PARADIGM pathway analysis of mRNASeq expression data - Bladder Urothelial Carcinoma (Primary solid tumor)

Pathway.Name	Avg.Num.Perturbations
FOXM1 transcription factor network	177
Aurora B signaling	123
Signaling events regulated by Ret tyrosine kinase	121
Glypican 2 network	116
TCGA08_retinoblastoma	99
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	98
IGF1 pathway	94
Endothelins	87
Nongenotropic Androgen signaling	84
Signaling mediated by p38-alpha and p38-beta	82

Pathway.Name	Significance.Ratio	Avg.Num.Perturbations	Total.Perturbations	Num.Entities	Min.Mean.Truth	Max.Mean.Truth	Min.Mean.Within	Max.Mean.Within	Min.Mean.Any	Max.Mean.Within.1
FOXM1 transcription factor network	0.4338	177	9036	51	-0.04	0.74	1000	-1000	-0.069	-1000
Aurora B signaling	0.3015	123	8295	67	-0.15	0.26	1000	-1000	-0.009	-1000
Signaling events regulated by Ret tyrosine kinase	0.2966	121	9956	82	-0.16	0.014	1000	-1000	-0.025	-1000
Glypican 2 network	0.2843	116	465	4	0.025	0.099	1000	-1000	0.006	-1000
TCGA08_retinoblastoma	0.2426	99	794	8	-0.058	0.14	1000	-1000	-0.002	-1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	0.2402	98	6678	68	-0.61	0.32	1000	-1000	-0.034	-1000
IGF1 pathway	0.2304	94	5372	57	-0.12	0.038	1000	-1000	-0.012	-1000
Endothelins	0.2132	87	8415	96	-0.36	0.19	1000	-1000	-0.005	-1000
Nongenotropic Androgen signaling	0.2059	84	4376	52	-0.24	0.14	1000	-1000	-0.006	-1000
Signaling mediated by p38-alpha and p38-beta	0.2010	82	3650	44	-0.19	0.01	1000	-1000	-0.005	-1000
Fc-epsilon receptor I signaling in mast cells	0.1936	79	7745	97	-0.12	0.022	1000	-1000	-0.024	-1000
Signaling events mediated by the Hedgehog family	0.1863	76	4000	52	-0.081	0.081	1000	-1000	-0.01	-1000
Syndecan-1-mediated signaling events	0.1838	75	2561	34	-0.049	0.16	1000	-1000	-0.003	-1000
Reelin signaling pathway	0.1789	73	4103	56	-0.093	0.058	1000	-1000	-0.002	-1000
PLK1 signaling events	0.1765	72	6150	85	-0.052	0.2	1000	-1000	-0.01	-1000
IL4-mediated signaling events	0.1691	69	6312	91	-0.6	0.4	1000	-1000	-0.11	-1000
IL23-mediated signaling events	0.1691	69	4163	60	-0.31	0.08	1000	-1000	-0.066	-1000
Signaling events mediated by Stem cell factor receptor (c-Kit)	0.1667	68	5310	78	-0.24	0.081	1000	-1000	-0.026	-1000
Thromboxane A2 receptor signaling	0.1569	64	6748	105	-0.22	0.055	1000	-1000	-0.026	-1000
p75(NTR)-mediated signaling	0.1544	63	7902	125	-0.076	0.071	1000	-1000	-0.019	-1000
Plasma membrane estrogen receptor signaling	0.1471	60	5180	86	-0.23	0.13	1000	-1000	-0.024	-1000
TCGA08_p53	0.1397	57	405	7	-0.044	0.024	1000	-1000	-0.001	-1000
Aurora C signaling	0.1373	56	392	7	0	0.13	1000	-1000	-0.003	-1000
S1P4 pathway	0.1373	56	1423	25	-0.084	0.019	1000	-1000	0	-1000
S1P5 pathway	0.1299	53	901	17	-0.084	0.064	1000	-1000	-0.006	-1000
HIF-1-alpha transcription factor network	0.1250	51	3918	76	-0.09	0.29	1000	-1000	-0.025	-1000
TCR signaling in naïve CD8+ T cells	0.1225	50	4676	93	-0.091	0.044	1000	-1000	-0.022	-1000
Ephrin A reverse signaling	0.1201	49	344	7	-0.033	0	1000	-1000	0	-1000
amb2 Integrin signaling	0.1201	49	4021	82	-0.22	0.069	1000	-1000	-0.01	-1000
Integrins in angiogenesis	0.1201	49	4187	84	-0.18	0.12	1000	-1000	-0.002	-1000
Ras signaling in the CD4+ TCR pathway	0.1201	49	839	17	-0.12	0.011	1000	-1000	-0.003	-1000
LPA receptor mediated events	0.1176	48	4913	102	-0.17	0.069	1000	-1000	-0.026	-1000
BMP receptor signaling	0.1152	47	3815	81	-0.16	0.043	1000	-1000	-0.021	-1000
S1P1 pathway	0.1152	47	1705	36	-0.28	0.01	1000	-1000	-0.01	-1000
Rapid glucocorticoid signaling	0.1152	47	957	20	-0.12	0.07	1000	-1000	-0.001	-1000
Osteopontin-mediated events	0.1127	46	1773	38	-0.084	0.12	1000	-1000	-0.009	-1000
Glucocorticoid receptor regulatory network	0.1078	44	5127	114	-0.43	0.16	1000	-1000	-0.026	-1000
Neurotrophic factor-mediated Trk receptor signaling	0.1078	44	5327	120	-0.15	0.13	1000	-1000	-0.021	-1000
JNK signaling in the CD4+ TCR pathway	0.1054	43	731	17	-0.15	0.011	1000	-1000	-0.011	-1000
Calcium signaling in the CD4+ TCR pathway	0.1054	43	1363	31	-0.077	0.014	1000	-1000	-0.017	-1000
Glypican 1 network	0.1029	42	2051	48	-0.13	0.041	1000	-1000	-0.005	-1000
FOXA2 and FOXA3 transcription factor networks	0.1005	41	1900	46	-0.11	0.31	1000	-1000	-0.015	-1000
IL6-mediated signaling events	0.0956	39	2995	75	-0.19	0.044	1000	-1000	-0.019	-1000
ErbB2/ErbB3 signaling events	0.0931	38	2526	65	-0.12	0.015	1000	-1000	-0.021	-1000
IL12-mediated signaling events	0.0907	37	3227	87	-0.36	0.059	1000	-1000	-0.071	-1000
Lissencephaly gene (LIS1) in neuronal migration and development	0.0907	37	1999	54	-0.093	0.058	1000	-1000	-0.003	-1000
PDGFR-alpha signaling pathway	0.0907	37	1657	44	-0.23	0.023	1000	-1000	0.003	-1000
BCR signaling pathway	0.0907	37	3719	99	-0.083	0.017	1000	-1000	-0.022	-1000
RXR and RAR heterodimerization with other nuclear receptor	0.0858	35	1821	52	-0.16	0.018	1000	-1000	-0.013	-1000
Aurora A signaling	0.0833	34	2056	60	-0.13	0.2	1000	-1000	0	-1000
Angiopoietin receptor Tie2-mediated signaling	0.0809	33	2909	88	-0.12	0.045	1000	-1000	-0.033	-1000
Nephrin/Neph1 signaling in the kidney podocyte	0.0784	32	1094	34	-0.01	0.013	1000	-1000	-0.007	-1000
Visual signal transduction: Cones	0.0784	32	1222	38	-0.054	0.078	1000	-1000	0	-1000
Arf6 signaling events	0.0784	32	1998	62	-0.12	0.029	1000	-1000	-0.006	-1000
FAS signaling pathway (CD95)	0.0784	32	1517	47	-0.5	0.022	1000	-1000	-0.003	-1000
S1P3 pathway	0.0784	32	1374	42	-0.085	0.016	1000	-1000	-0.009	-1000
Coregulation of Androgen receptor activity	0.0760	31	2376	76	-0.13	0.14	1000	-1000	-0.008	-1000
Syndecan-2-mediated signaling events	0.0760	31	2192	69	-0.033	0.056	1000	-1000	0	-1000
Wnt signaling	0.0760	31	223	7	-0.007	0.025	1000	-1000	0.002	-1000
Syndecan-4-mediated signaling events	0.0735	30	2018	67	-0.089	0.073	1000	-1000	-0.006	-1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)	0.0686	28	2393	85	-0.23	0.016	1000	-1000	-0.005	-1000
Noncanonical Wnt signaling pathway	0.0637	26	689	26	-0.042	0.025	1000	-1000	-0.006	-1000
Class IB PI3K non-lipid kinase events	0.0637	26	78	3	-0.009	-1000	1000	-1000	-0.009	-1000
Sphingosine 1-phosphate (S1P) pathway	0.0613	25	725	28	-0.084	0.045	1000	-1000	0	-1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha	0.0613	25	833	33	-0.14	0.14	1000	-1000	-0.007	-1000
Visual signal transduction: Rods	0.0613	25	1342	52	-0.054	0.12	1000	-1000	0	-1000
Presenilin action in Notch and Wnt signaling	0.0564	23	1442	61	-0.084	0.12	1000	-1000	-0.017	-1000
Canonical Wnt signaling pathway	0.0564	23	1204	51	-0.08	0.12	1000	-1000	-0.017	-1000
Regulation of Androgen receptor activity	0.0564	23	1662	70	-0.15	0.024	1000	-1000	-0.018	-1000
EGFR-dependent Endothelin signaling events	0.0539	22	473	21	-0.033	0.037	1000	-1000	0	-1000
Effects of Botulinum toxin	0.0515	21	563	26	-0.01	0.054	1000	-1000	-0.001	-1000
Hedgehog signaling events mediated by Gli proteins	0.0490	20	1357	65	-0.083	0.042	1000	-1000	-0.014	-1000
Ephrin B reverse signaling	0.0490	20	994	48	-0.024	0.029	1000	-1000	-0.017	-1000
IL27-mediated signaling events	0.0490	20	1045	51	-0.12	0.074	1000	-1000	-0.014	-1000
FoxO family signaling	0.0466	19	1273	64	0.001	0.23	1000	-1000	-0.013	-1000
Cellular roles of Anthrax toxin	0.0441	18	710	39	-0.008	0.023	1000	-1000	-0.006	-1000
Insulin Pathway	0.0441	18	1336	74	-0.13	0.045	1000	-1000	-0.017	-1000
Nectin adhesion pathway	0.0417	17	1074	63	-0.024	0.024	1000	-1000	-0.024	-1000
EPHB forward signaling	0.0417	17	1446	85	-0.01	0.038	1000	-1000	-0.022	-1000
Stabilization and expansion of the E-cadherin adherens junction	0.0417	17	1267	74	-0.12	0.029	1000	-1000	-0.019	-1000
Caspase cascade in apoptosis	0.0392	16	1211	74	-0.01	0.029	1000	-1000	-0.015	-1000
IL2 signaling events mediated by PI3K	0.0368	15	905	58	-0.022	0.12	1000	-1000	-0.012	-1000
IL2 signaling events mediated by STAT5	0.0368	15	336	22	-0.03	0.077	1000	-1000	-0.009	-1000
BARD1 signaling events	0.0343	14	814	57	-0.021	0.1	1000	-1000	-0.02	-1000
IL1-mediated signaling events	0.0343	14	928	62	0	0.033	1000	-1000	-0.007	-1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes	0.0343	14	1171	83	-0.18	0.037	1000	-1000	-0.005	-1000
Regulation of nuclear SMAD2/3 signaling	0.0319	13	1892	136	-0.099	0.087	1000	-1000	-0.027	-1000
ErbB4 signaling events	0.0319	13	899	69	-0.12	0.031	1000	-1000	-0.007	-1000
Signaling events mediated by PTP1B	0.0294	12	951	76	-0.12	0.039	1000	-1000	-0.023	-1000
IFN-gamma pathway	0.0294	12	825	68	-0.085	0.059	1000	-1000	-0.022	-1000
Regulation of Telomerase	0.0294	12	1250	102	-0.044	0.17	1000	-1000	-0.02	-1000
PDGFR-beta signaling pathway	0.0294	12	1169	97	-0.035	0.045	1000	-1000	-0.017	-1000
Signaling events mediated by HDAC Class III	0.0270	11	471	40	-0.11	0.02	1000	-1000	-0.019	-1000
Regulation of p38-alpha and p38-beta	0.0270	11	619	54	-0.077	0.026	1000	-1000	-0.025	-1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha	0.0245	10	456	45	-0.007	0.029	1000	-1000	-0.012	-1000
LPA4-mediated signaling events	0.0221	9	113	12	-0.041	0.008	1000	-1000	0	-1000
a4b1 and a4b7 Integrin signaling	0.0221	9	49	5	0.002	0.009	1000	-1000	0.006	-1000
Ceramide signaling pathway	0.0221	9	754	76	-0.12	0.028	1000	-1000	-0.008	-1000
Paxillin-independent events mediated by a4b1 and a4b7	0.0221	9	346	37	-0.001	0.03	1000	-1000	0	-1000
TCGA08_rtk_signaling	0.0221	9	234	26	-0.031	0.028	1000	-1000	-0.009	-1000
E-cadherin signaling events	0.0221	9	45	5	0	0.013	1000	-1000	0.006	-1000
EPO signaling pathway	0.0196	8	443	55	-0.022	0.042	1000	-1000	-0.003	-1000
TRAIL signaling pathway	0.0196	8	405	48	0	0.038	1000	-1000	-0.011	-1000
HIF-2-alpha transcription factor network	0.0196	8	357	43	-0.12	0.12	1000	-1000	-0.078	-1000
Signaling mediated by p38-gamma and p38-delta	0.0196	8	129	15	-0.009	0.019	1000	-1000	-0.002	-1000
Retinoic acid receptors-mediated signaling	0.0196	8	484	58	-0.05	0.025	1000	-1000	-0.009	-1000
Syndecan-3-mediated signaling events	0.0196	8	284	35	-0.038	0.03	1000	-1000	-0.003	-1000
E-cadherin signaling in the nascent adherens junction	0.0196	8	643	76	-0.006	0.022	1000	-1000	-0.025	-1000
Signaling events mediated by PRL	0.0196	8	280	34	-0.039	0.03	1000	-1000	-0.003	-1000
PLK2 and PLK4 events	0.0172	7	22	3	0.011	0.016	1000	-1000	0.008	-1000
Arf6 trafficking events	0.0172	7	500	71	-0.2	0.019	1000	-1000	-0.014	-1000
ceramide signaling pathway	0.0147	6	296	49	-0.004	0.028	1000	-1000	-0.008	-1000
E-cadherin signaling in keratinocytes	0.0147	6	285	43	-0.013	0.017	1000	-1000	-0.003	-1000
Class I PI3K signaling events mediated by Akt	0.0123	5	350	68	-0.094	0.028	1000	-1000	-0.011	-1000
Paxillin-dependent events mediated by a4b1	0.0123	5	214	36	-0.02	0.022	1000	-1000	-0.021	-1000
Class I PI3K signaling events	0.0123	5	395	73	-0.011	0.02	1000	-1000	-0.003	-1000
Signaling events mediated by HDAC Class II	0.0098	4	339	75	-0.043	0.024	1000	-1000	-0.011	-1000
Signaling events mediated by VEGFR1 and VEGFR2	0.0098	4	527	125	-0.024	0.033	1000	-1000	-0.022	-1000
p38 MAPK signaling pathway	0.0098	4	177	44	-0.001	0.037	1000	-1000	-0.011	-1000
Canonical NF-kappaB pathway	0.0049	2	110	39	0	0.044	1000	-1000	-0.008	-1000
Circadian rhythm pathway	0.0049	2	54	22	-0.007	0.027	1000	-1000	-0.01	-1000
Insulin-mediated glucose transport	0.0049	2	76	32	-0.11	0.027	1000	-1000	-0.004	-1000
mTOR signaling pathway	0.0049	2	150	53	-0.003	0.022	1000	-1000	-0.017	-1000
Atypical NF-kappaB pathway	0.0049	2	62	31	0	0.021	1000	-1000	-0.001	-1000
Signaling events mediated by HDAC Class I	0.0025	1	126	104	-0.02	0.035	1000	-1000	-0.014	-1000
Sumoylation by RanBP2 regulates transcriptional repression	0.0025	1	39	27	0	0.03	1000	-1000	-0.015	-1000
VEGFR1 specific signals	0.0025	1	82	56	-0.02	0.036	1000	-1000	-0.002	-1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling	0.0000	0	14	23	0.005	0.027	1000	-1000	-0.001	-1000
Arf6 downstream pathway	0.0000	0	16	43	-0.022	0.022	1000	-1000	-0.017	-1000
Arf1 pathway	0.0000	0	6	54	0	0.019	1000	-1000	-0.002	-1000
Alternative NF-kappaB pathway	0.0000	0	0	13	0	0.03	1000	-1000	0	-1000
Total	NA	4281	249111	7203	-13	-990	131000	-131000	-1.7	-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	0.6	0.56	1.1	193	-0.92	5	198
PLK1	0.33	0.29	0.63	173	-10000	0	173
BIRC5	0.42	0.3	0.63	236	-1.3	1	237
HSPA1B	0.6	0.56	1.1	204	-0.88	6	210
MAP2K1	0.18	0.15	0.32	208	-10000	0	208
BRCA2	0.61	0.58	1.1	205	-0.88	6	211
FOXM1	0.74	0.73	1.3	213	-0.81	21	234
XRCC1	0.6	0.56	1.1	199	-0.88	6	205
FOXM1B/p19	0.14	0.42	0.88	68	-0.77	18	86
Cyclin D1/CDK4	0.5	0.49	0.91	196	-0.8	7	203
CDC2	0.67	0.64	1.2	213	-0.74	20	233
TGFA	0.52	0.5	0.94	199	-0.78	6	205
SKP2	0.6	0.56	1.1	204	-0.88	6	210
CCNE1	0.082	0.1	0.31	64	-10000	0	64
CKS1B	0.6	0.57	1.1	204	-0.88	6	210
RB1	0.026	0.21	0.7	28	-0.62	2	30
FOXM1C/SP1	0.51	0.52	0.94	197	-0.77	21	218
AURKB	0.35	0.29	0.62	195	-10000	0	195
CENPF	0.7	0.63	1.2	217	-0.87	6	223
CDK4	0.073	0.059	0.15	98	-10000	0	98
MYC	0.5	0.5	0.91	202	-0.8	9	211
CHEK2	0.18	0.15	0.31	213	-10000	0	213
ONECUT1	0.54	0.52	0.98	199	-0.85	6	205
CDKN2A	0.005	0.16	0.21	112	-0.2	99	211
LAMA4	0.59	0.59	1.1	201	-1.1	8	209
FOXM1B/HNF6	0.54	0.54	1	191	-0.96	6	197
FOS	0.32	0.7	1.1	147	-0.99	33	180
SP1	0.009	0.016	-10000	0	-10000	0	0
CDC25B	0.6	0.57	1.1	204	-0.88	6	210
response to radiation	0.13	0.11	0.23	208	-10000	0	208
CENPB	0.6	0.56	1.1	193	-0.92	5	198
CENPA	0.7	0.63	1.2	220	-0.87	6	226
NEK2	0.7	0.63	1.2	212	-0.95	4	216
HIST1H2BA	0.59	0.56	1.1	194	-0.88	6	200
CCNA2	0.11	0.13	0.32	106	-10000	0	106
EP300	0.01	0	-10000	0	-10000	0	0
CCNB1/CDK1	0.65	0.63	1.2	200	-1	6	206
CCNB2	0.7	0.63	1.2	219	-0.87	6	225
CCNB1	0.7	0.67	1.2	211	-0.93	6	217
ETV5	0.6	0.57	1.1	204	-0.91	7	211
ESR1	0.45	0.69	1.1	183	-1.1	26	209
CCND1	0.54	0.53	0.99	201	-0.84	6	207
GSK3A	0.14	0.11	0.24	194	-10000	0	194
Cyclin A-E1/CDK1-2	0.2	0.16	0.34	212	-10000	0	212
CDK2	0.044	0.033	0.12	3	-10000	0	3
G2/M transition of mitotic cell cycle	0.17	0.15	0.29	229	-10000	0	229
FOXM1B/Cbp/p300	-0.04	0.2	-10000	0	-0.73	22	22
GAS1	0.43	0.77	1.1	186	-1	53	239
MMP2	0.53	0.64	1.1	201	-0.97	16	217
RB1/FOXM1C	0.5	0.49	0.91	197	-0.85	7	204
CREBBP	0.01	0	-10000	0	-10000	0	0

×

Aurora B signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Condensin I complex	0.14	0.095	0.22	210	-10000	0	210
STMN1	0.095	0.095	0.18	195	-10000	0	195
Aurora B/RasGAP/Survivin	0.21	0.13	0.27	296	-0.16	1	297
Chromosomal passenger complex/Cul3 protein complex	0.079	0.1	0.19	143	-0.16	23	166
BIRC5	0.2	0.12	0.28	292	-0.3	1	293
DES	-0.15	0.25	0.26	1	-0.4	185	186
Aurora C/Aurora B/INCENP	0.1	0.078	0.18	194	-10000	0	194
Aurora B/TACC1	0.084	0.078	0.17	182	-0.15	1	183
Aurora B/PP2A	0.095	0.086	0.19	184	-10000	0	184
mol:GTP	0	0	-10000	0	-10000	0	0
CBX5	0.033	0.029	-10000	0	-10000	0	0
mitotic metaphase/anaphase transition	-0.004	0.004	-10000	0	-10000	0	0
NDC80	0.13	0.13	0.24	212	-10000	0	212
Cul3 protein complex	-0.024	0.08	-10000	0	-0.16	98	98
KIF2C	0.17	0.11	0.24	256	-10000	0	256
PEBP1	0.014	0.003	-10000	0	-10000	0	0
KIF20A	0.2	0.11	0.27	300	-10000	0	300
mol:GDP	0	0	-10000	0	-10000	0	0
Aurora B/RasGAP	0.095	0.086	0.19	184	-10000	0	184
SEPT1	0.011	0.027	0.27	3	-0.29	1	4
SMC2	0.011	0.013	0.27	1	-10000	0	1
SMC4	0.01	0	-10000	0	-10000	0	0
NSUN2/NPM1/Nucleolin	0.11	0.11	0.22	182	-10000	0	182
PSMA3	0.01	0	-10000	0	-10000	0	0
G2/M transition of mitotic cell cycle	-0.006	0.005	-10000	0	-10000	0	0
H3F3B	0.067	0.062	0.14	184	-10000	0	184
AURKB	0.13	0.13	0.27	184	-10000	0	184
AURKC	0.018	0.045	0.27	13	-10000	0	13
CDCA8	0.088	0.12	0.28	109	-10000	0	109
cytokinesis	0.14	0.15	0.3	182	-0.18	1	183
Aurora B/Septin1	0.19	0.16	0.32	218	-0.16	1	219
AURKA	0.083	0.12	0.26	124	-10000	0	124
INCENP	0.02	0.014	0.28	1	-10000	0	1
KLHL13	-0.054	0.12	-10000	0	-0.29	88	88
BUB1	0.056	0.1	0.26	80	-10000	0	80
hSgo1/Aurora B/Survivin	0.26	0.17	0.33	316	-0.14	1	317
EVI5	0.016	0.004	-10000	0	-10000	0	0
RhoA/GTP	0.18	0.16	0.34	202	-10000	0	202
SGOL1	0.12	0.13	0.27	172	-10000	0	172
CENPA	0.2	0.13	0.26	282	-10000	0	282
NCAPG	0.12	0.13	0.27	181	-10000	0	181
Aurora B/HC8 Proteasome	0.095	0.086	0.19	184	-10000	0	184
NCAPD2	0.011	0.013	0.27	1	-10000	0	1
Aurora B/PP1-gamma	0.095	0.086	0.19	184	-10000	0	184
RHOA	0.01	0	-10000	0	-10000	0	0
NCAPH	0.17	0.13	0.27	253	-10000	0	253
NPM1	0.08	0.087	0.18	184	-10000	0	184
RASA1	0.01	0	-10000	0	-10000	0	0
KLHL9	-0.001	0.056	-10000	0	-0.29	15	15
mitotic prometaphase	0.004	0.003	-10000	0	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.095	0.085	0.19	184	-10000	0	184
PPP1CC	0.01	0	-10000	0	-10000	0	0
Centraspindlin	0.22	0.17	0.35	236	-10000	0	236
RhoA/GDP	0.007	0	-10000	0	-10000	0	0
NSUN2	0.08	0.087	0.18	182	-10000	0	182
MYLK	-0.015	0.13	0.13	119	-0.17	138	257
KIF23	0.14	0.13	0.28	202	-10000	0	202
VIM	0.076	0.079	0.16	181	-0.19	4	185
RACGAP1	0.023	0.027	0.29	4	-10000	0	4
mitosis	0	0	-10000	0	-10000	0	0
NCL	0.08	0.087	0.18	182	-10000	0	182
Chromosomal passenger complex	0.2	0.12	0.26	287	-0.12	1	288
Chromosomal passenger complex/EVI5	0.25	0.15	0.34	266	-0.13	1	267
TACC1	0.008	0.025	-10000	0	-0.29	3	3
PPP2R5D	0.01	0	-10000	0	-10000	0	0
CUL3	0.01	0	-10000	0	-10000	0	0
response to DNA damage stimulus	0	0	-10000	0	-10000	0	0

×

Signaling events regulated by Ret tyrosine kinase

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
PTK2	-0.019	0.03	-10000	0	-10000	0	0
Crk/p130 Cas/Paxillin	-0.11	0.096	-10000	0	-0.19	225	225
JUN	-0.08	0.091	-10000	0	-0.16	225	225
HRAS	0.01	0	-10000	0	-10000	0	0
RET51/GFRalpha1/GDNF/GRB10	-0.07	0.092	0.17	6	-0.15	227	233
RAP1A	0.01	0	-10000	0	-10000	0	0
FRS2	0.014	0.034	0.27	7	-10000	0	7
RAP1A/GDP	0.007	0	-10000	0	-10000	0	0
RET51/GFRalpha1/GDNF/DOK1	-0.068	0.09	0.17	7	-0.14	225	232
EntrezGene:5979	0	0	-10000	0	-10000	0	0
PTPN11	0.01	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.01	0	-10000	0	-10000	0	0
RET9/GFRalpha1/GDNF/Enigma	-0.071	0.077	-10000	0	-0.14	225	225
RHOA	0.01	0	-10000	0	-10000	0	0
RAP1A/GTP	-0.059	0.079	0.14	4	-0.13	225	229
GRB7	0.014	0.062	0.27	14	-0.29	7	21
RET51/GFRalpha1/GDNF	-0.068	0.09	0.17	6	-0.14	225	231
MAPKKK cascade	-0.074	0.088	-10000	0	-0.15	225	225
BCAR1	0.01	0	-10000	0	-10000	0	0
RET9/GFRalpha1/GDNF/IRS1	-0.074	0.082	-10000	0	-0.14	227	227
lamellipodium assembly	-0.1	0.1	-10000	0	-0.19	229	229
RET51/GFRalpha1/GDNF/SHC	-0.068	0.09	0.17	6	-0.14	224	230
PIK3CA	0.01	0	-10000	0	-10000	0	0
RET9/GFRalpha1/GDNF/SHC	-0.071	0.077	-10000	0	-0.14	224	224
RET9/GFRalpha1/GDNF/Shank3	-0.071	0.077	-10000	0	-0.14	225	225
MAPK3	-0.06	0.07	-10000	0	-0.12	225	225
DOK1	0.011	0.013	0.27	1	-10000	0	1
DOK6	-0.098	0.14	-10000	0	-0.29	148	148
PXN	0.01	0	-10000	0	-10000	0	0
neurite development	-0.079	0.081	-10000	0	-0.18	109	109
DOK5	-0.015	0.089	0.27	3	-0.29	37	40
GFRA1	-0.16	0.15	-10000	0	-0.29	228	228
MAPK8	-0.082	0.092	-10000	0	-0.16	225	225
HRAS/GTP	-0.081	0.1	-10000	0	-0.17	225	225
tube development	-0.064	0.072	-10000	0	-0.13	225	225
MAPK1	-0.06	0.07	-10000	0	-0.12	225	225
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.086	0.091	-10000	0	-0.17	222	222
Rac1/GDP	0.007	0	-10000	0	-10000	0	0
SRC	0.01	0	-10000	0	-10000	0	0
PDLIM7	0.01	0	-10000	0	-10000	0	0
RET51/GFRalpha1/GDNF/Dok6	-0.11	0.12	0.17	5	-0.18	267	272
SHC1	0.011	0.013	0.27	1	-10000	0	1
RET51/GFRalpha1/GDNF/Dok4	-0.068	0.09	0.17	6	-0.14	225	231
RET51/GFRalpha1/GDNF/Dok5	-0.081	0.1	0.18	8	-0.16	234	242
PRKCA	0.006	0.033	-10000	0	-0.29	5	5
HRAS/GDP	0.007	0	-10000	0	-10000	0	0
CREB1	-0.11	0.12	-10000	0	-0.21	223	223
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.087	0.09	-10000	0	-0.17	224	224
RET51/GFRalpha1/GDNF/Grb7	-0.068	0.093	0.17	9	-0.15	217	226
mol:GDP	0	0	-10000	0	-10000	0	0
RET	0.006	0.059	0.27	7	-0.29	11	18
DOK4	0.01	0	-10000	0	-10000	0	0
JNK cascade	-0.079	0.09	-10000	0	-0.16	225	225
RET9/GFRalpha1/GDNF/FRS2	-0.069	0.08	0.17	4	-0.14	222	226
SHANK3	0.01	0	-10000	0	-10000	0	0
RASA1	0.01	0	-10000	0	-10000	0	0
NCK1	0.01	0	-10000	0	-10000	0	0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.088	0.09	-10000	0	-0.17	224	224
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.087	0.1	0.2	1	-0.17	222	223
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK	-0.088	0.099	-10000	0	-0.17	225	225
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.089	0.1	-10000	0	-0.18	224	224
PI3K	-0.14	0.15	-10000	0	-0.26	229	229
SOS1	0.01	0	-10000	0	-10000	0	0
RET9/GFRalpha1/GDNF/Shank3/Grb2	-0.063	0.074	-10000	0	-0.13	225	225
GRB10	0.006	0.033	-10000	0	-0.29	5	5
activation of MAPKK activity	-0.08	0.092	0.16	1	-0.16	221	222
RET51/GFRalpha1/GDNF/FRS2	-0.066	0.093	0.19	9	-0.14	222	231
GAB1	0.01	0	-10000	0	-10000	0	0
IRS1	0.003	0.046	-10000	0	-0.29	10	10
IRS2	-0.002	0.058	-10000	0	-0.29	16	16
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.089	0.1	-10000	0	-0.18	224	224
RET51/GFRalpha1/GDNF/PKC alpha	-0.07	0.092	0.17	6	-0.15	225	231
GRB2	0.01	0	-10000	0	-10000	0	0
PRKACA	0.01	0	-10000	0	-10000	0	0
GDNF	0.007	0.023	0.27	3	-10000	0	3
RAC1	0.01	0	-10000	0	-10000	0	0
RET51/GFRalpha1/GDNF/IRS1	-0.072	0.094	0.17	6	-0.15	227	233
Rac1/GTP	-0.12	0.12	-10000	0	-0.22	226	226
RET9/GFRalpha1/GDNF	-0.084	0.084	-10000	0	-0.16	225	225
GFRalpha1/GDNF	-0.1	0.1	-10000	0	-0.19	225	225

×

Glypican 2 network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Total.Perturbations
MDK	0.025	0.06	0.27	23	-9999	23
GPC2	0.099	0.12	0.27	140	-9999	140
GPC2/Midkine	0.086	0.098	0.21	151	-9999	151
neuron projection morphogenesis	0.086	0.098	0.21	151	-9999	151

×

TCGA08_retinoblastoma

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2B	0.016	0.078	0.27	22	-0.28	11	33
CDKN2C	-0.003	0.025	0.27	2	-10000	0	2
CDKN2A	0.14	0.14	0.27	201	-0.26	4	205
CCND2	-0.051	0.065	0.17	7	-0.1	198	205
RB1	0.055	0.071	0.11	200	-0.19	8	208
CDK4	-0.056	0.069	0.18	7	-0.19	34	41
CDK6	-0.058	0.072	0.19	7	-0.2	42	49
G1/S progression	-0.055	0.072	0.17	12	-0.19	39	51

×

Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FOXP3	0.024	0.064	0.35	13	-10000	0	13
NFATC2	-0.093	0.22	0.37	4	-0.46	70	74
NFATC3	-0.094	0.13	-10000	0	-0.25	142	142
CD40LG	-0.39	0.48	0.46	2	-0.82	204	206
ITCH	0	0.062	0.32	1	-0.17	43	44
CBLB	0	0.061	-10000	0	-0.17	43	43
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment	-0.26	0.44	0.53	17	-0.75	129	146
JUNB	0.006	0.033	-10000	0	-0.29	5	5
CaM/Ca2+/Calcineurin A alpha-beta B1	0	0.075	0.19	4	-0.21	43	47
T cell anergy	-0.035	0.1	0.22	1	-0.31	43	44
TLE4	-0.066	0.17	-10000	0	-0.38	64	64
Jun/NFAT1-c-4/p21SNFT	-0.35	0.5	0.48	4	-0.81	202	206
AP-1/NFAT1-c-4	-0.42	0.57	0.62	6	-0.94	196	202
IKZF1	-0.062	0.17	0.38	2	-0.36	65	67
T-helper 2 cell differentiation	-0.2	0.32	-10000	0	-0.78	74	74
AP-1/NFAT1	-0.091	0.19	0.33	8	-0.3	137	145
CALM1	0.002	0.045	-10000	0	-10000	0	0
EGR2	-0.44	0.61	-10000	0	-1	178	178
EGR3	-0.6	0.7	-10000	0	-1.3	202	202
NFAT1/FOXP3	-0.044	0.19	0.42	19	-0.33	66	85
EGR1	-0.061	0.13	-10000	0	-0.29	99	99
JUN	0.001	0.06	-10000	0	-0.29	15	15
EGR4	0.007	0.062	0.27	7	-0.29	12	19
mol:Ca2+	-0.007	0.043	-10000	0	-0.13	43	43
GBP3	-0.06	0.16	-10000	0	-0.36	53	53
FOSL1	-0.011	0.075	-10000	0	-0.29	28	28
NFAT1-c-4/MAF/IRF4	-0.36	0.48	0.46	1	-0.81	202	203
DGKA	-0.057	0.15	-10000	0	-0.34	53	53
CREM	0.01	0	-10000	0	-10000	0	0
NFAT1-c-4/PPARG	-0.37	0.48	-10000	0	-0.83	202	202
CTLA4	-0.041	0.16	0.44	14	-0.32	51	65
NFAT1-c-4 (dimer)/EGR1	-0.39	0.52	0.49	3	-0.88	201	204
NFAT1-c-4 (dimer)/EGR4	-0.36	0.5	0.49	3	-0.83	202	205
FOS	-0.066	0.13	-10000	0	-0.29	103	103
IFNG	-0.12	0.31	0.4	19	-0.65	65	84
T cell activation	-0.19	0.27	-10000	0	-0.52	120	120
MAF	0.002	0.048	-10000	0	-0.29	11	11
T-helper 2 cell lineage commitment	0	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	0.32	0.43	0.71	199	-10000	0	199
TNF	-0.35	0.47	0.46	11	-0.79	201	212
FASLG	-0.61	0.75	-10000	0	-1.3	207	207
TBX21	0.017	0.088	0.16	10	-0.29	23	33
BATF3	0.009	0.042	0.27	4	-0.29	5	9
PRKCQ	-0.013	0.089	0.27	4	-0.29	35	39
PTPN1	-0.057	0.15	-10000	0	-0.32	64	64
NFAT1-c-4/ICER1	-0.36	0.49	0.43	1	-0.82	201	202
GATA3	-0.008	0.077	0.27	2	-0.29	27	29
T-helper 1 cell differentiation	-0.12	0.3	0.4	19	-0.64	66	85
IL2RA	-0.26	0.42	0.51	17	-0.7	147	164
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
CASP3	-0.057	0.15	-10000	0	-0.32	65	65
E2F1	0.074	0.11	0.27	97	-10000	0	97
PPARG	-0.008	0.075	0.27	2	-0.29	26	28
SLC3A2	-0.057	0.15	-10000	0	-0.32	65	65
IRF4	-0.009	0.08	0.27	3	-0.29	29	32
PTGS2	-0.4	0.49	0.46	2	-0.84	205	207
CSF2	-0.35	0.5	0.52	16	-0.81	198	214
JunB/Fra1/NFAT1-c-4	-0.36	0.48	-10000	0	-0.8	201	201
IL4	-0.21	0.34	-10000	0	-0.83	73	73
IL5	-0.38	0.47	0.5	4	-0.8	203	207
IL2	-0.2	0.28	-10000	0	-0.54	117	117
IL3	-0.071	0.064	-10000	0	-10000	0	0
RNF128	-0.022	0.13	0.32	3	-0.39	43	46
NFATC1	-0.32	0.44	-10000	0	-0.72	199	199
CDK4	0.22	0.28	0.55	123	-10000	0	123
PTPRK	-0.058	0.15	-10000	0	-0.33	61	61
IL8	-0.39	0.48	0.46	2	-0.82	204	206
POU2F1	0.01	0.001	-10000	0	-10000	0	0

×

IGF1 pathway

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
NCK2	0.01	0	-10000	0	-10000	0	0
PTK2	0.01	0	-10000	0	-10000	0	0
CRKL	-0.061	0.082	0.15	2	-0.15	183	185
GRB2/SOS1/SHC	0.021	0.008	0.18	1	-10000	0	1
HRAS	0.01	0	-10000	0	-10000	0	0
IRS1/Crk	-0.06	0.083	-10000	0	-0.15	183	183
IGF-1R heterotetramer/IGF1/PTP1B	-0.059	0.087	-10000	0	-0.15	183	183
AKT1	-0.049	0.07	-10000	0	-0.12	183	183
BAD	-0.046	0.066	-10000	0	-0.12	183	183
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	-0.062	0.081	-10000	0	-0.15	183	183
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.06	0.084	-10000	0	-0.15	183	183
RAF1	-0.04	0.066	-10000	0	-0.2	3	3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos	-0.05	0.083	-10000	0	-0.14	183	183
YWHAZ	0.01	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.067	0.091	-10000	0	-0.17	183	183
PIK3CA	0.01	0	-10000	0	-10000	0	0
RPS6KB1	-0.049	0.07	-10000	0	-0.12	183	183
GNB2L1	0.01	0	-10000	0	-10000	0	0
positive regulation of MAPKKK cascade	-0.038	0.059	-10000	0	-0.17	10	10
PXN	0.01	0	-10000	0	-10000	0	0
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
cell adhesion	0	0	-10000	0	-10000	0	0
GRB2/SOS1	0.015	0	-10000	0	-10000	0	0
HRAS/GTP	-0.049	0.069	-10000	0	-0.12	182	182
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc	-0.035	0.073	-10000	0	-0.12	182	182
IGF-1R heterotetramer	-0.016	0.035	-10000	0	-0.13	9	9
IGF-1R heterotetramer/IGF1/IRS/Nck	-0.057	0.086	-10000	0	-0.15	183	183
Crk/p130 Cas/Paxillin	-0.046	0.08	-10000	0	-0.13	183	183
IGF1R	-0.016	0.035	-10000	0	-0.13	9	9
IGF1	-0.002	0.05	-10000	0	-0.34	9	9
IRS2/Crk	-0.06	0.087	-10000	0	-0.15	184	184
PI3K	-0.05	0.083	-10000	0	-0.14	183	183
apoptosis	0.038	0.062	0.1	183	-10000	0	183
HRAS/GDP	0.007	0	-10000	0	-10000	0	0
PRKCD	-0.11	0.14	-10000	0	-0.26	183	183
RAF1/14-3-3 E	-0.033	0.062	-10000	0	-0.19	4	4
BAD/14-3-3	-0.04	0.065	-10000	0	-0.11	183	183
PRKCZ	-0.05	0.071	-10000	0	-0.13	183	183
Crk/p130 Cas/Paxillin/FAK1	-0.037	0.066	-10000	0	-0.19	10	10
PTPN1	0.01	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1	-0.12	0.15	-10000	0	-0.28	183	183
BCAR1	0.01	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/SHC/GRB10	-0.046	0.08	-10000	0	-0.13	184	184
mol:GDP	0	0	-10000	0	-10000	0	0
SOS1	0.01	0	-10000	0	-10000	0	0
IRS1/NCK2	-0.059	0.083	-10000	0	-0.15	183	183
GRB10	0.006	0.033	-10000	0	-0.29	5	5
PTPN11	-0.062	0.081	-10000	0	-0.15	183	183
IRS1	-0.069	0.089	-10000	0	-0.17	183	183
IRS2	-0.066	0.09	-10000	0	-0.16	183	183
IGF-1R heterotetramer/IGF1	-0.088	0.11	-10000	0	-0.21	183	183
GRB2	0.01	0	-10000	0	-10000	0	0
PDPK1	-0.052	0.074	-10000	0	-0.13	183	183
YWHAE	0.009	0.015	-10000	0	-0.29	1	1
PRKD1	-0.11	0.15	-10000	0	-0.27	183	183
SHC1	0.011	0.013	0.27	1	-10000	0	1

×

Endothelins

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
AKT1	-0.076	0.12	0.26	2	-0.3	58	60
PTK2B	0.009	0.015	-10000	0	-0.29	1	1
mol:Ca2+	-0.093	0.17	-10000	0	-0.53	36	36
EDN1	-0.036	0.066	0.21	7	-0.2	22	29
EDN3	0.008	0.035	0.27	7	-10000	0	7
EDN2	0.011	0.099	0.27	29	-0.29	23	52
HRAS/GDP	-0.13	0.17	-10000	0	-0.31	151	151
ETA receptor/Endothelin-1/Gq/GTP/PLC beta	-0.088	0.13	-10000	0	-0.26	108	108
ADCY4	-0.12	0.12	0.18	2	-0.25	143	145
ADCY5	-0.17	0.16	0.18	2	-0.29	229	231
ADCY6	-0.12	0.12	0.18	2	-0.25	142	144
ADCY7	-0.12	0.12	0.18	2	-0.25	142	144
ADCY1	-0.11	0.12	0.18	2	-0.25	141	143
ADCY2	-0.16	0.15	0.18	2	-0.28	209	211
ADCY3	-0.12	0.12	0.18	2	-0.25	142	144
ADCY8	-0.12	0.12	0.17	4	-0.25	141	145
ADCY9	-0.12	0.13	0.18	2	-0.25	144	146
arachidonic acid secretion	-0.19	0.24	-10000	0	-0.45	157	157
ETB receptor/Endothelin-1/Gq/GTP	-0.06	0.12	-10000	0	-0.25	88	88
GNAO1	-0.084	0.14	-10000	0	-0.29	129	129
HRAS	0.009	0.002	-10000	0	-10000	0	0
ETA receptor/Endothelin-1/G12/GTP	-0.066	0.11	0.31	2	-0.28	55	57
ETA receptor/Endothelin-1/Gs/GTP	-0.12	0.13	0.29	2	-0.26	138	140
mol:GTP	-0.002	0.005	-10000	0	-10000	0	0
COL3A1	-0.079	0.14	0.43	2	-0.36	52	54
EDNRB	-0.029	0.097	-10000	0	-0.29	47	47
response to oxidative stress	0	0	-10000	0	-10000	0	0
CYSLTR2	-0.071	0.12	0.29	5	-0.32	52	57
CYSLTR1	-0.083	0.14	0.28	3	-0.37	56	59
SLC9A1	-0.051	0.073	0.18	2	-0.2	53	55
mol:GDP	-0.14	0.18	-10000	0	-0.33	153	153
SLC9A3	-0.096	0.2	-10000	0	-0.53	57	57
RAF1	-0.17	0.21	-10000	0	-0.39	171	171
JUN	-0.11	0.23	-10000	0	-0.76	35	35
JAK2	-0.076	0.12	0.26	2	-0.31	58	60
mol:IP3	-0.094	0.14	-10000	0	-0.31	95	95
ETA receptor/Endothelin-1	-0.092	0.14	0.37	2	-0.36	58	60
PLCB1	-0.002	0.051	-10000	0	-0.29	12	12
PLCB2	0.004	0.022	-10000	0	-0.29	2	2
ETA receptor/Endothelin-3	-0.049	0.094	0.2	2	-0.24	62	64
FOS	-0.3	0.4	-10000	0	-0.84	141	141
Gai/GDP	-0.25	0.36	-10000	0	-0.78	129	129
CRK	0.01	0	-10000	0	-10000	0	0
mol:Ca ++	-0.13	0.17	0.26	2	-0.35	117	119
BCAR1	0.01	0	-10000	0	-10000	0	0
PRKCB1	-0.094	0.14	-10000	0	-0.3	99	99
GNAQ	0.005	0.009	-10000	0	-10000	0	0
GNAZ	-0.055	0.12	-10000	0	-0.29	89	89
GNAL	-0.12	0.15	-10000	0	-0.29	178	178
Gs family/GDP	-0.18	0.18	-10000	0	-0.34	185	185
ETA receptor/Endothelin-1/Gq/GTP	-0.089	0.13	-10000	0	-0.28	104	104
MAPK14	-0.059	0.11	-10000	0	-0.24	86	86
TRPC6	-0.096	0.18	-10000	0	-0.56	35	35
GNAI2	0.01	0	-10000	0	-10000	0	0
GNAI3	0.01	0	-10000	0	-10000	0	0
GNAI1	0.008	0.025	-10000	0	-0.29	3	3
ETB receptor/Endothelin-1/Gq/GTP/PLC beta	-0.064	0.12	-10000	0	-0.25	90	90
ETB receptor/Endothelin-2	-0.012	0.096	0.19	24	-0.21	61	85
ETB receptor/Endothelin-3	-0.013	0.072	0.19	7	-0.2	47	54
ETB receptor/Endothelin-1	-0.043	0.088	0.26	2	-0.22	64	66
MAPK3	-0.28	0.36	-10000	0	-0.72	152	152
MAPK1	-0.28	0.36	-10000	0	-0.72	152	152
Rac1/GDP	-0.13	0.16	-10000	0	-0.31	151	151
cAMP biosynthetic process	-0.19	0.16	-10000	0	-0.3	233	233
MAPK8	-0.11	0.19	-10000	0	-0.54	48	48
SRC	0.01	0	-10000	0	-10000	0	0
ETB receptor/Endothelin-1/Gi/GTP	-0.11	0.15	-10000	0	-0.25	180	180
p130Cas/CRK/Src/PYK2	-0.12	0.18	-10000	0	-0.4	85	85
mol:K +	0	0	-10000	0	-10000	0	0
G12/GDP	-0.13	0.16	-10000	0	-0.31	150	150
COL1A2	-0.11	0.2	0.45	2	-0.46	70	72
EntrezGene:2778	0	0	-10000	0	-10000	0	0
ETA receptor/Endothelin-2	-0.049	0.11	0.2	6	-0.23	88	94
mol:DAG	-0.094	0.14	-10000	0	-0.31	95	95
MAP2K2	-0.22	0.28	-10000	0	-0.54	156	156
MAP2K1	-0.22	0.28	-10000	0	-0.54	156	156
EDNRA	-0.081	0.13	0.18	2	-0.32	74	76
positive regulation of muscle contraction	-0.063	0.1	0.22	2	-0.26	58	60
Gq family/GDP	-0.12	0.17	-10000	0	-0.35	109	109
HRAS/GTP	-0.14	0.17	-10000	0	-0.31	156	156
PRKCH	-0.093	0.14	-10000	0	-0.3	98	98
RAC1	0.01	0	-10000	0	-10000	0	0
PRKCA	-0.094	0.14	-10000	0	-0.3	102	102
PRKCB	-0.13	0.16	-10000	0	-0.32	135	135
PRKCE	-0.092	0.14	-10000	0	-0.3	97	97
PRKCD	-0.094	0.14	-10000	0	-0.3	99	99
PRKCG	-0.093	0.14	-10000	0	-0.3	98	98
regulation of vascular smooth muscle contraction	-0.36	0.48	-10000	0	-0.99	141	141
PRKCQ	-0.1	0.15	-10000	0	-0.3	111	111
PLA2G4A	-0.2	0.26	-10000	0	-0.49	157	157
GNA14	-0.037	0.1	-10000	0	-0.29	58	58
GNA15	0.005	0.026	-10000	0	-0.29	3	3
GNA12	0.01	0	-10000	0	-10000	0	0
GNA11	0.007	0.016	-10000	0	-0.29	1	1
Rac1/GTP	-0.066	0.11	0.31	2	-0.29	54	56
MMP1	0.19	0.15	0.31	221	-0.55	1	222

×

Nongenotropic Androgen signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.005	0	-10000	0	-10000	0	0
GNB1/GNG2	-0.042	0.078	-10000	0	-0.14	152	152
regulation of S phase of mitotic cell cycle	-0.055	0.087	-10000	0	-0.17	149	149
GNAO1	-0.085	0.14	-10000	0	-0.29	129	129
HRAS	0.009	0.002	-10000	0	-10000	0	0
SHBG/T-DHT	0.006	0.001	-10000	0	-10000	0	0
PELP1	0.009	0.002	-10000	0	-10000	0	0
AKT1	0.005	0	-10000	0	-10000	0	0
MAP2K1	-0.067	0.083	-10000	0	-0.14	222	222
T-DHT/AR	-0.069	0.096	-10000	0	-0.2	148	148
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
mol:GTP	-0.002	0.003	-10000	0	-0.006	129	129
GNAI2	0.01	0	-10000	0	-10000	0	0
GNAI3	0.01	0	-10000	0	-10000	0	0
GNAI1	0.008	0.025	-10000	0	-0.29	3	3
mol:GDP	-0.1	0.14	-10000	0	-0.29	149	149
cell proliferation	-0.15	0.19	-10000	0	-0.42	129	129
PIK3CA	0.01	0	-10000	0	-10000	0	0
FOS	-0.24	0.34	-10000	0	-0.74	129	129
mol:Ca2+	-0.032	0.035	-10000	0	-0.07	166	166
MAPK3	-0.12	0.14	-10000	0	-0.3	129	129
MAPK1	-0.073	0.097	-10000	0	-0.21	129	129
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
mol:IP3	-0.001	0.002	-10000	0	-0.004	129	129
cAMP biosynthetic process	0.022	0.026	0.061	105	-10000	0	105
GNG2	0.006	0.036	-10000	0	-0.29	6	6
potassium channel inhibitor activity	-0.001	0.002	-10000	0	-0.004	129	129
HRAS/GTP	-0.051	0.074	-10000	0	-0.14	148	148
actin cytoskeleton reorganization	0.014	0.007	-10000	0	-0.12	1	1
SRC	0.009	0.002	-10000	0	-10000	0	0
voltage-gated calcium channel activity	-0.001	0.002	-10000	0	-0.004	129	129
PI3K	0.013	0.009	-10000	0	-0.16	1	1
apoptosis	0.14	0.19	0.42	129	-10000	0	129
T-DHT/AR/PELP1	-0.055	0.082	-10000	0	-0.16	148	148
HRAS/GDP	-0.098	0.14	-10000	0	-0.28	149	149
CREB1	-0.15	0.21	-10000	0	-0.45	129	129
RAC1-CDC42/GTP	0.018	0.007	-10000	0	-0.13	1	1
AR	-0.1	0.14	-10000	0	-0.29	148	148
GNB1	0.01	0	-10000	0	-10000	0	0
RAF1	-0.06	0.075	-10000	0	-0.14	147	147
RAC1-CDC42/GDP	-0.086	0.14	-10000	0	-0.27	148	148
T-DHT/AR/PELP1/Src	-0.048	0.076	-10000	0	-0.15	148	148
MAP2K2	-0.067	0.083	-10000	0	-0.14	222	222
T-DHT/AR/PELP1/Src/PI3K	-0.055	0.088	-10000	0	-0.17	149	149
GNAZ	-0.055	0.12	-10000	0	-0.29	89	89
SHBG	0.009	0.002	-10000	0	-10000	0	0
Gi family/GNB1/GNG2/GDP	-0.13	0.17	-10000	0	-0.34	147	147
mol:T-DHT	0	0.001	-10000	0	-0.002	46	46
RAC1	0.01	0	-10000	0	-10000	0	0
GNRH1	0.005	0	-10000	0	-10000	0	0
Gi family/GTP	-0.11	0.13	-10000	0	-0.24	164	164
CDC42	0.01	0	-10000	0	-10000	0	0

×

Signaling mediated by p38-alpha and p38-beta

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
PTGS2	-0.19	0.39	-10000	0	-0.87	100	100
MKNK1	0.01	0	-10000	0	-10000	0	0
MAPK14	-0.046	0.14	-10000	0	-0.27	105	105
ATF2/c-Jun	-0.048	0.14	-10000	0	-0.51	20	20
MAPK11	-0.046	0.14	-10000	0	-0.27	105	105
MITF	-0.074	0.18	-10000	0	-0.35	101	101
MAPKAPK5	-0.056	0.16	-10000	0	-0.32	98	98
KRT8	-0.061	0.17	-10000	0	-0.34	99	99
MAPKAPK3	0.01	0	-10000	0	-10000	0	0
MAPKAPK2	0.01	0	-10000	0	-10000	0	0
p38alpha-beta/CK2	-0.067	0.19	-10000	0	-0.38	105	105
CEBPB	-0.057	0.16	-10000	0	-0.33	98	98
SLC9A1	-0.056	0.16	-10000	0	-0.32	98	98
mol:GDP	0	0	-10000	0	-10000	0	0
ATF2	-0.055	0.16	-10000	0	-0.32	98	98
p38alpha-beta/MNK1	-0.045	0.16	-10000	0	-0.31	98	98
JUN	-0.048	0.14	-10000	0	-0.54	18	18
PPARGC1A	-0.16	0.21	-10000	0	-0.32	217	217
USF1	-0.056	0.16	-10000	0	-0.32	98	98
RAB5/GDP/GDI1	-0.04	0.11	-10000	0	-0.23	98	98
NOS2	-0.048	0.21	0.33	28	-0.62	16	44
DDIT3	-0.056	0.16	-10000	0	-0.32	98	98
RAB5A	0.01	0	-10000	0	-10000	0	0
HSPB1	-0.046	0.13	-10000	0	-0.26	105	105
p38alpha-beta/HBP1	-0.045	0.16	-10000	0	-0.31	98	98
CREB1	-0.065	0.18	-10000	0	-0.35	105	105
RAB5/GDP	0.007	0	-10000	0	-10000	0	0
EIF4E	-0.047	0.13	-10000	0	-0.27	98	98
RPS6KA4	-0.056	0.16	-10000	0	-0.32	98	98
PLA2G4A	-0.054	0.14	-10000	0	-0.29	100	100
GDI1	-0.056	0.16	-10000	0	-0.32	98	98
TP53	-0.074	0.19	-10000	0	-0.38	105	105
RPS6KA5	-0.062	0.17	-10000	0	-0.34	102	102
ESR1	-0.1	0.2	-10000	0	-0.34	144	144
HBP1	0.01	0	-10000	0	-10000	0	0
MEF2C	-0.064	0.17	-10000	0	-0.34	100	100
MEF2A	-0.056	0.16	-10000	0	-0.32	98	98
EIF4EBP1	-0.062	0.18	0.23	1	-0.35	105	106
KRT19	-0.067	0.17	-10000	0	-0.35	98	98
ELK4	-0.056	0.16	-10000	0	-0.32	98	98
ATF6	-0.056	0.16	-10000	0	-0.32	98	98
ATF1	-0.065	0.18	-10000	0	-0.35	105	105
p38alpha-beta/MAPKAPK2	-0.045	0.16	-10000	0	-0.31	98	98
p38alpha-beta/MAPKAPK3	-0.045	0.16	-10000	0	-0.31	98	98

×

Fc-epsilon receptor I signaling in mast cells

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PPAP2A	0.008	0.021	-10000	0	-0.29	2	2
LAT2	-0.077	0.13	0.18	1	-0.22	162	163
AP1	-0.12	0.18	-10000	0	-0.37	104	104
mol:PIP3	-0.092	0.15	0.19	3	-0.29	124	127
IKBKB	-0.07	0.1	0.14	3	-0.2	142	145
AKT1	-0.041	0.079	-10000	0	-0.16	102	102
IKBKG	-0.07	0.1	0.14	3	-0.2	142	145
MS4A2	-0.072	0.13	-10000	0	-0.29	111	111
mol:Sphingosine-1-phosphate	0	0	-10000	0	-10000	0	0
PIK3CA	0.009	0.001	-10000	0	-10000	0	0
MAP3K1	-0.075	0.14	-10000	0	-0.25	123	123
mol:Ca2+	-0.071	0.12	0.17	3	-0.22	124	127
LYN	0.009	0.003	-10000	0	-10000	0	0
CBLB	-0.077	0.13	-10000	0	-0.21	162	162
SHC1	0.011	0.013	0.27	1	-10000	0	1
RasGAP/p62DOK	-0.027	0.072	-10000	0	-0.14	118	118
positive regulation of cell migration	0	0	-10000	0	-10000	0	0
INPP5D	0.005	0.039	-10000	0	-0.29	7	7
PLD2	-0.053	0.088	-10000	0	-0.15	166	166
PTPN13	-0.085	0.14	-10000	0	-0.36	58	58
PTPN11	0.005	0.01	-10000	0	-10000	0	0
GO:0007205	0	0	-10000	0	-10000	0	0
regulation of mast cell degranulation	-0.051	0.097	-10000	0	-0.23	59	59
SYK	0.006	0.031	-10000	0	-0.3	4	4
GRB2	0.01	0.001	-10000	0	-10000	0	0
LAT/PLCgamma1/GRB2/SLP76/GADs	-0.11	0.14	-10000	0	-0.29	124	124
LAT	-0.076	0.13	0.18	1	-0.21	162	163
PAK2	-0.084	0.15	-10000	0	-0.28	123	123
NFATC2	-0.097	0.17	-10000	0	-0.46	72	72
HRAS	-0.091	0.16	-10000	0	-0.3	125	125
GAB2	0.009	0.015	-10000	0	-0.29	1	1
PLA2G1B	0.022	0.017	-10000	0	-10000	0	0
Fc epsilon R1	-0.067	0.12	0.18	7	-0.2	165	172
Antigen/IgE/Fc epsilon R1	-0.057	0.11	0.17	7	-0.17	165	172
mol:GDP	-0.1	0.18	0.18	2	-0.32	125	127
JUN	-0.002	0.058	-10000	0	-0.29	16	16
mol:Ca++	0	0	-10000	0	-10000	0	0
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
FOS	-0.084	0.14	-10000	0	-0.29	129	129
Antigen/IgE/Fc epsilon R1/LYN/SYK	-0.082	0.13	0.14	1	-0.23	163	164
CHUK	-0.07	0.1	0.14	3	-0.2	142	145
KLRG1	-0.064	0.11	0.16	1	-0.18	161	162
VAV1	-0.08	0.13	-10000	0	-0.22	162	162
calcium-dependent protein kinase C activity	0	0	-10000	0	-10000	0	0
CBL	-0.077	0.13	-10000	0	-0.21	162	162
negative regulation of mast cell degranulation	-0.06	0.11	0.15	1	-0.18	159	160
BTK	-0.11	0.19	-10000	0	-0.35	122	122
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK	-0.09	0.15	-10000	0	-0.24	172	172
GAB2/PI3K/SHP2	-0.055	0.076	-10000	0	-0.17	103	103
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP	-0.079	0.14	-10000	0	-0.25	120	120
RAF1	0.02	0.02	-10000	0	-10000	0	0
Fc epsilon R1/FcgammaRIIB/SHIP	-0.056	0.12	0.17	8	-0.21	120	128
FCER1G	0.02	0.057	0.27	14	-0.29	4	18
FCER1A	-0.069	0.14	0.27	1	-0.3	104	105
Antigen/IgE/Fc epsilon R1/Fyn	-0.05	0.1	0.16	7	-0.16	166	173
MAPK3	0.021	0.017	-10000	0	-10000	0	0
MAPK1	0.021	0.017	-10000	0	-10000	0	0
NFKB1	0.01	0	-10000	0	-10000	0	0
MAPK8	-0.018	0.068	-10000	0	-0.55	3	3
DUSP1	-0.077	0.14	-10000	0	-0.29	119	119
NF-kappa-B/RelA	-0.043	0.064	-10000	0	-0.14	108	108
actin cytoskeleton reorganization	-0.086	0.15	-10000	0	-0.38	54	54
mol:Glucocorticoid Dexamethasone	0	0	-10000	0	-10000	0	0
PI3K	-0.077	0.14	-10000	0	-0.26	123	123
FER	-0.077	0.13	-10000	0	-0.22	162	162
RELA	0.01	0	-10000	0	-10000	0	0
ITK	-0.05	0.12	-10000	0	-0.25	82	82
SOS1	0.01	0	-10000	0	-10000	0	0
PLCG1	-0.098	0.17	0.18	2	-0.32	125	127
cytokine secretion	-0.032	0.047	-10000	0	-0.1	87	87
SPHK1	-0.067	0.13	0.18	6	-0.22	150	156
PTK2	-0.089	0.15	-10000	0	-0.39	54	54
NTAL/PLCgamma1/GRB2/SLP76/GADs	-0.11	0.15	-10000	0	-0.3	123	123
EDG1	0	0	-10000	0	-10000	0	0
mol:DAG	-0.09	0.15	0.17	3	-0.29	123	126
MAP2K2	0.02	0.018	-10000	0	-10000	0	0
MAP2K1	0.02	0.018	-10000	0	-10000	0	0
MAP2K7	0.01	0	-10000	0	-10000	0	0
KLRG1/SHP2	-0.054	0.099	-10000	0	-0.19	104	104
MAP2K4	0.009	0.009	-10000	0	-10000	0	0
Fc epsilon R1/FcgammaRIIB	-0.062	0.12	0.17	8	-0.18	174	182
mol:Choline	-0.052	0.088	-10000	0	-0.15	166	166
SHC/Grb2/SOS1	-0.062	0.12	-10000	0	-0.23	115	115
FYN	0.008	0.025	-10000	0	-0.29	3	3
DOK1	0.011	0.013	0.27	1	-10000	0	1
PXN	-0.083	0.14	-10000	0	-0.36	54	54
HCLS1	-0.077	0.13	-10000	0	-0.22	162	162
PRKCB	-0.099	0.14	0.16	3	-0.27	142	145
FCGR2B	-0.008	0.078	0.27	3	-0.29	27	30
IGHE	-0.002	0.003	-10000	0	-10000	0	0
KLRG1/SHIP	-0.061	0.11	0.15	1	-0.18	159	160
LCP2	0.007	0.026	-10000	0	-0.29	3	3
PLA2G4A	-0.083	0.14	-10000	0	-0.23	162	162
RASA1	0.01	0	-10000	0	-10000	0	0
mol:Phosphatidic acid	-0.052	0.088	-10000	0	-0.15	166	166
IKK complex	-0.05	0.08	0.13	3	-0.16	108	111
WIPF1	0.001	0.05	-10000	0	-0.29	12	12

×

Signaling events mediated by the Hedgehog family

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
TGFB2	0.001	0.19	0.29	43	-0.46	48	91
IHH	0.038	0.083	0.22	47	-0.1	31	78
SHH Np/Cholesterol/GAS1	-0.078	0.089	-10000	0	-0.16	219	219
LRPAP1	0.011	0.013	0.27	1	-10000	0	1
dorsoventral neural tube patterning	0.078	0.088	0.15	219	-10000	0	219
SMO/beta Arrestin2	-0.017	0.13	0.25	1	-0.32	45	46
SMO	-0.02	0.14	0.27	1	-0.34	45	46
AKT1	0.003	0.075	-10000	0	-0.26	8	8
ARRB2	0.01	0	-10000	0	-10000	0	0
BOC	-0.016	0.087	0.27	1	-0.29	37	38
ADRBK1	0.01	0	-10000	0	-10000	0	0
heart looping	-0.02	0.14	0.27	1	-0.33	45	46
STIL	-0.02	0.11	0.24	9	-0.23	45	54
DHH N/PTCH2	-0.005	0.062	-10000	0	-0.2	38	38
DHH N/PTCH1	0.007	0.11	0.25	1	-0.25	48	49
PIK3CA	0.01	0	-10000	0	-10000	0	0
DHH	-0.005	0.063	-10000	0	-0.29	19	19
PTHLH	-0.027	0.28	0.34	40	-0.74	48	88
determination of left/right symmetry	-0.02	0.14	0.27	1	-0.33	45	46
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
skeletal system development	-0.026	0.28	0.34	40	-0.73	48	88
IHH N/Hhip	-0.032	0.12	0.17	26	-0.21	107	133
DHH N/Hhip	-0.048	0.1	0.19	2	-0.2	119	121
mol:Cholesterol	0	0	-10000	0	-10000	0	0
heart development	-0.02	0.14	0.27	1	-0.33	45	46
pancreas development	-0.067	0.13	0.27	2	-0.29	105	107
HHAT	0.01	0	-10000	0	-10000	0	0
PI3K	0.014	0.01	-10000	0	-0.19	1	1
EntrezGene:84976	0	0	-10000	0	-10000	0	0
GAS1	-0.059	0.13	0.27	2	-0.29	96	98
somite specification	-0.02	0.14	0.27	1	-0.33	45	46
SHH Np/Cholesterol/PTCH1	-0.038	0.11	0.23	1	-0.25	51	52
SHH Np/Cholesterol/PTCH2	-0.051	0.079	-10000	0	-0.14	163	163
SHH Np/Cholesterol/Megalin	-0.019	0.094	0.17	48	-0.14	114	162
SHH	-0.066	0.096	-10000	0	-0.19	150	150
catabolic process	0.013	0.12	0.22	29	-0.27	48	77
SMO/Vitamin D3	-0.039	0.13	0.29	1	-0.31	45	46
SHH Np/Cholesterol/Hhip	-0.081	0.099	0.17	1	-0.17	210	211
LRP2	0.062	0.1	0.27	84	-10000	0	84
receptor-mediated endocytosis	-0.035	0.13	0.23	5	-0.31	37	42
SHH Np/Cholesterol/BOC	-0.057	0.083	0.17	1	-0.15	175	176
SHH Np/Cholesterol/CDO	-0.064	0.084	-10000	0	-0.15	194	194
mesenchymal cell differentiation	0.081	0.098	0.17	210	-0.17	1	211
mol:Vitamin D3	-0.031	0.12	0.2	23	-0.27	41	64
IHH N/PTCH2	0.018	0.074	0.16	32	-0.2	25	57
CDON	-0.032	0.1	-10000	0	-0.29	57	57
IHH N/PTCH1	0.024	0.13	0.25	40	-0.27	48	88
Megalin/LRPAP1	0.051	0.072	0.19	85	-10000	0	85
PTCH2	-0.005	0.064	-10000	0	-0.29	20	20
SHH Np/Cholesterol	-0.047	0.072	-10000	0	-0.14	150	150
PTCH1	0.013	0.12	0.22	29	-0.27	48	77
HHIP	-0.067	0.13	0.27	2	-0.29	105	107

