PARADIGM pathway analysis of mRNASeq expression data - Colorectal Adenocarcinoma (Primary solid tumor)

Pathway.Name	Avg.Num.Perturbations
Ephrin A reverse signaling	99
IL23-mediated signaling events	98
Signaling mediated by p38-alpha and p38-beta	95
IL4-mediated signaling events	93
Wnt signaling	89
amb2 Integrin signaling	70
Syndecan-4-mediated signaling events	68
Noncanonical Wnt signaling pathway	65
Glypican 1 network	64
EGFR-dependent Endothelin signaling events	60

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
Ephrin A reverse signaling	0.1634	99	694	7	-0.1	0	1000	-1000	-0.016	-1000
IL23-mediated signaling events	0.1617	98	5927	60	-0.54	0.011	1000	-1000	-0.17	-1000
Signaling mediated by p38-alpha and p38-beta	0.1568	95	4212	44	-0.19	0.011	1000	-1000	-0.04	-1000
IL4-mediated signaling events	0.1535	93	8509	91	-0.68	0.61	1000	-1000	-0.17	-1000
Wnt signaling	0.1469	89	625	7	-0.14	0.005	1000	-1000	-0.026	-1000
amb2 Integrin signaling	0.1155	70	5781	82	-0.17	0.015	1000	-1000	-0.065	-1000
Syndecan-4-mediated signaling events	0.1122	68	4611	67	-0.18	0.038	1000	-1000	-0.074	-1000
Noncanonical Wnt signaling pathway	0.1073	65	1697	26	-0.14	0.011	1000	-1000	-0.05	-1000
Glypican 1 network	0.1056	64	3077	48	-0.21	0.015	1000	-1000	-0.039	-1000
EGFR-dependent Endothelin signaling events	0.0990	60	1263	21	-0.18	0.016	1000	-1000	-0.06	-1000
TCR signaling in naïve CD8+ T cells	0.0974	59	5506	93	-0.12	0.055	1000	-1000	-0.076	-1000
BCR signaling pathway	0.0974	59	5902	99	-0.17	0.014	1000	-1000	-0.078	-1000
Syndecan-1-mediated signaling events	0.0957	58	1972	34	-0.14	0.011	1000	-1000	-0.048	-1000
IL12-mediated signaling events	0.0941	57	5030	87	-0.3	0.067	1000	-1000	-0.14	-1000
FOXA2 and FOXA3 transcription factor networks	0.0941	57	2623	46	-0.43	0.016	1000	-1000	-0.12	-1000
Ephrin B reverse signaling	0.0875	53	2550	48	-0.14	0.044	1000	-1000	-0.063	-1000
Signaling events mediated by the Hedgehog family	0.0858	52	2742	52	-0.13	0.081	1000	-1000	-0.055	-1000
TCGA08_retinoblastoma	0.0858	52	418	8	-0.07	0.027	1000	-1000	-0.012	-1000
HIF-1-alpha transcription factor network	0.0842	51	3887	76	-0.31	0.016	1000	-1000	-0.18	-1000
Endothelins	0.0842	51	4970	96	-0.16	0.011	1000	-1000	-0.076	-1000
BMP receptor signaling	0.0809	49	4029	81	-0.17	0.027	1000	-1000	-0.084	-1000
Fc-epsilon receptor I signaling in mast cells	0.0809	49	4794	97	-0.15	0.03	1000	-1000	-0.074	-1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	0.0809	49	3357	68	-0.31	0.12	1000	-1000	-0.12	-1000
Nephrin/Neph1 signaling in the kidney podocyte	0.0792	48	1663	34	-0.06	0.011	1000	-1000	-0.039	-1000
Reelin signaling pathway	0.0792	48	2721	56	-0.12	0.021	1000	-1000	-0.069	-1000
Calcium signaling in the CD4+ TCR pathway	0.0776	47	1470	31	-0.21	0.011	1000	-1000	-0.062	-1000
p75(NTR)-mediated signaling	0.0759	46	5778	125	-0.18	0.03	1000	-1000	-0.086	-1000
TCGA08_p53	0.0726	44	314	7	-0.051	0.031	1000	-1000	-0.009	-1000
Thromboxane A2 receptor signaling	0.0677	41	4395	105	-0.18	0.046	1000	-1000	-0.055	-1000
Osteopontin-mediated events	0.0660	40	1533	38	-0.16	0.011	1000	-1000	-0.094	-1000
Syndecan-2-mediated signaling events	0.0660	40	2822	69	-0.11	0.022	1000	-1000	-0.032	-1000
Glucocorticoid receptor regulatory network	0.0660	40	4589	114	-0.34	0.21	1000	-1000	-0.068	-1000
Signaling events regulated by Ret tyrosine kinase	0.0627	38	3191	82	-0.11	0.011	1000	-1000	-0.073	-1000
Visual signal transduction: Cones	0.0594	36	1399	38	-0.054	0.007	1000	-1000	-0.049	-1000
LPA receptor mediated events	0.0594	36	3709	102	-0.11	0.012	1000	-1000	-0.079	-1000
Neurotrophic factor-mediated Trk receptor signaling	0.0578	35	4212	120	-0.18	0.14	1000	-1000	-0.068	-1000
Caspase cascade in apoptosis	0.0561	34	2519	74	-0.084	0.044	1000	-1000	-0.04	-1000
JNK signaling in the CD4+ TCR pathway	0.0561	34	592	17	-0.047	0.011	1000	-1000	-0.038	-1000
Canonical Wnt signaling pathway	0.0561	34	1753	51	-0.18	0.089	1000	-1000	-0.058	-1000
Presenilin action in Notch and Wnt signaling	0.0528	32	1970	61	-0.18	0.061	1000	-1000	-0.059	-1000
Glypican 2 network	0.0528	32	130	4	-0.012	-0.007	1000	-1000	-0.016	-1000
Angiopoietin receptor Tie2-mediated signaling	0.0528	32	2888	88	-0.12	0.044	1000	-1000	-0.091	-1000
Visual signal transduction: Rods	0.0528	32	1708	52	-0.12	0.011	1000	-1000	-0.067	-1000
Signaling events mediated by Stem cell factor receptor (c-Kit)	0.0528	32	2551	78	-0.084	0.057	1000	-1000	-0.087	-1000
Cellular roles of Anthrax toxin	0.0512	31	1214	39	-0.045	0.011	1000	-1000	-0.018	-1000
Arf6 signaling events	0.0512	31	1948	62	-0.18	0.024	1000	-1000	-0.045	-1000
IL1-mediated signaling events	0.0512	31	1973	62	-0.1	0.021	1000	-1000	-0.086	-1000
Effects of Botulinum toxin	0.0512	31	806	26	-0.12	0.01	1000	-1000	-0.059	-1000
Integrins in angiogenesis	0.0495	30	2592	84	-0.16	0.019	1000	-1000	-0.081	-1000
a4b1 and a4b7 Integrin signaling	0.0479	29	149	5	-0.024	-0.006	1000	-1000	-0.022	-1000
Retinoic acid receptors-mediated signaling	0.0479	29	1710	58	-0.15	0.019	1000	-1000	-0.065	-1000
Signaling events mediated by PTP1B	0.0462	28	2194	76	-0.18	0.029	1000	-1000	-0.073	-1000
FAS signaling pathway (CD95)	0.0462	28	1327	47	-0.17	0.014	1000	-1000	-0.041	-1000
IL27-mediated signaling events	0.0462	28	1442	51	-0.2	0.024	1000	-1000	-0.073	-1000
Ras signaling in the CD4+ TCR pathway	0.0446	27	468	17	-0.048	0.011	1000	-1000	-0.044	-1000
Lissencephaly gene (LIS1) in neuronal migration and development	0.0429	26	1455	54	-0.13	0.022	1000	-1000	-0.085	-1000
Plasma membrane estrogen receptor signaling	0.0413	25	2163	86	-0.075	0.019	1000	-1000	-0.074	-1000
LPA4-mediated signaling events	0.0396	24	293	12	-0.058	0.016	1000	-1000	-0.027	-1000
ErbB4 signaling events	0.0380	23	1625	69	-0.17	0.036	1000	-1000	-0.066	-1000
Paxillin-independent events mediated by a4b1 and a4b7	0.0380	23	880	37	-0.13	0.026	1000	-1000	-0.045	-1000
S1P1 pathway	0.0380	23	847	36	-0.1	0.011	1000	-1000	-0.053	-1000
Nongenotropic Androgen signaling	0.0380	23	1247	52	-0.05	0.012	1000	-1000	-0.047	-1000
IL6-mediated signaling events	0.0380	23	1798	75	-0.11	0.043	1000	-1000	-0.068	-1000
Coregulation of Androgen receptor activity	0.0363	22	1732	76	-0.17	0.041	1000	-1000	-0.026	-1000
IGF1 pathway	0.0363	22	1307	57	-0.076	0.023	1000	-1000	-0.08	-1000
EPHB forward signaling	0.0347	21	1847	85	-0.1	0.06	1000	-1000	-0.084	-1000
Class I PI3K signaling events	0.0347	21	1539	73	-0.11	0.024	1000	-1000	-0.056	-1000
PDGFR-alpha signaling pathway	0.0330	20	915	44	-0.062	0.017	1000	-1000	-0.059	-1000
RXR and RAR heterodimerization with other nuclear receptor	0.0314	19	1007	52	-0.12	0.034	1000	-1000	-0.044	-1000
IL2 signaling events mediated by STAT5	0.0314	19	419	22	-0.052	0.015	1000	-1000	-0.055	-1000
Nectin adhesion pathway	0.0281	17	1072	63	-0.033	0.02	1000	-1000	-0.064	-1000
Regulation of Telomerase	0.0281	17	1750	102	-0.18	0.036	1000	-1000	-0.1	-1000
FOXM1 transcription factor network	0.0281	17	906	51	-0.12	0.076	1000	-1000	-0.2	-1000
Sphingosine 1-phosphate (S1P) pathway	0.0264	16	461	28	-0.045	0.018	1000	-1000	-0.031	-1000
IFN-gamma pathway	0.0264	16	1118	68	-0.067	0.02	1000	-1000	-0.09	-1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha	0.0264	16	551	33	-0.08	0.029	1000	-1000	-0.046	-1000
ErbB2/ErbB3 signaling events	0.0248	15	1033	65	-0.07	0.016	1000	-1000	-0.06	-1000
Signaling events mediated by PRL	0.0248	15	536	34	-0.024	0.028	1000	-1000	-0.034	-1000
S1P4 pathway	0.0248	15	396	25	-0.045	0.016	1000	-1000	-0.033	-1000
Regulation of nuclear SMAD2/3 signaling	0.0231	14	1953	136	-0.078	0.04	1000	-1000	-0.065	-1000
Ceramide signaling pathway	0.0231	14	1100	76	-0.18	0.059	1000	-1000	-0.041	-1000
Signaling events mediated by HDAC Class III	0.0231	14	598	40	-0.047	0.018	1000	-1000	-0.024	-1000
Syndecan-3-mediated signaling events	0.0231	14	500	35	-0.11	0.03	1000	-1000	-0.039	-1000
PDGFR-beta signaling pathway	0.0231	14	1419	97	-0.096	0.031	1000	-1000	-0.074	-1000
PLK2 and PLK4 events	0.0215	13	39	3	-0.003	0.009	1000	-1000	-0.015	-1000
Regulation of p38-alpha and p38-beta	0.0215	13	709	54	-0.11	0.027	1000	-1000	-0.059	-1000
S1P3 pathway	0.0215	13	574	42	-0.045	0.018	1000	-1000	-0.035	-1000
Regulation of Androgen receptor activity	0.0215	13	959	70	-0.2	0.028	1000	-1000	-0.057	-1000
S1P5 pathway	0.0198	12	207	17	-0.045	0.011	1000	-1000	-0.025	-1000
Class IB PI3K non-lipid kinase events	0.0198	12	36	3	0	-1000	1000	-1000	-0.015	-1000
Hedgehog signaling events mediated by Gli proteins	0.0182	11	747	65	-0.045	0.035	1000	-1000	-0.053	-1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes	0.0182	11	948	83	-0.16	0.052	1000	-1000	-0.064	-1000
Signaling mediated by p38-gamma and p38-delta	0.0182	11	179	15	-0.024	0.017	1000	-1000	-0.032	-1000
IL2 signaling events mediated by PI3K	0.0182	11	658	58	-0.047	0.027	1000	-1000	-0.079	-1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha	0.0182	11	495	45	-0.06	0.039	1000	-1000	-0.085	-1000
Signaling events mediated by HDAC Class II	0.0165	10	777	75	-0.038	0.025	1000	-1000	-0.044	-1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)	0.0165	10	893	85	-0.039	0.028	1000	-1000	-0.065	-1000
Sumoylation by RanBP2 regulates transcriptional repression	0.0165	10	282	27	-0.017	0.016	1000	-1000	-0.051	-1000
Insulin Pathway	0.0165	10	743	74	-0.12	0.027	1000	-1000	-0.081	-1000
Aurora B signaling	0.0165	10	716	67	-0.12	0.029	1000	-1000	-0.06	-1000
BARD1 signaling events	0.0149	9	561	57	-0.045	0.049	1000	-1000	-0.054	-1000
Paxillin-dependent events mediated by a4b1	0.0149	9	326	36	-0.024	0.02	1000	-1000	-0.062	-1000
TCGA08_rtk_signaling	0.0149	9	245	26	-0.044	0.036	1000	-1000	-0.018	-1000
Stabilization and expansion of the E-cadherin adherens junction	0.0149	9	730	74	-0.18	0.052	1000	-1000	-0.078	-1000
p38 MAPK signaling pathway	0.0149	9	410	44	-0.056	0.02	1000	-1000	-0.064	-1000
VEGFR1 specific signals	0.0132	8	484	56	-0.016	0.031	1000	-1000	-0.049	-1000
Rapid glucocorticoid signaling	0.0132	8	160	20	-0.018	0.011	1000	-1000	-0.025	-1000
Signaling events mediated by VEGFR1 and VEGFR2	0.0116	7	905	125	-0.041	0.056	1000	-1000	-0.082	-1000
Canonical NF-kappaB pathway	0.0099	6	235	39	-0.017	0.055	1000	-1000	-0.075	-1000
Aurora A signaling	0.0099	6	400	60	-0.054	0.029	1000	-1000	-0.03	-1000
Arf6 downstream pathway	0.0099	6	292	43	-0.042	0.025	1000	-1000	-0.03	-1000
Aurora C signaling	0.0099	6	46	7	-0.01	0.011	1000	-1000	-0.02	-1000
EPO signaling pathway	0.0099	6	377	55	-0.026	0.041	1000	-1000	-0.088	-1000
Signaling events mediated by HDAC Class I	0.0099	6	710	104	-0.022	0.041	1000	-1000	-0.058	-1000
TRAIL signaling pathway	0.0083	5	269	48	-0.014	0.037	1000	-1000	-0.061	-1000
ceramide signaling pathway	0.0083	5	269	49	-0.017	0.029	1000	-1000	-0.043	-1000
HIF-2-alpha transcription factor network	0.0083	5	243	43	-0.083	0.085	1000	-1000	-0.085	-1000
Atypical NF-kappaB pathway	0.0083	5	159	31	-0.031	0.029	1000	-1000	-0.039	-1000
E-cadherin signaling in the nascent adherens junction	0.0083	5	400	76	-0.044	0.044	1000	-1000	-0.074	-1000
mTOR signaling pathway	0.0066	4	244	53	-0.006	0.025	1000	-1000	-0.058	-1000
Class I PI3K signaling events mediated by Akt	0.0066	4	302	68	-0.032	0.042	1000	-1000	-0.046	-1000
FoxO family signaling	0.0066	4	283	64	-0.081	0.1	1000	-1000	-0.069	-1000
Arf6 trafficking events	0.0066	4	343	71	-0.037	0.027	1000	-1000	-0.065	-1000
PLK1 signaling events	0.0050	3	283	85	-0.007	0.029	1000	-1000	-0.038	-1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling	0.0033	2	50	23	0.004	0.034	1000	-1000	-0.055	-1000
Circadian rhythm pathway	0.0033	2	59	22	-0.011	0.037	1000	-1000	-0.044	-1000
Insulin-mediated glucose transport	0.0033	2	91	32	0	0.033	1000	-1000	-0.053	-1000
E-cadherin signaling in keratinocytes	0.0033	2	116	43	-0.033	0.038	1000	-1000	-0.057	-1000
Arf1 pathway	0.0033	2	118	54	-0.013	0.021	1000	-1000	-0.032	-1000
Alternative NF-kappaB pathway	0.0033	2	32	13	0	0.029	1000	-1000	-0.033	-1000
E-cadherin signaling events	0.0017	1	5	5	0.01	0.022	1000	-1000	-0.025	-1000
Total	NA	3511	202482	7203	-14	-1000	131000	-131000	-7.9	-131000

Ephrin A reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAPKKK cascade	-0.063	0.14	-9999	-0.32	138	138
EFNA5	-0.1	0.22	-9999	-0.52	127	127
FYN	-0.054	0.14	-9999	-0.29	140	140
neuron projection morphogenesis	-0.063	0.14	-9999	-0.32	138	138
cell-cell signaling	0	0	-9999	-10000	0	0
Ephrin A5/EPHA5	-0.063	0.14	-9999	-0.32	138	138
EPHA5	-0.004	0.067	-9999	-0.46	13	13

×

IL23-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCL2	-0.43	0.54	-10000	0	-1.2	159	159
IL23A	-0.44	0.55	-10000	0	-1.3	140	140
NF kappa B1 p50/RelA/I kappa B alpha	-0.47	0.51	-10000	0	-1.2	167	167
positive regulation of T cell mediated cytotoxicity	-0.48	0.63	-10000	0	-1.4	161	161
ITGA3	-0.41	0.52	-10000	0	-1.2	143	143
IL17F	-0.29	0.34	-10000	0	-0.74	145	145
IL12B	-0.017	0.078	-10000	0	-0.48	14	14
STAT1 (dimer)	-0.46	0.59	-10000	0	-1.3	162	162
CD4	-0.42	0.52	-10000	0	-1.2	151	151
IL23	-0.42	0.52	-10000	0	-1.2	139	139
IL23R	-0.1	0.3	-10000	0	-1.4	27	27
IL1B	-0.46	0.58	-10000	0	-1.3	155	155
T-helper cell lineage commitment	0	0	-10000	0	-10000	0	0
IL24	-0.53	0.61	-10000	0	-1.3	205	205
TYK2	-0.002	0.033	-10000	0	-0.62	1	1
STAT4	-0.029	0.15	-10000	0	-0.56	43	43
STAT3	0.011	0.002	-10000	0	-10000	0	0
IL18RAP	-0.034	0.15	-10000	0	-0.55	48	48
IL12RB1	-0.047	0.16	-10000	0	-0.57	50	50
PIK3CA	0.009	0.034	-10000	0	-0.58	2	2
IL12Rbeta1/TYK2	-0.036	0.12	-10000	0	-0.43	51	51
IL23R/JAK2	-0.12	0.3	-10000	0	-1.3	29	29
positive regulation of chronic inflammatory response	-0.48	0.63	-10000	0	-1.4	161	161
natural killer cell activation	0.007	0.017	0.069	32	-10000	0	32
JAK2	-0.02	0.11	-10000	0	-0.57	21	21
PIK3R1	0.008	0.042	-10000	0	-0.58	3	3
NFKB1	0.008	0.025	-10000	0	-0.59	1	1
RELA	0.009	0.004	-10000	0	-10000	0	0
positive regulation of dendritic cell antigen processing and presentation	-0.4	0.49	-10000	0	-1.1	141	141
ALOX12B	-0.46	0.56	-10000	0	-1.2	168	168
CXCL1	-0.42	0.54	-10000	0	-1.2	159	159
T cell proliferation	-0.48	0.63	-10000	0	-1.4	161	161
NFKBIA	0.009	0.004	-10000	0	-10000	0	0
IL17A	-0.25	0.3	-10000	0	-0.61	156	156
PI3K	-0.48	0.52	-10000	0	-1.2	167	167
IFNG	-0.019	0.051	0.13	20	-0.12	55	75
STAT3 (dimer)	-0.47	0.48	-10000	0	-1.1	177	177
IL18R1	-0.013	0.11	-10000	0	-0.56	25	25
IL23/IL23R/JAK2/TYK2/SOCS3	-0.24	0.32	-10000	0	-0.73	109	109
IL18/IL18R	-0.025	0.14	-10000	0	-0.37	69	69
macrophage activation	-0.022	0.018	-10000	0	-0.045	134	134
TNF	-0.44	0.56	-10000	0	-1.3	150	150
STAT3/STAT4	-0.49	0.52	-10000	0	-1.2	166	166
STAT4 (dimer)	-0.47	0.6	-10000	0	-1.3	164	164
IL18	0.002	0.067	-10000	0	-0.54	9	9
IL19	-0.41	0.51	-10000	0	-1.1	147	147
STAT5A (dimer)	-0.46	0.59	-10000	0	-1.3	161	161
STAT1	0.006	0.054	-10000	0	-0.49	7	7
SOCS3	-0.002	0.082	-10000	0	-0.5	16	16
CXCL9	-0.47	0.58	-10000	0	-1.3	173	173
MPO	-0.44	0.54	-10000	0	-1.2	168	168
positive regulation of humoral immune response	-0.48	0.63	-10000	0	-1.4	161	161
IL23/IL23R/JAK2/TYK2	-0.54	0.75	-10000	0	-1.5	161	161
IL6	-0.48	0.58	-10000	0	-1.3	169	169
STAT5A	0.011	0	-10000	0	-10000	0	0
IL2	0.004	0.029	-10000	0	-0.46	2	2
positive regulation of tyrosine phosphorylation of STAT protein	0.007	0.017	0.069	32	-10000	0	32
CD3E	-0.42	0.53	-10000	0	-1.2	143	143
keratinocyte proliferation	-0.48	0.63	-10000	0	-1.4	161	161
NOS2	-0.48	0.58	-10000	0	-1.2	186	186

×

Signaling mediated by p38-alpha and p38-beta

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTGS2	-0.16	0.36	-9999	-0.96	81	81
MKNK1	0.011	0	-9999	-10000	0	0
MAPK14	-0.063	0.14	-9999	-0.31	117	117
ATF2/c-Jun	-0.045	0.15	-9999	-0.5	26	26
MAPK11	-0.078	0.17	-9999	-0.36	130	130
MITF	-0.094	0.2	-9999	-0.41	147	147
MAPKAPK5	-0.074	0.18	-9999	-0.39	126	126
KRT8	-0.075	0.18	-9999	-0.39	127	127
MAPKAPK3	0.011	0	-9999	-10000	0	0
MAPKAPK2	0.011	0	-9999	-10000	0	0
p38alpha-beta/CK2	-0.11	0.23	-9999	-0.5	128	128
CEBPB	-0.075	0.18	-9999	-0.39	128	128
SLC9A1	-0.075	0.18	-9999	-0.39	127	127
mol:GDP	0	0	-9999	-10000	0	0
ATF2	-0.071	0.18	-9999	-0.38	128	128
p38alpha-beta/MNK1	-0.075	0.19	-9999	-0.41	114	114
JUN	-0.044	0.14	-9999	-0.5	26	26
PPARGC1A	-0.11	0.22	-9999	-0.42	165	165
USF1	-0.074	0.18	-9999	-0.39	126	126
RAB5/GDP/GDI1	-0.073	0.12	-9999	-0.42	37	37
NOS2	-0.19	0.41	-9999	-1.1	89	89
DDIT3	-0.075	0.18	-9999	-0.39	127	127
RAB5A	0.007	0.054	-9999	-0.58	5	5
HSPB1	-0.06	0.16	-9999	-0.46	41	41
p38alpha-beta/HBP1	-0.075	0.19	-9999	-0.4	126	126
CREB1	-0.074	0.18	-9999	-0.4	127	127
RAB5/GDP	0.005	0.04	-9999	-0.43	5	5
EIF4E	-0.064	0.17	-9999	-0.56	34	34
RPS6KA4	-0.074	0.18	-9999	-0.39	127	127
PLA2G4A	-0.15	0.22	-9999	-0.47	145	145
GDI1	-0.074	0.18	-9999	-0.38	126	126
TP53	-0.12	0.24	-9999	-0.52	128	128
RPS6KA5	-0.076	0.18	-9999	-0.39	128	128
ESR1	-0.1	0.2	-9999	-0.42	150	150
HBP1	0.011	0	-9999	-10000	0	0
MEF2C	-0.08	0.18	-9999	-0.39	134	134
MEF2A	-0.075	0.18	-9999	-0.4	114	114
EIF4EBP1	-0.074	0.18	-9999	-0.4	127	127
KRT19	-0.076	0.18	-9999	-0.39	127	127
ELK4	-0.076	0.18	-9999	-0.4	126	126
ATF6	-0.074	0.18	-9999	-0.38	126	126
ATF1	-0.074	0.18	-9999	-0.41	115	115
p38alpha-beta/MAPKAPK2	-0.075	0.19	-9999	-0.4	126	126
p38alpha-beta/MAPKAPK3	-0.075	0.19	-9999	-0.4	126	126

×

IL4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.53	0.57	-10000	0	-1.3	178	178
STAT6 (cleaved dimer)	-0.58	0.56	-10000	0	-1.2	219	219
IGHG1	-0.16	0.18	-10000	0	-0.56	4	4
IGHG3	-0.52	0.55	-10000	0	-1.2	208	208
AKT1	-0.24	0.29	-10000	0	-0.72	85	85
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1	-0.19	0.26	-10000	0	-0.67	69	69
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1	-0.24	0.28	-10000	0	-0.7	79	79
THY1	-0.53	0.58	-10000	0	-1.3	179	179
MYB	0.003	0.072	-10000	0	-0.58	9	9
HMGA1	0.006	0.055	-10000	0	-0.54	6	6
IL4/IL4R/JAK1/IL2R gamma/JAK3	-0.32	0.35	-10000	0	-0.78	146	146
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP	-0.25	0.29	-10000	0	-0.68	96	96
SP1	0.015	0.025	-10000	0	-0.58	1	1
INPP5D	-0.018	0.13	-10000	0	-0.58	30	30
SOCS5	0.027	0.016	-10000	0	-10000	0	0
STAT6 (dimer)/ETS1	-0.55	0.6	-10000	0	-1.3	190	190
SOCS1	-0.35	0.36	-10000	0	-0.81	153	153
SOCS3	-0.26	0.31	-10000	0	-0.85	68	68
FCER2	-0.52	0.56	-10000	0	-1.2	176	176
PARP14	0.009	0.021	-10000	0	-0.46	1	1
CCL17	-0.57	0.61	-10000	0	-1.3	190	190
GRB2	0.011	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP	-0.2	0.23	-10000	0	-0.63	54	54
T cell proliferation	-0.54	0.59	-10000	0	-1.3	185	185
IL4R/JAK1	-0.54	0.57	-10000	0	-1.3	179	179
EGR2	-0.57	0.61	-10000	0	-1.4	178	178
JAK2	-0.033	0.11	-10000	0	-0.58	21	21
JAK3	0.002	0.077	-10000	0	-0.53	12	12
PIK3R1	0.008	0.042	-10000	0	-0.58	3	3
JAK1	0.003	0.043	-10000	0	-0.58	3	3
COL1A2	-0.21	0.34	-10000	0	-1.2	46	46
CCL26	-0.58	0.62	-10000	0	-1.3	201	201
IL4R	-0.57	0.62	-10000	0	-1.4	178	178
PTPN6	0.023	0.012	-10000	0	-10000	0	0
IL13RA2	-0.59	0.63	-10000	0	-1.4	197	197
IL13RA1	-0.016	0.052	-10000	0	-0.6	3	3
IRF4	-0.27	0.5	-10000	0	-1.4	81	81
ARG1	-0.14	0.18	-10000	0	-0.79	16	16
CBL	-0.3	0.33	-10000	0	-0.74	136	136
GTF3A	0.012	0.04	-10000	0	-0.51	3	3
PIK3CA	0.009	0.034	-10000	0	-0.58	2	2
IL13RA1/JAK2	-0.032	0.096	-10000	0	-0.45	22	22
IRF4/BCL6	-0.24	0.46	-10000	0	-1.3	81	81
CD40LG	-0.037	0.16	-10000	0	-0.58	49	49
MAPK14	-0.29	0.34	-10000	0	-0.78	121	121
mitosis	-0.23	0.27	-10000	0	-0.68	84	84
STAT6	-0.65	0.76	-10000	0	-1.5	201	201
SPI1	-0.014	0.12	-10000	0	-0.52	30	30
RPS6KB1	-0.22	0.27	-10000	0	-0.68	74	74
STAT6 (dimer)	-0.65	0.78	-10000	0	-1.5	201	201
STAT6 (dimer)/PARP14	-0.59	0.64	-10000	0	-1.4	190	190
mast cell activation	0.012	0.013	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2	-0.25	0.3	-10000	0	-0.74	88	88
FRAP1	-0.24	0.29	-10000	0	-0.72	85	85
LTA	-0.56	0.61	-10000	0	-1.3	181	181
FES	0	0.08	-10000	0	-0.56	12	12
T-helper 1 cell differentiation	0.61	0.68	1.4	202	-10000	0	202
CCL11	-0.57	0.62	-10000	0	-1.4	192	192
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES	-0.24	0.3	-10000	0	-0.74	83	83
IL2RG	0.001	0.083	-10000	0	-0.56	13	13
IL10	-0.57	0.62	-10000	0	-1.4	179	179
IRS1	0.002	0.076	-10000	0	-0.58	10	10
IRS2	0.003	0.067	-10000	0	-0.54	9	9
IL4	-0.11	0.12	-10000	0	-10000	0	0
IL5	-0.53	0.57	-10000	0	-1.3	171	171
IL4/IL4R/JAK1/IL13RA1/JAK2	-0.41	0.42	-10000	0	-0.92	188	188
COL1A1	-0.25	0.4	-10000	0	-1.2	65	65
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1	-0.55	0.6	-10000	0	-1.4	166	166
IL2R gamma/JAK3	-0.001	0.083	-10000	0	-0.39	25	25
TFF3	-0.57	0.61	-10000	0	-1.3	191	191
ALOX15	-0.62	0.64	-10000	0	-1.4	218	218
MYBL1	0	0.079	-10000	0	-0.55	12	12
T-helper 2 cell differentiation	-0.43	0.44	-10000	0	-0.98	186	186
SHC1	0.011	0	-10000	0	-10000	0	0
CEBPB	0.009	0.042	-10000	0	-0.49	4	4
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2	-0.24	0.28	-10000	0	-0.68	82	82
mol:PI-3-4-5-P3	-0.24	0.29	-10000	0	-0.72	85	85
PI3K	-0.26	0.31	-10000	0	-0.78	85	85
DOK2	-0.012	0.11	-10000	0	-0.55	25	25
ETS1	0.015	0.063	-10000	0	-0.46	10	10
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2	-0.18	0.22	-10000	0	-0.62	43	43
ITGB3	-0.54	0.58	-10000	0	-1.3	175	175
PIGR	-0.68	0.7	-10000	0	-1.5	237	237
IGHE	0.041	0.051	0.26	10	-0.31	1	11
MAPKKK cascade	-0.18	0.22	-10000	0	-0.61	43	43
BCL6	0.01	0.038	-10000	0	-0.45	4	4
OPRM1	-0.53	0.57	-10000	0	-1.3	175	175
RETNLB	-0.68	0.67	-10000	0	-1.4	244	244
SELP	-0.6	0.66	-10000	0	-1.4	193	193
AICDA	-0.52	0.55	-10000	0	-1.2	179	179

×

Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Noncanonical Wnts/FZD	-0.13	0.21	-9999	-0.38	200	200
FZD6	0.005	0.064	-9999	-0.58	7	7
WNT6	-0.1	0.21	-9999	-0.5	131	131
WNT4	-0.054	0.18	-9999	-0.54	72	72
FZD3	-0.008	0.11	-9999	-0.58	20	20
WNT5A	-0.01	0.11	-9999	-0.55	23	23
WNT11	-0.14	0.25	-9999	-0.53	172	172

×

amb2 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2	-0.084	0.22	-9999	-0.48	120	120
alphaM/beta2 Integrin/GPIbA	-0.075	0.19	-9999	-0.44	117	117
alphaM/beta2 Integrin/proMMP-9	-0.1	0.24	-9999	-0.49	137	137
PLAUR	0.009	0.039	-9999	-0.54	3	3
HMGB1	-0.012	0.097	-9999	-0.59	16	16
alphaM/beta2 Integrin/Talin	-0.059	0.18	-9999	-0.44	97	97
AGER	-0.012	0.096	-9999	-0.58	16	16
RAP1A	0.01	0.024	-9999	-0.58	1	1
SELPLG	-0.006	0.099	-9999	-0.55	19	19
mol:LDL	0	0	-9999	-10000	0	0
alphaM/beta2 Integrin/RAGE/HMGB1	-0.09	0.21	-9999	-0.47	106	106
mol:GTP	0	0	-9999	-10000	0	0
MMP9	-0.062	0.18	-9999	-0.52	83	83
CYR61	-0.022	0.12	-9999	-0.48	41	41
TLN1	0.01	0.024	-9999	-0.58	1	1
Rap1/GTP	-0.12	0.17	-9999	-0.45	91	91
RHOA	0.01	0.024	-9999	-0.58	1	1
P-selectin oligomer	-0.087	0.22	-9999	-0.55	105	105
MYH2	-0.13	0.2	-9999	-0.46	117	117
MST1R	0.007	0.054	-9999	-0.58	5	5
leukocyte activation during inflammatory response	-0.14	0.19	-9999	-0.4	158	158
APOB	-0.12	0.22	-9999	-0.5	147	147
mol:GDP	0	0	-9999	-10000	0	0
complement component iC3b receptor activity	0	0	-9999	-10000	0	0
MMP2	-0.033	0.15	-9999	-0.53	50	50
JAM3	0.007	0.046	-9999	-0.46	6	6
GP1BA	-0.015	0.11	-9999	-0.52	28	28
alphaM/beta2 Integrin/CTGF	-0.069	0.19	-9999	-0.44	108	108
alphaM/beta2 Integrin	-0.14	0.21	-9999	-0.46	128	128
JAM3 homodimer	0.007	0.046	-9999	-0.46	6	6
ICAM2	0.002	0.069	-9999	-0.5	11	11
ICAM1	0.005	0.056	-9999	-0.51	7	7
phagocytosis triggered by activation of immune response cell surface activating receptor	-0.14	0.2	-9999	-0.45	128	128
cell adhesion	-0.074	0.19	-9999	-0.44	117	117
NFKB1	-0.11	0.25	-9999	-0.62	70	70
THY1	-0.001	0.081	-9999	-0.55	13	13
RhoA/GDP	0.008	0.018	-9999	-0.43	1	1
Lipoprotein(a)	-0.086	0.15	-9999	-0.31	181	181
alphaM/beta2 Integrin/LRP/tPA	-0.055	0.18	-9999	-0.45	87	87
IL6	-0.17	0.33	-9999	-0.78	105	105
ITGB2	-0.038	0.15	-9999	-0.54	47	47
elevation of cytosolic calcium ion concentration	-0.055	0.18	-9999	-0.45	84	84
alphaM/beta2 Integrin/JAM2/JAM3	-0.082	0.22	-9999	-0.5	108	108
JAM2	-0.05	0.18	-9999	-0.55	67	67
alphaM/beta2 Integrin/ICAM1	-0.065	0.19	-9999	-0.45	94	94
alphaM/beta2 Integrin/uPA/Plg	-0.082	0.2	-9999	-0.45	115	115
RhoA/GTP	-0.14	0.21	-9999	-0.48	116	116
positive regulation of phagocytosis	-0.13	0.21	-9999	-0.55	95	95
Ron/MSP	-0.018	0.12	-9999	-0.38	55	55
alphaM/beta2 Integrin/uPAR/uPA	-0.055	0.18	-9999	-0.45	84	84
alphaM/beta2 Integrin/uPAR	-0.061	0.18	-9999	-0.44	99	99
PLAU	-0.001	0.081	-9999	-0.51	15	15
PLAT	0	0.078	-9999	-0.54	12	12
actin filament polymerization	-0.13	0.19	-9999	-0.44	117	117
MST1	-0.033	0.15	-9999	-0.51	51	51
alphaM/beta2 Integrin/lipoprotein(a)	-0.13	0.2	-9999	-0.41	159	159
TNF	-0.11	0.26	-9999	-0.72	62	62
RAP1B	0.011	0	-9999	-10000	0	0
alphaM/beta2 Integrin/uPA	-0.066	0.19	-9999	-0.44	105	105
fibrinolysis	-0.082	0.2	-9999	-0.45	115	115
HCK	-0.017	0.12	-9999	-0.54	31	31
dendritic cell antigen processing and presentation	-0.14	0.2	-9999	-0.45	128	128
VTN	-0.054	0.17	-9999	-0.5	76	76
alphaM/beta2 Integrin/CYR61	-0.078	0.2	-9999	-0.43	123	123
LPA	-0.027	0.12	-9999	-0.46	43	43
LRP1	0.006	0.057	-9999	-0.56	6	6
cell migration	-0.11	0.26	-9999	-0.55	125	125
FN1	-0.088	0.21	-9999	-0.52	112	112
alphaM/beta2 Integrin/Thy1	-0.065	0.2	-9999	-0.46	101	101
MPO	-0.039	0.16	-9999	-0.53	55	55
KNG1	-0.11	0.22	-9999	-0.52	138	138
RAP1/GDP	0.015	0.015	-9999	-0.36	1	1
ROCK1	-0.13	0.2	-9999	-0.46	117	117
ELA2	0	0	-9999	-10000	0	0
PLG	-0.04	0.16	-9999	-0.58	46	46
CTGF	-0.006	0.09	-9999	-0.47	22	22
alphaM/beta2 Integrin/Hck	-0.074	0.22	-9999	-0.5	104	104
ITGAM	-0.072	0.19	-9999	-0.53	86	86
alphaM/beta2 Integrin/P-Selectin/PSGL1	-0.11	0.24	-9999	-0.48	145	145
HP	-0.077	0.19	-9999	-0.5	102	102
leukocyte adhesion	-0.13	0.22	-9999	-0.59	88	88
SELP	-0.087	0.22	-9999	-0.55	105	105

×

Syndecan-4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.069	0.18	-9999	-0.52	69	69
Syndecan-4/Syndesmos	-0.14	0.24	-9999	-0.55	120	120
positive regulation of JNK cascade	-0.14	0.23	-9999	-0.53	127	127
Syndecan-4/ADAM12	-0.18	0.28	-9999	-0.6	150	150
CCL5	-0.038	0.15	-9999	-0.51	57	57
Rac1/GDP	0.009	0	-9999	-10000	0	0
DNM2	0.01	0.024	-9999	-0.58	1	1
ITGA5	-0.006	0.093	-9999	-0.49	21	21
SDCBP	0.003	0.072	-9999	-0.58	9	9
PLG	-0.036	0.15	-9999	-0.56	46	46
ADAM12	-0.078	0.2	-9999	-0.51	103	103
mol:GTP	0	0	-9999	-10000	0	0
NUDT16L1	0.01	0.027	-9999	-0.46	2	2
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
Syndecan-4/PKC alpha	-0.031	0.04	-9999	-10000	0	0
Syndecan-4/Laminin alpha1	-0.17	0.26	-9999	-0.59	138	138
Syndecan-4/CXCL12/CXCR4	-0.15	0.25	-9999	-0.57	127	127
Syndecan-4/Laminin alpha3	-0.15	0.24	-9999	-0.56	126	126
MDK	-0.009	0.1	-9999	-0.51	24	24
Syndecan-4/FZD7	-0.14	0.24	-9999	-0.56	122	122
Syndecan-4/Midkine	-0.15	0.24	-9999	-0.57	124	124
FZD7	0	0.078	-9999	-0.5	14	14
Syndecan-4/FGFR1/FGF	-0.18	0.23	-9999	-0.56	130	130
THBS1	-0.002	0.084	-9999	-0.52	15	15
integrin-mediated signaling pathway	-0.17	0.26	-9999	-0.57	139	139
positive regulation of MAPKKK cascade	-0.14	0.23	-9999	-0.53	127	127
Syndecan-4/TACI	-0.18	0.26	-9999	-0.58	141	141
CXCR4	-0.016	0.12	-9999	-0.5	33	33
cell adhesion	-0.027	0.12	-9999	-0.33	59	59
Syndecan-4/Dynamin	-0.14	0.24	-9999	-0.56	118	118
Syndecan-4/TSP1	-0.14	0.24	-9999	-0.56	124	124
Syndecan-4/GIPC	-0.14	0.24	-9999	-0.56	119	119
Syndecan-4/RANTES	-0.16	0.25	-9999	-0.57	131	131
ITGB1	0.011	0	-9999	-10000	0	0
LAMA1	-0.059	0.18	-9999	-0.54	77	77
LAMA3	-0.014	0.11	-9999	-0.51	30	30
RAC1	0.011	0	-9999	-10000	0	0
PRKCA	0.038	0.056	-9999	-0.47	2	2
Syndecan-4/alpha-Actinin	-0.14	0.24	-9999	-0.56	118	118
TFPI	-0.009	0.1	-9999	-0.54	22	22
F2	-0.12	0.22	-9999	-0.5	150	150
alpha5/beta1 Integrin	0.004	0.067	-9999	-0.35	21	21
positive regulation of cell adhesion	-0.17	0.26	-9999	-0.58	141	141
ACTN1	0.011	0	-9999	-10000	0	0
TNC	-0.063	0.19	-9999	-0.52	85	85
Syndecan-4/CXCL12	-0.15	0.25	-9999	-0.57	127	127
FGF6	-0.001	0.026	-9999	-0.46	2	2
RHOA	0.01	0.024	-9999	-0.58	1	1
CXCL12	-0.013	0.11	-9999	-0.49	29	29
TNFRSF13B	-0.064	0.18	-9999	-0.52	84	84
FGF2	-0.039	0.16	-9999	-0.52	57	57
FGFR1	-0.01	0.1	-9999	-0.52	24	24
Syndecan-4/PI-4-5-P2	-0.14	0.24	-9999	-0.56	118	118
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.083	0.21	-9999	-0.51	112	112
cell migration	-0.006	0.017	-9999	-10000	0	0
PRKCD	0.016	0.009	-9999	-10000	0	0
vasculogenesis	-0.14	0.23	-9999	-0.54	124	124
SDC4	-0.15	0.25	-9999	-0.6	118	118
Syndecan-4/Tenascin C	-0.17	0.27	-9999	-0.59	139	139
Syndecan-4/PI-4-5-P2/PKC alpha	-0.024	0.032	-9999	-10000	0	0
Syndecan-4/Syntenin	-0.14	0.24	-9999	-0.55	124	124
MMP9	-0.062	0.18	-9999	-0.52	83	83
Rac1/GTP	-0.028	0.12	-9999	-0.34	59	59
cytoskeleton organization	-0.13	0.23	-9999	-0.53	120	120
GIPC1	0.007	0.048	-9999	-0.58	4	4
Syndecan-4/TFPI	-0.15	0.25	-9999	-0.57	124	124

×

Noncanonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC2	-0.039	0.16	-9999	-0.57	52	52
GNB1/GNG2	-0.11	0.2	-9999	-0.5	82	82
mol:DAG	-0.095	0.18	-9999	-0.46	81	81
PLCG1	-0.099	0.19	-9999	-0.47	81	81
YES1	-0.12	0.2	-9999	-0.52	84	84
FZD3	-0.008	0.11	-9999	-0.58	20	20
FZD6	0.005	0.064	-9999	-0.58	7	7
G protein	-0.099	0.19	-9999	-0.51	64	64
MAP3K7	-0.084	0.16	-9999	-0.43	67	67
mol:Ca2+	-0.092	0.17	-9999	-0.44	81	81
mol:IP3	-0.095	0.18	-9999	-0.46	81	81
NLK	-0.005	0.009	-9999	-10000	0	0
GNB1	0.011	0	-9999	-10000	0	0
CAMK2A	-0.096	0.17	-9999	-0.46	74	74
MAP3K7IP1	0	0	-9999	-10000	0	0
Noncanonical Wnts/FZD	-0.13	0.21	-9999	-0.38	200	200
CSNK1A1	0.009	0.034	-9999	-0.58	2	2
GNAS	-0.12	0.2	-9999	-0.52	80	80
GO:0007205	-0.094	0.18	-9999	-0.48	64	64
WNT6	-0.1	0.21	-9999	-0.5	131	131
WNT4	-0.054	0.18	-9999	-0.54	72	72
NFAT1/CK1 alpha	-0.12	0.22	-9999	-0.55	87	87
GNG2	0.003	0.067	-9999	-0.54	9	9
WNT5A	-0.01	0.11	-9999	-0.55	23	23
WNT11	-0.14	0.25	-9999	-0.53	172	172
CDC42	-0.11	0.2	-9999	-0.51	83	83