×

Syndecan-1-mediated signaling events

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
TGFB1	0.01	0	-10000	0	-10000	0	0
CCL5	0.004	0.08	0.27	13	-0.29	20	33
SDCBP	0.01	0	-10000	0	-10000	0	0
FGFR/FGF2/Syndecan-1	0.084	0.1	0.2	123	-0.18	23	146
mol:PI-4-5-P2	0	0	-10000	0	-10000	0	0
RP11-540L11.1	0	0	-10000	0	-10000	0	0
Syndecan-1/Laminin-5	0.078	0.091	0.18	123	-0.2	11	134
Syndecan-1/Syntenin	0.078	0.091	0.18	123	-0.21	10	133
MAPK3	0.077	0.085	0.17	123	-0.19	10	133
HGF/MET	-0.026	0.09	0.19	9	-0.19	87	96
TGFB1/TGF beta receptor Type II	0.01	0	-10000	0	-10000	0	0
BSG	0.01	0	-10000	0	-10000	0	0
keratinocyte migration	0.077	0.09	0.17	123	-0.2	11	134
Syndecan-1/RANTES	0.079	0.11	0.19	126	-0.24	16	142
Syndecan-1/CD147	0.077	0.086	0.21	39	-0.2	10	49
Syndecan-1/Syntenin/PIP2	0.023	0.061	-10000	0	-0.2	10	10
LAMA5	0.01	0	-10000	0	-10000	0	0
positive regulation of cell-cell adhesion	0.023	0.059	-10000	0	-0.2	10	10
MMP7	0.044	0.13	0.27	78	-0.29	21	99
HGF	-0.049	0.13	0.27	7	-0.29	87	94
Syndecan-1/CASK	0.071	0.09	0.17	123	-0.17	23	146
Syndecan-1/HGF/MET	0.055	0.11	0.23	40	-0.25	20	60
regulation of cell adhesion	0.076	0.084	0.17	123	-0.23	5	128
HPSE	0.031	0.079	0.27	37	-0.29	3	40
positive regulation of cell migration	0.084	0.1	0.2	123	-0.18	23	146
SDC1	0.084	0.1	0.2	123	-0.18	23	146
Syndecan-1/Collagen	0.084	0.1	0.2	123	-0.18	23	146
PPIB	0.01	0	-10000	0	-10000	0	0
MET	0.011	0.018	0.27	2	-10000	0	2
PRKACA	0.01	0	-10000	0	-10000	0	0
MMP9	0.069	0.12	0.27	102	-0.29	8	110
MAPK1	0.077	0.085	0.21	42	-0.24	5	47
homophilic cell adhesion	0.084	0.1	0.2	123	-0.18	23	146
MMP1	0.16	0.13	0.27	230	-0.29	1	231

×

Reelin signaling pathway

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
CDK5R1/CDK5	0.024	0.04	0.19	22	-10000	0	22
VLDLR	0.003	0.046	-10000	0	-0.29	10	10
CRKL	0.011	0.018	0.27	2	-10000	0	2
LRPAP1	0.011	0.013	0.27	1	-10000	0	1
FYN	0.008	0.025	-10000	0	-0.29	3	3
ITGA3	0.014	0.034	0.27	7	-10000	0	7
RELN/VLDLR/Fyn	-0.046	0.09	0.18	4	-0.16	153	157
MAPK8IP1/MKK7/MAP3K11/JNK1	0.028	0.02	0.17	1	-0.13	6	7
AKT1	-0.059	0.1	-10000	0	-0.17	161	161
MAP2K7	0.01	0	-10000	0	-10000	0	0
RAPGEF1	0.01	0	-10000	0	-10000	0	0
DAB1	-0.002	0.11	0.27	25	-0.29	34	59
RELN/LRP8/DAB1	-0.021	0.11	0.18	54	-0.15	123	177
LRPAP1/LRP8	0.048	0.069	0.19	77	-10000	0	77
RELN/LRP8/DAB1/Fyn	-0.017	0.1	0.17	53	-0.14	125	178
DAB1/alpha3/beta1 Integrin	-0.02	0.087	0.2	8	-0.13	125	133
long-term memory	-0.042	0.12	0.17	39	-0.16	157	196
DAB1/LIS1	-0.016	0.097	0.16	33	-0.13	125	158
DAB1/CRLK/C3G	-0.021	0.085	0.2	5	-0.13	125	130
PIK3CA	0.01	0	-10000	0	-10000	0	0
DAB1/NCK2	-0.015	0.098	0.17	29	-0.13	125	154
ARHGEF2	0.01	0	-10000	0	-10000	0	0
mol:Src family inhibitors PP1 and PP2	0	0	-10000	0	-10000	0	0
GRIN2A	-0.055	0.12	0.27	3	-0.29	89	92
CDK5R1	0.024	0.058	0.27	22	-10000	0	22
RELN	-0.093	0.14	0.27	4	-0.29	143	147
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
RELN/LRP8/Fyn	-0.019	0.11	0.19	45	-0.16	114	159
GRIN2A/RELN/LRP8/DAB1/Fyn	-0.047	0.12	0.17	40	-0.17	162	202
MAPK8	0.008	0.025	-10000	0	-0.29	3	3
RELN/VLDLR/DAB1	-0.046	0.098	0.17	19	-0.16	160	179
ITGB1	0.01	0	-10000	0	-10000	0	0
MAP1B	-0.047	0.1	0.16	4	-0.17	131	135
RELN/LRP8	-0.017	0.11	0.19	46	-0.16	111	157
GRIN2B/RELN/LRP8/DAB1/Fyn	-0.012	0.11	0.17	57	-0.14	122	179
PI3K	0.014	0.01	-10000	0	-0.19	1	1
mol:PP2	0	0	-10000	0	-10000	0	0
alpha3/beta1 Integrin	0.018	0.023	0.19	7	-10000	0	7
RAP1A	-0.025	0.074	0.14	5	-0.12	125	130
PAFAH1B1	0.01	0	-10000	0	-10000	0	0
MAPK8IP1	0.008	0.029	0.27	1	-0.29	3	4
CRLK/C3G	0.016	0.012	0.19	2	-10000	0	2
GRIN2B	0.012	0.047	0.27	13	-10000	0	13
NCK2	0.01	0	-10000	0	-10000	0	0
neuron differentiation	-0.03	0.09	0.16	5	-0.2	33	38
neuron adhesion	-0.02	0.073	0.14	9	-0.19	17	26
LRP8	0.058	0.1	0.27	76	-10000	0	76
GSK3B	-0.055	0.095	-10000	0	-0.16	161	161
RELN/VLDLR/DAB1/Fyn	-0.04	0.093	0.16	18	-0.14	162	180
MAP3K11	0.01	0	-10000	0	-10000	0	0
RELN/VLDLR/DAB1/P13K	-0.064	0.11	-10000	0	-0.19	161	161
CDK5	0.01	0	-10000	0	-10000	0	0
MAPT	-0.009	0.075	0.18	2	-0.25	34	36
neuron migration	-0.057	0.12	0.18	8	-0.2	156	164
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1	-0.031	0.091	0.16	5	-0.2	33	38
RELN/VLDLR	-0.013	0.1	0.18	43	-0.14	115	158

×

PLK1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
regulation of centriole-centriole cohesion	-0.052	0.052	-10000	0	-0.11	172	172
BUB1B	0.073	0.066	0.14	169	-10000	0	169
PLK1	0.034	0.031	0.081	105	-10000	0	105
PLK1S1	0.019	0.014	-10000	0	-10000	0	0
KIF2A	0.032	0.028	0.078	80	-10000	0	80
regulation of mitotic centrosome separation	0.034	0.031	0.081	105	-10000	0	105
GOLGA2	0.01	0	-10000	0	-10000	0	0
Hec1/SPC24	0.15	0.14	0.29	195	-10000	0	195
WEE1	0.042	0.035	0.13	6	-10000	0	6
cytokinesis	0.12	0.078	0.18	212	-0.14	5	217
PP2A-alpha B56	0.058	0.057	0.3	1	-10000	0	1
AURKA	0.045	0.05	0.12	124	-10000	0	124
PICH/PLK1	0.084	0.088	0.18	167	-10000	0	167
CENPE	0.048	0.051	0.12	126	-10000	0	126
RhoA/GTP	0.007	0	-10000	0	-10000	0	0
positive regulation of microtubule depolymerization	0.032	0.028	0.078	80	-10000	0	80
PPP2CA	0.01	0	-10000	0	-10000	0	0
FZR1	0.01	0	-10000	0	-10000	0	0
TPX2	0.069	0.057	0.12	219	-10000	0	219
PAK1	0.009	0.015	-10000	0	-0.3	1	1
SPC24	0.11	0.12	0.27	153	-10000	0	153
FBXW11	0.01	0	-10000	0	-10000	0	0
CLSPN	0.061	0.061	0.14	152	-10000	0	152
GORASP1	0.01	0	-10000	0	-10000	0	0
metaphase	0	0.001	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
NLP	0.016	0.014	0.037	95	-10000	0	95
G2 phase of mitotic cell cycle	0.001	0.002	-10000	0	-10000	0	0
STAG2	0.008	0.021	-10000	0	-0.29	2	2
GRASP65/GM130/RAB1/GTP	0.011	0.01	-10000	0	-10000	0	0
spindle elongation	0.034	0.031	0.081	105	-10000	0	105
ODF2	0.011	0.002	-10000	0	-10000	0	0
BUB1	0.045	0.073	0.36	1	-10000	0	1
TPT1	0.019	0.014	-10000	0	-10000	0	0
CDC25C	0.097	0.068	0.15	252	-10000	0	252
CDC25B	0.018	0.032	0.28	6	-10000	0	6
SGOL1	0.052	0.052	0.11	172	-10000	0	172
RHOA	0.01	0	-10000	0	-10000	0	0
CCNB1/CDK1	0.073	0.084	0.18	145	-10000	0	145
CDC14B	0.005	0.01	-10000	0	-0.2	1	1
CDC20	0.16	0.13	0.27	231	-10000	0	231
PLK1/PBIP1	0.012	0.027	0.14	15	-10000	0	15
mitosis	0	0.002	-10000	0	-10000	0	0
FBXO5	0.029	0.025	0.077	43	-10000	0	43
CDC2	0.004	0.005	0.01	145	-10000	0	145
NDC80	0.096	0.12	0.27	135	-10000	0	135
metaphase plate congression	0.025	0.021	-10000	0	-10000	0	0
ERCC6L	0.083	0.087	0.18	167	-10000	0	167
NLP/gamma Tubulin	0.018	0.014	0.045	39	-10000	0	39
microtubule cytoskeleton organization	0.019	0.014	-10000	0	-10000	0	0
G2/M transition DNA damage checkpoint	0	0.001	0.009	1	-10000	0	1
PPP1R12A	0.01	0.001	-10000	0	-10000	0	0
interphase	0	0.001	0.009	1	-10000	0	1
PLK1/PRC1-2	0.18	0.12	0.24	302	-10000	0	302
GRASP65/GM130/RAB1/GTP/PLK1	0.039	0.02	-10000	0	-10000	0	0
RAB1A	0.01	0	-10000	0	-10000	0	0
prophase	0	0	-10000	0	-10000	0	0
Aurora A/BORA	0.03	0.029	0.077	98	-10000	0	98
mitotic prometaphase	0.001	0.001	-10000	0	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.059	0.038	-10000	0	-10000	0	0
microtubule-based process	0.16	0.09	0.21	300	-10000	0	300
Golgi organization	0.034	0.031	0.081	105	-10000	0	105
Cohesin/SA2	0.032	0.027	0.078	39	-0.13	2	41
PPP1CB/MYPT1	0.016	0.002	-10000	0	-10000	0	0
KIF20A	0.2	0.11	0.27	300	-10000	0	300
APC/C/CDC20	0.13	0.1	0.22	232	-10000	0	232
PPP2R1A	0.01	0	-10000	0	-10000	0	0
chromosome segregation	0.011	0.027	0.14	15	-10000	0	15
PRC1	0.06	0.1	0.27	79	-10000	0	79
ECT2	0.04	0.044	0.11	95	-10000	0	95
C13orf34	0.029	0.027	0.074	81	-10000	0	81
NUDC	0.025	0.021	-10000	0	-10000	0	0
regulation of attachment of spindle microtubules to kinetochore	0.072	0.066	0.14	169	-10000	0	169
spindle assembly	0.026	0.022	0.061	91	-10000	0	91
spindle stabilization	0.019	0.014	-10000	0	-10000	0	0
APC/C/HCDH1	0.011	0.008	-10000	0	-0.16	1	1
MKLP2/PLK1	0.16	0.09	0.21	300	-10000	0	300
CCNB1	0.1	0.12	0.27	145	-10000	0	145
PPP1CB	0.01	0.001	-10000	0	-10000	0	0
BTRC	0.01	0	-10000	0	-10000	0	0
ROCK2	0.023	0.052	-10000	0	-0.34	7	7
TUBG1	0.019	0.014	-10000	0	-10000	0	0
G2/M transition of mitotic cell cycle	0.05	0.059	0.13	145	-10000	0	145
MLF1IP	0.011	0.029	0.16	15	-10000	0	15
INCENP	0.011	0.013	0.27	1	-10000	0	1

×

IL4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.36	0.58	0.78	2	-1.1	113	115
STAT6 (cleaved dimer)	-0.47	0.52	-10000	0	-1	157	157
IGHG1	-0.091	0.24	0.48	12	-0.39	35	47
IGHG3	-0.35	0.55	0.66	2	-1	137	139
AKT1	-0.17	0.34	0.56	4	-0.67	69	73
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1	-0.13	0.3	0.51	5	-0.69	43	48
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1	-0.17	0.34	0.58	4	-0.66	68	72
THY1	-0.36	0.58	0.78	2	-1.1	114	116
MYB	0.045	0.091	0.27	56	-0.29	1	57
HMGA1	0.015	0.036	0.27	8	-10000	0	8
IL4/IL4R/JAK1/IL2R gamma/JAK3	-0.22	0.42	0.62	10	-0.76	100	110
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP	-0.17	0.34	0.58	4	-0.65	71	75
SP1	0.008	0.025	-10000	0	-10000	0	0
INPP5D	0.005	0.039	-10000	0	-0.29	7	7
SOCS5	0.017	0.028	-10000	0	-10000	0	0
STAT6 (dimer)/ETS1	-0.39	0.59	0.62	2	-1.1	136	138
SOCS1	-0.23	0.39	0.57	5	-0.71	115	120
SOCS3	-0.25	0.46	0.6	2	-1.2	57	59
FCER2	-0.58	0.73	0.8	5	-1.3	185	190
PARP14	0.002	0.023	-10000	0	-0.14	2	2
CCL17	-0.34	0.6	0.84	8	-1.1	110	118
GRB2	0.01	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP	-0.13	0.27	0.54	4	-0.52	55	59
T cell proliferation	-0.38	0.59	0.67	2	-1.1	123	125
IL4R/JAK1	-0.37	0.57	0.64	2	-1.1	134	136
EGR2	-0.52	0.73	0.83	2	-1.3	157	159
JAK2	-0.006	0.059	0.17	8	-0.32	1	9
JAK3	0.009	0.024	0.32	2	-10000	0	2
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
JAK1	0.012	0.022	-10000	0	-10000	0	0
COL1A2	-0.16	0.39	0.5	2	-1.4	27	29
CCL26	-0.36	0.59	0.77	2	-1.1	118	120
IL4R	-0.38	0.63	0.8	7	-1.2	123	130
PTPN6	0.015	0.022	0.22	1	-10000	0	1
IL13RA2	-0.37	0.6	0.85	3	-1.1	114	117
IL13RA1	-0.006	0.059	0.17	7	-0.33	1	8
IRF4	-0.2	0.44	0.66	3	-1.1	60	63
ARG1	-0.05	0.21	0.52	7	-0.65	5	12
CBL	-0.21	0.39	0.58	6	-0.7	105	111
GTF3A	0.012	0.021	0.15	5	-10000	0	5
PIK3CA	0.01	0	-10000	0	-10000	0	0
IL13RA1/JAK2	-0.001	0.085	0.24	10	-0.23	2	12
IRF4/BCL6	-0.17	0.4	0.47	1	-1	58	59
CD40LG	-0.028	0.097	0.25	3	-0.29	44	47
MAPK14	-0.23	0.42	0.62	4	-0.8	96	100
mitosis	-0.16	0.32	0.56	4	-0.63	69	73
STAT6	-0.41	0.7	0.87	9	-1.2	134	143
SPI1	0.018	0.048	0.27	5	-0.29	4	9
RPS6KB1	-0.16	0.31	0.54	4	-0.61	67	71
STAT6 (dimer)	-0.41	0.7	0.87	9	-1.2	134	143
STAT6 (dimer)/PARP14	-0.43	0.63	0.72	1	-1.1	152	153
mast cell activation	0.006	0.02	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2	-0.17	0.35	0.58	4	-0.69	67	71
FRAP1	-0.17	0.34	0.56	4	-0.67	69	73
LTA	-0.37	0.6	0.83	3	-1.1	116	119
FES	0.009	0.015	-10000	0	-0.29	1	1
T-helper 1 cell differentiation	0.4	0.68	1.2	134	-0.87	9	143
CCL11	-0.39	0.61	-10000	0	-1.2	120	120
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES	-0.17	0.34	0.58	4	-0.67	67	71
IL2RG	0.006	0.062	0.28	9	-0.28	10	19
IL10	-0.38	0.61	0.78	2	-1.2	117	119
IRS1	0.003	0.046	-10000	0	-0.29	10	10
IRS2	-0.002	0.058	-10000	0	-0.29	16	16
IL4	-0.055	0.19	0.63	2	-10000	0	2
IL5	-0.36	0.58	0.87	2	-1.1	113	115
IL4/IL4R/JAK1/IL13RA1/JAK2	-0.26	0.48	0.76	9	-0.84	114	123
COL1A1	-0.12	0.33	0.6	3	-1.5	12	15
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1	-0.38	0.59	-10000	0	-1.1	114	114
IL2R gamma/JAK3	0.01	0.053	0.25	9	-0.19	10	19
TFF3	-0.48	0.71	0.84	4	-1.3	149	153
ALOX15	-0.33	0.6	0.8	8	-1.1	109	117
MYBL1	0.012	0.026	0.27	4	-10000	0	4
T-helper 2 cell differentiation	-0.3	0.5	0.67	4	-0.9	123	127
SHC1	0.011	0.013	0.27	1	-10000	0	1
CEBPB	0.017	0.029	-10000	0	-0.29	1	1
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2	-0.16	0.33	0.56	4	-0.6	81	85
mol:PI-3-4-5-P3	-0.17	0.34	0.57	4	-0.67	69	73
PI3K	-0.18	0.36	0.57	4	-0.72	69	73
DOK2	0.002	0.056	0.27	2	-0.29	13	15
ETS1	0.011	0.028	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2	-0.12	0.26	0.46	10	-0.48	56	66
ITGB3	-0.42	0.65	0.78	2	-1.2	127	129
PIGR	-0.6	0.72	0.8	6	-1.2	198	204
IGHE	0.023	0.066	0.12	1	-0.2	9	10
MAPKKK cascade	-0.11	0.26	0.45	10	-0.48	55	65
BCL6	0.014	0.012	-10000	0	-10000	0	0
OPRM1	-0.36	0.58	0.77	2	-1.1	113	115
RETNLB	-0.36	0.58	0.77	2	-1.1	114	116
SELP	-0.47	0.7	0.78	2	-1.3	141	143
AICDA	-0.35	0.56	0.72	3	-1.1	114	117

×

IL23-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCL2	-0.067	0.64	0.83	40	-1.2	69	109
IL23A	-0.018	0.58	0.92	33	-1.1	50	83
NF kappa B1 p50/RelA/I kappa B alpha	-0.21	0.4	-10000	0	-0.99	70	70
positive regulation of T cell mediated cytotoxicity	-0.021	0.64	0.93	51	-1.1	70	121
ITGA3	-0.02	0.56	0.83	35	-1.1	50	85
IL17F	0.007	0.4	0.61	50	-0.65	69	119
IL12B	0.053	0.11	0.28	57	-10000	0	57
STAT1 (dimer)	-0.051	0.58	0.74	42	-1.1	70	112
CD4	-0.017	0.56	0.83	41	-0.97	69	110
IL23	-0.027	0.55	0.83	29	-1.1	49	78
IL23R	0.072	0.21	0.56	35	-10000	0	35
IL1B	-0.031	0.62	0.91	36	-1.2	51	87
T-helper cell lineage commitment	0	0	-10000	0	-10000	0	0
IL24	0.001	0.58	0.92	44	-1	57	101
TYK2	0.03	0.063	0.18	34	-10000	0	34
STAT4	-0.005	0.064	-10000	0	-0.29	20	20
STAT3	0.01	0.002	-10000	0	-10000	0	0
IL18RAP	-0.001	0.067	-10000	0	-0.29	21	21
IL12RB1	0.036	0.11	0.25	51	-0.32	10	61
PIK3CA	0.01	0.002	-10000	0	-10000	0	0
IL12Rbeta1/TYK2	0.04	0.1	0.22	59	-0.23	10	69
IL23R/JAK2	0.08	0.22	0.54	42	-10000	0	42
positive regulation of chronic inflammatory response	-0.021	0.64	0.93	51	-1.1	70	121
natural killer cell activation	-0.007	0.019	-10000	0	-0.058	25	25
JAK2	0.046	0.096	0.25	48	-0.32	1	49
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
NFKB1	0.012	0.01	-10000	0	-10000	0	0
RELA	0.012	0.01	-10000	0	-10000	0	0
positive regulation of dendritic cell antigen processing and presentation	-0.019	0.53	0.83	29	-1	50	79
ALOX12B	-0.005	0.56	0.87	42	-1	54	96
CXCL1	-0.046	0.64	0.9	44	-1.1	76	120
T cell proliferation	-0.021	0.64	0.93	51	-1.1	70	121
NFKBIA	0.012	0.01	-10000	0	-10000	0	0
IL17A	0.035	0.35	0.58	51	-0.52	57	108
PI3K	-0.21	0.41	-10000	0	-1	70	70
IFNG	0.038	0.079	0.17	87	-0.084	2	89
STAT3 (dimer)	-0.21	0.39	-10000	0	-0.97	70	70
IL18R1	0.012	0.027	-10000	0	-0.28	3	3
IL23/IL23R/JAK2/TYK2/SOCS3	0.025	0.43	0.68	56	-0.69	57	113
IL18/IL18R	0.029	0.072	0.15	1	-0.17	27	28
macrophage activation	0.002	0.037	0.07	66	-0.044	42	108
TNF	-0.016	0.59	0.92	36	-1.1	50	86
STAT3/STAT4	-0.22	0.42	-10000	0	-1	71	71
STAT4 (dimer)	-0.059	0.58	0.74	40	-1.1	70	110
IL18	0.01	0.037	-10000	0	-0.29	6	6
IL19	-0.007	0.56	0.85	41	-1	53	94
STAT5A (dimer)	-0.053	0.57	0.74	40	-1.1	70	110
STAT1	0.012	0.026	0.27	4	-10000	0	4
SOCS3	-0.022	0.092	-10000	0	-0.29	43	43
CXCL9	0.003	0.61	0.89	51	-1.1	53	104
MPO	-0.015	0.56	0.83	40	-1	54	94
positive regulation of humoral immune response	-0.021	0.64	0.93	51	-1.1	70	121
IL23/IL23R/JAK2/TYK2	-0.035	0.67	0.93	51	-1.2	70	121
IL6	-0.31	0.77	0.82	38	-1.1	181	219
STAT5A	0.009	0.015	-10000	0	-0.29	1	1
IL2	0.015	0.03	-10000	0	-10000	0	0
positive regulation of tyrosine phosphorylation of STAT protein	-0.007	0.019	-10000	0	-0.058	25	25
CD3E	-0.062	0.63	0.83	41	-1.1	77	118
keratinocyte proliferation	-0.021	0.64	0.93	51	-1.1	70	121
NOS2	-0.014	0.57	0.86	42	-1	58	100

×

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

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
MAP4K1	-0.072	0.17	0.19	2	-0.36	97	99
CRKL	-0.075	0.18	0.2	2	-0.38	97	99
HRAS	-0.071	0.17	-10000	0	-0.35	99	99
mol:PIP3	-0.073	0.16	-10000	0	-0.36	96	96
SPRED1	0.01	0	-10000	0	-10000	0	0
SPRED2	0.01	0	-10000	0	-10000	0	0
GAB1	-0.08	0.18	0.21	2	-0.4	97	99
FOXO3	-0.065	0.16	-10000	0	-0.36	90	90
AKT1	-0.072	0.17	-10000	0	-0.39	90	90
BAD	-0.065	0.16	-10000	0	-0.36	90	90
megakaryocyte differentiation	-0.079	0.18	0.21	2	-0.4	96	98
GSK3B	-0.065	0.16	-10000	0	-0.36	90	90
RAF1	-0.057	0.14	-10000	0	-0.29	99	99
SHC1	0.011	0.013	0.27	1	-10000	0	1
STAT3	-0.08	0.18	0.21	2	-0.4	97	99
STAT1	-0.19	0.41	-10000	0	-0.91	97	97
HRAS/SPRED1	-0.054	0.14	-10000	0	-0.29	99	99
cell proliferation	-0.079	0.18	0.21	2	-0.4	97	99
PIK3CA	0.01	0	-10000	0	-10000	0	0
TEC	0.01	0	-10000	0	-10000	0	0
RPS6KB1	-0.077	0.18	-10000	0	-0.4	96	96
HRAS/SPRED2	-0.054	0.14	-10000	0	-0.29	99	99
LYN/TEC/p62DOK	-0.065	0.18	-10000	0	-0.39	90	90
MAPK3	-0.037	0.1	-10000	0	-0.21	99	99
STAP1	-0.081	0.19	0.21	2	-0.41	97	99
GRAP2	-0.023	0.093	-10000	0	-0.29	45	45
JAK2	-0.16	0.35	-10000	0	-0.77	97	97
STAT1 (dimer)	-0.18	0.4	-10000	0	-0.89	97	97
mol:Gleevec	0.003	0.007	-10000	0	-10000	0	0
GRB2/SOCS1/VAV1	-0.069	0.18	-10000	0	-0.39	97	97
actin filament polymerization	-0.078	0.18	0.22	3	-0.39	97	100
LYN	0.01	0	-10000	0	-10000	0	0
STAP1/STAT5A (dimer)	-0.11	0.26	-10000	0	-0.56	97	97
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
CBL/CRKL/GRB2	-0.06	0.16	-10000	0	-0.36	90	90
PI3K	-0.067	0.18	-10000	0	-0.4	90	90
PTEN	0.01	0	-10000	0	-10000	0	0
SCF/KIT/EPO/EPOR	-0.21	0.48	-10000	0	-1.1	90	90
MAPK8	-0.081	0.18	0.21	2	-0.4	97	99
STAT3 (dimer)	-0.078	0.18	0.21	2	-0.39	97	99
positive regulation of transcription	-0.029	0.086	0.14	1	-0.17	98	99
mol:GDP	-0.072	0.17	-10000	0	-0.36	99	99
PIK3C2B	-0.08	0.18	0.21	2	-0.4	97	99
CBL/CRKL	-0.066	0.17	-10000	0	-0.36	97	97
FER	-0.081	0.18	0.21	2	-0.4	97	99
SH2B3	-0.08	0.18	0.21	2	-0.4	97	99
PDPK1	-0.067	0.15	-10000	0	-0.35	90	90
SNAI2	-0.081	0.19	0.21	2	-0.41	97	99
positive regulation of cell proliferation	-0.14	0.31	-10000	0	-0.68	97	97
KITLG	0	0.039	-10000	0	-0.31	5	5
cell motility	-0.14	0.31	-10000	0	-0.68	97	97
PTPN6	0.014	0.016	0.27	1	-10000	0	1
EPOR	-0.039	0.14	-10000	0	-10000	0	0
STAT5A (dimer)	-0.11	0.26	-10000	0	-0.56	97	97
SOCS1	0.011	0.013	0.27	1	-10000	0	1
cell migration	0.081	0.19	0.41	98	-0.21	2	100
SOS1	0.01	0	-10000	0	-10000	0	0
EPO	0.024	0.069	0.26	31	-10000	0	31
VAV1	-0.001	0.061	0.27	2	-0.29	16	18
GRB10	-0.081	0.18	0.21	2	-0.4	97	99
PTPN11	0.012	0.008	-10000	0	-10000	0	0
SCF/KIT	-0.085	0.19	0.22	2	-0.42	97	99
GO:0007205	0.004	0.01	-10000	0	-10000	0	0
MAP2K1	-0.043	0.11	-10000	0	-0.23	99	99
CBL	0.01	0	-10000	0	-10000	0	0
KIT	-0.24	0.5	-10000	0	-1.2	90	90
MAP2K2	-0.043	0.11	-10000	0	-0.23	99	99
SHC/Grb2/SOS1	-0.065	0.18	-10000	0	-0.38	96	96
STAT5A	-0.12	0.26	-10000	0	-0.58	97	97
GRB2	0.01	0	-10000	0	-10000	0	0
response to radiation	-0.079	0.18	0.21	2	-0.4	97	99
SHC/GRAP2	-0.008	0.066	0.19	1	-0.19	45	46
PTPRO	-0.081	0.18	0.21	2	-0.41	96	98
SH2B2	-0.079	0.18	0.22	3	-0.4	97	100
DOK1	0.011	0.013	0.27	1	-10000	0	1
MATK	-0.083	0.19	0.21	2	-0.41	98	100
CREBBP	-0.004	0.056	0.16	6	-0.16	8	14
BCL2	-0.077	0.26	-10000	0	-1.2	16	16

×

Thromboxane A2 receptor signaling

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
TGM2	0.004	0.063	0.27	7	-0.29	13	20
GNB1/GNG2	-0.077	0.088	-10000	0	-0.18	167	167
AKT1	-0.062	0.12	0.31	5	-0.19	166	171
EGF	0.025	0.062	0.27	25	-10000	0	25
mol:TXA2	0	0.001	-10000	0	-10000	0	0
FGR	0.004	0.03	-10000	0	-0.12	17	17
mol:Ca2+	-0.1	0.16	0.37	5	-0.29	166	171
LYN	0.004	0.03	-10000	0	-0.12	19	19
RhoA/GTP	-0.045	0.067	-10000	0	-0.12	166	166
mol:PGI2	0	0	-10000	0	-10000	0	0
SYK	-0.12	0.18	0.38	5	-0.33	166	171
GNG2	0.005	0.036	-10000	0	-0.29	6	6
ARRB2	0.01	0	-10000	0	-10000	0	0
TP alpha/Gq family/GDP/G beta5/gamma2	-0.004	0.05	-10000	0	-0.28	5	5
G beta5/gamma2	-0.099	0.12	-10000	0	-0.24	167	167
PRKCH	-0.12	0.19	0.38	5	-0.34	166	171
DNM1	0.002	0.048	-10000	0	-0.29	11	11
TXA2/TP beta/beta Arrestin3	0	0.027	-10000	0	-10000	0	0
mol:GTP	-0.001	0.002	-10000	0	-10000	0	0
PTGDR	-0.005	0.063	-10000	0	-0.29	19	19
G12 family/GTP	-0.12	0.14	-10000	0	-0.3	166	166
ADRBK1	0.01	0	-10000	0	-10000	0	0
ADRBK2	0.01	0.02	0.27	1	-0.29	1	2
RhoA/GTP/ROCK1	0.013	0.001	-10000	0	-10000	0	0
mol:GDP	0.055	0.1	0.19	80	-0.25	5	85
mol:NADP	0.01	0.013	0.27	1	-10000	0	1
RAB11A	0.01	0	-10000	0	-10000	0	0
PRKG1	-0.059	0.13	-10000	0	-0.29	94	94
mol:IP3	-0.13	0.2	0.4	5	-0.36	166	171
cell morphogenesis	0.013	0.001	-10000	0	-10000	0	0
PLCB2	-0.18	0.27	0.5	3	-0.49	166	169
mol:cGMP	0	0.001	-10000	0	-10000	0	0
BLK	0.008	0.044	0.15	16	-0.13	19	35
mol:PDG2	0	0	-10000	0	-10000	0	0
HCK	0.005	0.04	0.16	5	-0.14	19	24
RHOA	0.01	0	-10000	0	-10000	0	0
PTGIR	0.009	0.015	-10000	0	-0.29	1	1
PRKCB1	-0.13	0.2	0.39	5	-0.36	166	171
GNAQ	0.01	0	-10000	0	-10000	0	0
mol:L-citrulline	0.01	0.013	0.27	1	-10000	0	1
TXA2/TXA2-R family	-0.19	0.27	0.51	3	-0.51	166	169
LCK	0.005	0.033	0.15	2	-0.13	19	21
TXA2/TP beta/beta Arrestin3/RAB11/GDP	0.007	0.032	-10000	0	-0.13	19	19
TXA2-R family/G12 family/GDP/G beta/gamma	0.013	0.02	-10000	0	-10000	0	0
TXA2/TP beta/beta Arrestin2/RAB11/GDP	0.012	0.033	-10000	0	-0.13	19	19
MAPK14	-0.075	0.13	0.32	5	-0.22	166	171
TGM2/GTP	-0.15	0.23	0.42	5	-0.41	166	171
MAPK11	-0.075	0.13	0.32	5	-0.22	166	171
ARHGEF1	-0.058	0.1	0.25	5	-0.17	166	171
GNAI2	0.01	0	-10000	0	-10000	0	0
JNK cascade	-0.13	0.21	0.4	5	-0.38	166	171
RAB11/GDP	0.01	0.002	-10000	0	-10000	0	0
ICAM1	-0.095	0.16	0.38	5	-0.28	163	168
cAMP biosynthetic process	-0.12	0.19	0.36	5	-0.34	166	171
Gq family/GTP/EBP50	-0.006	0.056	-10000	0	-0.14	52	52
actin cytoskeleton reorganization	0.013	0.001	-10000	0	-10000	0	0
SRC	0.004	0.03	-10000	0	-0.12	19	19
GNB5	0.01	0	-10000	0	-10000	0	0
GNB1	0.01	0	-10000	0	-10000	0	0
EGF/EGFR	0.006	0.048	-10000	0	-0.17	11	11
VCAM1	-0.1	0.16	0.36	5	-0.3	164	169
TP beta/Gq family/GDP/G beta5/gamma2	-0.004	0.05	-10000	0	-0.28	5	5
platelet activation	-0.099	0.17	0.38	5	-0.29	166	171
PGI2/IP	0.006	0.01	-10000	0	-0.2	1	1
PRKACA	0.001	0.038	-10000	0	-0.16	20	20
Gq family/GDP/G beta5/gamma2	-0.005	0.049	-10000	0	-0.26	5	5
TXA2/TP beta/beta Arrestin2	-0.002	0.068	-10000	0	-0.4	11	11
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TBXA2R	0.001	0.036	-10000	0	-0.15	20	20
mol:DAG	-0.14	0.22	0.41	5	-0.4	166	171
EGFR	0.008	0.057	0.27	8	-0.29	9	17
TXA2/TP alpha	-0.17	0.25	0.49	3	-0.46	166	169
Gq family/GTP	-0.017	0.065	-10000	0	-0.17	61	61
YES1	0.004	0.03	-10000	0	-0.13	13	13
GNAI2/GTP	0	0.033	-10000	0	-0.14	19	19
PGD2/DP	-0.003	0.042	-10000	0	-0.2	19	19
SLC9A3R1	0.023	0.057	0.27	21	-10000	0	21
FYN	0.004	0.032	-10000	0	-0.13	19	19
mol:NO	0.01	0.013	0.27	1	-10000	0	1
GNA15	0.008	0.025	-10000	0	-0.29	3	3
PGK/cGMP	-0.027	0.073	0.17	1	-0.16	94	95
RhoA/GDP	0.01	0.002	-10000	0	-10000	0	0
TP alpha/TGM2/GDP/G beta/gamma	0.015	0.053	0.16	7	-0.16	23	30
NOS3	0.01	0.013	0.27	1	-10000	0	1
RAC1	0.01	0	-10000	0	-10000	0	0
PRKCA	-0.12	0.19	0.38	5	-0.34	166	171
PRKCB	-0.14	0.2	0.36	5	-0.38	166	171
PRKCE	-0.12	0.19	0.39	5	-0.34	166	171
PRKCD	-0.13	0.2	0.39	5	-0.37	166	171
PRKCG	-0.13	0.21	0.39	5	-0.37	166	171
muscle contraction	-0.17	0.26	0.42	5	-0.47	166	171
PRKCZ	-0.12	0.19	0.38	5	-0.33	166	171
ARR3	0.002	0.004	-10000	0	-10000	0	0
TXA2/TP beta	0.009	0.037	0.16	1	-0.15	19	20
PRKCQ	-0.12	0.2	0.38	5	-0.35	166	171
MAPKKK cascade	-0.16	0.24	0.4	5	-0.44	166	171
SELE	-0.13	0.2	0.36	5	-0.36	166	171
TP beta/GNAI2/GDP/G beta/gamma	0.016	0.038	-10000	0	-0.14	19	19
ROCK1	0.01	0	-10000	0	-10000	0	0
GNA14	-0.032	0.1	-10000	0	-0.29	58	58
chemotaxis	-0.22	0.31	0.54	3	-0.59	166	169
GNA12	0.01	0	-10000	0	-10000	0	0
GNA13	0.01	0	-10000	0	-10000	0	0
GNA11	0.009	0.015	-10000	0	-0.29	1	1
Rac1/GTP	0.007	0.002	-10000	0	-10000	0	0

×

p75(NTR)-mediated signaling

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
Sortilin/TRAF6	0.015	0	-10000	0	-10000	0	0
Necdin/E2F1	0.029	0.1	0.19	81	-0.19	33	114
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E	-0.024	0.092	0.17	5	-0.16	121	126
NGF (dimer)/p75(NTR)/BEX1	-0.05	0.12	0.2	10	-0.2	137	147
NT-4/5 (dimer)/p75(NTR)	-0.042	0.1	0.19	4	-0.2	108	112
IKBKB	0.01	0	-10000	0	-10000	0	0
AKT1	-0.035	0.081	-10000	0	-0.15	122	122
IKBKG	0.01	0	-10000	0	-10000	0	0
BDNF	-0.047	0.12	-10000	0	-0.29	78	78
MGDIs/NGR/p75(NTR)/LINGO1	0.013	0.11	0.2	66	-0.16	78	144
FURIN	0.011	0.013	0.27	1	-10000	0	1
proBDNF (dimer)/p75(NTR)/Sortilin	-0.049	0.1	0.18	5	-0.18	145	150
LINGO1	0.022	0.055	0.27	19	-10000	0	19
Sortilin/TRAF6/NRIF	0.013	0	-10000	0	-10000	0	0
proBDNF (dimer)	-0.047	0.12	-10000	0	-0.29	78	78
NTRK1	0.013	0.034	0.27	7	-10000	0	7
RTN4R	0.049	0.093	0.27	62	-10000	0	62
neuron apoptosis	-0.037	0.12	-10000	0	-0.28	40	40
IRAK1	0.01	0	-10000	0	-10000	0	0
SHC1	-0.045	0.096	0.12	5	-0.18	120	125
ARHGDIA	0.01	0	-10000	0	-10000	0	0
RhoA/GTP	0.007	0	-10000	0	-10000	0	0
Gamma Secretase	0.03	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1	-0.03	0.096	0.18	5	-0.17	121	126
MAGEH1	0.008	0.021	-10000	0	-0.29	2	2
proNGF (dimer)/p75(NTR)/Sortilin/Necdin	-0.047	0.11	0.18	4	-0.18	143	147
Mammalian IAPs/DIABLO	0.019	0.045	0.21	5	-0.14	22	27
proNGF (dimer)	-0.03	0.1	-10000	0	-0.29	54	54
MAGED1	0.01	0	-10000	0	-10000	0	0
APP	0.008	0.021	-10000	0	-0.29	2	2
NT-4/5 (dimer)	-0.01	0.074	-10000	0	-0.29	27	27
ZNF274	0.01	0	-10000	0	-10000	0	0
RhoA/GDP/RHOGDI	-0.032	0.084	-10000	0	-0.15	121	121
NGF	-0.03	0.1	-10000	0	-0.29	54	54
cell cycle arrest	-0.026	0.07	0.099	17	-0.12	121	138
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK	-0.045	0.1	-10000	0	-0.2	121	121
NT-4/5 (dimer)/p75(NTR)/TRAF6	-0.028	0.088	0.18	4	-0.17	107	111
NCSTN	0.01	0	-10000	0	-10000	0	0
mol:GTP	-0.04	0.1	0.18	5	-0.18	123	128
PSENEN	0.01	0	-10000	0	-10000	0	0
mol:ceramide	-0.038	0.086	-10000	0	-0.16	121	121
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs	-0.039	0.096	-10000	0	-0.3	24	24
p75(NTR)/beta APP	-0.03	0.091	0.19	5	-0.19	91	96
BEX1	-0.011	0.088	0.27	7	-0.29	32	39
mol:GDP	-0.05	0.095	0.11	5	-0.19	121	126
NGF (dimer)	0.021	0.094	0.17	76	-0.15	63	139
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI	0.019	0.1	0.2	66	-0.14	78	144
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
RAC1/GTP	-0.032	0.086	0.16	5	-0.15	121	126
MYD88	0.01	0	-10000	0	-10000	0	0
CHUK	0.01	0	-10000	0	-10000	0	0
NGF (dimer)/p75(NTR)/PKA	-0.04	0.1	0.18	5	-0.18	123	128
RHOB	0.01	0	-10000	0	-10000	0	0
RHOA	0.01	0	-10000	0	-10000	0	0
MAGE-G1/E2F1	0.057	0.075	0.19	97	-10000	0	97
NT3 (dimer)	-0.045	0.12	0.27	1	-0.29	76	77
TP53	-0.039	0.079	-10000	0	-0.14	145	145
PRDM4	-0.039	0.087	-10000	0	-0.16	121	121
BDNF (dimer)	0.003	0.13	0.18	90	-0.17	107	197
PIK3CA	0.01	0	-10000	0	-10000	0	0
SORT1	0.01	0	-10000	0	-10000	0	0
activation of caspase activity	-0.025	0.09	0.16	5	-0.15	121	126
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.029	0.094	0.18	5	-0.16	121	126
RHOC	0.01	0	-10000	0	-10000	0	0
XIAP	0.01	0.02	0.27	1	-0.29	1	2
MAPK10	-0.076	0.12	-10000	0	-0.26	105	105
DIABLO	0.01	0	-10000	0	-10000	0	0
SMPD2	-0.039	0.087	-10000	0	-0.16	121	121
APH1B	0.01	0	-10000	0	-10000	0	0
APH1A	0.01	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin	-0.039	0.1	0.18	5	-0.18	121	126
PSEN1	0.01	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0.015	0	-10000	0	-10000	0	0
NT3 (dimer)/p75(NTR)	-0.065	0.12	0.19	5	-0.22	143	148
MAPK8	-0.063	0.12	-10000	0	-0.24	102	102
MAPK9	-0.062	0.12	-10000	0	-0.24	102	102
APAF1	0.01	0	-10000	0	-10000	0	0
NTF3	-0.045	0.12	0.27	1	-0.29	76	77
NTF4	-0.01	0.074	-10000	0	-0.29	27	27
NDN	-0.026	0.097	-10000	0	-0.29	49	49
RAC1/GDP	0.007	0	-10000	0	-10000	0	0
RhoA-B-C/GDP	-0.022	0.081	-10000	0	-0.14	123	123
p75 CTF/Sortilin/TRAF6/NRIF	0.026	0.007	0.18	1	-10000	0	1
RhoA-B-C/GTP	-0.04	0.1	0.18	5	-0.18	123	128
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.032	0.092	0.17	5	-0.15	145	150
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.038	0.096	0.18	5	-0.16	145	150
PRKACB	0.008	0.021	-10000	0	-0.29	2	2
proBDNF (dimer)/p75 ECD	-0.025	0.081	-10000	0	-0.19	78	78
ChemicalAbstracts:86-01-1	0	0	-10000	0	-10000	0	0
BIRC3	-0.004	0.071	0.27	3	-0.29	22	25
BIRC2	0.011	0.018	0.27	2	-10000	0	2
neuron projection morphogenesis	-0.053	0.1	0.11	15	-0.2	114	129
BAD	-0.069	0.12	-10000	0	-0.25	105	105
RIPK2	0.01	0	-10000	0	-10000	0	0
NGFR	-0.053	0.13	0.27	5	-0.29	90	95
CYCS	-0.034	0.081	-10000	0	-0.15	121	121
ADAM17	0.011	0.013	0.27	1	-10000	0	1
NGF (dimer)/p75(NTR)/TRAF6/RIP2	-0.029	0.094	0.18	5	-0.16	121	126
BCL2L11	-0.069	0.12	-10000	0	-0.25	105	105
BDNF (dimer)/p75(NTR)	-0.066	0.12	0.19	5	-0.22	145	150
PI3K	-0.029	0.094	0.18	5	-0.16	122	127
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1	-0.029	0.094	0.18	5	-0.16	121	126
NDNL2	0.01	0	-10000	0	-10000	0	0
YWHAE	0.009	0.015	-10000	0	-0.29	1	1
PRKCI	0.01	0	-10000	0	-10000	0	0
NGF (dimer)/p75(NTR)	-0.054	0.12	0.19	5	-0.22	121	126
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE	-0.029	0.094	0.18	5	-0.16	121	126
TRAF6	0.01	0	-10000	0	-10000	0	0
RAC1	0.01	0	-10000	0	-10000	0	0
PRKCZ	0.008	0.025	-10000	0	-0.29	3	3
PLG	0.005	0.03	0.27	5	-10000	0	5
oligodendrocyte cell fate commitment	0	0	-10000	0	-10000	0	0
CASP6	-0.071	0.12	-10000	0	-0.2	164	164
SQSTM1	0.01	0	-10000	0	-10000	0	0
NGFRAP1	0.008	0.021	-10000	0	-0.29	2	2
CASP3	-0.065	0.12	-10000	0	-0.24	102	102
E2F1	0.071	0.11	0.27	97	-10000	0	97
CASP9	0.01	0	-10000	0	-10000	0	0
IKK complex	-0.03	0.1	0.19	2	-0.25	54	56
NGF (dimer)/TRKA	-0.011	0.075	0.19	7	-0.19	54	61
MMP7	0.044	0.13	0.27	78	-0.29	21	99
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.023	0.09	0.17	5	-0.15	121	126
MMP3	-0.007	0.13	0.27	33	-0.29	51	84
APAF-1/Caspase 9	-0.04	0.063	-10000	0	-0.21	31	31

×

Plasma membrane estrogen receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.005	0.063	0.16	2	-0.13	77	79
ER alpha/Gai/GDP/Gbeta gamma	-0.16	0.24	-10000	0	-0.41	155	155
AKT1	-0.14	0.31	-10000	0	-0.79	73	73
PIK3CA	0.01	0	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/PI3K	-0.14	0.32	-10000	0	-0.81	73	73
mol:Ca2+	-0.04	0.11	-10000	0	-0.29	63	63
IGF1R	0.008	0.025	-10000	0	-0.29	3	3
E2/ER alpha (dimer)/Striatin	-0.017	0.066	-10000	0	-0.16	73	73
SHC1	0.011	0.013	0.27	1	-10000	0	1
apoptosis	0.13	0.29	0.75	73	-10000	0	73
RhoA/GTP	-0.012	0.046	-10000	0	-0.11	72	72
E2/ER alpha (dimer)/PELP1/Src/p130 Cas	-0.12	0.2	-10000	0	-0.41	111	111
regulation of stress fiber formation	0.006	0.042	0.096	72	-10000	0	72
E2/ERA-ERB (dimer)	-0.016	0.067	0.17	2	-0.16	73	75
KRAS	0.011	0.013	0.27	1	-10000	0	1
G13/GTP	-0.015	0.059	-10000	0	-0.14	73	73
pseudopodium formation	-0.006	0.042	-10000	0	-0.096	72	72
E2/ER alpha (dimer)/PELP1	-0.017	0.066	-10000	0	-0.16	73	73
GRB2	0.01	0	-10000	0	-10000	0	0
GNG2	0.006	0.036	-10000	0	-0.29	6	6
GNAO1	-0.084	0.14	-10000	0	-0.29	129	129
HRAS	0.01	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
mol:NO	-0.12	0.23	-10000	0	-0.44	111	111
E2/ER beta (dimer)	0.008	0.012	0.18	2	-10000	0	2
mol:GDP	-0.035	0.11	-10000	0	-0.26	73	73
mol:NADP	-0.12	0.23	-10000	0	-0.44	111	111
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
mol:IP3	-0.042	0.12	-10000	0	-0.3	63	63
IGF-1R heterotetramer	0.008	0.025	-10000	0	-0.29	3	3
PLCB1	-0.043	0.12	-10000	0	-0.31	63	63
PLCB2	-0.042	0.12	-10000	0	-0.31	60	60
IGF1	-0.12	0.15	-10000	0	-0.29	182	182
mol:L-citrulline	-0.12	0.23	-10000	0	-0.44	111	111
RHOA	0.01	0	-10000	0	-10000	0	0
Gai/GDP	-0.23	0.34	-10000	0	-0.71	129	129
JNK cascade	0.008	0.012	0.18	2	-10000	0	2
BCAR1	0.01	0	-10000	0	-10000	0	0
ESR2	0.011	0.018	0.27	2	-10000	0	2
GNAQ	0.01	0	-10000	0	-10000	0	0
ESR1	-0.043	0.11	-10000	0	-0.29	73	73
Gq family/GDP/Gbeta gamma	-0.015	0.074	-10000	0	-0.38	5	5
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1	-0.035	0.09	-10000	0	-0.23	47	47
E2/ER alpha (dimer)/PELP1/Src/p52 SHC	-0.12	0.2	-10000	0	-0.41	111	111
GNAZ	-0.055	0.12	-10000	0	-0.29	89	89
E2/ER alpha (dimer)	-0.029	0.077	-10000	0	-0.19	73	73
STRN	0.01	0	-10000	0	-10000	0	0
GNAL	-0.12	0.15	-10000	0	-0.29	178	178
PELP1	0.01	0	-10000	0	-10000	0	0
MAPK11	0.009	0.007	0.11	2	-10000	0	2
GNAI2	0.01	0	-10000	0	-10000	0	0
GNAI3	0.01	0	-10000	0	-10000	0	0
GNAI1	0.008	0.025	-10000	0	-0.29	3	3
HBEGF	-0.13	0.23	-10000	0	-0.38	154	154
cAMP biosynthetic process	-0.069	0.088	0.11	1	-0.15	207	208
SRC	-0.15	0.23	-10000	0	-0.39	155	155
PI3K	0.014	0.01	-10000	0	-0.19	1	1
GNB1	0.01	0	-10000	0	-10000	0	0
G13/GDP/Gbeta gamma	-0.023	0.097	-10000	0	-0.23	73	73
SOS1	0.01	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1	-0.15	0.18	-10000	0	-0.34	161	161
Gs family/GTP	-0.069	0.09	0.13	1	-0.15	207	208
EntrezGene:2778	0	0	-10000	0	-10000	0	0
RAS family/GTP	0.02	0.007	0.17	1	-10000	0	1
vasodilation	-0.12	0.22	-10000	0	-0.42	111	111
mol:DAG	-0.042	0.12	-10000	0	-0.3	63	63
Gs family/GDP/Gbeta gamma	-0.077	0.11	-10000	0	-0.28	75	75
MSN	-0.007	0.045	-10000	0	-0.1	72	72
Gq family/GTP	-0.044	0.12	-10000	0	-0.32	60	60
mol:PI-3-4-5-P3	-0.14	0.3	-10000	0	-0.78	73	73
NRAS	0.01	0	-10000	0	-10000	0	0
mol:E2	0	0	-10000	0	-10000	0	0
cell adhesion	0.12	0.22	0.42	111	-10000	0	111
GRB2/SOS1	0.015	0	-10000	0	-10000	0	0
RhoA/GDP	-0.028	0.1	-10000	0	-0.25	73	73
NOS3	-0.13	0.24	-10000	0	-0.47	111	111
GNA11	0.009	0.015	-10000	0	-0.29	1	1
MAPKKK cascade	-0.12	0.24	-10000	0	-0.6	74	74
E2/ER alpha (dimer)/PELP1/Src	-0.13	0.21	-10000	0	-0.43	111	111
ruffle organization	-0.006	0.042	-10000	0	-0.096	72	72
ROCK2	-0.008	0.047	-10000	0	-0.11	72	72
GNA14	-0.032	0.1	-10000	0	-0.29	58	58
GNA15	0.008	0.025	-10000	0	-0.29	3	3
GNA13	0.01	0	-10000	0	-10000	0	0
MMP9	-0.12	0.23	-10000	0	-0.37	151	151
MMP2	-0.15	0.22	-10000	0	-0.38	157	157

×

TCGA08_p53

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
CDKN2A	0.078	0.08	0.16	201	-0.19	4	205
TP53	0.024	0.028	-10000	0	-10000	0	0
Senescence	0.024	0.028	-10000	0	-10000	0	0
Apoptosis	0.024	0.028	-10000	0	-10000	0	0
Activated_Oncogenes	0	0	-10000	0	-10000	0	0
MDM2	-0.044	0.054	0.13	6	-0.098	194	200
MDM4	0.01	0	-10000	0	-10000	0	0

×

Aurora C signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Total.Perturbations
INCENP	0.011	0.013	0.27	1	-9999	1
Aurora C/Aurora B/INCENP	0.092	0.078	0.17	194	-9999	194
metaphase	0	0	-10000	0	-9999	0
mitosis	0	0	-10000	0	-9999	0
H3F3B	0.004	0.004	-10000	0	-9999	0
AURKB	0.13	0.13	0.27	184	-9999	184
AURKC	0.018	0.045	0.27	13	-9999	13

×

S1P4 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	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
GNAO1	-0.084	0.14	-10000	0	-0.29	129	129
CDC42/GTP	-0.067	0.12	-10000	0	-0.2	165	165
PLCG1	-0.073	0.12	-10000	0	-0.2	165	165
mol:GTP	0	0	-10000	0	-10000	0	0
GNAI2	0.01	0	-10000	0	-10000	0	0
GNAI3	0.01	0	-10000	0	-10000	0	0
G12/G13	0.015	0	-10000	0	-10000	0	0
cell migration	-0.066	0.12	-10000	0	-0.19	165	165
S1PR5	0.017	0.052	0.27	14	-0.29	2	16
S1PR4	0.009	0.037	0.27	3	-0.29	4	7
MAPK3	-0.073	0.12	-10000	0	-0.2	165	165
MAPK1	-0.073	0.12	-10000	0	-0.2	165	165
S1P/S1P5/Gi	-0.075	0.13	-10000	0	-0.22	162	162
GNAI1	0.008	0.025	-10000	0	-0.29	3	3
CDC42/GDP	0.007	0	-10000	0	-10000	0	0
S1P/S1P5/G12	0.018	0.031	0.17	14	-0.16	2	16
RHOA	0.011	0.015	-10000	0	-0.13	4	4
S1P/S1P4/Gi	-0.078	0.13	-10000	0	-0.22	165	165
mol:GDP	0	0	-10000	0	-10000	0	0
GNAZ	-0.055	0.12	-10000	0	-0.29	89	89
S1P/S1P4/G12/G13	0.019	0.02	0.17	3	-0.14	4	7
GNA12	0.01	0	-10000	0	-10000	0	0
GNA13	0.01	0	-10000	0	-10000	0	0
CDC42	0.01	0	-10000	0	-10000	0	0

×

S1P5 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-10000	0	-10000	0	0
telencephalon oligodendrocyte cell migration	0.064	0.12	0.19	162	-10000	0	162
GNAI2	0.01	0	-10000	0	-10000	0	0
S1P/S1P5/G12	0.018	0.031	0.17	14	-0.16	2	16
mol:GDP	0	0	-10000	0	-10000	0	0
GNAO1	-0.084	0.14	-10000	0	-0.29	129	129
RhoA/GTP	-0.064	0.12	-10000	0	-0.2	162	162
negative regulation of cAMP metabolic process	-0.074	0.13	-10000	0	-0.22	162	162
GNAZ	-0.055	0.12	-10000	0	-0.29	89	89
GNAI3	0.01	0	-10000	0	-10000	0	0
GNA12	0.01	0	-10000	0	-10000	0	0
S1PR5	0.017	0.052	0.27	14	-0.29	2	16
mol:GTP	0	0	-10000	0	-10000	0	0
S1P/S1P5/Gi	-0.075	0.13	-10000	0	-0.22	162	162
RhoA/GDP	0.007	0	-10000	0	-10000	0	0
RHOA	0.01	0	-10000	0	-10000	0	0
GNAI1	0.008	0.025	-10000	0	-0.29	3	3

×

HIF-1-alpha transcription factor network

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
PKM2	0.15	0.27	0.57	40	-0.48	19	59
HDAC7	0.011	0.003	-10000	0	-10000	0	0
HIF1A/ARNT/Cbp/p300/Src-1	0.16	0.31	0.65	46	-0.5	23	69
SMAD4	0.01	0	-10000	0	-10000	0	0
ID2	0.15	0.27	0.57	40	-0.49	19	59
AP1	-0.056	0.11	-10000	0	-0.21	130	130
ABCG2	0.15	0.27	0.58	41	-0.48	19	60
HIF1A	0.058	0.076	0.2	41	-10000	0	41
TFF3	0.14	0.3	0.6	47	-0.5	30	77
GATA2	0.014	0.06	0.27	13	-0.29	7	20
AKT1	0.053	0.086	0.24	15	-0.14	15	30
response to hypoxia	0.041	0.085	0.19	48	-0.13	24	72
MCL1	0.15	0.27	0.57	40	-0.48	19	59
NDRG1	0.16	0.27	0.58	41	-0.47	19	60
SERPINE1	0.16	0.27	0.58	41	-0.5	19	60
FECH	0.15	0.27	0.57	40	-0.48	19	59
FURIN	0.15	0.27	0.57	41	-0.48	19	60
NCOA2	-0.003	0.072	-10000	0	-0.29	24	24
EP300	0.075	0.13	0.29	41	-0.26	26	67
HMOX1	0.16	0.27	0.59	44	-0.48	19	63
BHLHE40	0.15	0.27	0.57	40	-0.48	19	59
BHLHE41	0.15	0.27	0.57	40	-0.5	20	60
HIF1A/ARNT/SMAD3/SMAD4/SP1	0.087	0.11	0.35	13	-10000	0	13
ENG	0.071	0.087	0.26	12	-10000	0	12
JUN	-0.001	0.058	-10000	0	-0.29	16	16
RORA	0.15	0.27	0.57	40	-0.49	20	60
ABCB1	-0.09	0.23	-10000	0	-0.7	47	47
TFRC	0.15	0.27	0.58	40	-0.48	19	59
CXCR4	0.15	0.27	0.57	40	-0.5	19	59
TF	0.17	0.29	0.61	56	-0.48	19	75
CITED2	0.15	0.27	0.57	40	-0.48	19	59
HIF1A/ARNT	0.2	0.38	0.86	44	-0.61	10	54
LDHA	-0.012	0.028	-10000	0	-10000	0	0
ETS1	0.15	0.27	0.57	40	-0.48	19	59
PGK1	0.15	0.27	0.57	40	-0.48	19	59
NOS2	0.17	0.28	0.62	50	-0.48	21	71
ITGB2	0.15	0.27	0.59	43	-0.5	19	62
ALDOA	0.15	0.27	0.57	40	-0.48	19	59
Cbp/p300/CITED2	0.14	0.31	0.6	42	-0.54	25	67
FOS	-0.083	0.14	-10000	0	-0.29	128	128
HK2	0.15	0.27	0.58	40	-0.48	19	59
SP1	-0.004	0.047	-10000	0	-0.16	15	15
GCK	0.062	0.34	0.54	7	-1.1	27	34
HK1	0.15	0.27	0.57	40	-0.48	19	59
NPM1	0.15	0.27	0.57	40	-0.48	19	59
EGLN1	0.15	0.27	0.57	40	-0.48	19	59
CREB1	0.013	0	-10000	0	-10000	0	0
PGM1	0.15	0.27	0.57	40	-0.48	19	59
SMAD3	0.01	0	-10000	0	-10000	0	0
EDN1	0.031	0.19	0.47	2	-0.58	14	16
IGFBP1	0.17	0.28	0.6	50	-0.48	19	69
VEGFA	0.14	0.25	0.57	16	-0.45	22	38
HIF1A/JAB1	0.052	0.059	0.19	25	-10000	0	25
CP	0.15	0.31	0.62	56	-0.49	31	87
CXCL12	0.11	0.3	0.56	39	-0.5	32	71
COPS5	0.013	0.01	-10000	0	-10000	0	0
SMAD3/SMAD4	0.016	0	-10000	0	-10000	0	0
BNIP3	0.15	0.27	0.57	41	-0.48	19	60
EGLN3	0.15	0.27	0.57	40	-0.48	20	60
CA9	0.29	0.3	0.63	105	-0.47	14	119
TERT	0.24	0.3	0.62	92	-0.49	15	107
ENO1	0.15	0.27	0.57	40	-0.48	19	59
PFKL	0.15	0.27	0.57	40	-0.48	19	59
NCOA1	0.011	0.004	-10000	0	-10000	0	0
ADM	0.15	0.27	0.57	40	-0.48	19	59
ARNT	0.055	0.075	0.24	15	-10000	0	15
HNF4A	0.028	0.085	0.26	41	-0.12	11	52
ADFP	0.14	0.27	0.55	46	-0.48	19	65
SLC2A1	0.15	0.25	0.59	16	-0.45	22	38
LEP	0.15	0.29	0.59	43	-0.48	25	68
HIF1A/ARNT/Cbp/p300	0.16	0.32	0.68	44	-0.52	23	67
EPO	0.15	0.24	0.61	26	-0.47	6	32
CREBBP	0.075	0.13	0.29	40	-0.26	25	65
HIF1A/ARNT/Cbp/p300/HDAC7	0.16	0.31	0.65	45	-0.5	22	67
PFKFB3	0.15	0.27	0.57	40	-0.47	20	60
NT5E	0.14	0.28	0.57	42	-0.49	27	69

×

TCR signaling in naïve CD8+ T cells

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GRB2/SOS1/SHC	-0.049	0.19	-10000	0	-0.42	72	72
FYN	-0.071	0.25	0.24	10	-0.55	73	83
LAT/GRAP2/SLP76	-0.061	0.2	-10000	0	-0.45	71	71
IKBKB	0.01	0	-10000	0	-10000	0	0
AKT1	-0.04	0.17	0.23	11	-0.38	70	81
B2M	0.01	0.006	-10000	0	-10000	0	0
IKBKG	-0.008	0.047	-10000	0	-0.11	62	62
MAP3K8	0.008	0.025	-10000	0	-0.29	3	3
mol:Ca2+	-0.004	0.017	0.031	35	-0.039	52	87
integrin-mediated signaling pathway	0.012	0.017	-10000	0	-0.16	4	4
LAT/GRAP2/SLP76/VAV1/PI3K Class IA	-0.067	0.24	0.26	11	-0.55	70	81
TRPV6	-0.014	0.12	0.23	34	-0.29	47	81
CD28	-0.001	0.062	0.27	2	-0.29	16	18
SHC1	-0.065	0.24	0.24	10	-0.52	73	83
receptor internalization	-0.07	0.24	0.26	5	-0.51	74	79
PRF1	-0.07	0.29	0.38	11	-0.8	42	53
KRAS	0.011	0.013	0.27	1	-10000	0	1
GRB2	0.01	0	-10000	0	-10000	0	0
COT/AKT1	-0.026	0.14	0.21	11	-0.3	70	81
LAT	-0.065	0.24	0.24	10	-0.51	73	83
EntrezGene:6955	0	0.005	0.03	5	-10000	0	5
CD3D	-0.014	0.091	0.28	3	-0.3	36	39
CD3E	-0.021	0.094	-10000	0	-0.3	42	42
CD3G	-0.024	0.096	-10000	0	-0.29	46	46
RASGRP2	-0.039	0.074	-10000	0	-0.16	106	106
RASGRP1	-0.036	0.17	0.23	12	-0.38	66	78
HLA-A	0.009	0.017	-10000	0	-0.3	1	1
RASSF5	0.007	0.029	-10000	0	-0.29	4	4
RAP1A/GTP/RAPL	0.012	0.017	-10000	0	-0.16	4	4
mol:GTP	0	0	-10000	0	-10000	0	0
mol:GDP	-0.007	0.059	0.14	12	-0.12	60	72
PDK1/CARD11/BCL10/MALT1/TRAF6	-0.035	0.071	-10000	0	-0.18	71	71
PRKCA	-0.025	0.098	0.13	5	-0.23	65	70
GRAP2	-0.023	0.093	-10000	0	-0.29	45	45
mol:IP3	-0.049	0.16	0.16	43	-0.34	75	118
EntrezGene:6957	0	0.006	0.029	3	-10000	0	3
TCR/CD3/MHC I/CD8	-0.064	0.22	0.21	11	-0.54	59	70
ORAI1	0.008	0.074	0.17	48	-0.16	34	82
CSK	-0.066	0.24	0.24	10	-0.52	72	82
B7 family/CD28	-0.033	0.24	0.37	16	-0.52	63	79
CHUK	0.01	0	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8/LCK/ZAP-70	-0.079	0.27	0.25	10	-0.59	73	83
PTPN6	-0.065	0.24	0.25	10	-0.51	73	83
VAV1	-0.068	0.24	0.24	11	-0.53	73	84
Monovalent TCR/CD3	-0.046	0.16	0.19	2	-0.34	73	75
CBL	0.01	0	-10000	0	-10000	0	0
LCK	-0.071	0.25	0.23	11	-0.54	73	84
PAG1	-0.066	0.24	0.24	10	-0.52	72	82
RAP1A	0.01	0	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8/LCK	-0.076	0.27	0.26	10	-0.57	73	83
CD80	0.044	0.088	0.27	54	-10000	0	54
CD86	0.008	0.033	0.27	1	-0.29	4	5
PDK1/CARD11/BCL10/MALT1	-0.042	0.085	0.083	1	-0.22	71	72
HRAS	0.01	0	-10000	0	-10000	0	0
GO:0035030	-0.038	0.19	0.28	14	-0.43	64	78
CD8A	-0.018	0.092	0.3	1	-0.3	39	40
CD8B	-0.013	0.096	0.28	7	-0.3	37	44
PTPRC	-0.024	0.1	0.27	2	-0.29	48	50
PDK1/PKC theta	-0.053	0.21	0.25	11	-0.45	72	83
CSK/PAG1	-0.061	0.23	0.24	10	-0.52	69	79
SOS1	0.01	0	-10000	0	-10000	0	0
peptide-MHC class I	0.014	0.016	-10000	0	-0.21	1	1
GRAP2/SLP76	-0.069	0.24	0.21	7	-0.5	77	84
STIM1	0.004	0.03	-10000	0	-10000	0	0
RAS family/GTP	0.001	0.071	0.16	11	-0.15	56	67
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin	-0.076	0.26	0.26	5	-0.55	74	79
mol:DAG	-0.054	0.13	-10000	0	-0.3	78	78
RAP1A/GDP	-0.003	0.027	0.064	11	-0.055	50	61
PLCG1	0.01	0	-10000	0	-10000	0	0
CD247	0.006	0.042	0.27	1	-0.3	7	8
cytotoxic T cell degranulation	-0.065	0.27	0.38	11	-0.75	42	53
RAP1A/GTP	-0.017	0.026	-10000	0	-0.06	106	106
mol:PI-3-4-5-P3	-0.051	0.2	0.25	11	-0.45	70	81
LAT/GRAP2/SLP76/VAV1/PLCgamma1	-0.065	0.2	0.17	44	-0.47	65	109
NRAS	0.01	0	-10000	0	-10000	0	0
ZAP70	-0.001	0.058	0.27	1	-0.29	15	16
GRB2/SOS1	0.015	0	-10000	0	-10000	0	0
LAT/GRAP2/SLP76/VAV1	-0.066	0.19	-10000	0	-0.45	70	70
MALT1	0.01	0	-10000	0	-10000	0	0
TRAF6	0.01	0	-10000	0	-10000	0	0
CD8 heterodimer	-0.018	0.11	0.24	7	-0.27	55	62
CARD11	0.007	0.049	0.27	4	-0.29	8	12
PRKCB	-0.038	0.12	0.13	5	-0.25	83	88
PRKCE	-0.024	0.097	0.13	5	-0.23	65	70
PRKCQ	-0.065	0.24	0.26	11	-0.52	72	83
LCP2	0.008	0.025	-10000	0	-0.29	3	3
BCL10	0.01	0	-10000	0	-10000	0	0
regulation of survival gene product expression	-0.031	0.15	0.22	11	-0.32	70	81
IKK complex	-0.007	0.052	0.12	11	-0.099	66	77
RAS family/GDP	-0.007	0.011	-10000	0	-0.035	32	32
MAP3K14	-0.017	0.11	0.18	11	-0.23	70	81
PDPK1	-0.036	0.16	0.23	11	-0.36	70	81
TCR/CD3/MHC I/CD8/Fyn	-0.091	0.3	0.28	5	-0.67	69	74