×

Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer	-0.028	0.14	-10000	0	-0.43	48	48
fibroblast growth factor receptor signaling pathway	-0.028	0.14	-10000	0	-0.43	48	48
LAMA1	-0.059	0.18	-10000	0	-0.54	77	77
PRNP	-0.003	0.091	-10000	0	-0.58	15	15
GPC1/SLIT2	-0.089	0.18	-10000	0	-0.39	159	159
SMAD2	0.015	0.065	-10000	0	-0.34	17	17
GPC1/PrPc/Cu2+	-0.002	0.078	-10000	0	-0.35	29	29
GPC1/Laminin alpha1	-0.043	0.15	-10000	0	-0.4	87	87
TDGF1	-0.073	0.21	-10000	0	-0.58	86	86
CRIPTO/GPC1	-0.055	0.16	-10000	0	-0.42	100	100
APP/GPC1	0.007	0.065	-10000	0	-0.4	15	15
mol:NO	0	0	-10000	0	-10000	0	0
YES1	-0.043	0.14	-10000	0	-0.35	106	106
FLT1	0.007	0.052	-10000	0	-0.56	5	5
GPC1/TGFB/TGFBR1/TGFBR2	0.012	0.062	-10000	0	-0.33	19	19
SERPINC1	-0.014	0.096	-10000	0	-0.46	27	27
FYN	-0.043	0.14	-10000	0	-0.36	105	105
FGR	-0.062	0.16	-10000	0	-0.37	131	131
positive regulation of MAPKKK cascade	-0.096	0.21	-10000	0	-0.46	125	125
SLIT2	-0.12	0.24	-10000	0	-0.53	150	150
GPC1/NRG	-0.052	0.16	-10000	0	-0.39	103	103
NRG1	-0.07	0.2	-10000	0	-0.53	91	91
GPC1/VEGF165 homodimer/VEGFR1 homodimer	0.012	0.066	-10000	0	-0.34	19	19
LYN	-0.039	0.14	-10000	0	-0.35	100	100
mol:Spermine	0	0.062	-10000	0	-0.4	14	14
cell growth	-0.028	0.14	-10000	0	-0.43	48	48
BMP signaling pathway	0.001	0.084	0.55	14	-10000	0	14
SRC	-0.039	0.14	-10000	0	-0.35	100	100
TGFBR1	0.007	0.048	-10000	0	-0.58	4	4
mol:Cu2+	0	0	-10000	0	-10000	0	0
PLA2G2A	-0.21	0.27	-10000	0	-0.53	244	244
GPC1	-0.001	0.085	-10000	0	-0.55	14	14
TGFBR1 (dimer)	0.007	0.048	-10000	0	-0.58	4	4
VEGFA	0.011	0.019	-10000	0	-0.46	1	1
BLK	-0.11	0.2	-10000	0	-0.38	206	206
HCK	-0.056	0.16	-10000	0	-0.36	123	123
FGF2	-0.039	0.16	-10000	0	-0.52	57	57
FGFR1	-0.01	0.1	-10000	0	-0.52	24	24
VEGFR1 homodimer	0.007	0.052	-10000	0	-0.56	5	5
TGFBR2	0.011	0.019	-10000	0	-0.46	1	1
cell death	0.007	0.064	-10000	0	-0.4	15	15
ATIII/GPC1	-0.01	0.091	-10000	0	-0.34	41	41
PLA2G2A/GPC1	-0.15	0.21	-10000	0	-0.39	250	250
LCK	-0.064	0.17	-10000	0	-0.38	130	130
neuron differentiation	-0.052	0.16	-10000	0	-0.39	103	103
PrPc/Cu2+	-0.002	0.067	-10000	0	-0.42	15	15
APP	0.01	0.024	-10000	0	-0.58	1	1
TGFBR2 (dimer)	0.011	0.019	-10000	0	-0.46	1	1

×

EGFR-dependent Endothelin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HRAS	0.008	0.041	-9999	-0.49	4	4
EGFR	0.005	0.058	-9999	-0.53	7	7
EGF/EGFR	-0.12	0.15	-9999	-0.34	132	132
EGF/EGFR dimer/SHC/GRB2/SOS1	-0.072	0.14	-9999	-0.3	95	95
mol:GTP	0	0	-9999	-10000	0	0
EDNRA	-0.021	0.13	-9999	-0.52	37	37
response to oxidative stress	0	0	-9999	-10000	0	0
EGF	-0.18	0.25	-9999	-0.51	222	222
EGF/EGFR dimer/SHC	-0.099	0.16	-9999	-0.3	228	228
mol:GDP	-0.073	0.14	-9999	-0.29	95	95
mol:Ca2+	0	0	-9999	-10000	0	0
EDN1	-0.023	0.13	-9999	-0.52	39	39
GRB2/SOS1	0.016	0.018	-9999	-0.42	1	1
HRAS/GTP	-0.085	0.11	-9999	-0.45	3	3
SHC1	0.011	0	-9999	-10000	0	0
HRAS/GDP	-0.087	0.11	-9999	-0.46	3	3
FRAP1	-0.071	0.13	-9999	-0.28	95	95
EGF/EGFR dimer	-0.13	0.19	-9999	-0.36	228	228
SOS1	0.01	0.024	-9999	-0.58	1	1
GRB2	0.011	0	-9999	-10000	0	0
ETA receptor/Endothelin-1	-0.031	0.13	-9999	-0.38	73	73

×

TCR signaling in naïve CD8+ T 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
GRB2/SOS1/SHC	-0.094	0.19	-10000	0	-0.54	79	79
FYN	-0.09	0.29	-10000	0	-0.7	88	88
LAT/GRAP2/SLP76	-0.11	0.23	-10000	0	-0.58	97	97
IKBKB	0.011	0.019	-10000	0	-0.46	1	1
AKT1	-0.052	0.19	-10000	0	-0.45	92	92
B2M	0.007	0.044	-10000	0	-0.52	4	4
IKBKG	-0.036	0.054	-10000	0	-0.16	70	70
MAP3K8	0.01	0.031	-10000	0	-0.52	2	2
mol:Ca2+	-0.024	0.04	-10000	0	-0.1	110	110
integrin-mediated signaling pathway	0.008	0.05	-10000	0	-0.32	13	13
LAT/GRAP2/SLP76/VAV1/PI3K Class IA	-0.091	0.28	-10000	0	-0.68	92	92
TRPV6	-0.094	0.19	-10000	0	-0.48	120	120
CD28	-0.031	0.15	-10000	0	-0.56	45	45
SHC1	-0.086	0.27	-10000	0	-0.67	87	87
receptor internalization	-0.095	0.3	-10000	0	-0.74	84	84
PRF1	-0.1	0.33	-10000	0	-1	55	55
KRAS	0.006	0.057	-10000	0	-0.56	6	6
GRB2	0.011	0	-10000	0	-10000	0	0
COT/AKT1	-0.034	0.15	-10000	0	-0.36	83	83
LAT	-0.094	0.28	-10000	0	-0.68	90	90
EntrezGene:6955	-0.001	0.004	-10000	0	-10000	0	0
CD3D	-0.033	0.15	-10000	0	-0.57	46	46
CD3E	-0.026	0.14	-10000	0	-0.57	39	39
CD3G	-0.055	0.18	-10000	0	-0.57	69	69
RASGRP2	-0.01	0.043	-10000	0	-0.17	31	31
RASGRP1	-0.057	0.2	-10000	0	-0.48	92	92
HLA-A	0.002	0.069	-10000	0	-0.53	10	10
RASSF5	0.001	0.076	-10000	0	-0.53	12	12
RAP1A/GTP/RAPL	0.008	0.05	-10000	0	-0.33	13	13
mol:GTP	0	0	-10000	0	-10000	0	0
mol:GDP	0	0.06	-10000	0	-0.12	77	77
PDK1/CARD11/BCL10/MALT1/TRAF6	-0.065	0.096	-10000	0	-0.27	88	88
PRKCA	-0.049	0.1	-10000	0	-0.28	78	78
GRAP2	-0.023	0.14	-10000	0	-0.55	37	37
mol:IP3	-0.058	0.19	0.2	77	-0.45	82	159
EntrezGene:6957	-0.001	0.005	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.089	0.29	-10000	0	-0.75	75	75
ORAI1	0.055	0.11	0.27	117	-0.33	1	118
CSK	-0.09	0.28	-10000	0	-0.71	82	82
B7 family/CD28	-0.12	0.32	-10000	0	-0.73	106	106
CHUK	0.007	0.048	-10000	0	-0.58	4	4
TCR/CD3/MHC I/CD8/LCK/ZAP-70	-0.11	0.33	-10000	0	-0.8	89	89
PTPN6	-0.09	0.28	-10000	0	-0.71	83	83
VAV1	-0.1	0.29	-10000	0	-0.71	93	93
Monovalent TCR/CD3	-0.067	0.26	-10000	0	-0.59	86	86
CBL	0.011	0	-10000	0	-10000	0	0
LCK	-0.099	0.3	-10000	0	-0.73	89	89
PAG1	-0.091	0.28	-10000	0	-0.7	87	87
RAP1A	0.01	0.024	-10000	0	-0.58	1	1
TCR/CD3/MHC I/CD8/LCK	-0.11	0.33	-10000	0	-0.8	88	88
CD80	-0.04	0.16	-10000	0	-0.57	53	53
CD86	-0.036	0.16	-10000	0	-0.54	52	52
PDK1/CARD11/BCL10/MALT1	-0.079	0.12	-10000	0	-0.32	93	93
HRAS	0.008	0.041	-10000	0	-0.49	4	4
GO:0035030	-0.09	0.25	-10000	0	-0.59	103	103
CD8A	-0.06	0.19	-10000	0	-0.54	79	79
CD8B	-0.047	0.17	-10000	0	-0.56	61	61
PTPRC	-0.044	0.17	-10000	0	-0.55	59	59
PDK1/PKC theta	-0.07	0.23	-10000	0	-0.56	93	93
CSK/PAG1	-0.084	0.27	-10000	0	-0.7	81	81
SOS1	0.01	0.024	-10000	0	-0.58	1	1
peptide-MHC class I	0.006	0.06	-10000	0	-0.38	14	14
GRAP2/SLP76	-0.12	0.27	-10000	0	-0.68	94	94
STIM1	0.03	0.053	0.2	3	-10000	0	3
RAS family/GTP	-0.003	0.083	-10000	0	-0.18	68	68
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin	-0.11	0.33	-10000	0	-0.82	84	84
mol:DAG	-0.069	0.15	0.13	1	-0.39	92	93
RAP1A/GDP	0.001	0.027	-10000	0	-0.15	1	1
PLCG1	0.01	0.024	-10000	0	-0.58	1	1
CD247	-0.017	0.12	-10000	0	-0.55	30	30
cytotoxic T cell degranulation	-0.097	0.31	-10000	0	-0.96	55	55
RAP1A/GTP	-0.006	0.015	-10000	0	-0.071	19	19
mol:PI-3-4-5-P3	-0.068	0.22	-10000	0	-0.54	92	92
LAT/GRAP2/SLP76/VAV1/PLCgamma1	-0.084	0.24	0.22	67	-0.58	88	155
NRAS	0.002	0.076	-10000	0	-0.58	10	10
ZAP70	-0.036	0.15	-10000	0	-0.53	52	52
GRB2/SOS1	0.016	0.018	-10000	0	-0.42	1	1
LAT/GRAP2/SLP76/VAV1	-0.11	0.22	-10000	0	-0.56	99	99
MALT1	0.007	0.054	-10000	0	-0.58	5	5
TRAF6	0.01	0.024	-10000	0	-0.58	1	1
CD8 heterodimer	-0.075	0.2	-10000	0	-0.46	118	118
CARD11	-0.12	0.22	-10000	0	-0.49	156	156
PRKCB	-0.064	0.13	-10000	0	-0.34	88	88
PRKCE	-0.049	0.1	-10000	0	-0.28	78	78
PRKCQ	-0.089	0.27	-10000	0	-0.64	96	96
LCP2	-0.015	0.12	-10000	0	-0.55	29	29
BCL10	0.007	0.048	-10000	0	-0.58	4	4
regulation of survival gene product expression	-0.041	0.16	-10000	0	-0.38	92	92
IKK complex	0.005	0.057	-10000	0	-0.12	59	59
RAS family/GDP	-0.007	0.016	-10000	0	-0.096	9	9
MAP3K14	-0.019	0.12	-10000	0	-0.29	65	65
PDPK1	-0.046	0.18	-10000	0	-0.42	92	92
TCR/CD3/MHC I/CD8/Fyn	-0.11	0.34	-10000	0	-0.78	94	94

×

BCR signaling pathway

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
JUN	-0.063	0.16	-10000	0	-0.4	86	86
IKBKB	-0.029	0.092	-10000	0	-0.25	34	34
AKT1	-0.051	0.11	0.21	1	-0.25	93	94
IKBKG	-0.03	0.098	-10000	0	-0.27	42	42
CALM1	-0.041	0.16	0.25	24	-0.47	51	75
PIK3CA	0.009	0.034	-10000	0	-0.58	2	2
MAP3K1	-0.11	0.24	-10000	0	-0.56	106	106
MAP3K7	0.011	0	-10000	0	-10000	0	0
mol:Ca2+	-0.05	0.17	0.25	24	-0.48	55	79
DOK1	0.011	0	-10000	0	-10000	0	0
AP-1	-0.023	0.1	0.2	19	-0.25	53	72
LYN	0.011	0	-10000	0	-10000	0	0
BLNK	-0.01	0.11	-10000	0	-0.58	22	22
SHC1	0.011	0	-10000	0	-10000	0	0
BCR complex	-0.1	0.22	-10000	0	-0.47	145	145
CD22	-0.16	0.28	-10000	0	-0.57	146	146
CAMK2G	-0.033	0.15	0.24	23	-0.44	49	72
CSNK2A1	0.011	0	-10000	0	-10000	0	0
INPP5D	-0.018	0.13	-10000	0	-0.58	30	30
SHC/GRB2/SOS1	-0.078	0.14	-10000	0	-0.46	45	45
GO:0007205	-0.051	0.17	0.25	24	-0.49	55	79
SYK	0.011	0.019	-10000	0	-0.46	1	1
ELK1	-0.043	0.16	0.24	23	-0.48	51	74
NFATC1	-0.1	0.22	-10000	0	-0.49	105	105
B-cell antigen/BCR complex	-0.1	0.22	-10000	0	-0.47	145	145
PAG1/CSK	0.012	0.048	-10000	0	-0.4	8	8
NFKBIB	-0.001	0.033	0.084	15	-0.12	2	17
HRAS	-0.039	0.16	0.23	23	-0.43	55	78
NFKBIA	-0.001	0.033	0.084	15	-0.12	2	17
NF-kappa-B/RelA/I kappa B beta	0.005	0.028	-10000	0	-0.17	1	1
RasGAP/Csk	-0.11	0.22	-10000	0	-0.44	145	145
mol:GDP	-0.046	0.16	0.26	24	-0.46	55	79
PTEN	0.006	0.059	-10000	0	-0.58	6	6
CD79B	-0.029	0.14	-10000	0	-0.51	47	47
NF-kappa-B/RelA/I kappa B alpha	0.005	0.028	-10000	0	-0.17	1	1
GRB2	0.011	0	-10000	0	-10000	0	0
PI3K/BCAP/CD19	-0.11	0.22	-10000	0	-0.49	126	126
PIK3R1	0.008	0.042	-10000	0	-0.58	3	3
mol:IP3	-0.052	0.18	0.26	24	-0.5	55	79
CSK	0.01	0.024	-10000	0	-0.58	1	1
FOS	-0.051	0.16	0.24	20	-0.42	71	91
CHUK	-0.032	0.1	-10000	0	-0.28	40	40
IBTK	0.002	0.076	-10000	0	-0.58	10	10
CARD11/BCL10/MALT1/TAK1	-0.1	0.17	-10000	0	-0.45	86	86
PTPN6	-0.13	0.27	-10000	0	-0.64	103	103
RELA	0.011	0	-10000	0	-10000	0	0
BCL2A1	-0.002	0.036	-10000	0	-0.11	28	28
VAV2	-0.16	0.29	-10000	0	-0.61	135	135
ubiquitin-dependent protein catabolic process	0.002	0.032	0.087	15	-0.11	2	17
BTK	-0.055	0.27	0.36	27	-1.1	36	63
CD19	-0.17	0.28	-10000	0	-0.53	171	171
MAP4K1	-0.045	0.17	-10000	0	-0.56	60	60
CD72	-0.005	0.089	-10000	0	-0.5	19	19
PAG1	0.005	0.06	-10000	0	-0.55	7	7
MAPK14	-0.089	0.2	-10000	0	-0.46	103	103
SH3BP5	0.003	0.072	-10000	0	-0.58	9	9
PIK3AP1	-0.055	0.18	0.3	2	-0.51	58	60
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72	-0.076	0.23	-10000	0	-0.52	98	98
RAF1	-0.031	0.15	0.23	23	-0.44	42	65
RasGAP/p62DOK/SHIP	-0.14	0.21	-10000	0	-0.6	72	72
CD79A	-0.11	0.23	-10000	0	-0.54	138	138
re-entry into mitotic cell cycle	-0.023	0.1	0.2	20	-0.25	54	74
RASA1	0.009	0.034	-10000	0	-0.58	2	2
MAPK3	-0.016	0.12	0.22	22	-0.41	28	50
MAPK1	-0.016	0.12	0.22	2	-0.41	28	30
CD72/SHP1	-0.12	0.26	-10000	0	-0.63	99	99
NFKB1	0.01	0.024	-10000	0	-0.58	1	1
MAPK8	-0.089	0.2	-10000	0	-0.47	101	101
actin cytoskeleton organization	-0.12	0.24	-10000	0	-0.54	116	116
NF-kappa-B/RelA	0.014	0.054	0.17	15	-0.22	2	17
Calcineurin	-0.054	0.12	-10000	0	-0.41	48	48
PI3K	-0.15	0.21	-10000	0	-0.53	115	115
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2	-0.056	0.17	0.31	2	-0.5	56	58
SOS1	0.01	0.024	-10000	0	-0.58	1	1
Bam32/HPK1	-0.15	0.34	-10000	0	-0.82	103	103
DAPP1	-0.17	0.36	-10000	0	-0.96	88	88
cytokine secretion	-0.093	0.2	-10000	0	-0.44	106	106
mol:DAG	-0.052	0.18	0.26	24	-0.5	55	79
PLCG2	-0.01	0.11	-10000	0	-0.55	23	23
MAP2K1	-0.024	0.14	0.22	22	-0.43	35	57
B-cell antigen/BCR complex/FcgammaRIIB	-0.14	0.25	-10000	0	-0.44	210	210
mol:PI-3-4-5-P3	-0.1	0.14	0.28	1	-0.36	112	113
ETS1	-0.027	0.14	0.24	23	-0.41	50	73
B-cell antigen/BCR complex/LYN/SYK/BLNK	-0.066	0.18	-10000	0	-0.38	128	128
B-cell antigen/BCR complex/LYN	-0.12	0.25	-10000	0	-0.53	121	121
MALT1	0.007	0.054	-10000	0	-0.58	5	5
TRAF6	0.011	0.024	-10000	0	-0.58	1	1
RAC1	-0.14	0.26	-10000	0	-0.59	115	115
B-cell antigen/BCR complex/LYN/SYK	-0.15	0.26	-10000	0	-0.66	98	98
CARD11	-0.1	0.22	0.25	20	-0.5	99	119
FCGR2B	-0.087	0.21	-10000	0	-0.54	109	109
PPP3CA	0.011	0	-10000	0	-10000	0	0
BCL10	0.008	0.048	-10000	0	-0.58	4	4
IKK complex	-0.006	0.041	0.092	15	-0.11	11	26
PTPRC	-0.043	0.17	-10000	0	-0.55	59	59
PDPK1	-0.053	0.11	0.19	1	-0.25	97	98
PPP3CB	0.011	0	-10000	0	-10000	0	0
PPP3CC	0.006	0.059	-10000	0	-0.58	6	6
POU2F2	0.004	0.029	-10000	0	-0.11	12	12

×

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	-0.002	0.088	-9999	-0.55	15	15
CCL5	-0.038	0.15	-9999	-0.51	57	57
SDCBP	0.003	0.072	-9999	-0.58	9	9
FGFR/FGF2/Syndecan-1	-0.12	0.2	-9999	-0.54	70	70
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
Syndecan-1/Laminin-5	-0.13	0.21	-9999	-0.5	102	102
Syndecan-1/Syntenin	-0.11	0.19	-9999	-0.51	77	77
MAPK3	-0.088	0.18	-9999	-0.52	54	54
HGF/MET	-0.021	0.12	-9999	-0.39	57	57
TGFB1/TGF beta receptor Type II	-0.002	0.088	-9999	-0.55	15	15
BSG	0.01	0.024	-9999	-0.58	1	1
keratinocyte migration	-0.13	0.21	-9999	-0.49	102	102
Syndecan-1/RANTES	-0.13	0.21	-9999	-0.51	103	103
Syndecan-1/CD147	-0.098	0.19	-9999	-0.5	70	70
Syndecan-1/Syntenin/PIP2	-0.11	0.19	-9999	-0.49	77	77
LAMA5	-0.031	0.15	-9999	-0.57	44	44
positive regulation of cell-cell adhesion	-0.11	0.18	-9999	-0.48	77	77
MMP7	-0.14	0.24	-9999	-0.52	170	170
HGF	-0.039	0.16	-9999	-0.55	55	55
Syndecan-1/CASK	-0.11	0.19	-9999	-0.52	70	70
Syndecan-1/HGF/MET	-0.12	0.22	-9999	-0.53	95	95
regulation of cell adhesion	-0.081	0.17	-9999	-0.5	54	54
HPSE	-0.005	0.092	-9999	-0.51	19	19
positive regulation of cell migration	-0.12	0.2	-9999	-0.54	70	70
SDC1	-0.12	0.2	-9999	-0.55	70	70
Syndecan-1/Collagen	-0.12	0.2	-9999	-0.54	70	70
PPIB	0.011	0	-9999	-10000	0	0
MET	0.01	0.031	-9999	-0.52	2	2
PRKACA	0.011	0	-9999	-10000	0	0
MMP9	-0.062	0.18	-9999	-0.52	83	83
MAPK1	-0.088	0.18	-9999	-0.52	53	53
homophilic cell adhesion	-0.12	0.2	-9999	-0.54	70	70
MMP1	-0.13	0.24	-9999	-0.53	161	161

×

IL12-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1	-0.068	0.19	-10000	0	-0.45	77	77
TBX21	-0.24	0.51	-10000	0	-1.1	120	120
B2M	0.005	0.045	-10000	0	-0.52	4	4
TYK2	0.007	0.034	-10000	0	-0.61	1	1
IL12RB1	-0.038	0.16	-10000	0	-0.57	50	50
GADD45B	-0.15	0.37	-10000	0	-0.92	73	73
IL12RB2	-0.039	0.16	-10000	0	-0.53	55	55
GADD45G	-0.16	0.38	-10000	0	-0.94	74	74
natural killer cell activation	-0.003	0.023	-10000	0	-10000	0	0
RELB	0.009	0.036	-10000	0	-0.5	3	3
RELA	0.011	0	-10000	0	-10000	0	0
IL18	0.003	0.069	-10000	0	-0.55	9	9
IL2RA	-0.047	0.17	-10000	0	-0.55	63	63
IFNG	-0.068	0.19	-10000	0	-0.52	89	89
STAT3 (dimer)	-0.15	0.37	-10000	0	-0.79	113	113
HLA-DRB5	-0.083	0.21	-10000	0	-0.52	107	107
FASLG	-0.24	0.52	-10000	0	-1.1	123	123
NF kappa B2 p52/RelB	-0.27	0.4	-10000	0	-0.96	124	124
CD4	-0.013	0.12	-10000	0	-0.56	26	26
SOCS1	-0.028	0.14	-10000	0	-0.5	47	47
EntrezGene:6955	-0.004	0.015	-10000	0	-10000	0	0
CD3D	-0.035	0.15	-10000	0	-0.57	46	46
CD3E	-0.028	0.14	-10000	0	-0.56	39	39
CD3G	-0.058	0.19	-10000	0	-0.57	69	69
IL12Rbeta2/JAK2	-0.035	0.15	-10000	0	-0.41	74	74
CCL3	-0.24	0.51	-10000	0	-1.1	120	120
CCL4	-0.22	0.49	-10000	0	-1.1	108	108
HLA-A	-0.001	0.069	-10000	0	-0.52	10	10
IL18/IL18R	-0.011	0.15	-10000	0	-0.38	72	72
NOS2	-0.28	0.56	-10000	0	-1.2	134	134
IL12/IL12R/TYK2/JAK2/SPHK2	-0.053	0.16	-10000	0	-0.41	71	71
IL1R1	-0.21	0.46	-10000	0	-1	111	111
IL4	0.005	0.024	-10000	0	-10000	0	0
JAK2	-0.012	0.11	-10000	0	-0.57	21	21
EntrezGene:6957	-0.004	0.015	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.18	0.45	-10000	0	-0.97	116	116
RAB7A	-0.11	0.32	-10000	0	-0.78	62	62
lysosomal transport	-0.1	0.3	-10000	0	-0.73	65	65
FOS	-0.17	0.41	-10000	0	-1.1	84	84
STAT4 (dimer)	-0.17	0.42	-10000	0	-0.92	109	109
STAT5A (dimer)	-0.3	0.42	-10000	0	-0.96	144	144
GZMA	-0.24	0.5	-10000	0	-1.1	112	112
GZMB	-0.25	0.51	-10000	0	-1.1	127	127
HLX	0.006	0.055	-10000	0	-0.54	6	6
LCK	-0.24	0.52	-10000	0	-1.1	129	129
TCR/CD3/MHC II/CD4	-0.12	0.33	-10000	0	-0.74	97	97
IL2/IL2R	-0.034	0.15	-10000	0	-0.42	68	68
MAPK14	-0.15	0.39	-10000	0	-0.89	92	92
CCR5	-0.17	0.42	-10000	0	-1.1	77	77
IL1B	-0.062	0.19	-10000	0	-0.54	79	79
STAT6	-0.036	0.12	0.2	10	-0.25	48	58
STAT4	-0.029	0.15	-10000	0	-0.56	43	43
STAT3	0.011	0	-10000	0	-10000	0	0
STAT1	0.006	0.054	-10000	0	-0.49	7	7
NFKB1	0.01	0.024	-10000	0	-0.58	1	1
NFKB2	0.01	0.031	-10000	0	-0.52	2	2
IL12B	-0.005	0.075	-10000	0	-0.47	14	14
CD8A	-0.063	0.19	-10000	0	-0.54	79	79
CD8B	-0.049	0.17	-10000	0	-0.56	61	61
T-helper 1 cell differentiation	0	0	-10000	0	-10000	0	0
natural killer cell mediated cytotoxicity	0.067	0.18	0.45	77	-10000	0	77
IL2RB	-0.018	0.13	-10000	0	-0.55	32	32
proteasomal ubiquitin-dependent protein catabolic process	-0.15	0.38	-10000	0	-0.82	109	109
IL2RG	-0.001	0.084	-10000	0	-0.56	13	13
IL12	-0.029	0.13	-10000	0	-0.4	61	61
STAT5A	0.011	0	-10000	0	-10000	0	0
CD247	-0.02	0.12	-10000	0	-0.55	30	30
IL2	0.001	0.027	-10000	0	-0.46	2	2
SPHK2	0.009	0.036	-10000	0	-0.5	3	3
FRAP1	0	0	-10000	0	-10000	0	0
IL12A	-0.039	0.16	-10000	0	-0.57	48	48
IL12/IL12R/TYK2/JAK2	-0.26	0.59	-10000	0	-1.2	127	127
MAP2K3	-0.16	0.39	-10000	0	-0.89	94	94
RIPK2	0.011	0	-10000	0	-10000	0	0
MAP2K6	-0.16	0.4	-10000	0	-0.9	95	95
regulation of dendritic cell antigen processing and presentation	0	0	-10000	0	-10000	0	0
HLA-DRA	-0.045	0.17	-10000	0	-0.52	64	64
IL18RAP	-0.033	0.16	-10000	0	-0.56	48	48
IL12Rbeta1/TYK2	-0.023	0.13	-10000	0	-0.43	51	51
EOMES	-0.14	0.41	-10000	0	-1.3	63	63
STAT1 (dimer)	-0.18	0.38	-10000	0	-0.82	125	125
T cell proliferation	-0.11	0.3	0.4	1	-0.65	107	108
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
IL18R1	-0.012	0.12	-10000	0	-0.57	25	25
CD8-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.2	0.28	-10000	0	-0.71	109	109
ATF2	-0.13	0.36	-10000	0	-0.84	81	81

×

FOXA2 and FOXA3 transcription factor networks

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
ACADVL	-0.28	0.36	-10000	0	-0.94	86	86
PCK1	-0.27	0.45	-10000	0	-1.3	81	81
HNF4A	-0.36	0.45	-10000	0	-1.1	111	111
KCNJ11	-0.27	0.38	-10000	0	-1	76	76
AKT1	-0.14	0.16	-10000	0	-0.46	20	20
response to starvation	-0.019	0.035	-10000	0	-10000	0	0
DLK1	-0.28	0.37	-10000	0	-1	75	75
NKX2-1	-0.18	0.35	-10000	0	-1.1	48	48
ACADM	-0.29	0.38	-10000	0	-0.98	89	89
TAT	-0.18	0.22	-10000	0	-0.68	44	44
CEBPB	0.004	0.042	-10000	0	-0.49	4	4
CEBPA	-0.007	0.098	-10000	0	-0.58	17	17
TTR	-0.3	0.41	-10000	0	-1.1	103	103
PKLR	-0.43	0.48	-10000	0	-1	185	185
APOA1	-0.38	0.49	-10000	0	-1.2	103	103
CPT1C	-0.3	0.4	-10000	0	-1	97	97
ALAS1	-0.12	0.18	-10000	0	-0.81	3	3
TFRC	-0.18	0.27	-10000	0	-0.96	27	27
FOXF1	0.012	0.11	0.28	8	-0.56	17	25
NF1	0.014	0.042	-10000	0	-0.58	3	3
HNF1A (dimer)	0.002	0.072	-10000	0	-0.58	6	6
CPT1A	-0.28	0.36	-10000	0	-0.98	75	75
HMGCS1	-0.29	0.37	-10000	0	-1	77	77
NR3C1	-0.037	0.13	-10000	0	-0.56	28	28
CPT1B	-0.3	0.39	-10000	0	-1	88	88
chromatin remodeling	0	0	-10000	0	-10000	0	0
SP1	0.008	0.044	-10000	0	-0.58	1	1
GCK	-0.3	0.39	-10000	0	-1	96	96
CREB1	-0.008	0.061	-10000	0	-0.61	2	2
IGFBP1	-0.27	0.4	-10000	0	-0.94	117	117
PDX1	-0.18	0.36	-10000	0	-1.4	38	38
UCP2	-0.29	0.38	-10000	0	-0.96	96	96
ALDOB	-0.38	0.49	-10000	0	-1.1	140	140
AFP	-0.069	0.17	-10000	0	-0.53	42	42
BDH1	-0.28	0.37	-10000	0	-1	74	74
HADH	-0.26	0.36	-10000	0	-1	69	69
F2	-0.42	0.53	-10000	0	-1.3	124	124
HNF1A	0.002	0.072	-10000	0	-0.58	6	6
G6PC	-0.032	0.14	-10000	0	-0.71	9	9
SLC2A2	-0.17	0.24	-10000	0	-0.88	18	18
INS	0.016	0.065	0.22	9	-0.47	3	12
FOXA1	-0.071	0.21	0.29	1	-0.57	81	82
FOXA3	-0.033	0.12	-10000	0	-0.53	20	20
FOXA2	-0.31	0.42	-10000	0	-1.1	89	89
ABCC8	-0.29	0.39	-10000	0	-1	80	80
ALB	-0.077	0.18	-10000	0	-0.54	37	37

×

Ephrin B reverse signaling

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
EFNB2	0.01	0.031	-10000	0	-0.52	2	2
EPHB2	0	0.079	-10000	0	-0.56	12	12
EFNB1	0.004	0.072	-10000	0	-0.36	23	23
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	-0.063	0.16	-10000	0	-0.49	35	35
Ephrin B2/EPHB1-2	-0.049	0.13	-10000	0	-0.27	136	136
neuron projection morphogenesis	-0.084	0.14	-10000	0	-0.47	35	35
Ephrin B1/EPHB1-2/Tiam1	-0.072	0.17	-10000	0	-0.42	63	63
DNM1	-0.007	0.096	-10000	0	-0.5	22	22
cell-cell signaling	0	0.002	-10000	0	-10000	0	0
MAP2K4	-0.079	0.23	-10000	0	-0.66	80	80
YES1	-0.12	0.3	-10000	0	-0.89	79	79
Ephrin B1/EPHB1-2/NCK2	-0.043	0.14	-10000	0	-0.34	56	56
PI3K	-0.079	0.24	-10000	0	-0.66	83	83
mol:GDP	-0.072	0.16	-10000	0	-0.42	63	63
ITGA2B	-0.043	0.16	-10000	0	-0.5	63	63
endothelial cell proliferation	0.014	0.019	-10000	0	-0.32	2	2
FYN	-0.12	0.3	-10000	0	-0.89	79	79
MAP3K7	-0.088	0.24	-10000	0	-0.7	79	79
FGR	-0.13	0.3	-10000	0	-0.88	81	81
TIAM1	-0.044	0.16	-10000	0	-0.52	63	63
PIK3R1	0.008	0.042	-10000	0	-0.58	3	3
RGS3	0.011	0	-10000	0	-10000	0	0
cell adhesion	-0.097	0.24	-10000	0	-0.63	86	86
LYN	-0.12	0.3	-10000	0	-0.89	79	79
Ephrin B1/EPHB1-2/Src Family Kinases	-0.11	0.28	-10000	0	-0.83	79	79
Ephrin B1/EPHB1-2	-0.11	0.26	-10000	0	-0.76	79	79
SRC	-0.12	0.3	-10000	0	-0.88	79	79
ITGB3	-0.008	0.1	-10000	0	-0.55	21	21
EPHB1	-0.1	0.21	-10000	0	-0.49	139	139
EPHB4	0.011	0	-10000	0	-10000	0	0
RAC1	0.011	0	-10000	0	-10000	0	0
Ephrin B2/EPHB4	0.014	0.019	-10000	0	-0.32	2	2
alphaIIb/beta3 Integrin	-0.037	0.14	-10000	0	-0.37	83	83
BLK	-0.14	0.31	-10000	0	-0.9	82	82
HCK	-0.12	0.3	-10000	0	-0.88	81	81
regulation of stress fiber formation	0.044	0.13	0.33	56	-10000	0	56
MAPK8	-0.07	0.22	-10000	0	-0.62	81	81
Ephrin B1/EPHB1-2/RGS3	-0.043	0.13	-10000	0	-0.33	57	57
endothelial cell migration	-0.072	0.21	-10000	0	-0.6	80	80
NCK2	0.01	0.024	-10000	0	-0.58	1	1
PTPN13	-0.093	0.25	-10000	0	-0.65	97	97
regulation of focal adhesion formation	0.044	0.13	0.33	56	-10000	0	56
chemotaxis	0.043	0.13	0.33	57	-10000	0	57
PIK3CA	0.009	0.034	-10000	0	-0.58	2	2
Rac1/GTP	-0.085	0.14	-10000	0	-0.48	35	35
angiogenesis	-0.11	0.25	-10000	0	-0.75	79	79
LCK	-0.13	0.31	-10000	0	-0.9	80	80

×

Signaling events mediated by the Hedgehog family

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB2	-0.052	0.22	-10000	0	-0.63	55	55
IHH	-0.039	0.17	-10000	0	-0.63	43	43
SHH Np/Cholesterol/GAS1	-0.082	0.16	-10000	0	-0.31	190	190
LRPAP1	0.01	0.024	-10000	0	-0.58	1	1
dorsoventral neural tube patterning	0.081	0.16	0.3	190	-10000	0	190
SMO/beta Arrestin2	-0.038	0.19	-10000	0	-0.64	35	35
SMO	-0.046	0.2	-10000	0	-0.67	37	37
AKT1	-0.005	0.11	-10000	0	-0.5	11	11
ARRB2	0.011	0	-10000	0	-10000	0	0
BOC	-0.032	0.14	-10000	0	-0.48	54	54
ADRBK1	0.01	0.031	-10000	0	-0.52	2	2
heart looping	-0.044	0.2	-10000	0	-0.64	39	39
STIL	-0.027	0.16	-10000	0	-0.58	30	30
DHH N/PTCH2	-0.041	0.16	-10000	0	-0.43	78	78
DHH N/PTCH1	-0.047	0.17	-10000	0	-0.44	54	54
PIK3CA	0.009	0.034	-10000	0	-0.58	2	2
DHH	-0.03	0.14	-10000	0	-0.54	44	44
PTHLH	-0.078	0.3	-10000	0	-0.92	54	54
determination of left/right symmetry	-0.044	0.2	-10000	0	-0.64	39	39
PIK3R1	0.008	0.042	-10000	0	-0.58	3	3
skeletal system development	-0.077	0.29	-10000	0	-0.91	54	54
IHH N/Hhip	-0.085	0.2	-10000	0	-0.46	128	128
DHH N/Hhip	-0.079	0.19	-10000	0	-0.42	132	132
mol:Cholesterol	0	0	-10000	0	-10000	0	0
heart development	-0.044	0.2	-10000	0	-0.64	39	39
pancreas development	-0.081	0.21	-10000	0	-0.55	100	100
HHAT	0.004	0.068	-10000	0	-0.58	8	8
PI3K	0.013	0.04	-10000	0	-0.43	5	5
EntrezGene:84976	0	0	-10000	0	-10000	0	0
GAS1	-0.13	0.24	-10000	0	-0.52	163	163
somite specification	-0.044	0.2	-10000	0	-0.64	39	39
SHH Np/Cholesterol/PTCH1	-0.033	0.17	-10000	0	-0.6	32	32
SHH Np/Cholesterol/PTCH2	-0.025	0.12	-10000	0	-0.32	80	80
SHH Np/Cholesterol/Megalin	-0.023	0.11	-10000	0	-0.36	36	36
SHH	-0.01	0.11	-10000	0	-0.41	40	40
catabolic process	-0.033	0.16	-10000	0	-0.43	60	60
SMO/Vitamin D3	-0.041	0.19	-10000	0	-0.63	40	40
SHH Np/Cholesterol/Hhip	-0.054	0.15	-10000	0	-0.36	95	95
LRP2	-0.027	0.12	-10000	0	-0.46	43	43
receptor-mediated endocytosis	-0.044	0.19	-10000	0	-0.63	37	37
SHH Np/Cholesterol/BOC	-0.026	0.12	-10000	0	-0.36	45	45
SHH Np/Cholesterol/CDO	-0.008	0.1	-10000	0	-0.36	41	41
mesenchymal cell differentiation	0.054	0.15	0.36	95	-10000	0	95
mol:Vitamin D3	-0.031	0.17	-10000	0	-0.6	32	32
IHH N/PTCH2	-0.044	0.16	-10000	0	-0.44	81	81
CDON	-0.001	0.081	-10000	0	-0.52	14	14
IHH N/PTCH1	-0.032	0.17	-10000	0	-0.43	60	60
Megalin/LRPAP1	-0.011	0.087	-10000	0	-0.32	44	44
PTCH2	-0.029	0.14	-10000	0	-0.54	44	44
SHH Np/Cholesterol	-0.009	0.083	-10000	0	-0.32	40	40
PTCH1	-0.033	0.16	-10000	0	-0.44	54	54
HHIP	-0.081	0.21	-10000	0	-0.55	100	100

×

TCGA08_retinoblastoma

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
CDKN2B	-0.012	0.1	-10000	0	-0.51	25	25
CDKN2C	0.019	0.017	-10000	0	-10000	0	0
CDKN2A	-0.07	0.19	-10000	0	-0.5	96	96
CCND2	0.019	0.074	0.2	56	-0.14	28	84
RB1	-0.016	0.079	-10000	0	-0.22	54	54
CDK4	0.027	0.077	0.24	49	-10000	0	49
CDK6	0.026	0.078	0.22	56	-10000	0	56
G1/S progression	0.016	0.079	0.22	54	-10000	0	54

×

HIF-1-alpha transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PKM2	-0.23	0.46	-9999	-1.1	68	68
HDAC7	0.011	0.025	-9999	-0.58	1	1
HIF1A/ARNT/Cbp/p300/Src-1	-0.19	0.33	-9999	-0.92	50	50
SMAD4	0.005	0.068	-9999	-0.58	8	8
ID2	-0.23	0.46	-9999	-1.1	67	67
AP1	-0.013	0.11	-9999	-0.39	45	45
ABCG2	-0.26	0.49	-9999	-1.2	81	81
HIF1A	-0.029	0.11	-9999	-0.68	9	9
TFF3	-0.25	0.49	-9999	-1.2	86	86
GATA2	-0.021	0.13	-9999	-0.56	34	34
AKT1	-0.023	0.088	-9999	-0.72	1	1
response to hypoxia	-0.037	0.086	-9999	-0.25	7	7
MCL1	-0.23	0.46	-9999	-1.1	69	69
NDRG1	-0.23	0.46	-9999	-1.1	68	68
SERPINE1	-0.24	0.48	-9999	-1.2	77	77
FECH	-0.23	0.46	-9999	-1.1	72	72
FURIN	-0.23	0.46	-9999	-1.1	70	70
NCOA2	0.004	0.066	-9999	-0.57	8	8
EP300	-0.015	0.12	-9999	-0.37	20	20
HMOX1	-0.23	0.47	-9999	-1.1	72	72
BHLHE40	-0.23	0.46	-9999	-1.1	69	69
BHLHE41	-0.24	0.48	-9999	-1.2	73	73
HIF1A/ARNT/SMAD3/SMAD4/SP1	-0.037	0.11	-9999	-0.49	17	17
ENG	-0.004	0.13	-9999	-0.5	13	13
JUN	0.006	0.052	-9999	-0.56	5	5
RORA	-0.24	0.48	-9999	-1.2	75	75
ABCB1	-0.22	0.39	-9999	-1.1	94	94
TFRC	-0.23	0.47	-9999	-1.1	69	69
CXCR4	-0.24	0.48	-9999	-1.2	78	78
TF	-0.28	0.5	-9999	-1.1	92	92
CITED2	-0.23	0.46	-9999	-1.2	66	66
HIF1A/ARNT	-0.3	0.51	-9999	-1.3	80	80
LDHA	-0.036	0.077	-9999	-1.1	2	2
ETS1	-0.23	0.47	-9999	-1.2	67	67
PGK1	-0.23	0.46	-9999	-1.2	66	66
NOS2	-0.28	0.51	-9999	-1.2	93	93
ITGB2	-0.24	0.49	-9999	-1.2	81	81
ALDOA	-0.23	0.46	-9999	-1.1	67	67
Cbp/p300/CITED2	-0.22	0.48	-9999	-1.2	63	63
FOS	-0.026	0.14	-9999	-0.54	41	41
HK2	-0.23	0.46	-9999	-1.1	73	73
SP1	0.005	0.043	-9999	-0.58	1	1
GCK	-0.054	0.3	-9999	-1.4	21	21
HK1	-0.23	0.46	-9999	-1.1	67	67
NPM1	-0.23	0.47	-9999	-1.2	68	68
EGLN1	-0.23	0.46	-9999	-1.1	67	67
CREB1	0.016	0.035	-9999	-0.58	2	2
PGM1	-0.23	0.46	-9999	-1.1	73	73
SMAD3	0.005	0.066	-9999	-0.57	8	8
EDN1	-0.064	0.28	-9999	-1.1	27	27
IGFBP1	-0.28	0.5	-9999	-1.1	103	103
VEGFA	-0.11	0.34	-9999	-0.85	31	31
HIF1A/JAB1	-0.024	0.069	-9999	-0.49	10	10
CP	-0.29	0.51	-9999	-1.2	100	100
CXCL12	-0.24	0.48	-9999	-1.2	73	73
COPS5	0.011	0.019	-9999	-0.46	1	1
SMAD3/SMAD4	0.007	0.07	-9999	-0.42	16	16
BNIP3	-0.26	0.49	-9999	-1.2	84	84
EGLN3	-0.24	0.47	-9999	-1.2	73	73
CA9	-0.31	0.52	-9999	-1.1	118	118
TERT	-0.25	0.48	-9999	-1.1	83	83
ENO1	-0.23	0.46	-9999	-1.1	67	67
PFKL	-0.23	0.47	-9999	-1.2	67	67
NCOA1	0.011	0.024	-9999	-0.58	1	1
ADM	-0.23	0.47	-9999	-1.1	77	77
ARNT	-0.021	0.078	-9999	-0.64	1	1
HNF4A	0.004	0.065	-9999	-0.58	7	7
ADFP	-0.23	0.46	-9999	-1.1	76	76
SLC2A1	-0.12	0.34	-9999	-0.88	34	34
LEP	-0.24	0.47	-9999	-1.2	73	73
HIF1A/ARNT/Cbp/p300	-0.2	0.34	-9999	-0.95	49	49
EPO	-0.094	0.3	-9999	-1	12	12
CREBBP	-0.013	0.12	-9999	-0.36	17	17
HIF1A/ARNT/Cbp/p300/HDAC7	-0.19	0.34	-9999	-0.95	45	45
PFKFB3	-0.23	0.46	-9999	-1.1	67	67
NT5E	-0.24	0.48	-9999	-1.2	71	71