×

Ephrin A reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAPKKK cascade	-0.017	0.066	0.17	3	-0.16	66	69
EFNA5	0	0.056	0.27	1	-0.29	14	15
FYN	-0.015	0.058	-10000	0	-0.14	66	66
neuron projection morphogenesis	-0.017	0.066	0.17	3	-0.16	66	69
cell-cell signaling	0	0	-10000	0	-10000	0	0
Ephrin A5/EPHA5	-0.017	0.066	0.17	3	-0.16	66	69
EPHA5	-0.033	0.1	0.27	2	-0.29	54	56

×

amb2 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2	-0.028	0.092	0.2	8	-0.23	49	57
alphaM/beta2 Integrin/GPIbA	-0.012	0.078	0.21	13	-0.23	22	35
alphaM/beta2 Integrin/proMMP-9	0.024	0.12	0.2	85	-0.28	22	107
PLAUR	0.01	0	-10000	0	-10000	0	0
HMGB1	-0.01	0.027	-10000	0	-10000	0	0
alphaM/beta2 Integrin/Talin	-0.014	0.072	0.2	7	-0.23	21	28
AGER	-0.006	0.041	0.26	6	-10000	0	6
RAP1A	0.01	0	-10000	0	-10000	0	0
SELPLG	0.006	0.043	0.27	2	-0.29	7	9
mol:LDL	0	0	-10000	0	-10000	0	0
alphaM/beta2 Integrin/RAGE/HMGB1	-0.053	0.12	0.34	1	-0.18	180	181
mol:GTP	0	0	-10000	0	-10000	0	0
MMP9	0.069	0.12	0.27	102	-0.29	8	110
CYR61	-0.075	0.13	-10000	0	-0.29	116	116
TLN1	0.01	0	-10000	0	-10000	0	0
Rap1/GTP	-0.025	0.097	-10000	0	-0.36	22	22
RHOA	0.01	0	-10000	0	-10000	0	0
P-selectin oligomer	-0.052	0.12	-10000	0	-0.29	84	84
MYH2	-0.011	0.11	0.17	6	-0.26	38	44
MST1R	0.002	0.072	0.27	8	-0.29	18	26
leukocyte activation during inflammatory response	-0.038	0.086	0.18	8	-0.17	92	100
APOB	-0.031	0.11	0.27	7	-0.29	59	66
mol:GDP	0	0	-10000	0	-10000	0	0
complement component iC3b receptor activity	0	0	-10000	0	-10000	0	0
MMP2	-0.016	0.085	-10000	0	-0.29	36	36
JAM3	-0.011	0.075	-10000	0	-0.29	28	28
GP1BA	0.013	0.039	0.27	8	-0.29	1	9
alphaM/beta2 Integrin/CTGF	-0.047	0.11	0.19	9	-0.23	91	100
alphaM/beta2 Integrin	-0.019	0.12	0.17	3	-0.3	39	42
JAM3 homodimer	-0.011	0.075	-10000	0	-0.29	28	28
ICAM2	0.009	0.015	-10000	0	-0.29	1	1
ICAM1	0.015	0.041	0.27	9	-0.29	1	10
phagocytosis triggered by activation of immune response cell surface activating receptor	-0.018	0.12	0.17	3	-0.3	39	42
cell adhesion	-0.012	0.077	0.21	13	-0.23	22	35
NFKB1	-0.11	0.18	0.25	20	-0.29	187	207
THY1	0.012	0.022	0.27	3	-10000	0	3
RhoA/GDP	0.007	0	-10000	0	-10000	0	0
Lipoprotein(a)	-0.023	0.081	0.17	11	-0.17	83	94
alphaM/beta2 Integrin/LRP/tPA	-0.015	0.082	0.22	8	-0.22	34	42
IL6	-0.22	0.29	-10000	0	-0.54	188	188
ITGB2	-0.011	0.062	0.26	8	-0.31	8	16
elevation of cytosolic calcium ion concentration	0.013	0.089	0.19	45	-0.21	21	66
alphaM/beta2 Integrin/JAM2/JAM3	-0.056	0.12	0.2	7	-0.21	120	127
JAM2	-0.07	0.13	-10000	0	-0.29	109	109
alphaM/beta2 Integrin/ICAM1	0.003	0.082	0.19	23	-0.17	36	59
alphaM/beta2 Integrin/uPA/Plg	0.012	0.09	0.19	45	-0.21	21	66
RhoA/GTP	-0.009	0.11	0.18	7	-0.27	38	45
positive regulation of phagocytosis	-0.028	0.11	0.26	5	-0.36	28	33
Ron/MSP	0.018	0.068	0.2	28	-0.19	19	47
alphaM/beta2 Integrin/uPAR/uPA	0.014	0.091	0.19	45	-0.21	21	66
alphaM/beta2 Integrin/uPAR	-0.014	0.072	0.18	10	-0.23	21	31
PLAU	0.044	0.088	0.27	54	-10000	0	54
PLAT	-0.002	0.064	0.27	2	-0.29	18	20
actin filament polymerization	-0.011	0.1	0.17	7	-0.28	29	36
MST1	0.023	0.06	0.27	22	-0.29	1	23
alphaM/beta2 Integrin/lipoprotein(a)	-0.037	0.088	0.19	8	-0.17	92	100
TNF	-0.092	0.17	0.33	20	-0.27	176	196
RAP1B	0.01	0	-10000	0	-10000	0	0
alphaM/beta2 Integrin/uPA	0.008	0.097	0.19	48	-0.23	21	69
fibrinolysis	0.011	0.088	0.18	45	-0.21	21	66
HCK	0.004	0.058	0.27	5	-0.29	12	17
dendritic cell antigen processing and presentation	-0.018	0.12	0.17	3	-0.3	39	42
VTN	-0.034	0.12	0.27	7	-0.29	66	73
alphaM/beta2 Integrin/CYR61	-0.059	0.12	0.2	7	-0.23	116	123
LPA	-0.013	0.086	0.27	6	-0.29	32	38
LRP1	0.007	0.029	-10000	0	-0.29	4	4
cell migration	-0.001	0.11	0.2	20	-0.23	48	68
FN1	0.018	0.083	0.27	26	-0.29	12	38
alphaM/beta2 Integrin/Thy1	-0.013	0.073	0.18	12	-0.23	21	33
MPO	0.01	0.019	0.27	2	-10000	0	2
KNG1	0	0	-10000	0	-10000	0	0
RAP1/GDP	0.014	0	-10000	0	-10000	0	0
ROCK1	-0.007	0.1	0.17	5	-0.33	21	26
ELA2	0	0	-10000	0	-10000	0	0
PLG	0.005	0.03	0.27	5	-10000	0	5
CTGF	-0.051	0.12	-10000	0	-0.29	84	84
alphaM/beta2 Integrin/Hck	-0.016	0.091	0.25	9	-0.27	25	34
ITGAM	-0.022	0.073	0.26	3	-0.31	19	22
alphaM/beta2 Integrin/P-Selectin/PSGL1	-0.04	0.1	0.22	8	-0.19	90	98
HP	0.036	0.086	0.27	46	-0.29	2	48
leukocyte adhesion	-0.086	0.14	0.2	7	-0.3	90	97
SELP	-0.052	0.12	-10000	0	-0.29	84	84

×

Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer	0.014	0.014	-10000	0	-0.19	2	2
alphaV beta3 Integrin	-0.056	0.11	-10000	0	-0.19	146	146
PTK2	-0.08	0.14	-10000	0	-0.35	69	69
IGF1R	0.008	0.025	-10000	0	-0.29	3	3
PI4KB	0.01	0	-10000	0	-10000	0	0
MFGE8	0.008	0.021	-10000	0	-0.29	2	2
SRC	0.01	0	-10000	0	-10000	0	0
CDKN1B	-0.083	0.17	-10000	0	-0.45	66	66
VEGFA	0.01	0	-10000	0	-10000	0	0
ILK	-0.083	0.17	-10000	0	-0.45	66	66
ROCK1	0.01	0	-10000	0	-10000	0	0
AKT1	-0.077	0.16	-10000	0	-0.42	66	66
PTK2B	-0.003	0.047	-10000	0	-0.13	47	47
alphaV/beta3 Integrin/JAM-A	-0.061	0.12	0.18	6	-0.19	168	174
CBL	0.01	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
alphaV beta3 Integrin/ANGPTL3	0	0.059	0.18	4	-0.16	45	49
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.052	0.087	-10000	0	-0.14	186	186
VEGF/Rho/ROCK/alphaV/beta3 Integrin	-0.026	0.089	-10000	0	-0.31	17	17
alphaV/beta3 Integrin/Syndecan-1	-0.003	0.061	-10000	0	-0.16	53	53
PI4KA	0.01	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.096	0.14	-10000	0	-0.22	206	206
PI4 Kinase	0.015	0	-10000	0	-10000	0	0
PIK3CA	0.01	0	-10000	0	-10000	0	0
alphaV/beta3 Integrin/Osteopontin	0.063	0.11	0.18	160	-0.16	41	201
RPS6KB1	-0.094	0.13	-10000	0	-0.26	127	127
TLN1	0.01	0	-10000	0	-10000	0	0
MAPK3	-0.18	0.25	-10000	0	-0.49	148	148
GPR124	-0.024	0.094	-10000	0	-0.29	46	46
MAPK1	-0.18	0.25	-10000	0	-0.49	148	148
PXN	0.01	0	-10000	0	-10000	0	0
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
alphaV/beta3 Integrin/Tumstatin	-0.046	0.1	0.18	4	-0.18	140	144
cell adhesion	-0.001	0.062	-10000	0	-0.17	45	45
ANGPTL3	0.01	0.029	0.27	5	-10000	0	5
VEGFR2 homodimer/VEGFA homodimer/Src	0.019	0.012	-10000	0	-0.16	2	2
IGF-1R heterotetramer	0.008	0.025	-10000	0	-0.29	3	3
Rac1/GDP	0.007	0	-10000	0	-10000	0	0
TGFBR2	0.008	0.025	-10000	0	-0.29	3	3
ITGB3	-0.024	0.094	-10000	0	-0.29	46	46
IGF1	-0.12	0.15	-10000	0	-0.29	182	182
RAC1	0.01	0	-10000	0	-10000	0	0
regulation of cell-matrix adhesion	-0.018	0.09	-10000	0	-0.21	69	69
apoptosis	0.009	0.015	-10000	0	-0.29	1	1
CD47	0.01	0	-10000	0	-10000	0	0
alphaV/beta3 Integrin/CD47	0	0.057	-10000	0	-0.16	46	46
VCL	0.009	0.015	-10000	0	-0.29	1	1
alphaV/beta3 Integrin/Del1	-0.023	0.093	-10000	0	-0.2	80	80
CSF1	-0.001	0.056	-10000	0	-0.29	15	15
PIK3C2A	-0.083	0.17	-10000	0	-0.45	66	66
PI4 Kinase/Pyk2	-0.056	0.1	-10000	0	-0.24	68	68
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.006	0.055	-10000	0	-0.14	47	47
FAK1/Vinculin	-0.063	0.12	-10000	0	-0.28	69	69
alphaV beta3/Integrin/ppsTEM5	-0.018	0.09	-10000	0	-0.21	69	69
RHOA	0.01	0	-10000	0	-10000	0	0
VTN	-0.034	0.12	0.27	7	-0.29	66	73
BCAR1	0.01	0	-10000	0	-10000	0	0
FGF2	-0.089	0.14	-10000	0	-0.29	136	136
F11R	-0.057	0.095	-10000	0	-0.19	135	135
alphaV/beta3 Integrin/Lactadherin	-0.001	0.059	-10000	0	-0.16	47	47
alphaV/beta3 Integrin/TGFBR2	-0.001	0.06	-10000	0	-0.16	48	48
alphaV/beta3 Integrin/c-FMS/Cbl/Cas	0.019	0.032	-10000	0	-0.14	16	16
HSP90AA1	0.01	0	-10000	0	-10000	0	0
alphaV/beta3 Integrin/Talin	0.001	0.052	-10000	0	-0.14	46	46
mol:GDP	0	0	-10000	0	-10000	0	0
FN1	0.018	0.083	0.27	26	-0.29	12	38
alphaV/beta3 Integrin/Pyk2	0.004	0.051	-10000	0	-0.13	48	48
SDC1	0.005	0.039	-10000	0	-0.29	7	7
VAV3	0.01	0.032	0.17	5	-0.13	16	21
PTPN11	0.01	0	-10000	0	-10000	0	0
IRS1	0.003	0.046	-10000	0	-0.29	10	10
FAK1/Paxillin	-0.063	0.12	-10000	0	-0.28	69	69
cell migration	-0.057	0.11	-10000	0	-0.26	69	69
ITGAV	0.009	0.015	-10000	0	-0.29	1	1
PI3K	-0.052	0.11	-10000	0	-0.26	68	68
SPP1	0.12	0.13	0.27	165	-10000	0	165
KDR	0.008	0.021	-10000	0	-0.29	2	2
mol:PI-4-5-P2	0	0	-10000	0	-10000	0	0
alphaV/beta3 Integrin/Caspase 8	0.009	0.015	-10000	0	-0.29	1	1
COL4A3	-0.07	0.14	0.27	4	-0.29	112	116
angiogenesis	-0.18	0.25	-10000	0	-0.48	158	158
Rac1/GTP	0.014	0.032	0.16	5	-0.11	19	24
EDIL3	-0.032	0.1	-10000	0	-0.29	57	57
cell proliferation	-0.001	0.059	-10000	0	-0.16	48	48

×

Ras signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ERK1-2/ELK1	-0.12	0.18	-10000	0	-0.34	132	132
MAP3K8	0.004	0.026	-10000	0	-0.29	3	3
FOS	-0.093	0.14	-10000	0	-0.37	54	54
PRKCA	0.001	0.034	-10000	0	-0.29	5	5
PTPN7	0.001	0.049	0.25	5	-0.29	7	12
HRAS	0.009	0.001	-10000	0	-10000	0	0
PRKCB	-0.081	0.13	-10000	0	-0.29	118	118
NRAS	0.009	0.001	-10000	0	-10000	0	0
RAS family/GTP	0.011	0.015	0.14	1	-10000	0	1
MAPK3	-0.053	0.1	-10000	0	-0.43	12	12
MAP2K1	-0.1	0.17	-10000	0	-0.35	120	120
ELK1	0.002	0.013	-10000	0	-10000	0	0
BRAF	-0.094	0.15	-10000	0	-0.32	120	120
mol:GTP	-0.001	0.002	-10000	0	-0.004	129	129
MAPK1	-0.053	0.1	-10000	0	-0.43	12	12
RAF1	-0.094	0.16	-10000	0	-0.32	120	120
KRAS	0.01	0.013	0.27	1	-10000	0	1

×

LPA receptor mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.007	0.073	-10000	0	-0.17	63	63
NF kappa B1 p50/RelA/I kappa B alpha	-0.013	0.073	-10000	0	-0.19	36	36
AP1	-0.062	0.11	-10000	0	-0.17	172	172
mol:PIP3	-0.03	0.063	-10000	0	-0.14	84	84
AKT1	-0.001	0.053	-10000	0	-0.21	10	10
PTK2B	-0.019	0.071	-10000	0	-0.18	58	58
RHOA	-0.001	0.03	-10000	0	-10000	0	0
PIK3CB	0.01	0	-10000	0	-10000	0	0
mol:Ca2+	-0.015	0.056	-10000	0	-0.15	44	44
MAGI3	0.01	0	-10000	0	-10000	0	0
RELA	0.01	0	-10000	0	-10000	0	0
apoptosis	-0.03	0.089	-10000	0	-0.19	84	84
HRAS/GDP	0.007	0	-10000	0	-10000	0	0
positive regulation of microtubule depolymerization	-0.024	0.071	-10000	0	-0.19	36	36
NF kappa B1 p50/RelA	-0.026	0.08	-10000	0	-0.19	61	61
endothelial cell migration	-0.035	0.12	-10000	0	-0.3	60	60
ADCY4	-0.087	0.14	-10000	0	-0.3	101	101
ADCY5	-0.17	0.19	-10000	0	-0.37	161	161
ADCY6	-0.087	0.14	-10000	0	-0.3	101	101
ADCY7	-0.087	0.14	-10000	0	-0.3	101	101
ADCY1	-0.086	0.14	-10000	0	-0.3	100	100
ADCY2	-0.15	0.18	-10000	0	-0.35	147	147
ADCY3	-0.087	0.14	-10000	0	-0.3	101	101
ADCY8	-0.088	0.14	-10000	0	-0.3	101	101
ADCY9	-0.09	0.15	-10000	0	-0.31	102	102
GSK3B	-0.017	0.067	-10000	0	-0.17	58	58
arachidonic acid secretion	-0.092	0.15	-10000	0	-0.31	103	103
GNG2	0.006	0.036	-10000	0	-0.29	6	6
TRIP6	0.009	0.013	-10000	0	-10000	0	0
GNAO1	-0.033	0.11	-10000	0	-0.27	60	60
HRAS	0.01	0	-10000	0	-10000	0	0
NFKBIA	-0.022	0.076	-10000	0	-0.2	45	45
GAB1	0.01	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
lamellipodium assembly	0.012	0.075	-10000	0	-0.86	3	3
JUN	-0.002	0.058	-10000	0	-0.29	16	16
LPA/LPA2/NHERF2	0.009	0.024	0.17	2	-10000	0	2
TIAM1	0.007	0.087	-10000	0	-1	3	3
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
mol:IP3	-0.015	0.056	-10000	0	-0.15	44	44
PLCB3	0.006	0.019	-10000	0	-10000	0	0
FOS	-0.084	0.14	-10000	0	-0.29	129	129
positive regulation of mitosis	-0.092	0.15	-10000	0	-0.31	103	103
LPA/LPA1-2-3	-0.015	0.085	0.17	6	-0.17	83	89
mol:Ca ++	0	0	-10000	0	-10000	0	0
JNK cascade	0	0	-10000	0	-10000	0	0
BCAR1	0.01	0	-10000	0	-10000	0	0
stress fiber formation	-0.017	0.072	-10000	0	-0.2	37	37
GNAZ	-0.027	0.091	-10000	0	-0.23	60	60
EGFR/PI3K-beta/Gab1	-0.023	0.069	-10000	0	-0.15	84	84
positive regulation of dendritic cell cytokine production	-0.016	0.084	0.17	6	-0.17	83	89
LPA/LPA2/MAGI-3	0.009	0.024	0.17	2	-10000	0	2
ARHGEF1	-0.01	0.061	-10000	0	-0.15	60	60
GNAI2	-0.018	0.072	-10000	0	-0.19	60	60
GNAI3	-0.018	0.072	-10000	0	-0.19	60	60
GNAI1	-0.018	0.072	-10000	0	-0.19	60	60
LPA/LPA3	-0.013	0.063	0.18	4	-0.15	59	63
LPA/LPA2	0.002	0.028	0.15	3	-0.083	28	31
LPA/LPA1	-0.023	0.087	-10000	0	-0.23	60	60
HB-EGF/EGFR	0.032	0.079	0.14	94	-0.19	22	116
HBEGF	0.041	0.078	0.16	102	-0.19	13	115
mol:DAG	-0.015	0.056	-10000	0	-0.15	44	44
cAMP biosynthetic process	-0.11	0.16	-10000	0	-0.28	149	149
NFKB1	0.01	0	-10000	0	-10000	0	0
SRC	0.01	0	-10000	0	-10000	0	0
GNB1	0.01	0	-10000	0	-10000	0	0
LYN	-0.022	0.076	-10000	0	-0.19	52	52
GNAQ	-0.008	0.053	0.099	5	-0.17	33	38
LPAR2	0.012	0.022	0.27	3	-10000	0	3
LPAR3	-0.011	0.087	0.27	5	-0.29	33	38
LPAR1	-0.023	0.091	-10000	0	-0.22	60	60
IL8	-0.075	0.19	0.3	1	-0.45	72	73
PTK2	-0.021	0.074	-10000	0	-0.16	83	83
Rac1/GDP	0.007	0	-10000	0	-10000	0	0
CASP3	-0.03	0.089	-10000	0	-0.2	84	84
EGFR	0.008	0.057	0.27	8	-0.29	9	17
PLCG1	-0.013	0.064	0.1	4	-0.19	44	48
PLD2	-0.021	0.074	-10000	0	-0.16	83	83
G12/G13	-0.004	0.069	-10000	0	-0.16	60	60
PI3K-beta	-0.02	0.051	-10000	0	-0.23	10	10
cell migration	0.001	0.045	-10000	0	-0.23	4	4
SLC9A3R2	0.01	0	-10000	0	-10000	0	0
PXN	-0.018	0.073	-10000	0	-0.2	37	37
HRAS/GTP	-0.094	0.15	-10000	0	-0.32	103	103
RAC1	0.01	0	-10000	0	-10000	0	0
MMP9	0.069	0.12	0.27	102	-0.29	8	110
PRKCE	0.01	0	-10000	0	-10000	0	0
PRKCD	-0.013	0.054	-10000	0	-0.15	44	44
Gi(beta/gamma)	-0.085	0.14	-10000	0	-0.29	103	103
mol:LPA	-0.009	0.036	-10000	0	-0.12	36	36
TRIP6/p130 Cas/FAK1/Paxillin	-0.011	0.083	-10000	0	-0.23	27	27
MAPKKK cascade	-0.092	0.15	-10000	0	-0.31	103	103
contractile ring contraction involved in cytokinesis	-0.001	0.029	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
GNA14	-0.016	0.066	0.099	4	-0.19	45	49
GNA15	-0.008	0.054	-10000	0	-0.17	34	34
GNA12	0.01	0	-10000	0	-10000	0	0
GNA13	0.01	0	-10000	0	-10000	0	0
MAPT	-0.024	0.073	-10000	0	-0.2	37	37
GNA11	-0.008	0.055	0.098	6	-0.18	33	39
Rac1/GTP	0.012	0.079	-10000	0	-0.91	3	3
MMP2	-0.035	0.12	-10000	0	-0.31	60	60

×

BMP receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS	-0.022	0.093	0.18	28	-0.14	136	164
SMAD6-7/SMURF1	0.021	0.018	0.18	3	-0.16	2	5
NOG	0.028	0.069	0.27	31	-10000	0	31
SMAD9	-0.12	0.21	-10000	0	-0.46	106	106
SMAD4	0.01	0	-10000	0	-10000	0	0
SMAD5	-0.015	0.068	-10000	0	-0.2	15	15
BMP7/USAG1	-0.12	0.13	0.19	3	-0.23	227	230
SMAD5/SKI	-0.011	0.066	-10000	0	-0.2	15	15
SMAD1	0.021	0.009	-10000	0	-10000	0	0
BMP2	-0.022	0.092	-10000	0	-0.29	43	43
SMAD1/SMAD1/SMAD4	0	0.01	-10000	0	-10000	0	0
BMPR1A	0.01	0	-10000	0	-10000	0	0
BMPR1B	0.039	0.097	0.27	54	-0.29	6	60
BMPR1A-1B/BAMBI	0.025	0.074	0.18	50	-0.16	28	78
AHSG	0.033	0.084	0.27	46	-10000	0	46
CER1	0.002	0.004	-10000	0	-10000	0	0
BMP2-4/CER1	-0.008	0.065	0.17	5	-0.16	59	64
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA	-0.036	0.096	-10000	0	-0.28	18	18
BMP2-4 (homodimer)	-0.013	0.078	0.19	5	-0.2	59	64
RGMB	0.01	0	-10000	0	-10000	0	0
BMP6/BMPR2/BMPR1A-1B	0.043	0.057	0.18	56	-0.14	7	63
RGMA	-0.077	0.14	-10000	0	-0.29	119	119
SMURF1	0.01	0	-10000	0	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP	-0.039	0.096	-10000	0	-0.25	27	27
BMP2-4/USAG1	-0.058	0.11	0.18	10	-0.18	166	176
SMAD6/SMURF1/SMAD5	-0.011	0.066	-10000	0	-0.2	15	15
SOSTDC1	-0.083	0.14	0.27	7	-0.29	130	137
BMP7/BMPR2/BMPR1A-1B	-0.021	0.092	0.18	29	-0.14	127	156
SKI	0.01	0	-10000	0	-10000	0	0
BMP6 (homodimer)	0.01	0.023	0.27	2	-0.29	1	3
HFE2	0.007	0.027	0.27	4	-10000	0	4
ZFYVE16	0.01	0	-10000	0	-10000	0	0
MAP3K7	0.01	0	-10000	0	-10000	0	0
BMP2-4/CHRD	-0.019	0.087	0.18	6	-0.18	88	94
SMAD5/SMAD5/SMAD4	-0.011	0.066	-10000	0	-0.2	15	15
MAPK1	0.01	0	-10000	0	-10000	0	0
TAK1/TAB family	-0.037	0.076	-10000	0	-0.26	19	19
BMP7 (homodimer)	-0.097	0.14	-10000	0	-0.29	147	147
NUP214	0.01	0	-10000	0	-10000	0	0
BMP6/FETUA	0.031	0.06	0.19	48	-0.19	1	49
SMAD1/SKI	0.026	0.008	-10000	0	-10000	0	0
SMAD6	0.011	0.027	0.27	3	-0.29	1	4
CTDSP2	0.01	0	-10000	0	-10000	0	0
BMP2-4/FETUA	0.009	0.082	0.18	42	-0.16	50	92
MAP3K7IP1	0	0	-10000	0	-10000	0	0
GREM1	0.006	0.15	0.27	62	-0.29	59	121
BMPR2 (homodimer)	0.01	0	-10000	0	-10000	0	0
GADD34/PP1CA	0.02	0	-10000	0	-10000	0	0
BMPR1A-1B (homodimer)	0.035	0.066	0.19	54	-0.19	6	60
CHRDL1	-0.16	0.15	-10000	0	-0.29	235	235
ENDOFIN/SMAD1	0.026	0.008	-10000	0	-10000	0	0
SMAD6-7/SMURF1/SMAD1	0.034	0.016	-10000	0	-10000	0	0
SMAD6/SMURF1	0.01	0	-10000	0	-10000	0	0
BAMBI	-0.01	0.089	0.27	7	-0.29	33	40
SMURF2	0.01	0	-10000	0	-10000	0	0
BMP2-4/CHRDL1	-0.1	0.1	-10000	0	-0.18	254	254
BMP2-4/GREM1	-0.005	0.11	0.18	64	-0.16	112	176
SMAD7	0.009	0.015	-10000	0	-0.29	1	1
SMAD8A/SMAD8A/SMAD4	-0.11	0.2	-10000	0	-0.43	106	106
SMAD1/SMAD6	0.026	0.008	-10000	0	-10000	0	0
TAK1/SMAD6	0.015	0	-10000	0	-10000	0	0
BMP7	-0.098	0.14	-10000	0	-0.29	147	147
BMP6	0.01	0.023	0.27	2	-0.29	1	3
MAP3K7IP2	0	0	-10000	0	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1	-0.038	0.094	-10000	0	-0.29	19	19
PPM1A	0.01	0	-10000	0	-10000	0	0
SMAD1/SMURF2	0.026	0.008	-10000	0	-10000	0	0
SMAD7/SMURF1	0.014	0.01	-10000	0	-0.19	1	1
CTDSPL	0.01	0	-10000	0	-10000	0	0
PPP1CA	0.01	0	-10000	0	-10000	0	0
XIAP	0.01	0.02	0.27	1	-0.29	1	2
CTDSP1	0.01	0	-10000	0	-10000	0	0
PPP1R15A	0.01	0	-10000	0	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS	-0.051	0.12	0.16	2	-0.19	123	125
CHRD	-0.018	0.089	0.27	1	-0.29	39	40
BMPR2	0.01	0	-10000	0	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM	-0.046	0.1	-10000	0	-0.17	145	145
BMP4	0.001	0.067	0.27	5	-0.29	17	22
FST	0	0.08	0.27	10	-0.29	22	32
BMP2-4/NOG	0.006	0.076	0.19	23	-0.16	48	71
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1	-0.015	0.087	0.17	29	-0.13	127	156

×

S1P1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	0.009	0.018	-10000	0	-0.19	2	2
PDGFRB	-0.001	0.047	-10000	0	-0.3	10	10
SPHK1	0.001	0.081	-10000	0	-0.87	1	1
mol:S1P	-0.008	0.08	-10000	0	-0.79	1	1
S1P1/S1P/Gi	-0.15	0.22	-10000	0	-0.36	187	187
GNAO1	-0.089	0.14	-10000	0	-0.29	129	129
PDGFB-D/PDGFRB/PLCgamma1	-0.14	0.19	-10000	0	-0.37	146	146
PLCG1	-0.15	0.2	-10000	0	-0.39	145	145
mol:GTP	0	0	-10000	0	-10000	0	0
PDGFB-D/PDGFRB	-0.001	0.047	-10000	0	-0.3	10	10
GNAI2	0.005	0.009	-10000	0	-10000	0	0
GNAI3	0.005	0.009	-10000	0	-10000	0	0
GNAI1	0.003	0.027	-10000	0	-0.3	3	3
mol:GDP	0	0	-10000	0	-10000	0	0
EDG1	0	0.016	-10000	0	-0.16	2	2
S1P1/S1P	-0.031	0.067	-10000	0	-0.18	16	16
negative regulation of cAMP metabolic process	-0.15	0.21	-10000	0	-0.35	187	187
MAPK3	-0.2	0.27	-10000	0	-0.52	145	145
calcium-dependent phospholipase C activity	-0.003	0.004	-10000	0	-10000	0	0
Rac1/GDP	0.007	0	-10000	0	-10000	0	0
RhoA/GDP	0.007	0	-10000	0	-10000	0	0
KDR	0.006	0.022	-10000	0	-0.29	2	2
PLCB2	-0.016	0.077	-10000	0	-0.16	18	18
RAC1	0.01	0	-10000	0	-10000	0	0
RhoA/GTP	-0.033	0.054	-10000	0	-0.16	16	16
receptor internalization	-0.03	0.064	-10000	0	-0.14	46	46
PTGS2	-0.28	0.41	-10000	0	-0.95	103	103
Rac1/GTP	-0.033	0.054	-10000	0	-0.16	16	16
RHOA	0.01	0	-10000	0	-10000	0	0
VEGFA	0.007	0.007	-10000	0	-10000	0	0
negative regulation of T cell proliferation	-0.15	0.21	-10000	0	-0.35	187	187
GO:0007205	0	0	-10000	0	-10000	0	0
GNAZ	-0.06	0.12	-10000	0	-0.29	89	89
MAPK1	-0.2	0.27	-10000	0	-0.52	145	145
S1P1/S1P/PDGFB-D/PDGFRB	-0.04	0.083	-10000	0	-0.17	97	97
ABCC1	0.007	0.02	0.27	2	-10000	0	2

×

Rapid glucocorticoid signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma	-0.049	0.076	-10000	0	-0.13	180	180
MAPK9	0.004	0	-10000	0	-10000	0	0
adrenocorticotropin secretion	0.04	0.074	0.16	107	-0.19	7	114
GNB1/GNG2	0.011	0.021	-10000	0	-0.16	6	6
GNB1	0.01	0	-10000	0	-10000	0	0
regulation of calcium ion transport via voltage-gated calcium channel activity	0	0	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
MAPK14	0.004	0	-10000	0	-10000	0	0
Gs family/GTP	-0.059	0.074	-10000	0	-0.14	178	178
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	0.018	0.021	0.042	178	-10000	0	178
GNAL	-0.12	0.15	-10000	0	-0.29	178	178
GNG2	0.006	0.036	-10000	0	-0.29	6	6
CRH	0.07	0.12	0.27	107	-0.29	7	114
mol:cortisol	0	0	-10000	0	-10000	0	0
MAPK8	0.002	0.02	-10000	0	-0.23	3	3
MAPK11	0.004	0	-10000	0	-10000	0	0

×

Osteopontin-mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IKK alpha homodimer	0.051	0.083	0.21	35	-0.14	9	44
NF kappa B1 p50/RelA/I kappa B alpha	0.06	0.087	0.25	35	-10000	0	35
alphaV/beta3 Integrin/Osteopontin/Src	0.093	0.091	0.2	165	-0.16	1	166
AP1	0	0.14	0.26	20	-0.28	47	67
ILK	0.041	0.08	-10000	0	-0.17	6	6
bone resorption	0.037	0.079	0.23	1	-0.22	10	11
PTK2B	0.009	0.015	-10000	0	-0.29	1	1
PYK2/p130Cas	0.078	0.1	0.23	35	-0.19	1	36
ITGAV	0.014	0.008	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
CD44/Rho Family GTPase/ROCK2	0.005	0.047	0.19	1	-0.19	21	22
alphaV/beta3 Integrin/Osteopontin	0.078	0.12	0.2	159	-0.16	41	200
MAP3K1	0.04	0.08	0.17	35	-0.14	41	76
JUN	-0.002	0.058	-10000	0	-0.29	16	16
MAPK3	0.054	0.095	0.24	53	-0.14	8	61
MAPK1	0.054	0.095	0.24	53	-0.14	8	61
Rac1/GDP	0.007	0	-10000	0	-10000	0	0
NFKB1	0.01	0	-10000	0	-10000	0	0
MAPK8	0.036	0.076	0.16	35	-0.13	41	76
ITGB3	-0.019	0.095	-10000	0	-0.29	45	45
NFKBIA	0.056	0.096	0.25	53	-10000	0	53
FOS	-0.084	0.14	-10000	0	-0.29	129	129
CD44	0	0.056	0.27	1	-0.29	14	15
CHUK	0.01	0	-10000	0	-10000	0	0
PLAU	0.069	0.13	0.38	46	-10000	0	46
NF kappa B1 p50/RelA	0.067	0.093	0.26	53	-10000	0	53
BCAR1	0.01	0	-10000	0	-10000	0	0
RELA	0.01	0	-10000	0	-10000	0	0
alphaV beta3 Integrin	0	0.071	-10000	0	-0.2	46	46
mol:GDP	0	0	-10000	0	-10000	0	0
SYK	0.04	0.078	0.16	35	-0.14	41	76
VAV3	0.037	0.072	0.15	37	-0.13	41	78
MAP3K14	0.05	0.09	0.2	52	-0.14	41	93
ROCK2	0.005	0.039	-10000	0	-0.29	7	7
SPP1	0.12	0.13	0.27	165	-10000	0	165
RAC1	0.01	0	-10000	0	-10000	0	0
Rac1/GTP	0.035	0.067	0.18	3	-0.13	9	12
MMP2	-0.019	0.14	0.19	20	-0.3	57	77

×

Glucocorticoid receptor regulatory network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PCK2	-0.024	0.047	0.25	1	-10000	0	1
SMARCC2	0.008	0.014	-10000	0	-10000	0	0
SMARCC1	0.008	0.015	-10000	0	-10000	0	0
TBX21	0.001	0.16	0.48	1	-0.52	26	27
SUMO2	0.006	0.009	-10000	0	-10000	0	0
STAT1 (dimer)	0.016	0.025	0.27	4	-10000	0	4
FKBP4	0.01	0	-10000	0	-10000	0	0
FKBP5	-0.003	0.06	-10000	0	-0.29	17	17
GR alpha/HSP90/FKBP51/HSP90	0.026	0.093	0.22	18	-0.17	6	24
PRL	-0.018	0.1	0.45	2	-10000	0	2
cortisol/GR alpha (dimer)/TIF2	0.031	0.23	0.42	51	-0.42	25	76
RELA	-0.11	0.11	-10000	0	-0.21	215	215
FGG	0.08	0.24	0.41	77	-0.41	22	99
GR beta/TIF2	0.016	0.11	0.23	27	-0.23	14	41
IFNG	-0.021	0.3	0.52	46	-0.49	47	93
apoptosis	-0.045	0.18	0.48	3	-0.45	17	20
CREB1	0.018	0.028	-10000	0	-10000	0	0
histone acetylation	-0.092	0.13	-10000	0	-0.33	51	51
BGLAP	0.005	0.11	0.35	1	-0.37	1	2
GR/PKAc	0.034	0.087	0.22	19	-10000	0	19
NF kappa B1 p50/RelA	-0.2	0.2	0.28	2	-0.36	238	240
SMARCD1	0.008	0.015	-10000	0	-10000	0	0
MDM2	0.038	0.091	0.18	67	-0.14	7	74
GATA3	-0.005	0.078	0.26	3	-0.29	27	30
AKT1	0.007	0.007	-10000	0	-0.14	1	1
CSF2	-0.041	0.12	-10000	0	-0.44	5	5
GSK3B	0.006	0.009	-10000	0	-10000	0	0
NR1I3	-0.031	0.16	0.5	2	-0.45	7	9
CSN2	0.051	0.2	0.33	60	-0.37	24	84
BRG1/BAF155/BAF170/BAF60A	0.02	0.048	-10000	0	-0.22	15	15
NFATC1	-0.003	0.063	-10000	0	-0.29	19	19
POU2F1	0.013	0.014	-10000	0	-10000	0	0
CDKN1A	0.011	0.087	-10000	0	-1.2	2	2
response to stress	0	0	-10000	0	-10000	0	0
response to UV	-0.002	0.007	-10000	0	-10000	0	0
SFN	0.027	0.076	0.27	32	-0.29	4	36
GR alpha/HSP90/FKBP51/HSP90/14-3-3	0.043	0.087	0.22	19	-0.17	1	20
prolactin receptor activity	0	0	-10000	0	-10000	0	0
EGR1	-0.14	0.32	0.48	2	-0.69	100	102
JUN	0.039	0.21	0.4	61	-0.32	36	97
IL4	-0.011	0.12	-10000	0	-0.43	13	13
CDK5R1	0.022	0.059	0.27	22	-10000	0	22
PRKACA	0.01	0	-10000	0	-10000	0	0
cortisol/GR alpha (monomer)/AP-1	-0.037	0.068	-10000	0	-0.22	32	32
GR alpha/HSP90/FKBP51/HSP90/PP5C	0.033	0.088	0.22	16	-0.17	1	17
cortisol/GR alpha (monomer)	0.044	0.26	0.48	57	-0.48	23	80
NCOA2	-0.008	0.07	-10000	0	-0.29	24	24
response to hypoxia	0	0	-10000	0	-10000	0	0
FOS	-0.019	0.17	0.24	53	-0.3	77	130
AP-1/NFAT1-c-4	-0.008	0.32	0.52	60	-0.46	78	138
AFP	0.005	0.18	0.46	10	-10000	0	10
SUV420H1	0.01	0	-10000	0	-10000	0	0
IRF1	0.045	0.14	0.35	13	-10000	0	13
TP53	0.017	0.035	-10000	0	-0.49	2	2
PPP5C	0.01	0	-10000	0	-10000	0	0
KRT17	-0.063	0.37	0.57	36	-0.77	49	85
KRT14	0.1	0.25	0.44	41	-1.1	4	45
TBP	0.015	0.009	-10000	0	-10000	0	0
CREBBP	-0.059	0.083	0.25	4	-0.29	16	20
HDAC1	0.008	0.011	-10000	0	-10000	0	0
HDAC2	0.004	0.011	-10000	0	-10000	0	0
AP-1	-0.008	0.32	0.52	60	-0.46	78	138
MAPK14	0.006	0.008	-10000	0	-10000	0	0
MAPK10	-0.021	0.085	-10000	0	-0.29	37	37
MAPK11	0.006	0.009	-10000	0	-10000	0	0
KRT5	-0.2	0.52	0.55	42	-0.93	120	162
interleukin-1 receptor activity	-0.005	0.009	-10000	0	-10000	0	0
NCOA1	0.011	0.001	-10000	0	-10000	0	0
STAT1	0.016	0.026	0.27	4	-10000	0	4
CGA	0.009	0.12	0.35	9	-0.3	9	18
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2	-0.11	0.18	0.31	1	-0.4	81	82
MAPK3	0.006	0.009	-10000	0	-10000	0	0
MAPK1	0.006	0.008	-10000	0	-10000	0	0
ICAM1	-0.16	0.23	0.38	4	-0.44	124	128
NFKB1	-0.11	0.11	-10000	0	-0.2	224	224
MAPK8	0.032	0.17	0.36	46	-0.26	39	85
MAPK9	0.006	0.008	-10000	0	-10000	0	0
cortisol/GR alpha (dimer)	-0.057	0.18	0.48	3	-0.47	17	20
BAX	0.016	0.027	-10000	0	-10000	0	0
POMC	-0.16	0.26	0.45	1	-0.84	19	20
EP300	-0.059	0.083	0.25	4	-0.29	16	20
cortisol/GR alpha (dimer)/p53	0.046	0.23	0.43	54	-0.42	20	74
proteasomal ubiquitin-dependent protein catabolic process	0.025	0.073	0.16	20	-10000	0	20
SGK1	-0.076	0.26	-10000	0	-1.2	16	16
IL13	-0.055	0.23	0.5	7	-0.59	16	23
IL6	-0.43	0.48	-10000	0	-0.89	201	201
PRKACG	0.001	0.003	-10000	0	-10000	0	0
IL5	-0.055	0.2	0.46	7	-0.52	13	20
IL2	-0.06	0.26	0.46	27	-0.47	61	88
CDK5	0.008	0.006	-10000	0	-10000	0	0
PRKACB	0.008	0.021	-10000	0	-0.29	2	2
HSP90AA1	0.01	0	-10000	0	-10000	0	0
IL8	-0.24	0.36	0.47	1	-0.72	109	110
CDK5R1/CDK5	0.02	0.041	0.19	22	-10000	0	22
NF kappa B1 p50/RelA/PKAc	-0.14	0.16	0.23	2	-0.27	212	214
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90	0.049	0.21	0.4	55	-0.38	23	78
SMARCA4	0.008	0.014	-10000	0	-10000	0	0
chromatin remodeling	0.039	0.16	0.32	27	-0.34	12	39
NF kappa B1 p50/RelA/Cbp	-0.22	0.18	0.3	1	-0.38	191	192
JUN (dimer)	0.039	0.21	0.4	61	-0.32	36	97
YWHAH	0.01	0	-10000	0	-10000	0	0
VIPR1	0.004	0.15	0.28	2	-0.48	25	27
NR3C1	0.036	0.15	0.3	46	-0.26	20	66
NR4A1	-0.16	0.16	-10000	0	-0.29	226	226
TIF2/SUV420H1	0.003	0.049	-10000	0	-0.19	24	24
MAPKKK cascade	-0.045	0.18	0.48	3	-0.45	17	20
cortisol/GR alpha (dimer)/Src-1	0.044	0.23	0.42	56	-0.41	23	79
PBX1	0	0.061	-10000	0	-0.29	17	17
POU1F1	0.008	0.027	0.27	3	-10000	0	3
SELE	-0.4	0.46	0.31	2	-0.86	193	195
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A	0.038	0.16	0.32	27	-0.35	12	39
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90	0.049	0.21	0.4	55	-0.38	23	78
mol:cortisol	0.03	0.15	0.27	62	-0.26	24	86
MMP1	0.16	0.21	0.44	76	-0.87	1	77

×

Neurotrophic factor-mediated Trk receptor signaling

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
CRKL	0.011	0.018	0.27	2	-10000	0	2
RAS family/GTP/Tiam1	-0.056	0.068	-10000	0	-0.17	49	49
NT3 (dimer)/TRKC	-0.12	0.13	0.19	1	-0.23	225	226
NT3 (dimer)/TRKB	-0.11	0.14	0.2	8	-0.22	218	226
SHC/Grb2/SOS1/GAB1/PI3K	0.017	0.01	-10000	0	-0.16	1	1
RAPGEF1	0.01	0	-10000	0	-10000	0	0
BDNF	-0.047	0.12	-10000	0	-0.29	78	78
PIK3CA	0.01	0	-10000	0	-10000	0	0
DYNLT1	0.01	0	-10000	0	-10000	0	0
NTRK1	0.013	0.034	0.27	7	-10000	0	7
NTRK2	-0.1	0.15	0.27	7	-0.29	157	164
NTRK3	-0.14	0.15	-10000	0	-0.29	196	196
NT-4/5 (dimer)/TRKB	-0.09	0.13	0.2	8	-0.21	203	211
neuron apoptosis	0.13	0.18	0.35	132	-10000	0	132
SHC 2-3/Grb2	-0.14	0.19	-10000	0	-0.38	132	132
SHC1	0.011	0.013	0.27	1	-10000	0	1
SHC2	-0.15	0.21	-10000	0	-0.46	101	101
SHC3	-0.14	0.19	-10000	0	-0.42	109	109
STAT3 (dimer)	0.015	0.047	0.16	14	-0.28	7	21
NT3 (dimer)/TRKA	-0.046	0.11	0.2	10	-0.18	143	153
RIN/GDP	-0.05	0.068	0.15	1	-0.16	58	59
GIPC1	0.01	0	-10000	0	-10000	0	0
KRAS	0.011	0.013	0.27	1	-10000	0	1
DNAJA3	-0.058	0.12	0.18	2	-0.23	121	123
RIN/GTP	0.001	0.009	0.18	1	-10000	0	1
CCND1	0.015	0.091	0.31	14	-0.54	7	21
MAGED1	0.01	0	-10000	0	-10000	0	0
PTPN11	0.01	0	-10000	0	-10000	0	0
RICS	0	0	-10000	0	-10000	0	0
NT-4/5 (dimer)	-0.01	0.074	-10000	0	-0.29	27	27
SHC/GRB2/SOS1	0.021	0.008	0.18	1	-10000	0	1
GRB2	0.01	0	-10000	0	-10000	0	0
NGF (dimer)/TRKA/MATK	-0.008	0.081	0.18	12	-0.17	68	80
TRKA/NEDD4-2	0.017	0.023	0.19	7	-10000	0	7
ELMO1	0.008	0.025	-10000	0	-0.29	3	3
RhoG/GTP/ELMO1/DOCK1	0.011	0.022	-10000	0	-0.2	4	4
NGF	-0.03	0.1	-10000	0	-0.29	54	54
HRAS	0.01	0	-10000	0	-10000	0	0
DOCK1	0.008	0.021	-10000	0	-0.29	2	2
GAB2	0.009	0.015	-10000	0	-0.29	1	1
RIT2	0.001	0.014	0.27	1	-10000	0	1
RIT1	0.01	0	-10000	0	-10000	0	0
FRS2	0.014	0.034	0.27	7	-10000	0	7
DNM1	0.002	0.048	-10000	0	-0.29	11	11
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.01	0	-10000	0	-10000	0	0
SH2B1 (homopentamer)	0	0	-10000	0	-10000	0	0
RhoG/GTP	-0.054	0.12	0.18	2	-0.22	121	123
mol:GDP	-0.072	0.094	-10000	0	-0.22	69	69
NGF (dimer)	-0.03	0.1	-10000	0	-0.29	54	54
RhoG/GDP	0.006	0.017	-10000	0	-0.19	3	3
RIT1/GDP	-0.049	0.068	-10000	0	-0.16	55	55
TIAM1	0.008	0.025	-10000	0	-0.29	3	3
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
BDNF (dimer)/TRKB	-0.076	0.12	0.18	7	-0.19	194	201
KIDINS220/CRKL/C3G	0.016	0.012	0.19	2	-10000	0	2
SHC/RasGAP	0.015	0.009	0.19	1	-10000	0	1
FRS2 family/SHP2	0.023	0.021	0.18	7	-10000	0	7
SHC/GRB2/SOS1/GAB1	0.026	0.007	0.18	1	-10000	0	1
RIT1/GTP	0.007	0	-10000	0	-10000	0	0
NT3 (dimer)	-0.045	0.12	0.27	1	-0.29	76	77
RAP1/GDP	-0.046	0.054	-10000	0	-0.14	55	55
KIDINS220/CRKL	0.011	0.018	0.27	2	-10000	0	2
BDNF (dimer)	-0.047	0.12	-10000	0	-0.29	78	78
ubiquitin-dependent protein catabolic process	-0.001	0.064	0.18	7	-0.16	54	61
Schwann cell development	-0.034	0.027	-10000	0	-0.093	4	4
EHD4	0.01	0	-10000	0	-10000	0	0
FRS2 family/GRB2/SOS1	0.028	0.02	0.18	7	-10000	0	7
FRS2 family/SHP2/CRK family/C3G/GAB2	0.02	0.014	-10000	0	-0.15	1	1
RAP1B	0.01	0	-10000	0	-10000	0	0
RAP1A	0.01	0	-10000	0	-10000	0	0
CDC42/GTP	-0.14	0.13	-10000	0	-0.21	285	285
ABL1	0.01	0	-10000	0	-10000	0	0
SH2B family/GRB2/SOS1	0.015	0	-10000	0	-10000	0	0
Rap1/GTP	-0.022	0.056	-10000	0	-10000	0	0
STAT3	0.015	0.047	0.16	14	-0.28	7	21
axon guidance	-0.14	0.13	-10000	0	-0.2	285	285
MAPK3	-0.013	0.067	-10000	0	-0.15	68	68
MAPK1	-0.013	0.067	-10000	0	-0.15	68	68
CDC42/GDP	-0.049	0.068	-10000	0	-0.16	55	55
NTF3	-0.045	0.12	0.27	1	-0.29	76	77
NTF4	-0.01	0.074	-10000	0	-0.29	27	27
NGF (dimer)/TRKA/FAIM	-0.001	0.064	0.18	7	-0.16	54	61
PI3K	0.014	0.01	-10000	0	-0.19	1	1
FRS3	0.01	0	-10000	0	-10000	0	0
FAIM	0.01	0	-10000	0	-10000	0	0
GAB1	0.01	0	-10000	0	-10000	0	0
RASGRF1	-0.047	0.13	0.23	3	-0.23	119	122
SOS1	0.01	0	-10000	0	-10000	0	0
MCF2L	-0.1	0.12	0.12	1	-0.2	225	226
RGS19	0.011	0.013	0.27	1	-10000	0	1
CDC42	0.01	0	-10000	0	-10000	0	0
RAS family/GTP	0.005	0.055	-10000	0	-10000	0	0
Rac1/GDP	-0.049	0.068	-10000	0	-0.16	55	55
NGF (dimer)/TRKA/GRIT	-0.007	0.063	0.17	7	-0.16	54	61
neuron projection morphogenesis	-0.054	0.13	-10000	0	-0.39	25	25
NGF (dimer)/TRKA/NEDD4-2	-0.001	0.064	0.18	7	-0.16	54	61
MAP2K1	0.014	0.004	-10000	0	-10000	0	0
NGFR	-0.053	0.13	0.27	5	-0.29	90	95
NGF (dimer)/TRKA/GIPC/GAIP	-0.01	0.075	-10000	0	-0.18	59	59
RAS family/GTP/PI3K	0.014	0.01	-10000	0	-0.17	1	1
FRS2 family/SHP2/GRB2/SOS1	0.032	0.018	0.17	7	-10000	0	7
NRAS	0.01	0	-10000	0	-10000	0	0
GRB2/SOS1	0.015	0	-10000	0	-10000	0	0
PRKCI	0.01	0	-10000	0	-10000	0	0
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
RAC1	0.01	0	-10000	0	-10000	0	0
PRKCZ	0.008	0.025	-10000	0	-0.29	3	3
MAPKKK cascade	-0.094	0.21	-10000	0	-0.61	54	54
RASA1	0.01	0	-10000	0	-10000	0	0
TRKA/c-Abl	0.017	0.023	0.19	7	-10000	0	7
SQSTM1	0.01	0	-10000	0	-10000	0	0
BDNF (dimer)/TRKB/GIPC	-0.063	0.11	0.18	7	-0.17	194	201
NGF (dimer)/TRKA/p62/Atypical PKCs	0.009	0.058	0.17	6	-0.13	55	61
MATK	-0.003	0.076	0.27	6	-0.29	23	29
NEDD4L	0.01	0	-10000	0	-10000	0	0
RAS family/GDP	-0.048	0.046	-10000	0	-0.13	45	45
NGF (dimer)/TRKA	-0.062	0.12	0.2	2	-0.24	121	123
Rac1/GTP	-0.065	0.079	-10000	0	-0.18	117	117
FRS2 family/SHP2/CRK family	0.033	0.021	0.17	9	-10000	0	9

×

JNK signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1	0.004	0.067	0.18	4	-0.16	50	54
MAP4K1	0.005	0.051	0.27	3	-0.29	10	13
MAP3K8	0.008	0.025	-10000	0	-0.29	3	3
PRKCB	-0.076	0.14	-10000	0	-0.29	118	118
DBNL	0.01	0	-10000	0	-10000	0	0
CRKL	0.011	0.018	0.27	2	-10000	0	2
MAP3K1	-0.005	0.07	-10000	0	-0.18	50	50
JUN	-0.15	0.25	-10000	0	-0.53	121	121
MAP3K7	-0.005	0.07	-10000	0	-0.18	50	50
GRAP2	-0.023	0.093	-10000	0	-0.29	45	45
CRK	0.01	0	-10000	0	-10000	0	0
MAP2K4	-0.004	0.073	-10000	0	-0.18	46	46
LAT	0.011	0.013	0.27	1	-10000	0	1
LCP2	0.008	0.025	-10000	0	-0.29	3	3
MAPK8	-0.15	0.26	-10000	0	-0.55	121	121
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family	-0.006	0.074	-10000	0	-0.19	50	50
LAT/GRAP2/SLP76/HPK1/HIP-55	0.009	0.064	0.17	4	-0.15	50	54

×

Calcium signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC1	0.007	0.051	0.11	20	-0.19	15	35
NFATC2	-0.002	0.064	0.13	7	-0.19	33	40
NFATC3	0.014	0.034	0.11	20	-10000	0	20
CD40LG	-0.063	0.21	0.38	16	-0.36	95	111
PTGS2	-0.077	0.22	0.38	15	-0.38	115	130
JUNB	0.006	0.033	-10000	0	-0.29	5	5
CaM/Ca2+/Calcineurin A alpha-beta B1	0.007	0.02	0.098	2	-10000	0	2
CaM/Ca2+	0.007	0.02	0.098	2	-10000	0	2
CALM1	0.01	0.012	-10000	0	-10000	0	0
JUN	-0.001	0.059	-10000	0	-0.29	15	15
mol:Ca2+	0	0.011	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0.007	0.007	-10000	0	-10000	0	0
FOSL1	-0.011	0.075	-10000	0	-0.29	28	28
CREM	0.01	0	-10000	0	-10000	0	0
Jun/NFAT1-c-4/p21SNFT	-0.007	0.14	0.33	16	-0.26	56	72
FOS	-0.058	0.13	-10000	0	-0.29	90	90
IFNG	-0.015	0.24	0.41	54	-0.34	83	137
AP-1/NFAT1-c-4	-0.042	0.24	0.54	15	-0.38	83	98
FASLG	-0.053	0.21	0.4	19	-0.35	89	108
NFAT1-c-4/ICER1	-0.006	0.1	0.22	14	-0.22	42	56
IL2RA	-0.044	0.22	0.43	24	-0.36	84	108
FKBP12/FK506	0.007	0	-10000	0	-10000	0	0
CSF2	-0.018	0.23	0.4	50	-0.34	83	133
JunB/Fra1/NFAT1-c-4	-0.013	0.11	0.21	14	-0.22	51	65
IL4	-0.053	0.19	0.37	16	-0.34	83	99
IL2	-0.005	0.009	-10000	0	-10000	0	0
IL3	-0.012	0.016	-10000	0	-10000	0	0
FKBP1A	0.01	0	-10000	0	-10000	0	0
BATF3	0.009	0.042	0.27	4	-0.29	5	9
mol:FK506	0	0	-10000	0	-10000	0	0
POU2F1	0.01	0.001	-10000	0	-10000	0	0

×

Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer	-0.073	0.13	0.18	1	-0.23	156	157
fibroblast growth factor receptor signaling pathway	-0.073	0.13	0.18	1	-0.22	156	157
LAMA1	0.041	0.12	0.27	66	-0.29	15	81
PRNP	0.003	0.046	-10000	0	-0.29	10	10
GPC1/SLIT2	-0.079	0.1	-10000	0	-0.19	184	184
SMAD2	0.012	0.013	-10000	0	-0.14	3	3
GPC1/PrPc/Cu2+	0.01	0.028	0.17	1	-0.16	10	11
GPC1/Laminin alpha1	0.036	0.08	0.2	66	-0.19	15	81
TDGF1	0.007	0.023	0.27	3	-10000	0	3
CRIPTO/GPC1	0.013	0.018	0.19	4	-10000	0	4
APP/GPC1	0.014	0.017	0.19	1	-0.19	2	3
mol:NO	0	0	-10000	0	-10000	0	0
YES1	0.011	0.01	0.12	3	-10000	0	3
FLT1	0.01	0	-10000	0	-10000	0	0
GPC1/TGFB/TGFBR1/TGFBR2	0.019	0.017	0.18	1	-0.16	3	4
SERPINC1	0.027	0.068	0.27	30	-10000	0	30
FYN	0.011	0.01	0.11	4	-10000	0	4
FGR	0.011	0.01	0.11	4	-10000	0	4
positive regulation of MAPKKK cascade	0.004	0.047	-10000	0	-0.26	3	3
SLIT2	-0.13	0.15	-10000	0	-0.29	185	185
GPC1/NRG	-0.014	0.091	0.19	19	-0.19	73	92
NRG1	-0.032	0.13	0.27	18	-0.29	73	91
GPC1/VEGF165 homodimer/VEGFR1 homodimer	0.021	0.008	0.18	1	-10000	0	1
LYN	0.011	0.01	0.12	3	-10000	0	3
mol:Spermine	0.005	0.008	0.16	1	-10000	0	1
cell growth	-0.073	0.13	0.18	1	-0.22	156	157
BMP signaling pathway	-0.011	0.013	-10000	0	-0.27	1	1
SRC	0.011	0.01	0.11	4	-10000	0	4
TGFBR1	0.01	0	-10000	0	-10000	0	0
mol:Cu2+	0	0	-10000	0	-10000	0	0
PLA2G2A	-0.12	0.15	0.27	3	-0.29	182	185
GPC1	0.011	0.013	0.27	1	-10000	0	1
TGFBR1 (dimer)	0.01	0	-10000	0	-10000	0	0
VEGFA	0.01	0	-10000	0	-10000	0	0
BLK	0.015	0.032	0.16	16	-10000	0	16
HCK	0.013	0.02	0.14	9	-10000	0	9
FGF2	-0.089	0.14	-10000	0	-0.29	136	136
FGFR1	-0.058	0.12	-10000	0	-0.29	93	93
VEGFR1 homodimer	0.01	0	-10000	0	-10000	0	0
TGFBR2	0.008	0.025	-10000	0	-0.29	3	3
cell death	0.014	0.017	0.19	1	-0.19	2	3
ATIII/GPC1	0.027	0.047	0.19	31	-10000	0	31
PLA2G2A/GPC1	-0.076	0.1	0.19	3	-0.19	181	184
LCK	0.012	0.015	0.13	6	-10000	0	6
neuron differentiation	-0.014	0.091	0.19	19	-0.19	73	92
PrPc/Cu2+	0.002	0.031	-10000	0	-0.19	10	10
APP	0.008	0.021	-10000	0	-0.29	2	2
TGFBR2 (dimer)	0.008	0.025	-10000	0	-0.29	3	3

×

FOXA2 and FOXA3 transcription factor networks

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
ACADVL	0.19	0.19	0.59	31	-10000	0	31
PCK1	0.19	0.19	0.6	45	-10000	0	45
HNF4A	0.23	0.24	0.71	52	-10000	0	52
KCNJ11	0.19	0.27	0.61	35	-0.7	18	53
AKT1	0.13	0.14	0.38	49	-0.38	1	50
response to starvation	0.016	0.032	0.15	12	-10000	0	12
DLK1	0.18	0.27	0.61	39	-0.62	19	58
NKX2-1	0.24	0.2	0.67	41	-10000	0	41
ACADM	0.19	0.2	0.57	36	-0.53	2	38
TAT	0.19	0.19	0.59	44	-10000	0	44
CEBPB	0.023	0.029	0.15	10	-10000	0	10
CEBPA	0.033	0.062	0.25	20	-0.29	2	22
TTR	0.18	0.25	0.6	70	-0.44	3	73
PKLR	0.2	0.21	0.58	49	-10000	0	49
APOA1	0.26	0.28	0.82	48	-10000	0	48
CPT1C	0.19	0.2	0.57	40	-0.68	1	41
ALAS1	0.16	0.14	0.5	17	-10000	0	17
TFRC	0.24	0.22	0.65	58	-10000	0	58
FOXF1	-0.11	0.15	-10000	0	-0.3	148	148
NF1	0.013	0	-10000	0	-10000	0	0
HNF1A (dimer)	0.071	0.071	0.25	24	-10000	0	24
CPT1A	0.19	0.19	0.57	37	-0.7	1	38
HMGCS1	0.19	0.19	0.57	35	-10000	0	35
NR3C1	0.022	0.064	0.21	8	-0.29	10	18
CPT1B	0.19	0.19	0.58	35	-0.7	1	36
chromatin remodeling	0	0	-10000	0	-10000	0	0
SP1	0.057	0.054	-10000	0	-10000	0	0
GCK	0.16	0.27	0.57	35	-0.63	25	60
CREB1	0.025	0.036	0.18	6	-10000	0	6
IGFBP1	0.16	0.17	0.57	30	-10000	0	30
PDX1	0.26	0.23	0.57	99	-10000	0	99
UCP2	0.19	0.19	0.56	40	-10000	0	40
ALDOB	0.23	0.25	0.72	48	-10000	0	48
AFP	0.05	0.11	0.34	18	-10000	0	18
BDH1	0.19	0.19	0.57	38	-10000	0	38
HADH	0.21	0.21	0.6	35	-10000	0	35
F2	0.25	0.27	0.82	43	-10000	0	43
HNF1A	0.071	0.071	0.25	24	-10000	0	24
G6PC	0.1	0.12	0.5	25	-10000	0	25
SLC2A2	0.21	0.21	0.61	49	-10000	0	49
INS	-0.017	0.033	-10000	0	-10000	0	0
FOXA1	0.007	0.12	0.25	22	-0.29	40	62
FOXA3	0.13	0.14	0.33	116	-10000	0	116
FOXA2	0.31	0.32	0.83	69	-10000	0	69
ABCC8	0.21	0.21	0.61	36	-10000	0	36
ALB	0.064	0.13	0.31	61	-10000	0	61

×

IL6-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
BCL2L1	0.012	0.22	0.56	12	-0.62	11	23
CRP	0.014	0.23	0.61	14	-0.6	13	27
cell cycle arrest	0.002	0.24	0.59	12	-0.65	17	29
TIMP1	0.014	0.21	0.53	13	-0.51	15	28
IL6ST	-0.022	0.1	-10000	0	-0.29	51	51
Rac1/GDP	-0.068	0.19	0.3	10	-0.38	80	90
AP1	0.004	0.12	0.31	8	-0.31	9	17
GAB2	0.012	0.016	-10000	0	-0.28	1	1
TNFSF11	0.011	0.24	0.58	13	-0.7	15	28
HSP90B1	0.027	0.072	-10000	0	-0.57	1	1
GAB1	0.012	0.004	-10000	0	-10000	0	0
MAPK14	-0.12	0.23	-10000	0	-0.55	77	77
AKT1	0.03	0.022	-10000	0	-10000	0	0
FOXO1	0.029	0.021	-10000	0	-10000	0	0
MAP2K6	-0.1	0.21	0.25	3	-0.45	82	85
mol:GTP	0.001	0.002	-10000	0	-10000	0	0
MAP2K4	-0.038	0.21	0.36	23	-0.41	60	83
MITF	-0.086	0.2	0.27	10	-0.39	88	98
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TYK2	0.01	0	-10000	0	-10000	0	0
A2M	-0.1	0.35	-10000	0	-1.2	37	37
CEBPB	0.016	0.017	-10000	0	-0.29	1	1
GRB2/SOS1/GAB family/SHP2	-0.005	0.088	0.26	4	-0.35	3	7
STAT3	-0.006	0.25	0.59	12	-0.69	17	29
STAT1	0.014	0.04	0.27	4	-10000	0	4
CEBPD	0.01	0.22	0.56	11	-0.78	7	18
PIK3CA	0.011	0.001	-10000	0	-10000	0	0
PI3K	0.015	0.01	-10000	0	-0.19	1	1
JUN	-0.001	0.058	-10000	0	-0.29	16	16
PIAS3/MITF	-0.082	0.19	0.25	10	-0.37	87	97
MAPK11	-0.12	0.23	-10000	0	-0.55	77	77
STAT3 (dimer)/FOXO1	-0.011	0.22	0.47	19	-0.51	24	43
GRB2/SOS1/GAB family	-0.068	0.16	0.24	2	-0.32	78	80
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK	-0.095	0.18	0.21	5	-0.38	82	87
GRB2	0.012	0.004	-10000	0	-10000	0	0
JAK2	0.009	0.015	-10000	0	-0.29	1	1
LBP	0.044	0.23	0.56	24	-0.55	6	30
PIK3R1	0.01	0.015	-10000	0	-0.29	1	1
JAK1	0.011	0.011	-10000	0	-10000	0	0
MYC	-0.012	0.28	0.56	12	-0.86	23	35
FGG	0.022	0.24	0.59	22	-0.61	12	34
macrophage differentiation	0.002	0.24	0.59	12	-0.65	17	29
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4	-0.064	0.13	-10000	0	-0.27	75	75
JUNB	0.006	0.23	0.54	12	-0.69	15	27
FOS	-0.084	0.14	-10000	0	-0.29	129	129
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4	-0.082	0.2	0.3	10	-0.41	77	87
STAT1/PIAS1	-0.046	0.18	0.3	21	-0.37	54	75
GRB2/SOS1/GAB family/SHP2/PI3K	0.028	0.024	-10000	0	-0.23	1	1
STAT3 (dimer)	-0.004	0.24	0.59	12	-0.68	17	29
PRKCD	-0.015	0.22	0.42	23	-0.47	40	63
IL6R	-0.013	0.084	-10000	0	-0.29	34	34
SOCS3	-0.19	0.34	-10000	0	-0.99	55	55
gp130 (dimer)/JAK1/JAK1/LMO4	0.009	0.08	0.22	3	-0.16	54	57
Rac1/GTP	-0.061	0.2	0.3	19	-0.38	77	96
HCK	0.005	0.058	0.27	5	-0.29	12	17
MAPKKK cascade	0.022	0.079	0.27	2	-0.64	1	3
bone resorption	0.013	0.23	0.58	13	-0.66	15	28
IRF1	0.011	0.22	0.56	11	-0.68	8	19
mol:GDP	-0.077	0.2	0.3	10	-0.39	81	91
SOS1	0.013	0.006	-10000	0	-10000	0	0
VAV1	-0.078	0.2	0.3	10	-0.4	81	91
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3	-0.11	0.27	-10000	0	-0.6	80	80
PTPN11	0.013	0.032	-10000	0	-10000	0	0
IL6/IL6RA	-0.086	0.13	-10000	0	-0.21	193	193
gp130 (dimer)/TYK2/TYK2/LMO4	0.004	0.072	0.22	1	-0.16	59	60
gp130 (dimer)/JAK2/JAK2/LMO4	0.004	0.074	0.22	1	-0.16	59	60
IL6	-0.1	0.15	-10000	0	-0.29	155	155
PIAS3	0.01	0	-10000	0	-10000	0	0
PTPRE	0	0.032	0.27	2	-0.2	2	4
PIAS1	0.01	0	-10000	0	-10000	0	0
RAC1	0.011	0.002	-10000	0	-10000	0	0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4	-0.097	0.17	0.2	3	-0.25	170	173
LMO4	0.015	0.024	-10000	0	-0.3	1	1
STAT3 (dimer)/PIAS3	-0.018	0.23	0.53	10	-0.66	17	27
MCL1	0.031	0.021	-10000	0	-10000	0	0

×

ErbB2/ErbB3 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
USP8	0.004	0.004	-10000	0	-10000	0	0
RAS family/GTP	-0.004	0.085	0.2	2	-0.16	67	69
NFATC4	-0.014	0.058	-10000	0	-0.12	75	75
ERBB2IP	0.01	0.002	-10000	0	-10000	0	0
HSP90 (dimer)	0.01	0	-10000	0	-10000	0	0
mammary gland morphogenesis	-0.012	0.075	0.16	12	-0.15	75	87
JUN	-0.01	0.082	0.23	6	-0.3	1	7
HRAS	0.01	0.001	-10000	0	-10000	0	0
DOCK7	-0.016	0.066	-10000	0	-0.14	75	75
ErbB2/ErbB3/neuregulin 1 beta/SHC	-0.003	0.074	0.17	17	-0.14	75	92
AKT1	0.003	0.003	-10000	0	-10000	0	0
BAD	0.005	0.002	-10000	0	-10000	0	0
MAPK10	-0.009	0.043	-10000	0	-0.11	29	29
mol:GTP	0	0.002	-10000	0	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta	-0.012	0.08	0.17	12	-0.16	75	87
RAF1	-0.004	0.092	0.18	34	-0.21	21	55
ErbB2/ErbB3/neuregulin 2	-0.056	0.081	0.17	2	-0.15	170	172
STAT3	0.013	0.004	-10000	0	-10000	0	0
cell migration	-0.014	0.051	-10000	0	-0.13	22	22
mol:PI-3-4-5-P3	-0.001	0.001	-10000	0	-10000	0	0
cell proliferation	-0.059	0.22	0.37	5	-0.55	32	37
FOS	-0.1	0.25	0.3	34	-0.44	130	164
NRAS	0.01	0.001	-10000	0	-10000	0	0
mol:Ca2+	-0.012	0.075	0.16	12	-0.15	75	87
MAPK3	-0.029	0.17	0.34	5	-0.41	32	37
MAPK1	-0.029	0.17	0.34	5	-0.41	32	37
JAK2	-0.016	0.066	-10000	0	-0.14	75	75
NF2	0.004	0.007	-10000	0	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1	-0.017	0.082	-10000	0	-0.19	70	70
NRG1	-0.033	0.13	0.27	18	-0.29	73	91
GRB2/SOS1	0.015	0.001	-10000	0	-10000	0	0
MAPK8	-0.027	0.092	-10000	0	-0.2	84	84
MAPK9	-0.007	0.039	-10000	0	-0.091	24	24
ERBB2	0.001	0.028	0.15	13	-10000	0	13
ERBB3	0.003	0.05	0.27	2	-0.29	10	12
SHC1	0.011	0.013	0.27	1	-10000	0	1
RAC1	0.01	0	-10000	0	-10000	0	0
apoptosis	0.004	0.01	-10000	0	-10000	0	0
STAT3 (dimer)	0.013	0.004	-10000	0	-10000	0	0
RNF41	0.004	0.005	-10000	0	-10000	0	0
FRAP1	0.002	0.002	-10000	0	-10000	0	0
RAC1-CDC42/GTP	-0.019	0.045	-10000	0	-0.11	70	70
ErbB2/ErbB2/HSP90 (dimer)	0.009	0.02	0.12	10	-10000	0	10
CHRNA1	-0.004	0.16	0.34	34	-0.38	15	49
myelination	-0.016	0.056	-10000	0	-0.12	77	77
PPP3CB	-0.015	0.063	-10000	0	-0.14	75	75
KRAS	0.011	0.013	0.27	1	-10000	0	1
RAC1-CDC42/GDP	-0.008	0.076	-10000	0	-0.16	75	75
NRG2	-0.12	0.15	-10000	0	-0.29	172	172
mol:GDP	-0.019	0.083	-10000	0	-0.18	75	75
SOS1	0.01	0.001	-10000	0	-10000	0	0
MAP2K2	-0.005	0.1	0.21	34	-0.2	31	65
SRC	0.01	0	-10000	0	-10000	0	0
mol:cAMP	0	0.001	-10000	0	-10000	0	0
PTPN11	-0.016	0.066	-10000	0	-0.14	75	75
MAP2K1	-0.045	0.17	0.34	2	-0.41	31	33
heart morphogenesis	-0.012	0.075	0.16	12	-0.15	75	87
RAS family/GDP	-0.004	0.079	-10000	0	-0.16	70	70
GRB2	0.01	0.001	-10000	0	-10000	0	0
PRKACA	0.003	0.007	-10000	0	-10000	0	0
CHRNE	0.003	0.026	0.19	2	-0.16	1	3
HSP90AA1	0.01	0	-10000	0	-10000	0	0
activation of caspase activity	-0.003	0.003	-10000	0	-10000	0	0
nervous system development	-0.012	0.075	0.16	12	-0.15	75	87
CDC42	0.01	0	-10000	0	-10000	0	0

×

IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1	0.023	0.12	0.3	27	-0.27	16	43
TBX21	-0.11	0.47	0.74	8	-1.1	59	67
B2M	0.009	0.01	-10000	0	-10000	0	0
TYK2	0.007	0.033	0.17	3	-10000	0	3
IL12RB1	0.013	0.091	0.32	20	-0.33	10	30
GADD45B	-0.069	0.37	0.64	7	-0.9	48	55
IL12RB2	0.043	0.11	0.28	64	-0.31	5	69
GADD45G	-0.063	0.35	0.64	7	-0.86	46	53
natural killer cell activation	-0.001	0.03	0.14	5	-10000	0	5
RELB	0.01	0	-10000	0	-10000	0	0
RELA	0.01	0	-10000	0	-10000	0	0
IL18	0.007	0.039	-10000	0	-0.29	6	6
IL2RA	0.009	0.084	0.27	19	-0.29	18	37
IFNG	0.059	0.1	0.27	81	-10000	0	81
STAT3 (dimer)	-0.063	0.34	0.59	8	-0.74	64	72
HLA-DRB5	-0.001	0.072	0.26	12	-0.29	15	27
FASLG	-0.12	0.47	0.83	7	-1.1	62	69
NF kappa B2 p52/RelB	-0.16	0.38	-10000	0	-0.96	62	62
CD4	0.001	0.024	-10000	0	-0.29	2	2
SOCS1	0.011	0.013	0.27	1	-10000	0	1
EntrezGene:6955	-0.008	0.015	-10000	0	-10000	0	0
CD3D	-0.024	0.089	0.26	3	-0.3	36	39
CD3E	-0.029	0.091	-10000	0	-0.29	42	42
CD3G	-0.033	0.095	-10000	0	-0.3	46	46
IL12Rbeta2/JAK2	0.037	0.092	0.22	60	-0.22	7	67
CCL3	-0.11	0.47	0.76	9	-1.1	59	68
CCL4	-0.13	0.51	0.74	8	-1.2	64	72
HLA-A	0.008	0.018	-10000	0	-0.29	1	1
IL18/IL18R	0.027	0.076	0.24	2	-0.19	26	28
NOS2	-0.076	0.4	0.72	7	-0.91	56	63
IL12/IL12R/TYK2/JAK2/SPHK2	0.023	0.12	0.29	27	-0.27	16	43
IL1R1	-0.093	0.43	0.71	8	-1	56	64
IL4	0.002	0.03	-10000	0	-0.16	3	3
JAK2	0.007	0.036	0.19	2	-0.3	1	3
EntrezGene:6957	-0.007	0.013	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.11	0.29	0.26	2	-0.66	67	69
RAB7A	-0.041	0.3	0.62	5	-0.71	46	51
lysosomal transport	-0.036	0.29	0.6	6	-0.67	46	52
FOS	-0.36	0.57	0.56	4	-1	159	163
STAT4 (dimer)	-0.07	0.37	0.61	8	-0.83	63	71
STAT5A (dimer)	-0.1	0.43	0.47	36	-0.97	62	98
GZMA	-0.13	0.5	0.79	7	-1.2	59	66
GZMB	-0.11	0.48	0.76	9	-1.1	58	67
HLX	0.011	0.013	0.27	1	-10000	0	1
LCK	-0.11	0.47	0.68	9	-1.1	62	71
TCR/CD3/MHC II/CD4	-0.11	0.2	0.16	1	-0.3	169	170
IL2/IL2R	0.019	0.07	0.2	25	-0.18	25	50
MAPK14	-0.065	0.36	0.63	7	-0.83	55	62
CCR5	-0.079	0.39	0.66	7	-1	46	53
IL1B	0.002	0.092	0.27	16	-0.31	20	36
STAT6	-0.002	0.15	0.42	10	-0.28	41	51
STAT4	-0.005	0.064	-10000	0	-0.29	20	20
STAT3	0.01	0	-10000	0	-10000	0	0
STAT1	0.012	0.026	0.27	4	-10000	0	4
NFKB1	0.01	0	-10000	0	-10000	0	0
NFKB2	0.01	0	-10000	0	-10000	0	0
IL12B	0.014	0.062	0.29	15	-10000	0	15
CD8A	-0.019	0.09	0.3	1	-0.29	39	40
CD8B	-0.014	0.095	0.28	7	-0.29	37	44
T-helper 1 cell differentiation	0	0	-10000	0	-10000	0	0
natural killer cell mediated cytotoxicity	-0.023	0.12	0.26	16	-0.3	27	43
IL2RB	0.008	0.038	0.27	2	-0.29	5	7
proteasomal ubiquitin-dependent protein catabolic process	-0.058	0.34	0.61	8	-0.75	63	71
IL2RG	0.008	0.06	0.27	9	-0.29	10	19
IL12	0.021	0.069	0.22	25	-10000	0	25
STAT5A	0.009	0.015	-10000	0	-0.29	1	1
CD247	-0.003	0.043	0.27	1	-0.29	7	8
IL2	0.003	0.004	-10000	0	-10000	0	0
SPHK2	0.011	0.013	0.27	1	-10000	0	1
FRAP1	0	0	-10000	0	-10000	0	0
IL12A	0.012	0.049	0.25	11	-10000	0	11
IL12/IL12R/TYK2/JAK2	-0.12	0.53	0.79	10	-1.2	62	72
MAP2K3	-0.065	0.36	0.63	7	-0.8	60	67
RIPK2	0.01	0	-10000	0	-10000	0	0
MAP2K6	-0.068	0.36	0.63	7	-0.81	60	67
regulation of dendritic cell antigen processing and presentation	0	0	-10000	0	-10000	0	0
HLA-DRA	-0.008	0.055	0.27	1	-0.29	13	14
IL18RAP	-0.003	0.067	-10000	0	-0.29	20	20
IL12Rbeta1/TYK2	0.015	0.077	0.25	20	-0.25	10	30
EOMES	-0.064	0.25	-10000	0	-1.1	20	20
STAT1 (dimer)	-0.03	0.36	0.58	21	-0.74	61	82
T cell proliferation	-0.049	0.28	0.53	6	-0.6	60	66
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
IL18R1	0.009	0.029	-10000	0	-0.3	3	3
CD8-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.13	0.23	-10000	0	-0.63	63	63
ATF2	-0.056	0.33	0.59	7	-0.76	55	62

×

Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1	0.01	0	-10000	0	-10000	0	0
VLDLR	0.003	0.046	-10000	0	-0.29	10	10
LRPAP1	0.011	0.013	0.27	1	-10000	0	1
NUDC	0.01	0	-10000	0	-10000	0	0
RELN/LRP8	-0.017	0.11	0.19	46	-0.16	111	157
CaM/Ca2+	0.007	0	-10000	0	-10000	0	0
KATNA1	0.01	0	-10000	0	-10000	0	0
GO:0030286	0	0	-10000	0	-10000	0	0
ABL1	-0.024	0.078	0.18	3	-0.14	111	114
IQGAP1/CaM	0.015	0	-10000	0	-10000	0	0
DAB1	-0.002	0.11	0.27	25	-0.29	34	59
IQGAP1	0.01	0	-10000	0	-10000	0	0
PLA2G7	0.043	0.086	0.27	52	-10000	0	52
CALM1	0.01	0	-10000	0	-10000	0	0
DYNLT1	0.01	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
LRPAP1/LRP8	0.048	0.069	0.19	77	-10000	0	77
UniProt:Q4QZ09	0	0	-10000	0	-10000	0	0
CLIP1	0.01	0	-10000	0	-10000	0	0
CDK5R1	0.024	0.058	0.27	22	-10000	0	22
LIS1/Poliovirus Protein 3A	0.007	0	-10000	0	-10000	0	0
CDK5R2	0.024	0.065	0.27	27	-10000	0	27
mol:PP1	0	0	-10000	0	-10000	0	0
RELN/VLDLR/DAB1	-0.052	0.11	0.18	19	-0.17	160	179
YWHAE	0.009	0.015	-10000	0	-0.29	1	1
NDEL1/14-3-3 E	-0.002	0.073	0.18	16	-10000	0	16
MAP1B	-0.02	0.068	-10000	0	-0.21	45	45
RAC1	0.009	0	-10000	0	-10000	0	0
p35/CDK5	-0.009	0.081	0.22	16	-0.12	107	123
RELN	-0.093	0.14	0.27	4	-0.29	143	147
PAFAH/LIS1	0.037	0.059	0.19	52	-10000	0	52
LIS1/CLIP170	0.014	0	-10000	0	-10000	0	0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain	-0.013	0.045	-10000	0	-10000	0	0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3	-0.053	0.11	0.2	2	-0.18	152	154
GO:0005869	0	0	-10000	0	-10000	0	0
NDEL1	-0.007	0.075	0.18	17	-10000	0	17
LIS1/IQGAP1	0.014	0	-10000	0	-10000	0	0
RHOA	0.009	0	-10000	0	-10000	0	0
PAFAH1B1	0.009	0	-10000	0	-10000	0	0
PAFAH1B3	0.025	0.06	0.27	23	-10000	0	23
PAFAH1B2	0.01	0	-10000	0	-10000	0	0
MAP1B/LIS1/Dynein heavy chain	-0.002	0.045	-10000	0	-0.13	45	45
NDEL1/Katanin 60/Dynein heavy chain	0.001	0.072	0.24	4	-10000	0	4
LRP8	0.058	0.1	0.27	76	-10000	0	76
NDEL1/Katanin 60	-0.002	0.073	0.18	17	-10000	0	17
P39/CDK5	-0.008	0.085	0.22	22	-0.12	108	130
LIS1/NudC/Dynein intermediate chain/microtubule organizing center	0.014	0	-10000	0	-10000	0	0
CDK5	-0.022	0.071	0.16	3	-0.13	111	114
PPP2R5D	0.01	0	-10000	0	-10000	0	0
LIS1/CLIP170/Dynein Complex/Dynactin Complex	0.012	0	-10000	0	-10000	0	0
CSNK2A1	0.01	0	-10000	0	-10000	0	0
RELN/VLDLR/DAB1/LIS1	-0.037	0.094	0.17	19	-0.14	160	179
RELN/VLDLR	-0.013	0.1	0.18	43	-0.14	115	158
CDC42	0.009	0	-10000	0	-10000	0	0

×

PDGFR-alpha signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.022	0.079	-10000	0	-0.33	24	24
PDGF/PDGFRA/CRKL	-0.022	0.072	0.17	1	-0.2	55	56
positive regulation of JUN kinase activity	-0.001	0.056	0.17	1	-0.14	56	57
CRKL	0.011	0.018	0.27	2	-10000	0	2
PDGF/PDGFRA/Caveolin-3	-0.025	0.072	0.19	2	-0.2	55	57
AP1	-0.23	0.34	-10000	0	-0.74	129	129
mol:IP3	-0.037	0.078	-10000	0	-0.22	56	56
PLCG1	-0.037	0.078	-10000	0	-0.22	56	56
PDGF/PDGFRA/alphaV Integrin	-0.023	0.073	-10000	0	-0.2	56	56
RAPGEF1	0.01	0	-10000	0	-10000	0	0
CRK	0.01	0	-10000	0	-10000	0	0
mol:Ca2+	-0.037	0.078	-10000	0	-0.22	56	56
CAV3	0.005	0.023	0.27	3	-10000	0	3
CAV1	-0.004	0.063	-10000	0	-0.29	19	19
SHC/Grb2/SOS1	-0.001	0.057	0.18	1	-0.14	56	57
PDGF/PDGFRA/Shf	-0.026	0.078	-10000	0	-0.21	60	60
FOS	-0.23	0.34	-10000	0	-0.73	129	129
JUN	-0.028	0.053	-10000	0	-0.25	16	16
oligodendrocyte development	-0.023	0.073	-10000	0	-0.2	56	56
GRB2	0.01	0	-10000	0	-10000	0	0
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
mol:DAG	-0.037	0.078	-10000	0	-0.22	56	56
PDGF/PDGFRA	-0.022	0.079	-10000	0	-0.33	24	24
actin cytoskeleton reorganization	-0.023	0.071	-10000	0	-0.2	56	56
SRF	0.017	0.011	-10000	0	-10000	0	0
SHC1	0.011	0.013	0.27	1	-10000	0	1
PI3K	-0.013	0.061	-10000	0	-0.16	57	57
PDGF/PDGFRA/Crk/C3G	-0.013	0.06	-10000	0	-0.16	56	56
JAK1	-0.011	0.052	-10000	0	-0.21	24	24
ELK1/SRF	-0.023	0.063	-10000	0	-0.17	56	56
SHB	0.01	0	-10000	0	-10000	0	0
SHF	0.005	0.039	-10000	0	-0.29	7	7
CSNK2A1	0.023	0.019	-10000	0	-10000	0	0
GO:0007205	-0.045	0.09	-10000	0	-0.26	56	56
SOS1	0.01	0	-10000	0	-10000	0	0
Ras protein signal transduction	-0.001	0.056	0.17	1	-0.14	56	57
PDGF/PDGFRA/SHB	-0.023	0.072	-10000	0	-0.2	56	56
PDGF/PDGFRA/Caveolin-1	-0.031	0.09	-10000	0	-0.23	64	64
ITGAV	0.009	0.015	-10000	0	-0.29	1	1
ELK1	-0.048	0.085	-10000	0	-0.23	56	56
PIK3CA	0.01	0	-10000	0	-10000	0	0
PDGF/PDGFRA/Crk	-0.023	0.072	-10000	0	-0.2	56	56
JAK-STAT cascade	-0.011	0.052	-10000	0	-0.21	24	24
cell proliferation	-0.026	0.078	-10000	0	-0.21	60	60

×

BCR signaling pathway

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
JUN	-0.044	0.13	0.24	6	-0.28	71	77
IKBKB	-0.008	0.059	0.23	2	-0.22	8	10
AKT1	-0.032	0.087	0.27	7	-0.18	75	82
IKBKG	-0.009	0.061	0.22	2	-0.21	11	13
CALM1	-0.031	0.11	0.25	2	-0.34	30	32
PIK3CA	0.01	0	-10000	0	-10000	0	0
MAP3K1	-0.058	0.17	0.29	7	-0.38	67	74
MAP3K7	0.01	0	-10000	0	-10000	0	0
mol:Ca2+	-0.034	0.11	0.26	2	-0.34	33	35
DOK1	0.011	0.013	0.27	1	-10000	0	1
AP-1	-0.038	0.082	0.18	6	-0.19	64	70
LYN	0.01	0	-10000	0	-10000	0	0
BLNK	0	0.052	-10000	0	-0.29	13	13
SHC1	0.011	0.013	0.27	1	-10000	0	1
BCR complex	-0.02	0.11	0.29	14	-0.22	78	92
CD22	-0.067	0.19	0.33	7	-0.37	90	97
CAMK2G	-0.027	0.1	0.24	2	-0.31	30	32
CSNK2A1	0.01	0	-10000	0	-10000	0	0
INPP5D	0.005	0.039	-10000	0	-0.29	7	7
SHC/GRB2/SOS1	-0.019	0.064	-10000	0	-0.13	87	87
GO:0007205	-0.035	0.11	0.26	2	-0.34	33	35
SYK	0.007	0.029	-10000	0	-0.29	4	4
ELK1	-0.032	0.11	0.25	2	-0.34	30	32
NFATC1	-0.06	0.16	0.25	7	-0.35	69	76
B-cell antigen/BCR complex	-0.02	0.11	0.29	14	-0.22	78	92
PAG1/CSK	0.015	0	-10000	0	-10000	0	0
NFKBIB	0.004	0.022	0.12	2	-10000	0	2
HRAS	-0.026	0.095	0.23	2	-0.28	33	35
NFKBIA	0.004	0.022	0.12	2	-10000	0	2
NF-kappa-B/RelA/I kappa B beta	0.007	0.02	0.12	2	-10000	0	2
RasGAP/Csk	-0.005	0.1	0.24	15	-0.17	83	98
mol:GDP	-0.033	0.11	0.26	2	-0.35	30	32
PTEN	0.01	0	-10000	0	-10000	0	0
CD79B	0.003	0.068	0.27	7	-0.29	16	23
NF-kappa-B/RelA/I kappa B alpha	0.007	0.019	0.12	2	-10000	0	2
GRB2	0.01	0	-10000	0	-10000	0	0
PI3K/BCAP/CD19	-0.071	0.18	0.38	7	-0.39	80	87
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
mol:IP3	-0.035	0.12	0.26	2	-0.35	33	35
CSK	0.01	0	-10000	0	-10000	0	0
FOS	-0.065	0.12	-10000	0	-0.3	55	55
CHUK	-0.009	0.061	0.22	2	-0.21	12	14
IBTK	0.01	0	-10000	0	-10000	0	0
CARD11/BCL10/MALT1/TAK1	-0.022	0.098	-10000	0	-0.29	34	34
PTPN6	-0.062	0.18	0.31	7	-0.35	90	97
RELA	0.01	0	-10000	0	-10000	0	0
BCL2A1	0.006	0.021	0.14	2	-10000	0	2
VAV2	-0.071	0.18	0.3	7	-0.42	65	72
ubiquitin-dependent protein catabolic process	0.006	0.022	0.12	2	-10000	0	2
BTK	-0.047	0.23	-10000	0	-1	21	21
CD19	-0.06	0.18	0.28	11	-0.34	90	101
MAP4K1	0.005	0.051	0.27	3	-0.29	10	13
CD72	0.017	0.048	0.27	13	-0.29	1	14
PAG1	0.01	0	-10000	0	-10000	0	0
MAPK14	-0.048	0.14	0.26	8	-0.33	64	72
SH3BP5	0.009	0.015	-10000	0	-0.29	1	1
PIK3AP1	-0.033	0.12	0.22	7	-0.37	34	41
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72	-0.045	0.16	0.26	8	-0.34	77	85
RAF1	-0.023	0.091	0.23	2	-0.27	33	35
RasGAP/p62DOK/SHIP	-0.006	0.1	0.28	7	-0.17	84	91
CD79A	-0.035	0.13	0.27	14	-0.29	73	87
re-entry into mitotic cell cycle	-0.038	0.082	0.18	6	-0.19	64	70
RASA1	0.01	0	-10000	0	-10000	0	0
MAPK3	-0.017	0.078	0.21	2	-0.25	26	28
MAPK1	-0.017	0.078	0.21	2	-0.25	26	28
CD72/SHP1	-0.058	0.18	0.32	13	-0.33	89	102
NFKB1	0.01	0	-10000	0	-10000	0	0
MAPK8	-0.048	0.14	0.26	8	-0.33	66	74
actin cytoskeleton organization	-0.063	0.16	0.29	7	-0.37	64	71
NF-kappa-B/RelA	0.016	0.037	0.22	2	-10000	0	2
Calcineurin	-0.019	0.093	-10000	0	-0.29	30	30
PI3K	-0.082	0.13	-10000	0	-0.29	95	95
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2	-0.034	0.12	0.2	7	-0.35	35	42
SOS1	0.01	0	-10000	0	-10000	0	0
Bam32/HPK1	-0.071	0.22	0.35	4	-0.61	48	52
DAPP1	-0.083	0.24	0.31	2	-0.68	46	48
cytokine secretion	-0.056	0.15	0.24	7	-0.32	69	76
mol:DAG	-0.035	0.12	0.26	2	-0.35	33	35
PLCG2	0.01	0.03	0.27	3	-0.29	2	5
MAP2K1	-0.02	0.085	0.22	2	-0.26	29	31
B-cell antigen/BCR complex/FcgammaRIIB	-0.019	0.12	0.26	15	-0.21	83	98
mol:PI-3-4-5-P3	-0.056	0.098	-10000	0	-0.22	87	87
ETS1	-0.024	0.092	0.23	2	-0.29	30	32
B-cell antigen/BCR complex/LYN/SYK/BLNK	-0.002	0.093	0.24	14	-0.16	87	101
B-cell antigen/BCR complex/LYN	-0.055	0.17	0.28	7	-0.31	94	101
MALT1	0.01	0	-10000	0	-10000	0	0
TRAF6	0.01	0	-10000	0	-10000	0	0
RAC1	-0.067	0.17	0.29	7	-0.39	64	71
B-cell antigen/BCR complex/LYN/SYK	-0.053	0.17	0.38	7	-0.32	87	94
CARD11	-0.033	0.11	0.25	2	-0.34	34	36
FCGR2B	-0.008	0.078	0.27	3	-0.29	27	30
PPP3CA	0.01	0	-10000	0	-10000	0	0
BCL10	0.01	0	-10000	0	-10000	0	0
IKK complex	0	0.03	0.13	7	-0.083	7	14
PTPRC	-0.024	0.098	0.27	2	-0.29	48	50
PDPK1	-0.032	0.078	0.23	7	-0.15	87	94
PPP3CB	0.01	0	-10000	0	-10000	0	0
PPP3CC	0.01	0	-10000	0	-10000	0	0
POU2F2	0.006	0.018	0.14	2	-0.073	2	4

×

RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1	0.015	0.008	-10000	0	-10000	0	0
VDR	0.009	0.024	0.27	1	-0.29	2	3
FAM120B	0.01	0	-10000	0	-10000	0	0
RXRs/LXRs/DNA/9cRA	-0.011	0.092	-10000	0	-0.38	1	1
RXRs/LXRs/DNA/Oxysterols	-0.001	0.091	-10000	0	-0.35	1	1
MED1	0.01	0	-10000	0	-10000	0	0
mol:9cRA	0.005	0.01	-10000	0	-10000	0	0
RARs/THRs/DNA/Src-1	-0.008	0.071	-10000	0	-0.19	51	51
RXRs/NUR77	-0.098	0.11	0.18	1	-0.17	259	260
RXRs/PPAR	-0.037	0.09	-10000	0	-0.17	118	118
NCOR2	0.01	0	-10000	0	-10000	0	0
VDR/VDR/Vit D3	0.007	0.017	0.18	1	-0.19	2	3
RARs/VDR/DNA/Vit D3	0.011	0.045	0.16	1	-0.13	35	36
RARA	0.01	0	-10000	0	-10000	0	0
NCOA1	0.01	0	-10000	0	-10000	0	0
VDR/VDR/DNA	0.009	0.024	0.27	1	-0.29	2	3
RARs/RARs/DNA/9cRA	0.008	0.041	-10000	0	-0.13	34	34
RARG	0.01	0	-10000	0	-10000	0	0
RPS6KB1	0.017	0.016	-10000	0	-10000	0	0
RARs/THRs/DNA/SMRT	-0.008	0.071	-10000	0	-0.19	51	51
THRA	0.01	0	-10000	0	-10000	0	0
mol:Bile acids	0	0	-10000	0	-10000	0	0
VDR/Vit D3/DNA	0.007	0.017	0.18	1	-0.19	2	3
RXRs/PPAR/9cRA/PGJ2/DNA	-0.008	0.081	-10000	0	-0.27	1	1
NR1H4	-0.037	0.13	0.27	16	-0.29	73	89
RXRs/LXRs/DNA	0.007	0.081	-10000	0	-0.25	1	1
NR1H2	0.015	0.009	-10000	0	-10000	0	0
NR1H3	0.015	0.01	-10000	0	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.008	0.074	0.22	2	-0.13	101	103
NR4A1	-0.16	0.15	-10000	0	-0.29	230	230
mol:ATRA	0	0	-10000	0	-10000	0	0
RXRs/FXR/9cRA/MED1	-0.05	0.11	0.18	2	-0.18	143	145
RXRG	-0.063	0.13	0.27	1	-0.29	100	101
RXR alpha/CCPG	0.018	0.012	-10000	0	-0.19	1	1
RXRA	0.014	0.018	-10000	0	-0.29	1	1
RXRB	0.015	0.01	-10000	0	-10000	0	0
THRB	-0.008	0.07	-10000	0	-0.29	24	24
PPARG	-0.008	0.075	0.27	2	-0.29	26	28
PPARD	0.01	0	-10000	0	-10000	0	0
TNF	0.007	0.098	-10000	0	-10000	0	0
mol:Oxysterols	0.005	0.009	-10000	0	-10000	0	0
cholesterol transport	-0.001	0.091	-10000	0	-0.35	1	1
PPARA	0.008	0.021	-10000	0	-0.29	2	2
mol:Vit D3	0	0	-10000	0	-10000	0	0
RARB	-0.015	0.082	-10000	0	-0.29	34	34
RXRs/NUR77/BCL2	-0.14	0.13	-10000	0	-0.21	275	275
SREBF1	0.003	0.085	0.34	1	-10000	0	1
RXRs/RXRs/DNA/9cRA	-0.008	0.081	-10000	0	-0.27	1	1
ABCA1	0.002	0.083	-10000	0	-10000	0	0
RARs/THRs	0.008	0.06	-10000	0	-0.14	51	51
RXRs/FXR	-0.033	0.1	0.21	9	-0.16	143	152
BCL2	-0.002	0.058	-10000	0	-0.29	16	16

×

Aurora A signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Aurora A/GADD45A	0.012	0.04	-10000	0	-10000	0	0
BIRC5	0.2	0.12	0.27	292	-0.29	1	293
NFKBIA	0.011	0.04	-10000	0	-10000	0	0
CPEB1	-0.13	0.15	-10000	0	-0.29	192	192
AKT1	0.011	0.04	-10000	0	-10000	0	0
NDEL1	0.01	0	-10000	0	-10000	0	0
Aurora A/BRCA1	0.011	0.037	0.22	1	-10000	0	1
NDEL1/TACC3	0.027	0.056	0.2	19	-10000	0	19
GADD45A	0.01	0	-10000	0	-10000	0	0
GSK3B	-0.01	0.013	-10000	0	-10000	0	0
PAK1/Aurora A	0.012	0.04	-10000	0	-10000	0	0
MDM2	0.018	0.045	0.27	13	-10000	0	13
JUB	0.012	0.022	0.27	3	-10000	0	3
TPX2	0.091	0.076	0.16	219	-10000	0	219
TP53	0.018	0.038	0.17	6	-10000	0	6
DLG7	0.009	0.04	-10000	0	-10000	0	0
AURKAIP1	0.011	0.013	0.27	1	-10000	0	1
ARHGEF7	0.01	0	-10000	0	-10000	0	0
G2 phase of mitotic cell cycle	0	0	-10000	0	-10000	0	0
Aurora A/NDEL1/TACC3	0.028	0.059	0.21	19	-10000	0	19
G2/M transition of mitotic cell cycle	0.011	0.037	0.22	1	-10000	0	1
AURKA	0.013	0.053	-10000	0	-10000	0	0
AURKB	0.099	0.07	0.16	207	-10000	0	207
CDC25B	0.015	0.043	0.18	6	-10000	0	6
G2/M transition checkpoint	0.012	0.038	0.19	3	-10000	0	3
mRNA polyadenylation	-0.06	0.074	-10000	0	-0.15	116	116
Aurora A/CPEB	-0.06	0.074	-10000	0	-0.16	116	116
Aurora A/TACC1/TRAP/chTOG	0.019	0.039	-10000	0	-0.16	1	1
BRCA1	0.011	0.013	0.27	1	-10000	0	1
centrosome duplication	0.012	0.04	-10000	0	-10000	0	0
regulation of centrosome cycle	0.026	0.054	0.2	19	-10000	0	19
spindle assembly	0.018	0.038	-10000	0	-0.16	1	1
TDRD7	0.01	0	-10000	0	-10000	0	0
Aurora A/RasGAP/Survivin	0.13	0.077	0.2	154	-10000	0	154
CENPA	0.12	0.074	0.16	281	-10000	0	281
Aurora A/PP2A	0.012	0.04	-10000	0	-10000	0	0
meiosis	0	0	-10000	0	-10000	0	0
protein catabolic process	0.015	0.038	-10000	0	-10000	0	0
negative regulation of DNA binding	0.018	0.038	0.17	6	-10000	0	6
prophase	0	0	-10000	0	-10000	0	0
GIT1/beta-PIX	0.015	0	-10000	0	-10000	0	0
RASA1	0.01	0	-10000	0	-10000	0	0
Ajuba/Aurora A	0.012	0.039	0.19	3	-10000	0	3
mitotic prometaphase	-0.013	0.013	-10000	0	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.013	0.053	-10000	0	-10000	0	0
TACC1	0.008	0.025	-10000	0	-0.29	3	3
TACC3	0.03	0.069	0.27	31	-10000	0	31
Aurora A/Antizyme1	0.016	0.038	-10000	0	-10000	0	0
Aurora A/RasGAP	0.012	0.04	-10000	0	-10000	0	0
OAZ1	0.01	0	-10000	0	-10000	0	0
RAN	0.01	0	-10000	0	-10000	0	0
mitosis	0	0	-10000	0	-10000	0	0
PRKACA	-0.01	0.013	-10000	0	-10000	0	0
GIT1	0.01	0	-10000	0	-10000	0	0
GIT1/beta-PIX/PAK1	0.02	0.009	-10000	0	-0.16	1	1
Importin alpha/Importin beta/TPX2	0.091	0.076	0.16	219	-10000	0	219
PPP2R5D	0.01	0	-10000	0	-10000	0	0
Aurora A/TPX2	0.075	0.077	0.18	120	-10000	0	120
PAK1	0.009	0.015	-10000	0	-0.29	1	1
CKAP5	0.01	0	-10000	0	-10000	0	0

×

Angiopoietin receptor Tie2-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	-0.046	0.25	-10000	0	-0.76	42	42
NCK1/PAK1/Dok-R	-0.044	0.12	-10000	0	-0.39	42	42
NCK1/Dok-R	-0.058	0.28	-10000	0	-0.88	42	42
PIK3CA	0.01	0.001	-10000	0	-10000	0	0
mol:beta2-estradiol	0.014	0.064	0.22	34	-0.1	2	36
RELA	0.01	0	-10000	0	-10000	0	0
SHC1	0.011	0.013	0.27	1	-10000	0	1
Rac/GDP	0.007	0	-10000	0	-10000	0	0
F2	0.037	0.098	0.27	60	-10000	0	60
TNIP2	0.01	0	-10000	0	-10000	0	0
NF kappa B/RelA	-0.048	0.27	-10000	0	-0.83	42	42
FN1	0.018	0.083	0.27	26	-0.29	12	38
PLD2	-0.065	0.28	-10000	0	-0.9	42	42
PTPN11	0.01	0	-10000	0	-10000	0	0
GRB14	0.045	0.089	0.27	56	-10000	0	56
ELK1	-0.057	0.26	-10000	0	-0.83	42	42
GRB7	0.014	0.062	0.27	14	-0.29	7	21
PAK1	0.009	0.015	-10000	0	-0.29	1	1
Tie2/Ang1/alpha5/beta1 Integrin	-0.049	0.29	-10000	0	-0.89	42	42
CDKN1A	-0.04	0.18	-10000	0	-0.52	44	44
ITGA5	-0.002	0.058	-10000	0	-0.29	16	16
mol:GTP	0	0	-10000	0	-10000	0	0
RasGAP/Dok-R	-0.058	0.28	-10000	0	-0.88	42	42
CRK	0.01	0	-10000	0	-10000	0	0
mol:NO	-0.029	0.19	-10000	0	-0.58	42	42
PLG	-0.066	0.28	-10000	0	-0.9	42	42
mol:GDP	0	0	-10000	0	-10000	0	0
chemokinesis	-0.046	0.24	-10000	0	-0.74	42	42
GRB2	0.01	0	-10000	0	-10000	0	0
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
ANGPT2	-0.073	0.16	0.33	1	-0.51	30	31
BMX	-0.079	0.29	-10000	0	-0.94	42	42
ANGPT1	-0.077	0.31	-10000	0	-1.1	34	34
tube development	-0.047	0.19	-10000	0	-0.57	43	43
ANGPT4	0.012	0.037	0.27	8	-10000	0	8
response to hypoxia	-0.005	0.02	-10000	0	-10000	0	0
Tie2/Ang1/GRB14	-0.043	0.3	-10000	0	-0.91	42	42
alpha5/beta1 Integrin	0.007	0.04	-10000	0	-0.19	16	16
FGF2	-0.089	0.14	-10000	0	-0.29	136	136
STAT5A (dimer)	-0.049	0.21	-10000	0	-0.63	44	44
mol:L-citrulline	-0.029	0.19	-10000	0	-0.58	42	42
AGTR1	-0.12	0.15	-10000	0	-0.29	175	175
MAPK14	-0.067	0.29	-10000	0	-0.91	42	42
Tie2/SHP2	-0.015	0.15	-10000	0	-0.93	9	9
TEK	-0.02	0.17	-10000	0	-1	9	9
RPS6KB1	-0.047	0.24	-10000	0	-0.74	42	42
Angiotensin II/AT1	-0.078	0.1	-10000	0	-0.19	175	175
Tie2/Ang1/GRB2	-0.064	0.29	-10000	0	-0.92	42	42
MAPK3	-0.06	0.27	-10000	0	-0.84	42	42
MAPK1	-0.06	0.27	-10000	0	-0.84	42	42
Tie2/Ang1/GRB7	-0.059	0.3	-10000	0	-0.92	42	42
NFKB1	0.01	0	-10000	0	-10000	0	0
MAPK8	-0.065	0.28	-10000	0	-0.9	42	42
PI3K	-0.059	0.27	-10000	0	-0.85	42	42
FES	-0.068	0.29	-10000	0	-0.9	42	42
Crk/Dok-R	-0.058	0.28	-10000	0	-0.88	42	42
Tie2/Ang1/ABIN2	-0.064	0.29	-10000	0	-0.92	42	42
blood circulation	0	0	-10000	0	-10000	0	0
negative regulation of caspase activity	-0.039	0.22	-10000	0	-0.69	42	42
STAT5A	0.009	0.015	-10000	0	-0.29	1	1
mol:ROS	0	0	-10000	0	-10000	0	0
PTK2	-0.047	0.24	-10000	0	-0.74	42	42
Tie2/Ang2	-0.064	0.24	-10000	0	-0.72	43	43
Tie2/Ang1	-0.07	0.3	-10000	0	-0.95	42	42
FOXO1	-0.036	0.22	-10000	0	-0.69	42	42
ELF1	0.009	0.019	-10000	0	-10000	0	0
ELF2	-0.064	0.28	-10000	0	-0.89	42	42
mol:Choline	-0.062	0.28	-10000	0	-0.87	42	42
cell migration	-0.025	0.069	-10000	0	-0.22	42	42
FYN	-0.054	0.21	-10000	0	-0.63	43	43
DOK2	0.002	0.056	0.27	2	-0.29	13	15
negative regulation of cell cycle	-0.035	0.16	-10000	0	-0.48	44	44
ETS1	-0.005	0.065	-10000	0	-0.22	34	34
PXN	-0.036	0.2	-10000	0	-0.62	42	42
ITGB1	0.01	0	-10000	0	-10000	0	0
NOS3	-0.035	0.21	-10000	0	-0.65	42	42
RAC1	0.01	0	-10000	0	-10000	0	0
TNF	0.008	0.088	0.27	20	-0.22	33	53
MAPKKK cascade	-0.062	0.28	-10000	0	-0.87	42	42
RASA1	0.01	0	-10000	0	-10000	0	0
Tie2/Ang1/Shc	-0.063	0.29	-10000	0	-0.92	42	42
NCK1	0.01	0	-10000	0	-10000	0	0
vasculogenesis	-0.023	0.17	-10000	0	-0.52	42	42
mol:Phosphatidic acid	-0.062	0.28	-10000	0	-0.87	42	42
mol:Angiotensin II	0.001	0.002	-10000	0	-10000	0	0
mol:NADP	-0.029	0.19	-10000	0	-0.58	42	42
Rac1/GTP	-0.045	0.22	-10000	0	-0.69	42	42
MMP2	-0.071	0.29	-10000	0	-0.92	42	42

×

Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity	0.01	0.071	0.2	46	-0.18	6	52
KIRREL	0.008	0.023	-10000	0	-0.32	2	2
Nephrin/NEPH1Par3/Par6/Atypical PKCs	-0.01	0.071	0.18	6	-0.2	46	52
PLCG1	0.01	0	-10000	0	-10000	0	0
ARRB2	0.01	0	-10000	0	-10000	0	0
WASL	0.01	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/CD2AP	0.007	0.059	0.16	20	-0.14	41	61
ChemicalAbstracts:57-88-5	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP	-0.002	0.061	-10000	0	-0.17	41	41
FYN	-0.004	0.051	-10000	0	-0.14	41	41
mol:Ca2+	0.006	0.058	0.16	20	-0.14	41	61
mol:DAG	0.007	0.059	0.16	20	-0.14	41	61
NPHS2	0.013	0.055	0.26	19	-10000	0	19
mol:IP3	0.007	0.059	0.16	20	-0.14	41	61
regulation of endocytosis	0.006	0.053	0.15	6	-0.13	41	47
Nephrin/NEPH1/podocin/Cholesterol	0.001	0.058	0.16	20	-0.14	41	61
establishment of cell polarity	-0.01	0.071	0.18	6	-0.2	46	52
Nephrin/NEPH1/podocin/NCK1-2	0.013	0.056	0.16	20	-0.12	41	61
Nephrin/NEPH1/beta Arrestin2	0.007	0.054	0.16	6	-0.13	41	47
NPHS1	0.005	0.034	0.26	6	-10000	0	6
Nephrin/NEPH1/podocin	0.002	0.06	0.16	20	-0.14	41	61
TJP1	0.01	0	-10000	0	-10000	0	0
NCK1	0.01	0	-10000	0	-10000	0	0
NCK2	0.01	0	-10000	0	-10000	0	0
heterophilic cell adhesion	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/PLCgamma1	0.007	0.059	0.16	20	-0.14	41	61
CD2AP	0.01	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/GRB2	0.007	0.059	0.16	20	-0.14	41	61
GRB2	0.01	0	-10000	0	-10000	0	0
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
TRPC6	-0.002	0.047	-10000	0	-0.13	41	41
cytoskeleton organization	-0.002	0.06	-10000	0	-0.17	41	41
Nephrin/NEPH1	-0.005	0.049	0.15	6	-0.13	46	52
Nephrin/NEPH1/ZO-1	0	0.057	0.17	6	-0.15	46	52

×

Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin	0.016	0.025	0.16	5	-0.13	7	12
RGS9BP	0.001	0.059	0.27	3	-0.29	14	17
mol:GTP	0	0	-10000	0	-10000	0	0
GRK1	0.001	0.014	0.27	1	-10000	0	1
mol:Na +	0.034	0.086	0.17	96	-0.16	28	124
mol:ADP	0.005	0.011	0.16	2	-10000	0	2
GNAT2	0.01	0.026	0.27	4	-10000	0	4
RGS9-1/Gbeta5/R9AP	-0.022	0.081	0.18	3	-0.16	97	100
mol:GDP	0	0	-10000	0	-10000	0	0
PDE6H/GNAT2/GTP	0.009	0.02	0.17	6	-10000	0	6
GRK7	0.009	0.013	0.27	1	-10000	0	1
CNGB3	0.078	0.12	0.27	108	-10000	0	108
Cone Metarhodopsin II/X-Arrestin	0.001	0.003	-10000	0	-10000	0	0
mol:Ca2+	0.023	0.07	0.2	21	-0.14	27	48
Cone PDE6	-0.016	0.069	0.16	4	-0.13	96	100
Cone Metarhodopsin II	0.006	0.011	0.16	2	-10000	0	2
Na + (4 Units)	0.044	0.092	0.18	107	-0.14	27	134
GNAT2/GDP	-0.013	0.071	0.16	7	-0.13	97	104
GNB5	0.01	0	-10000	0	-10000	0	0
mol:GMP (4 units)	0.005	0.01	-10000	0	-10000	0	0
Cone Transducin	0.017	0.027	0.17	5	-0.14	7	12
SLC24A2	0.021	0.059	0.27	22	-10000	0	22
GNB3/GNGT2	0.012	0.028	0.19	1	-0.19	7	8
GNB3	0.008	0.029	0.27	1	-0.29	3	4
GNAT2/GTP	0.008	0.018	0.18	4	-10000	0	4
CNGA3	-0.022	0.088	-10000	0	-0.29	40	40
ARR3	0.002	0.004	-10000	0	-10000	0	0
absorption of light	0	0	-10000	0	-10000	0	0
cGMP/Cone CNG Channel	0.034	0.087	0.17	96	-0.16	28	124
mol:Pi	-0.022	0.08	0.18	3	-0.16	97	100
Cone CNG Channel	0.032	0.068	0.14	2	-0.12	28	30
mol:all-trans-retinal	0	0	-10000	0	-10000	0	0
mol:K +	0.021	0.059	0.27	22	-10000	0	22
RGS9	-0.054	0.12	-10000	0	-0.29	87	87
PDE6C	0.002	0.004	-10000	0	-10000	0	0
GNGT2	0.007	0.029	-10000	0	-0.29	4	4
mol:cGMP (4 units)	0	0	-10000	0	-10000	0	0
PDE6H	0.003	0.019	0.27	2	-10000	0	2

×

Arf6 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CENTA1/KIF3B	0.012	0.017	-10000	0	-0.16	4	4
ARNO/beta Arrestin1-2	-0.001	0.043	-10000	0	-10000	0	0
EGFR	0.008	0.057	0.27	8	-0.29	9	17
EPHA2	0.006	0.033	-10000	0	-0.29	5	5
USP6	0.01	0	-10000	0	-10000	0	0
IQSEC1	0.01	0.013	0.27	1	-10000	0	1
EGFR/EGFR/EGF/EGF	0.024	0.058	0.19	33	-0.19	9	42
ARRB2	0.006	0.009	0.14	2	-10000	0	2
mol:GTP	0.004	0.024	-10000	0	-0.15	5	5
ARRB1	0.007	0.029	-10000	0	-0.29	4	4
FBXO8	0.01	0	-10000	0	-10000	0	0
TSHR	0.012	0.034	0.27	7	-10000	0	7
EGF	0.025	0.062	0.27	25	-10000	0	25
somatostatin receptor activity	0	0	-10000	0	0	101	101
ARAP2	0.008	0.021	-10000	0	-0.29	2	2
mol:GDP	-0.06	0.086	-10000	0	-0.18	102	102
mol:PI-3-4-5-P3	0	0	-10000	0	0	66	66
ITGA2B	0.029	0.069	0.27	31	-10000	0	31
ARF6	0.01	0	-10000	0	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	0.027	0.029	0.18	9	-0.14	5	14
ADAP1	0.007	0.029	-10000	0	-0.29	4	4
KIF13B	0.01	0	-10000	0	-10000	0	0
HGF/MET	-0.026	0.091	0.19	9	-0.19	87	96
PXN	0.01	0	-10000	0	-10000	0	0
ARF6/GTP	-0.054	0.085	-10000	0	-0.18	93	93
EGFR/EGFR/EGF/EGF/ARFGEP100	0.029	0.052	0.18	34	-0.16	9	43
ADRB2	-0.028	0.099	-10000	0	-0.29	52	52
receptor agonist activity	0	0	-10000	0	0	105	105
actin filament binding	0	0	-10000	0	0	101	101
SRC	0.01	0	-10000	0	-10000	0	0
ITGB3	-0.024	0.094	-10000	0	-0.29	46	46
GNAQ	0.01	0	-10000	0	-10000	0	0
EFA6/PI-4-5-P2	0	0	-10000	0	-0.001	73	73
ARF6/GDP	-0.013	0.071	-10000	0	-0.28	19	19
ARF6/GDP/GULP/ACAP1	-0.067	0.11	0.18	3	-0.22	106	109
alphaIIb/beta3 Integrin/paxillin/GIT1	0.018	0.065	0.18	26	-0.14	41	67
ACAP1	0	0.065	0.27	4	-0.29	17	21
ACAP2	0.01	0	-10000	0	-10000	0	0
LHCGR/beta Arrestin2	0.005	0.016	0.22	2	-10000	0	2
EFNA1	0.016	0.038	0.27	9	-10000	0	9
HGF	-0.05	0.13	0.27	7	-0.29	87	94
CYTH3	0.005	0	-10000	0	-10000	0	0
CYTH2	0.006	0.002	-10000	0	-10000	0	0
NCK1	0.01	0	-10000	0	-10000	0	0
fibronectin binding	0	0	-10000	0	0	73	73
endosomal lumen acidification	0	0	-10000	0	0	92	92
microtubule-based process	0	0	-10000	0	-10000	0	0
GULP1	-0.036	0.11	-10000	0	-0.29	63	63
GNAQ/ARNO	0.011	0.003	-10000	0	-10000	0	0
mol:Phosphatidic acid	0	0	-10000	0	0	1	1
PIP3-E	0	0	-10000	0	0	10	10
MET	0.011	0.018	0.27	2	-10000	0	2
GNA14	-0.033	0.1	-10000	0	-0.29	58	58
GNA15	0.008	0.025	-10000	0	-0.29	3	3
GIT1	0.01	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0	0	-10000	0	0	87	87
GNA11	0.009	0.015	-10000	0	-0.29	1	1
LHCGR	0.004	0.019	0.27	2	-10000	0	2
AGTR1	-0.12	0.15	-10000	0	-0.29	175	175
desensitization of G-protein coupled receptor protein signaling pathway	0.005	0.016	0.22	2	-10000	0	2
IPCEF1/ARNO	0.024	0.044	-10000	0	-10000	0	0
alphaIIb/beta3 Integrin	0.004	0.08	0.19	26	-0.19	41	67

×

FAS signaling pathway (CD95)

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
SPTAN1	0.005	0.035	0.16	20	-10000	0	20
RFC1	0.005	0.035	0.16	20	-10000	0	20
PRKDC	0.005	0.035	0.16	20	-10000	0	20
RIPK1	0.014	0.005	-10000	0	-10000	0	0
CASP7	-0.025	0.047	-10000	0	-10000	0	0
FASLG/FAS/FADD/FAF1	-0.025	0.059	0.15	5	-0.2	23	28
MAP2K4	-0.11	0.15	-10000	0	-0.27	191	191
mol:ceramide	-0.066	0.11	-10000	0	-0.3	24	24
GSN	0.002	0.038	0.16	18	-0.15	5	23
FASLG/FAS/FADD/FAF1/Caspase 8	-0.038	0.077	-10000	0	-0.26	22	22
FAS	-0.006	0.038	-10000	0	-0.3	6	6
BID	-0.001	0.03	0.25	4	-0.14	4	8
MAP3K1	-0.058	0.09	-10000	0	-0.23	17	17
MAP3K7	0.004	0.007	-10000	0	-10000	0	0
RB1	0.005	0.036	0.16	20	-0.16	1	21
CFLAR	0.014	0.005	-10000	0	-10000	0	0
HGF/MET	-0.017	0.081	0.18	9	-0.16	93	102
ARHGDIB	0.005	0.035	0.16	20	-10000	0	20
FADD	0.002	0.034	0.26	6	-10000	0	6
actin filament polymerization	-0.002	0.038	0.15	5	-0.16	18	23
NFKB1	-0.082	0.1	-10000	0	-0.2	179	179
MAPK8	-0.18	0.23	-10000	0	-0.43	184	184
DFFA	0.005	0.035	0.16	20	-10000	0	20
DNA fragmentation during apoptosis	0.005	0.035	0.16	20	-10000	0	20
FAS/FADD/MET	0.005	0.036	0.17	8	-0.17	6	14
CFLAR/RIP1	0.022	0.008	-10000	0	-10000	0	0
FAIM3	0.012	0.039	0.27	4	-0.29	4	8
FAF1	-0.004	0.016	-10000	0	-10000	0	0
PARP1	0.005	0.035	0.16	20	-10000	0	20
DFFB	0.005	0.035	0.16	20	-10000	0	20
CHUK	-0.073	0.096	-10000	0	-0.22	17	17
FASLG	-0.015	0.076	0.26	7	-0.3	21	28
FAS/FADD	-0.002	0.038	0.18	6	-0.21	6	12
HGF	-0.049	0.13	0.27	7	-0.29	87	94
LMNA	0.006	0.032	0.14	20	-10000	0	20
CASP6	0.005	0.035	0.16	20	-10000	0	20
CASP10	-0.001	0.013	-10000	0	-10000	0	0
CASP3	0.004	0.042	0.18	20	-10000	0	20
PTPN13	0.004	0.041	-10000	0	-0.29	8	8
CASP8	-0.006	0.034	0.28	4	-0.18	4	8
IL6	-0.5	0.57	-10000	0	-1.1	184	184
MET	0.011	0.018	0.27	2	-10000	0	2
ICAD/CAD	0.006	0.032	0.14	20	-10000	0	20
FASLG/FAS/FADD/FAF1/Caspase 10	-0.067	0.11	-10000	0	-0.31	24	24
activation of caspase activity by cytochrome c	-0.001	0.03	0.25	4	-0.14	4	8
PAK2	0.003	0.036	0.15	20	-10000	0	20
BCL2	-0.001	0.058	-10000	0	-0.29	16	16

×

S1P3 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.003	0.046	-10000	0	-0.29	10	10
mol:S1P	0	0.004	-10000	0	-10000	0	0
S1P1/S1P/Gi	-0.079	0.13	-10000	0	-0.22	164	164
GNAO1	-0.085	0.14	-10000	0	-0.29	129	129
S1P/S1P3/G12/G13	0.016	0.025	0.17	1	-0.14	8	9
AKT1	-0.028	0.12	-10000	0	-0.52	15	15
AKT3	-0.069	0.21	-10000	0	-1.1	14	14
mol:GTP	0	0	-10000	0	-10000	0	0
PDGFB-D/PDGFRB	0.003	0.046	-10000	0	-0.29	10	10
GNAI2	0.009	0.006	-10000	0	-10000	0	0
GNAI3	0.01	0.005	-10000	0	-10000	0	0
GNAI1	0.007	0.026	-10000	0	-0.29	3	3
mol:GDP	0	0	-10000	0	-10000	0	0
S1PR3	0.004	0.044	0.27	1	-0.29	8	9
S1PR2	0.01	0	-10000	0	-10000	0	0
EDG1	0	0	-10000	0	-10000	0	0
mol:Ca2+	-0.084	0.14	-10000	0	-0.35	70	70
MAPK3	-0.079	0.14	-10000	0	-0.33	70	70
MAPK1	-0.079	0.14	-10000	0	-0.33	70	70
JAK2	-0.083	0.14	-10000	0	-0.35	70	70
CXCR4	-0.081	0.14	-10000	0	-0.34	70	70
FLT1	0.01	0.008	-10000	0	-10000	0	0
RhoA/GDP	0.007	0	-10000	0	-10000	0	0
Rac1/GDP	0.007	0	-10000	0	-10000	0	0
SRC	-0.079	0.14	-10000	0	-0.33	70	70
S1P/S1P3/Gi	-0.085	0.14	-10000	0	-0.35	70	70
RAC1	0.01	0	-10000	0	-10000	0	0
RhoA/GTP	-0.073	0.13	-10000	0	-0.32	70	70
VEGFA	0.01	0.008	-10000	0	-10000	0	0
S1P/S1P2/Gi	-0.079	0.13	-10000	0	-0.22	164	164
VEGFR1 homodimer/VEGFA homodimer	0.016	0.013	-10000	0	-10000	0	0
RHOA	0.01	0	-10000	0	-10000	0	0
S1P/S1P3/Gq	-0.016	0.074	-10000	0	-0.18	66	66
GNAQ	0.01	0	-10000	0	-10000	0	0
GNAZ	-0.055	0.12	-10000	0	-0.29	89	89
G12/G13	0.015	0	-10000	0	-10000	0	0
GNA14	-0.032	0.1	-10000	0	-0.29	58	58
GNA15	0.008	0.025	-10000	0	-0.29	3	3
GNA12	0.01	0	-10000	0	-10000	0	0
GNA13	0.01	0	-10000	0	-10000	0	0
GNA11	0.009	0.015	-10000	0	-0.29	1	1
Rac1/GTP	-0.073	0.13	-10000	0	-0.32	70	70

×

Coregulation of Androgen receptor activity

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NRIP1	0.009	0.021	0.27	1	-10000	0	1
SVIL	0.006	0.029	-10000	0	-0.29	3	3
ZNF318	0.014	0.033	0.17	16	-10000	0	16
JMJD2C	0.017	0.041	0.14	41	-10000	0	41
T-DHT/AR/Ubc9	-0.049	0.098	0.19	3	-0.18	135	138
CARM1	0.009	0.004	-10000	0	-10000	0	0
PRDX1	0.01	0.002	-10000	0	-10000	0	0
PELP1	0.01	0.005	-10000	0	-10000	0	0
CTNNB1	0.008	0.012	-10000	0	-10000	0	0
AKT1	0.01	0.01	-10000	0	-10000	0	0
PTK2B	0.008	0.018	-10000	0	-0.29	1	1
MED1	0.011	0.01	-10000	0	-10000	0	0
MAK	0.019	0.049	0.2	25	-10000	0	25
response to oxidative stress	0	0.002	-10000	0	-10000	0	0
HIP1	0.007	0.026	-10000	0	-0.29	2	2
GSN	0.004	0.039	-10000	0	-0.29	6	6
NCOA2	-0.008	0.07	-10000	0	-0.29	24	24
NCOA6	0.009	0.019	0.27	1	-10000	0	1
DNA-PK	0.023	0.031	0.17	16	-10000	0	16
NCOA4	0.01	0.002	-10000	0	-10000	0	0
PIAS3	0.008	0.012	-10000	0	-10000	0	0
cell proliferation	0	0.049	0.22	9	-10000	0	9
XRCC5	0.01	0.008	-10000	0	-10000	0	0
UBE3A	0.007	0.022	-10000	0	-10000	0	0
T-DHT/AR/SNURF	-0.061	0.11	0.19	3	-0.19	151	154
FHL2	-0.021	0.086	-10000	0	-0.79	3	3
RANBP9	0.008	0.015	-10000	0	-10000	0	0
JMJD1A	-0.012	0.058	0.16	12	-0.12	73	85
CDK6	0.002	0.048	-10000	0	-0.29	11	11
TGFB1I1	-0.001	0.055	-10000	0	-0.29	13	13
T-DHT/AR/CyclinD1	-0.05	0.1	0.19	7	-0.18	133	140
XRCC6	0.01	0.008	-10000	0	-10000	0	0
T-DHT/AR	-0.044	0.13	0.22	19	-0.18	162	181
CTDSP1	0.009	0.006	-10000	0	-10000	0	0
CTDSP2	0.012	0.021	-10000	0	-10000	0	0
BRCA1	0.009	0.021	0.29	1	-10000	0	1
TCF4	0.007	0.039	-10000	0	-0.29	6	6
CDKN2A	0.14	0.14	0.27	201	-0.29	4	205
SRF	0.013	0.015	-10000	0	-0.13	1	1
NKX3-1	-0.049	0.13	0.42	2	-0.32	44	46
KLK3	-0.041	0.26	-10000	0	-1.3	16	16
TMF1	0.009	0.004	-10000	0	-10000	0	0
HNRNPA1	0.011	0.011	-10000	0	-10000	0	0
AOF2	-0.001	0.014	-10000	0	-0.065	16	16
APPL1	0.011	0.019	-10000	0	-10000	0	0
T-DHT/AR/Caspase 8	-0.048	0.098	0.17	3	-0.17	141	144
AR	-0.094	0.15	0.14	1	-0.3	135	136
UBA3	0.009	0.006	-10000	0	-10000	0	0
PATZ1	0.011	0.011	-10000	0	-10000	0	0
PAWR	0.009	0.015	-10000	0	-0.29	1	1
PRKDC	0.01	0.008	-10000	0	-10000	0	0
PA2G4	0.011	0.015	-10000	0	-10000	0	0
UBE2I	0.01	0	-10000	0	-10000	0	0
T-DHT/AR/Cyclin D3/CDK11 p58	-0.042	0.089	0.16	3	-0.16	135	138
RPS6KA3	0.008	0.016	-10000	0	-10000	0	0
T-DHT/AR/ARA70	-0.05	0.098	0.2	3	-0.18	135	138
LATS2	0.01	0.019	-10000	0	-0.29	1	1
T-DHT/AR/PRX1	-0.042	0.09	0.2	1	-0.16	131	132
Cyclin D3/CDK11 p58	0.008	0.002	-10000	0	-10000	0	0
VAV3	0.009	0.039	0.26	5	-0.28	3	8
KLK2	0.002	0.11	0.3	36	-10000	0	36
CASP8	0.01	0.005	-10000	0	-10000	0	0
T-DHT/AR/TIF2/CARM1	-0.048	0.1	0.2	3	-0.17	147	150
TMPRSS2	-0.13	0.3	0.36	8	-0.78	69	77
CCND1	0.013	0.061	0.27	14	-0.29	6	20
PIAS1	0.007	0.022	-10000	0	-10000	0	0
mol:T-DHT	-0.002	0.023	0.096	3	-0.056	29	32
CDC2L1	0	0.001	-10000	0	-10000	0	0
PIAS4	0.006	0.034	-10000	0	-0.16	16	16
T-DHT/AR/CDK6	-0.053	0.1	0.18	3	-0.18	147	150
CMTM2	0.013	0.029	0.27	5	-10000	0	5
SNURF	-0.013	0.078	-10000	0	-0.29	30	30
ZMIZ1	0.007	0.025	0.14	1	-10000	0	1
CCND3	0.01	0.001	-10000	0	-10000	0	0
TGIF1	0.011	0.011	-10000	0	-10000	0	0
FKBP4	0.008	0.015	-10000	0	-10000	0	0

×

Syndecan-2-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Syndecan-2/Fibronectin	0.008	0.07	0.19	25	-0.16	38	63
EPHB2	0.028	0.065	0.27	28	-10000	0	28
Syndecan-2/TACI	-0.01	0.068	0.19	7	-0.16	59	66
LAMA1	0.041	0.12	0.27	66	-0.29	15	81
Syndecan-2/alpha2 ITGB1	0.015	0.081	0.18	37	-0.14	59	96
HRAS	0.01	0	-10000	0	-10000	0	0
Syndecan-2/CASK	-0.005	0.042	-10000	0	-0.16	29	29
ITGA5	-0.002	0.058	-10000	0	-0.29	16	16
BAX	0.013	0.004	-10000	0	-10000	0	0
EPB41	0.01	0	-10000	0	-10000	0	0
positive regulation of cell-cell adhesion	0.002	0.038	-10000	0	-0.14	29	29
LAMA3	0.005	0.12	0.27	35	-0.29	37	72
EZR	0.01	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0	0	-10000	0	-10000	0	0
CAV2	0.007	0.029	-10000	0	-0.29	4	4
Syndecan-2/MMP2	-0.013	0.072	-10000	0	-0.19	52	52
RP11-540L11.1	0	0	-10000	0	-10000	0	0
alpha2 ITGB1	0.016	0.022	0.19	5	-0.19	1	6
dendrite morphogenesis	0.014	0.063	0.19	27	-0.15	28	55
Syndecan-2/GM-CSF	0.033	0.083	0.19	71	-0.16	25	96
determination of left/right symmetry	-0.006	0.051	-10000	0	-0.19	29	29
Syndecan-2/PKC delta	0.002	0.043	-10000	0	-0.16	29	29
GNB2L1	0.01	0	-10000	0	-10000	0	0
MAPK3	0.02	0.057	0.12	71	-0.14	25	96
MAPK1	0.02	0.057	-10000	0	-0.14	25	25
Syndecan-2/RACK1	0.008	0.037	-10000	0	-0.13	29	29
NF1	0.01	0	-10000	0	-10000	0	0
FGFR/FGF/Syndecan-2	-0.006	0.051	-10000	0	-0.19	29	29
ITGA2	0.012	0.032	0.27	5	-0.29	1	6
MAPK8	0.011	0.003	-10000	0	-10000	0	0
Syndecan-2/alpha2/beta1 Integrin	0.033	0.079	0.18	64	-0.13	38	102
Syndecan-2/Kininogen	-0.005	0.042	-10000	0	-0.16	29	29
ITGB1	0.01	0	-10000	0	-10000	0	0
SRC	0.004	0.034	-10000	0	-0.12	29	29
Syndecan-2/CASK/Protein 4.1	0.002	0.039	-10000	0	-0.14	29	29
extracellular matrix organization	0.002	0.043	-10000	0	-0.15	29	29
actin cytoskeleton reorganization	0.008	0.07	0.19	25	-0.16	38	63
Syndecan-2/Caveolin-2/Ras	0.007	0.044	-10000	0	-0.14	32	32
Syndecan-2/Laminin alpha3	0.002	0.088	0.19	34	-0.17	59	93
Syndecan-2/RasGAP	0.013	0.037	-10000	0	-0.12	29	29
alpha5/beta1 Integrin	0.007	0.04	-10000	0	-0.19	16	16
PRKCD	0.01	0	-10000	0	-10000	0	0
Syndecan-2 dimer	0.014	0.064	0.19	27	-0.16	28	55
GO:0007205	0.002	0	-10000	0	-10000	0	0
DNA mediated transformation	0	0	-10000	0	-10000	0	0
Syndecan-2/RasGAP/Src	0.011	0.035	-10000	0	-0.11	29	29
RHOA	0.01	0	-10000	0	-10000	0	0
SDCBP	0.01	0	-10000	0	-10000	0	0
TNFRSF13B	-0.012	0.089	0.27	7	-0.29	33	40
RASA1	0.01	0	-10000	0	-10000	0	0
alpha2/beta1 Integrin	0.016	0.022	0.19	5	-0.19	1	6
Syndecan-2/Synbindin	0.002	0.043	-10000	0	-0.16	29	29
TGFB1	0.01	0	-10000	0	-10000	0	0
CASP3	0.002	0.038	-10000	0	-0.14	29	29
FN1	0.018	0.083	0.27	26	-0.29	12	38
Syndecan-2/IL8	-0.022	0.074	0.19	1	-0.16	83	84
SDC2	-0.006	0.051	-10000	0	-0.19	29	29
KNG1	0	0	-10000	0	-10000	0	0
Syndecan-2/Neurofibromin	0.002	0.043	-10000	0	-0.16	29	29
TRAPPC4	0.01	0	-10000	0	-10000	0	0
CSF2	0.056	0.1	0.27	75	-10000	0	75
Syndecan-2/TGFB1	0.002	0.043	-10000	0	-0.16	29	29
Syndecan-2/Syntenin/PI-4-5-P2	0.002	0.039	-10000	0	-0.14	29	29
Syndecan-2/Ezrin	0.008	0.04	-10000	0	-0.14	29	29
PRKACA	0.002	0.038	-10000	0	-0.14	29	29
angiogenesis	-0.022	0.074	0.19	1	-0.16	83	84
MMP2	-0.016	0.085	-10000	0	-0.29	36	36
IL8	-0.033	0.11	0.27	1	-0.29	59	60
calcineurin-NFAT signaling pathway	-0.01	0.068	0.19	7	-0.16	59	66