×

Endothelins

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
AKT1	-0.037	0.23	-10000	0	-0.62	54	54
PTK2B	0.01	0.034	-10000	0	-0.59	2	2
mol:Ca2+	-0.027	0.25	-10000	0	-0.94	35	35
EDN1	-0.023	0.17	-10000	0	-0.44	56	56
EDN3	-0.097	0.22	-10000	0	-0.56	116	116
EDN2	-0.065	0.19	-10000	0	-0.53	86	86
HRAS/GDP	-0.046	0.19	-10000	0	-0.5	60	60
ETA receptor/Endothelin-1/Gq/GTP/PLC beta	-0.022	0.17	-10000	0	-0.45	50	50
ADCY4	-0.05	0.2	-10000	0	-0.54	59	59
ADCY5	-0.11	0.24	-10000	0	-0.54	95	95
ADCY6	-0.046	0.2	-10000	0	-0.54	55	55
ADCY7	-0.047	0.2	-10000	0	-0.54	57	57
ADCY1	-0.074	0.22	-10000	0	-0.54	74	74
ADCY2	-0.072	0.24	-10000	0	-0.6	72	72
ADCY3	-0.046	0.2	-10000	0	-0.54	55	55
ADCY8	-0.058	0.2	-10000	0	-0.54	58	58
ADCY9	-0.047	0.2	-10000	0	-0.54	56	56
arachidonic acid secretion	-0.068	0.2	-10000	0	-0.54	58	58
ETB receptor/Endothelin-1/Gq/GTP	-0.011	0.14	-10000	0	-0.47	30	30
GNAO1	-0.045	0.16	-10000	0	-0.49	68	68
HRAS	0.008	0.041	-10000	0	-0.49	4	4
ETA receptor/Endothelin-1/G12/GTP	-0.032	0.24	0.35	55	-0.6	49	104
ETA receptor/Endothelin-1/Gs/GTP	-0.046	0.24	0.33	55	-0.56	58	113
mol:GTP	0.001	0.004	-10000	0	-10000	0	0
COL3A1	-0.059	0.29	-10000	0	-0.75	67	67
EDNRB	-0.009	0.11	-10000	0	-0.57	20	20
response to oxidative stress	0	0	-10000	0	-10000	0	0
CYSLTR2	-0.072	0.29	-10000	0	-0.68	86	86
CYSLTR1	-0.066	0.29	-10000	0	-0.72	77	77
SLC9A1	-0.026	0.12	0.19	48	-0.31	49	97
mol:GDP	-0.054	0.2	-10000	0	-0.51	65	65
SLC9A3	-0.16	0.32	-10000	0	-0.62	160	160
RAF1	-0.049	0.18	-10000	0	-0.49	52	52
JUN	-0.01	0.2	-10000	0	-0.74	28	28
JAK2	-0.048	0.24	-10000	0	-0.6	66	66
mol:IP3	-0.023	0.17	-10000	0	-0.46	45	45
ETA receptor/Endothelin-1	-0.047	0.29	0.42	55	-0.65	64	119
PLCB1	-0.032	0.15	-10000	0	-0.57	45	45
PLCB2	0.004	0.061	-10000	0	-0.52	8	8
ETA receptor/Endothelin-3	-0.099	0.21	-10000	0	-0.45	139	139
FOS	-0.052	0.23	-10000	0	-0.82	35	35
Gai/GDP	-0.026	0.16	-10000	0	-0.82	20	20
CRK	0.011	0.019	-10000	0	-0.46	1	1
mol:Ca ++	-0.054	0.26	-10000	0	-0.66	68	68
BCAR1	0.008	0.043	-10000	0	-0.52	4	4
PRKCB1	-0.023	0.16	-10000	0	-0.44	45	45
GNAQ	0.006	0.059	-10000	0	-0.58	6	6
GNAZ	-0.013	0.11	-10000	0	-0.55	26	26
GNAL	-0.018	0.12	-10000	0	-0.51	34	34
Gs family/GDP	-0.091	0.17	-10000	0	-0.47	73	73
ETA receptor/Endothelin-1/Gq/GTP	-0.016	0.18	-10000	0	-0.49	46	46
MAPK14	-0.012	0.13	-10000	0	-0.46	28	28
TRPC6	-0.032	0.27	-10000	0	-1	35	35
GNAI2	0.011	0	-10000	0	-10000	0	0
GNAI3	0.011	0	-10000	0	-10000	0	0
GNAI1	-0.003	0.089	-10000	0	-0.56	15	15
ETB receptor/Endothelin-1/Gq/GTP/PLC beta	-0.019	0.14	-10000	0	-0.44	36	36
ETB receptor/Endothelin-2	-0.053	0.16	-10000	0	-0.39	105	105
ETB receptor/Endothelin-3	-0.077	0.18	-10000	0	-0.41	133	133
ETB receptor/Endothelin-1	-0.02	0.16	-10000	0	-0.41	58	58
MAPK3	-0.051	0.22	-10000	0	-0.68	43	43
MAPK1	-0.051	0.22	-10000	0	-0.69	41	41
Rac1/GDP	-0.044	0.19	-10000	0	-0.5	53	53
cAMP biosynthetic process	-0.074	0.21	-10000	0	-0.53	74	74
MAPK8	-0.021	0.23	-10000	0	-0.72	39	39
SRC	0.01	0.024	-10000	0	-0.59	1	1
ETB receptor/Endothelin-1/Gi/GTP	-0.02	0.12	-10000	0	-0.41	31	31
p130Cas/CRK/Src/PYK2	-0.056	0.22	-10000	0	-0.62	52	52
mol:K +	0	0	-10000	0	-10000	0	0
G12/GDP	-0.044	0.19	-10000	0	-0.49	59	59
COL1A2	-0.064	0.32	-10000	0	-0.83	66	66
EntrezGene:2778	0	0	-10000	0	-10000	0	0
ETA receptor/Endothelin-2	-0.076	0.19	-10000	0	-0.41	118	118
mol:DAG	-0.024	0.17	-10000	0	-0.46	45	45
MAP2K2	-0.047	0.19	-10000	0	-0.54	47	47
MAP2K1	-0.047	0.19	-10000	0	-0.54	48	48
EDNRA	-0.024	0.19	0.22	29	-0.52	55	84
positive regulation of muscle contraction	-0.026	0.21	-10000	0	-0.57	48	48
Gq family/GDP	-0.082	0.17	-10000	0	-0.56	49	49
HRAS/GTP	-0.053	0.18	-10000	0	-0.46	65	65
PRKCH	-0.02	0.16	-10000	0	-0.47	44	44
RAC1	0.011	0	-10000	0	-10000	0	0
PRKCA	-0.018	0.16	-10000	0	-0.49	34	34
PRKCB	-0.044	0.2	-10000	0	-0.5	69	69
PRKCE	-0.016	0.16	-10000	0	-0.48	36	36
PRKCD	-0.017	0.16	-10000	0	-0.47	37	37
PRKCG	-0.099	0.2	-10000	0	-0.47	81	81
regulation of vascular smooth muscle contraction	-0.062	0.26	-10000	0	-0.94	36	36
PRKCQ	-0.048	0.19	-10000	0	-0.5	57	57
PLA2G4A	-0.075	0.22	-10000	0	-0.59	58	58
GNA14	-0.006	0.1	-10000	0	-0.56	19	19
GNA15	-0.008	0.1	-10000	0	-0.55	22	22
GNA12	0.011	0	-10000	0	-10000	0	0
GNA11	0.007	0.05	-10000	0	-0.54	5	5
Rac1/GTP	-0.032	0.24	0.35	55	-0.6	49	104
MMP1	-0.16	0.37	-10000	0	-0.74	146	146

×

BMP 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS	-0.13	0.2	-9999	-0.38	189	189
SMAD6-7/SMURF1	0.019	0.045	-9999	-0.38	7	7
NOG	-0.024	0.12	-9999	-0.47	41	41
SMAD9	-0.064	0.17	-9999	-0.53	57	57
SMAD4	0.004	0.068	-9999	-0.58	8	8
SMAD5	-0.044	0.14	-9999	-0.46	27	27
BMP7/USAG1	-0.17	0.24	-9999	-0.44	245	245
SMAD5/SKI	-0.036	0.13	-9999	-0.45	24	24
SMAD1	0.022	0.045	-9999	-0.47	3	3
BMP2	-0.003	0.09	-9999	-0.55	16	16
SMAD1/SMAD1/SMAD4	-0.007	0.048	-9999	-0.48	3	3
BMPR1A	0.01	0.024	-9999	-0.58	1	1
BMPR1B	-0.092	0.21	-9999	-0.51	119	119
BMPR1A-1B/BAMBI	-0.078	0.17	-9999	-0.33	175	175
AHSG	-0.044	0.15	-9999	-0.46	66	66
CER1	-0.006	0.067	-9999	-0.46	13	13
BMP2-4/CER1	-0.011	0.1	-9999	-0.32	53	53
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA	-0.05	0.14	-9999	-0.42	46	46
BMP2-4 (homodimer)	-0.011	0.1	-9999	-0.38	42	42
RGMB	-0.013	0.1	-9999	-0.46	31	31
BMP6/BMPR2/BMPR1A-1B	-0.044	0.14	-9999	-0.34	68	68
RGMA	-0.074	0.2	-9999	-0.54	93	93
SMURF1	0.011	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP	-0.05	0.13	-9999	-0.39	44	44
BMP2-4/USAG1	-0.073	0.17	-9999	-0.35	155	155
SMAD6/SMURF1/SMAD5	-0.036	0.13	-9999	-0.45	25	25
SOSTDC1	-0.1	0.23	-9999	-0.56	124	124
BMP7/BMPR2/BMPR1A-1B	-0.11	0.19	-9999	-0.38	151	151
SKI	0.011	0	-9999	-10000	0	0
BMP6 (homodimer)	-0.009	0.1	-9999	-0.52	23	23
HFE2	-0.001	0.042	-9999	-0.46	5	5
ZFYVE16	-0.004	0.096	-9999	-0.58	16	16
MAP3K7	0.011	0	-9999	-10000	0	0
BMP2-4/CHRD	-0.02	0.13	-9999	-0.34	71	71
SMAD5/SMAD5/SMAD4	-0.04	0.13	-9999	-0.45	26	26
MAPK1	0.01	0.024	-9999	-0.58	1	1
TAK1/TAB family	-0.057	0.098	-9999	-0.38	29	29
BMP7 (homodimer)	-0.13	0.24	-9999	-0.54	155	155
NUP214	0.011	0	-9999	-10000	0	0
BMP6/FETUA	-0.037	0.13	-9999	-0.34	88	88
SMAD1/SKI	0.027	0.043	-9999	-0.44	3	3
SMAD6	0.006	0.055	-9999	-0.54	6	6
CTDSP2	0.011	0	-9999	-10000	0	0
BMP2-4/FETUA	-0.034	0.13	-9999	-0.3	103	103
MAP3K7IP1	0	0	-9999	-10000	0	0
GREM1	-0.086	0.21	-9999	-0.54	106	106
BMPR2 (homodimer)	0.007	0.054	-9999	-0.58	5	5
GADD34/PP1CA	0.013	0.062	-9999	-0.35	17	17
BMPR1A-1B (homodimer)	-0.059	0.15	-9999	-0.36	120	120
CHRDL1	-0.16	0.25	-9999	-0.52	199	199
ENDOFIN/SMAD1	0.019	0.071	-9999	-0.51	5	5
SMAD6-7/SMURF1/SMAD1	-0.001	0.05	-9999	-0.54	3	3
SMAD6/SMURF1	0.011	0	-9999	-10000	0	0
BAMBI	-0.049	0.17	-9999	-0.53	68	68
SMURF2	0.007	0.05	-9999	-0.53	5	5
BMP2-4/CHRDL1	-0.11	0.18	-9999	-0.33	227	227
BMP2-4/GREM1	-0.061	0.16	-9999	-0.34	140	140
SMAD7	0.009	0.034	-9999	-0.58	2	2
SMAD8A/SMAD8A/SMAD4	-0.059	0.16	-9999	-0.49	62	62
SMAD1/SMAD6	0.027	0.043	-9999	-0.44	3	3
TAK1/SMAD6	0.017	0	-9999	-10000	0	0
BMP7	-0.13	0.24	-9999	-0.54	155	155
BMP6	-0.009	0.1	-9999	-0.52	23	23
MAP3K7IP2	0	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1	-0.04	0.12	-9999	-0.36	45	45
PPM1A	0.011	0	-9999	-10000	0	0
SMAD1/SMURF2	0.025	0.054	-9999	-0.48	4	4
SMAD7/SMURF1	0.016	0.025	-9999	-0.42	2	2
CTDSPL	0.011	0	-9999	-10000	0	0
PPP1CA	0.011	0	-9999	-10000	0	0
XIAP	0.01	0.024	-9999	-0.58	1	1
CTDSP1	0.01	0.024	-9999	-0.58	1	1
PPP1R15A	0.011	0.019	-9999	-0.46	1	1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS	-0.082	0.18	-9999	-0.49	71	71
CHRD	-0.02	0.13	-9999	-0.55	34	34
BMPR2	0.007	0.054	-9999	-0.58	5	5
BMP2-4/BMPR2/BMPR1A-1B/RGM	-0.057	0.14	-9999	-0.43	44	44
BMP4	-0.012	0.11	-9999	-0.5	28	28
FST	-0.052	0.18	-9999	-0.53	71	71
BMP2-4/NOG	-0.022	0.12	-9999	-0.31	79	79
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1	-0.1	0.18	-9999	-0.35	151	151

×

Fc-epsilon receptor I signaling in mast cells

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
PPAP2A	0.01	0.031	-10000	0	-0.52	2	2
LAT2	-0.066	0.17	-10000	0	-0.49	59	59
AP1	-0.11	0.2	-10000	0	-0.6	73	73
mol:PIP3	-0.085	0.22	-10000	0	-0.57	74	74
IKBKB	-0.036	0.13	0.15	14	-0.31	79	93
AKT1	-0.054	0.16	-10000	0	-0.47	45	45
IKBKG	-0.036	0.13	0.15	14	-0.31	80	94
MS4A2	-0.082	0.21	-10000	0	-0.54	102	102
mol:Sphingosine-1-phosphate	0	0	-10000	0	-10000	0	0
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
MAP3K1	-0.055	0.19	-10000	0	-0.51	65	65
mol:Ca2+	-0.059	0.16	-10000	0	-0.41	74	74
LYN	0.009	0.006	-10000	0	-10000	0	0
CBLB	-0.063	0.17	-10000	0	-0.42	83	83
SHC1	0.011	0	-10000	0	-10000	0	0
RasGAP/p62DOK	0.011	0.054	-10000	0	-0.32	5	5
positive regulation of cell migration	0	0	-10000	0	-10000	0	0
INPP5D	-0.018	0.13	-10000	0	-0.58	30	30
PLD2	-0.079	0.18	-10000	0	-0.4	102	102
PTPN13	-0.098	0.2	-10000	0	-0.58	58	58
PTPN11	0.003	0.056	-10000	0	-0.6	5	5
GO:0007205	0	0	-10000	0	-10000	0	0
regulation of mast cell degranulation	-0.028	0.13	-10000	0	-0.36	44	44
SYK	0.008	0.02	-10000	0	-0.46	1	1
GRB2	0.011	0.001	-10000	0	-10000	0	0
LAT/PLCgamma1/GRB2/SLP76/GADs	-0.12	0.21	-10000	0	-0.59	75	75
LAT	-0.072	0.18	-10000	0	-0.48	66	66
PAK2	-0.067	0.21	-10000	0	-0.56	70	70
NFATC2	-0.084	0.18	-10000	0	-0.65	49	49
HRAS	-0.08	0.23	-10000	0	-0.61	72	72
GAB2	0.009	0.034	-10000	0	-0.58	2	2
PLA2G1B	0.03	0.026	-10000	0	-10000	0	0
Fc epsilon R1	-0.12	0.2	-10000	0	-0.4	189	189
Antigen/IgE/Fc epsilon R1	-0.11	0.19	-10000	0	-0.36	189	189
mol:GDP	-0.091	0.25	-10000	0	-0.67	72	72
JUN	0.007	0.052	-10000	0	-0.56	5	5
mol:Ca++	0	0	-10000	0	-10000	0	0
PIK3R1	0.008	0.042	-10000	0	-0.59	3	3
FOS	-0.026	0.14	-10000	0	-0.54	41	41
Antigen/IgE/Fc epsilon R1/LYN/SYK	-0.071	0.18	-10000	0	-0.43	84	84
CHUK	-0.037	0.13	0.15	14	-0.31	78	92
KLRG1	-0.067	0.17	-10000	0	-0.42	73	73
VAV1	-0.081	0.2	-10000	0	-0.53	73	73
calcium-dependent protein kinase C activity	0	0	-10000	0	-10000	0	0
CBL	-0.061	0.17	-10000	0	-0.47	59	59
negative regulation of mast cell degranulation	-0.071	0.17	-10000	0	-0.43	77	77
BTK	-0.095	0.26	-10000	0	-0.71	71	71
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK	-0.12	0.25	-10000	0	-0.55	112	112
GAB2/PI3K/SHP2	-0.093	0.16	-10000	0	-0.5	49	49
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP	-0.062	0.16	-10000	0	-0.45	58	58
RAF1	0.024	0.025	-10000	0	-10000	0	0
Fc epsilon R1/FcgammaRIIB/SHIP	-0.15	0.26	-10000	0	-0.47	189	189
FCER1G	-0.023	0.14	-10000	0	-0.54	39	39
FCER1A	-0.08	0.21	-10000	0	-0.56	95	95
Antigen/IgE/Fc epsilon R1/Fyn	-0.09	0.19	-10000	0	-0.38	138	138
MAPK3	0.03	0.026	-10000	0	-10000	0	0
MAPK1	0.03	0.026	-10000	0	-10000	0	0
NFKB1	0.01	0.024	-10000	0	-0.58	1	1
MAPK8	-0.006	0.073	-10000	0	-0.5	5	5
DUSP1	-0.006	0.091	-10000	0	-0.47	22	22
NF-kappa-B/RelA	-0.039	0.064	-10000	0	-0.22	22	22
actin cytoskeleton reorganization	-0.063	0.18	-10000	0	-0.59	41	41
mol:Glucocorticoid Dexamethasone	0	0	-10000	0	-10000	0	0
PI3K	-0.1	0.19	-10000	0	-0.56	69	69
FER	-0.066	0.17	-10000	0	-0.48	60	60
RELA	0.011	0	-10000	0	-10000	0	0
ITK	-0.051	0.13	-10000	0	-0.45	46	46
SOS1	0.01	0.024	-10000	0	-0.58	1	1
PLCG1	-0.088	0.25	-10000	0	-0.67	71	71
cytokine secretion	-0.029	0.046	-10000	0	-10000	0	0
SPHK1	-0.082	0.19	-10000	0	-0.46	88	88
PTK2	-0.066	0.19	-10000	0	-0.64	40	40
NTAL/PLCgamma1/GRB2/SLP76/GADs	-0.12	0.21	-10000	0	-0.61	73	73
EDG1	0	0	-10000	0	-10000	0	0
mol:DAG	-0.077	0.21	-10000	0	-0.55	74	74
MAP2K2	0.027	0.026	-10000	0	-10000	0	0
MAP2K1	0.026	0.03	-10000	0	-10000	0	0
MAP2K7	0.01	0.024	-10000	0	-0.58	1	1
KLRG1/SHP2	-0.063	0.16	-10000	0	-0.46	54	54
MAP2K4	0.008	0.078	-10000	0	-0.94	4	4
Fc epsilon R1/FcgammaRIIB	-0.14	0.26	-10000	0	-0.5	169	169
mol:Choline	-0.078	0.18	-10000	0	-0.39	102	102
SHC/Grb2/SOS1	-0.049	0.16	-10000	0	-0.51	41	41
FYN	0.005	0.06	-10000	0	-0.55	7	7
DOK1	0.011	0	-10000	0	-10000	0	0
PXN	-0.055	0.17	-10000	0	-0.58	40	40
HCLS1	-0.068	0.18	-10000	0	-0.46	74	74
PRKCB	-0.062	0.18	-10000	0	-0.44	84	84
FCGR2B	-0.087	0.21	-10000	0	-0.54	109	109
IGHE	-0.003	0.007	-10000	0	-10000	0	0
KLRG1/SHIP	-0.073	0.18	-10000	0	-0.44	77	77
LCP2	-0.016	0.12	-10000	0	-0.55	29	29
PLA2G4A	-0.14	0.22	-10000	0	-0.46	147	147
RASA1	0.009	0.034	-10000	0	-0.58	2	2
mol:Phosphatidic acid	-0.078	0.18	-10000	0	-0.39	102	102
IKK complex	-0.015	0.1	0.15	14	-0.24	59	73
WIPF1	-0.001	0.081	-10000	0	-0.55	13	13

×

Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FOXP3	-0.039	0.17	-10000	0	-0.62	48	48
NFATC2	-0.092	0.26	-10000	0	-0.67	67	67
NFATC3	-0.019	0.077	-10000	0	-0.29	3	3
CD40LG	-0.28	0.42	-10000	0	-1	111	111
ITCH	0.028	0.084	-10000	0	-0.81	5	5
CBLB	0.029	0.08	-10000	0	-0.85	4	4
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment	-0.28	0.46	-10000	0	-1.2	98	98
JUNB	0.007	0.05	-10000	0	-0.53	5	5
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.008	0.059	-10000	0	-0.37	14	14
T cell anergy	0.005	0.1	-10000	0	-0.55	14	14
TLE4	-0.057	0.21	-10000	0	-0.68	39	39
Jun/NFAT1-c-4/p21SNFT	-0.18	0.37	-10000	0	-1	69	69
AP-1/NFAT1-c-4	-0.3	0.48	-10000	0	-1.1	110	110
IKZF1	-0.076	0.26	-10000	0	-0.78	54	54
T-helper 2 cell differentiation	-0.13	0.26	-10000	0	-0.79	55	55
AP-1/NFAT1	-0.094	0.21	-10000	0	-0.55	67	67
CALM1	0.019	0.033	-10000	0	-0.3	3	3
EGR2	-0.14	0.36	-10000	0	-1.2	43	43
EGR3	-0.15	0.38	-10000	0	-1.2	51	51
NFAT1/FOXP3	-0.095	0.27	-10000	0	-0.74	69	69
EGR1	-0.01	0.1	-10000	0	-0.5	25	25
JUN	-0.009	0.059	-10000	0	-0.58	5	5
EGR4	-0.055	0.17	-10000	0	-0.51	75	75
mol:Ca2+	0.007	0.035	-10000	0	-0.32	3	3
GBP3	-0.11	0.31	-10000	0	-0.8	86	86
FOSL1	-0.024	0.13	-10000	0	-0.51	41	41
NFAT1-c-4/MAF/IRF4	-0.18	0.38	-10000	0	-1	77	77
DGKA	-0.053	0.2	-10000	0	-0.65	36	36
CREM	0.011	0.019	-10000	0	-0.46	1	1
NFAT1-c-4/PPARG	-0.15	0.35	-10000	0	-0.97	64	64
CTLA4	-0.097	0.29	-10000	0	-0.77	76	76
NFAT1-c-4 (dimer)/EGR1	-0.16	0.36	-10000	0	-0.98	68	68
NFAT1-c-4 (dimer)/EGR4	-0.19	0.37	-10000	0	-1	70	70
FOS	-0.042	0.14	-10000	0	-0.55	41	41
IFNG	-0.24	0.4	-10000	0	-0.98	110	110
T cell activation	-0.11	0.2	-10000	0	-0.72	20	20
MAF	0.001	0.074	-10000	0	-0.54	11	11
T-helper 2 cell lineage commitment	0	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	0.12	0.3	0.91	48	-10000	0	48
TNF	-0.18	0.35	-10000	0	-0.93	75	75
FASLG	-0.24	0.51	-10000	0	-1.4	77	77
TBX21	-0.062	0.19	-10000	0	-0.56	73	73
BATF3	-0.006	0.093	-10000	0	-0.51	20	20
PRKCQ	-0.052	0.18	-10000	0	-0.59	62	62
PTPN1	-0.049	0.19	-10000	0	-0.62	34	34
NFAT1-c-4/ICER1	-0.15	0.35	-10000	0	-1	59	59
GATA3	-0.017	0.12	-10000	0	-0.52	32	32
T-helper 1 cell differentiation	-0.22	0.4	-10000	0	-0.94	112	112
IL2RA	-0.27	0.42	-10000	0	-1.1	100	100
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
CASP3	-0.051	0.19	-10000	0	-0.63	34	34
E2F1	0.014	0.036	-10000	0	-0.49	3	3
PPARG	0.004	0.068	-10000	0	-0.58	8	8
SLC3A2	-0.049	0.19	-10000	0	-0.64	28	28
IRF4	-0.075	0.2	-10000	0	-0.54	95	95
PTGS2	-0.3	0.44	-10000	0	-0.98	133	133
CSF2	-0.31	0.44	-10000	0	-0.98	134	134
JunB/Fra1/NFAT1-c-4	-0.16	0.34	-10000	0	-0.97	62	62
IL4	-0.13	0.27	-10000	0	-0.84	54	54
IL5	-0.27	0.4	-10000	0	-0.98	95	95
IL2	-0.11	0.2	-10000	0	-0.75	18	18
IL3	-0.064	0.099	-10000	0	-0.79	7	7
RNF128	0.025	0.091	-10000	0	-0.63	11	11
NFATC1	-0.12	0.3	-10000	0	-0.93	47	47
CDK4	0.082	0.18	0.59	26	-10000	0	26
PTPRK	-0.049	0.19	-10000	0	-0.63	32	32
IL8	-0.31	0.45	-10000	0	-1	130	130
POU2F1	0.002	0.071	-10000	0	-0.55	10	10