×

Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Noncanonical Wnts/FZD	0.004	0.093	0.2	9	-0.19	57	66
FZD6	0.01	0	-10000	0	-10000	0	0
WNT6	0.025	0.095	0.27	39	-0.29	13	52
WNT4	-0.007	0.077	0.27	3	-0.29	26	29
FZD3	0.008	0.025	-10000	0	-0.29	3	3
WNT5A	0.011	0.056	0.27	10	-0.29	7	17
WNT11	0.015	0.1	0.27	34	-0.29	22	56

×

Syndecan-4-mediated signaling events

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
PTK2	0.022	0.081	0.22	1	-0.38	12	13
Syndecan-4/Syndesmos	0.052	0.1	0.23	26	-0.41	9	35
positive regulation of JNK cascade	0.011	0.12	-10000	0	-0.36	18	18
Syndecan-4/ADAM12	0.067	0.12	0.28	42	-0.41	9	51
CCL5	0.004	0.08	0.27	13	-0.29	20	33
Rac1/GDP	0.007	0	-10000	0	-10000	0	0
DNM2	0.01	0	-10000	0	-10000	0	0
ITGA5	-0.002	0.058	-10000	0	-0.29	16	16
SDCBP	0.01	0	-10000	0	-10000	0	0
PLG	0.004	0.03	0.27	5	-10000	0	5
ADAM12	0.035	0.077	0.27	40	-10000	0	40
mol:GTP	0	0	-10000	0	-10000	0	0
NUDT16L1	0.01	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0	0	-10000	0	-10000	0	0
Syndecan-4/PKC alpha	0.004	0.011	-10000	0	-10000	0	0
Syndecan-4/Laminin alpha1	0.073	0.13	0.28	50	-0.41	11	61
Syndecan-4/CXCL12/CXCR4	0.016	0.13	0.25	7	-0.38	18	25
Syndecan-4/Laminin alpha3	0.058	0.12	0.28	43	-0.41	10	53
MDK	0.025	0.06	0.27	23	-10000	0	23
Syndecan-4/FZD7	0.049	0.1	0.23	26	-0.41	9	35
Syndecan-4/Midkine	0.06	0.1	0.24	31	-0.4	9	40
FZD7	-0.004	0.063	-10000	0	-0.29	19	19
Syndecan-4/FGFR1/FGF	-0.052	0.12	-10000	0	-0.27	67	67
THBS1	0	0.052	-10000	0	-0.29	13	13
integrin-mediated signaling pathway	0.048	0.11	0.25	30	-0.38	15	45
positive regulation of MAPKKK cascade	0.011	0.12	-10000	0	-0.36	18	18
Syndecan-4/TACI	0.049	0.1	0.24	25	-0.42	9	34
CXCR4	0.004	0.041	-10000	0	-0.29	8	8
cell adhesion	0.007	0.063	0.12	14	-0.28	12	26
Syndecan-4/Dynamin	0.052	0.1	0.23	20	-0.41	9	29
Syndecan-4/TSP1	0.05	0.1	0.23	20	-0.41	10	30
Syndecan-4/GIPC	0.052	0.1	0.23	26	-0.41	9	35
Syndecan-4/RANTES	0.054	0.11	0.25	33	-0.43	11	44
ITGB1	0.01	0	-10000	0	-10000	0	0
LAMA1	0.041	0.12	0.27	66	-0.29	15	81
LAMA3	0.005	0.12	0.27	35	-0.29	37	72
RAC1	0.01	0	-10000	0	-10000	0	0
PRKCA	-0.015	0.035	-10000	0	-0.23	6	6
Syndecan-4/alpha-Actinin	0.052	0.1	0.23	26	-0.41	9	35
TFPI	0.003	0.044	-10000	0	-0.29	9	9
F2	0.029	0.07	0.28	30	-10000	0	30
alpha5/beta1 Integrin	0.007	0.04	-10000	0	-0.19	16	16
positive regulation of cell adhesion	0.064	0.12	0.26	58	-0.39	12	70
ACTN1	0.01	0	-10000	0	-10000	0	0
TNC	-0.008	0.091	0.27	9	-0.29	33	42
Syndecan-4/CXCL12	0.036	0.11	0.23	17	-0.4	16	33
FGF6	0	0.001	-10000	0	-10000	0	0
RHOA	0.01	0	-10000	0	-10000	0	0
CXCL12	-0.073	0.13	-10000	0	-0.29	114	114
TNFRSF13B	-0.012	0.089	0.27	7	-0.29	33	40
FGF2	-0.089	0.14	-10000	0	-0.29	136	136
FGFR1	-0.058	0.12	-10000	0	-0.29	93	93
Syndecan-4/PI-4-5-P2	0.045	0.099	0.22	26	-0.41	9	35
mol:GDP	0	0	-10000	0	-10000	0	0
FN1	0.017	0.081	0.27	26	-0.27	12	38
cell migration	-0.006	0.006	-10000	0	-10000	0	0
PRKCD	0.008	0.005	-10000	0	-10000	0	0
vasculogenesis	0.049	0.099	0.22	25	-0.4	10	35
SDC4	0.049	0.1	0.24	26	-0.43	9	35
Syndecan-4/Tenascin C	0.049	0.12	0.25	30	-0.39	15	45
Syndecan-4/PI-4-5-P2/PKC alpha	-0.003	0.005	-10000	0	-10000	0	0
Syndecan-4/Syntenin	0.052	0.1	0.23	26	-0.41	9	35
MMP9	0.071	0.12	0.27	102	-0.28	8	110
Rac1/GTP	0.007	0.064	0.12	14	-0.29	12	26
cytoskeleton organization	0.051	0.097	0.22	26	-0.4	9	35
GIPC1	0.01	0	-10000	0	-10000	0	0
Syndecan-4/TFPI	0.05	0.1	0.23	20	-0.42	11	31

×

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MET/RANBP9	0.016	0.012	0.19	2	-10000	0	2
CRKL	-0.016	0.068	-10000	0	-0.23	2	2
mol:PIP3	-0.003	0.005	-10000	0	-10000	0	0
AKT1	0.001	0.004	-10000	0	-10000	0	0
PTK2B	0.009	0.015	-10000	0	-0.29	1	1
RAPGEF1	-0.014	0.065	-10000	0	-0.22	2	2
RANBP10	0.01	0	-10000	0	-10000	0	0
PIK3CA	0.01	0	-10000	0	-10000	0	0
HGF/MET/SHIP2	-0.014	0.078	0.18	9	-0.16	87	96
MAP3K5	-0.013	0.073	-10000	0	-0.23	13	13
HGF/MET/CIN85/CBL/ENDOPHILINS	-0.006	0.072	0.18	9	-0.14	87	96
AP1	-0.05	0.094	-10000	0	-0.18	130	130
mol:SU11274	0	0	-10000	0	-10000	0	0
SHC1	0.011	0.013	0.27	1	-10000	0	1
apoptosis	-0.23	0.35	-10000	0	-0.73	130	130
STAT3 (dimer)	-0.021	0.08	-10000	0	-0.17	87	87
GAB1/CRKL/SHP2/PI3K	-0.003	0.068	-10000	0	-0.22	3	3
INPP5D	0.005	0.039	-10000	0	-0.29	7	7
CBL/CRK	-0.01	0.067	-10000	0	-0.22	2	2
PTPN11	0.01	0	-10000	0	-10000	0	0
GO:0007205	0	0	-10000	0	-10000	0	0
PLCG1	0.01	0	-10000	0	-10000	0	0
PTEN	0.01	0	-10000	0	-10000	0	0
ELK1	-0.005	0.006	-10000	0	-10000	0	0
mol:SU5416	0	0	-10000	0	-10000	0	0
SHP2/GRB2/SOS1GAB1	-0.011	0.05	-10000	0	-0.11	87	87
PAK1	0.002	0.007	-10000	0	-0.12	1	1
HGF/MET/RANBP10	-0.014	0.078	0.18	9	-0.16	87	96
HRAS	-0.023	0.087	-10000	0	-0.24	1	1
DOCK1	-0.014	0.066	-10000	0	-0.23	3	3
GAB1	-0.019	0.072	-10000	0	-0.25	2	2
CRK	-0.016	0.069	-10000	0	-0.23	2	2
mol:PHA665752	0	0	-10000	0	-10000	0	0
mol:GDP	-0.065	0.17	-10000	0	-0.38	87	87
JUN	-0.002	0.058	-10000	0	-0.29	16	16
EntrezGene:200958	0	0	-10000	0	-10000	0	0
HGF/MET	-0.022	0.062	0.1	2	-0.14	87	89
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
cell morphogenesis	-0.018	0.087	-10000	0	-0.18	86	86
GRB2/SHC	-0.009	0.059	0.17	1	-0.12	87	88
FOS	-0.084	0.14	-10000	0	-0.29	129	129
GLMN	0.002	0	-10000	0	-10000	0	0
cell motility	-0.005	0.006	-10000	0	-10000	0	0
HGF/MET/MUC20	-0.02	0.076	0.17	9	-0.16	87	96
cell migration	-0.009	0.058	0.17	1	-0.12	87	88
GRB2	0.01	0	-10000	0	-10000	0	0
CBL	0.01	0	-10000	0	-10000	0	0
MET/RANBP10	0.016	0.012	0.19	2	-10000	0	2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP	-0.02	0.078	-10000	0	-0.17	87	87
MET/MUC20	0.008	0.012	0.18	2	-10000	0	2
RAP1B	-0.011	0.063	-10000	0	-0.21	2	2
RAP1A	-0.011	0.063	-10000	0	-0.21	2	2
HGF/MET/RANBP9	-0.014	0.078	0.18	9	-0.16	87	96
RAF1	-0.02	0.083	-10000	0	-0.23	1	1
STAT3	-0.021	0.08	-10000	0	-0.17	87	87
cell proliferation	-0.036	0.11	-10000	0	-0.25	87	87
RPS6KB1	-0.004	0.024	-10000	0	-0.12	1	1
MAPK3	-0.007	0.005	-10000	0	-10000	0	0
MAPK1	-0.007	0.005	-10000	0	-10000	0	0
RANBP9	0.01	0	-10000	0	-10000	0	0
MAPK8	-0.006	0.069	-10000	0	-0.29	7	7
SRC	-0.018	0.072	-10000	0	-0.16	87	87
PI3K	-0.009	0.059	-10000	0	-0.12	87	87
MET/Glomulin	0.01	0.013	0.2	2	-10000	0	2
SOS1	0.01	0	-10000	0	-10000	0	0
MAP2K1	-0.018	0.079	-10000	0	-0.22	1	1
MET	0.011	0.018	0.27	2	-10000	0	2
MAP4K1	-0.015	0.076	-10000	0	-0.25	12	12
PTK2	0.01	0	-10000	0	-10000	0	0
MAP2K2	-0.018	0.079	-10000	0	-0.22	1	1
BAD	0.002	0.004	-10000	0	-10000	0	0
MAP2K4	-0.011	0.069	-10000	0	-0.22	13	13
SHP2/GRB2/SOS1/GAB1	-0.01	0.064	-10000	0	-0.2	2	2
INPPL1	0.01	0	-10000	0	-10000	0	0
PXN	0.01	0	-10000	0	-10000	0	0
SH3KBP1	0.01	0	-10000	0	-10000	0	0
HGS	-0.019	0.057	-10000	0	-0.13	87	87
PLCgamma1/PKC	0.007	0	-10000	0	-10000	0	0
HGF	-0.049	0.13	0.27	7	-0.29	87	94
RASA1	0.01	0	-10000	0	-10000	0	0
NCK1	0.01	0	-10000	0	-10000	0	0
PTPRJ	0.009	0.015	-10000	0	-0.29	1	1
NCK/PLCgamma1	-0.012	0.065	-10000	0	-0.13	87	87
PDPK1	-0.001	0.004	-10000	0	-10000	0	0
HGF/MET/SHIP	-0.017	0.082	0.18	9	-0.16	90	99

×

Noncanonical Wnt signaling pathway

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
NFATC2	-0.042	0.11	-10000	0	-0.29	71	71
GNB1/GNG2	0.011	0.088	0.18	8	-0.36	7	15
mol:DAG	0.006	0.079	0.15	9	-0.33	7	16
PLCG1	0.006	0.081	0.16	8	-0.34	7	15
YES1	0.003	0.086	0.17	9	-0.18	57	66
FZD3	0.008	0.025	-10000	0	-0.29	3	3
FZD6	0.01	0	-10000	0	-10000	0	0
G protein	0.011	0.083	-10000	0	-0.34	7	7
MAP3K7	-0.01	0.083	0.14	7	-0.25	30	37
mol:Ca2+	0.006	0.077	0.15	9	-0.32	7	16
mol:IP3	0.006	0.079	0.15	9	-0.33	7	16
NLK	0.003	0.007	-10000	0	-10000	0	0
GNB1	0.01	0	-10000	0	-10000	0	0
CAMK2A	-0.011	0.088	0.14	7	-0.27	30	37
MAP3K7IP1	0	0	-10000	0	-10000	0	0
Noncanonical Wnts/FZD	0.004	0.093	0.2	9	-0.19	57	66
CSNK1A1	0.01	0	-10000	0	-10000	0	0
GNAS	0.003	0.086	0.17	9	-0.18	57	66
GO:0007205	0.004	0.078	0.15	8	-0.33	7	15
WNT6	0.025	0.095	0.27	39	-0.29	13	52
WNT4	-0.007	0.077	0.27	3	-0.29	26	29
NFAT1/CK1 alpha	-0.006	0.096	-10000	0	-0.29	17	17
GNG2	0.006	0.036	-10000	0	-0.29	6	6
WNT5A	0.011	0.056	0.27	10	-0.29	7	17
WNT11	0.015	0.1	0.27	34	-0.29	22	56
CDC42	0.004	0.081	0.16	9	-0.17	57	66

×

Class IB PI3K non-lipid kinase events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
cAMP biosynthetic process	0.009	0.073	0.29	26	-10000	0	26
PI3K Class IB/PDE3B	-0.009	0.073	-10000	0	-0.29	26	26
PDE3B	-0.009	0.073	-10000	0	-0.29	26	26

×

Sphingosine 1-phosphate (S1P) pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.011	0.013	0.27	1	-10000	0	1
SPHK1	0.045	0.091	0.27	56	-0.29	1	57
GNAI2	0.01	0	-10000	0	-10000	0	0
mol:S1P	0.025	0.039	0.12	59	-0.2	1	60
GNAO1	-0.084	0.14	-10000	0	-0.29	129	129
mol:Sphinganine-1-P	0.03	0.054	0.16	57	-0.19	1	58
growth factor activity	0	0	-10000	0	-10000	0	0
S1P/S1P2/G12/G13	0.034	0.023	-10000	0	-0.14	1	1
GNAI3	0.01	0	-10000	0	-10000	0	0
G12/G13	0.015	0	-10000	0	-10000	0	0
S1PR3	0.005	0.043	0.27	1	-0.29	8	9
S1PR2	0.01	0	-10000	0	-10000	0	0
EDG1	0	0	-10000	0	-10000	0	0
S1P1/S1P	0.017	0.027	-10000	0	-0.17	1	1
S1PR5	0.017	0.052	0.27	14	-0.29	2	16
S1PR4	0.009	0.037	0.27	3	-0.29	4	7
GNAI1	0.008	0.025	-10000	0	-0.29	3	3
S1P/S1P5/G12	0.034	0.041	0.19	14	-0.14	3	17
S1P/S1P3/Gq	-0.011	0.088	-10000	0	-0.21	56	56
S1P/S1P4/Gi	-0.069	0.13	-10000	0	-0.22	157	157
GNAQ	0.01	0	-10000	0	-10000	0	0
GNAZ	-0.055	0.12	-10000	0	-0.29	89	89
GNA14	-0.032	0.1	-10000	0	-0.29	58	58
GNA15	0.008	0.025	-10000	0	-0.29	3	3
GNA12	0.01	0	-10000	0	-10000	0	0
GNA13	0.01	0	-10000	0	-10000	0	0
GNA11	0.009	0.015	-10000	0	-0.29	1	1
ABCC1	0.011	0.018	0.27	2	-10000	0	2

×

Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A	-0.14	0.15	-10000	0	-0.29	206	206
oxygen homeostasis	0	0	-10000	0	-10000	0	0
TCEB2	0.011	0.013	0.27	1	-10000	0	1
TCEB1	0.01	0	-10000	0	-10000	0	0
HIF1A/p53	0.014	0.008	-10000	0	-10000	0	0
HIF1A	0.008	0.008	-10000	0	-10000	0	0
COPS5	0.01	0	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C/RBX1/CUL2	0.03	0.007	0.17	1	-10000	0	1
FIH (dimer)	0.01	0	-10000	0	-10000	0	0
CDKN2A	0.14	0.14	0.27	201	-0.29	4	205
ARNT/IPAS	-0.09	0.1	-10000	0	-0.19	206	206
HIF1AN	0.01	0	-10000	0	-10000	0	0
GNB2L1	0.01	0	-10000	0	-10000	0	0
HIF1A/ARNT	0.014	0.008	-10000	0	-10000	0	0
CUL2	0.01	0	-10000	0	-10000	0	0
OS9	0.01	0	-10000	0	-10000	0	0
RACK1/Elongin B/Elongin C	0.021	0.008	0.18	1	-10000	0	1
response to hypoxia	0	0	-10000	0	-10000	0	0
HIF1A/Hsp90	0.014	0.008	-10000	0	-10000	0	0
PHD1-3/OS9	0.022	0.023	-10000	0	-0.14	8	8
HIF1A/RACK1/Elongin B/Elongin C	0.023	0.011	-10000	0	-10000	0	0
VHL	0.01	0	-10000	0	-10000	0	0
HSP90AA1	0.01	0	-10000	0	-10000	0	0
HIF1A/JAB1	0.014	0.008	-10000	0	-10000	0	0
EGLN3	0.004	0.041	-10000	0	-0.29	8	8
EGLN2	0.01	0	-10000	0	-10000	0	0
EGLN1	0.01	0	-10000	0	-10000	0	0
TP53	0.01	0	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A	0.021	0.004	-10000	0	-10000	0	0
ARNT	0.01	0	-10000	0	-10000	0	0
ARD1A	0	0	-10000	0	-10000	0	0
RBX1	0.01	0	-10000	0	-10000	0	0
HIF1A/p19ARF	0.091	0.078	0.17	197	-10000	0	197

×

Visual signal transduction: Rods

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
mol:K +	0.01	0	-10000	0	-10000	0	0
GNAT1/GTP	0.006	0.018	0.18	4	-10000	0	4
Metarhodopsin II/Arrestin	0.002	0.003	-10000	0	-10000	0	0
PDE6G/GNAT1/GTP	0.018	0.034	0.17	19	-10000	0	19
mol:GTP	0	0	-10000	0	-10000	0	0
absorption of light	0	0	-10000	0	-10000	0	0
GNAT1	0.009	0.026	0.27	4	-10000	0	4
GRK1	0.001	0.014	0.27	1	-10000	0	1
CNG Channel	0.05	0.072	0.2	28	-0.12	25	53
mol:Na +	0.068	0.076	0.22	36	-0.12	15	51
mol:ADP	0.001	0.014	0.27	1	-10000	0	1
RGS9-1/Gbeta5/R9AP	-0.022	0.081	0.18	3	-0.16	97	100
mol:GDP	0	0	-10000	0	-10000	0	0
cGMP/CNG Channel	0.084	0.088	0.26	36	-0.12	3	39
CNGB1	0.12	0.13	0.27	174	-10000	0	174
RDH5	0.009	0.015	-10000	0	-0.29	1	1
SAG	0	0	-10000	0	-10000	0	0
mol:Ca2+	0.047	0.054	0.15	36	-0.11	15	51
Na + (4 Units)	0.04	0.055	0.17	24	-10000	0	24
RGS9	-0.054	0.12	-10000	0	-0.29	87	87
GNB1/GNGT1	0.023	0.039	0.19	20	-10000	0	20
GNAT1/GDP	-0.014	0.071	0.16	7	-0.13	97	104
GUCY2D	0.037	0.082	0.27	45	-10000	0	45
GNGT1	0.021	0.056	0.27	20	-10000	0	20
GUCY2F	0.001	0.003	-10000	0	-10000	0	0
GNB5	0.01	0	-10000	0	-10000	0	0
mol:GMP (4 units)	0.015	0.039	0.16	6	-0.13	16	22
mol:11-cis-retinal	0.009	0.015	-10000	0	-0.29	1	1
mol:cGMP	0.033	0.048	0.18	23	-0.13	1	24
GNB1	0.01	0	-10000	0	-10000	0	0
Rhodopsin	0.009	0.01	-10000	0	-0.19	1	1
SLC24A1	0.01	0	-10000	0	-10000	0	0
CNGA1	0.008	0.098	0.27	25	-0.29	25	50
Metarhodopsin II	0.002	0.008	0.16	1	-10000	0	1
mol:Ca ++	0	0	-10000	0	-10000	0	0
GC1/GCAP Family	0.042	0.061	0.18	66	-0.14	1	67
RGS9BP	0.001	0.059	0.27	3	-0.29	14	17
Metarhodopsin II/Transducin	0.013	0.021	-10000	0	-10000	0	0
GCAP Family/Ca ++	0.02	0.038	0.17	23	-0.14	1	24
PDE6A/B	0.008	0.046	0.19	6	-0.19	16	22
mol:Pi	-0.022	0.08	0.18	3	-0.16	97	100
mol:all-trans-retinal	0	0	-10000	0	-10000	0	0
Transducin	0.025	0.036	0.17	24	-10000	0	24
PDE6B	-0.002	0.061	0.27	1	-0.29	17	18
PDE6A	0.013	0.031	0.27	6	-10000	0	6
PDE6G	0.019	0.049	0.27	15	-10000	0	15
RHO	0.002	0.004	-10000	0	-10000	0	0
PDE6	-0.007	0.082	0.28	1	-0.14	102	103
GUCA1A	0.021	0.058	0.27	21	-10000	0	21
GC2/GCAP Family	0.021	0.038	0.17	23	-0.14	1	24
GUCA1C	0.001	0.014	0.27	1	-10000	0	1
GUCA1B	0.01	0.023	0.27	2	-0.29	1	3

×

Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved)	0.019	0.018	-10000	0	-10000	0	0
HDAC1	0.009	0.011	-10000	0	-10000	0	0
AES	0.01	0.004	-10000	0	-10000	0	0
FBXW11	0.01	0	-10000	0	-10000	0	0
DTX1	0.004	0.062	0.27	6	-0.29	13	19
LRP6/FZD1	0.015	0.014	0.19	1	-0.19	1	2
TLE1	0.008	0.026	-10000	0	-0.29	3	3
AP1	-0.066	0.12	-10000	0	-0.21	141	141
NCSTN	0.01	0	-10000	0	-10000	0	0
ADAM10	0.01	0	-10000	0	-10000	0	0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4	0.013	0.066	-10000	0	-0.3	3	3
NICD/RBPSUH	0.02	0.001	-10000	0	-10000	0	0
WIF1	-0.048	0.13	0.27	9	-0.29	81	90
NOTCH1	0.015	0.001	-10000	0	-10000	0	0
PSENEN	0.01	0	-10000	0	-10000	0	0
KREMEN2	0.11	0.13	0.27	158	-10000	0	158
DKK1	-0.022	0.12	0.27	15	-0.29	57	72
beta catenin/beta TrCP1	0.014	0.035	-10000	0	-10000	0	0
APH1B	0.01	0	-10000	0	-10000	0	0
APH1A	0.01	0	-10000	0	-10000	0	0
AXIN1	0.003	0.008	-10000	0	-10000	0	0
CtBP/CBP/TCF1/TLE1/AES	0.015	0.043	0.26	3	-0.17	3	6
PSEN1	0.01	0	-10000	0	-10000	0	0
FOS	-0.084	0.14	-10000	0	-0.29	129	129
JUN	-0.002	0.058	-10000	0	-0.29	16	16
MAP3K7	0.01	0.005	-10000	0	-10000	0	0
CTNNB1	0.009	0.036	-10000	0	-10000	0	0
MAPK3	0.01	0	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	0.12	0.11	0.21	207	-0.16	1	208
HNF1A	0.013	0.029	0.27	5	-10000	0	5
CTBP1	0.011	0.013	0.26	1	-10000	0	1
MYC	-0.043	0.25	-10000	0	-1.2	18	18
NKD1	-0.005	0.079	0.27	6	-0.29	25	31
FZD1	0.01	0.02	0.27	1	-0.29	1	2
NOTCH1 precursor/Deltex homolog 1	0.022	0.02	-10000	0	-10000	0	0
apoptosis	-0.066	0.12	-10000	0	-0.21	141	141
Delta 1/NOTCHprecursor	0.021	0.012	-10000	0	-10000	0	0
DLL1	0.008	0.035	0.27	2	-0.29	4	6
PPARD	0.008	0.024	-10000	0	-10000	0	0
Gamma Secretase	0.03	0.002	-10000	0	-10000	0	0
APC	0.003	0.008	-10000	0	-10000	0	0
DVL1	0.006	0.017	-10000	0	-10000	0	0
CSNK2A1	0.01	0.001	-10000	0	-10000	0	0
MAP3K7IP1	0	0.005	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	0.058	0.11	0.19	142	-0.16	32	174
LRP6	0.01	0	-10000	0	-10000	0	0
CSNK1A1	0.01	0.001	-10000	0	-10000	0	0
NLK	0.008	0.011	-10000	0	-10000	0	0
CCND1	-0.003	0.17	-10000	0	-1.2	7	7
WNT1	0.009	0.023	0.27	3	-10000	0	3
Axin1/APC/beta catenin	0.016	0.026	-10000	0	-10000	0	0
DKK2	0.068	0.11	0.27	93	-0.29	1	94
NOTCH1 precursor/DVL1	0.018	0.015	-10000	0	-10000	0	0
GSK3B	0.01	0.001	-10000	0	-10000	0	0
FRAT1	0.01	0.002	-10000	0	-10000	0	0
NOTCH/Deltex homolog 1	0.018	0.031	-10000	0	-10000	0	0
PPP2R5D	0.014	0.044	0.18	21	-10000	0	21
MAPK1	0.01	0	-10000	0	-10000	0	0
WNT1/LRP6/FZD1	-0.007	0.071	0.18	12	-0.14	80	92
RBPJ	0.01	0	-10000	0	-10000	0	0
CREBBP	0.011	0.004	-10000	0	-10000	0	0

×

Canonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.016	0.028	0.18	3	-10000	0	3
AES	0.015	0.023	0.15	3	-10000	0	3
FBXW11	0.01	0	-10000	0	-10000	0	0
mol:GTP	0	0.001	-10000	0	-10000	0	0
LRP6/FZD1	0.015	0.014	0.19	1	-0.19	1	2
SMAD4	0.01	0	-10000	0	-10000	0	0
DKK2	0.068	0.11	0.27	93	-0.29	1	94
TLE1	0.012	0.035	0.16	3	-0.29	3	6
MACF1	0.01	0	-10000	0	-10000	0	0
CTNNB1	0.065	0.058	0.19	26	-10000	0	26
WIF1	-0.048	0.12	0.27	9	-0.29	81	90
beta catenin/RanBP3	0.039	0.12	0.38	46	-10000	0	46
KREMEN2	0.11	0.13	0.27	158	-10000	0	158
DKK1	-0.022	0.12	0.27	15	-0.29	57	72
beta catenin/beta TrCP1	0.067	0.055	0.19	20	-10000	0	20
FZD1	0.01	0.02	0.27	1	-0.29	1	2
AXIN2	-0.08	0.31	-10000	0	-1.2	29	29
AXIN1	0.01	0.001	-10000	0	-10000	0	0
RAN	0.01	0.001	-10000	0	-10000	0	0
Axin1/APC/GSK3/beta catenin	0.034	0.021	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4	0.05	0.044	0.21	2	-0.23	2	4
Axin1/APC/GSK3	0.032	0.035	0.15	5	-10000	0	5
Axin1/APC/GSK3/beta catenin/Macf1	0.038	0.024	-10000	0	-10000	0	0
HNF1A	0.018	0.037	0.22	8	-10000	0	8
CTBP1	0.016	0.027	0.19	4	-10000	0	4
MYC	-0.061	0.27	-10000	0	-1.3	18	18
RANBP3	0.01	0.001	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	0.12	0.11	0.21	207	-0.16	1	208
NKD1	-0.005	0.079	0.27	6	-0.29	25	31
TCF4	0.012	0.036	0.16	3	-0.29	3	6
TCF3	0.015	0.024	0.16	3	-10000	0	3
WNT1/LRP6/FZD1/Axin1	0.026	0.017	0.18	4	-0.14	1	5
Ran/GTP	0.008	0.002	-10000	0	-10000	0	0
CtBP/CBP/TCF/TLE1/AES	0.045	0.15	0.43	46	-10000	0	46
LEF1	0.019	0.04	0.23	10	-10000	0	10
DVL1	0.016	0.021	-10000	0	-10000	0	0
CSNK2A1	0.01	0	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES	0.031	0.075	0.21	1	-0.26	8	9
DKK1/LRP6/Kremen 2	0.058	0.11	0.19	142	-0.16	32	174
LRP6	0.01	0	-10000	0	-10000	0	0
CSNK1A1	0.016	0.028	0.18	3	-10000	0	3
NLK	0.008	0.006	-10000	0	-10000	0	0
CCND1	-0.024	0.19	-10000	0	-1.3	7	7
WNT1	0.01	0.023	0.27	3	-10000	0	3
GSK3A	0.01	0.001	-10000	0	-10000	0	0
GSK3B	0.01	0.001	-10000	0	-10000	0	0
FRAT1	0.01	0	-10000	0	-10000	0	0
PPP2R5D	0.027	0.049	0.19	25	-10000	0	25
APC	0.015	0.01	-10000	0	-0.12	1	1
WNT1/LRP6/FZD1	0.043	0.062	0.16	80	-10000	0	80
CREBBP	0.015	0.024	0.16	3	-10000	0	3

×

Regulation of Androgen receptor activity

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
HDAC1	0.009	0.004	-10000	0	-10000	0	0
SMARCC1	0.008	0.01	-10000	0	-10000	0	0
REL	0.008	0.032	0.28	2	-0.29	3	5
HDAC7	-0.036	0.1	0.19	3	-0.23	63	66
JUN	-0.002	0.058	-10000	0	-0.29	16	16
EP300	0.01	0.001	-10000	0	-10000	0	0
KAT2B	0.009	0.015	-10000	0	-0.29	1	1
KAT5	0.01	0.001	-10000	0	-10000	0	0
MAPK14	0.003	0.029	0.16	1	-0.2	5	6
FOXO1	0.009	0.015	-10000	0	-0.29	1	1
T-DHT/AR	-0.032	0.11	0.23	9	-0.25	61	70
MAP2K6	0.003	0.037	0.27	1	-0.29	5	6
BRM/BAF57	0.015	0.011	-10000	0	-10000	0	0
MAP2K4	0.006	0.011	-10000	0	-10000	0	0
SMARCA2	0.01	0.006	-10000	0	-10000	0	0
PDE9A	-0.12	0.33	-10000	0	-1	49	49
NCOA2	-0.006	0.07	-10000	0	-0.29	24	24
CEBPA	0.015	0.045	0.27	10	-0.29	2	12
EHMT2	0.01	0.003	-10000	0	-10000	0	0
cell proliferation	-0.024	0.13	0.26	7	-0.26	64	71
NR0B1	0.024	0.072	0.27	32	-10000	0	32
EGR1	-0.06	0.13	-10000	0	-0.29	96	96
RXRs/9cRA	-0.024	0.071	0.17	1	-0.14	106	107
AR/RACK1/Src	-0.001	0.084	0.21	30	-0.17	14	44
AR/GR	-0.061	0.1	-10000	0	-0.19	146	146
GNB2L1	0.011	0.002	-10000	0	-10000	0	0
PKN1	0.009	0.015	-10000	0	-0.29	1	1
RCHY1	0.01	0	-10000	0	-10000	0	0
epidermal growth factor receptor activity	0.001	0.003	-10000	0	-10000	0	0
MAPK8	0.004	0.022	-10000	0	-0.19	2	2
T-DHT/AR/TIF2/CARM1	-0.01	0.089	0.21	22	-0.18	34	56
SRC	0.002	0.037	0.12	3	-0.094	14	17
NR3C1	0.001	0.05	-10000	0	-0.29	12	12
KLK3	-0.071	0.24	0.34	13	-0.93	21	34
APPBP2	0.005	0.011	-10000	0	-10000	0	0
TRIM24	0.012	0.022	0.26	3	-10000	0	3
T-DHT/AR/TIP60	-0.02	0.062	-10000	0	-0.17	25	25
TMPRSS2	-0.15	0.38	0.39	1	-0.97	69	70
RXRG	-0.071	0.13	0.27	1	-0.29	106	107
mol:9cRA	0	0.001	-10000	0	-10000	0	0
RXRA	0.009	0.015	-10000	0	-0.29	1	1
RXRB	0.01	0.001	-10000	0	-10000	0	0
CARM1	0.011	0.003	-10000	0	-10000	0	0
NR2C2	0.01	0.02	0.27	1	-0.29	1	2
KLK2	0.01	0.11	0.32	35	-0.26	5	40
AR	-0.069	0.11	-10000	0	-0.21	147	147
SENP1	0.01	0.001	-10000	0	-10000	0	0
HSP90AA1	0.01	0	-10000	0	-10000	0	0
MDM2	0.018	0.047	0.27	13	-10000	0	13
SRY	0.007	0.033	0.27	6	-10000	0	6
GATA2	0.013	0.06	0.27	13	-0.29	7	20
MYST2	0.01	0.001	-10000	0	-10000	0	0
HOXB13	-0.026	0.11	0.28	9	-0.29	56	65
T-DHT/AR/RACK1/Src	-0.011	0.067	0.18	3	-0.16	24	27
positive regulation of transcription	0.013	0.06	0.27	13	-0.29	7	20
DNAJA1	0.005	0.011	-10000	0	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.016	0.021	0.13	12	-10000	0	12
NCOA1	0.014	0.007	-10000	0	-10000	0	0
SPDEF	-0.002	0.13	0.27	34	-0.29	47	81
T-DHT/AR/TIF2	-0.017	0.063	-10000	0	-0.21	18	18
T-DHT/AR/Hsp90	-0.02	0.063	-10000	0	-0.17	25	25
GSK3B	0.009	0.005	-10000	0	-10000	0	0
NR2C1	0.009	0.004	-10000	0	-10000	0	0
mol:T-DHT	0.001	0.035	0.12	3	-0.078	26	29
SIRT1	0.01	0.001	-10000	0	-10000	0	0
ZMIZ2	0.009	0.01	-10000	0	-10000	0	0
POU2F1	-0.007	0.059	0.15	9	-0.15	27	36
T-DHT/AR/DAX-1	-0.01	0.076	0.19	17	-0.17	24	41
CREBBP	0.01	0.001	-10000	0	-10000	0	0
SMARCE1	0.01	0.006	-10000	0	-10000	0	0

×

EGFR-dependent Endothelin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HRAS	0.01	0	-10000	0	-10000	0	0
EGFR	0.008	0.057	0.27	8	-0.29	9	17
EGF/EGFR	0.005	0.067	0.14	34	-0.13	65	99
EGF/EGFR dimer/SHC/GRB2/SOS1	0.037	0.047	0.18	33	-0.13	9	42
mol:GTP	0	0	-10000	0	-10000	0	0
EDNRA	-0.033	0.1	-10000	0	-0.29	59	59
response to oxidative stress	0	0	-10000	0	-10000	0	0
EGF	0.025	0.062	0.27	25	-10000	0	25
EGF/EGFR dimer/SHC	0.029	0.053	0.18	33	-0.16	9	42
mol:GDP	0.034	0.044	0.16	33	-0.13	9	42
mol:Ca2+	0	0	-10000	0	-10000	0	0
EDN1	0.011	0.038	0.27	5	-0.29	3	8
GRB2/SOS1	0.015	0	-10000	0	-10000	0	0
HRAS/GTP	0.022	0.031	0.19	1	-0.12	9	10
SHC1	0.011	0.013	0.27	1	-10000	0	1
HRAS/GDP	0.031	0.037	0.25	1	-0.12	9	10
FRAP1	0.011	0.028	0.14	1	-0.12	9	10
EGF/EGFR dimer	0.024	0.058	0.19	33	-0.19	9	42
SOS1	0.01	0	-10000	0	-10000	0	0
GRB2	0.01	0	-10000	0	-10000	0	0
ETA receptor/Endothelin-1	-0.014	0.079	0.19	5	-0.2	61	66

×

Effects of Botulinum toxin

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
STX1A	0.006	0.015	0.16	4	-10000	0	4
UniProt:P19321	0	0	-10000	0	-10000	0	0
RIMS1/UNC13B	0.005	0.038	0.19	1	-0.19	14	15
STXBP1	-0.002	0.058	-10000	0	-0.29	16	16
ACh/CHRNA1	0.039	0.079	0.21	71	-0.067	26	97
RAB3GAP2/RIMS1/UNC13B	0.012	0.033	0.18	1	-0.16	14	15
mol:Ca2+	0	0	-10000	0	-10000	0	0
UniProt:P30996	0	0	-10000	0	-10000	0	0
UniProt:Q60393	0	0	-10000	0	-10000	0	0
CST086	0	0	-10000	0	-10000	0	0
RIMS1	-0.003	0.055	0.27	1	-0.29	14	15
mol:ACh	-0.001	0.026	0.062	12	-0.091	27	39
RAB3GAP2	0.01	0	-10000	0	-10000	0	0
STX1A/SNAP25/VAMP2	0.002	0.049	0.23	1	-0.14	28	29
UniProt:P10844	0	0	-10000	0	-10000	0	0
muscle contraction	0.039	0.079	0.21	71	-0.066	26	97
UNC13B	0.01	0	-10000	0	-10000	0	0
CHRNA1	0.054	0.098	0.27	71	-10000	0	71
UniProt:P10845	0	0	-10000	0	-10000	0	0
ACh/Synaptotagmin 1	0.006	0.048	0.22	8	-0.12	27	35
SNAP25	-0.008	0.057	0.11	12	-0.21	27	39
VAMP2	0.003	0	-10000	0	-10000	0	0
SYT1	-0.01	0.091	0.27	8	-0.29	34	42
UniProt:Q00496	0	0	-10000	0	-10000	0	0
STXIA/STXBP1	0.005	0.035	0.12	4	-0.16	16	20
STX1A/SNAP25 fragment 1/VAMP2	0.002	0.049	0.23	1	-0.14	28	29

×

Hedgehog signaling events mediated by Gli proteins

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.01	0.001	-10000	0	-10000	0	0
HDAC2	0.01	0.001	-10000	0	-10000	0	0
GNB1/GNG2	0.01	0.045	-10000	0	-0.16	26	26
forebrain development	-0.058	0.19	-10000	0	-0.46	60	60
GNAO1	-0.083	0.14	-10000	0	-0.29	129	129
SMO/beta Arrestin2	0.008	0.047	-10000	0	-0.19	21	21
SMO	-0.003	0.066	-10000	0	-0.29	21	21
ARRB2	0.011	0.003	-10000	0	-10000	0	0
GLI3/SPOP	0.021	0.044	-10000	0	-0.19	12	12
mol:GTP	0.001	0.002	-10000	0	-10000	0	0
GSK3B	0.01	0	-10000	0	-10000	0	0
GNAI2	0.011	0.002	-10000	0	-10000	0	0
SIN3/HDAC complex	0.024	0.002	-10000	0	-10000	0	0
GNAI1	0.009	0.026	-10000	0	-0.29	3	3
XPO1	0.014	0.007	-10000	0	-10000	0	0
GLI1/Su(fu)	-0.034	0.16	-10000	0	-0.49	29	29
SAP30	0.01	0.001	-10000	0	-10000	0	0
mol:GDP	-0.003	0.066	-10000	0	-0.29	21	21
MIM/GLI2A	0.033	0.052	0.16	62	-10000	0	62
IFT88	0.01	0	-10000	0	-10000	0	0
GNAI3	0.011	0.002	-10000	0	-10000	0	0
GLI2	-0.004	0.053	-10000	0	-10000	0	0
GLI3	0.016	0.046	-10000	0	-0.2	12	12
CSNK1D	0.01	0	-10000	0	-10000	0	0
CSNK1E	0.01	0	-10000	0	-10000	0	0
SAP18	0.01	0.001	-10000	0	-10000	0	0
embryonic digit morphogenesis	0.01	0	-10000	0	-10000	0	0
GNG2	0.006	0.036	-10000	0	-0.29	6	6
Gi family/GTP	-0.081	0.14	-10000	0	-0.24	157	157
SIN3B	0.01	0.001	-10000	0	-10000	0	0
SIN3A	0.01	0.001	-10000	0	-10000	0	0
GLI3/Su(fu)	0.022	0.03	-10000	0	-10000	0	0
GLI2/Su(fu)	0.004	0.059	-10000	0	-0.2	15	15
FOXA2	0.042	0.12	0.33	52	-10000	0	52
neural tube patterning	-0.058	0.19	-10000	0	-0.46	60	60
SPOP	0.01	0	-10000	0	-10000	0	0
Su(fu)/PIAS1	0.014	0.029	-10000	0	-10000	0	0
GNB1	0.01	0	-10000	0	-10000	0	0
CSNK1G2	0.01	0	-10000	0	-10000	0	0
CSNK1G3	0.01	0	-10000	0	-10000	0	0
MTSS1	0.033	0.052	0.16	62	-10000	0	62
embryonic limb morphogenesis	-0.058	0.19	-10000	0	-0.46	60	60
SUFU	0.009	0.031	-10000	0	-10000	0	0
LGALS3	0.009	0.015	-10000	0	-0.29	1	1
catabolic process	0.015	0.056	-10000	0	-0.26	6	6
GLI3A/CBP	-0.027	0.1	-10000	0	-0.28	61	61
KIF3A	0.01	0	-10000	0	-10000	0	0
GLI1	-0.059	0.2	-10000	0	-0.48	60	60
RAB23	0.009	0.015	-10000	0	-0.29	1	1
CSNK1A1	0.01	0	-10000	0	-10000	0	0
IFT172	0.01	0	-10000	0	-10000	0	0
RBBP7	0.01	0.001	-10000	0	-10000	0	0
Su(fu)/Galectin3	0.014	0.029	-10000	0	-10000	0	0
GNAZ	-0.054	0.12	-10000	0	-0.29	89	89
RBBP4	0.01	0.001	-10000	0	-10000	0	0
CSNK1G1	0.01	0	-10000	0	-10000	0	0
PIAS1	0.01	0	-10000	0	-10000	0	0
PRKACA	0.01	0	-10000	0	-10000	0	0
GLI2/SPOP	0.002	0.051	-10000	0	-10000	0	0
STK36	0.014	0.007	-10000	0	-10000	0	0
Gi family/GNB1/GNG2/GDP	-0.077	0.14	-10000	0	-0.23	154	154
PTCH1	-0.05	0.18	-10000	0	-0.57	26	26
MIM/GLI1	-0.03	0.21	0.3	34	-0.46	56	90
CREBBP	-0.027	0.1	-10000	0	-0.28	61	61
Su(fu)/SIN3/HDAC complex	0.018	0.01	-10000	0	-10000	0	0

×

Ephrin B reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EFNB2	0.011	0.018	0.27	2	-10000	0	2
EPHB2	0.028	0.065	0.27	28	-10000	0	28
EFNB1	0.004	0.033	-10000	0	-0.19	11	11
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.024	0.061	0.16	31	-0.2	6	37
Ephrin B2/EPHB1-2	0.021	0.06	0.17	32	-0.14	27	59
neuron projection morphogenesis	0.013	0.052	-10000	0	-0.12	37	37
Ephrin B1/EPHB1-2/Tiam1	0.022	0.066	0.18	31	-0.14	37	68
DNM1	0.002	0.048	-10000	0	-0.29	11	11
cell-cell signaling	0	0.001	-10000	0	-10000	0	0
MAP2K4	-0.002	0.069	-10000	0	-0.49	8	8
YES1	-0.007	0.1	-10000	0	-0.72	8	8
Ephrin B1/EPHB1-2/NCK2	0.023	0.065	0.18	32	-0.14	36	68
PI3K	0.007	0.071	-10000	0	-0.49	8	8
mol:GDP	0.02	0.065	0.17	31	-0.14	37	68
ITGA2B	0.029	0.069	0.27	31	-10000	0	31
endothelial cell proliferation	0.014	0.011	0.17	2	-10000	0	2
FYN	-0.008	0.1	-10000	0	-0.74	8	8
MAP3K7	-0.004	0.073	-10000	0	-0.52	8	8
FGR	-0.006	0.1	-10000	0	-0.72	8	8
TIAM1	0.008	0.025	-10000	0	-0.29	3	3
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
RGS3	0.01	0	-10000	0	-10000	0	0
cell adhesion	0.001	0.082	-10000	0	-0.46	8	8
LYN	-0.007	0.1	-10000	0	-0.72	8	8
Ephrin B1/EPHB1-2/Src Family Kinases	-0.009	0.093	-10000	0	-0.66	8	8
Ephrin B1/EPHB1-2	-0.006	0.079	-10000	0	-0.56	8	8
SRC	-0.005	0.1	-10000	0	-0.71	8	8
ITGB3	-0.024	0.094	-10000	0	-0.29	46	46
EPHB1	-0.008	0.08	0.27	4	-0.29	28	32
EPHB4	0.01	0	-10000	0	-10000	0	0
RAC1	0.01	0	-10000	0	-10000	0	0
Ephrin B2/EPHB4	0.014	0.011	0.17	2	-10000	0	2
alphaIIb/beta3 Integrin	0.004	0.08	0.19	26	-0.19	41	67
BLK	-0.018	0.11	-10000	0	-0.72	8	8
HCK	-0.01	0.1	-10000	0	-0.72	8	8
regulation of stress fiber formation	-0.022	0.064	0.14	36	-0.17	32	68
MAPK8	-0.001	0.071	-10000	0	-0.5	8	8
Ephrin B1/EPHB1-2/RGS3	0.023	0.065	0.18	32	-0.14	36	68
endothelial cell migration	-0.001	0.06	-10000	0	-0.42	8	8
NCK2	0.01	0	-10000	0	-10000	0	0
PTPN13	0.009	0.021	-10000	0	-0.42	1	1
regulation of focal adhesion formation	-0.022	0.064	0.14	36	-0.17	32	68
chemotaxis	-0.022	0.064	0.14	36	-0.17	32	68
PIK3CA	0.01	0	-10000	0	-10000	0	0
Rac1/GTP	0.019	0.057	-10000	0	-0.16	12	12
angiogenesis	-0.006	0.079	-10000	0	-0.56	8	8
LCK	-0.007	0.1	-10000	0	-0.71	8	8

×

IL27-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.011	0.002	-10000	0	-10000	0	0
CD4-positive alpha-beta T cell lineage commitment	0	0.001	-10000	0	-10000	0	0
cytokine production during immune response	-0.041	0.12	0.36	1	-0.31	19	20
IL27/IL27R/JAK1	0.065	0.14	0.48	19	-10000	0	19
TBX21	0.05	0.16	0.36	49	-0.4	8	57
IL12B	0.021	0.052	0.29	14	-10000	0	14
IL12A	0.011	0.022	0.16	8	-10000	0	8
IL6ST	-0.017	0.099	-10000	0	-0.3	45	45
IL27RA/JAK1	0.03	0.045	-10000	0	-10000	0	0
IL27	0.03	0.066	0.29	23	-10000	0	23
TYK2	0.021	0.02	-10000	0	-10000	0	0
T-helper cell lineage commitment	-0.087	0.1	-10000	0	-10000	0	0
T-helper 2 cell differentiation	-0.041	0.12	0.36	1	-0.31	19	20
T cell proliferation during immune response	-0.041	0.12	0.36	1	-0.31	19	20
MAPKKK cascade	0.041	0.12	0.31	19	-0.36	1	20
STAT3	0.01	0	-10000	0	-10000	0	0
STAT2	0.01	0	-10000	0	-10000	0	0
STAT1	0.014	0.027	0.28	4	-10000	0	4
IL12RB1	0.018	0.075	0.28	20	-0.29	10	30
positive regulation of tyrosine phosphorylation of STAT protein	0	0	-10000	0	-10000	0	0
IL12RB2	0.074	0.18	0.39	70	-0.35	8	78
IL27/IL27R/JAK2/TYK2	0.041	0.12	0.31	18	-0.37	1	19
positive regulation of T cell mediated cytotoxicity	0.041	0.12	0.31	19	-0.36	1	20
STAT1 (dimer)	0.067	0.2	0.51	47	-0.41	3	50
JAK2	0.017	0.021	-10000	0	-0.29	1	1
JAK1	0.012	0.006	-10000	0	-10000	0	0
STAT2 (dimer)	0.039	0.11	0.31	11	-0.35	1	12
T cell proliferation	0.02	0.11	0.3	14	-0.31	15	29
IL12/IL12R/TYK2/JAK2	0.07	0.11	0.41	15	-10000	0	15
IL17A	-0.086	0.1	-10000	0	-10000	0	0
mast cell activation	-0.041	0.12	0.36	1	-0.31	19	20
IFNG	0.029	0.056	0.14	77	-0.065	1	78
T cell differentiation	0	0.005	0.012	37	-0.014	7	44
STAT3 (dimer)	0.039	0.11	0.31	11	-0.35	1	12
STAT5A (dimer)	0.039	0.11	0.31	11	-0.35	1	12
STAT4 (dimer)	0.036	0.11	0.31	11	-0.31	6	17
STAT4	-0.005	0.064	-10000	0	-0.29	20	20
T cell activation	-0.006	0.011	-10000	0	-0.12	4	4
IL27R/JAK2/TYK2	0.034	0.098	0.33	1	-10000	0	1
GATA3	-0.081	0.29	-10000	0	-1.2	27	27
IL18	0.003	0.024	-10000	0	-0.19	6	6
positive regulation of mast cell cytokine production	0.039	0.11	0.3	11	-0.34	1	12
IL27/EBI3	0.038	0.067	0.24	30	-0.2	4	34
IL27RA	0.025	0.046	0.34	1	-10000	0	1
IL6	-0.12	0.15	-10000	0	-0.29	184	184
STAT5A	0.009	0.015	-10000	0	-0.29	1	1
monocyte differentiation	0.001	0.003	-10000	0	-10000	0	0
IL2	-0.017	0.035	-10000	0	-0.31	1	1
IL1B	0.002	0.053	0.16	15	-0.19	20	35
EBI3	0.019	0.048	0.28	7	-0.29	4	11
TNF	0.014	0.034	0.16	21	-10000	0	21

×

FoxO family signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G6PC	0.043	0.077	0.34	23	-10000	0	23
PLK1	0.23	0.24	0.59	92	-10000	0	92
CDKN1B	0.18	0.13	0.37	93	-10000	0	93
FOXO3	0.21	0.21	0.53	93	-0.39	1	94
KAT2B	0.044	0.042	0.13	1	-0.28	1	2
FOXO1/SIRT1	0.018	0.04	0.2	14	-10000	0	14
CAT	0.19	0.19	0.48	92	-10000	0	92
CTNNB1	0.01	0	-10000	0	-10000	0	0
AKT1	0.048	0.04	0.14	9	-10000	0	9
FOXO1	0.04	0.059	0.26	24	-10000	0	24
MAPK10	0.026	0.017	0.13	1	-10000	0	1
mol:GTP	0.001	0	-10000	0	-10000	0	0
FOXO4	0.054	0.044	-10000	0	-10000	0	0
response to oxidative stress	0.039	0.04	0.1	95	-10000	0	95
FOXO3A/SIRT1	0.17	0.16	0.43	87	-10000	0	87
XPO1	0.01	0	-10000	0	-10000	0	0
EP300	0.014	0.01	-10000	0	-10000	0	0
BCL2L11	0.058	0.059	-10000	0	-10000	0	0
FOXO1/SKP2	0.042	0.051	0.21	31	-10000	0	31
mol:GDP	0.039	0.04	0.1	95	-10000	0	95
RAN	0.011	0	-10000	0	-10000	0	0
GADD45A	0.14	0.11	-10000	0	-10000	0	0
YWHAQ	0.01	0	-10000	0	-10000	0	0
FOXO1/14-3-3 family	0.043	0.027	-10000	0	-10000	0	0
MST1	0.058	0.067	0.29	22	-10000	0	22
CSNK1D	0.01	0	-10000	0	-10000	0	0
CSNK1E	0.01	0	-10000	0	-10000	0	0
FOXO4/14-3-3 family	0.033	0.034	-10000	0	-10000	0	0
YWHAB	0.01	0	-10000	0	-10000	0	0
MAPK8	0.03	0.016	0.13	1	-10000	0	1
MAPK9	0.03	0.016	0.13	1	-10000	0	1
YWHAG	0.01	0	-10000	0	-10000	0	0
YWHAE	0.009	0.015	-10000	0	-0.29	1	1
YWHAZ	0.01	0	-10000	0	-10000	0	0
SIRT1	0.006	0.02	0.13	3	-10000	0	3
SOD2	0.18	0.13	0.5	5	-10000	0	5
RBL2	0.17	0.16	0.46	7	-10000	0	7
RAL/GDP	0.042	0.028	0.24	1	-10000	0	1
CHUK	0.044	0.039	-10000	0	-10000	0	0
Ran/GTP	0.009	0	-10000	0	-10000	0	0
CSNK1G2	0.01	0	-10000	0	-10000	0	0
RAL/GTP	0.043	0.027	0.23	1	-10000	0	1
CSNK1G1	0.01	0	-10000	0	-10000	0	0
FASLG	0.003	0.29	0.46	5	-1.2	21	26
SKP2	0.016	0.038	0.27	9	-10000	0	9
USP7	0.011	0	-10000	0	-10000	0	0
IKBKB	0.044	0.039	-10000	0	-10000	0	0
CCNB1	0.23	0.24	0.59	93	-10000	0	93
FOXO1-3a-4/beta catenin	0.16	0.12	0.35	80	-10000	0	80
proteasomal ubiquitin-dependent protein catabolic process	0.042	0.051	0.21	31	-10000	0	31
CSNK1A1	0.01	0	-10000	0	-10000	0	0
SGK1	0.036	0.064	0.13	5	-0.29	10	15
CSNK1G3	0.01	0	-10000	0	-10000	0	0
Ran/GTP/Exportin 1	0.016	0	-10000	0	-10000	0	0
ZFAND5	0.054	0.04	-10000	0	-10000	0	0
SFN	0.027	0.076	0.27	32	-0.29	4	36
CDK2	0.013	0.016	-10000	0	-10000	0	0
FOXO3A/14-3-3	0.082	0.067	0.24	17	-10000	0	17
CREBBP	0.013	0.016	-10000	0	-10000	0	0
FBXO32	0.19	0.2	0.48	92	-0.74	1	93
BCL6	0.17	0.16	0.4	78	-10000	0	78
RALB	0.01	0	-10000	0	-10000	0	0
RALA	0.011	0.013	0.27	1	-10000	0	1
YWHAH	0.01	0	-10000	0	-10000	0	0

×

Cellular roles of Anthrax toxin

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ANTXR1	0.007	0.029	-10000	0	-0.29	4	4
ANTXR2	-0.008	0.071	-10000	0	-0.29	25	25
negative regulation of myeloid dendritic cell antigen processing and presentation	-0.003	0.01	-10000	0	-0.041	28	28
monocyte activation	0	0.081	-10000	0	-0.36	17	17
MAP2K2	0.006	0.006	-10000	0	-10000	0	0
MAP2K1	0	0.01	-10000	0	-0.036	28	28
MAP2K7	0	0.01	-10000	0	-0.036	28	28
MAP2K6	0	0.013	0.078	1	-0.041	28	29
CYAA	-0.006	0.036	-10000	0	-0.14	28	28
MAP2K4	0	0.01	-10000	0	-0.036	28	28
IL1B	-0.005	0.039	0.075	14	-0.12	32	46
Channel	0.002	0.041	-10000	0	-0.15	28	28
NLRP1	0	0.013	-10000	0	-0.041	28	28
CALM1	0.01	0	-10000	0	-10000	0	0
negative regulation of phagocytosis	0.003	0.012	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
regulation of endothelial cell proliferation	0.003	0.01	0.041	28	-10000	0	28
MAPK3	0	0.01	-10000	0	-0.036	28	28
MAPK1	0	0.01	-10000	0	-0.036	28	28
PGR	-0.007	0.037	-10000	0	-0.13	28	28
PA/Cellular Receptors	0.001	0.045	-10000	0	-0.16	28	28
apoptosis	-0.003	0.01	-10000	0	-0.041	28	28
LOC728358	0	0	-10000	0	-10000	0	0
Lethal toxin (unfolded)	0.002	0.04	-10000	0	-0.14	28	28
macrophage activation	0.002	0.009	-10000	0	-10000	0	0
TNF	0.023	0.057	0.27	21	-10000	0	21
VCAM1	0	0.081	-10000	0	-0.36	17	17
platelet activation	0.003	0.012	-10000	0	-10000	0	0
MAPKKK cascade	-0.001	0.012	0.07	2	-10000	0	2
IL18	-0.003	0.029	-10000	0	-0.12	17	17
negative regulation of macrophage activation	-0.003	0.01	-10000	0	-0.041	28	28
LEF	-0.003	0.011	-10000	0	-0.041	28	28
CASP1	-0.001	0.017	-10000	0	-0.051	28	28
mol:cAMP	0.003	0.012	-10000	0	-10000	0	0
necrosis	-0.003	0.01	-10000	0	-0.041	28	28
intracellular pH reduction	0	0	-10000	0	-10000	0	0
PAGA	0	0	-10000	0	-10000	0	0
Edema toxin (unfolded)	0.002	0.038	-10000	0	-0.14	28	28
mol:Epigallocatechin-3-gallate (EGCG)	0	0	-10000	0	-10000	0	0

×

Insulin Pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CBL/APS/CAP	-0.047	0.073	-10000	0	-0.12	193	193
TC10/GTP	-0.042	0.068	-10000	0	-0.12	189	189
Insulin Receptor/Insulin/IRS1/Shp2	0.016	0.025	-10000	0	-0.14	10	10
HRAS	0.01	0	-10000	0	-10000	0	0
APS homodimer	0.013	0.028	0.27	5	-10000	0	5
GRB14	0.045	0.089	0.27	56	-10000	0	56
FOXO3	-0.009	0.1	-10000	0	-0.51	16	16
AKT1	0.02	0.028	-10000	0	-0.1	9	9
INSR	0.011	0	-10000	0	-10000	0	0
Insulin Receptor/Insulin	0.021	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
GRB10	0.006	0.033	-10000	0	-0.29	5	5
SORBS1	-0.13	0.15	-10000	0	-0.29	189	189
CRK	0.01	0	-10000	0	-10000	0	0
PTPN1	0.01	0	-10000	0	-10000	0	0
CAV1	0.006	0.032	-10000	0	-0.18	10	10
CBL/APS/CAP/Crk-II/C3G	-0.041	0.081	0.17	5	-0.13	189	194
Insulin Receptor/Insulin/IRS1/NCK2	0.016	0.025	-10000	0	-0.14	10	10
mol:GDP	0	0	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	0.013	0.023	-10000	0	-0.12	11	11
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B	0.013	0.023	-10000	0	-10000	0	0
RPS6KB1	0.019	0.027	-10000	0	-0.097	9	9
PARD6A	0.009	0.015	-10000	0	-0.29	1	1
CBL	0.01	0	-10000	0	-10000	0	0
tumor necrosis factor-mediated signaling pathway	0	0	-10000	0	-10000	0	0
DOK1	0.009	0.012	0.24	1	-10000	0	1
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
Insulin Receptor/Insuli/IRS1/GRB2/Shc	0.013	0.019	-10000	0	-10000	0	0
HRAS/GTP	-0.004	0.021	-10000	0	-0.1	17	17
Insulin Receptor	0.011	0	-10000	0	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC	0.022	0.025	0.17	1	-0.13	10	11
PRKCI	0.014	0.021	-10000	0	-0.38	1	1
Insulin Receptor/Insulin/GRB14/PDK1	0.007	0.019	-10000	0	-0.11	9	9
SHC1	0.011	0.013	0.27	1	-10000	0	1
negative regulation of MAPKKK cascade	0.02	0.008	-10000	0	-10000	0	0
PI3K	0.017	0.023	-10000	0	-0.12	11	11
NCK2	0.01	0	-10000	0	-10000	0	0
RHOQ	0.01	0	-10000	0	-10000	0	0
mol:H2O2	0	0	-10000	0	-10000	0	0
HRAS/GDP	0.007	0	-10000	0	-10000	0	0
AKT2	0.02	0.028	-10000	0	-0.1	9	9
PRKCZ	0.011	0.041	-10000	0	-0.39	4	4
SH2B2	0.013	0.028	0.27	5	-10000	0	5
SHC/SHIP	0.011	0.029	0.17	1	-0.12	17	18
F2RL2	0.007	0.073	0.27	13	-0.29	15	28
TRIP10	0.009	0.015	-10000	0	-0.29	1	1
Insulin Receptor/Insulin/Shc	0.014	0.008	0.17	1	-10000	0	1
TC10/GTP/CIP4/Exocyst	0.013	0.008	-10000	0	-0.16	1	1
Insulin Receptor/Insulin/SHC/GRB2/Sos1	0.025	0.007	0.17	1	-10000	0	1
RAPGEF1	0.01	0	-10000	0	-10000	0	0
RASA1	0.01	0	-10000	0	-10000	0	0
NCK1	0.01	0	-10000	0	-10000	0	0
CBL/APS/CAP/Crk-II	-0.048	0.085	0.18	5	-0.14	189	194
TC10/GDP	0.007	0	-10000	0	-10000	0	0
Insulin Receptor/Insulin/SHC/GRB10	0.019	0.02	0.17	1	-0.14	5	6
INPP5D	0.007	0.022	-10000	0	-0.13	10	10
SOS1	0.01	0	-10000	0	-10000	0	0
SGK1	-0.023	0.15	-10000	0	-0.75	16	16
mol:cAMP	0	0	-10000	0	-10000	0	0
PTPN11	0.01	0	-10000	0	-10000	0	0
IRS1	0.003	0.046	-10000	0	-0.29	10	10
p62DOK/RasGAP	0.02	0.008	-10000	0	-10000	0	0
INS	0.001	0	-10000	0	-10000	0	0
mol:PI-3-4-P2	0.007	0.022	-10000	0	-0.13	10	10
GRB2	0.01	0	-10000	0	-10000	0	0
EIF4EBP1	0.023	0.033	0.17	3	-0.097	9	12
PTPRA	0.011	0	-10000	0	-10000	0	0
PIK3CA	0.01	0	-10000	0	-10000	0	0
TC10/GTP/CIP4	0.013	0.008	-10000	0	-0.16	1	1
PDPK1	0.01	0	-10000	0	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos	0.011	0.028	-10000	0	-0.16	10	10
Insulin Receptor/Insulin/IRS1	0.01	0.025	-10000	0	-0.14	10	10
Insulin Receptor/Insulin/IRS3	0.009	0	-10000	0	-10000	0	0
Par3/Par6	0.022	0.04	0.16	13	-0.13	17	30

×

Nectin adhesion 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.003	0.046	-10000	0	-0.29	10	10
alphaV beta3 Integrin	-0.009	0.067	-10000	0	-0.2	46	46
PTK2	-0.013	0.094	-10000	0	-0.32	30	30
positive regulation of JNK cascade	-0.021	0.07	-10000	0	-0.27	29	29
CDC42/GDP	-0.001	0.1	-10000	0	-0.36	29	29
Rac1/GDP	-0.001	0.1	-10000	0	-0.36	29	29
RAP1B	0.01	0	-10000	0	-10000	0	0
RAP1A	0.01	0	-10000	0	-10000	0	0
CTNNB1	0.01	0	-10000	0	-10000	0	0
CDC42/GTP	-0.004	0.092	-10000	0	-0.33	29	29
nectin-3/I-afadin	0.001	0.055	0.19	2	-0.19	29	31
RAPGEF1	-0.01	0.11	-10000	0	-0.39	29	29
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	-0.014	0.12	-10000	0	-0.44	29	29
PDGFB-D/PDGFRB	0.003	0.046	-10000	0	-0.29	10	10
TLN1	-0.001	0.04	-10000	0	-0.12	35	35
Rap1/GTP	-0.022	0.074	-10000	0	-0.29	29	29
IQGAP1	0.01	0	-10000	0	-10000	0	0
Rap1/GTP/I-afadin	0.019	0	-10000	0	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin	0.001	0.055	0.19	2	-0.19	29	31
PVR	0.01	0	-10000	0	-10000	0	0
Necl-5(dimer)	0.01	0	-10000	0	-10000	0	0
mol:GDP	-0.009	0.12	-10000	0	-0.43	29	29
MLLT4	0.01	0	-10000	0	-10000	0	0
PIK3CA	0.01	0	-10000	0	-10000	0	0
PI3K	0.015	0.049	0.17	2	-0.13	39	41
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin	0.014	0.01	-10000	0	-0.19	1	1
positive regulation of lamellipodium assembly	-0.023	0.075	-10000	0	-0.28	31	31
PVRL1	0.009	0.015	-10000	0	-0.29	1	1
PVRL3	-0.01	0.079	0.27	2	-0.29	29	31
PVRL2	0.01	0	-10000	0	-10000	0	0
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
CDH1	0	0.054	-10000	0	-0.29	14	14
CLDN1	0.003	0.07	0.27	8	-0.29	17	25
JAM-A/CLDN1	0.01	0.057	0.18	8	-0.14	44	52
SRC	-0.017	0.13	-10000	0	-0.48	29	29
ITGB3	-0.024	0.094	-10000	0	-0.29	46	46
nectin-1(dimer)/I-afadin/I-afadin	0.014	0.01	-10000	0	-0.19	1	1
FARP2	-0.009	0.12	-10000	0	-0.42	29	29
RAC1	0.01	0	-10000	0	-10000	0	0
CTNNA1	0.01	0	-10000	0	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer)	0.009	0.047	0.18	2	-0.16	29	31
nectin-1/I-afadin	0.014	0.01	-10000	0	-0.19	1	1
nectin-2/I-afadin	0.015	0	-10000	0	-10000	0	0
RAC1/GTP/IQGAP1/filamentous actin	0.014	0	-10000	0	-10000	0	0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin	0.008	0.048	0.18	2	-0.16	30	32
CDC42/GTP/IQGAP1/filamentous actin	0.014	0	-10000	0	-10000	0	0
F11R	0.009	0.015	-10000	0	-0.29	1	1
positive regulation of filopodium formation	-0.021	0.07	-10000	0	-0.27	29	29
alphaV/beta3 Integrin/Talin	-0.005	0.063	-10000	0	-0.23	15	15
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.015	0	-10000	0	-10000	0	0
nectin-2(dimer)/I-afadin/I-afadin	0.015	0	-10000	0	-10000	0	0
PIP5K1C	-0.003	0.043	-10000	0	-0.13	35	35
VAV2	-0.011	0.12	-10000	0	-0.43	31	31
RAP1/GDP	-0.001	0.095	-10000	0	-0.34	29	29
ITGAV	0.009	0.015	-10000	0	-0.29	1	1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin	0.009	0.047	0.18	2	-0.16	29	31
nectin-3(dimer)/I-afadin/I-afadin	0.001	0.055	0.19	2	-0.19	29	31
Rac1/GTP	-0.005	0.097	-10000	0	-0.34	31	31
PTPRM	-0.005	0.048	-10000	0	-0.15	35	35
E-cadherin/beta catenin/alpha catenin	0.024	0.029	-10000	0	-0.13	14	14
adherens junction assembly	0	0	-10000	0	-10000	0	0
CDC42	0.01	0	-10000	0	-10000	0	0