×

Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity	0.06	0.16	0.4	107	-10000	0	107
KIRREL	-0.032	0.15	-10000	0	-0.58	39	39
Nephrin/NEPH1Par3/Par6/Atypical PKCs	-0.06	0.17	-10000	0	-0.4	107	107
PLCG1	0.01	0.024	-10000	0	-0.58	1	1
ARRB2	0.011	0	-10000	0	-10000	0	0
WASL	0.011	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/CD2AP	-0.057	0.16	-10000	0	-0.38	89	89
ChemicalAbstracts:57-88-5	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP	-0.023	0.11	-10000	0	-0.35	37	37
FYN	-0.042	0.13	-10000	0	-0.34	67	67
mol:Ca2+	-0.041	0.14	-10000	0	-0.37	63	63
mol:DAG	-0.041	0.14	-10000	0	-0.37	63	63
NPHS2	-0.02	0.09	-10000	0	-0.47	22	22
mol:IP3	-0.041	0.14	-10000	0	-0.37	63	63
regulation of endocytosis	-0.032	0.12	-10000	0	-0.32	63	63
Nephrin/NEPH1/podocin/Cholesterol	-0.047	0.13	-10000	0	-0.3	121	121
establishment of cell polarity	-0.06	0.16	-10000	0	-0.4	107	107
Nephrin/NEPH1/podocin/NCK1-2	-0.031	0.13	-10000	0	-0.48	18	18
Nephrin/NEPH1/beta Arrestin2	-0.032	0.12	-10000	0	-0.33	63	63
NPHS1	-0.058	0.17	-10000	0	-0.51	75	75
Nephrin/NEPH1/podocin	-0.042	0.13	-10000	0	-0.35	67	67
TJP1	0.01	0.024	-10000	0	-0.58	1	1
NCK1	0.009	0.034	-10000	0	-0.58	2	2
NCK2	0.01	0.024	-10000	0	-0.58	1	1
heterophilic cell adhesion	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/PLCgamma1	-0.041	0.14	-10000	0	-0.37	63	63
CD2AP	-0.016	0.12	-10000	0	-0.58	28	28
Nephrin/NEPH1/podocin/GRB2	-0.04	0.14	-10000	0	-0.36	63	63
GRB2	0.011	0	-10000	0	-10000	0	0
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
TRPC6	-0.053	0.15	-10000	0	-0.38	78	78
cytoskeleton organization	-0.027	0.13	-10000	0	-0.41	41	41
Nephrin/NEPH1	-0.041	0.12	-10000	0	-0.28	107	107
Nephrin/NEPH1/ZO-1	-0.04	0.14	-10000	0	-0.32	107	107

×

Reelin signaling 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDK5R1/CDK5	0.015	0.023	-9999	-0.32	3	3
VLDLR	-0.041	0.16	-9999	-0.55	57	57
CRKL	0.011	0	-9999	-10000	0	0
LRPAP1	0.01	0.024	-9999	-0.58	1	1
FYN	0.005	0.06	-9999	-0.55	7	7
ITGA3	0.008	0.043	-9999	-0.52	4	4
RELN/VLDLR/Fyn	-0.079	0.17	-9999	-0.4	101	101
MAPK8IP1/MKK7/MAP3K11/JNK1	0.021	0.068	-9999	-0.89	1	1
AKT1	-0.071	0.15	-9999	-0.47	34	34
MAP2K7	0.01	0.024	-9999	-0.58	1	1
RAPGEF1	0.01	0.024	-9999	-0.58	1	1
DAB1	-0.081	0.2	-9999	-0.52	104	104
RELN/LRP8/DAB1	-0.091	0.17	-9999	-0.32	200	200
LRPAP1/LRP8	0.014	0.036	-9999	-0.42	4	4
RELN/LRP8/DAB1/Fyn	-0.083	0.16	-9999	-0.36	115	115
DAB1/alpha3/beta1 Integrin	-0.11	0.16	-9999	-0.5	49	49
long-term memory	-0.11	0.2	-9999	-0.53	60	60
DAB1/LIS1	-0.11	0.16	-9999	-0.52	47	47
DAB1/CRLK/C3G	-0.11	0.16	-9999	-0.5	48	48
PIK3CA	0.009	0.034	-9999	-0.58	2	2
DAB1/NCK2	-0.12	0.16	-9999	-0.52	48	48
ARHGEF2	0.011	0	-9999	-10000	0	0
mol:Src family inhibitors PP1 and PP2	0	0	-9999	-10000	0	0
GRIN2A	-0.02	0.11	-9999	-0.48	35	35
CDK5R1	0.009	0.033	-9999	-0.46	3	3
RELN	-0.096	0.22	-9999	-0.52	121	121
PIK3R1	0.008	0.042	-9999	-0.58	3	3
RELN/LRP8/Fyn	-0.049	0.14	-9999	-0.36	70	70
GRIN2A/RELN/LRP8/DAB1/Fyn	-0.093	0.18	-9999	-0.38	131	131
MAPK8	0.01	0.024	-9999	-0.58	1	1
RELN/VLDLR/DAB1	-0.12	0.19	-9999	-0.34	235	235
ITGB1	0.011	0	-9999	-10000	0	0
MAP1B	-0.11	0.19	-9999	-0.38	158	158
RELN/LRP8	-0.046	0.14	-9999	-0.31	125	125
GRIN2B/RELN/LRP8/DAB1/Fyn	-0.1	0.19	-9999	-0.38	150	150
PI3K	0.013	0.04	-9999	-0.43	5	5
mol:PP2	0	0	-9999	-10000	0	0
alpha3/beta1 Integrin	0.014	0.032	-9999	-0.37	4	4
RAP1A	-0.076	0.16	-9999	-0.47	48	48
PAFAH1B1	0.011	0	-9999	-10000	0	0
MAPK8IP1	-0.01	0.11	-9999	-0.53	24	24
CRLK/C3G	0.016	0.018	-9999	-0.42	1	1
GRIN2B	-0.038	0.16	-9999	-0.56	52	52
NCK2	0.01	0.024	-9999	-0.58	1	1
neuron differentiation	-0.036	0.12	-9999	-0.38	28	28
neuron adhesion	-0.064	0.16	-9999	-0.48	37	37
LRP8	0.008	0.042	-9999	-0.58	3	3
GSK3B	-0.062	0.14	-9999	-0.45	36	36
RELN/VLDLR/DAB1/Fyn	-0.11	0.19	-9999	-0.38	147	147
MAP3K11	0.01	0.024	-9999	-0.58	1	1
RELN/VLDLR/DAB1/P13K	-0.081	0.15	-9999	-0.32	146	146
CDK5	0.011	0	-9999	-10000	0	0
MAPT	-0.063	0.18	-9999	-0.46	103	103
neuron migration	-0.065	0.16	-9999	-0.46	39	39
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1	-0.037	0.12	-9999	-0.38	28	28
RELN/VLDLR	-0.063	0.16	-9999	-0.35	99	99

×

Calcium signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC1	-0.02	0.085	-9999	-0.34	33	33
NFATC2	-0.035	0.11	-9999	-0.39	52	52
NFATC3	-0.002	0.033	-9999	-10000	0	0
CD40LG	-0.18	0.32	-9999	-0.72	111	111
PTGS2	-0.2	0.33	-9999	-0.69	145	145
JUNB	0.007	0.05	-9999	-0.53	5	5
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.01	0.015	-9999	-10000	0	0
CaM/Ca2+	-0.01	0.015	-9999	-10000	0	0
CALM1	0.006	0.011	-9999	-10000	0	0
JUN	0.001	0.053	-9999	-0.57	5	5
mol:Ca2+	-0.009	0.013	-9999	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0.004	0.007	-9999	-10000	0	0
FOSL1	-0.024	0.13	-9999	-0.51	41	41
CREM	0.011	0.019	-9999	-0.46	1	1
Jun/NFAT1-c-4/p21SNFT	-0.1	0.2	-9999	-0.52	74	74
FOS	-0.032	0.14	-9999	-0.54	41	41
IFNG	-0.19	0.33	-9999	-0.67	152	152
AP-1/NFAT1-c-4	-0.2	0.35	-9999	-0.74	132	132
FASLG	-0.19	0.32	-9999	-0.7	130	130
NFAT1-c-4/ICER1	-0.064	0.14	-9999	-0.4	58	58
IL2RA	-0.18	0.33	-9999	-0.76	107	107
FKBP12/FK506	0.009	0	-9999	-10000	0	0
CSF2	-0.21	0.34	-9999	-0.69	154	154
JunB/Fra1/NFAT1-c-4	-0.077	0.15	-9999	-0.4	75	75
IL4	-0.16	0.28	-9999	-0.63	117	117
IL2	-0.007	0.024	-9999	-10000	0	0
IL3	-0.031	0.092	-9999	-0.84	7	7
FKBP1A	0.011	0	-9999	-10000	0	0
BATF3	-0.006	0.093	-9999	-0.51	20	20
mol:FK506	0	0	-9999	-10000	0	0
POU2F1	0.002	0.071	-9999	-0.55	10	10

×

p75(NTR)-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Sortilin/TRAF6	0.016	0.025	-10000	0	-0.42	2	2
Necdin/E2F1	0.006	0.065	-10000	0	-0.37	17	17
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E	-0.056	0.16	-10000	0	-0.36	107	107
NGF (dimer)/p75(NTR)/BEX1	-0.1	0.2	-10000	0	-0.38	181	181
NT-4/5 (dimer)/p75(NTR)	-0.066	0.16	-10000	0	-0.37	124	124
IKBKB	0.011	0.019	-10000	0	-0.46	1	1
AKT1	-0.042	0.14	-10000	0	-0.34	88	88
IKBKG	0.01	0.024	-10000	0	-0.58	1	1
BDNF	-0.021	0.13	-10000	0	-0.53	36	36
MGDIs/NGR/p75(NTR)/LINGO1	-0.062	0.16	-10000	0	-0.42	62	62
FURIN	0.01	0.031	-10000	0	-0.52	2	2
proBDNF (dimer)/p75(NTR)/Sortilin	-0.053	0.15	-10000	0	-0.33	131	131
LINGO1	-0.023	0.12	-10000	0	-0.47	44	44
Sortilin/TRAF6/NRIF	-0.008	0.051	-10000	0	-0.8	1	1
proBDNF (dimer)	-0.021	0.13	-10000	0	-0.53	36	36
NTRK1	-0.037	0.15	-10000	0	-0.53	53	53
RTN4R	-0.003	0.085	-10000	0	-0.48	18	18
neuron apoptosis	-0.06	0.17	-10000	0	-0.59	26	26
IRAK1	0.01	0.031	-10000	0	-0.52	2	2
SHC1	-0.059	0.16	-10000	0	-0.35	132	132
ARHGDIA	0.008	0.042	-10000	0	-0.58	3	3
RhoA/GTP	0.008	0.018	-10000	0	-0.43	1	1
Gamma Secretase	0.03	0.035	-10000	0	-0.3	7	7
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1	-0.053	0.16	-10000	0	-0.38	89	89
MAGEH1	0.001	0.078	-10000	0	-0.57	11	11
proNGF (dimer)/p75(NTR)/Sortilin/Necdin	-0.053	0.16	-10000	0	-0.39	89	89
Mammalian IAPs/DIABLO	0.006	0.1	-10000	0	-0.45	22	22
proNGF (dimer)	-0.032	0.15	-10000	0	-0.52	48	48
MAGED1	0.011	0	-10000	0	-10000	0	0
APP	0.01	0.024	-10000	0	-0.58	1	1
NT-4/5 (dimer)	-0.013	0.089	-10000	0	-0.46	23	23
ZNF274	0.002	0.076	-10000	0	-0.58	10	10
RhoA/GDP/RHOGDI	-0.046	0.14	-10000	0	-0.34	86	86
NGF	-0.032	0.15	-10000	0	-0.53	48	48
cell cycle arrest	-0.051	0.14	-10000	0	-0.34	82	82
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK	-0.024	0.11	-10000	0	-0.31	24	24
NT-4/5 (dimer)/p75(NTR)/TRAF6	-0.049	0.14	-10000	0	-0.38	49	49
NCSTN	0.011	0	-10000	0	-10000	0	0
mol:GTP	-0.078	0.18	-10000	0	-0.37	154	154
PSENEN	0.01	0.024	-10000	0	-0.58	1	1
mol:ceramide	-0.048	0.15	-10000	0	-0.37	82	82
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs	-0.012	0.098	-10000	0	-0.44	8	8
p75(NTR)/beta APP	-0.05	0.15	-10000	0	-0.36	107	107
BEX1	-0.058	0.17	-10000	0	-0.5	79	79
mol:GDP	-0.067	0.16	-10000	0	-0.36	132	132
NGF (dimer)	-0.11	0.18	-10000	0	-0.38	144	144
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI	-0.05	0.15	-10000	0	-0.39	63	63
PIK3R1	0.008	0.042	-10000	0	-0.58	3	3
RAC1/GTP	-0.05	0.14	-10000	0	-0.35	82	82
MYD88	0.011	0	-10000	0	-10000	0	0
CHUK	0.007	0.048	-10000	0	-0.58	4	4
NGF (dimer)/p75(NTR)/PKA	-0.078	0.18	-10000	0	-0.38	154	154
RHOB	0.009	0.039	-10000	0	-0.54	3	3
RHOA	0.01	0.024	-10000	0	-0.58	1	1
MAGE-G1/E2F1	0.015	0.026	-10000	0	-0.36	3	3
NT3 (dimer)	-0.018	0.12	-10000	0	-0.53	33	33
TP53	-0.061	0.16	-10000	0	-0.55	20	20
PRDM4	-0.048	0.15	-10000	0	-0.37	82	82
BDNF (dimer)	-0.18	0.22	-10000	0	-0.43	212	212
PIK3CA	0.009	0.034	-10000	0	-0.58	2	2
SORT1	0.01	0.024	-10000	0	-0.58	1	1
activation of caspase activity	-0.058	0.16	-10000	0	-0.36	107	107
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.047	0.15	-10000	0	-0.37	83	83
RHOC	0.011	0	-10000	0	-10000	0	0
XIAP	0.01	0.024	-10000	0	-0.58	1	1
MAPK10	-0.042	0.16	-10000	0	-0.5	31	31
DIABLO	0.011	0	-10000	0	-10000	0	0
SMPD2	-0.048	0.15	-10000	0	-0.37	82	82
APH1B	0.006	0.059	-10000	0	-0.58	6	6
APH1A	0.011	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin	-0.06	0.16	-10000	0	-0.36	132	132
PSEN1	0.011	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0.014	0.036	-10000	0	-0.42	4	4
NT3 (dimer)/p75(NTR)	-0.07	0.17	-10000	0	-0.39	128	128
MAPK8	-0.026	0.14	-10000	0	-0.52	17	17
MAPK9	-0.025	0.14	-10000	0	-0.52	17	17
APAF1	0.008	0.042	-10000	0	-0.58	3	3
NTF3	-0.018	0.12	-10000	0	-0.53	33	33
NTF4	-0.013	0.09	-10000	0	-0.46	23	23
NDN	-0.001	0.082	-10000	0	-0.53	14	14
RAC1/GDP	0.009	0	-10000	0	-10000	0	0
RhoA-B-C/GDP	-0.074	0.14	-10000	0	-0.47	33	33
p75 CTF/Sortilin/TRAF6/NRIF	0.022	0.061	-10000	0	-0.37	12	12
RhoA-B-C/GTP	-0.078	0.18	-10000	0	-0.37	154	154
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.038	0.14	-10000	0	-0.58	15	15
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.041	0.14	-10000	0	-0.37	61	61
PRKACB	-0.02	0.13	-10000	0	-0.57	33	33
proBDNF (dimer)/p75 ECD	-0.008	0.097	-10000	0	-0.38	38	38
ChemicalAbstracts:86-01-1	0	0	-10000	0	-10000	0	0
BIRC3	-0.016	0.12	-10000	0	-0.53	31	31
BIRC2	-0.001	0.086	-10000	0	-0.58	13	13
neuron projection morphogenesis	-0.065	0.16	0.19	18	-0.39	84	102
BAD	-0.027	0.15	-10000	0	-0.49	22	22
RIPK2	0.011	0	-10000	0	-10000	0	0
NGFR	-0.08	0.2	-10000	0	-0.51	106	106
CYCS	-0.047	0.15	-10000	0	-0.36	95	95
ADAM17	0.009	0.034	-10000	0	-0.58	2	2
NGF (dimer)/p75(NTR)/TRAF6/RIP2	-0.047	0.15	-10000	0	-0.37	83	83
BCL2L11	-0.026	0.15	-10000	0	-0.49	22	22
BDNF (dimer)/p75(NTR)	-0.071	0.18	-10000	0	-0.39	131	131
PI3K	-0.049	0.15	-10000	0	-0.36	87	87
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1	-0.047	0.15	-10000	0	-0.37	82	82
NDNL2	0.011	0	-10000	0	-10000	0	0
YWHAE	0.011	0	-10000	0	-10000	0	0
PRKCI	0.008	0.042	-10000	0	-0.58	3	3
NGF (dimer)/p75(NTR)	-0.079	0.19	-10000	0	-0.42	132	132
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE	-0.047	0.15	-10000	0	-0.37	82	82
TRAF6	0.01	0.024	-10000	0	-0.58	1	1
RAC1	0.011	0	-10000	0	-10000	0	0
PRKCZ	0.01	0.031	-10000	0	-0.52	2	2
PLG	-0.04	0.16	-10000	0	-0.58	46	46
oligodendrocyte cell fate commitment	0	0	-10000	0	-10000	0	0
CASP6	-0.057	0.16	-10000	0	-0.42	65	65
SQSTM1	0.011	0	-10000	0	-10000	0	0
NGFRAP1	-0.023	0.14	-10000	0	-0.58	35	35
CASP3	-0.023	0.14	-10000	0	-0.45	22	22
E2F1	0.009	0.036	-10000	0	-0.5	3	3
CASP9	0.01	0.024	-10000	0	-0.58	1	1
IKK complex	-0.06	0.12	-10000	0	-0.52	20	20
NGF (dimer)/TRKA	-0.049	0.16	-10000	0	-0.41	91	91
MMP7	-0.14	0.24	-10000	0	-0.52	170	170
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.044	0.15	-10000	0	-0.36	89	89
MMP3	-0.13	0.24	-10000	0	-0.54	161	161
APAF-1/Caspase 9	-0.067	0.14	-10000	0	-0.57	25	25

×

TCGA08_p53

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
CDKN2A	-0.051	0.14	-10000	0	-0.37	96	96
TP53	-0.048	0.11	0.25	1	-0.36	56	57
Senescence	-0.048	0.11	0.25	1	-0.36	56	57
Apoptosis	-0.048	0.11	0.25	1	-0.36	56	57
Activated_Oncogenes	0	0	-10000	0	-10000	0	0
MDM2	0.031	0.084	0.26	41	-0.34	4	45
MDM4	0.01	0.031	-10000	0	-0.52	2	2