×

EPHB forward signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Ephrin A5/EPHB2	0.019	0.053	0.17	29	-0.16	14	43
cell-cell adhesion	0.01	0.031	0.18	2	-10000	0	2
Ephrin B/EPHB2/RasGAP	0.037	0.051	0.17	35	-0.13	12	47
ITSN1	0.01	0	-10000	0	-10000	0	0
PIK3CA	0.01	0	-10000	0	-10000	0	0
SHC1	0.011	0.013	0.27	1	-10000	0	1
Ephrin B1/EPHB3	0.019	0.033	0.17	16	-0.16	2	18
Ephrin B1/EPHB1	0.003	0.046	0.17	4	-0.16	28	32
HRAS/GDP	0.004	0.043	0.19	1	-0.15	13	14
Ephrin B/EPHB1/GRB7	0.02	0.064	0.18	23	-0.13	44	67
Endophilin/SYNJ1	0.014	0.031	0.15	1	-0.12	12	13
KRAS	0.011	0.013	0.27	1	-10000	0	1
Ephrin B/EPHB1/Src	0.018	0.055	0.18	10	-0.13	38	48
endothelial cell migration	0.022	0.012	0.15	2	-0.13	1	3
GRB2	0.01	0	-10000	0	-10000	0	0
GRB7	0.014	0.062	0.27	14	-0.29	7	21
PAK1	0.016	0.033	0.15	1	-0.12	14	15
HRAS	0.01	0	-10000	0	-10000	0	0
RRAS	0.014	0.033	0.15	1	-0.13	12	13
DNM1	0.002	0.048	-10000	0	-0.29	11	11
cell-cell signaling	0	0	-10000	0	-10000	0	0
CRK	0.002	0.043	0.15	1	-0.12	38	39
lamellipodium assembly	-0.01	0.031	-10000	0	-0.18	2	2
Ephrin B/EPHB1/Src/p52 SHC/GRB2	0.003	0.056	0.18	1	-0.16	38	39
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
EPHB2	0.028	0.065	0.27	28	-10000	0	28
EPHB3	0.019	0.055	0.27	16	-0.29	2	18
EPHB1	-0.008	0.08	0.27	4	-0.29	28	32
EPHB4	0.01	0	-10000	0	-10000	0	0
mol:GDP	0.005	0.043	0.14	2	-0.17	12	14
Ephrin B/EPHB2	0.031	0.05	0.17	35	-0.13	12	47
Ephrin B/EPHB3	0.026	0.044	0.16	23	-0.13	13	36
JNK cascade	0.009	0.043	-10000	0	-0.13	28	28
Ephrin B/EPHB1	0.012	0.054	0.18	10	-0.13	38	48
RAP1/GDP	0.014	0.042	-10000	0	-0.15	11	11
EFNB2	0.011	0.018	0.27	2	-10000	0	2
EFNB3	0.005	0.066	0.27	8	-0.29	14	22
EFNB1	0.01	0	-10000	0	-10000	0	0
Ephrin B2/EPHB1-2	0.021	0.06	0.18	32	-0.14	27	59
RAP1B	0.01	0	-10000	0	-10000	0	0
RAP1A	0.01	0	-10000	0	-10000	0	0
CDC42/GTP	0.02	0.054	0.22	2	-0.16	11	13
Rap1/GTP	0.001	0.035	-10000	0	-0.18	2	2
axon guidance	0.019	0.052	0.17	29	-0.16	14	43
MAPK3	0.004	0.05	0.15	1	-0.15	28	29
MAPK1	0.004	0.05	0.15	1	-0.15	28	29
Rac1/GDP	0.01	0.042	0.14	1	-0.16	12	13
actin cytoskeleton reorganization	-0.009	0.027	-10000	0	-0.12	11	11
CDC42/GDP	0.01	0.042	0.14	1	-0.16	12	13
PI3K	0.024	0.012	0.16	2	-0.13	1	3
EFNA5	0	0.056	0.27	1	-0.29	14	15
Ephrin B2/EPHB4	0.014	0.011	0.17	2	-10000	0	2
Ephrin B/EPHB2/Intersectin/N-WASP	0.019	0.042	0.19	1	-0.16	12	13
CDC42	0.01	0	-10000	0	-10000	0	0
RAS family/GTP	-0.01	0.031	-10000	0	-0.18	2	2
PTK2	0.006	0.009	-10000	0	-10000	0	0
MAP4K4	0.009	0.043	-10000	0	-0.13	28	28
SRC	0.01	0	-10000	0	-10000	0	0
KALRN	0.011	0.033	0.27	4	-0.29	2	6
Intersectin/N-WASP	0.015	0	-10000	0	-10000	0	0
neuron projection morphogenesis	0.017	0.046	0.16	2	-0.19	3	5
MAP2K1	0.004	0.053	0.16	1	-0.16	28	29
WASL	0.01	0	-10000	0	-10000	0	0
Ephrin B1/EPHB1-2/NCK1	0.026	0.06	0.18	32	-0.14	28	60
cell migration	0.001	0.062	0.18	1	-0.18	38	39
NRAS	0.01	0	-10000	0	-10000	0	0
SYNJ1	0.015	0.031	0.15	1	-0.12	12	13
PXN	0.01	0	-10000	0	-10000	0	0
TF	0.023	0.041	0.12	41	-0.11	10	51
HRAS/GTP	0.018	0.049	0.2	2	-0.2	2	4
Ephrin B1/EPHB1-2	0.02	0.059	0.17	32	-0.14	28	60
cell adhesion mediated by integrin	-0.003	0.027	0.13	13	-10000	0	13
RAC1	0.01	0	-10000	0	-10000	0	0
mol:GTP	0.022	0.056	0.18	9	-0.12	37	46
RAC1-CDC42/GTP	-0.01	0.031	-10000	0	-0.18	2	2
RASA1	0.01	0	-10000	0	-10000	0	0
RAC1-CDC42/GDP	0.014	0.042	-10000	0	-0.18	3	3
ruffle organization	0.011	0.042	0.14	2	-0.19	2	4
NCK1	0.01	0	-10000	0	-10000	0	0
receptor internalization	0.013	0.031	0.14	1	-0.12	12	13
Ephrin B/EPHB2/KALRN	0.038	0.053	0.17	39	-0.13	14	53
ROCK1	0.013	0.019	-10000	0	-0.14	2	2
RAS family/GDP	-0.008	0.026	-10000	0	-0.13	11	11
Rac1/GTP	-0.01	0.033	-10000	0	-0.19	2	2
Ephrin B/EPHB1/Src/Paxillin	0.002	0.059	0.2	1	-0.17	38	39

×

Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization	0.008	0.033	-10000	0	-0.17	14	14
epithelial cell differentiation	0.016	0.027	-10000	0	-0.13	14	14
CYFIP2	0.002	0.048	-10000	0	-0.29	11	11
ENAH	0.013	0.023	-10000	0	-0.16	1	1
EGFR	0.008	0.057	0.27	8	-0.29	9	17
EPHA2	0.006	0.033	-10000	0	-0.29	5	5
MYO6	0.008	0.024	-10000	0	-0.12	14	14
CTNNB1	0.01	0	-10000	0	-10000	0	0
ABI1/Sra1/Nap1	0.016	0.029	-10000	0	-0.16	11	11
AQP5	0.021	0.04	-10000	0	-10000	0	0
CTNND1	0.01	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.008	0.024	-10000	0	-0.12	14	14
regulation of calcium-dependent cell-cell adhesion	0.016	0.04	0.17	19	-0.12	12	31
EGF	0.025	0.062	0.27	25	-10000	0	25
NCKAP1	0.01	0	-10000	0	-10000	0	0
AQP3	-0.06	0.16	-10000	0	-0.37	80	80
cortical microtubule organization	0.016	0.027	-10000	0	-0.13	14	14
GO:0000145	0.005	0.022	-10000	0	-0.11	14	14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.018	0.028	-10000	0	-0.13	14	14
MLLT4	0.01	0	-10000	0	-10000	0	0
ARF6/GDP	-0.005	0.023	-10000	0	-0.21	1	1
ARF6	0.01	0	-10000	0	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	0.027	0.029	0.18	9	-0.14	5	14
mol:Ca2+	0	0	-10000	0	-10000	0	0
VASP	0.01	0.025	-10000	0	-0.18	1	1
PVRL2	0.01	0	-10000	0	-10000	0	0
ZYX	0.008	0.024	-10000	0	-0.12	14	14
ARF6/GTP	0.029	0.026	0.16	9	-0.12	5	14
CDH1	0	0.054	-10000	0	-0.29	14	14
EGFR/EGFR/EGF/EGF	0.018	0.04	-10000	0	-0.12	20	20
RhoA/GDP	0.017	0.026	-10000	0	-0.12	14	14
actin cytoskeleton organization	0.008	0.024	-10000	0	-0.12	14	14
IGF-1R heterotetramer	0.008	0.025	-10000	0	-0.29	3	3
GIT1	0.01	0	-10000	0	-10000	0	0
IGF1R	0.008	0.025	-10000	0	-0.29	3	3
IGF1	-0.12	0.15	-10000	0	-0.29	182	182
DIAPH1	0.009	0.088	-10000	0	-0.52	11	11
Wnt receptor signaling pathway	-0.016	0.027	0.13	14	-10000	0	14
RHOA	0.01	0	-10000	0	-10000	0	0
RhoA/GTP	-0.005	0.023	-10000	0	-0.21	1	1
CTNNA1	0.01	0	-10000	0	-10000	0	0
VCL	0.008	0.025	-10000	0	-0.12	14	14
EFNA1	0.016	0.038	0.27	9	-10000	0	9
LPP	0.008	0.023	-10000	0	-0.11	14	14
Ephrin A1/EPHA2	0.015	0.032	-10000	0	-0.12	18	18
SEC6/SEC8	-0.004	0.019	-10000	0	-0.11	14	14
MGAT3	0.016	0.041	0.17	19	-0.12	12	31
HGF/MET	-0.013	0.06	-10000	0	-0.12	99	99
HGF	-0.049	0.13	0.27	7	-0.29	87	94
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN	0.008	0.033	-10000	0	-0.17	14	14
actin cable formation	0.019	0.025	-10000	0	-0.13	1	1
KIAA1543	0.005	0.039	-10000	0	-0.19	14	14
KIFC3	0.008	0.024	-10000	0	-0.12	14	14
NCK1	0.01	0	-10000	0	-10000	0	0
EXOC3	0.01	0	-10000	0	-10000	0	0
ACTN1	0.008	0.024	-10000	0	-0.12	14	14
NCK1/GIT1	0.015	0	-10000	0	-10000	0	0
mol:GDP	0.016	0.027	-10000	0	-0.13	14	14
EXOC4	0.01	0	-10000	0	-10000	0	0
STX4	0.008	0.024	-10000	0	-0.12	14	14
PIP5K1C	0.008	0.024	-10000	0	-0.12	14	14
LIMA1	0.01	0	-10000	0	-10000	0	0
ABI1	0.01	0	-10000	0	-10000	0	0
ROCK1	0.013	0.025	-10000	0	-0.19	1	1
adherens junction assembly	0.008	0.048	-10000	0	-0.27	9	9
IGF-1R heterotetramer/IGF1	-0.046	0.07	-10000	0	-0.12	194	194
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.015	0	-10000	0	-10000	0	0
MET	0.011	0.018	0.27	2	-10000	0	2
PLEKHA7	0.008	0.027	-10000	0	-0.13	14	14
mol:GTP	0.026	0.028	0.17	9	-0.14	5	14
establishment of epithelial cell apical/basal polarity	0.013	0.022	-10000	0	-10000	0	0
cortical actin cytoskeleton stabilization	0.008	0.033	-10000	0	-0.17	14	14
regulation of cell-cell adhesion	0.008	0.024	-10000	0	-0.12	14	14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton	0.008	0.033	-10000	0	-0.17	14	14

×

Caspase cascade in apoptosis

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
TOP1	0.008	0.081	0.17	9	-0.27	22	31
ACTA1	-0.001	0.1	0.15	20	-0.32	26	46
NUMA1	0.008	0.081	0.17	9	-0.27	22	31
SPTAN1	-0.001	0.097	0.18	9	-0.32	24	33
LIMK1	-0.001	0.097	0.18	9	-0.32	24	33
BIRC3	-0.004	0.071	0.27	3	-0.29	22	25
BIRC2	0.011	0.018	0.27	2	-10000	0	2
BAX	0.01	0	-10000	0	-10000	0	0
CASP10	0.012	0.054	0.14	34	-0.16	18	52
CRMA	0	0	-10000	0	-10000	0	0
XIAP	0.01	0.02	0.27	1	-0.29	1	2
PTK2	0.008	0.081	0.17	9	-0.27	22	31
DIABLO	0.01	0	-10000	0	-10000	0	0
apoptotic nuclear changes	0	0.096	0.18	9	-0.32	24	33
response to UV	0	0	-10000	0	-10000	0	0
CRADD	0.01	0	-10000	0	-10000	0	0
GSN	-0.003	0.1	0.18	9	-0.33	26	35
MADD	0.01	0	-10000	0	-10000	0	0
TFAP2A	0.029	0.062	0.32	3	-0.46	2	5
BID	0.003	0.057	0.14	11	-0.16	31	42
MAP3K1	0.006	0.038	-10000	0	-0.18	7	7
TRADD	0.01	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0.015	0	-10000	0	-10000	0	0
mol:Activated DNA	0	0	-10000	0	-10000	0	0
ARHGDIB	-0.001	0.097	0.18	9	-0.32	24	33
CASP9	0.01	0	-10000	0	-10000	0	0
DNA repair	-0.008	0.034	0.12	4	-0.13	12	16
neuron apoptosis	0.011	0.051	-10000	0	-0.7	2	2
mol:NAD	0	0	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	0.005	0.094	0.18	9	-0.31	24	33
APAF1	0.01	0	-10000	0	-10000	0	0
CASP6	0.015	0.053	-10000	0	-10000	0	0
TRAF2	0.01	0	-10000	0	-10000	0	0
ICAD/CAD	0.001	0.094	0.18	9	-0.31	24	33
CASP7	0.008	0.057	0.23	22	-0.15	4	26
KRT18	0.015	0.04	-10000	0	-0.47	1	1
apoptosis	0.007	0.085	0.17	10	-0.29	22	32
DFFA	-0.001	0.097	0.18	9	-0.32	24	33
DFFB	-0.001	0.097	0.18	9	-0.32	24	33
PARP1	0.008	0.034	0.13	12	-0.12	4	16
actin filament polymerization	0	0.092	0.3	24	-0.18	9	33
TNF	0.023	0.057	0.27	21	-10000	0	21
CYCS	0.005	0.037	0.11	9	-0.15	10	19
SATB1	0.011	0.055	-10000	0	-10000	0	0
SLK	-0.001	0.097	0.18	9	-0.32	24	33
p15 BID/BAX	0.008	0.05	0.12	9	-0.14	31	40
CASP2	0.016	0.036	0.15	1	-10000	0	1
JNK cascade	-0.006	0.038	0.17	7	-10000	0	7
CASP3	-0.002	0.1	0.16	20	-0.34	24	44
LMNB2	0.021	0.033	-10000	0	-10000	0	0
RIPK1	0.01	0	-10000	0	-10000	0	0
CASP4	0.011	0.013	0.27	1	-10000	0	1
Mammalian IAPs/DIABLO	0.019	0.045	0.21	5	-0.14	22	27
negative regulation of DNA binding	0.029	0.062	0.32	3	-0.46	2	5
stress fiber formation	0	0.096	0.15	20	-0.32	24	44
GZMB	0.015	0.075	0.2	34	-0.19	21	55
CASP1	0.003	0.036	0.14	1	-0.23	9	10
LMNB1	0.024	0.036	-10000	0	-10000	0	0
APP	0.011	0.052	-10000	0	-0.7	2	2
TNFRSF1A	0.01	0	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
CASP8	0.005	0	-10000	0	-10000	0	0
VIM	0.006	0.084	0.17	10	-0.28	22	32
LMNA	0.02	0.033	-10000	0	-10000	0	0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD	0.016	0.039	0.16	1	-10000	0	1
LRDD	0.01	0	-10000	0	-10000	0	0
SREBF1	0	0.097	0.15	20	-0.32	24	44
APAF-1/Caspase 9	0.007	0.03	0.24	1	-10000	0	1
nuclear fragmentation during apoptosis	0.008	0.08	0.17	9	-0.27	22	31
CFL2	0	0.094	0.18	9	-0.31	24	33
GAS2	-0.01	0.11	0.18	9	-0.33	25	34
positive regulation of apoptosis	0.025	0.033	-10000	0	-10000	0	0
PRF1	0.005	0.073	0.27	11	-0.29	16	27

×

IL2 signaling events mediated by PI3K

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.02	0.054	0.34	1	-0.46	1	2
UGCG	-0.022	0.15	-10000	0	-0.61	23	23
AKT1/mTOR/p70S6K/Hsp90/TERT	0.058	0.1	0.26	2	-0.26	22	24
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucosylceramide	-0.022	0.14	-10000	0	-0.6	23	23
mol:DAG	0.005	0.004	-10000	0	-10000	0	0
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.002	0.12	-10000	0	-0.38	34	34
FRAP1	0.011	0.15	0.26	1	-0.44	34	35
FOXO3	0.013	0.12	0.26	1	-0.4	26	27
AKT1	0.011	0.13	0.27	1	-0.42	27	28
GAB2	0.009	0.015	-10000	0	-0.29	1	1
SMPD1	0.012	0.023	-10000	0	-10000	0	0
SGMS1	0.012	0.023	-10000	0	-10000	0	0
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
mol:GDP	0.007	0.01	-10000	0	-0.16	1	1
CALM1	0.01	0	-10000	0	-10000	0	0
cell proliferation	-0.007	0.12	-10000	0	-0.31	39	39
EIF3A	0.01	0	-10000	0	-10000	0	0
PI3K	0.016	0.013	-10000	0	-0.19	1	1
RPS6KB1	0.031	0.05	-10000	0	-10000	0	0
mol:sphingomyelin	0.005	0.004	-10000	0	-10000	0	0
natural killer cell activation	0	0.003	-10000	0	-10000	0	0
JAK3	0.012	0.019	0.27	2	-10000	0	2
PIK3R1	0.01	0.015	-10000	0	-0.29	1	1
JAK1	0.011	0.004	-10000	0	-10000	0	0
NFKB1	0.01	0	-10000	0	-10000	0	0
MYC	-0.006	0.2	-10000	0	-0.72	26	26
MYB	0.081	0.13	0.42	30	-1	1	31
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.017	0.096	0.25	2	-0.3	23	25
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.038	0.044	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	0.018	0.094	0.25	2	-0.29	23	25
Rac1/GDP	0.013	0.01	-10000	0	-0.14	1	1
T cell proliferation	0.018	0.088	0.24	2	-0.28	23	25
SHC1	0.01	0.013	0.27	1	-10000	0	1
RAC1	0.01	0	-10000	0	-10000	0	0
positive regulation of cyclin-dependent protein kinase activity	0.017	0.038	0.11	56	-0.082	1	57
PRKCZ	0.017	0.091	0.24	2	-0.28	23	25
NF kappa B1 p50/RelA	0.018	0.13	-10000	0	-0.38	34	34
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K	0.019	0.057	0.25	2	-0.35	7	9
HSP90AA1	0.01	0	-10000	0	-10000	0	0
RELA	0.01	0	-10000	0	-10000	0	0
IL2RA	0.009	0.084	0.27	19	-0.29	18	37
IL2RB	0.008	0.038	0.27	2	-0.29	5	7
TERT	0.12	0.13	0.27	176	-10000	0	176
E2F1	0.079	0.11	0.32	56	-0.28	1	57
SOS1	0.01	0.003	-10000	0	-10000	0	0
RPS6	0.01	0	-10000	0	-10000	0	0
mol:cAMP	-0.008	0.018	0.034	1	-0.054	56	57
PTPN11	0.01	0.004	-10000	0	-10000	0	0
IL2RG	0.009	0.061	0.27	9	-0.29	10	19
actin cytoskeleton organization	0.018	0.088	0.24	2	-0.28	23	25
GRB2	0.01	0.003	-10000	0	-10000	0	0
IL2	0.004	0.006	-10000	0	-10000	0	0
PIK3CA	0.011	0.004	-10000	0	-10000	0	0
Rac1/GTP	0.023	0.015	-10000	0	-0.13	1	1
LCK	0.009	0.035	0.27	2	-0.29	4	6
BCL2	0.001	0.18	-10000	0	-0.73	20	20

×

IL2 signaling events mediated by STAT5

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
GAB2	0.009	0.015	-10000	0	-0.29	1	1
ELF1	0.009	0.069	0.16	19	-0.28	18	37
CCNA2	0.077	0.11	0.27	106	-10000	0	106
PIK3CA	0.01	0	-10000	0	-10000	0	0
JAK3	0.011	0.018	0.27	2	-10000	0	2
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
JAK1	0.01	0	-10000	0	-10000	0	0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.024	0.073	0.3	1	-0.46	4	5
SHC1	0.011	0.013	0.27	1	-10000	0	1
SP1	-0.008	0.079	-10000	0	-0.28	32	32
IL2RA	0.004	0.13	0.31	19	-0.54	18	37
IL2RB	0.008	0.038	0.27	2	-0.29	5	7
SOS1	0.01	0	-10000	0	-10000	0	0
IL2RG	0.009	0.06	0.27	9	-0.29	10	19
G1/S transition of mitotic cell cycle	-0.008	0.2	-10000	0	-0.58	37	37
PTPN11	0.01	0	-10000	0	-10000	0	0
CCND2	-0.03	0.15	-10000	0	-0.54	32	32
LCK	0.009	0.035	0.27	2	-0.29	4	6
GRB2	0.01	0	-10000	0	-10000	0	0
IL2	0.003	0.004	-10000	0	-10000	0	0
CDK6	0.002	0.048	-10000	0	-0.29	11	11
CCND3	0.026	0.065	-10000	0	-0.47	2	2

×

BARD1 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BARD1/CSTF1	0.01	0.032	-10000	0	-0.19	10	10
ATM	0.01	0	-10000	0	-10000	0	0
UBE2D3	0.01	0	-10000	0	-10000	0	0
PRKDC	0.01	0	-10000	0	-10000	0	0
ATR	0.01	0	-10000	0	-10000	0	0
UBE2L3	0.01	0	-10000	0	-10000	0	0
FANCD2	0.013	0.013	0.14	4	-10000	0	4
protein ubiquitination	0.043	0.054	0.16	64	-0.13	9	73
XRCC5	0.01	0	-10000	0	-10000	0	0
XRCC6	0.01	0	-10000	0	-10000	0	0
M/R/N Complex	0.02	0	-10000	0	-10000	0	0
MRE11A	0.01	0	-10000	0	-10000	0	0
DNA-PK	0.02	0	-10000	0	-10000	0	0
FA complex/FANCD2/Ubiquitin	0.025	0.025	-10000	0	-10000	0	0
FANCF	0.01	0.02	0.27	1	-0.29	1	2
BRCA1	0.011	0.013	0.27	1	-10000	0	1
CCNE1	0.051	0.094	0.27	64	-10000	0	64
CDK2/Cyclin E1	0.043	0.064	0.19	64	-10000	0	64
FANCG	0.01	0	-10000	0	-10000	0	0
BRCA1/BACH1/BARD1	0.01	0.033	0.19	1	-0.19	10	11
FANCE	0.011	0.013	0.27	1	-10000	0	1
FANCC	0.011	0.013	0.27	1	-10000	0	1
NBN	0.01	0	-10000	0	-10000	0	0
FANCA	0.027	0.064	0.27	27	-10000	0	27
DNA repair	0.053	0.044	0.22	2	-10000	0	2
BRCA1/BARD1/ubiquitin	0.01	0.033	0.19	1	-0.19	10	11
BARD1/DNA-PK	0.022	0.025	-10000	0	-0.14	10	10
FANCL	0.011	0.013	0.27	1	-10000	0	1
mRNA polyadenylation	-0.01	0.032	0.19	10	-10000	0	10
BRCA1/BARD1/CTIP/M/R/N Complex	0.013	0.028	-10000	0	-0.16	10	10
BRCA1/BACH1/BARD1/TopBP1	0.016	0.028	0.18	1	-0.16	10	11
BRCA1/BARD1/P53	0.022	0.026	0.18	1	-0.14	10	11
BARD1/CSTF1/BRCA1	0.016	0.028	0.18	1	-0.16	10	11
BRCA1/BACH1	0.011	0.013	0.27	1	-10000	0	1
BARD1	0.002	0.046	-10000	0	-0.29	10	10
PCNA	0.011	0.013	0.27	1	-10000	0	1
BRCA1/BARD1/UbcH5C	0.016	0.028	0.18	1	-0.16	10	11
BRCA1/BARD1/UbcH7	0.016	0.028	0.18	1	-0.16	10	11
BRCA1/BARD1/RAD51/PCNA	0.075	0.078	0.18	144	-0.14	7	151
BARD1/DNA-PK/P53	0.026	0.024	-10000	0	-0.13	10	10
BRCA1/BARD1/Ubiquitin	0.01	0.033	0.19	1	-0.19	10	11
BRCA1/BARD1/CTIP	0.016	0.026	0.18	1	-0.14	10	11
FA complex	0.024	0.026	0.18	2	-10000	0	2
BARD1/EWS	0.01	0.032	-10000	0	-0.19	10	10
RBBP8	0.009	0	-10000	0	-10000	0	0
TP53	0.01	0	-10000	0	-10000	0	0
TOPBP1	0.01	0	-10000	0	-10000	0	0
G1/S transition of mitotic cell cycle	-0.021	0.026	0.14	10	-0.17	1	11
BRCA1/BARD1	0.048	0.058	0.17	64	-0.13	9	73
CSTF1	0.01	0	-10000	0	-10000	0	0
BARD1/EWS-Fli1	0.002	0.031	-10000	0	-0.19	10	10
CDK2	0.01	0	-10000	0	-10000	0	0
UniProt:Q9BZD1	0	0	-10000	0	-10000	0	0
RAD51	0.1	0.12	0.27	145	-10000	0	145
RAD50	0.01	0	-10000	0	-10000	0	0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme	0.01	0.033	0.19	1	-0.19	10	11
EWSR1	0.01	0	-10000	0	-10000	0	0

×

IL1-mediated signaling events

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
UBC13/UEV1A	0.011	0.004	-10000	0	-10000	0	0
PRKCZ	0.008	0.025	-10000	0	-0.29	3	3
MAP3K7IP2	0	0	-10000	0	-10000	0	0
ERC1	0.01	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4	0.012	0.035	-10000	0	-0.18	2	2
IRAK/TOLLIP	0.016	0.001	-10000	0	-10000	0	0
IKBKB	0.01	0	-10000	0	-10000	0	0
IKBKG	0.01	0	-10000	0	-10000	0	0
IL1 alpha/IL1R2	0.026	0.11	0.21	71	-0.19	43	114
IL1A	0.008	0.12	0.27	40	-0.29	37	77
IL1B	0.002	0.059	0.16	15	-0.19	27	42
IRAK/TRAF6/p62/Atypical PKCs	0.028	0.012	-10000	0	-10000	0	0
IL1R2	0.029	0.086	0.27	38	-0.29	7	45
IL1R1	0.009	0.015	-10000	0	-0.29	1	1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	0.016	0.039	-10000	0	-0.23	2	2
TOLLIP	0.01	0	-10000	0	-10000	0	0
TICAM2	0.009	0.015	-10000	0	-0.29	1	1
MAP3K3	0.01	0	-10000	0	-10000	0	0
TAK1/TAB1/TAB2	0.007	0	-10000	0	-10000	0	0
IKK complex/ELKS	0.026	0.005	-10000	0	-10000	0	0
JUN	0.011	0.005	-10000	0	-10000	0	0
MAP3K7	0.01	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/PI3K	0.025	0.052	0.19	11	-0.24	2	13
IL1 alpha/IL1R1/IL1RAP/MYD88	0.029	0.075	0.18	49	-0.14	37	86
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4	0.033	0.071	0.18	49	-0.13	37	86
IL1 beta fragment/IL1R1/IL1RAP	0.016	0.056	0.2	11	-0.15	28	39
NFKB1	0.01	0	-10000	0	-10000	0	0
MAPK8	0.011	0.005	0.1	1	-10000	0	1
IRAK1	0.01	0.001	-10000	0	-10000	0	0
IL1RN/IL1R1	0.017	0.039	0.19	11	-0.24	4	15
IRAK4	0.01	0	-10000	0	-10000	0	0
PRKCI	0.01	0	-10000	0	-10000	0	0
TRAF6	0.01	0	-10000	0	-10000	0	0
PI3K	0.014	0.01	-10000	0	-0.19	1	1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	0.014	0.04	0.16	2	-0.25	2	4
CHUK	0.01	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s	0.016	0.056	0.2	11	-0.15	28	39
IL1 beta/IL1R2	0.018	0.076	0.19	36	-0.17	31	67
IRAK/TRAF6/TAK1/TAB1/TAB2	0.018	0.001	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	0.014	0.04	0.16	2	-0.22	2	4
IRAK3	0.001	0.05	-10000	0	-0.29	12	12
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4	0.025	0.052	0.19	11	-0.24	2	13
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	0.012	0.065	0.19	2	-0.17	37	39
IL1 alpha/IL1R1/IL1RAP	0.024	0.08	0.19	49	-0.16	37	86
RELA	0.01	0	-10000	0	-10000	0	0
MAP3K7IP1	0	0	-10000	0	-10000	0	0
SQSTM1	0.01	0	-10000	0	-10000	0	0
MYD88	0.01	0	-10000	0	-10000	0	0
IRAK/TRAF6/MEKK3	0.021	0.001	-10000	0	-10000	0	0
IL1RAP	0.017	0.042	0.27	11	-10000	0	11
UBE2N	0.01	0	-10000	0	-10000	0	0
IRAK/TRAF6	0.008	0.034	-10000	0	-0.21	2	2
CASP1	0.003	0.044	-10000	0	-0.29	9	9
IL1RN/IL1R2	0.031	0.072	0.2	47	-0.21	10	57
IL1 beta fragment/IL1R1/IL1RAP/MYD88	0.022	0.054	0.19	11	-0.14	28	39
TMEM189-UBE2V1	0.005	0.005	-10000	0	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	0.014	0.056	-10000	0	-0.4	1	1
PIK3CA	0.01	0	-10000	0	-10000	0	0
IL1RN	0.014	0.052	0.27	11	-0.29	4	15
TRAF6/TAK1/TAB1/TAB2	0.017	0.002	-10000	0	-10000	0	0
MAP2K6	0.012	0.008	0.16	1	-10000	0	1

×

Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.011	0.013	0.27	1	-10000	0	1
NFATC1	0.003	0.057	-10000	0	-0.24	19	19
NFATC2	-0.033	0.052	-10000	0	-0.15	46	46
NFATC3	0.002	0.025	-10000	0	-0.28	3	3
YWHAE	0.009	0.015	-10000	0	-0.29	1	1
Calcineurin A alpha-beta B1/CABIN1	-0.041	0.1	-10000	0	-0.32	29	29
Exportin 1/Ran/NUP214	0.017	0.003	-10000	0	-10000	0	0
mol:DAG	-0.002	0.002	-10000	0	-10000	0	0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV	-0.043	0.091	-10000	0	-0.28	35	35
BCL2/BAX	0.007	0.04	-10000	0	-0.19	16	16
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.003	0.009	-10000	0	-10000	0	0
CaM/Ca2+	-0.003	0.009	-10000	0	-10000	0	0
BAX	0.01	0	-10000	0	-10000	0	0
MAPK14	0.007	0.003	-10000	0	-10000	0	0
BAD	0.01	0	-10000	0	-10000	0	0
CABIN1/MEF2D	-0.038	0.097	-10000	0	-0.3	29	29
Calcineurin A alpha-beta B1/BCL2	-0.002	0.058	-10000	0	-0.29	16	16
FKBP8	0.01	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	0.037	0.095	0.3	29	-10000	0	29
KPNB1	0.01	0	-10000	0	-10000	0	0
KPNA2	0.012	0.026	0.27	4	-10000	0	4
XPO1	0.009	0.001	-10000	0	-10000	0	0
SFN	0.027	0.076	0.27	32	-0.29	4	36
MAP3K8	0.005	0.026	-10000	0	-0.29	3	3
NFAT4/CK1 alpha	0.002	0.017	-10000	0	-0.13	3	3
MEF2D/NFAT1/Cbp/p300	-0.1	0.12	-10000	0	-0.2	230	230
CABIN1	-0.041	0.1	-10000	0	-0.32	29	29
CALM1	0.007	0.003	-10000	0	-10000	0	0
RAN	0.009	0.001	-10000	0	-10000	0	0
MAP3K1	0.01	0	-10000	0	-10000	0	0
CAMK4	0.003	0.048	0.27	1	-0.29	10	11
mol:Ca2+	-0.006	0.006	-10000	0	-10000	0	0
MAPK3	0.01	0	-10000	0	-10000	0	0
YWHAH	0.01	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/AKAP79/PKA	0.014	0.017	0.19	4	-10000	0	4
YWHAB	0.01	0	-10000	0	-10000	0	0
MAPK8	0.004	0.025	-10000	0	-0.29	3	3
MAPK9	0.01	0	-10000	0	-10000	0	0
YWHAG	0.01	0	-10000	0	-10000	0	0
FKBP1A	0.01	0	-10000	0	-10000	0	0
NFAT1-c-4/YWHAQ	-0.01	0.059	-10000	0	-0.24	19	19
PRKCH	0.01	0	-10000	0	-10000	0	0
CABIN1/Cbp/p300	-0.002	0.016	-10000	0	-10000	0	0
CASP3	0.007	0.003	-10000	0	-10000	0	0
PIM1	0.01	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0.001	0.005	-10000	0	-10000	0	0
apoptosis	0.01	0.006	-10000	0	-10000	0	0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1	0.019	0.023	-10000	0	-10000	0	0
PRKCB	-0.076	0.14	-10000	0	-0.29	118	118
PRKCE	0.01	0	-10000	0	-10000	0	0
JNK2/NFAT4	0.009	0.023	-10000	0	-0.25	3	3
BAD/BCL-XL	0.015	0.009	0.19	1	-10000	0	1
PRKCD	0.01	0	-10000	0	-10000	0	0
NUP214	0.009	0.001	-10000	0	-10000	0	0
PRKCZ	0.004	0.026	-10000	0	-0.29	3	3
PRKCA	0.006	0.033	-10000	0	-0.29	5	5
PRKCG	0.014	0.048	0.27	14	-10000	0	14
PRKCQ	-0.013	0.088	0.27	4	-0.29	35	39
FKBP38/BCL2	0.007	0.04	-10000	0	-0.19	16	16
EP300	-0.001	0.01	-10000	0	-10000	0	0
PRKCB1	0	0	-10000	0	-10000	0	0
CSNK2A1	0.01	0	-10000	0	-10000	0	0
NFATc/JNK1	0.004	0.056	-10000	0	-0.23	19	19
CaM/Ca2+/FKBP38	0.002	0.01	-10000	0	-10000	0	0
FKBP12/FK506	0.007	0	-10000	0	-10000	0	0
CSNK1A1	-0.003	0.01	-10000	0	-10000	0	0
CaM/Ca2+/CAMK IV	-0.002	0.029	0.15	1	-0.16	10	11
NFATc/ERK1	0.009	0.055	-10000	0	-0.23	19	19
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV	-0.037	0.091	-10000	0	-0.27	35	35
NR4A1	-0.18	0.17	-10000	0	-0.32	230	230
GSK3B	0.006	0.003	-10000	0	-10000	0	0
positive T cell selection	0.002	0.025	-10000	0	-0.27	3	3
NFAT1/CK1 alpha	-0.028	0.043	-10000	0	-0.12	46	46
RCH1/ KPNB1	0.017	0.017	0.19	4	-10000	0	4
YWHAQ	0.01	0	-10000	0	-10000	0	0
PRKACA	0.007	0.003	-10000	0	-10000	0	0
AKAP5	0.012	0.026	0.27	4	-10000	0	4
MEF2D	-0.001	0.01	-10000	0	-10000	0	0
mol:FK506	0	0	-10000	0	-10000	0	0
YWHAZ	0.01	0	-10000	0	-10000	0	0
NFATc/p38 alpha	0.005	0.055	-10000	0	-0.23	19	19
CREBBP	-0.001	0.01	-10000	0	-10000	0	0
BCL2	-0.002	0.058	-10000	0	-0.29	16	16

×

Regulation of nuclear SMAD2/3 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
EP300	0.008	0.009	-10000	0	-10000	0	0
HSPA8	0.01	0.002	-10000	0	-10000	0	0
SMAD3/SMAD4/ER alpha	-0.014	0.087	0.24	1	-0.19	68	69
AKT1	0.011	0.017	-10000	0	-10000	0	0
GSC	0.033	0.071	0.37	3	-10000	0	3
NKX2-5	0.044	0.098	0.27	65	-10000	0	65
muscle cell differentiation	-0.001	0.052	0.25	11	-10000	0	11
SMAD2-3/SMAD4/SP1	0.025	0.076	-10000	0	-0.24	15	15
SMAD4	0.001	0.037	-10000	0	-0.13	15	15
CBFB	0.01	0	-10000	0	-10000	0	0
SAP18	0.01	0.001	-10000	0	-10000	0	0
Cbp/p300/MSG1	0.021	0.026	0.18	8	-10000	0	8
SMAD3/SMAD4/VDR	0.02	0.038	-10000	0	-0.2	2	2
MYC	-0.007	0.065	-10000	0	-0.29	18	18
CDKN2B	0	0.22	-10000	0	-1.2	11	11
AP1	-0.034	0.11	-10000	0	-0.33	26	26
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1	0.027	0.017	-10000	0	-10000	0	0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1	0.024	0.07	0.2	3	-0.31	11	14
SP3	0.011	0	-10000	0	-10000	0	0
CREB1	0.01	0	-10000	0	-10000	0	0
FOXH1	0.07	0.11	0.27	92	-10000	0	92
SMAD3/SMAD4/GR	0.003	0.056	-10000	0	-0.2	15	15
GATA3	-0.011	0.079	0.27	2	-0.29	26	28
SKI/SIN3/HDAC complex/NCoR1	0.022	0.005	-10000	0	-10000	0	0
MEF2C/TIF2	0.034	0.079	0.26	1	-0.3	13	14
endothelial cell migration	0	0.14	1.2	5	-0.33	5	10
MAX	0.008	0.01	-10000	0	-10000	0	0
RBBP7	0.01	0.001	-10000	0	-10000	0	0
RBBP4	0.01	0.001	-10000	0	-10000	0	0
RUNX2	0.012	0.032	0.27	5	-0.29	1	6
RUNX3	0	0.054	-10000	0	-0.29	14	14
RUNX1	0.01	0	-10000	0	-10000	0	0
CTBP1	0.011	0.013	0.27	1	-10000	0	1
NR3C1	0	0.051	-10000	0	-0.29	12	12
VDR	0.009	0.024	0.27	1	-0.29	2	3
CDKN1A	-0.002	0.094	-10000	0	-1.1	2	2
KAT2B	0.008	0.015	-10000	0	-0.29	1	1
SMAD2/SMAD2/SMAD4/FOXH1	0.062	0.08	0.2	74	-0.17	2	76
DCP1A	0.01	0	-10000	0	-10000	0	0
SKI	0.01	0.001	-10000	0	-10000	0	0
SERPINE1	0	0.14	0.33	5	-1.2	5	10
SMAD3/SMAD4/ATF2	0.011	0.043	-10000	0	-0.15	5	5
SMAD3/SMAD4/ATF3	-0.02	0.089	-10000	0	-0.19	77	77
SAP30	0.01	0.001	-10000	0	-10000	0	0
Cbp/p300/PIAS3	0.018	0.018	0.15	1	-10000	0	1
JUN	-0.039	0.1	-10000	0	-0.33	26	26
SMAD3/SMAD4/IRF7	0.019	0.061	0.22	11	-0.18	6	17
TFE3	0.012	0.012	-10000	0	-0.16	1	1
COL1A2	-0.027	0.19	0.32	2	-0.72	27	29
mesenchymal cell differentiation	-0.013	0.046	0.14	8	-0.2	2	10
DLX1	0.035	0.079	0.27	42	-10000	0	42
TCF3	0.01	0	-10000	0	-10000	0	0
FOS	-0.008	0.073	-10000	0	-0.34	19	19
SMAD3/SMAD4/Max	0.008	0.043	-10000	0	-0.15	5	5
Cbp/p300/SNIP1	0.019	0.008	-10000	0	-10000	0	0
ZBTB17	0.007	0.017	-10000	0	-10000	0	0
LAMC1	0.009	0.038	-10000	0	-0.24	2	2
TGIF2/HDAC complex/SMAD3/SMAD4	0.011	0.043	-10000	0	-0.15	5	5
IRF7	0.018	0.052	0.27	13	-0.29	2	15
ESR1	-0.035	0.11	-10000	0	-0.29	62	62
HNF4A	0.034	0.079	0.27	41	-10000	0	41
MEF2C	0.037	0.079	0.24	2	-0.3	14	16
SMAD2-3/SMAD4	0.016	0.054	-10000	0	-0.17	10	10
Cbp/p300/Src-1	0.018	0.012	-10000	0	-10000	0	0
IGHV3OR16-13	0.004	0.012	-10000	0	-10000	0	0
TGIF2/HDAC complex	0.01	0	-10000	0	-10000	0	0
CREBBP	0.008	0.007	-10000	0	-10000	0	0
SKIL	0.011	0.013	0.27	1	-10000	0	1
HDAC1	0.01	0.001	-10000	0	-10000	0	0
HDAC2	0.01	0.001	-10000	0	-10000	0	0
SNIP1	0.01	0.002	-10000	0	-10000	0	0
GCN5L2	-0.001	0.006	-10000	0	-10000	0	0
SMAD3/SMAD4/TFE3	0.018	0.048	-10000	0	-0.16	6	6
MSG1/HSC70	0.019	0.025	0.19	8	-10000	0	8
SMAD2	0.013	0.021	-10000	0	-10000	0	0
SMAD3	0	0.034	-10000	0	-0.12	10	10
SMAD3/E2F4-5/DP1/p107/SMAD4	0.013	0.028	-10000	0	-0.17	1	1
SMAD2/SMAD2/SMAD4	0	0.021	-10000	0	-0.25	1	1
NCOR1	0.01	0.001	-10000	0	-10000	0	0
NCOA2	-0.008	0.07	-10000	0	-0.29	24	24
NCOA1	0.01	0	-10000	0	-10000	0	0
MYOD/E2A	0.007	0	-10000	0	-10000	0	0
SMAD2-3/SMAD4/SP1/MIZ-1	0.032	0.076	-10000	0	-0.23	14	14
IFNB1	0.011	0.059	0.31	9	-0.18	3	12
SMAD3/SMAD4/MEF2C	0.042	0.088	0.3	2	-0.32	14	16
CITED1	0.015	0.036	0.27	8	-10000	0	8
SMAD2-3/SMAD4/ARC105	0.021	0.051	-10000	0	-0.19	4	4
RBL1	0.011	0.018	0.27	2	-10000	0	2
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB	0.016	0.098	0.23	1	-0.5	11	12
RUNX1-3/PEBPB2	0.014	0.032	-10000	0	-0.16	14	14
SMAD7	-0.033	0.12	-10000	0	-0.37	23	23
MYC/MIZ-1	0.001	0.054	0.15	11	-0.2	18	29
SMAD3/SMAD4	-0.007	0.07	0.32	1	-0.39	6	7
IL10	-0.013	0.092	0.32	1	-0.35	21	22
PIASy/HDAC complex	0.011	0.006	-10000	0	-10000	0	0
PIAS3	0.009	0.003	-10000	0	-10000	0	0
CDK2	0.009	0.006	-10000	0	-10000	0	0
IL5	-0.008	0.065	0.31	2	-0.19	22	24
CDK4	0.009	0.015	0.27	1	-10000	0	1
PIAS4	0.011	0.006	-10000	0	-10000	0	0
ATF3	-0.043	0.11	-10000	0	-0.29	72	72
SMAD3/SMAD4/SP1	0.011	0.069	-10000	0	-0.22	20	20
FOXG1	0.038	0.091	0.27	55	-10000	0	55
FOXO3	0.012	0.021	-10000	0	-0.094	1	1
FOXO1	0.011	0.024	-10000	0	-0.2	1	1
FOXO4	0.012	0.023	0.16	1	-0.093	2	3
heart looping	0.037	0.078	0.24	2	-0.3	14	16
CEBPB	0.01	0.018	-10000	0	-0.29	1	1
SMAD3/SMAD4/DLX1	0.028	0.067	0.2	26	-0.14	8	34
MYOD1	0	0	-10000	0	-10000	0	0
SMAD3/SMAD4/HNF4	0.026	0.066	0.2	26	-0.14	7	33
SMAD3/SMAD4/GATA3	-0.001	0.078	0.21	2	-0.2	42	44
SnoN/SIN3/HDAC complex/NCoR1	0.011	0.013	0.27	1	-10000	0	1
SMAD3/SMAD4/RUNX1-3/PEBPB2	0.016	0.051	-10000	0	-0.17	15	15
SMAD3/SMAD4/SP1-3	0.022	0.063	-10000	0	-0.2	14	14
MED15	0.01	0	-10000	0	-10000	0	0
SP1	0.005	0.032	-10000	0	-10000	0	0
SIN3B	0.01	0.001	-10000	0	-10000	0	0
SIN3A	0.01	0.001	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5	0.087	0.1	0.29	32	-0.19	11	43
ITGB5	0.007	0.049	-10000	0	-0.2	10	10
TGIF/SIN3/HDAC complex/CtBP	0.021	0.004	-10000	0	-10000	0	0
SMAD3/SMAD4/AR	-0.056	0.096	-10000	0	-0.18	144	144
AR	-0.099	0.14	-10000	0	-0.29	148	148
negative regulation of cell growth	-0.007	0.066	-10000	0	-0.23	8	8
SMAD3/SMAD4/MYOD	0.006	0.041	-10000	0	-0.15	6	6
E2F5	0.01	0.023	0.27	2	-0.29	1	3
E2F4	0.01	0	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF	0.066	0.07	0.25	8	-10000	0	8
SMAD2-3/SMAD4/FOXO1-3a-4	0.017	0.073	0.2	1	-0.34	12	13
TFDP1	0.01	0	-10000	0	-10000	0	0
SMAD3/SMAD4/AP1	-0.027	0.11	-10000	0	-0.34	26	26
SMAD3/SMAD4/RUNX2	0.013	0.047	0.2	2	-0.14	8	10
TGIF2	0.01	0	-10000	0	-10000	0	0
TGIF1	0.01	0	-10000	0	-10000	0	0
ATF2	0.01	0	-10000	0	-10000	0	0

×

ErbB4 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF	0.02	0.023	-10000	0	-10000	0	0
epithelial cell differentiation	-0.003	0.059	-10000	0	-0.24	2	2
ITCH	0.01	0.014	0.27	1	-10000	0	1
WWP1	0.02	0.015	-10000	0	-10000	0	0
FYN	0.008	0.025	-10000	0	-0.29	3	3
EGFR	0.008	0.057	0.27	8	-0.29	9	17
PRL	0.008	0.035	0.27	7	-10000	0	7
neuron projection morphogenesis	0.004	0.05	-10000	0	-0.19	2	2
PTPRZ1	-0.032	0.16	0.27	42	-0.29	91	133
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC	0.011	0.06	-10000	0	-0.21	2	2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta	0.019	0.029	-10000	0	-0.22	1	1
ADAM17	0.01	0.014	0.27	1	-10000	0	1
ErbB4/ErbB4	0.019	0.028	-10000	0	-10000	0	0
ErbB4/ErbB4/neuregulin 3/neuregulin 3	0.023	0.041	0.25	1	-10000	0	1
NCOR1	0.01	0	-10000	0	-10000	0	0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn	0.001	0.061	-10000	0	-0.23	2	2
GRIN2B	0.001	0.057	-10000	0	-0.22	2	2
ErbB4/ErbB2/betacellulin	0.008	0.053	-10000	0	-0.2	2	2
STAT1	0.012	0.026	0.27	4	-10000	0	4
HBEGF	0	0.052	-10000	0	-0.29	13	13
PRLR	0.014	0.093	0.27	28	-0.29	19	47
E4ICDs/ETO2	0.02	0.023	-10000	0	-10000	0	0
axon guidance	0.009	0.074	-10000	0	-0.26	1	1
NEDD4	0.008	0.016	-10000	0	-0.29	1	1
Prolactin receptor/Prolactin receptor/Prolactin	0.016	0.068	0.19	35	-0.19	19	54
CBFA2T3	0	0.052	-10000	0	-0.29	13	13
ErbB4/ErbB2/HBEGF	0.022	0.032	-10000	0	-10000	0	0
MAPK3	0.004	0.052	-10000	0	-0.2	2	2
STAT1 (dimer)	0.022	0.029	-10000	0	-10000	0	0
MAPK1	0.004	0.052	-10000	0	-0.2	2	2
JAK2	0.009	0.015	-10000	0	-0.29	1	1
ErbB4/ErbB2/neuregulin 1 beta	0.001	0.06	-10000	0	-0.2	1	1
NRG1	-0.021	0.089	0.17	19	-0.2	73	92
NRG3	0.014	0.048	0.27	14	-10000	0	14
NRG2	-0.12	0.15	-10000	0	-0.29	172	172
NRG4	-0.019	0.088	-10000	0	-0.29	39	39
heart development	0.009	0.074	-10000	0	-0.26	1	1
neural crest cell migration	0.001	0.059	-10000	0	-0.2	1	1
ERBB2	0.014	0.029	0.16	14	-10000	0	14
WWOX/E4ICDs	0.021	0.023	-10000	0	-10000	0	0
SHC1	0.011	0.013	0.27	1	-10000	0	1
ErbB4/EGFR/neuregulin 4	0.011	0.06	-10000	0	-0.25	4	4
apoptosis	-0.026	0.036	-10000	0	-0.22	1	1
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta	0.01	0.033	-10000	0	-0.25	4	4
ErbB4/ErbB2/epiregulin	0.029	0.079	0.2	1	-0.2	2	3
ErbB4/ErbB4/betacellulin/betacellulin	0.017	0.029	-10000	0	-0.25	2	2
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2	0.031	0.06	-10000	0	-0.21	1	1
MDM2	0.02	0.029	-10000	0	-10000	0	0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta	-0.003	0.061	0.18	1	-0.18	1	2
STAT5A	0.009	0.069	-10000	0	-0.25	1	1
ErbB4/EGFR/neuregulin 1 beta	0.002	0.069	-10000	0	-0.24	4	4
DLG4	0.009	0.015	-10000	0	-0.29	1	1
GRB2/SHC	0.015	0.009	0.19	1	-10000	0	1
E4ICDs/TAB2/NCoR1	0.019	0.02	-10000	0	-10000	0	0
STAT5A (dimer)	0.004	0.067	-10000	0	-0.26	2	2
MAP3K7IP2	0	0	-10000	0	-10000	0	0
STAT5B (dimer)	0.013	0.069	-10000	0	-0.25	1	1
LRIG1	-0.018	0.087	-10000	0	-0.29	38	38
EREG	0.002	0.15	0.27	54	-0.29	57	111
BTC	-0.027	0.098	-10000	0	-0.29	50	50
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta	0.008	0.074	-10000	0	-0.27	1	1
ERBB4	0.022	0.019	-10000	0	-10000	0	0
STAT5B	0.01	0	-10000	0	-10000	0	0
YAP1	0.012	0.033	0.22	1	-0.6	1	2
GRB2	0.01	0	-10000	0	-10000	0	0
ErbB4/ErbB2/neuregulin 4	0.013	0.044	-10000	0	-0.2	1	1
glial cell differentiation	-0.018	0.02	-10000	0	-10000	0	0
WWOX	0.009	0.015	-10000	0	-0.29	1	1
cell proliferation	-0.03	0.098	-10000	0	-0.29	19	19

×

Signaling events mediated by PTP1B

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
PDGFRB	0.003	0.046	-10000	0	-0.29	10	10
Jak2/Leptin Receptor	0.028	0.074	0.24	6	-0.25	6	12
PTP1B/AKT1	0.022	0.035	-10000	0	-0.18	1	1
FYN	0.008	0.025	-10000	0	-0.29	3	3
p210 bcr-abl/PTP1B	0.019	0.038	-10000	0	-0.2	1	1
EGFR	0.01	0.058	0.27	8	-0.29	9	17
EGF/EGFR	0.027	0.057	0.19	28	-0.18	2	30
CSF1	-0.001	0.056	-10000	0	-0.29	15	15
AKT1	0.01	0	-10000	0	-10000	0	0
INSR	0.01	0	-10000	0	-10000	0	0
PTP1B/N-cadherin	0.039	0.066	0.21	38	-0.18	2	40
Insulin Receptor/Insulin	0.015	0.025	-10000	0	-10000	0	0
HCK	0.004	0.058	0.27	5	-0.29	12	17
CRK	0.01	0	-10000	0	-10000	0	0
TYK2	0.02	0.036	-10000	0	-0.19	1	1
EGF	0.025	0.062	0.27	25	-10000	0	25
YES1	0.01	0	-10000	0	-10000	0	0
CAV1	0.019	0.047	-10000	0	-0.18	4	4
TXN	0.012	0.018	0.27	2	-10000	0	2
PTP1B/IRS1/GRB2	0.025	0.042	-10000	0	-0.2	4	4
cell migration	-0.019	0.038	0.2	1	-10000	0	1
STAT3	0.01	0.001	-10000	0	-10000	0	0
PRLR	0.015	0.094	0.27	28	-0.29	19	47
ITGA2B	0.029	0.069	0.27	31	-10000	0	31
CSF1R	-0.003	0.067	0.27	2	-0.29	20	22
Prolactin Receptor/Prolactin	0.02	0.071	0.2	35	-0.19	19	54
FGR	0.008	0.021	-10000	0	-0.29	2	2
PTP1B/p130 Cas	0.023	0.036	-10000	0	-0.19	1	1
Crk/p130 Cas	0.028	0.036	-10000	0	-0.19	1	1
DOK1	0.019	0.044	-10000	0	-0.19	7	7
JAK2	0.019	0.067	0.21	4	-0.21	19	23
Jak2/Leptin Receptor/Leptin	-0.011	0.08	0.18	4	-0.2	33	37
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
PTPN1	0.019	0.038	-10000	0	-0.21	1	1
LYN	0.01	0	-10000	0	-10000	0	0
CDH2	0.033	0.084	0.27	41	-0.29	4	45
SRC	0.019	0.017	-10000	0	-10000	0	0
ITGB3	-0.023	0.095	-10000	0	-0.29	46	46
CAT1/PTP1B	0.007	0.076	-10000	0	-0.26	8	8
CAPN1	0.011	0.002	-10000	0	-10000	0	0
CSK	0.01	0	-10000	0	-10000	0	0
PI3K	0.013	0.023	-10000	0	-10000	0	0
mol:H2O2	0.001	0.002	-10000	0	-10000	0	0
STAT3 (dimer)	-0.014	0.085	0.17	3	-0.22	35	38
negative regulation of transcription	0.022	0.067	0.21	4	-0.21	19	23
FCGR2A	0.017	0.046	0.27	12	-0.29	1	13
FER	0.008	0.026	-10000	0	-0.29	3	3
alphaIIb/beta3 Integrin	0.004	0.08	0.19	26	-0.19	41	67
BLK	-0.009	0.1	0.27	16	-0.29	37	53
Insulin Receptor/Insulin/Shc	0.015	0.008	0.17	1	-10000	0	1
RHOA	0.011	0.002	-10000	0	-10000	0	0
LEPR	0.001	0.052	-10000	0	-0.28	13	13
BCAR1	0.01	0	-10000	0	-10000	0	0
p210 bcr-abl/Grb2	0.01	0	-10000	0	-10000	0	0
mol:NADPH	0.001	0.002	-10000	0	-10000	0	0
TRPV6	-0.011	0.094	0.17	3	-0.23	29	32
PRL	0.01	0.035	0.27	7	-10000	0	7
SOCS3	-0.12	0.36	-10000	0	-1.2	43	43
SPRY2	0.004	0.042	-10000	0	-0.29	8	8
Insulin Receptor/Insulin/IRS1	0.01	0.027	-10000	0	-0.16	10	10
CSF1/CSF1R	0.017	0.058	0.23	1	-0.21	11	12
Ras protein signal transduction	-0.004	0.013	-10000	0	-10000	0	0
IRS1	0.003	0.046	-10000	0	-0.29	10	10
INS	0	0.001	-10000	0	-10000	0	0
LEP	-0.009	0.1	0.27	16	-0.29	36	52
STAT5B	0.024	0.044	0.16	3	-0.17	3	6
STAT5A	0.024	0.044	0.16	2	-0.17	3	5
GRB2	0.01	0	-10000	0	-10000	0	0
PDGFB-D/PDGFRB	0.021	0.042	-10000	0	-0.17	7	7
CSN2	-0.002	0.031	-10000	0	-10000	0	0
PIK3CA	0.01	0	-10000	0	-10000	0	0
LAT	0.022	0.035	-10000	0	-0.36	1	1
YBX1	0.016	0.013	0.27	1	-10000	0	1
LCK	0.008	0.035	0.27	2	-0.29	4	6
SHC1	0.011	0.013	0.27	1	-10000	0	1
NOX4	0.03	0.067	0.27	30	-10000	0	30

×

IFN-gamma pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2	0.053	0.057	0.17	80	-0.13	1	81
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
CRKL	0.011	0.018	0.27	2	-10000	0	2
STAT1 (dimer)/Cbp/p300	0.044	0.03	0.22	4	-10000	0	4
IFN-gammaR/JAK1/JAK1/JAK2/JAK2	0.025	0.013	-10000	0	-0.16	1	1
antigen processing and presentation of peptide antigen via MHC class I	-0.007	0.04	-10000	0	-0.19	9	9
CaM/Ca2+	0.048	0.047	-10000	0	-0.12	1	1
RAP1A	0.01	0	-10000	0	-10000	0	0
STAT1 (dimer)/SHP2	0.034	0.034	0.22	4	-0.12	1	5
AKT1	0.027	0.024	-10000	0	-0.11	1	1
MAP2K1	0.026	0.026	-10000	0	-0.11	1	1
MAP3K11	0.027	0.027	-10000	0	-0.12	1	1
IFNGR1	0.012	0.003	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
CaM/Ca2+/CAMKII	-0.056	0.14	-10000	0	-0.27	127	127
Rap1/GTP	0	0.005	-10000	0	-10000	0	0
CRKL/C3G	0.016	0.012	0.19	2	-10000	0	2
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP	0.057	0.057	0.17	80	-0.13	1	81
CEBPB	0.037	0.052	0.26	2	-0.39	4	6
STAT3	0.01	0	-10000	0	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1	0.056	0.057	0.35	1	-10000	0	1
STAT1	0.029	0.033	0.23	4	-0.12	1	5
CALM1	0.01	0	-10000	0	-10000	0	0
IFN-gamma (dimer)	0.059	0.1	0.26	81	-10000	0	81
PIK3CA	0.01	0	-10000	0	-10000	0	0
STAT1 (dimer)/PIAS1	0.033	0.031	0.22	4	-10000	0	4
CEBPB/PTGES2/Cbp/p300	0.019	0.032	-10000	0	-0.26	4	4
mol:Ca2+	0.05	0.054	0.16	80	-0.12	1	81
MAPK3	0.032	0.031	-10000	0	-10000	0	0
STAT1 (dimer)	-0.004	0.056	-10000	0	-0.25	9	9
MAPK1	0.032	0.031	-10000	0	-10000	0	0
JAK2	0.012	0.003	-10000	0	-10000	0	0
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
JAK1	0.012	0.003	-10000	0	-10000	0	0
CAMK2D	0.008	0.021	-10000	0	-0.29	2	2
DAPK1	0.032	0.065	0.32	2	-0.55	4	6
SMAD7	0.009	0.033	-10000	0	-0.14	4	4
CBL/CRKL/C3G	0.036	0.027	0.2	2	-10000	0	2
PI3K	0.043	0.04	-10000	0	-0.12	1	1
IFNG	0.059	0.1	0.26	81	-10000	0	81
apoptosis	0.025	0.052	0.27	2	-0.42	4	6
CAMK2G	0.01	0	-10000	0	-10000	0	0
STAT3 (dimer)	0.01	0	-10000	0	-10000	0	0
CAMK2A	-0.085	0.14	-10000	0	-0.29	129	129
CAMK2B	0.037	0.08	0.27	43	-10000	0	43
FRAP1	0.023	0.023	-10000	0	-0.1	1	1
PRKCD	0.027	0.024	-10000	0	-0.11	1	1
RAP1B	0.01	0	-10000	0	-10000	0	0
negative regulation of cell growth	-0.007	0.04	-10000	0	-0.19	9	9
PTPN2	0.01	0	-10000	0	-10000	0	0
EP300	0.01	0	-10000	0	-10000	0	0
IRF1	0.031	0.024	0.2	1	-10000	0	1
STAT1 (dimer)/PIASy	0.032	0.031	0.22	4	-10000	0	4
SOCS1	0.008	0.016	0.32	1	-10000	0	1
mol:GDP	0.033	0.025	0.18	2	-10000	0	2
CASP1	0.007	0.041	-10000	0	-0.19	10	10
PTGES2	0.01	0	-10000	0	-10000	0	0
IRF9	0.025	0.019	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	0.032	0.031	-10000	0	-0.11	1	1
RAP1/GDP	0.016	0.012	0.14	1	-10000	0	1
CBL	0.027	0.027	-10000	0	-0.12	1	1
MAP3K1	0.028	0.028	-10000	0	-0.12	1	1
PIAS1	0.01	0	-10000	0	-10000	0	0
PIAS4	0.01	0.001	-10000	0	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class II	-0.007	0.04	-10000	0	-0.19	9	9
PTPN11	0.025	0.027	-10000	0	-0.12	1	1
CREBBP	0.01	0	-10000	0	-10000	0	0
RAPGEF1	0.01	0	-10000	0	-10000	0	0

×

Regulation of Telomerase

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Telomerase catalytic core complex	0.17	0.18	0.38	117	-0.39	3	120
RAD9A	0.014	0.031	0.27	6	-10000	0	6
AP1	-0.044	0.11	-10000	0	-0.2	130	130
IFNAR2	0.024	0.015	-10000	0	-10000	0	0
AKT1	0.01	0.059	0.12	3	-0.13	35	38
ER alpha/Oestrogen	-0.021	0.078	-10000	0	-0.19	73	73
NFX1/SIN3/HDAC complex	0.042	0.025	-10000	0	-10000	0	0
EGF	0.03	0.063	0.28	25	-10000	0	25
SMG5	0.01	0	-10000	0	-10000	0	0
SMG6	0.01	0	-10000	0	-10000	0	0
SP3/HDAC2	0.038	0.026	-10000	0	-10000	0	0
TERT/c-Abl	0.015	0.052	-10000	0	-0.36	3	3
SAP18	0.012	0.003	-10000	0	-10000	0	0
MRN complex	0.02	0	-10000	0	-10000	0	0
WT1	0.054	0.089	0.28	52	-10000	0	52
WRN	0.01	0	-10000	0	-10000	0	0
SP1	0.029	0.022	-10000	0	-10000	0	0
SP3	0.016	0.008	-10000	0	-10000	0	0
TERF2IP	0.01	0	-10000	0	-10000	0	0
Telomerase/Nucleolin	0.004	0.04	-10000	0	-0.34	3	3
Mad/Max	0.032	0.021	0.22	1	-10000	0	1
TERT	0.17	0.18	0.41	71	-0.39	3	74
CCND1	0.16	0.21	0.48	15	-0.91	7	22
MAX	0.017	0.008	-10000	0	-10000	0	0
RBBP7	0.013	0.003	-10000	0	-10000	0	0
RBBP4	0.012	0.003	-10000	0	-10000	0	0
TERF2	0.009	0	-10000	0	-10000	0	0
PTGES3	0.01	0	-10000	0	-10000	0	0
SIN3A	0.012	0.003	-10000	0	-10000	0	0
Telomerase/911	0.065	0.048	0.21	6	-10000	0	6
CDKN1B	0.045	0.044	-10000	0	-10000	0	0
RAD1	0.01	0	-10000	0	-10000	0	0
XRCC5	0.01	0	-10000	0	-10000	0	0
XRCC6	0.01	0	-10000	0	-10000	0	0
SAP30	0.013	0.003	-10000	0	-10000	0	0
TRF2/PARP2	0.014	0	-10000	0	-10000	0	0
UBE3A	0.016	0.007	-10000	0	-10000	0	0
JUN	0.003	0.058	-10000	0	-0.28	16	16
E6	0.006	0.006	-10000	0	-10000	0	0
HPV-16 E6/E6AP	0.022	0.016	-10000	0	-10000	0	0
FOS	-0.04	0.12	-10000	0	-0.29	72	72
IFN-gamma/IRF1	0.07	0.076	0.22	81	-10000	0	81
PARP2	0.01	0	-10000	0	-10000	0	0
BLM	0.018	0.044	0.27	12	-10000	0	12
Telomerase	0.043	0.058	0.2	15	-0.3	1	16
IRF1	0.019	0.008	-10000	0	-10000	0	0
ESR1	-0.039	0.11	-10000	0	-0.28	72	72
KU/TER	0.015	0	-10000	0	-10000	0	0
ATM/TRF2	0.015	0	-10000	0	-10000	0	0
ubiquitin-dependent protein catabolic process	0.044	0.024	-10000	0	-10000	0	0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex	0.044	0.024	-10000	0	-10000	0	0
HDAC1	0.012	0.003	-10000	0	-10000	0	0
HDAC2	0.026	0.019	-10000	0	-10000	0	0
ATM	0.003	0	-10000	0	-10000	0	0
SMAD3	0	0.011	-10000	0	-10000	0	0
ABL1	0.01	0	-10000	0	-10000	0	0
MXD1	0.017	0.015	0.28	1	-10000	0	1
MRE11A	0.01	0	-10000	0	-10000	0	0
HUS1	0.01	0	-10000	0	-10000	0	0
RPS6KB1	0.01	0	-10000	0	-10000	0	0
TERT/NF kappa B1/14-3-3	0.02	0.068	-10000	0	-0.37	3	3
NR2F2	-0.006	0.022	-10000	0	-0.29	1	1
MAPK3	0.018	0.014	-10000	0	-10000	0	0
MAPK1	0.018	0.014	-10000	0	-10000	0	0
TGFB1/TGF beta receptor Type II	0.003	0.008	-10000	0	-10000	0	0
NFKB1	0.01	0	-10000	0	-10000	0	0
HNRNPC	0.01	0	-10000	0	-10000	0	0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis	0.003	0	-10000	0	-10000	0	0
NBN	0.01	0	-10000	0	-10000	0	0
EGFR	0.018	0.042	0.27	8	-0.29	2	10
mol:Oestrogen	0.003	0.004	-10000	0	-10000	0	0
EGF/EGFR	0.036	0.06	0.2	33	-0.18	9	42
MYC	0.005	0.061	-10000	0	-0.28	17	17
IL2	0.022	0.022	-10000	0	-10000	0	0
KU	0.015	0	-10000	0	-10000	0	0
RAD50	0.01	0	-10000	0	-10000	0	0
HSP90AA1	0.01	0	-10000	0	-10000	0	0
TGFB1	0.003	0.008	-10000	0	-10000	0	0
TRF2/BLM	0.019	0.029	0.18	12	-10000	0	12
FRAP1	0	0	-10000	0	-10000	0	0
KU/TERT	0.14	0.14	0.34	48	-0.36	3	51
SP1/HDAC2	0.052	0.041	0.17	5	-10000	0	5
PINX1	0.01	0	-10000	0	-10000	0	0
Telomerase/EST1A	0.004	0.04	-10000	0	-0.34	3	3
Smad3/Myc	-0.003	0.035	-10000	0	-0.16	18	18
911 complex	0.023	0.019	0.18	6	-10000	0	6
IFNG	0.068	0.1	0.28	81	-10000	0	81
Telomerase/PinX1	0.004	0.04	-10000	0	-0.34	3	3
Telomerase/AKT1/mTOR/p70S6K	0.079	0.077	0.2	36	-10000	0	36
SIN3B	0.013	0.003	-10000	0	-10000	0	0
YWHAE	0.009	0.015	-10000	0	-0.29	1	1
Telomerase/EST1B	0.004	0.04	-10000	0	-0.34	3	3
response to DNA damage stimulus	0.002	0	-10000	0	-10000	0	0
MRN complex/TRF2/Rap1	0.028	0	-10000	0	-10000	0	0
TRF2/WRN	0.014	0	-10000	0	-10000	0	0
Telomerase/hnRNP C1/C2	0.004	0.04	-10000	0	-0.34	3	3
E2F1	0.085	0.11	0.28	97	-10000	0	97
ZNFX1	0.012	0.003	-10000	0	-10000	0	0
PIF1	0.031	0.073	0.27	34	-0.29	1	35
NCL	0.01	0	-10000	0	-10000	0	0
DKC1	0.01	0	-10000	0	-10000	0	0
telomeric DNA binding	0	0	-10000	0	-10000	0	0

×

PDGFR-beta signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate	0.022	0.089	0.17	50	-0.4	10	60
PDGFB-D/PDGFRB/SLAP	0.004	0.056	0.2	1	-0.24	18	19
PDGFB-D/PDGFRB/APS/CBL	0.018	0.033	0.18	5	-0.16	10	15
AKT1	0.016	0.024	-10000	0	-0.11	3	3
mol:PI-4-5-P2	0	0	-10000	0	-10000	0	0
mol:Sphingosine-1-phosphate	0.025	0.095	0.18	50	-0.43	10	60
PIK3CA	0.01	0	-10000	0	-10000	0	0
FGR	-0.001	0.049	-10000	0	-0.26	12	12
mol:Ca2+	0.003	0.079	-10000	0	-0.46	10	10
MYC	-0.013	0.16	-10000	0	-0.59	27	27
SHC1	0.011	0.013	0.27	1	-10000	0	1
HRAS/GDP	0.014	0.023	-10000	0	-0.13	10	10
LRP1/PDGFRB/PDGFB	0.015	0.033	0.18	1	-0.16	14	15
GRB10	0.006	0.033	-10000	0	-0.29	5	5
PTPN11	0.01	0	-10000	0	-10000	0	0
GO:0007205	0.003	0.08	-10000	0	-0.47	10	10
PTEN	0.01	0	-10000	0	-10000	0	0
GRB2	0.01	0	-10000	0	-10000	0	0
GRB7	0.014	0.062	0.27	14	-0.29	7	21
PDGFB-D/PDGFRB/SHP2	0.01	0.032	-10000	0	-0.19	10	10
PDGFB-D/PDGFRB/GRB10	0.007	0.039	-10000	0	-0.19	15	15
cell cycle arrest	0.004	0.056	0.2	1	-0.24	18	19
HRAS	0.01	0	-10000	0	-10000	0	0
HIF1A	0.016	0.022	-10000	0	-0.1	3	3
GAB1	0.005	0.081	-10000	0	-0.43	10	10
mol:GTP	0	0	-10000	0	-10000	0	0
DNM2	0.007	0.075	-10000	0	-0.39	10	10
PDGFB-D/PDGFRB	0.016	0.03	-10000	0	-0.17	10	10
mol:GDP	0	0	-10000	0	-10000	0	0
PDGFB-D/PDGFRB/LMW-PTP	0.01	0.032	-10000	0	-0.19	10	10
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB	0.023	0.088	0.17	56	-0.32	12	68
positive regulation of MAPKKK cascade	0.01	0.032	-10000	0	-0.19	10	10
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
mol:IP3	0.003	0.08	-10000	0	-0.47	10	10
E5	0	0.001	-10000	0	-10000	0	0
CSK	0.01	0.001	-10000	0	-10000	0	0
PDGFB-D/PDGFRB/GRB7	0.012	0.054	0.19	14	-0.19	17	31
SHB	0.01	0	-10000	0	-10000	0	0
BLK	-0.035	0.15	-10000	0	-0.43	43	43
PTPN2	0.01	0.004	-10000	0	-10000	0	0
PDGFB-D/PDGFRB/SNX15	0.01	0.032	-10000	0	-0.19	10	10
BCAR1	0.01	0	-10000	0	-10000	0	0
VAV2	0.001	0.095	-10000	0	-0.32	27	27
CBL	0.01	0	-10000	0	-10000	0	0
PDGFB-D/PDGFRB/DEP1	0.01	0.036	-10000	0	-0.21	10	10
LCK	-0.003	0.069	-10000	0	-0.32	13	13
PDGFRB	0.003	0.047	-10000	0	-0.3	10	10
ACP1	0.01	0	-10000	0	-10000	0	0
HCK	-0.011	0.12	-10000	0	-0.48	18	18
ABL1	0.003	0.071	-10000	0	-0.37	10	10
PDGFB-D/PDGFRB/CBL	0.002	0.092	-10000	0	-0.51	10	10
PTPN1	0.01	0.004	-10000	0	-10000	0	0
SNX15	0.01	0	-10000	0	-10000	0	0
STAT3	0.01	0	-10000	0	-10000	0	0
STAT1	0.012	0.026	0.27	4	-10000	0	4
cell proliferation	-0.01	0.15	-10000	0	-0.53	27	27
SLA	0.001	0.054	0.27	1	-0.29	13	14
actin cytoskeleton reorganization	0.017	0.023	-10000	0	-0.12	7	7
SRC	0.002	0.037	-10000	0	-0.22	10	10
PI3K	-0.003	0.018	-10000	0	-0.12	10	10
PDGFB-D/PDGFRB/GRB7/SHC	0.019	0.047	0.18	15	-0.16	17	32
SH2B2	0.013	0.028	0.27	5	-10000	0	5
PLCgamma1/SPHK1	0.025	0.097	0.18	50	-0.45	10	60
LYN	0.002	0.037	-10000	0	-0.22	10	10
LRP1	0.007	0.029	-10000	0	-0.29	4	4
SOS1	0.01	0	-10000	0	-10000	0	0
STAT5B	0.01	0	-10000	0	-10000	0	0
STAT5A	0.009	0.015	-10000	0	-0.29	1	1
NCK1-2/p130 Cas	0.026	0.025	-10000	0	-0.13	3	3
SPHK1	0.045	0.091	0.27	56	-0.3	1	57
EDG1	0	0.002	-10000	0	-10000	0	0
mol:DAG	0.003	0.08	-10000	0	-0.47	10	10
PLCG1	0.003	0.082	-10000	0	-0.49	10	10
NHERF/PDGFRB	0.024	0.046	0.18	21	-0.16	10	31
YES1	0.002	0.037	-10000	0	-0.22	10	10
cell migration	0.024	0.045	0.18	21	-0.16	10	31
SHC/Grb2/SOS1	0.026	0.026	-10000	0	-0.13	10	10
SLC9A3R2	0.01	0	-10000	0	-10000	0	0
SLC9A3R1	0.023	0.057	0.27	21	-10000	0	21
NHERF1-2/PDGFRB/PTEN	0.03	0.043	0.18	21	-0.14	10	31
FYN	-0.001	0.054	-10000	0	-0.27	13	13
DOK1	0.009	0.026	0.17	1	-0.14	10	11
HRAS/GTP	0.007	0	-10000	0	-10000	0	0
PDGFB	0.011	0.013	0.27	1	-10000	0	1
RAC1	-0.003	0.12	-10000	0	-0.42	27	27
PRKCD	0.009	0.025	-10000	0	-0.15	10	10
FER	0.009	0.025	-10000	0	-0.15	10	10
MAPKKK cascade	-0.003	0.019	-10000	0	-0.12	10	10
RASA1	0.009	0.025	-10000	0	-0.15	10	10
NCK1	0.01	0	-10000	0	-10000	0	0
NCK2	0.01	0	-10000	0	-10000	0	0
p62DOK/Csk	0.015	0.024	0.16	1	-0.13	10	11
PDGFB-D/PDGFRB/SHB	0.01	0.032	-10000	0	-0.19	10	10
chemotaxis	0.003	0.07	-10000	0	-0.36	10	10
STAT1-3-5/STAT1-3-5	0.021	0.026	-10000	0	-0.12	11	11
Bovine Papilomavirus E5/PDGFRB	0.003	0.032	-10000	0	-0.2	10	10
PTPRJ	0.009	0.015	-10000	0	-0.29	1	1

×

Signaling events mediated by HDAC Class III

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	0.01	0	-10000	0	-10000	0	0
HDAC4	0.01	0	-10000	0	-10000	0	0
induction of apoptosis	0	0	-10000	0	-10000	0	0
regulation of S phase of mitotic cell cycle	-0.02	0.042	-10000	0	-0.16	32	32
CDKN1A	0.001	0.036	-10000	0	-0.52	2	2
KAT2B	0.009	0.015	-10000	0	-0.29	1	1
BAX	0.01	0	-10000	0	-10000	0	0
FOXO3	-0.003	0	-10000	0	-10000	0	0
FOXO1	0.009	0.015	-10000	0	-0.29	1	1
FOXO4	0.01	0.005	-10000	0	-10000	0	0
response to UV	0	0	-10000	0	-10000	0	0
XRCC6	0.01	0	-10000	0	-10000	0	0
TAT	0.018	0.054	0.27	18	-10000	0	18
mol:Lysophosphatidic acid	0	0	-10000	0	-10000	0	0
MYOD1	0.004	0.01	-10000	0	-0.19	1	1
PPARGC1A	-0.11	0.15	0.27	1	-0.29	169	170
FHL2	0.008	0.025	-10000	0	-0.29	3	3
response to nutrient levels	0	0	-10000	0	-10000	0	0
KU70/SIRT1	0.014	0.008	0.13	2	-10000	0	2
HIST2H4A	0.02	0.042	0.16	32	-10000	0	32
SIRT1/FOXO3a	0.004	0.008	-10000	0	-10000	0	0
SIRT1	0.009	0.011	0.17	2	-10000	0	2
response to hypoxia	0	0	-10000	0	-10000	0	0
SIRT1/MEF2D/HDAC4	0.019	0.007	-10000	0	-10000	0	0
SIRT1/Histone H1b	0.02	0.023	0.13	2	-10000	0	2
apoptosis	-0.019	0.007	-10000	0	-10000	0	0
SIRT1/PGC1A	-0.059	0.085	0.17	1	-0.16	168	169
p53/SIRT1	0.011	0.022	0.33	2	-10000	0	2
SIRT1/FOXO4	0.014	0.009	0.13	2	-10000	0	2
FOXO1/FHL2/SIRT1	0.017	0.015	-10000	0	-0.14	3	3
HIST1H1E	0.02	0.032	-10000	0	-10000	0	0
SIRT1/p300	0.014	0.008	0.13	2	-10000	0	2
muscle cell differentiation	-0.013	0.011	0.16	1	-10000	0	1
TP53	0.009	0.011	0.17	2	-10000	0	2
KU70/SIRT1/BAX	0.019	0.007	-10000	0	-10000	0	0
CREBBP	0.01	0	-10000	0	-10000	0	0
MEF2D	0.01	0	-10000	0	-10000	0	0
HIV-1 Tat/SIRT1	0.019	0.038	0.18	20	-10000	0	20
ACSS2	0.009	0.011	0.14	3	-10000	0	3
SIRT1/PCAF/MYOD	0.013	0.011	-10000	0	-0.16	1	1

×

Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3	0.014	0	-10000	0	-10000	0	0
response to insulin stimulus	0	0	-10000	0	-10000	0	0
RIPK1	0.01	0	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
MAP2K6	0.007	0.035	0.27	1	-0.29	5	6
mol:GTP	0	0	-10000	0	-10000	0	0
MAP2K4	0.01	0	-10000	0	-10000	0	0
RAC1-CDC42/GTP/PAK family	0.013	0.015	-10000	0	-0.15	1	1
response to UV	0	0	-10000	0	-10000	0	0
YES1	0.01	0	-10000	0	-10000	0	0
interleukin-1 receptor activity	0	0	-10000	0	-10000	0	0
tumor necrosis factor receptor activity	0	0	-10000	0	-10000	0	0
MAP3K3	0.01	0	-10000	0	-10000	0	0
FYN	0.008	0.025	-10000	0	-0.29	3	3
MAP3K12	0.009	0.015	-10000	0	-0.29	1	1
FGR	0.008	0.021	-10000	0	-0.29	2	2
p38 alpha/TAB1	-0.019	0.048	-10000	0	-0.22	13	13
PRKG1	-0.059	0.12	-10000	0	-0.29	94	94
DUSP8	-0.013	0.079	-10000	0	-0.29	31	31
PGK/cGMP/p38 alpha	-0.025	0.08	-10000	0	-0.23	33	33
apoptosis	-0.019	0.046	-10000	0	-0.21	13	13
RAL/GTP	0.014	0.008	0.17	1	-10000	0	1
LYN	0.01	0	-10000	0	-10000	0	0
DUSP1	-0.077	0.14	-10000	0	-0.29	119	119
PAK1	0.009	0.015	-10000	0	-0.29	1	1
SRC	0.01	0	-10000	0	-10000	0	0
RAC1/OSM/MEKK3/MKK3	0.026	0.007	0.18	1	-10000	0	1
TRAF6	0.01	0	-10000	0	-10000	0	0
RAC1	0.01	0	-10000	0	-10000	0	0
epidermal growth factor receptor activity	0	0	-10000	0	-10000	0	0
mol:LPS	0	0	-10000	0	-10000	0	0
mol:cGMP	0	0	-10000	0	-10000	0	0
CCM2	0.011	0.013	0.27	1	-10000	0	1
RAC1-CDC42/GTP	0.014	0	-10000	0	-10000	0	0
MAPK11	0	0.072	-10000	0	-0.26	13	13
BLK	-0.009	0.1	0.27	16	-0.29	37	53
HCK	0.004	0.058	0.27	5	-0.29	12	17
MAP2K3	0.01	0	-10000	0	-10000	0	0
DUSP16	0.01	0	-10000	0	-10000	0	0
DUSP10	0.013	0.028	0.27	5	-10000	0	5
TRAF6/MEKK3	0.013	0	-10000	0	-10000	0	0
MAP3K7IP1	0	0	-10000	0	-10000	0	0
MAPK14	0.003	0.062	-10000	0	-0.23	13	13
positive regulation of innate immune response	0.002	0.08	-10000	0	-0.29	13	13
LCK	0.008	0.035	0.27	2	-0.29	4	6
p38alpha-beta/MKP7	0.006	0.079	-10000	0	-0.28	13	13
p38alpha-beta/MKP5	0.008	0.08	-10000	0	-0.28	13	13
PGK/cGMP	-0.039	0.085	-10000	0	-0.19	94	94
PAK2	0.01	0	-10000	0	-10000	0	0
p38alpha-beta/MKP1	-0.012	0.1	-10000	0	-0.26	46	46
CDC42	0.01	0	-10000	0	-10000	0	0
RALB	0.01	0	-10000	0	-10000	0	0
RALA	0.011	0.013	0.27	1	-10000	0	1
PAK3	0.013	0.045	0.27	12	-10000	0	12

×

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

Figure S95. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S95. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BAG4	0.01	0	-10000	0	-10000	0	0
Caspase 8 (4 units)	0.011	0.05	-10000	0	-0.18	22	22
NEF	-0.004	0.033	-10000	0	-0.14	21	21
NFKBIA	0.007	0.019	-10000	0	-10000	0	0
BIRC3	-0.001	0.084	0.32	3	-0.33	22	25
CYCS	0.006	0.058	-10000	0	-0.2	25	25
RIPK1	0.01	0	-10000	0	-10000	0	0
CD247	0.001	0.053	0.27	1	-0.17	28	29
MAP2K7	0.015	0.055	-10000	0	-0.39	2	2
protein ubiquitination	0.024	0.034	-10000	0	-0.24	1	1
CRADD	0.01	0	-10000	0	-10000	0	0
DAXX	0.01	0	-10000	0	-10000	0	0
FAS	0.006	0.036	-10000	0	-0.29	6	6
BID	0.005	0.061	-10000	0	-0.21	25	25
NF-kappa-B/RelA/I kappa B alpha	0.015	0.051	0.21	3	-0.19	22	25
TRADD	0.01	0	-10000	0	-10000	0	0
MAP3K5	0.009	0.015	-10000	0	-0.29	1	1
CFLAR	0.01	0	-10000	0	-10000	0	0
FADD	0.014	0.031	0.27	6	-10000	0	6
NF-kappa-B/RelA/I kappa B alpha/ubiquitin	0.016	0.052	0.21	3	-0.19	22	25
MAPK8	0.015	0.053	-10000	0	-0.37	2	2
APAF1	0.01	0	-10000	0	-10000	0	0
TRAF1	0.009	0.024	0.27	1	-0.29	2	3
TRAF2	0.01	0	-10000	0	-10000	0	0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG	0.005	0.063	0.15	7	-0.22	25	32
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD	0.024	0.04	-10000	0	-0.31	1	1
CHUK	0.024	0.035	-10000	0	-0.26	1	1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8	0.029	0.028	0.17	6	-0.15	6	12
TCRz/NEF	0	0.063	0.18	8	-0.21	28	36
TNF	0.023	0.057	0.27	21	-10000	0	21
FASLG	-0.007	0.1	0.31	7	-0.4	21	28
NFKB1	0.007	0.019	-10000	0	-10000	0	0
TNFR1A/BAG4/TNF-alpha	0.028	0.035	0.18	21	-10000	0	21
CASP6	0.019	0.043	-10000	0	-0.38	1	1
CASP7	0.003	0.11	0.24	3	-0.4	24	27
RELA	0.007	0.019	-10000	0	-10000	0	0
CASP2	0.01	0	-10000	0	-10000	0	0
CASP3	0.003	0.11	0.24	3	-0.4	24	27
TNFRSF1A	0.01	0	-10000	0	-10000	0	0
TNFR1A/BAG4	0.015	0	-10000	0	-10000	0	0
CASP8	0.01	0	-10000	0	-10000	0	0
CASP9	0.01	0	-10000	0	-10000	0	0
MAP3K14	0.024	0.038	-10000	0	-0.29	1	1
APAF-1/Caspase 9	0.002	0.073	0.19	3	-0.25	24	27
BCL2	0.012	0.055	-10000	0	-0.31	3	3

×

LPA4-mediated signaling events

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
ADCY4	0.006	0	-10000	0	-10000	0	0
ADCY5	0.003	0.003	-10000	0	-10000	0	0
ADCY6	0.006	0	-10000	0	-10000	0	0
ADCY7	0.006	0	-10000	0	-10000	0	0
ADCY1	0.008	0.017	0.11	10	-10000	0	10
ADCY2	0.003	0.003	-10000	0	-10000	0	0
ADCY3	0.006	0	-10000	0	-10000	0	0
ADCY8	0.005	0.011	0.11	4	-10000	0	4
PRKCE	0.005	0	-10000	0	-10000	0	0
ADCY9	0.006	0.001	-10000	0	-10000	0	0
mol:DAG	0	0	-10000	0	-10000	0	0
cAMP biosynthetic process	-0.041	0.047	-10000	0	-0.11	99	99

×

a4b1 and a4b7 Integrin signaling

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
ITGB1	0.01	0	-10000	0	-10000	0	0
ITGB7	0.006	0.033	-10000	0	-0.29	5	5
ITGA4	0.002	0.052	0.27	1	-0.29	12	13
alpha4/beta7 Integrin	0.007	0.042	0.19	1	-0.19	17	18
alpha4/beta1 Integrin	0.009	0.036	0.19	1	-0.19	12	13

×

Ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.01	0.011	0.16	2	-10000	0	2
MAP4K4	0.014	0.039	0.15	1	-10000	0	1
BAG4	0.01	0	-10000	0	-10000	0	0
PKC zeta/ceramide	0.006	0.007	-10000	0	-10000	0	0
NFKBIA	0.01	0	-10000	0	-10000	0	0
BIRC3	-0.004	0.071	0.27	3	-0.29	22	25
BAX	0.005	0.004	-10000	0	-10000	0	0
RIPK1	0.01	0	-10000	0	-10000	0	0
AKT1	0.003	0.001	-10000	0	-10000	0	0
BAD	0.001	0.008	-10000	0	-10000	0	0
SMPD1	0.012	0.018	-10000	0	-10000	0	0
RB1	0.001	0.01	-10000	0	-0.13	1	1
FADD/Caspase 8	0.02	0.04	-10000	0	-10000	0	0
MAP2K4	0.002	0.007	-10000	0	-10000	0	0
NSMAF	0.01	0	-10000	0	-10000	0	0
response to UV	0	0	-10000	0	-10000	0	0
RAF1	0.003	0.008	0.094	1	-10000	0	1
EGF	0.025	0.062	0.27	25	-10000	0	25
mol:ceramide	-0.001	0.008	-10000	0	-0.065	2	2
MADD	0.01	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
mol:Free Fatty acid	0.01	0.008	0.16	1	-10000	0	1
ASAH1	0.01	0	-10000	0	-10000	0	0
negative regulation of cell cycle	0.001	0.01	-10000	0	-0.13	1	1
cell proliferation	-0.037	0.059	-10000	0	-0.1	174	174
BID	0.018	0.031	-10000	0	-10000	0	0
MAP3K1	0.001	0.008	-10000	0	-10000	0	0
EIF2A	0.004	0.007	-10000	0	-10000	0	0
TRADD	0.01	0	-10000	0	-10000	0	0
CRADD	0.01	0	-10000	0	-10000	0	0
MAPK3	0.006	0.008	0.092	1	-10000	0	1
response to heat	0	0	-10000	0	-10000	0	0
MAPK1	0.006	0.008	0.092	1	-10000	0	1
Cathepsin D/ceramide	0.006	0.008	-10000	0	-10000	0	0
FADD	0.016	0.041	0.16	3	-10000	0	3
KSR1	0.001	0.008	-10000	0	-10000	0	0
MAPK8	0.004	0.024	-10000	0	-0.19	6	6
PRKRA	0.001	0.008	-10000	0	-10000	0	0
PDGFA	0.011	0.013	0.27	1	-10000	0	1
TRAF2	0.01	0	-10000	0	-10000	0	0
IGF1	-0.12	0.15	-10000	0	-0.29	182	182
mol:GD3	0	0	-10000	0	-10000	0	0
ganglioside biosynthetic process	-0.001	0.008	-10000	0	-0.064	2	2
CTSD	0.01	0	-10000	0	-10000	0	0
regulation of nitric oxide biosynthetic process	0.015	0	-10000	0	-10000	0	0
response to radiation	0	0	-10000	0	-10000	0	0
ERK1/PKC delta	-0.038	0.063	-10000	0	-0.11	174	174
PRKCD	0.01	0	-10000	0	-10000	0	0
PRKCZ	0.008	0.025	-10000	0	-0.29	3	3
mol:GW4869	0	0	-10000	0	-10000	0	0
mol:sphingosine	0.01	0.008	0.16	1	-10000	0	1
RelA/NF kappa B1	0.015	0	-10000	0	-10000	0	0
mol:glutathione	0	0	-10000	0	-10000	0	0
PAWR	0.009	0.015	-10000	0	-0.29	1	1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD	0.014	0.042	0.16	1	-10000	0	1
TNFR1A/BAG4/TNF-alpha	0.028	0.035	0.18	21	-10000	0	21
mol:Sphingosine-1-phosphate	0.01	0.011	0.16	2	-10000	0	2
MAP2K1	0.004	0.008	0.092	1	-10000	0	1
mol:C11AG	0	0	-10000	0	-10000	0	0
RELA	0.01	0	-10000	0	-10000	0	0
CYCS	0.008	0.024	0.13	15	-10000	0	15
TNFRSF1A	0.01	0	-10000	0	-10000	0	0
NFKB1	0.01	0	-10000	0	-10000	0	0
TNFR1A/BAG4	0.015	0	-10000	0	-10000	0	0
EIF2AK2	0.002	0.007	-10000	0	-10000	0	0
TNF-alpha/TNFR1A/FAN	0.028	0.035	0.18	21	-10000	0	21
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
CASP8	0.019	0.026	-10000	0	-10000	0	0
MAP2K2	0.004	0.008	0.092	1	-10000	0	1
SMPD3	0.015	0.024	-10000	0	-10000	0	0
TNF	0.023	0.057	0.27	21	-10000	0	21
PKC zeta/PAR4	0.013	0.02	-10000	0	-0.19	4	4
mol:PHOSPHOCHOLINE	-0.008	0.025	-10000	0	-0.1	24	24
NF kappa B1/RelA/I kappa B alpha	0.028	0.015	-10000	0	-0.13	4	4
AIFM1	0.008	0.024	0.13	15	-10000	0	15
BCL2	-0.002	0.058	-10000	0	-0.29	16	16

×

Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2	0.005	0.045	0.14	1	-0.2	17	18
CRKL	0.011	0.018	0.27	2	-10000	0	2
Rac1/GDP	0.007	0	-10000	0	-10000	0	0
DOCK1	0.008	0.021	-10000	0	-0.29	2	2
ITGA4	0.002	0.052	0.27	1	-0.29	12	13
alpha4/beta7 Integrin/MAdCAM1	0.023	0.042	0.18	13	-0.14	15	28
EPO	0.028	0.069	0.27	31	-10000	0	31
alpha4/beta7 Integrin	0.007	0.042	0.19	1	-0.19	17	18
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.01	0	-10000	0	-10000	0	0
alpha4/beta1 Integrin	0.009	0.036	0.19	1	-0.19	12	13
EPO/EPOR (dimer)	0.03	0.053	0.19	39	-10000	0	39
lamellipodium assembly	0.016	0.01	-10000	0	-0.18	1	1
PIK3CA	0.01	0	-10000	0	-10000	0	0
PI3K	0.014	0.01	-10000	0	-0.19	1	1
ARF6	0.01	0	-10000	0	-10000	0	0
JAK2	0.018	0.041	-10000	0	-0.17	11	11
PXN	0.01	0	-10000	0	-10000	0	0
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
MADCAM1	0.017	0.048	0.27	14	-10000	0	14
cell adhesion	0.022	0.041	0.17	13	-0.14	15	28
CRKL/CBL	0.016	0.012	0.19	2	-10000	0	2
ITGB1	0.01	0	-10000	0	-10000	0	0
SRC	0.003	0.046	-10000	0	-0.17	23	23
ITGB7	0.006	0.033	-10000	0	-0.29	5	5
RAC1	0.01	0	-10000	0	-10000	0	0
alpha4/beta1 Integrin/VCAM1	0.009	0.054	0.18	3	-0.2	23	26
p130Cas/Crk/Dock1	0.013	0.042	-10000	0	-0.23	6	6
VCAM1	-0.001	0.063	0.27	2	-0.29	17	19
RHOA	0.01	0	-10000	0	-10000	0	0
alpha4/beta1 Integrin/Paxillin/GIT1	0.021	0.029	0.18	1	-0.14	12	13
BCAR1	0.003	0.042	-10000	0	-0.16	23	23
EPOR	0.015	0.036	0.27	8	-10000	0	8
mol:GDP	0	0	-10000	0	-10000	0	0
CBL	0.01	0	-10000	0	-10000	0	0
GIT1	0.01	0	-10000	0	-10000	0	0
Rac1/GTP	0.016	0.011	-10000	0	-0.18	1	1

×

TCGA08_rtk_signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.031	0.1	-10000	0	-0.29	56	56
HRAS	0.01	0	-10000	0	-10000	0	0
EGFR	0.008	0.057	0.27	8	-0.29	9	17
AKT	0.022	0.017	-10000	0	-10000	0	0
FOXO3	0.01	0	-10000	0	-10000	0	0
AKT1	0.01	0	-10000	0	-10000	0	0
FOXO1	0.009	0.015	-10000	0	-0.29	1	1
AKT3	0	0.054	-10000	0	-0.29	14	14
FOXO4	0.011	0.013	0.27	1	-10000	0	1
MET	0.011	0.018	0.27	2	-10000	0	2
PIK3CA	0.01	0	-10000	0	-10000	0	0
PIK3CB	0.01	0	-10000	0	-10000	0	0
NRAS	0.01	0	-10000	0	-10000	0	0
PIK3CG	0.002	0.056	0.27	2	-0.29	13	15
PIK3R3	0.01	0	-10000	0	-10000	0	0
PIK3R2	0.01	0	-10000	0	-10000	0	0
NF1	0.01	0	-10000	0	-10000	0	0
RAS	-0.003	0.049	-10000	0	-0.11	59	59
ERBB2	0.018	0.045	0.27	13	-10000	0	13
proliferation/survival/translation	-0.015	0.029	0.2	2	-10000	0	2
PI3K	0.005	0.042	-10000	0	-0.098	51	51
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
KRAS	0.011	0.013	0.27	1	-10000	0	1
FOXO	0.028	0.019	0.13	1	-10000	0	1
AKT2	0.01	0	-10000	0	-10000	0	0
PTEN	0.01	0	-10000	0	-10000	0	0

×

E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin	0.013	0.036	-9999	-0.17	15	15
E-cadherin/beta catenin	0.008	0.038	-9999	-0.19	14	14
CTNNB1	0.01	0	-9999	-10000	0	0
JUP	0.008	0.021	-9999	-0.29	2	2
CDH1	0	0.054	-9999	-0.29	14	14

×

EPO signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.029	0.07	0.34	1	-10000	0	1
CRKL	0.021	0.029	0.17	2	-0.11	1	3
mol:DAG	0.027	0.039	-10000	0	-10000	0	0
HRAS	0.023	0.024	-10000	0	-10000	0	0
MAPK8	0.02	0.023	-10000	0	-10000	0	0
RAP1A	0.02	0.027	-10000	0	-0.11	1	1
GAB1	0.02	0.027	-10000	0	-0.11	1	1
MAPK14	0.02	0.023	-10000	0	-10000	0	0
EPO	0.028	0.068	0.26	31	-10000	0	31
PLCG1	0.027	0.04	-10000	0	-10000	0	0
EPOR/TRPC2/IP3 Receptors	0.016	0.035	0.26	8	-10000	0	8
RAPGEF1	0.01	0	-10000	0	-10000	0	0
EPO/EPOR (dimer)/SOCS3	0.014	0.072	0.17	32	-0.17	37	69
GAB1/SHC/GRB2/SOS1	0.029	0.025	0.15	1	-10000	0	1
EPO/EPOR (dimer)	0.031	0.051	0.18	39	-10000	0	39
IRS2	0.019	0.031	-10000	0	-0.17	3	3
STAT1	0.03	0.055	0.22	1	-0.2	13	14
STAT5B	0.028	0.047	-10000	0	-0.16	13	13
cell proliferation	0.018	0.02	-10000	0	-10000	0	0
GAB1/SHIP/PIK3R1/SHP2/SHC	0.015	0.024	-10000	0	-0.13	1	1
TEC	0.02	0.027	-10000	0	-0.11	1	1
SOCS3	-0.022	0.092	-10000	0	-0.29	43	43
STAT1 (dimer)	0.03	0.055	0.22	1	-0.2	13	14
JAK2	0.011	0.004	-10000	0	-10000	0	0
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
EPO/EPOR (dimer)/JAK2	0.042	0.048	0.22	1	-10000	0	1
EPO/EPOR	0.031	0.051	0.18	39	-10000	0	39
LYN	0.01	0.005	-10000	0	-10000	0	0
TEC/VAV2	0.026	0.03	-10000	0	-10000	0	0
elevation of cytosolic calcium ion concentration	0.016	0.035	0.26	8	-10000	0	8
SHC1	0.011	0.013	0.27	1	-10000	0	1
EPO/EPOR (dimer)/LYN	0.036	0.045	0.18	36	-10000	0	36
mol:IP3	0.027	0.039	-10000	0	-10000	0	0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP	0.021	0.042	-10000	0	-0.18	4	4
SH2B3	0.011	0.004	-10000	0	-10000	0	0
NFKB1	0.02	0.023	-10000	0	-10000	0	0
EPO/EPOR (dimer)/JAK2/SOCS3	-0.003	0.059	-10000	0	-0.16	37	37
PTPN6	0.019	0.028	0.16	1	-0.12	1	2
TEC/VAV2/GRB2	0.03	0.03	-10000	0	-10000	0	0
EPOR	0.016	0.035	0.26	8	-10000	0	8
INPP5D	0.005	0.039	-10000	0	-0.29	7	7
mol:GDP	0.029	0.025	0.15	1	-10000	0	1
SOS1	0.01	0	-10000	0	-10000	0	0
PLCG2	0.01	0.03	0.27	3	-0.29	2	5
CRKL/CBL/C3G	0.032	0.029	-10000	0	-10000	0	0
VAV2	0.02	0.027	-10000	0	-0.11	1	1
CBL	0.02	0.027	-10000	0	-0.11	1	1
SHC/Grb2/SOS1	0.022	0.026	-10000	0	-10000	0	0
STAT5A	0.027	0.048	-10000	0	-0.17	4	4
GRB2	0.01	0	-10000	0	-10000	0	0
STAT5 (dimer)	0.034	0.068	0.28	1	-0.25	16	17
LYN/PLCgamma2	0.015	0.021	0.19	3	-0.19	2	5
PTPN11	0.01	0	-10000	0	-10000	0	0
BTK	0.019	0.034	0.19	2	-0.18	4	6
BCL2	0.011	0.15	-10000	0	-0.72	16	16

×

TRAIL signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TNFSF10	0.022	0.055	0.27	19	-10000	0	19
positive regulation of NF-kappaB transcription factor activity	0.02	0.044	0.19	19	-0.19	5	24
MAP2K4	0.024	0.02	-10000	0	-10000	0	0
IKBKB	0.01	0	-10000	0	-10000	0	0
TNFRSF10B	0.01	0	-10000	0	-10000	0	0
TNFRSF10A	0.009	0.015	-10000	0	-0.29	1	1
SMPD1	0.012	0.015	-10000	0	-10000	0	0
IKBKG	0.01	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
TNFRSF10D	0.006	0.033	-10000	0	-0.29	5	5
TRAIL/TRAILR2	0.023	0.037	0.19	19	-10000	0	19
TRAIL/TRAILR3	0.023	0.047	0.19	24	-0.19	4	28
TRAIL/TRAILR1	0.023	0.039	0.19	19	-0.19	1	20
TRAIL/TRAILR4	0.02	0.044	0.19	19	-0.19	5	24
TRAIL/TRAILR1/DAP3/GTP	0.026	0.033	0.17	19	-0.14	1	20
IKK complex	0.018	0.005	-10000	0	-10000	0	0
RIPK1	0.01	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
DAP3/GTP	0.007	0	-10000	0	-10000	0	0
MAPK3	0.016	0.032	0.16	19	-10000	0	19
MAP3K1	0.024	0.021	-10000	0	-10000	0	0
TRAILR4 (trimer)	0.006	0.033	-10000	0	-0.29	5	5
TRADD	0.01	0	-10000	0	-10000	0	0
TRAILR1 (trimer)	0.009	0.015	-10000	0	-0.29	1	1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2	0.023	0.023	-10000	0	-0.16	1	1
CFLAR	0.01	0	-10000	0	-10000	0	0
MAPK1	0.016	0.032	0.16	19	-10000	0	19
TRAIL/TRAILR1/FADD/TRADD/RIP	0.038	0.035	0.17	25	-0.13	1	26
mol:ceramide	0.012	0.015	-10000	0	-10000	0	0
FADD	0.014	0.031	0.27	6	-10000	0	6
MAPK8	0.023	0.022	-10000	0	-10000	0	0
TRAF2	0.01	0	-10000	0	-10000	0	0
TRAILR3 (trimer)	0.01	0.041	0.27	5	-0.29	4	9
CHUK	0.01	0	-10000	0	-10000	0	0
TRAIL/TRAILR1/FADD	0.03	0.039	0.18	25	-0.16	1	26
DAP3	0.01	0	-10000	0	-10000	0	0
CASP10	0.016	0.029	0.18	5	-10000	0	5
JNK cascade	0.02	0.044	0.19	19	-0.19	5	24
TRAIL (trimer)	0.022	0.054	0.27	19	-10000	0	19
TNFRSF10C	0.01	0.041	0.27	5	-0.29	4	9
TRAIL/TRAILR1/DAP3/GTP/FADD	0.032	0.035	0.16	25	-0.13	1	26
TRAIL/TRAILR2/FADD	0.03	0.038	0.18	25	-10000	0	25
cell death	0.012	0.015	-10000	0	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2	0.023	0.021	-10000	0	-10000	0	0
TRAILR2 (trimer)	0.01	0	-10000	0	-10000	0	0
CASP8	0.004	0.009	-10000	0	-10000	0	0
negative regulation of caspase activity	0	0	-10000	0	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP	0.038	0.034	0.17	25	-10000	0	25

×

HIF-2-alpha transcription factor network

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
MMP14	0.015	0.027	0.35	1	-10000	0	1
oxygen homeostasis	0.006	0.012	-10000	0	-10000	0	0
TCEB2	0.011	0.013	0.27	1	-10000	0	1
TCEB1	0.01	0	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C/HIF2A	0.044	0.059	0.27	1	-0.2	3	4
EPO	0.096	0.16	0.5	15	-0.35	3	18
FIH (dimer)	0.015	0.013	-10000	0	-10000	0	0
APEX1	0.016	0.017	-10000	0	-10000	0	0
SERPINE1	0.081	0.15	0.47	8	-0.42	5	13
FLT1	0.015	0.025	-10000	0	-10000	0	0
ADORA2A	0.075	0.14	0.4	15	-0.36	3	18
germ cell development	0.1	0.17	0.54	14	-0.34	5	19
SLC11A2	0.08	0.14	0.44	8	-0.37	3	11
BHLHE40	0.079	0.14	0.44	8	-0.36	4	12
HIF1AN	0.015	0.013	-10000	0	-10000	0	0
HIF2A/ARNT/SIRT1	0.077	0.12	0.38	15	-0.24	4	19
ETS1	0.016	0.007	-10000	0	-10000	0	0
CITED2	0.014	0.02	-10000	0	-10000	0	0
KDR	0.011	0.075	-10000	0	-1	2	2
PGK1	0.08	0.14	0.44	8	-0.37	3	11
SIRT1	0.011	0.002	-10000	0	-10000	0	0
response to hypoxia	0.001	0.002	-10000	0	-10000	0	0
HIF2A/ARNT	0.12	0.18	0.55	15	-0.42	3	18
EPAS1	0.043	0.073	0.26	8	-0.24	3	11
SP1	0.014	0.007	-10000	0	-10000	0	0
ABCG2	0.077	0.15	0.49	9	-0.35	13	22
EFNA1	0.083	0.14	0.49	8	-0.37	3	11
FXN	0.074	0.13	0.4	15	-0.36	3	18
POU5F1	0.1	0.17	0.55	14	-0.36	5	19
neuron apoptosis	-0.12	0.17	0.41	3	-0.54	15	18
EP300	0.01	0	-10000	0	-10000	0	0
EGLN3	0.01	0.042	-10000	0	-0.29	7	7
EGLN2	0.015	0.013	-10000	0	-10000	0	0
EGLN1	0.015	0.013	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C	0.021	0.008	0.18	1	-10000	0	1
VHL	0.01	0	-10000	0	-10000	0	0
ARNT	0.017	0.017	-10000	0	-10000	0	0
SLC2A1	0.076	0.14	0.4	15	-0.36	3	18
TWIST1	0.052	0.18	0.4	15	-0.34	47	62
ELK1	0.013	0	-10000	0	-10000	0	0
HIF2A/ARNT/Cbp/p300	0.069	0.1	0.34	8	-0.24	4	12
VEGFA	0.08	0.14	0.44	8	-0.37	3	11
CREBBP	0.01	0	-10000	0	-10000	0	0

×

Signaling mediated by p38-gamma and p38-delta

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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EEF2K	0.009	0.005	0.12	1	-10000	0	1
SNTA1	0.01	0	-10000	0	-10000	0	0
response to hypoxia	0	0	-10000	0	-10000	0	0
STMN1	0.019	0.032	0.12	41	-10000	0	41
MAPK12	0.007	0.022	-10000	0	-0.14	7	7
CCND1	0.007	0.055	0.14	14	-0.36	7	21
p38 gamma/SNTA1	0.013	0.021	-10000	0	-0.13	7	7
MAP2K3	0.01	0	-10000	0	-10000	0	0
PKN1	0.009	0.015	-10000	0	-0.29	1	1
G2/M transition checkpoint	0.007	0.022	-10000	0	-0.14	7	7
MAP2K6	0.006	0.023	-10000	0	-0.16	7	7
MAPT	-0.009	0.066	-10000	0	-0.22	34	34
MAPK13	0.01	0.008	0.16	1	-10000	0	1
hyperosmotic response	0	0	-10000	0	-10000	0	0
ZAK	0.007	0.017	-10000	0	-0.23	2	2

×

Retinoic acid receptors-mediated signaling

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
HDAC1	0.01	0	-10000	0	-10000	0	0
HDAC3	0.01	0	-10000	0	-10000	0	0
VDR	0.009	0.024	0.27	1	-0.29	2	3
Cbp/p300/PCAF	0.02	0.009	-10000	0	-0.16	1	1
EP300	0.01	0	-10000	0	-10000	0	0
RARs/AIB1/Cbp/p300/PCAF/9cRA	0.008	0.044	-10000	0	-0.19	3	3
KAT2B	0.009	0.015	-10000	0	-0.29	1	1
MAPK14	0.01	0	-10000	0	-10000	0	0
AKT1	0.005	0.058	0.16	17	-0.17	27	44
RAR alpha/9cRA/Cyclin H	0.021	0.028	-10000	0	-0.19	4	4
mol:9cRA	0	0	-10000	0	-10000	0	0
RARs/Src-1/Cbp/p300/PCAF/9cRA	0.005	0.048	-10000	0	-0.15	35	35
CDC2	0	0	-10000	0	-10000	0	0
response to UV	0.001	0	-10000	0	-10000	0	0
RAR alpha/Jnk1	0.009	0.029	-10000	0	-0.21	6	6
NCOR2	0.01	0	-10000	0	-10000	0	0
VDR/VDR/Vit D3	0.007	0.017	0.18	1	-0.19	2	3
RXRs/RARs/NRIP1/9cRA	-0.006	0.069	-10000	0	-0.33	5	5
NCOA2	-0.008	0.07	-10000	0	-0.29	24	24
NCOA3	0.01	0	-10000	0	-10000	0	0
NCOA1	0.01	0	-10000	0	-10000	0	0
VDR/VDR/DNA	0.009	0.024	0.27	1	-0.29	2	3
RARG	0.01	0	-10000	0	-10000	0	0
RAR gamma1/9cRA	0.014	0	-10000	0	-10000	0	0
MAPK3	0.01	0	-10000	0	-10000	0	0
MAPK1	0.01	0	-10000	0	-10000	0	0
MAPK8	0.008	0.025	-10000	0	-0.29	3	3
mol:Vit D3	0	0	-10000	0	-10000	0	0
RXRs/VDR/DNA/Vit D3	0.005	0.05	-10000	0	-0.3	4	4
RARA	0.012	0.031	-10000	0	-0.18	7	7
negative regulation of phosphoinositide 3-kinase cascade	0	0	-10000	0	-10000	0	0
RARs/TIF2/Cbp/p300/PCAF/9cRA	-0.005	0.066	-10000	0	-0.16	55	55
PRKCA	0.008	0.029	-10000	0	-0.29	4	4
RXRs/RARs/NRIP1/9cRA/HDAC1	-0.013	0.076	-10000	0	-0.36	5	5
RXRG	-0.05	0.11	0.14	9	-0.23	106	115
RXRA	0.013	0.027	-10000	0	-0.16	7	7
RXRB	0.013	0.033	-10000	0	-0.22	4	4
VDR/Vit D3/DNA	0.007	0.017	0.18	1	-0.19	2	3
RBP1	-0.006	0.074	0.27	3	-0.29	24	27
CRBP1/9-cic-RA	-0.003	0.05	0.18	3	-0.19	24	27
RARB	-0.014	0.083	-10000	0	-0.29	34	34
PRKCG	0.015	0.048	0.27	14	-10000	0	14
MNAT1	0.01	0	-10000	0	-10000	0	0
RAR alpha/RXRs	0.002	0.067	-10000	0	-0.32	6	6
RXRs/RARs/SMRT(N-CoR2)/9cRA	-0.002	0.064	-10000	0	-0.26	9	9
proteasomal ubiquitin-dependent protein catabolic process	0.008	0.048	-10000	0	-0.25	3	3
RXRs/RARs/NRIP1/9cRA/HDAC3	-0.013	0.076	-10000	0	-0.36	5	5
positive regulation of DNA binding	0.016	0.026	-10000	0	-0.17	6	6
NRIP1	-0.013	0.076	-10000	0	-0.54	1	1
RXRs/RARs	-0.018	0.083	-10000	0	-0.34	9	9
RXRs/RXRs/DNA/9cRA	0.001	0.048	-10000	0	-0.31	4	4
PRKACA	0.01	0	-10000	0	-10000	0	0
CDK7	0.01	0	-10000	0	-10000	0	0
TFIIH	0.02	0	-10000	0	-10000	0	0
RAR alpha/9cRA	0.025	0.02	-10000	0	-10000	0	0
CCNH	0.01	0	-10000	0	-10000	0	0
CREBBP	0.01	0	-10000	0	-10000	0	0
RAR gamma2/9cRA	0.019	0	-10000	0	-10000	0	0

×

Syndecan-3-mediated signaling events

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
CTTN	0.011	0.013	0.27	1	-10000	0	1
Syndecan-3/Src/Cortactin	0.003	0.072	-10000	0	-0.56	1	1
Syndecan-3/Neurocan	0.014	0.036	0.18	11	-0.48	1	12
POMC	0.012	0.054	0.27	10	-0.29	6	16
EGFR	0.008	0.057	0.27	8	-0.29	9	17
Syndecan-3/EGFR	0.016	0.033	0.18	8	-0.48	1	9
AGRP	0.007	0.023	0.27	3	-10000	0	3
NCSTN	0.01	0	-10000	0	-10000	0	0
PSENEN	0.01	0	-10000	0	-10000	0	0
RP11-540L11.1	0	0	-10000	0	-10000	0	0
APH1B	0.01	0	-10000	0	-10000	0	0
APH1A	0.01	0	-10000	0	-10000	0	0
NCAN	0.012	0.043	0.27	11	-10000	0	11
long-term memory	0.018	0.031	-10000	0	-0.56	1	1
Syndecan-3/IL8	0.011	0.032	0.18	1	-0.6	1	2
PSEN1	0.01	0	-10000	0	-10000	0	0
Src/Cortactin	0.015	0.009	0.19	1	-10000	0	1
FYN	0.008	0.025	-10000	0	-0.29	3	3
limb bud formation	0.007	0.025	-10000	0	-0.49	1	1
MC4R	0.007	0.03	0.27	5	-10000	0	5
SRC	0.01	0	-10000	0	-10000	0	0
PTN	-0.038	0.14	0.27	20	-0.29	83	103
FGFR/FGF/Syndecan-3	0.007	0.025	-10000	0	-0.5	1	1
neuron projection morphogenesis	-0.003	0.065	0.22	1	-0.54	1	2
Syndecan-3/AgRP	0.011	0.028	0.18	3	-0.48	1	4
Syndecan-3/AgRP/MC4R	0.015	0.032	-10000	0	-0.46	1	1
Fyn/Cortactin	0.014	0.02	0.19	1	-0.19	3	4
SDC3	0.007	0.025	-10000	0	-0.5	1	1
GO:0007205	0	0	-10000	0	-10000	0	0
positive regulation of leukocyte migration	0.011	0.031	0.17	1	-0.59	1	2
IL8	-0.033	0.11	0.27	1	-0.29	59	60
Syndecan-3/Fyn/Cortactin	0.018	0.032	-10000	0	-0.58	1	1
Syndecan-3/CASK	0.006	0.024	-10000	0	-0.48	1	1
alpha-MSH/MC4R	0.013	0.042	0.19	15	-0.19	6	21
Gamma Secretase	0.03	0	-10000	0	-10000	0	0

×

E-cadherin signaling in the nascent adherens junction

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	0.005	0.067	-10000	0	-0.35	14	14
KLHL20	0.017	0.044	0.16	14	-0.14	10	24
CYFIP2	0.002	0.048	-10000	0	-0.29	11	11
Rac1/GDP	0.016	0.04	-10000	0	-0.19	14	14
ENAH	0.005	0.067	-10000	0	-0.35	14	14
AP1M1	0.01	0	-10000	0	-10000	0	0
RAP1B	0.01	0	-10000	0	-10000	0	0
RAP1A	0.01	0	-10000	0	-10000	0	0
CTNNB1	0.01	0	-10000	0	-10000	0	0
CDC42/GTP	0.013	0.024	-10000	0	-10000	0	0
ABI1/Sra1/Nap1	-0.006	0.022	-10000	0	-0.1	10	10
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin	0.018	0.036	-10000	0	-0.14	18	18
RAPGEF1	0.007	0.059	-10000	0	-0.31	14	14
CTNND1	0.01	0	-10000	0	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	0.005	0.069	-10000	0	-0.36	14	14
CRK	0.006	0.063	-10000	0	-0.33	14	14
E-cadherin/gamma catenin/alpha catenin	0.013	0.036	-10000	0	-0.17	15	15
alphaE/beta7 Integrin	0.012	0.023	-10000	0	-0.19	5	5
IQGAP1	0.01	0	-10000	0	-10000	0	0
NCKAP1	0.01	0	-10000	0	-10000	0	0
Rap1/GTP/I-afadin	0.019	0	-10000	0	-10000	0	0
DLG1	0.005	0.067	-10000	0	-0.35	14	14
ChemicalAbstracts:7440-70-2	0	0	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	-0.003	0.016	-10000	0	-0.087	14	14
MLLT4	0.01	0	-10000	0	-10000	0	0
ARF6/GTP/NME1/Tiam1	0.019	0.016	0.17	1	-0.14	3	4
PI3K	-0.004	0.02	-10000	0	-0.11	14	14
ARF6	0.01	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
E-cadherin/gamma catenin	0.007	0.042	-10000	0	-0.2	15	15
TIAM1	0.008	0.025	-10000	0	-0.29	3	3
E-cadherin(dimer)/Ca2+	0.019	0.028	-10000	0	-0.13	14	14
AKT1	0.011	0.015	-10000	0	-10000	0	0
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
CDH1	0	0.054	-10000	0	-0.29	14	14
RhoA/GDP	0.015	0.04	-10000	0	-0.19	14	14
actin cytoskeleton organization	0.014	0.035	0.14	14	-0.11	10	24
CDC42/GDP	0.015	0.04	-10000	0	-0.19	14	14
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin	0.005	0.037	-10000	0	-0.18	15	15
ITGB7	0.006	0.033	-10000	0	-0.29	5	5
RAC1	0.01	0	-10000	0	-10000	0	0
E-cadherin/beta catenin/alpha catenin/p120 catenin	0.02	0.03	-10000	0	-0.14	14	14
E-cadherin/Ca2+/beta catenin/alpha catenin	0.013	0.027	-10000	0	-0.13	14	14
mol:GDP	0.011	0.045	-10000	0	-0.22	14	14
CDC42/GTP/IQGAP1	0.014	0	-10000	0	-10000	0	0
JUP	0.008	0.021	-10000	0	-0.29	2	2
p120 catenin/RhoA/GDP	0.017	0.041	-10000	0	-0.2	14	14
RAC1/GTP/IQGAP1	0.014	0	-10000	0	-10000	0	0
PIP5K1C/AP1M1	0.015	0	-10000	0	-10000	0	0
RHOA	0.01	0	-10000	0	-10000	0	0
CDC42	0.01	0	-10000	0	-10000	0	0
CTNNA1	0.01	0	-10000	0	-10000	0	0
positive regulation of S phase of mitotic cell cycle	0.014	0.046	0.22	14	-0.13	9	23
NME1	0.011	0.013	0.27	1	-10000	0	1
clathrin coat assembly	0	0	-10000	0	-10000	0	0
TJP1	0.005	0.067	-10000	0	-0.35	14	14
regulation of cell-cell adhesion	-0.003	0.019	-10000	0	-0.1	14	14
WASF2	0.006	0.015	-10000	0	-0.075	3	3
Rap1/GTP	0.017	0.027	-10000	0	-0.13	14	14
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin	0.022	0.037	-10000	0	-0.14	19	19
CCND1	0.016	0.054	0.25	14	-0.16	9	23
VAV2	0.008	0.078	-10000	0	-0.37	16	16
RAP1/GDP	0.018	0.032	-10000	0	-0.15	13	13
adherens junction assembly	0.005	0.065	-10000	0	-0.34	14	14
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
ABI1	0.01	0	-10000	0	-10000	0	0
PIP5K1C	0.01	0	-10000	0	-10000	0	0
regulation of heterotypic cell-cell adhesion	0.02	0.035	-10000	0	-0.13	19	19
E-cadherin/beta catenin	-0.001	0.048	-10000	0	-0.25	14	14
mol:GTP	0	0	-10000	0	-10000	0	0
SRC	0.005	0.067	-10000	0	-0.35	14	14
PIK3CA	0.01	0	-10000	0	-10000	0	0
Rac1/GTP	-0.003	0.066	0.25	14	-0.22	10	24
E-cadherin/beta catenin/alpha catenin	0.014	0.032	-10000	0	-0.16	14	14
ITGAE	0.01	0	-10000	0	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.005	0.07	-10000	0	-0.37	14	14

×

Signaling events mediated by PRL

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCNE1	0.051	0.094	0.27	64	-10000	0	64
mol:Halofuginone	0.003	0	-10000	0	-10000	0	0
ITGA1	0.01	0	-10000	0	-10000	0	0
CDKN1A	0.009	0.035	-10000	0	-0.48	2	2
PRL-3/alpha Tubulin	0.015	0	-10000	0	-10000	0	0
mol:Ca2+	-0.027	0.066	0.15	3	-0.2	51	54
AGT	-0.025	0.1	0.27	3	-0.29	51	54
CCNA2	0.025	0.032	-10000	0	-10000	0	0
TUBA1B	0.01	0	-10000	0	-10000	0	0
EGR1	-0.039	0.086	-10000	0	-0.19	100	100
CDK2/Cyclin E1	0.03	0.071	-10000	0	-0.37	2	2
MAPK3	0.009	0	-10000	0	-10000	0	0
PRL-2 /Rab GGTase beta	0.015	0	-10000	0	-10000	0	0
MAPK1	0.009	0	-10000	0	-10000	0	0
PTP4A1	0.009	0.005	-10000	0	-10000	0	0
PTP4A3	0.01	0	-10000	0	-10000	0	0
PTP4A2	0.01	0	-10000	0	-10000	0	0
ITGB1	0.009	0	-10000	0	-10000	0	0
SRC	0.01	0	-10000	0	-10000	0	0
RAC1	0.011	0.006	-10000	0	-10000	0	0
Rab GGTase beta/Rab GGTase alpha	0.015	0	-10000	0	-10000	0	0
PRL-1/ATF-5	-0.016	0.061	-10000	0	-10000	0	0
RABGGTA	0.01	0	-10000	0	-10000	0	0
BCAR1	-0.003	0	-10000	0	-10000	0	0
RHOC	0.011	0.006	-10000	0	-10000	0	0
RHOA	0.011	0.006	-10000	0	-10000	0	0
cell motility	-0.002	0.034	-10000	0	-10000	0	0
PRL-1/alpha Tubulin	-0.017	0.06	-10000	0	-10000	0	0
PRL-3/alpha1 Integrin	0.015	0	-10000	0	-10000	0	0
ROCK1	-0.002	0.034	-10000	0	-10000	0	0
RABGGTB	0.01	0	-10000	0	-10000	0	0
CDK2	0.01	0	-10000	0	-10000	0	0
mitosis	0.009	0.005	-10000	0	-10000	0	0
ATF5	0.012	0.026	0.27	4	-10000	0	4

×

PLK2 and PLK4 events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Total.Perturbations
PLK2	0.011	0.013	0.27	1	-9999	1
PLK4	0.016	0.04	0.27	10	-9999	10
regulation of centriole replication	0.013	0.025	0.16	11	-9999	11

×

Arf6 trafficking events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SLC2A4	-0.2	0.13	-10000	0	-0.29	294	294
CLTC	0.014	0.004	-10000	0	-10000	0	0
calcium ion-dependent exocytosis	0.011	0.007	-10000	0	-10000	0	0
Dynamin 2/GTP	0.013	0.005	-10000	0	-10000	0	0
EXOC4	0.01	0	-10000	0	-10000	0	0
CD59	0.012	0.003	-10000	0	-10000	0	0
CPE	0.009	0.008	0.16	1	-10000	0	1
CTNNB1	0.01	0	-10000	0	-10000	0	0
membrane fusion	0.011	0.003	-10000	0	-10000	0	0
CTNND1	0.011	0.004	-10000	0	-10000	0	0
DNM2	0.01	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.013	0.004	-10000	0	-10000	0	0
TSHR	0.01	0.02	0.16	7	-10000	0	7
INS	0.005	0.001	-10000	0	-10000	0	0
BIN1	-0.03	0.1	-10000	0	-0.29	54	54
mol:Choline	0.011	0.003	-10000	0	-10000	0	0
growth hormone secretagogue receptor activity	0	0	-10000	0	-10000	0	0
mol:GDP	0.009	0.007	0.16	1	-10000	0	1
membrane depolarization	0	0	-10000	0	-10000	0	0
ARF6	0.01	0	-10000	0	-10000	0	0
mol:Ca2+	0.013	0.005	-10000	0	-10000	0	0
JUP	0.011	0.01	-10000	0	-10000	0	0
ASAP2/amphiphysin II	-0.002	0.054	-10000	0	-0.14	54	54
ARF6/GTP	0.007	0	-10000	0	-10000	0	0
CDH1	0.007	0.026	-10000	0	-10000	0	0
clathrin-independent pinocytosis	0.007	0	-10000	0	-10000	0	0
MAPK8IP3	0.012	0.03	0.27	4	-0.29	1	5
positive regulation of endocytosis	0.007	0	-10000	0	-10000	0	0
EXOC2	0.01	0	-10000	0	-10000	0	0
substrate adhesion-dependent cell spreading	0.019	0	-10000	0	-10000	0	0
insulin receptor binding	0	0	-10000	0	-10000	0	0
SPAG9	0.01	0	-10000	0	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.017	0.019	-10000	0	-10000	0	0
positive regulation of phagocytosis	0.008	0	-10000	0	-10000	0	0
ARF6/GTP/JIP3	0.015	0.018	0.17	4	-0.16	1	5
ACAP1	0.007	0.027	-10000	0	-0.12	17	17
mol:GTP	0	0	-10000	0	-10000	0	0
CHRM2	-0.042	0.069	-10000	0	-0.18	1	1
clathrin heavy chain/ACAP1	0.014	0.008	-10000	0	-10000	0	0
JIP4/KLC1	0.019	0	-10000	0	-10000	0	0
EXOC1	0.01	0	-10000	0	-10000	0	0
exocyst	0.019	0	-10000	0	-10000	0	0
RALA/GTP	0.008	0.009	0.18	1	-10000	0	1
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex	0.014	0	-10000	0	-10000	0	0
receptor recycling	0.007	0	-10000	0	-10000	0	0
CTNNA1	0.011	0.004	-10000	0	-10000	0	0
NME1	0.009	0.008	0.16	1	-10000	0	1
clathrin coat assembly	0.014	0.004	-10000	0	-10000	0	0
IL2RA	0.009	0.033	-10000	0	-10000	0	0
VAMP3	0.009	0	-10000	0	-10000	0	0
GLUT4/clathrin heavy chain/ACAP1	-0.07	0.055	-10000	0	-0.17	1	1
EXOC6	0.01	0	-10000	0	-10000	0	0
PLD1	0.009	0.011	-10000	0	-0.21	1	1
PLD2	0.01	0.003	-10000	0	-10000	0	0
EXOC5	0.01	0	-10000	0	-10000	0	0
PIP5K1C	0.013	0.003	-10000	0	-10000	0	0
SDC1	0.01	0.019	-10000	0	-10000	0	0
ARF6/GDP	0.011	0.005	0.12	1	-10000	0	1
EXOC7	0.01	0	-10000	0	-10000	0	0
E-cadherin/beta catenin	0.018	0.02	-10000	0	-10000	0	0
mol:Phosphatidic acid	0.011	0.003	-10000	0	-10000	0	0
endocytosis	0.002	0.053	0.14	54	-10000	0	54
SCAMP2	0.01	0	-10000	0	-10000	0	0
ADRB2	-0.001	0.042	-10000	0	-10000	0	0
EXOC3	0.01	0	-10000	0	-10000	0	0
ASAP2	0.01	0	-10000	0	-10000	0	0
Dynamin 2/GDP	0.015	0.006	0.14	1	-10000	0	1
KLC1	0.01	0	-10000	0	-10000	0	0
AVPR2	0.003	0.038	-10000	0	-10000	0	0
RALA	0.011	0.013	0.27	1	-10000	0	1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.019	0.019	-10000	0	-10000	0	0

×

ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K4	0.014	0.055	-10000	0	-0.21	22	22
BAG4	0.01	0	-10000	0	-10000	0	0
BAD	0.01	0.019	-10000	0	-10000	0	0
NFKBIA	0.01	0	-10000	0	-10000	0	0
BIRC3	-0.004	0.071	0.27	3	-0.29	22	25
BAX	0.01	0.019	-10000	0	-10000	0	0
EnzymeConsortium:3.1.4.12	0.005	0.014	0.059	1	-10000	0	1
IKBKB	0.014	0.053	-10000	0	-0.2	22	22
MAP2K2	0.013	0.016	-10000	0	-10000	0	0
MAP2K1	0.013	0.016	-10000	0	-10000	0	0
SMPD1	0.007	0.014	-10000	0	-10000	0	0
GO:0005551	0	0	-10000	0	-10000	0	0
FADD/Caspase 8	0.018	0.055	-10000	0	-0.2	2	2
MAP2K4	0.011	0.018	-10000	0	-10000	0	0
protein ubiquitination	0.014	0.054	-10000	0	-0.2	22	22
EnzymeConsortium:2.7.1.37	0.015	0.016	-10000	0	-10000	0	0
response to UV	0	0	-10000	0	-10000	0	0
RAF1	0.012	0.017	-10000	0	-10000	0	0
CRADD	0.01	0	-10000	0	-10000	0	0
mol:ceramide	0.008	0.02	0.081	1	-10000	0	1
I-kappa-B-alpha/RELA/p50/ubiquitin	0.014	0	-10000	0	-10000	0	0
MADD	0.01	0	-10000	0	-10000	0	0
MAP3K1	0.01	0.019	-10000	0	-10000	0	0
TRADD	0.01	0	-10000	0	-10000	0	0
RELA/p50	0.01	0	-10000	0	-10000	0	0
MAPK3	0.014	0.016	-10000	0	-10000	0	0
MAPK1	0.014	0.016	-10000	0	-10000	0	0
p50/RELA/I-kappa-B-alpha	0.015	0	-10000	0	-10000	0	0
FADD	0.015	0.056	-10000	0	-0.21	22	22
KSR1	0.01	0.018	-10000	0	-10000	0	0
MAPK8	0.011	0.019	-10000	0	-0.1	3	3
TRAF2	0.01	0	-10000	0	-10000	0	0
response to radiation	0	0	-10000	0	-10000	0	0
CHUK	0.014	0.053	-10000	0	-0.2	22	22
TNF R/SODD	0.015	0	-10000	0	-10000	0	0
TNF	0.023	0.057	0.27	21	-10000	0	21
CYCS	0.013	0.025	0.1	15	-10000	0	15
IKBKG	0.014	0.053	-10000	0	-0.2	22	22
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD	0.013	0.058	-10000	0	-0.22	22	22
RELA	0.01	0	-10000	0	-10000	0	0
RIPK1	0.01	0	-10000	0	-10000	0	0
AIFM1	0.013	0.025	0.1	15	-10000	0	15
TNF/TNF R/SODD	0.028	0.035	0.18	21	-10000	0	21
TNFRSF1A	0.01	0	-10000	0	-10000	0	0
response to heat	0	0	-10000	0	-10000	0	0
CASP8	0.016	0.016	-10000	0	-10000	0	0
NSMAF	0.014	0.054	-10000	0	-0.2	22	22
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
BCL2	-0.002	0.058	-10000	0	-0.29	16	16