×

Thromboxane A2 receptor 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
TGM2	-0.005	0.093	-10000	0	-0.55	17	17
GNB1/GNG2	-0.054	0.07	-10000	0	-0.2	84	84
AKT1	-0.024	0.093	-10000	0	-0.21	60	60
EGF	-0.18	0.25	-10000	0	-0.51	222	222
mol:TXA2	0	0.001	-10000	0	-10000	0	0
FGR	-0.034	0.12	-10000	0	-0.41	27	27
mol:Ca2+	-0.049	0.13	-10000	0	-0.3	86	86
LYN	-0.018	0.095	-10000	0	-0.42	10	10
RhoA/GTP	-0.031	0.046	-10000	0	-0.14	46	46
mol:PGI2	0	0	-10000	0	-10000	0	0
SYK	-0.054	0.14	-10000	0	-0.35	81	81
GNG2	0.003	0.067	-10000	0	-0.54	9	9
ARRB2	0.011	0	-10000	0	-10000	0	0
TP alpha/Gq family/GDP/G beta5/gamma2	-0.006	0.11	-10000	0	-0.47	24	24
G beta5/gamma2	-0.069	0.093	-10000	0	-0.26	88	88
PRKCH	-0.055	0.15	-10000	0	-0.35	83	83
DNM1	-0.007	0.096	-10000	0	-0.5	22	22
TXA2/TP beta/beta Arrestin3	-0.016	0.037	-10000	0	-0.25	7	7
mol:GTP	0	0.001	-10000	0	-10000	0	0
PTGDR	-0.12	0.23	-10000	0	-0.51	155	155
G12 family/GTP	-0.075	0.11	-10000	0	-0.31	84	84
ADRBK1	0.01	0.031	-10000	0	-0.52	2	2
ADRBK2	-0.002	0.088	-10000	0	-0.58	14	14
RhoA/GTP/ROCK1	0.006	0.056	-10000	0	-0.39	11	11
mol:GDP	0.046	0.11	0.32	47	-10000	0	47
mol:NADP	-0.008	0.1	-10000	0	-0.54	21	21
RAB11A	0.011	0	-10000	0	-10000	0	0
PRKG1	-0.025	0.14	-10000	0	-0.56	38	38
mol:IP3	-0.064	0.16	-10000	0	-0.38	86	86
cell morphogenesis	0.006	0.056	-10000	0	-0.39	11	11
PLCB2	-0.09	0.21	-10000	0	-0.52	85	85
mol:cGMP	0	0.001	-10000	0	-10000	0	0
BLK	-0.073	0.14	-10000	0	-0.4	52	52
mol:PDG2	0	0	-10000	0	-10000	0	0
HCK	-0.03	0.12	-10000	0	-0.44	21	21
RHOA	0.01	0.024	-10000	0	-0.58	1	1
PTGIR	-0.007	0.095	-10000	0	-0.51	21	21
PRKCB1	-0.061	0.15	-10000	0	-0.37	84	84
GNAQ	0.006	0.059	-10000	0	-0.58	6	6
mol:L-citrulline	-0.008	0.1	-10000	0	-0.54	21	21
TXA2/TXA2-R family	-0.093	0.21	-10000	0	-0.53	87	87
LCK	-0.036	0.12	-10000	0	-0.42	24	24
TXA2/TP beta/beta Arrestin3/RAB11/GDP	-0.05	0.097	-10000	0	-0.5	9	9
TXA2-R family/G12 family/GDP/G beta/gamma	0.006	0.041	-10000	0	-0.3	1	1
TXA2/TP beta/beta Arrestin2/RAB11/GDP	-0.047	0.095	-10000	0	-0.49	9	9
MAPK14	-0.03	0.1	-10000	0	-0.23	74	74
TGM2/GTP	-0.078	0.18	-10000	0	-0.45	84	84
MAPK11	-0.034	0.1	-10000	0	-0.24	78	78
ARHGEF1	-0.024	0.08	-10000	0	-0.18	63	63
GNAI2	0.011	0	-10000	0	-10000	0	0
JNK cascade	-0.066	0.16	-10000	0	-0.39	87	87
RAB11/GDP	0.012	0.001	-10000	0	-10000	0	0
ICAM1	-0.043	0.12	-10000	0	-0.29	75	75
cAMP biosynthetic process	-0.067	0.15	-10000	0	-0.37	85	85
Gq family/GTP/EBP50	0.004	0.079	-10000	0	-0.34	20	20
actin cytoskeleton reorganization	0.006	0.056	-10000	0	-0.39	11	11
SRC	-0.019	0.096	-10000	0	-0.42	11	11
GNB5	0.007	0.048	-10000	0	-0.58	4	4
GNB1	0.011	0	-10000	0	-10000	0	0
EGF/EGFR	-0.063	0.12	-10000	0	-0.33	58	58
VCAM1	-0.052	0.14	-10000	0	-0.33	88	88
TP beta/Gq family/GDP/G beta5/gamma2	-0.006	0.11	-10000	0	-0.47	24	24
platelet activation	-0.043	0.14	-10000	0	-0.3	85	85
PGI2/IP	-0.005	0.069	-10000	0	-0.37	21	21
PRKACA	-0.048	0.12	-10000	0	-0.31	69	69
Gq family/GDP/G beta5/gamma2	-0.01	0.1	-10000	0	-0.44	25	25
TXA2/TP beta/beta Arrestin2	-0.017	0.066	-10000	0	-0.49	9	9
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TBXA2R	-0.042	0.12	-10000	0	-0.3	72	72
mol:DAG	-0.068	0.17	-10000	0	-0.42	84	84
EGFR	0.005	0.058	-10000	0	-0.53	7	7
TXA2/TP alpha	-0.092	0.2	-10000	0	-0.51	85	85
Gq family/GTP	-0.011	0.079	-10000	0	-0.28	35	35
YES1	-0.021	0.1	-10000	0	-0.44	12	12
GNAI2/GTP	-0.05	0.093	-10000	0	-0.46	12	12
PGD2/DP	-0.088	0.17	-10000	0	-0.37	155	155
SLC9A3R1	0.011	0	-10000	0	-10000	0	0
FYN	-0.021	0.098	-10000	0	-0.42	11	11
mol:NO	-0.008	0.1	-10000	0	-0.54	21	21
GNA15	-0.009	0.1	-10000	0	-0.54	22	22
PGK/cGMP	-0.019	0.11	-10000	0	-0.34	58	58
RhoA/GDP	0.011	0.024	-10000	0	-0.57	1	1
TP alpha/TGM2/GDP/G beta/gamma	-0.031	0.12	-10000	0	-0.49	16	16
NOS3	-0.008	0.1	-10000	0	-0.54	21	21
RAC1	0.011	0	-10000	0	-10000	0	0
PRKCA	-0.054	0.14	-10000	0	-0.35	82	82
PRKCB	-0.068	0.17	-10000	0	-0.39	100	100
PRKCE	-0.051	0.14	-10000	0	-0.35	78	78
PRKCD	-0.057	0.15	-10000	0	-0.38	82	82
PRKCG	-0.092	0.18	-10000	0	-0.41	108	108
muscle contraction	-0.086	0.2	-10000	0	-0.5	87	87
PRKCZ	-0.054	0.14	-10000	0	-0.35	82	82
ARR3	-0.001	0.042	-10000	0	-0.46	5	5
TXA2/TP beta	-0.038	0.12	-10000	0	-0.52	12	12
PRKCQ	-0.07	0.16	-10000	0	-0.37	99	99
MAPKKK cascade	-0.081	0.19	-10000	0	-0.47	88	88
SELE	-0.065	0.16	-10000	0	-0.37	100	100
TP beta/GNAI2/GDP/G beta/gamma	-0.023	0.11	-10000	0	-0.5	12	12
ROCK1	0.001	0.08	-10000	0	-0.58	11	11
GNA14	-0.007	0.1	-10000	0	-0.56	19	19
chemotaxis	-0.1	0.23	-10000	0	-0.6	84	84
GNA12	0.011	0	-10000	0	-10000	0	0
GNA13	0.009	0.034	-10000	0	-0.58	2	2
GNA11	0.007	0.05	-10000	0	-0.53	5	5
Rac1/GTP	0.007	0.004	-10000	0	-10000	0	0

×

Osteopontin-mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IKK alpha homodimer	-0.065	0.16	-9999	-0.46	31	31
NF kappa B1 p50/RelA/I kappa B alpha	-0.039	0.15	-9999	-0.52	18	18
alphaV/beta3 Integrin/Osteopontin/Src	-0.11	0.19	-9999	-0.37	206	206
AP1	-0.074	0.2	-9999	-0.6	43	43
ILK	-0.075	0.16	-9999	-0.46	30	30
bone resorption	-0.051	0.16	-9999	-0.55	20	20
PTK2B	0.009	0.034	-9999	-0.58	2	2
PYK2/p130Cas	-0.059	0.16	-9999	-0.51	20	20
ITGAV	0.004	0.076	-9999	-0.58	10	10
mol:GTP	0	0	-9999	-10000	0	0
CD44/Rho Family GTPase/ROCK2	0.006	0.071	-9999	-0.45	14	14
alphaV/beta3 Integrin/Osteopontin	-0.09	0.18	-9999	-0.37	129	129
MAP3K1	-0.079	0.18	-9999	-0.36	119	119
JUN	0.007	0.052	-9999	-0.56	5	5
MAPK3	-0.062	0.16	-9999	-0.43	36	36
MAPK1	-0.062	0.16	-9999	-0.5	25	25
Rac1/GDP	0.009	0	-9999	-10000	0	0
NFKB1	0.01	0.024	-9999	-0.58	1	1
MAPK8	-0.069	0.17	-9999	-0.46	39	39
ITGB3	-0.005	0.1	-9999	-0.55	21	21
NFKBIA	-0.054	0.16	-9999	-0.5	26	26
FOS	-0.026	0.14	-9999	-0.54	41	41
CD44	0.007	0.048	-9999	-0.58	4	4
CHUK	0.007	0.048	-9999	-0.58	4	4
PLAU	-0.051	0.19	-9999	-0.74	22	22
NF kappa B1 p50/RelA	-0.078	0.13	-9999	-0.53	20	20
BCAR1	0.008	0.043	-9999	-0.52	4	4
RELA	0.011	0	-9999	-10000	0	0
alphaV beta3 Integrin	0.001	0.097	-9999	-0.42	30	30
mol:GDP	0	0	-9999	-10000	0	0
SYK	-0.076	0.16	-9999	-0.34	118	118
VAV3	-0.1	0.19	-9999	-0.48	64	64
MAP3K14	-0.074	0.17	-9999	-0.34	121	121
ROCK2	0.001	0.08	-9999	-0.58	11	11
SPP1	-0.16	0.25	-9999	-0.51	197	197
RAC1	0.011	0	-9999	-10000	0	0
Rac1/GTP	-0.092	0.18	-9999	-0.5	46	46
MMP2	-0.074	0.21	-9999	-0.6	56	56

×

Syndecan-2-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Syndecan-2/Fibronectin	-0.053	0.16	-9999	-0.35	120	120
EPHB2	0	0.079	-9999	-0.55	12	12
Syndecan-2/TACI	-0.039	0.13	-9999	-0.32	103	103
LAMA1	-0.059	0.18	-9999	-0.54	77	77
Syndecan-2/alpha2 ITGB1	0.005	0.091	-9999	-0.31	34	34
HRAS	0.008	0.041	-9999	-0.49	4	4
Syndecan-2/CASK	0	0.066	-9999	-0.34	21	21
ITGA5	-0.006	0.093	-9999	-0.49	21	21
BAX	0.018	0.077	-9999	-1.1	1	1
EPB41	0.007	0.048	-9999	-0.58	4	4
positive regulation of cell-cell adhesion	0.002	0.074	-9999	-0.32	29	29
LAMA3	-0.014	0.11	-9999	-0.51	30	30
EZR	0.011	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
CAV2	-0.003	0.087	-9999	-0.51	17	17
Syndecan-2/MMP2	-0.019	0.13	-9999	-0.4	56	56
RP11-540L11.1	0	0	-9999	-10000	0	0
alpha2 ITGB1	0.013	0.044	-9999	-0.42	6	6
dendrite morphogenesis	0.001	0.083	-9999	-0.34	33	33
Syndecan-2/GM-CSF	-0.06	0.15	-9999	-0.32	142	142
determination of left/right symmetry	0.001	0.078	-9999	-0.4	22	22
Syndecan-2/PKC delta	0.008	0.066	-9999	-0.34	21	21
GNB2L1	0.011	0.019	-9999	-0.46	1	1
MAPK3	-0.047	0.13	-9999	-0.32	81	81
MAPK1	-0.047	0.13	-9999	-0.32	81	81
Syndecan-2/RACK1	0.012	0.064	-9999	-0.32	19	19
NF1	0.008	0.042	-9999	-0.58	3	3
FGFR/FGF/Syndecan-2	0.001	0.078	-9999	-0.4	22	22
ITGA2	0.006	0.059	-9999	-0.58	6	6
MAPK8	0.014	0.07	-9999	-0.35	19	19
Syndecan-2/alpha2/beta1 Integrin	-0.019	0.12	-9999	-0.31	71	71
Syndecan-2/Kininogen	-0.068	0.15	-9999	-0.32	156	156
ITGB1	0.011	0	-9999	-10000	0	0
SRC	0.017	0.065	-9999	-0.31	19	19
Syndecan-2/CASK/Protein 4.1	0.005	0.066	-9999	-0.31	25	25
extracellular matrix organization	0	0.095	-9999	-0.39	31	31
actin cytoskeleton reorganization	-0.052	0.16	-9999	-0.35	120	120
Syndecan-2/Caveolin-2/Ras	0.005	0.087	-9999	-0.37	22	22
Syndecan-2/Laminin alpha3	-0.008	0.095	-9999	-0.32	51	51
Syndecan-2/RasGAP	0.017	0.066	-9999	-0.31	21	21
alpha5/beta1 Integrin	0.004	0.067	-9999	-0.35	21	21
PRKCD	0.011	0	-9999	-10000	0	0
Syndecan-2 dimer	0.001	0.083	-9999	-0.34	33	33
GO:0007205	0.003	0.006	-9999	-10000	0	0
DNA mediated transformation	0	0	-9999	-10000	0	0
Syndecan-2/RasGAP/Src	0.022	0.068	-9999	-0.52	3	3
RHOA	0.01	0.024	-9999	-0.58	1	1
SDCBP	0.003	0.072	-9999	-0.58	9	9
TNFRSF13B	-0.064	0.18	-9999	-0.52	84	84
RASA1	0.009	0.034	-9999	-0.58	2	2
alpha2/beta1 Integrin	0.013	0.044	-9999	-0.42	6	6
Syndecan-2/Synbindin	0.008	0.066	-9999	-0.34	21	21
TGFB1	-0.002	0.088	-9999	-0.55	15	15
CASP3	0.014	0.063	-9999	-0.32	19	19
FN1	-0.088	0.21	-9999	-0.52	112	112
Syndecan-2/IL8	-0.066	0.16	-9999	-0.33	150	150
SDC2	0.001	0.078	-9999	-0.4	22	22
KNG1	-0.11	0.22	-9999	-0.52	138	138
Syndecan-2/Neurofibromin	0.006	0.071	-9999	-0.34	24	24
TRAPPC4	0.011	0	-9999	-10000	0	0
CSF2	-0.098	0.22	-9999	-0.52	123	123
Syndecan-2/TGFB1	0	0.096	-9999	-0.39	31	31
Syndecan-2/Syntenin/PI-4-5-P2	0.002	0.075	-9999	-0.32	29	29
Syndecan-2/Ezrin	0.015	0.062	-9999	-0.32	18	18
PRKACA	0.013	0.065	-9999	-0.32	20	20
angiogenesis	-0.066	0.16	-9999	-0.33	150	150
MMP2	-0.033	0.15	-9999	-0.53	50	50
IL8	-0.11	0.22	-9999	-0.52	137	137
calcineurin-NFAT signaling pathway	-0.039	0.13	-9999	-0.32	103	103

×

Glucocorticoid receptor regulatory network

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
PCK2	0.022	0.075	0.32	14	-10000	0	14
SMARCC2	0.012	0.006	-10000	0	-10000	0	0
SMARCC1	0.012	0.006	-10000	0	-10000	0	0
TBX21	-0.11	0.27	-10000	0	-0.71	84	84
SUMO2	0.01	0.025	-10000	0	-0.58	1	1
STAT1 (dimer)	0.012	0.057	-10000	0	-0.51	7	7
FKBP4	0.009	0.033	-10000	0	-0.46	3	3
FKBP5	0.01	0.031	-10000	0	-0.52	2	2
GR alpha/HSP90/FKBP51/HSP90	0.076	0.11	0.3	48	-0.39	6	54
PRL	-0.064	0.14	-10000	0	-0.58	15	15
cortisol/GR alpha (dimer)/TIF2	0.18	0.24	0.53	125	-0.48	6	131
RELA	-0.036	0.093	-10000	0	-0.33	11	11
FGG	0.12	0.21	0.48	66	-0.43	16	82
GR beta/TIF2	0.075	0.13	0.32	55	-0.46	12	67
IFNG	-0.27	0.38	-10000	0	-0.95	106	106
apoptosis	0.008	0.16	0.47	21	-0.63	5	26
CREB1	0.009	0.041	-10000	0	-0.58	2	2
histone acetylation	-0.033	0.12	0.33	1	-0.37	39	40
BGLAP	-0.054	0.15	-10000	0	-0.61	17	17
GR/PKAc	0.056	0.13	0.29	36	-0.36	18	54
NF kappa B1 p50/RelA	-0.068	0.18	-10000	0	-0.53	37	37
SMARCD1	0.011	0.025	-10000	0	-0.58	1	1
MDM2	0.073	0.088	0.27	52	-0.28	3	55
GATA3	-0.016	0.12	-10000	0	-0.52	32	32
AKT1	0.003	0.024	-10000	0	-0.59	1	1
CSF2	-0.19	0.38	-10000	0	-1.2	71	71
GSK3B	0.009	0.035	-10000	0	-0.59	2	2
NR1I3	0.023	0.18	0.46	18	-0.82	13	31
CSN2	0.12	0.15	0.41	54	-0.38	3	57
BRG1/BAF155/BAF170/BAF60A	0.032	0.029	-10000	0	-0.32	2	2
NFATC1	-0.016	0.12	-10000	0	-0.51	33	33
POU2F1	0.001	0.075	-10000	0	-0.55	10	10
CDKN1A	-0.018	0.16	-10000	0	-1.5	3	3
response to stress	0	0	-10000	0	-10000	0	0
response to UV	0	0.007	-10000	0	-10000	0	0
SFN	0.005	0.055	-10000	0	-0.47	8	8
GR alpha/HSP90/FKBP51/HSP90/14-3-3	0.077	0.11	0.3	36	-0.41	5	41
prolactin receptor activity	0	0	-10000	0	-10000	0	0
EGR1	0.02	0.17	0.45	18	-0.79	11	29
JUN	-0.16	0.19	-10000	0	-0.5	83	83
IL4	-0.078	0.14	-10000	0	-0.5	25	25
CDK5R1	0.009	0.033	-10000	0	-0.46	3	3
PRKACA	0.011	0	-10000	0	-10000	0	0
cortisol/GR alpha (monomer)/AP-1	-0.13	0.2	0.22	30	-0.48	92	122
GR alpha/HSP90/FKBP51/HSP90/PP5C	0.08	0.1	0.3	39	-0.39	4	43
cortisol/GR alpha (monomer)	0.21	0.28	0.64	127	-0.46	4	131
NCOA2	0.004	0.066	-10000	0	-0.57	8	8
response to hypoxia	0	0	-10000	0	-10000	0	0
FOS	-0.078	0.15	-10000	0	-0.58	41	41
AP-1/NFAT1-c-4	-0.27	0.31	-10000	0	-0.71	139	139
AFP	-0.12	0.17	-10000	0	-0.77	11	11
SUV420H1	0.01	0.024	-10000	0	-0.58	1	1
IRF1	0.12	0.14	0.48	27	-0.59	1	28
TP53	-0.031	0.18	-10000	0	-0.57	60	60
PPP5C	0.011	0	-10000	0	-10000	0	0
KRT17	-0.34	0.45	-10000	0	-1	156	156
KRT14	-0.12	0.2	-10000	0	-0.65	36	36
TBP	0.017	0.029	-10000	0	-0.36	3	3
CREBBP	0.034	0.054	0.29	2	-10000	0	2
HDAC1	0.011	0.009	-10000	0	-10000	0	0
HDAC2	0.022	0.027	-10000	0	-10000	0	0
AP-1	-0.28	0.31	-10000	0	-0.72	140	140
MAPK14	0.011	0.006	-10000	0	-10000	0	0
MAPK10	-0.032	0.15	-10000	0	-0.55	47	47
MAPK11	-0.002	0.079	-10000	0	-0.48	16	16
KRT5	-0.32	0.41	-10000	0	-0.96	133	133
interleukin-1 receptor activity	0.011	0.028	-10000	0	-10000	0	0
NCOA1	0.013	0.024	-10000	0	-0.58	1	1
STAT1	0.012	0.057	-10000	0	-0.51	7	7
CGA	-0.064	0.13	-10000	0	-0.49	21	21
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2	0.12	0.2	0.48	97	-0.53	5	102
MAPK3	0.01	0.025	-10000	0	-0.58	1	1
MAPK1	0.01	0.025	-10000	0	-0.58	1	1
ICAM1	-0.14	0.24	-10000	0	-0.74	46	46
NFKB1	-0.037	0.098	-10000	0	-0.41	8	8
MAPK8	-0.13	0.17	-10000	0	-0.43	82	82
MAPK9	0.011	0.006	-10000	0	-10000	0	0
cortisol/GR alpha (dimer)	0.001	0.16	0.48	21	-0.67	5	26
BAX	-0.013	0.13	-10000	0	-1.4	1	1
POMC	-0.15	0.33	-10000	0	-1.1	47	47
EP300	0.032	0.073	0.28	3	-0.55	4	7
cortisol/GR alpha (dimer)/p53	0.15	0.26	0.56	106	-0.42	18	124
proteasomal ubiquitin-dependent protein catabolic process	0.049	0.069	0.24	18	-0.24	3	21
SGK1	0.065	0.13	0.42	1	-1.4	3	4
IL13	-0.18	0.22	-10000	0	-0.67	56	56
IL6	-0.25	0.42	-10000	0	-0.93	128	128
PRKACG	0	0.038	-10000	0	-0.46	4	4
IL5	-0.15	0.18	-10000	0	-0.68	24	24
IL2	-0.2	0.24	-10000	0	-0.64	79	79
CDK5	0.012	0.003	-10000	0	-10000	0	0
PRKACB	-0.02	0.13	-10000	0	-0.57	33	33
HSP90AA1	0.01	0.024	-10000	0	-0.58	1	1
IL8	-0.25	0.41	-10000	0	-0.99	117	117
CDK5R1/CDK5	0.015	0.025	-10000	0	-0.32	3	3
NF kappa B1 p50/RelA/PKAc	-0.049	0.16	-10000	0	-0.52	32	32
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90	0.18	0.22	0.5	126	-0.38	2	128
SMARCA4	0.011	0.025	-10000	0	-0.58	1	1
chromatin remodeling	0.12	0.14	0.39	67	-0.41	4	71
NF kappa B1 p50/RelA/Cbp	-0.016	0.17	0.31	2	-0.62	16	18
JUN (dimer)	-0.16	0.19	-10000	0	-0.5	83	83
YWHAH	0.011	0	-10000	0	-10000	0	0
VIPR1	-0.079	0.21	-10000	0	-0.66	53	53
NR3C1	0.12	0.18	0.45	81	-0.46	12	93
NR4A1	-0.033	0.15	-10000	0	-0.48	56	56
TIF2/SUV420H1	0.011	0.052	-10000	0	-0.41	9	9
MAPKKK cascade	0.008	0.16	0.47	21	-0.63	5	26
cortisol/GR alpha (dimer)/Src-1	0.19	0.23	0.54	128	-0.43	4	132
PBX1	-0.003	0.089	-10000	0	-0.57	14	14
POU1F1	-0.001	0.036	-10000	0	-0.51	2	2
SELE	-0.23	0.4	-10000	0	-0.96	110	110
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A	0.12	0.14	0.39	67	-0.42	4	71
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90	0.18	0.22	0.5	126	-0.38	2	128
mol:cortisol	0.12	0.17	0.37	132	-10000	0	132
MMP1	-0.27	0.46	-10000	0	-1.1	129	129