×

E-cadherin signaling in keratinocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
keratinocyte differentiation	0.014	0.025	-10000	0	-0.2	2	2
adherens junction organization	0.01	0.043	-10000	0	-0.2	15	15
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.017	0.033	-10000	0	-0.21	2	2
FMN1	0.011	0.044	-10000	0	-0.2	14	14
mol:IP3	0.012	0.024	-10000	0	-0.18	2	2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.008	0.044	-10000	0	-0.21	15	15
CTNNB1	0.01	0.002	-10000	0	-10000	0	0
AKT1	0.014	0.029	-10000	0	-0.28	1	1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.009	0.059	-10000	0	-0.3	14	14
CTNND1	0.01	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.009	0.041	-10000	0	-0.19	15	15
VASP	0.009	0.042	-10000	0	-0.2	15	15
ZYX	0.009	0.042	-10000	0	-0.2	15	15
JUB	0.009	0.042	-10000	0	-0.2	14	14
EGFR(dimer)	0.016	0.05	0.18	8	-0.2	15	23
E-cadherin/beta catenin-gamma catenin	0.013	0.032	-10000	0	-0.15	15	15
mol:PI-3-4-5-P3	0.017	0.031	-10000	0	-0.3	1	1
PIK3CA	0.01	0.001	-10000	0	-10000	0	0
PI3K	0.017	0.031	-10000	0	-0.3	1	1
FYN	0.015	0.032	-10000	0	-0.22	4	4
mol:Ca2+	0.012	0.024	-10000	0	-0.18	2	2
JUP	0.009	0.021	-10000	0	-0.28	2	2
PIK3R1	0.01	0.015	-10000	0	-0.29	1	1
mol:DAG	0.012	0.024	-10000	0	-0.18	2	2
CDH1	0	0.054	-10000	0	-0.29	14	14
RhoA/GDP	0.017	0.033	-10000	0	-0.21	2	2
establishment of polarity of embryonic epithelium	0.009	0.041	-10000	0	-0.19	15	15
SRC	0.01	0	-10000	0	-10000	0	0
RAC1	0.01	0	-10000	0	-10000	0	0
RHOA	0.01	0	-10000	0	-10000	0	0
EGFR	0.008	0.057	0.27	8	-0.29	9	17
CASR	0.014	0.027	-10000	0	-0.17	2	2
RhoA/GTP	0.016	0.023	-10000	0	-0.22	1	1
AKT2	0.014	0.029	-10000	0	-0.28	1	1
actin cable formation	0.012	0.043	-10000	0	-0.19	14	14
apoptosis	-0.013	0.028	0.21	2	-10000	0	2
CTNNA1	0.01	0	-10000	0	-10000	0	0
mol:GDP	0.012	0.033	-10000	0	-0.23	2	2
PIP5K1A	0.009	0.042	-10000	0	-0.2	15	15
PLCG1	0.012	0.025	-10000	0	-0.18	2	2
Rac1/GTP	0.017	0.049	0.16	8	-0.19	15	23
homophilic cell adhesion	0	0.001	-10000	0	-10000	0	0

×

Class I PI3K signaling events mediated by Akt

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
BCL2L1	0.01	0.008	0.16	1	-10000	0	1
BAD/BCL-XL/YWHAZ	0.02	0.005	-10000	0	-10000	0	0
CDKN1B	0.014	0	-10000	0	-10000	0	0
CDKN1A	0.014	0.009	-10000	0	-10000	0	0
FRAP1	0	0	-10000	0	-10000	0	0
PRKDC	0.01	0	-10000	0	-10000	0	0
FOXO3	0.014	0	-10000	0	-10000	0	0
AKT1	0.013	0	-10000	0	-10000	0	0
BAD	0.01	0	-10000	0	-10000	0	0
AKT3	0	0.043	-10000	0	-0.23	14	14
mol:GTP	0	0	-10000	0	-10000	0	0
FOXO4	0.014	0.003	-10000	0	-10000	0	0
AKT1/ASK1	0.018	0.006	-10000	0	-10000	0	0
BAD/YWHAZ	0.02	0	-10000	0	-10000	0	0
RICTOR	0.01	0	-10000	0	-10000	0	0
RAF1	0.011	0.013	0.27	1	-10000	0	1
JNK cascade	-0.017	0.006	-10000	0	-10000	0	0
TSC1	0.014	0	-10000	0	-10000	0	0
YWHAZ	0.01	0	-10000	0	-10000	0	0
AKT1/RAF1	0.019	0.008	0.18	1	-10000	0	1
EP300	0.01	0	-10000	0	-10000	0	0
mol:GDP	0.013	0	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	0	0	-10000	0	-10000	0	0
TSC2	0.014	0	-10000	0	-10000	0	0
YWHAQ	0.01	0	-10000	0	-10000	0	0
TBC1D4	0.008	0	-10000	0	-10000	0	0
MAP3K5	0.009	0.015	-10000	0	-0.29	1	1
MAPKAP1	0.01	0	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.022	0.018	-10000	0	-10000	0	0
YWHAH	0.01	0	-10000	0	-10000	0	0
AKT1S1	0.014	0	-10000	0	-10000	0	0
CASP9	0.014	0	-10000	0	-10000	0	0
YWHAB	0.01	0	-10000	0	-10000	0	0
p27Kip1/KPNA1	0.02	0	-10000	0	-10000	0	0
GBL	0	0	-10000	0	-10000	0	0
PDK1/Src/Hsp90	0.02	0	-10000	0	-10000	0	0
YWHAE	0.009	0.015	-10000	0	-0.29	1	1
SRC	0.01	0	-10000	0	-10000	0	0
AKT2/p21CIP1	0.015	0.009	-10000	0	-10000	0	0
KIAA1303	0	0	-10000	0	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL	0.009	0	-10000	0	-10000	0	0
CHUK	0.014	0	-10000	0	-10000	0	0
BAD/BCL-XL	0.024	0.005	-10000	0	-10000	0	0
mTORC2	0.013	0	-10000	0	-10000	0	0
AKT2	0.008	0	-10000	0	-10000	0	0
FOXO1-3a-4/14-3-3 family	0.028	0.02	-10000	0	-10000	0	0
PDPK1	0.01	0	-10000	0	-10000	0	0
MDM2	0.016	0.012	-10000	0	-10000	0	0
MAPKKK cascade	-0.019	0.008	-10000	0	-0.18	1	1
MDM2/Cbp/p300	0.027	0.011	-10000	0	-10000	0	0
TSC1/TSC2	0.015	0	-10000	0	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.026	0.01	-10000	0	-10000	0	0
glucose import	-0.094	0.064	-10000	0	-0.13	294	294
mTOR/RHEB/GDP/Raptor/GBL/PRAS40	0.013	0	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
SLC2A4	0.002	0.004	-10000	0	-10000	0	0
GSK3A	0.014	0	-10000	0	-10000	0	0
FOXO1	0.014	0.006	-10000	0	-10000	0	0
GSK3B	0.014	0	-10000	0	-10000	0	0
SFN	0.027	0.076	0.27	32	-0.29	4	36
G1/S transition of mitotic cell cycle	0.015	0	-10000	0	-10000	0	0
p27Kip1/14-3-3 family	0.025	0.023	-10000	0	-10000	0	0
PRKACA	0.01	0	-10000	0	-10000	0	0
KPNA1	0.01	0	-10000	0	-10000	0	0
HSP90AA1	0.01	0	-10000	0	-10000	0	0
YWHAG	0.01	0	-10000	0	-10000	0	0
RHEB	0.01	0	-10000	0	-10000	0	0
CREBBP	0.01	0	-10000	0	-10000	0	0

×

Paxillin-dependent events mediated by a4b1

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.011	0.018	0.27	2	-10000	0	2
Rac1/GDP	0.008	0.004	-10000	0	-10000	0	0
DOCK1	0.008	0.021	-10000	0	-0.29	2	2
ITGA4	0.002	0.052	0.27	1	-0.29	12	13
RAC1	0.01	0	-10000	0	-10000	0	0
alpha4/beta7 Integrin	0.007	0.042	0.19	1	-0.19	17	18
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.01	0	-10000	0	-10000	0	0
alpha4/beta1 Integrin	0.015	0.031	0.18	1	-0.16	12	13
alpha4/beta7 Integrin/Paxillin	0.014	0.033	0.18	1	-0.14	17	18
lamellipodium assembly	0.021	0.02	-10000	0	-0.29	1	1
PIK3CA	0.01	0	-10000	0	-10000	0	0
PI3K	0.014	0.01	-10000	0	-0.19	1	1
ARF6	0.01	0	-10000	0	-10000	0	0
TLN1	0.01	0	-10000	0	-10000	0	0
PXN	0.009	0	-10000	0	-10000	0	0
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
ARF6/GTP	0.02	0.024	-10000	0	-0.12	12	12
cell adhesion	0.02	0.026	0.17	1	-0.13	12	13
CRKL/CBL	0.016	0.012	0.19	2	-10000	0	2
alpha4/beta1 Integrin/Paxillin	0.016	0.028	0.18	1	-0.14	12	13
ITGB1	0.01	0	-10000	0	-10000	0	0
ITGB7	0.006	0.033	-10000	0	-0.29	5	5
ARF6/GDP	0.008	0.004	-10000	0	-10000	0	0
alpha4/beta1 Integrin/Paxillin/VCAM1	0.016	0.047	0.18	3	-0.16	23	26
p130Cas/Crk/Dock1	0.019	0.012	-10000	0	-0.16	2	2
VCAM1	-0.001	0.063	0.27	2	-0.29	17	19
alpha4/beta1 Integrin/Paxillin/Talin	0.021	0.027	0.18	1	-0.13	12	13
alpha4/beta1 Integrin/Paxillin/GIT1	0.021	0.027	0.18	1	-0.13	12	13
BCAR1	0.01	0	-10000	0	-10000	0	0
mol:GDP	-0.02	0.026	0.13	12	-0.17	1	13
CBL	0.01	0	-10000	0	-10000	0	0
PRKACA	0.01	0	-10000	0	-10000	0	0
GIT1	0.01	0	-10000	0	-10000	0	0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton	0.021	0.027	0.18	1	-0.13	12	13
Rac1/GTP	0.022	0.022	-10000	0	-0.32	1	1

×

Class I PI3K signaling events

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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ARF5/GTP	0.014	0.003	-10000	0	-10000	0	0
DAPP1	-0.001	0.068	0.15	2	-0.3	7	9
Src family/SYK family/BLNK-LAT/BTK-ITK	-0.011	0.11	0.21	2	-0.35	24	26
mol:DAG	0.001	0.055	0.2	2	-0.16	22	24
HRAS	0.01	0	-10000	0	-10000	0	0
RAP1A	0.01	0	-10000	0	-10000	0	0
ARF5/GDP	0.013	0.036	-10000	0	-0.18	3	3
PLCG2	0.01	0.03	0.27	3	-0.29	2	5
PLCG1	0.01	0	-10000	0	-10000	0	0
ARF5	0.01	0	-10000	0	-10000	0	0
mol:GTP	0.006	0.003	-10000	0	-10000	0	0
ARF1/GTP	0.01	0.003	-10000	0	-10000	0	0
RHOA	0.01	0	-10000	0	-10000	0	0
YES1	0.01	0	-10000	0	-10000	0	0
RAP1A/GTP	0.011	0.003	-10000	0	-10000	0	0
ADAP1	0.007	0.003	-10000	0	-10000	0	0
ARAP3	0.006	0.003	-10000	0	-10000	0	0
INPPL1	0.01	0	-10000	0	-10000	0	0
PREX1	0.01	0	-10000	0	-10000	0	0
ARHGEF6	0.008	0.025	-10000	0	-0.29	3	3
ARHGEF7	0.01	0	-10000	0	-10000	0	0
ARF1	0.01	0	-10000	0	-10000	0	0
NRAS	0.01	0	-10000	0	-10000	0	0
FYN	0.008	0.025	-10000	0	-0.29	3	3
ARF6	0.01	0	-10000	0	-10000	0	0
FGR	0.008	0.021	-10000	0	-0.29	2	2
mol:Ca2+	0.003	0.032	0.13	2	-0.096	16	18
mol:IP4	0	0	-10000	0	-10000	0	0
TIAM1	0.008	0.025	-10000	0	-0.29	3	3
ZAP70	0	0.058	0.27	1	-0.29	15	16
mol:IP3	0.001	0.043	0.16	2	-0.11	36	38
LYN	0.01	0	-10000	0	-10000	0	0
ARF1/GDP	0.013	0.036	-10000	0	-0.18	3	3
RhoA/GDP	0.019	0.017	-10000	0	-10000	0	0
PDK1/Src/Hsp90	0.02	0	-10000	0	-10000	0	0
BLNK	0	0.052	-10000	0	-0.29	13	13
actin cytoskeleton reorganization	0.016	0.027	-10000	0	-10000	0	0
SRC	0.01	0	-10000	0	-10000	0	0
PLEKHA2	0.006	0.021	-10000	0	-0.16	7	7
RAC1	0.01	0	-10000	0	-10000	0	0
PTEN	0.009	0	-10000	0	-10000	0	0
HSP90AA1	0.01	0	-10000	0	-10000	0	0
ARF6/GTP	0.014	0.003	-10000	0	-10000	0	0
RhoA/GTP	0.012	0.003	-10000	0	-10000	0	0
Src family/SYK family/BLNK-LAT	-0.004	0.082	-10000	0	-0.33	13	13
BLK	-0.009	0.1	0.27	16	-0.29	37	53
PDPK1	0.01	0	-10000	0	-10000	0	0
CYTH1	0.007	0.003	-10000	0	-10000	0	0
HCK	0.004	0.058	0.27	5	-0.29	12	17
CYTH3	0.007	0.003	-10000	0	-10000	0	0
CYTH2	0.007	0.003	-10000	0	-10000	0	0
KRAS	0.011	0.013	0.27	1	-10000	0	1
GO:0030676	0	0	-10000	0	-10000	0	0
FOXO3	0.002	0.075	-10000	0	-0.37	16	16
SGK1	0	0.08	-10000	0	-0.4	16	16
INPP5D	0.005	0.039	-10000	0	-0.29	7	7
mol:GDP	0.008	0.037	-10000	0	-0.14	22	22
SOS1	0.01	0	-10000	0	-10000	0	0
SYK	0.007	0.029	-10000	0	-0.29	4	4
ARF6/GDP	0.015	0.016	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	0.006	0.003	-10000	0	-10000	0	0
ARAP3/RAP1A/GTP	0.011	0.003	-10000	0	-10000	0	0
VAV1	-0.001	0.061	0.27	2	-0.29	16	18
mol:PI-3-4-P2	0.006	0.026	-10000	0	-0.19	7	7
RAS family/GTP/PI3K Class I	0.018	0.007	0.16	1	-10000	0	1
PLEKHA1	0.006	0.021	-10000	0	-0.16	7	7
Rac1/GDP	0.013	0.036	-10000	0	-0.18	3	3
LAT	0.011	0.013	0.27	1	-10000	0	1
Rac1/GTP	0.009	0.041	-10000	0	-0.22	6	6
ITK	0.007	0.004	-10000	0	-10000	0	0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma	-0.002	0.072	0.22	2	-0.22	22	24
LCK	0.008	0.035	0.27	2	-0.29	4	6
BTK	0.008	0.008	-10000	0	-10000	0	0

×

Signaling events mediated by HDAC Class II

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G beta1gamma2/HDAC5	0.023	0.02	-10000	0	-0.14	6	6
HDAC3	0.01	0	-10000	0	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	0	0	-10000	0	-10000	0	0
GATA1/HDAC4	0.012	0.003	-10000	0	-10000	0	0
GATA1/HDAC5	0.012	0.003	-10000	0	-10000	0	0
GATA2/HDAC5	0.017	0.042	0.19	13	-0.19	7	20
HDAC5/BCL6/BCoR	0.02	0	-10000	0	-10000	0	0
HDAC9	-0.011	0.075	-10000	0	-0.29	28	28
Glucocorticoid receptor/Hsp90/HDAC6	0.015	0.03	-10000	0	-0.16	12	12
HDAC4/ANKRA2	0.015	0	-10000	0	-10000	0	0
HDAC5/YWHAB	0.015	0	-10000	0	-10000	0	0
NPC/RanGAP1/SUMO1/Ubc9	0.009	0	-10000	0	-10000	0	0
GATA2	0.013	0.06	0.27	13	-0.29	7	20
HDAC4/RFXANK	0.015	0.009	0.19	1	-10000	0	1
BCOR	0.01	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
HDAC10	0.01	0	-10000	0	-10000	0	0
HDAC5	0.01	0	-10000	0	-10000	0	0
GNB1/GNG2	0.012	0.025	-10000	0	-0.19	6	6
Histones	0.005	0.045	-10000	0	-0.16	4	4
ADRBK1	0.01	0	-10000	0	-10000	0	0
HDAC4	0.01	0	-10000	0	-10000	0	0
XPO1	0.01	0	-10000	0	-10000	0	0
HDAC5/ANKRA2	0.015	0	-10000	0	-10000	0	0
HDAC4/Ubc9	0.015	0	-10000	0	-10000	0	0
HDAC7	0.01	0	-10000	0	-10000	0	0
HDAC5/14-3-3 E	0.014	0.01	-10000	0	-0.19	1	1
TUBA1B	0.01	0	-10000	0	-10000	0	0
HDAC6	0.01	0	-10000	0	-10000	0	0
HDAC5/RFXANK	0.015	0.009	0.19	1	-10000	0	1
CAMK4	0.003	0.048	0.27	1	-0.29	10	11
Tubulin/HDAC6	0.019	0.012	-10000	0	-0.16	2	2
SUMO1	0.01	0	-10000	0	-10000	0	0
EntrezGene:9972	0	0	-10000	0	-10000	0	0
YWHAB	0.01	0	-10000	0	-10000	0	0
GATA1	0.007	0.005	-10000	0	-10000	0	0
EntrezGene:8021	0	0	-10000	0	-10000	0	0
YWHAE	0.009	0.015	-10000	0	-0.29	1	1
NR3C1	0.001	0.05	-10000	0	-0.29	12	12
SUMO1/HDAC4	0.019	0	-10000	0	-10000	0	0
SRF	0.01	0	-10000	0	-10000	0	0
HDAC4/YWHAB	0.015	0	-10000	0	-10000	0	0
Tubulin	0.014	0.014	-10000	0	-0.19	2	2
HDAC4/14-3-3 E	0.014	0.01	-10000	0	-0.19	1	1
GNB1	0.01	0	-10000	0	-10000	0	0
RANGAP1	0.01	0	-10000	0	-10000	0	0
BCL6/BCoR	0.015	0	-10000	0	-10000	0	0
HDAC4/HDAC3/SMRT (N-CoR2)	0.02	0	-10000	0	-10000	0	0
HDAC4/SRF	0.016	0.028	0.18	1	-0.16	10	11
HDAC4/ER alpha	-0.022	0.079	-10000	0	-0.19	73	73
EntrezGene:23225	0	0	-10000	0	-10000	0	0
positive regulation of chromatin silencing	0.005	0.045	-10000	0	-0.16	4	4
cell motility	0.019	0.012	-10000	0	-0.16	2	2
EntrezGene:23636	0	0	-10000	0	-10000	0	0
UBE2I	0.01	0	-10000	0	-10000	0	0
HDAC7/HDAC3	0.015	0	-10000	0	-10000	0	0
BCL6	0.01	0	-10000	0	-10000	0	0
HDAC4/CaMK II delta B	0.01	0	-10000	0	-10000	0	0
Hsp90/HDAC6	0.015	0	-10000	0	-10000	0	0
ESR1	-0.043	0.11	-10000	0	-0.29	73	73
HDAC6/HDAC11	0.013	0.022	0.19	1	-0.19	4	5
Ran/GTP/Exportin 1	0.02	0	-10000	0	-10000	0	0
NPC	0.006	0	-10000	0	-10000	0	0
MEF2C	0	0.054	-10000	0	-0.29	14	14
RAN	0.01	0	-10000	0	-10000	0	0
HDAC4/MEF2C	0.024	0.028	-10000	0	-0.13	14	14
GNG2	0.006	0.036	-10000	0	-0.29	6	6
NCOR2	0.01	0	-10000	0	-10000	0	0
TUBB2A	0.008	0.021	-10000	0	-0.29	2	2
HDAC11	0.008	0.032	0.27	1	-0.29	4	5
HSP90AA1	0.01	0	-10000	0	-10000	0	0
RANBP2	0.01	0	-10000	0	-10000	0	0
ANKRA2	0.01	0	-10000	0	-10000	0	0
RFXANK	0.011	0.013	0.27	1	-10000	0	1
nuclear import	-0.016	0.01	0.19	1	-10000	0	1

×

Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin	-0.009	0.067	-10000	0	-0.2	46	46
AKT1	0.026	0.045	-10000	0	-0.52	2	2
PTK2B	0.001	0.057	-10000	0	-0.33	5	5
VEGFR2 homodimer/Frs2	0.019	0.044	0.2	7	-0.5	2	9
CAV1	-0.004	0.063	-10000	0	-0.29	19	19
CALM1	0.01	0	-10000	0	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2	0.025	0.043	-10000	0	-0.48	2	2
endothelial cell proliferation	0	0.065	-10000	0	-0.36	5	5
mol:Ca2+	0.015	0.041	-10000	0	-0.28	6	6
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac	0.027	0.036	-10000	0	-0.46	2	2
RP11-342D11.1	0.01	0.04	-10000	0	-0.28	6	6
CDH5	0.008	0.021	-10000	0	-0.29	2	2
VEGFA homodimer	0.026	0.009	0.18	1	-10000	0	1
SHC1	0.011	0.013	0.27	1	-10000	0	1
SHC2	-0.008	0.073	0.27	1	-0.29	25	26
HRAS/GDP	0.018	0.036	-10000	0	-0.24	6	6
SH2D2A	0.012	0.026	0.27	4	-10000	0	4
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS	0.033	0.039	-10000	0	-0.42	2	2
VEGFR2 homodimer/VEGFA homodimer/TsAd	0.023	0.041	-10000	0	-0.48	2	2
VEGFR1 homodimer	0.01	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1	0.031	0.041	-10000	0	-0.26	6	6
GRB10	0.014	0.055	-10000	0	-0.42	6	6
PTPN11	0.01	0	-10000	0	-10000	0	0
GRB2	0.01	0	-10000	0	-10000	0	0
PAK1	0.009	0.015	-10000	0	-0.29	1	1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin	0.03	0.043	-10000	0	-0.56	2	2
HRAS	0.01	0	-10000	0	-10000	0	0
VEGF/Rho/ROCK1/Integrin Complex	0.001	0.06	-10000	0	-0.3	5	5
HIF1A	0.011	0.013	0.27	1	-10000	0	1
FRS2	0.014	0.034	0.27	7	-10000	0	7
oxygen and reactive oxygen species metabolic process	0.026	0.036	-10000	0	-0.45	2	2
mol:GTP	0	0	-10000	0	-10000	0	0
FLT4	0.009	0.015	-10000	0	-0.29	1	1
Nck/Pak	0.014	0.01	-10000	0	-0.19	1	1
VEGFR2 homodimer/VEGFA homodimer/Fyn	0.021	0.04	-10000	0	-0.48	2	2
mol:GDP	0.024	0.039	-10000	0	-0.26	6	6
mol:NADP	0.024	0.033	-10000	0	-0.37	2	2
eNOS/Hsp90	0.028	0.032	-10000	0	-0.35	2	2
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
mol:IP3	0.015	0.041	-10000	0	-0.28	6	6
HIF1A/ARNT	0.015	0.009	0.19	1	-10000	0	1
SHB	0.01	0	-10000	0	-10000	0	0
VEGFA	0.01	0.006	-10000	0	-10000	0	0
VEGFC	0.008	0.029	0.27	1	-0.29	3	4
FAK1/Vinculin	0.009	0.065	-10000	0	-0.37	5	5
mol:Ca ++	0	0	-10000	0	-10000	0	0
RHOA	0.01	0	-10000	0	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.01	0.064	-10000	0	-0.35	5	5
PTPN6	0.011	0.013	0.27	1	-10000	0	1
EPAS1	0.013	0.022	-10000	0	-0.29	2	2
mol:L-citrulline	0.024	0.033	-10000	0	-0.37	2	2
ITGAV	0.009	0.015	-10000	0	-0.29	1	1
PIK3CA	0.01	0	-10000	0	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2	0.03	0.041	-10000	0	-0.46	2	2
VEGFR2 homodimer/VEGFA homodimer	0.024	0.045	-10000	0	-0.31	6	6
VEGFR2/3 heterodimer	0.015	0.042	-10000	0	-0.57	2	2
VEGFB	0.01	0	-10000	0	-10000	0	0
MAPK11	0.012	0.043	-10000	0	-0.3	6	6
VEGFR2 homodimer	0.012	0.042	-10000	0	-0.58	2	2
FLT1	0.01	0	-10000	0	-10000	0	0
NEDD4	0.009	0.016	-10000	0	-0.29	1	1
MAPK3	-0.01	0.053	-10000	0	-0.28	7	7
MAPK1	-0.01	0.053	-10000	0	-0.28	7	7
VEGFA145/NRP2	0.005	0.044	-10000	0	-0.19	19	19
VEGFR1/2 heterodimer	0.016	0.037	-10000	0	-0.5	2	2
KDR	0.012	0.042	-10000	0	-0.58	2	2
VEGFA165/NRP1/VEGFR2 homodimer	0.018	0.052	-10000	0	-0.3	6	6
SRC	0.01	0	-10000	0	-10000	0	0
platelet activating factor biosynthetic process	-0.008	0.052	-10000	0	-0.29	7	7
PI3K	0.026	0.049	-10000	0	-0.57	2	2
VEGFR2 homodimer/VEGFA homodimer/NCK1	0.022	0.038	-10000	0	-0.48	2	2
FES	0.015	0.042	-10000	0	-0.28	6	6
GAB1	0.022	0.042	-10000	0	-0.53	2	2
VEGFR2 homodimer/VEGFA homodimer/Src	0.022	0.038	-10000	0	-0.48	2	2
CTNNB1	0.01	0	-10000	0	-10000	0	0
SOS1	0.01	0	-10000	0	-10000	0	0
ARNT	0.01	0	-10000	0	-10000	0	0
eNOS/Caveolin-1	0.027	0.033	-10000	0	-0.35	2	2
VEGFR2 homodimer/VEGFA homodimer/Yes	0.022	0.038	-10000	0	-0.48	2	2
PI3K/GAB1	0.031	0.047	-10000	0	-0.54	2	2
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak	0.033	0.041	-10000	0	-0.44	2	2
PRKACA	0.01	0	-10000	0	-10000	0	0
VEGFR2/3 heterodimer/VEGFC homodimer	0.02	0.042	-10000	0	-0.52	2	2
HSP90AA1	0.01	0	-10000	0	-10000	0	0
CDC42	0.015	0.042	-10000	0	-0.28	6	6
actin cytoskeleton reorganization	0.023	0.041	-10000	0	-0.48	2	2
PTK2	0.003	0.067	-10000	0	-0.39	5	5
EDG1	0.01	0.04	-10000	0	-0.28	6	6
mol:DAG	0.015	0.041	-10000	0	-0.28	6	6
CaM/Ca2+	0.019	0.038	-10000	0	-0.26	6	6
MAP2K3	0.015	0.041	-10000	0	-0.27	6	6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4	0.024	0.057	-10000	0	-0.42	6	6
PLCG1	0.015	0.042	-10000	0	-0.28	6	6
VEGFR2 homodimer/VEGFA homodimer/Src/Shb	0.027	0.036	-10000	0	-0.46	2	2
IQGAP1	0.01	0	-10000	0	-10000	0	0
YES1	0.01	0	-10000	0	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/SHP2	0.022	0.038	-10000	0	-0.48	2	2
VEGFR2 homodimer/VEGFA homodimer/SHP1	0.022	0.039	-10000	0	-0.48	2	2
cell migration	0.016	0.06	-10000	0	-0.55	2	2
mol:PI-3-4-5-P3	0.026	0.045	-10000	0	-0.52	2	2
FYN	0.008	0.025	-10000	0	-0.29	3	3
VEGFB/NRP1	0.016	0.039	-10000	0	-0.26	6	6
mol:NO	0.024	0.033	-10000	0	-0.37	2	2
PXN	0.01	0	-10000	0	-10000	0	0
HRAS/GTP	-0.004	0.033	-10000	0	-0.24	6	6
VEGFR2 homodimer/VEGFA homodimer/GRB10	0.022	0.057	-10000	0	-0.42	6	6
VHL	0.01	0	-10000	0	-10000	0	0
ITGB3	-0.024	0.094	-10000	0	-0.29	46	46
NOS3	0.025	0.037	-10000	0	-0.41	2	2
VEGFR2 homodimer/VEGFA homodimer/Sck	0.013	0.057	-10000	0	-0.44	3	3
RAC1	0.01	0	-10000	0	-10000	0	0
PRKCA	0.013	0.04	-10000	0	-0.26	7	7
PRKCB	0.007	0.049	-10000	0	-0.35	6	6
VCL	0.009	0.015	-10000	0	-0.29	1	1
VEGFA165/NRP1	0.016	0.041	-10000	0	-0.28	6	6
VEGFR1/2 heterodimer/VEGFA homodimer	0.022	0.038	-10000	0	-0.48	2	2
VEGFA165/NRP2	0.005	0.044	-10000	0	-0.19	19	19
MAPKKK cascade	0.025	0.049	-10000	0	-0.36	6	6
NRP2	-0.004	0.063	-10000	0	-0.29	19	19
VEGFC homodimer	0.008	0.029	0.27	1	-0.29	3	4
NCK1	0.01	0	-10000	0	-10000	0	0
ROCK1	0.01	0	-10000	0	-10000	0	0
FAK1/Paxillin	0.009	0.065	-10000	0	-0.37	5	5
MAP3K13	0.016	0.044	-10000	0	-0.28	6	6
PDPK1	0.022	0.041	-10000	0	-0.47	2	2

×

p38 MAPK signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TRAF6/ASK1	0.009	0.007	-10000	0	-0.13	1	1
TRAF2/ASK1	0.013	0.008	-10000	0	-0.16	1	1
ATM	0.01	0	-10000	0	-10000	0	0
MAP2K3	0.02	0.011	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
MAP2K6	0.019	0.023	-10000	0	-0.18	2	2
hyperosmotic response	0	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
GADD45G	0.006	0.036	-10000	0	-0.29	6	6
TXN	0.005	0.009	0.13	2	-10000	0	2
CALM1	0.01	0	-10000	0	-10000	0	0
GADD45A	0.01	0	-10000	0	-10000	0	0
GADD45B	0.002	0.048	-10000	0	-0.29	11	11
MAP3K1	0.01	0	-10000	0	-10000	0	0
MAP3K6	0.01	0	-10000	0	-10000	0	0
MAP3K7	0.01	0	-10000	0	-10000	0	0
MAP3K4	0.01	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
ASK1/ASK2	0.014	0.01	-10000	0	-0.19	1	1
TAK1/TAB family	-0.001	0	-10000	0	-10000	0	0
RAC1/OSM/MEKK3	0.02	0.007	0.17	1	-10000	0	1
TRAF2	0.01	0	-10000	0	-10000	0	0
RAC1/OSM/MEKK3/MKK3	0.02	0.011	-10000	0	-10000	0	0
TRAF6	0.004	0	-10000	0	-10000	0	0
RAC1	0.01	0	-10000	0	-10000	0	0
mol:LPS	0	0	-10000	0	-10000	0	0
CAMK2B	0.037	0.08	0.27	43	-10000	0	43
CCM2	0.011	0.013	0.27	1	-10000	0	1
CaM/Ca2+/CAMKIIB	0.03	0.049	0.17	43	-10000	0	43
MAPK11	0.01	0	-10000	0	-10000	0	0
response to DNA damage stimulus	0	0	-10000	0	-10000	0	0
CaM/Ca2+/CAMKIIB/ASK1	0.035	0.047	0.17	43	-0.14	1	44
OSM/MEKK3	0.015	0.009	0.19	1	-10000	0	1
TAOK1	0.008	0.012	-10000	0	-0.23	1	1
TAOK2	0.008	0	-10000	0	-10000	0	0
TAOK3	0.008	0	-10000	0	-10000	0	0
MAP3K7IP1	0	0	-10000	0	-10000	0	0
MAPK14	0.01	0	-10000	0	-10000	0	0
MAP3K7IP2	0	0	-10000	0	-10000	0	0
MAP3K5	0.009	0.015	-10000	0	-0.29	1	1
MAP3K10	0.011	0.013	0.27	1	-10000	0	1
MAP3K3	0.01	0	-10000	0	-10000	0	0
TRX/ASK1	0.01	0.01	-10000	0	-0.15	1	1
GADD45/MTK1/MTK1	0.017	0.032	-10000	0	-0.14	16	16

×

Canonical NF-kappaB pathway

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
FBXW11	0.011	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.037	0.018	-10000	0	-10000	0	0
ERC1	0.01	0	-10000	0	-10000	0	0
RIP2/NOD2	0.025	0.045	0.19	25	-0.19	2	27
NFKBIA	0.014	0	-10000	0	-10000	0	0
BIRC2	0.011	0.018	0.27	2	-10000	0	2
IKBKB	0.01	0	-10000	0	-10000	0	0
RIPK2	0.01	0	-10000	0	-10000	0	0
IKBKG	0.024	0.021	-10000	0	-10000	0	0
IKK complex/A20	0.044	0.038	0.23	5	-10000	0	5
NEMO/A20/RIP2	0.01	0	-10000	0	-10000	0	0
XPO1	0.01	0	-10000	0	-10000	0	0
NEMO/ATM	0.029	0.02	-10000	0	-10000	0	0
tumor necrosis factor receptor activity	0	0	-10000	0	-10000	0	0
RAN	0.01	0	-10000	0	-10000	0	0
Exportin 1/RanGTP	0.014	0	-10000	0	-10000	0	0
IKK complex/ELKS	0.025	0.012	-10000	0	-10000	0	0
BCL10/MALT1/TRAF6	0.02	0	-10000	0	-10000	0	0
NOD2	0.024	0.066	0.27	25	-0.29	2	27
NFKB1	0.011	0	-10000	0	-10000	0	0
RELA	0.011	0	-10000	0	-10000	0	0
MALT1	0.01	0	-10000	0	-10000	0	0
cIAP1/UbcH5C	0.016	0.012	0.19	2	-10000	0	2
ATM	0.01	0	-10000	0	-10000	0	0
TNF/TNFR1A	0.024	0.039	0.19	21	-10000	0	21
TRAF6	0.01	0	-10000	0	-10000	0	0
PRKCA	0.006	0.033	-10000	0	-0.29	5	5
CHUK	0.01	0	-10000	0	-10000	0	0
UBE2D3	0.01	0	-10000	0	-10000	0	0
TNF	0.023	0.057	0.27	21	-10000	0	21
NF kappa B1 p50/RelA	0.026	0	-10000	0	-10000	0	0
BCL10	0.01	0	-10000	0	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.014	0	-10000	0	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.011	0	-10000	0	-10000	0	0
TNFRSF1A	0.01	0	-10000	0	-10000	0	0
IKK complex	0.034	0.019	-10000	0	-10000	0	0
CYLD	0.01	0	-10000	0	-10000	0	0
IKK complex/PKC alpha	0.035	0.023	-10000	0	-10000	0	0

×

Circadian rhythm pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
chromatin modification	0.027	0.018	-10000	0	-10000	0	0
CLOCK	0.011	0.002	-10000	0	-10000	0	0
TIMELESS/CRY2	0.022	0.02	-10000	0	-10000	0	0
DEC1/BMAL1	0.014	0.028	0.19	10	-10000	0	10
ATR	0.01	0	-10000	0	-10000	0	0
NR1D1	0.018	0.016	-10000	0	-10000	0	0
ARNTL	0.011	0.002	-10000	0	-10000	0	0
TIMELESS	0.019	0.027	-10000	0	-10000	0	0
NPAS2	0.01	0.021	-10000	0	-0.29	2	2
CRY2	0.01	0	-10000	0	-10000	0	0
mol:CO	-0.007	0.009	-10000	0	-0.11	3	3
CHEK1	0.013	0.028	0.27	5	-10000	0	5
mol:HEME	0.007	0.009	0.11	3	-10000	0	3
PER1	-0.002	0.058	-10000	0	-0.29	16	16
BMAL/CLOCK/NPAS2	0.027	0.016	-10000	0	-0.15	2	2
BMAL1/CLOCK	0.022	0.026	-10000	0	-10000	0	0
S phase of mitotic cell cycle	0.027	0.018	-10000	0	-10000	0	0
TIMELESS/CHEK1/ATR	0.027	0.018	-10000	0	-10000	0	0
mol:NADPH	0.007	0.009	0.11	3	-10000	0	3
PER1/TIMELESS	0.021	0.023	-10000	0	-10000	0	0
PER1-2 / CRY1-2	0	0	-10000	0	-10000	0	0
DEC1	0.008	0.042	0.27	10	-10000	0	10

×

Insulin-mediated glucose transport

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Insulin responsive Vesicles	-0.093	0.078	-10000	0	-0.25	10	10
CaM/Ca2+	0.007	0	-10000	0	-10000	0	0
AKT1	0.01	0	-10000	0	-10000	0	0
AKT2	0.01	0	-10000	0	-10000	0	0
STXBP4	0.01	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucose	-0.1	0.08	-10000	0	-0.27	10	10
YWHAZ	0.01	0	-10000	0	-10000	0	0
CALM1	0.01	0	-10000	0	-10000	0	0
YWHAQ	0.01	0	-10000	0	-10000	0	0
TBC1D4	0.009	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
YWHAH	0.01	0	-10000	0	-10000	0	0
YWHAB	0.01	0	-10000	0	-10000	0	0
SNARE/Synip	0.02	0	-10000	0	-10000	0	0
YWHAG	0.01	0	-10000	0	-10000	0	0
ASIP	0.009	0.026	0.27	4	-10000	0	4
PRKCI	0.01	0	-10000	0	-10000	0	0
AS160/CaM/Ca2+	0.007	0	-10000	0	-10000	0	0
RHOQ	0.01	0	-10000	0	-10000	0	0
GYS1	0.011	0	-10000	0	-10000	0	0
PRKCZ	0.008	0.025	-10000	0	-0.29	3	3
TRIP10	0.009	0.015	-10000	0	-0.29	1	1
TC10/GTP/CIP4/Exocyst	0.013	0.008	-10000	0	-0.16	1	1
AS160/14-3-3	0.023	0.026	-10000	0	-10000	0	0
VAMP2	0.01	0	-10000	0	-10000	0	0
SLC2A4	-0.11	0.087	-10000	0	-0.3	10	10
STX4	0.01	0	-10000	0	-10000	0	0
GSK3B	0.012	0	-10000	0	-10000	0	0
SFN	0.027	0.076	0.27	32	-0.29	4	36
LNPEP	0.01	0	-10000	0	-10000	0	0
YWHAE	0.009	0.015	-10000	0	-0.29	1	1

×

mTOR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GBL	0	0	-10000	0	-10000	0	0
MKNK1	0.01	0	-10000	0	-10000	0	0
mol:PIP3	0	0.036	-10000	0	-0.22	11	11
FRAP1	0.005	0.006	-10000	0	-10000	0	0
AKT1	0.003	0.031	-10000	0	-0.18	11	11
INSR	0.01	0	-10000	0	-10000	0	0
Insulin Receptor/Insulin	0.007	0	-10000	0	-10000	0	0
mol:GTP	0.013	0.026	-10000	0	-0.15	10	10
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit	-0.001	0.008	-10000	0	-10000	0	0
TSC2	0.01	0	-10000	0	-10000	0	0
RHEB/GDP	0.01	0.022	-10000	0	-0.12	11	11
TSC1	0.01	0	-10000	0	-10000	0	0
Insulin Receptor/IRS1	0.004	0.043	-10000	0	-0.27	10	10
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA	0.013	0.012	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
EIF3A	0.01	0	-10000	0	-10000	0	0
RPS6KB1	0.008	0.016	-10000	0	-10000	0	0
MAP3K5	0.004	0.014	-10000	0	-0.28	1	1
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
apoptosis	0.004	0.014	-10000	0	-0.28	1	1
mol:LY294002	0	0	-10000	0	-0.001	10	10
EIF4B	0.009	0.015	-10000	0	-10000	0	0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.016	0.015	-10000	0	-10000	0	0
eIF4E/eIF4G1/eIF4A1	0.009	0.004	-10000	0	-10000	0	0
KIAA1303	0	0	-10000	0	-10000	0	0
PI3K	0.01	0.041	-10000	0	-0.23	11	11
mTOR/RHEB/GTP/Raptor/GBL	0.009	0.01	-10000	0	-10000	0	0
FKBP1A	0.01	0	-10000	0	-10000	0	0
RHEB/GTP	0.014	0.023	-10000	0	-0.13	10	10
mol:Amino Acids	0	0	-10000	0	-0.001	10	10
FKBP12/Rapamycin	0.007	0	-10000	0	-10000	0	0
PDPK1	0.001	0.034	-10000	0	-0.2	11	11
EIF4E	0.01	0	-10000	0	-10000	0	0
ASK1/PP5C	0.013	0.03	-10000	0	-0.58	1	1
mTOR/RHEB/GTP/Raptor/GBL/eIF4E	0.008	0	-10000	0	-10000	0	0
TSC1/TSC2	0.014	0.028	-10000	0	-0.16	10	10
tumor necrosis factor receptor activity	0	0	0.001	10	-10000	0	10
RPS6	0.01	0	-10000	0	-10000	0	0
PPP5C	0.01	0	-10000	0	-10000	0	0
EIF4G1	0.01	0	-10000	0	-10000	0	0
IRS1	-0.003	0.045	-10000	0	-0.29	10	10
INS	0	0	-10000	0	-10000	0	0
PTEN	0.01	0	-10000	0	-10000	0	0
PDK2	0.001	0.034	-10000	0	-0.2	11	11
EIF4EBP1	0.02	0.05	-10000	0	-10000	0	0
PIK3CA	0.01	0	-10000	0	-10000	0	0
PPP2R5D	0.006	0.006	-10000	0	-10000	0	0
peptide biosynthetic process	0.008	0	-10000	0	-10000	0	0
RHEB	0.01	0	-10000	0	-10000	0	0
EIF4A1	0.01	0	-10000	0	-10000	0	0
mol:Rapamycin	0	0	-10000	0	-10000	0	0
EEF2	0.008	0	-10000	0	-10000	0	0
eIF4E/4E-BP1	0.022	0.034	-10000	0	-10000	0	0

×

Atypical NF-kappaB pathway

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
BCL3/RelA	0.014	0.01	-10000	0	-0.19	1	1
FBXW11	0.01	0	-10000	0	-10000	0	0
NF kappa B1 p50/c-Rel	0.014	0.019	0.19	2	-0.16	3	5
NF kappa B1 p50/RelA/I kappa B alpha	0.019	0.021	-10000	0	-10000	0	0
NFKBIA	0.009	0.023	-10000	0	-0.15	8	8
MAPK14	0.01	0	-10000	0	-10000	0	0
NF kappa B1 p105/p50	0.014	0	-10000	0	-10000	0	0
ARRB2	0.008	0	-10000	0	-10000	0	0
REL	0.009	0.031	0.27	2	-0.29	3	5
response to oxidative stress	0	0	-10000	0	-10000	0	0
BCL3/NF kappa B1 p50	0.014	0.008	-10000	0	-0.16	1	1
response to UV	0	0	-10000	0	-10000	0	0
NF kappa B1 p105/RelA	0.014	0	-10000	0	-10000	0	0
PIK3CA	0.01	0	-10000	0	-10000	0	0
NF kappa B1 p50 dimer	0.01	0	-10000	0	-10000	0	0
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
NFKB1	0.009	0	-10000	0	-10000	0	0
RELA	0.01	0	-10000	0	-10000	0	0
positive regulation of anti-apoptosis	0.012	0.024	-10000	0	-0.15	8	8
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2	0.021	0.021	-10000	0	-10000	0	0
SRC	0.01	0	-10000	0	-10000	0	0
PI3K	0.014	0.01	-10000	0	-0.19	1	1
NF kappa B1 p50/RelA	0.012	0.024	-10000	0	-0.15	8	8
IKBKB	0.01	0	-10000	0	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.01	0	-10000	0	-10000	0	0
SYK	0.007	0.029	-10000	0	-0.29	4	4
I kappa B alpha/PIK3R1	0.014	0.025	-10000	0	-0.16	8	8
cell death	0.02	0.02	-10000	0	-10000	0	0
NF kappa B1 p105/c-Rel	0.014	0.019	0.19	2	-0.16	3	5
LCK	0.008	0.035	0.27	2	-0.29	4	6
BCL3	0.009	0.015	-10000	0	-0.29	1	1

×

Signaling events mediated by HDAC Class I

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NF kappa B/RelA	0.035	0.033	0.18	21	-10000	0	21
Ran/GTP/Exportin 1/HDAC1	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.029	0.02	-10000	0	-10000	0	0
SUMO1	0.01	0	-10000	0	-10000	0	0
ZFPM1	0.01	0	-10000	0	-10000	0	0
NPC/RanGAP1/SUMO1/Ubc9	0.009	0	-10000	0	-10000	0	0
FKBP3	0.01	0	-10000	0	-10000	0	0
Histones	0.031	0.011	-10000	0	-10000	0	0
YY1/LSF	0.016	0.009	-10000	0	-0.17	1	1
SMG5	0.01	0	-10000	0	-10000	0	0
RAN	0.01	0	-10000	0	-10000	0	0
I kappa B alpha/HDAC3	0.02	0.019	-10000	0	-10000	0	0
I kappa B alpha/HDAC1	0.021	0.012	-10000	0	-10000	0	0
SAP18	0.01	0	-10000	0	-10000	0	0
RELA	0.021	0.018	-10000	0	-10000	0	0
HDAC1/Smad7	0.02	0.009	-10000	0	-0.16	1	1
RANGAP1	0.01	0	-10000	0	-10000	0	0
HDAC3/TR2	0.021	0.012	-10000	0	-10000	0	0
NuRD/MBD3 Complex	0.021	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	0.024	0.015	-10000	0	-10000	0	0
EntrezGene:23225	0	0	-10000	0	-10000	0	0
GATA2	0.013	0.06	0.27	13	-0.29	7	20
GATA1	0.007	0.005	-10000	0	-10000	0	0
Mad/Max	0.015	0.009	0.19	1	-10000	0	1
NuRD/MBD3 Complex/GATA1/Fog1	0.025	0.001	-10000	0	-10000	0	0
RBBP7	0.01	0	-10000	0	-10000	0	0
NPC	0.006	0	-10000	0	-10000	0	0
RBBP4	0.01	0	-10000	0	-10000	0	0
MAX	0.01	0	-10000	0	-10000	0	0
EntrezGene:9972	0	0	-10000	0	-10000	0	0
FBXW11	0.01	0	-10000	0	-10000	0	0
NFKBIA	0.017	0.015	-10000	0	-10000	0	0
KAT2B	0.009	0.015	-10000	0	-0.29	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
SIN3/HDAC complex	0.019	0	-10000	0	-10000	0	0
SIN3 complex	0.026	0	-10000	0	-10000	0	0
SMURF1	0.01	0	-10000	0	-10000	0	0
CHD3	0.01	0	-10000	0	-10000	0	0
SAP30	0.01	0	-10000	0	-10000	0	0
EntrezGene:23636	0	0	-10000	0	-10000	0	0
NCOR1	0.01	0	-10000	0	-10000	0	0
YY1/HDAC3	0.023	0.015	-10000	0	-10000	0	0
YY1/HDAC2	0.016	0.009	-10000	0	-0.17	1	1
YY1/HDAC1	0.016	0.009	-10000	0	-0.17	1	1
NuRD/MBD2 Complex (MeCP1)	0.021	0	-10000	0	-10000	0	0
PPARG	0.01	0.053	-10000	0	-0.22	18	18
HDAC8/hEST1B	0.02	0	-10000	0	-10000	0	0
UBE2I	0.01	0	-10000	0	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.01	0	-10000	0	-10000	0	0
TNFRSF1A	0.01	0	-10000	0	-10000	0	0
HDAC3/SMRT (N-CoR2)	0.021	0.012	-10000	0	-10000	0	0
MBD3L2	0	0	-10000	0	-10000	0	0
ubiquitin-dependent protein catabolic process	0.02	0.009	-10000	0	-0.16	1	1
CREBBP	0.01	0	-10000	0	-10000	0	0
NuRD/MBD3/MBD3L2 Complex	0.023	0	-10000	0	-10000	0	0
HDAC1	0.01	0	-10000	0	-10000	0	0
HDAC3	0.017	0.015	-10000	0	-10000	0	0
HDAC2	0.01	0	-10000	0	-10000	0	0
YY1	0.013	0.011	-10000	0	-0.2	1	1
HDAC8	0.01	0	-10000	0	-10000	0	0
SMAD7	0.009	0.015	-10000	0	-0.29	1	1
NCOR2	0.01	0	-10000	0	-10000	0	0
MXD1	0.011	0.013	0.27	1	-10000	0	1
STAT3	0.012	0	-10000	0	-10000	0	0
NFKB1	0.01	0	-10000	0	-10000	0	0
EntrezGene:8021	0	0	-10000	0	-10000	0	0
RANBP2	0.01	0	-10000	0	-10000	0	0
YY1/LSF/HDAC1	0.022	0.009	-10000	0	-0.15	1	1
YY1/SAP30/HDAC1	0.022	0.009	-10000	0	-0.15	1	1
EP300	0.01	0	-10000	0	-10000	0	0
STAT3 (dimer non-phopshorylated)	0.012	0	-10000	0	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.017	0.015	-10000	0	-10000	0	0
histone deacetylation	0.021	0	-10000	0	-10000	0	0
STAT3 (dimer non-phopshorylated)/HDAC3	0.022	0.012	-10000	0	-10000	0	0
nuclear export	-0.02	0	-10000	0	-10000	0	0
PRKACA	0.01	0	-10000	0	-10000	0	0
GATAD2B	0.01	0	-10000	0	-10000	0	0
GATAD2A	0.01	0	-10000	0	-10000	0	0
GATA2/HDAC3	0.024	0.038	0.19	13	-10000	0	13
GATA1/HDAC1	0.012	0.003	-10000	0	-10000	0	0
GATA1/HDAC3	0.019	0.013	-10000	0	-10000	0	0
CHD4	0.01	0	-10000	0	-10000	0	0
TNF-alpha/TNFR1A	0.024	0.039	0.19	21	-10000	0	21
SIN3/HDAC complex/Mad/Max	0.021	0.003	-10000	0	-10000	0	0
NuRD Complex	0.025	0	-10000	0	-10000	0	0
positive regulation of chromatin silencing	0.03	0.01	-10000	0	-10000	0	0
SIN3B	0.01	0	-10000	0	-10000	0	0
MTA2	0.01	0	-10000	0	-10000	0	0
SIN3A	0.01	0	-10000	0	-10000	0	0
XPO1	0.01	0	-10000	0	-10000	0	0
SUMO1/HDAC1	0.019	0	-10000	0	-10000	0	0
HDAC complex	0.026	0	-10000	0	-10000	0	0
GATA1/Fog1	0.012	0.003	-10000	0	-10000	0	0
FKBP25/HDAC1/HDAC2	0.02	0	-10000	0	-10000	0	0
TNF	0.023	0.057	0.27	21	-10000	0	21
negative regulation of cell growth	0.021	0.003	-10000	0	-10000	0	0
NuRD/MBD2/PRMT5 Complex	0.021	0	-10000	0	-10000	0	0
Ran/GTP/Exportin 1	0.02	0	-10000	0	-10000	0	0
NF kappa B/RelA/I kappa B alpha	0.024	0.022	-10000	0	-10000	0	0
SIN3/HDAC complex/NCoR1	0.02	0	-10000	0	-10000	0	0
TFCP2	0.01	0	-10000	0	-10000	0	0
NR2C1	0.01	0	-10000	0	-10000	0	0
MBD3	0.01	0	-10000	0	-10000	0	0
MBD2	0.01	0	-10000	0	-10000	0	0

×

Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.01	0	-10000	0	-9999	0
Ran/GTP/Exportin 1/HDAC4	0	0	-10000	0	-9999	0
MDM2/SUMO1	0.024	0.027	0.18	13	-9999	13
HDAC4	0.01	0	-10000	0	-9999	0
Ran/GTP/Exportin 1/HDAC1	0	0	-10000	0	-9999	0
SUMO1	0.01	0	-10000	0	-9999	0
NPC/RanGAP1/SUMO1	0.008	0	-10000	0	-9999	0
mol:GTP	0	0	-10000	0	-9999	0
XPO1	0.01	0	-10000	0	-9999	0
EntrezGene:23636	0	0	-10000	0	-9999	0
RAN	0.01	0	-10000	0	-9999	0
EntrezGene:8021	0	0	-10000	0	-9999	0
RANBP2	0.01	0	-10000	0	-9999	0
SUMO1/HDAC4	0.019	0	-10000	0	-9999	0
SUMO1/HDAC1	0.019	0	-10000	0	-9999	0
RANGAP1	0.01	0	-10000	0	-9999	0
MDM2/SUMO1/SUMO1	0.03	0.026	0.18	13	-9999	13
NPC/RanGAP1/SUMO1/RanBP2/Ubc9	0.009	0	-10000	0	-9999	0
Ran/GTP	0.014	0	-10000	0	-9999	0
EntrezGene:23225	0	0	-10000	0	-9999	0
MDM2	0.018	0.045	0.27	13	-9999	13
UBE2I	0.01	0	-10000	0	-9999	0
Ran/GTP/Exportin 1	0.016	0	-10000	0	-9999	0
NPC	0.006	0	-10000	0	-9999	0
PIAS2	0.01	0	-10000	0	-9999	0
PIAS1	0.01	0	-10000	0	-9999	0
EntrezGene:9972	0	0	-10000	0	-9999	0

×

VEGFR1 specific signals

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer	0.018	0.005	-10000	0	-10000	0	0
VEGFR1 homodimer/NRP1	0.011	0.005	-10000	0	-10000	0	0
mol:DAG	0.018	0.019	-10000	0	-10000	0	0
VEGFR1 homodimer/NRP1/VEGFR 121	0.017	0.005	-10000	0	-10000	0	0
CaM/Ca2+	0.023	0.017	-10000	0	-10000	0	0
HIF1A	0.015	0.013	0.27	1	-10000	0	1
GAB1	0.01	0	-10000	0	-10000	0	0
AKT1	0.021	0.016	-10000	0	-10000	0	0
PLCG1	0.018	0.019	-10000	0	-10000	0	0
NOS3	0.025	0.015	-10000	0	-10000	0	0
CBL	0.01	0	-10000	0	-10000	0	0
mol:NO	0.025	0.015	-10000	0	-10000	0	0
FLT1	0.015	0.007	-10000	0	-10000	0	0
PGF	0.018	0.045	0.27	13	-10000	0	13
VEGFR1 homodimer/NRP2/VEGFR121	0.016	0.034	-10000	0	-10000	0	0
CALM1	0.01	0	-10000	0	-10000	0	0
PIK3CA	0.01	0	-10000	0	-10000	0	0
eNOS/Hsp90	0.03	0.014	-10000	0	-10000	0	0
endothelial cell proliferation	-0.02	0.065	-10000	0	-0.23	3	3
mol:Ca2+	0.018	0.019	-10000	0	-10000	0	0
MAPK3	0.016	0.013	-10000	0	-10000	0	0
MAPK1	0.016	0.013	-10000	0	-10000	0	0
PIK3R1	0.009	0.015	-10000	0	-0.29	1	1
PLGF homodimer	0.018	0.045	0.27	13	-10000	0	13
PRKACA	0.01	0	-10000	0	-10000	0	0
RP11-342D11.1	0	0	-10000	0	-10000	0	0
CAV1	-0.004	0.063	-10000	0	-0.29	19	19
VEGFA homodimer	0.01	0	-10000	0	-10000	0	0
VEGFR1 homodimer/VEGFA homodimer	0.018	0.005	-10000	0	-10000	0	0
platelet activating factor biosynthetic process	0.016	0.012	-10000	0	-10000	0	0
PI3K	0.033	0.028	-10000	0	-10000	0	0
PRKCA	0.016	0.015	-10000	0	-10000	0	0
PRKCB	0.012	0.014	-10000	0	-10000	0	0
VEGFR1 homodimer/PLGF homodimer	0.024	0.032	0.2	13	-10000	0	13
VEGFA	0.01	0	-10000	0	-10000	0	0
VEGFB	0.01	0	-10000	0	-10000	0	0
mol:IP3	0.018	0.019	-10000	0	-10000	0	0
RASA1	0.015	0.004	-10000	0	-10000	0	0
NRP2	-0.004	0.063	-10000	0	-0.29	19	19
VEGFR1 homodimer	0.015	0.007	-10000	0	-10000	0	0
VEGFB homodimer	0.01	0	-10000	0	-10000	0	0
NCK1	0.01	0	-10000	0	-10000	0	0
eNOS/Caveolin-1	0.028	0.015	-10000	0	-10000	0	0
PTPN11	0.01	0	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	0.032	0.027	-10000	0	-10000	0	0
mol:L-citrulline	0.025	0.015	-10000	0	-10000	0	0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP	0.029	0.005	-10000	0	-10000	0	0
VEGFR1 homodimer/VEGFA homodimer/NCK1	0.023	0.005	-10000	0	-10000	0	0
CD2AP	0.01	0	-10000	0	-10000	0	0
PI3K/GAB1	0.036	0.026	-10000	0	-10000	0	0
PDPK1	0.019	0.015	-10000	0	-10000	0	0
VEGFR1 homodimer/VEGFA homodimer/SHP2	0.023	0.005	-10000	0	-10000	0	0
mol:NADP	0.025	0.015	-10000	0	-10000	0	0
HSP90AA1	0.01	0	-10000	0	-10000	0	0
ubiquitin-dependent protein catabolic process	0.028	0.004	-10000	0	-10000	0	0
VEGFR1 homodimer/NRP2	0.01	0.037	-10000	0	-10000	0	0

×

Regulation of cytoplasmic and nuclear SMAD2/3 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
SMAD4	0.01	0	-10000	0	-10000	0	0
SMAD2	0.005	0	-10000	0	-10000	0	0
SMAD3	0.016	0	-10000	0	-10000	0	0
SMAD3/SMAD4	0.024	0.011	-10000	0	-10000	0	0
SMAD4/Ubc9/PIASy	0.02	0	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4	0.027	0.013	-10000	0	-10000	0	0
PPM1A	0.01	0	-10000	0	-10000	0	0
CALM1	0.01	0	-10000	0	-10000	0	0
SMAD2/SMAD4	0.011	0	-10000	0	-10000	0	0
MAP3K1	0.01	0	-10000	0	-10000	0	0
TRAP-1/SMAD4	0.012	0.023	-10000	0	-0.19	5	5
MAPK3	0.01	0	-10000	0	-10000	0	0
MAPK1	0.01	0	-10000	0	-10000	0	0
NUP214	0.01	0	-10000	0	-10000	0	0
CTDSP1	0.01	0	-10000	0	-10000	0	0
CTDSP2	0.01	0	-10000	0	-10000	0	0
CTDSPL	0.01	0	-10000	0	-10000	0	0
KPNB1	0.01	0	-10000	0	-10000	0	0
TGFBRAP1	0.006	0.033	-10000	0	-0.29	5	5
UBE2I	0.01	0	-10000	0	-10000	0	0
NUP153	0.01	0	-10000	0	-10000	0	0
KPNA2	0.012	0.026	0.27	4	-10000	0	4
PIAS4	0.01	0	-10000	0	-10000	0	0

×

Arf6 downstream pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLAUR	0.017	0.003	-10000	0	-10000	0	0
regulation of axonogenesis	-0.012	0.001	-10000	0	-10000	0	0
myoblast fusion	-0.011	0.006	-10000	0	-10000	0	0
mol:GTP	0.008	0.003	-10000	0	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.022	0.016	0.15	3	-0.18	1	4
ARF1/GTP	0.014	0.002	-10000	0	-10000	0	0
mol:GM1	0.006	0.002	-10000	0	-10000	0	0
mol:Choline	0.011	0.002	-10000	0	-10000	0	0
lamellipodium assembly	0.012	0.005	-10000	0	-10000	0	0
MAPK3	0.014	0.002	-10000	0	-10000	0	0
ARF6/GTP/NME1/Tiam1	0.022	0.017	0.18	1	-0.15	3	4
ARF1	0.01	0	-10000	0	-10000	0	0
ARF6/GDP	0.011	0.006	-10000	0	-10000	0	0
ARF1/GDP	0.015	0.007	-10000	0	-10000	0	0
ARF6	0.011	0.002	-10000	0	-10000	0	0
RAB11A	0.01	0	-10000	0	-10000	0	0
TIAM1	0.008	0.026	-10000	0	-0.29	3	3
fibronectin binding	0	0	-10000	0	-10000	0	0
MAPK1	0.014	0.002	-10000	0	-10000	0	0
actin filament bundle formation	-0.015	0.005	-10000	0	-10000	0	0
KALRN	0.011	0.009	0.099	4	-10000	0	4
RAB11FIP3/RAB11A	0.015	0	-10000	0	-10000	0	0
RhoA/GDP	0.015	0.006	-10000	0	-10000	0	0
NME1	0.011	0.013	0.27	1	-10000	0	1
Rac1/GDP	0.015	0.006	-10000	0	-10000	0	0
substrate adhesion-dependent cell spreading	0.008	0.003	-10000	0	-10000	0	0
cortical actin cytoskeleton organization	0.012	0.005	-10000	0	-10000	0	0
RAC1	0.01	0	-10000	0	-10000	0	0
liver development	0.008	0.003	-10000	0	-10000	0	0
ARF6/GTP	0.008	0.003	-10000	0	-10000	0	0
RhoA/GTP	0.014	0.002	-10000	0	-10000	0	0
mol:GDP	0.011	0.005	-10000	0	-10000	0	0
ARF6/GTP/RAB11FIP3/RAB11A	0.02	0.001	-10000	0	-10000	0	0
RHOA	0.01	0	-10000	0	-10000	0	0
PLD1	0.011	0.002	-10000	0	-10000	0	0
RAB11FIP3	0.01	0	-10000	0	-10000	0	0
tube morphogenesis	0.012	0.005	-10000	0	-10000	0	0
ruffle organization	0.012	0.001	-10000	0	-10000	0	0
regulation of epithelial cell migration	0.008	0.003	-10000	0	-10000	0	0
PLD2	0.011	0.002	-10000	0	-10000	0	0
PIP5K1A	0.012	0.001	-10000	0	-10000	0	0
mol:Phosphatidic acid	0.011	0.002	-10000	0	-10000	0	0
Rac1/GTP	0.013	0.005	-10000	0	-10000	0	0

×

Arf1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
coatomer protein complex	0.008	0	-9999	-10000	0	0
EntrezGene:79658	0	0	-9999	-10000	0	0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A	0.009	0	-9999	-10000	0	0
AP2	0.015	0	-9999	-10000	0	0
mol:DAG	0	0	-9999	-10000	0	0
Arfaptin 2/Rac/GTP	0.014	0	-9999	-10000	0	0
CLTB	0.01	0	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ER cargo protein	0.012	0	-9999	-10000	0	0
CD4	0.008	0.021	-9999	-0.29	2	2
CLTA	0.01	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
ARFGAP1	0.005	0	-9999	-10000	0	0
mol:PI-4-5-P2	0.005	0	-9999	-10000	0	0
ARF1/GTP	0.012	0	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein	0.01	0	-9999	-10000	0	0
mol:Choline	0.005	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
ARF1	0.01	0	-9999	-10000	0	0
DDEF1	0.005	0	-9999	-10000	0	0
ARF1/GDP	0.004	0	-9999	-10000	0	0
AP2M1	0.01	0	-9999	-10000	0	0
EntrezGene:1313	0	0	-9999	-10000	0	0
actin filament polymerization	0.008	0	-9999	-10000	0	0
Rac/GTP	0.008	0	-9999	-10000	0	0
ARF1/GTP/GGA3/ARF-GAP1	0.016	0	-9999	-10000	0	0
ARFIP2	0.009	0	-9999	-10000	0	0
COPA	0.01	0	-9999	-10000	0	0
RAC1	0.01	0	-9999	-10000	0	0
ARF1/GTP/coatomer protein complex	0.011	0	-9999	-10000	0	0
ARF1/GTP/ARHGAP10	0.007	0	-9999	-10000	0	0
GGA3	0.01	0	-9999	-10000	0	0
ARF1/GTP/Membrin	0.011	0	-9999	-10000	0	0
AP2A1	0.01	0	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ARF-GAP1	0.012	0	-9999	-10000	0	0
ARF1/GDP/Membrin	0.011	0	-9999	-10000	0	0
Arfaptin 2/Rac/GDP	0.013	0	-9999	-10000	0	0
CYTH2	0.01	0	-9999	-10000	0	0
ARF1/GTP/GGA3	0.014	0	-9999	-10000	0	0
mol:ATP	0	0	-9999	-10000	0	0
Rac/GDP	0.007	0	-9999	-10000	0	0
mol:Brefeldin A	0	0	-9999	-10000	0	0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP	0.015	0.012	-9999	-0.15	2	2
PLD2	0.005	0	-9999	-10000	0	0
ARF-GAP1/v-SNARE	0.005	0	-9999	-10000	0	0
PIP5K1A	0.005	0	-9999	-10000	0	0
ARF1/GTP/Membrin/GBF1/p115	0.012	0	-9999	-10000	0	0
mol:Phosphatic acid	0	0	-9999	-10000	0	0
mol:Phosphatidic acid	0.005	0	-9999	-10000	0	0
KDEL Receptor/Ligand/ARF-GAP1	0.005	0	-9999	-10000	0	0
GOSR2	0.007	0	-9999	-10000	0	0
USO1	0.007	0	-9999	-10000	0	0
GBF1	0.007	0	-9999	-10000	0	0
ARF1/GTP/Arfaptin 2	0.015	0	-9999	-10000	0	0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex	0.019	0.012	-9999	-0.16	2	2

×

Alternative NF-kappaB pathway

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

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

Entity	Mean	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations
IKK alpha homodimer	0.015	-9999	-9999
FBXW11	0.01	-9999	-9999
proteasomal ubiquitin-dependent protein catabolic process	0	-9999	-9999
beta TrCP1/SCF ubiquitin ligase complex	0.01	-9999	-9999
CHUK	0.01	-9999	-9999
NF kappa B2 p100/RelB	0.03	-9999	-9999
NFKB1	0.01	-9999	-9999
MAP3K14	0.01	-9999	-9999
NF kappa B1 p50/RelB	0.015	-9999	-9999
RELB	0.01	-9999	-9999
NFKB2	0.01	-9999	-9999
NF kappa B2 p52/RelB	0.014	-9999	-9999
regulation of B cell activation	0.013	-9999	-9999

pid_entity	TCGA.ZF.AA5P	TCGA.ZF.AA5N	TCGA.ZF.AA5H	TCGA.ZF.AA58
109_MAP3K5	0.022	-0.12	0.096	0.022
47_PPARGC1A	0.0099	0	-0.29	-0.29
105_BMP4	0.0099	0.0099	0.0099	0.0099
105_BMP6	0.0099	0.0099	0.0099	0.0099
105_BMP7	0.0099	0.0099	-0.29	-0.29
105_BMP2	0.0099	0.0099	0.0099	0.0099
131_RELN/VLDLR	0.026	0.019	0.026	-0.14
30_TGFB1/TGF beta receptor Type II	-0.007	-0.0065	-0.0073	0.0096
84_STAT5B	0.011	-0.11	0.02	0.0092
84_STAT5A	0.011	-0.11	0.02	0.0092