×

Signaling events regulated by Ret tyrosine kinase

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.026	0.051	-9999	-0.56	2	2
Crk/p130 Cas/Paxillin	-0.061	0.11	-9999	-0.39	28	28
JUN	-0.031	0.12	-9999	-0.44	24	24
HRAS	0.008	0.041	-9999	-0.49	4	4
RET51/GFRalpha1/GDNF/GRB10	-0.076	0.17	-9999	-0.41	90	90
RAP1A	0.01	0.024	-9999	-0.58	1	1
FRS2	0.009	0.034	-9999	-0.58	2	2
RAP1A/GDP	0.008	0.018	-9999	-0.43	1	1
RET51/GFRalpha1/GDNF/DOK1	-0.074	0.17	-9999	-0.4	89	89
EntrezGene:5979	0	0	-9999	-10000	0	0
PTPN11	0.007	0.054	-9999	-0.58	5	5
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.011	0.019	-9999	-0.46	1	1
RET9/GFRalpha1/GDNF/Enigma	-0.031	0.12	-9999	-0.29	100	100
RHOA	0.01	0.024	-9999	-0.58	1	1
RAP1A/GTP	-0.083	0.14	-9999	-0.36	90	90
GRB7	0.002	0.065	-9999	-0.46	12	12
RET51/GFRalpha1/GDNF	-0.074	0.17	-9999	-0.4	89	89
MAPKKK cascade	-0.075	0.13	-9999	-0.48	33	33
BCAR1	0.008	0.043	-9999	-0.52	4	4
RET9/GFRalpha1/GDNF/IRS1	-0.034	0.12	-9999	-0.3	103	103
lamellipodium assembly	-0.056	0.098	-9999	-0.32	44	44
RET51/GFRalpha1/GDNF/SHC	-0.074	0.17	-9999	-0.4	89	89
PIK3CA	0.009	0.034	-9999	-0.58	2	2
RET9/GFRalpha1/GDNF/SHC	-0.028	0.12	-9999	-0.29	95	95
RET9/GFRalpha1/GDNF/Shank3	-0.031	0.12	-9999	-0.3	97	97
MAPK3	-0.055	0.15	-9999	-0.49	28	28
DOK1	0.011	0	-9999	-10000	0	0
DOK6	-0.029	0.14	-9999	-0.55	43	43
PXN	0.011	0	-9999	-10000	0	0
neurite development	-0.05	0.15	-9999	-0.47	35	35
DOK5	-0.053	0.18	-9999	-0.55	70	70
GFRA1	-0.071	0.2	-9999	-0.53	92	92
MAPK8	-0.036	0.12	-9999	-0.45	21	21
HRAS/GTP	-0.084	0.14	-9999	-0.38	91	91
tube development	-0.024	0.12	-9999	-0.32	59	59
MAPK1	-0.055	0.15	-9999	-0.49	28	28
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.015	0.095	-9999	-0.27	62	62
Rac1/GDP	0.009	0	-9999	-10000	0	0
SRC	0.01	0.024	-9999	-0.58	1	1
PDLIM7	0.006	0.052	-9999	-0.48	7	7
RET51/GFRalpha1/GDNF/Dok6	-0.085	0.19	-9999	-0.41	114	114
SHC1	0.011	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/Dok4	-0.074	0.17	-9999	-0.4	89	89
RET51/GFRalpha1/GDNF/Dok5	-0.11	0.2	-9999	-0.43	129	129
PRKCA	0.01	0.031	-9999	-0.52	2	2
HRAS/GDP	0.006	0.029	-9999	-0.35	4	4
CREB1	-0.029	0.12	-9999	-0.35	56	56
PIK3R1	0.008	0.042	-9999	-0.58	3	3
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.011	0.087	-9999	-0.26	56	56
RET51/GFRalpha1/GDNF/Grb7	-0.079	0.17	-9999	-0.4	90	90
mol:GDP	0	0	-9999	-10000	0	0
RET	-0.084	0.2	-9999	-0.5	113	113
DOK4	0.01	0.024	-9999	-0.58	1	1
JNK cascade	-0.03	0.12	-9999	-0.44	24	24
RET9/GFRalpha1/GDNF/FRS2	-0.03	0.12	-9999	-0.29	97	97
SHANK3	0.006	0.055	-9999	-0.54	6	6
RASA1	0.009	0.034	-9999	-0.58	2	2
NCK1	0.009	0.034	-9999	-0.58	2	2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.012	0.088	-9999	-0.26	57	57
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.046	0.13	-9999	-0.41	33	33
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK	-0.044	0.13	-9999	-0.4	31	31
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.046	0.14	-9999	-0.54	23	23
PI3K	-0.047	0.17	-9999	-0.45	62	62
SOS1	0.01	0.024	-9999	-0.58	1	1
RET9/GFRalpha1/GDNF/Shank3/Grb2	-0.023	0.12	-9999	-0.32	59	59
GRB10	0.007	0.048	-9999	-0.58	4	4
activation of MAPKK activity	-0.036	0.12	-9999	-0.42	23	23
RET51/GFRalpha1/GDNF/FRS2	-0.075	0.17	-9999	-0.4	91	91
GAB1	0.011	0	-9999	-10000	0	0
IRS1	0.002	0.076	-9999	-0.58	10	10
IRS2	0.003	0.067	-9999	-0.54	9	9
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.046	0.14	-9999	-0.38	51	51
RET51/GFRalpha1/GDNF/PKC alpha	-0.075	0.17	-9999	-0.4	89	89
GRB2	0.011	0	-9999	-10000	0	0
PRKACA	0.011	0	-9999	-10000	0	0
GDNF	0.005	0.043	-9999	-0.52	4	4
RAC1	0.011	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/IRS1	-0.079	0.18	-9999	-0.41	95	95
Rac1/GTP	-0.066	0.12	-9999	-0.43	28	28
RET9/GFRalpha1/GDNF	-0.04	0.13	-9999	-0.33	95	95
GFRalpha1/GDNF	-0.048	0.15	-9999	-0.38	95	95

×

Visual signal transduction: Cones

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin	-0.016	0.099	-9999	-0.28	73	73
RGS9BP	-0.01	0.1	-9999	-0.54	22	22
mol:GTP	0	0	-9999	-10000	0	0
GRK1	-0.003	0.046	-9999	-0.46	6	6
mol:Na +	-0.048	0.12	-9999	-0.3	110	110
mol:ADP	-0.002	0.057	-9999	-0.34	16	16
GNAT2	-0.007	0.096	-9999	-0.52	20	20
RGS9-1/Gbeta5/R9AP	-0.021	0.12	-9999	-0.33	75	75
mol:GDP	0	0	-9999	-10000	0	0
PDE6H/GNAT2/GTP	-0.004	0.06	-9999	-0.32	21	21
GRK7	-0.001	0.062	-9999	-0.46	11	11
CNGB3	-0.03	0.12	-9999	-0.46	44	44
Cone Metarhodopsin II/X-Arrestin	0	0.03	-9999	-0.32	5	5
mol:Ca2+	-0.049	0.12	-9999	-0.28	126	126
Cone PDE6	-0.017	0.1	-9999	-0.32	44	44
Cone Metarhodopsin II	-0.001	0.044	-9999	-0.26	16	16
Na + (4 Units)	-0.048	0.12	-9999	-0.28	126	126
GNAT2/GDP	-0.021	0.11	-9999	-0.32	55	55
GNB5	0.007	0.048	-9999	-0.58	4	4
mol:GMP (4 units)	-0.004	0.058	-9999	-0.28	25	25
Cone Transducin	-0.017	0.11	-9999	-0.3	73	73
SLC24A2	-0.011	0.092	-9999	-0.48	22	22
GNB3/GNGT2	-0.019	0.12	-9999	-0.4	53	53
GNB3	-0.018	0.12	-9999	-0.54	32	32
GNAT2/GTP	-0.005	0.07	-9999	-0.38	20	20
CNGA3	-0.05	0.17	-9999	-0.52	67	67
ARR3	-0.001	0.042	-9999	-0.46	5	5
absorption of light	0	0	-9999	-10000	0	0
cGMP/Cone CNG Channel	-0.048	0.12	-9999	-0.3	110	110
mol:Pi	-0.021	0.12	-9999	-0.32	75	75
Cone CNG Channel	-0.054	0.11	-9999	-0.32	43	43
mol:all-trans-retinal	0	0	-9999	-10000	0	0
mol:K +	-0.011	0.092	-9999	-0.48	22	22
RGS9	-0.034	0.15	-9999	-0.52	51	51
PDE6C	0	0.038	-9999	-0.46	4	4
GNGT2	-0.009	0.11	-9999	-0.56	22	22
mol:cGMP (4 units)	0	0	-9999	-10000	0	0
PDE6H	0	0.019	-9999	-0.46	1	1

×

LPA receptor mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.015	0.12	-9999	-0.41	39	39
NF kappa B1 p50/RelA/I kappa B alpha	-0.014	0.11	-9999	-0.4	13	13
AP1	-0.086	0.14	-9999	-0.49	38	38
mol:PIP3	-0.065	0.12	-9999	-0.49	23	23
AKT1	0.01	0.094	-9999	-0.43	13	13
PTK2B	-0.014	0.094	-9999	-0.32	25	25
RHOA	0.011	0.051	-9999	-0.35	3	3
PIK3CB	0.008	0.046	-9999	-0.55	4	4
mol:Ca2+	-0.017	0.11	-9999	-0.31	42	42
MAGI3	0.009	0.042	-9999	-0.58	3	3
RELA	0.011	0	-9999	-10000	0	0
apoptosis	-0.052	0.14	-9999	-0.33	95	95
HRAS/GDP	0.006	0.029	-9999	-0.35	4	4
positive regulation of microtubule depolymerization	-0.043	0.13	-9999	-0.37	33	33
NF kappa B1 p50/RelA	-0.064	0.12	-9999	-0.47	28	28
endothelial cell migration	-0.046	0.19	-9999	-0.52	78	78
ADCY4	-0.039	0.16	-9999	-0.5	51	51
ADCY5	-0.072	0.2	-9999	-0.55	64	64
ADCY6	-0.037	0.16	-9999	-0.53	44	44
ADCY7	-0.038	0.16	-9999	-0.5	49	49
ADCY1	-0.05	0.17	-9999	-0.51	55	55
ADCY2	-0.055	0.19	-9999	-0.52	67	67
ADCY3	-0.038	0.16	-9999	-0.52	45	45
ADCY8	-0.042	0.16	-9999	-0.5	49	49
ADCY9	-0.038	0.16	-9999	-0.5	49	49
GSK3B	-0.008	0.092	-9999	-0.35	19	19
arachidonic acid secretion	-0.034	0.16	-9999	-0.5	45	45
GNG2	0.003	0.067	-9999	-0.54	9	9
TRIP6	-0.015	0.12	-9999	-0.42	42	42
GNAO1	-0.054	0.16	-9999	-0.35	118	118
HRAS	0.008	0.041	-9999	-0.49	4	4
NFKBIA	-0.02	0.12	-9999	-0.41	21	21
GAB1	0.011	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
lamellipodium assembly	-0.032	0.2	-9999	-0.91	31	31
JUN	0.007	0.052	-9999	-0.56	5	5
LPA/LPA2/NHERF2	0.007	0.046	-9999	-0.33	7	7
TIAM1	-0.059	0.24	-9999	-1.1	31	31
PIK3R1	0.008	0.042	-9999	-0.58	3	3
mol:IP3	-0.018	0.11	-9999	-0.32	42	42
PLCB3	0.012	0.055	-9999	-0.36	8	8
FOS	-0.026	0.14	-9999	-0.54	41	41
positive regulation of mitosis	-0.034	0.16	-9999	-0.5	45	45
LPA/LPA1-2-3	-0.063	0.15	-9999	-0.38	77	77
mol:Ca ++	0	0	-9999	-10000	0	0
JNK cascade	0	0.001	-9999	-10000	0	0
BCAR1	0.008	0.043	-9999	-0.52	4	4
stress fiber formation	-0.023	0.11	-9999	-0.36	26	26
GNAZ	-0.035	0.14	-9999	-0.37	79	79
EGFR/PI3K-beta/Gab1	-0.067	0.13	-9999	-0.52	23	23
positive regulation of dendritic cell cytokine production	-0.063	0.15	-9999	-0.38	77	77
LPA/LPA2/MAGI-3	0.006	0.049	-9999	-0.33	9	9
ARHGEF1	-0.007	0.11	-9999	-0.35	40	40
GNAI2	-0.02	0.12	-9999	-0.36	58	58
GNAI3	-0.02	0.12	-9999	-0.36	58	58
GNAI1	-0.029	0.14	-9999	-0.39	66	66
LPA/LPA3	-0.056	0.14	-9999	-0.37	92	92
LPA/LPA2	-0.001	0.046	-9999	-0.34	7	7
LPA/LPA1	-0.034	0.14	-9999	-0.38	78	78
HB-EGF/EGFR	-0.036	0.13	-9999	-0.32	99	99
HBEGF	-0.042	0.14	-9999	-0.37	94	94
mol:DAG	-0.018	0.11	-9999	-0.32	42	42
cAMP biosynthetic process	-0.051	0.18	-9999	-0.48	65	65
NFKB1	0.01	0.024	-9999	-0.58	1	1
SRC	0.01	0.024	-9999	-0.58	1	1
GNB1	0.011	0.001	-9999	-10000	0	0
LYN	-0.02	0.12	-9999	-0.4	22	22
GNAQ	-0.031	0.1	-9999	-0.32	47	47
LPAR2	0.006	0.052	-9999	-0.48	7	7
LPAR3	-0.07	0.19	-9999	-0.51	92	92
LPAR1	-0.034	0.15	-9999	-0.61	37	37
IL8	-0.11	0.21	-9999	-0.48	107	107
PTK2	-0.051	0.15	-9999	-0.36	76	76
Rac1/GDP	0.009	0	-9999	-10000	0	0
CASP3	-0.053	0.14	-9999	-0.33	95	95
EGFR	0.005	0.058	-9999	-0.53	7	7
PLCG1	-0.031	0.12	-9999	-0.34	50	50
PLD2	-0.051	0.15	-9999	-0.36	75	75
G12/G13	-0.012	0.11	-9999	-0.38	38	38
PI3K-beta	-0.031	0.09	-9999	-0.44	17	17
cell migration	-0.018	0.089	-9999	-0.26	40	40
SLC9A3R2	0.01	0.024	-9999	-0.58	1	1
PXN	-0.023	0.11	-9999	-0.37	26	26
HRAS/GTP	-0.035	0.16	-9999	-0.51	45	45
RAC1	0.011	0	-9999	-10000	0	0
MMP9	-0.062	0.18	-9999	-0.52	83	83
PRKCE	0.011	0	-9999	-10000	0	0
PRKCD	-0.011	0.11	-9999	-0.42	13	13
Gi(beta/gamma)	-0.034	0.16	-9999	-0.5	45	45
mol:LPA	-0.009	0.044	-9999	-0.19	21	21
TRIP6/p130 Cas/FAK1/Paxillin	-0.075	0.14	-9999	-0.5	31	31
MAPKKK cascade	-0.034	0.16	-9999	-0.5	45	45
contractile ring contraction involved in cytokinesis	0.011	0.051	-9999	-0.34	3	3
mol:GDP	0	0	-9999	-10000	0	0
GNA14	-0.037	0.12	-9999	-0.34	59	59
GNA15	-0.038	0.11	-9999	-0.33	57	57
GNA12	0.011	0	-9999	-10000	0	0
GNA13	0.009	0.034	-9999	-0.58	2	2
MAPT	-0.044	0.13	-9999	-0.39	33	33
GNA11	-0.03	0.1	-9999	-0.32	45	45
Rac1/GTP	-0.035	0.22	-9999	-0.97	31	31
MMP2	-0.046	0.19	-9999	-0.52	78	78

×

Neurotrophic factor-mediated Trk receptor signaling

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
CRKL	0.011	0	-10000	0	-10000	0	0
RAS family/GTP/Tiam1	-0.027	0.11	-10000	0	-0.32	50	50
NT3 (dimer)/TRKC	-0.044	0.15	-10000	0	-0.39	90	90
NT3 (dimer)/TRKB	-0.16	0.21	-10000	0	-0.45	145	145
SHC/Grb2/SOS1/GAB1/PI3K	0.028	0.032	-10000	0	-0.52	1	1
RAPGEF1	0.01	0.024	-10000	0	-0.58	1	1
BDNF	-0.021	0.13	-10000	0	-0.53	36	36
PIK3CA	0.009	0.034	-10000	0	-0.58	2	2
DYNLT1	0.011	0	-10000	0	-10000	0	0
NTRK1	-0.037	0.15	-10000	0	-0.53	53	53
NTRK2	-0.18	0.25	-10000	0	-0.5	219	219
NTRK3	-0.044	0.16	-10000	0	-0.51	62	62
NT-4/5 (dimer)/TRKB	-0.16	0.2	-10000	0	-0.37	225	225
neuron apoptosis	0.14	0.19	0.45	118	-10000	0	118
SHC 2-3/Grb2	-0.15	0.21	-10000	0	-0.5	118	118
SHC1	0.011	0	-10000	0	-10000	0	0
SHC2	-0.13	0.2	-10000	0	-0.56	81	81
SHC3	-0.14	0.21	-10000	0	-0.56	90	90
STAT3 (dimer)	0.017	0.021	-10000	0	-0.35	2	2
NT3 (dimer)/TRKA	-0.08	0.18	-10000	0	-0.44	93	93
RIN/GDP	-0.003	0.07	-10000	0	-0.27	10	10
GIPC1	0.007	0.048	-10000	0	-0.58	4	4
KRAS	0.006	0.057	-10000	0	-0.56	6	6
DNAJA3	-0.058	0.14	-10000	0	-0.36	69	69
RIN/GTP	-0.001	0.019	-10000	0	-0.32	2	2
CCND1	0.023	0.048	-10000	0	-0.82	2	2
MAGED1	0.011	0	-10000	0	-10000	0	0
PTPN11	0.007	0.054	-10000	0	-0.58	5	5
RICS	0	0	-10000	0	-10000	0	0
NT-4/5 (dimer)	-0.013	0.089	-10000	0	-0.46	23	23
SHC/GRB2/SOS1	0.023	0.015	-10000	0	-0.36	1	1
GRB2	0.011	0	-10000	0	-10000	0	0
NGF (dimer)/TRKA/MATK	-0.082	0.19	-10000	0	-0.38	158	158
TRKA/NEDD4-2	-0.019	0.11	-10000	0	-0.38	54	54
ELMO1	0.001	0.075	-10000	0	-0.52	12	12
RhoG/GTP/ELMO1/DOCK1	0.008	0.049	-10000	0	-0.32	13	13
NGF	-0.032	0.15	-10000	0	-0.53	48	48
HRAS	0.008	0.041	-10000	0	-0.49	4	4
DOCK1	0.01	0.024	-10000	0	-0.58	1	1
GAB2	0.009	0.034	-10000	0	-0.58	2	2
RIT2	-0.001	0.026	-10000	0	-0.46	2	2
RIT1	0.011	0	-10000	0	-10000	0	0
FRS2	0.009	0.034	-10000	0	-0.58	2	2
DNM1	-0.007	0.096	-10000	0	-0.5	22	22
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.011	0.019	-10000	0	-0.46	1	1
SH2B1 (homopentamer)	0	0	-10000	0	-10000	0	0
RhoG/GTP	-0.074	0.14	-10000	0	-0.38	61	61
mol:GDP	-0.006	0.099	-10000	0	-0.38	14	14
NGF (dimer)	-0.032	0.15	-10000	0	-0.52	48	48
RhoG/GDP	0.001	0.054	-10000	0	-0.38	12	12
RIT1/GDP	0.002	0.07	-10000	0	-0.27	8	8
TIAM1	-0.044	0.16	-10000	0	-0.52	63	63
PIK3R1	0.008	0.042	-10000	0	-0.58	3	3
BDNF (dimer)/TRKB	-0.11	0.18	-10000	0	-0.32	239	239
KIDINS220/CRKL/C3G	0.016	0.018	-10000	0	-0.42	1	1
SHC/RasGAP	0.016	0.025	-10000	0	-0.42	2	2
FRS2 family/SHP2	0.018	0.051	-10000	0	-0.44	7	7
SHC/GRB2/SOS1/GAB1	0.029	0.014	-10000	0	-0.32	1	1
RIT1/GTP	0.009	0	-10000	0	-10000	0	0
NT3 (dimer)	-0.018	0.12	-10000	0	-0.53	33	33
RAP1/GDP	-0.021	0.046	-10000	0	-0.27	5	5
KIDINS220/CRKL	0.011	0	-10000	0	-10000	0	0
BDNF (dimer)	-0.021	0.13	-10000	0	-0.53	36	36
ubiquitin-dependent protein catabolic process	-0.034	0.14	-10000	0	-0.35	92	92
Schwann cell development	-0.032	0.032	-10000	0	-10000	0	0
EHD4	0.011	0	-10000	0	-10000	0	0
FRS2 family/GRB2/SOS1	0.027	0.03	-10000	0	-0.32	4	4
FRS2 family/SHP2/CRK family/C3G/GAB2	0.028	0.049	-10000	0	-0.42	6	6
RAP1B	0.011	0	-10000	0	-10000	0	0
RAP1A	0.01	0.024	-10000	0	-0.58	1	1
CDC42/GTP	-0.13	0.16	-10000	0	-0.48	65	65
ABL1	0.01	0.024	-10000	0	-0.58	1	1
SH2B family/GRB2/SOS1	0.016	0.018	-10000	0	-0.42	1	1
Rap1/GTP	-0.017	0.08	-10000	0	-0.39	3	3
STAT3	0.017	0.021	-10000	0	-0.35	2	2
axon guidance	-0.12	0.15	-10000	0	-0.46	65	65
MAPK3	-0.069	0.17	-10000	0	-0.39	109	109
MAPK1	-0.069	0.17	-10000	0	-0.39	109	109
CDC42/GDP	0.001	0.074	-10000	0	-0.31	9	9
NTF3	-0.018	0.12	-10000	0	-0.53	33	33
NTF4	-0.013	0.09	-10000	0	-0.46	23	23
NGF (dimer)/TRKA/FAIM	-0.037	0.14	-10000	0	-0.35	96	96
PI3K	0.013	0.04	-10000	0	-0.43	5	5
FRS3	0.01	0.031	-10000	0	-0.52	2	2
FAIM	0.006	0.057	-10000	0	-0.56	6	6
GAB1	0.011	0	-10000	0	-10000	0	0
RASGRF1	-0.092	0.17	-10000	0	-0.38	107	107
SOS1	0.01	0.024	-10000	0	-0.58	1	1
MCF2L	-0.033	0.13	-10000	0	-0.32	95	95
RGS19	-0.001	0.081	-10000	0	-0.55	13	13
CDC42	0.007	0.054	-10000	0	-0.58	5	5
RAS family/GTP	-0.002	0.095	-10000	0	-0.54	9	9
Rac1/GDP	0.002	0.07	-10000	0	-0.27	8	8
NGF (dimer)/TRKA/GRIT	-0.041	0.14	-10000	0	-0.35	91	91
neuron projection morphogenesis	-0.041	0.14	-10000	0	-0.6	10	10
NGF (dimer)/TRKA/NEDD4-2	-0.034	0.14	-10000	0	-0.35	92	92
MAP2K1	0.03	0.023	-10000	0	-0.29	3	3
NGFR	-0.08	0.2	-10000	0	-0.51	106	106
NGF (dimer)/TRKA/GIPC/GAIP	-0.022	0.12	-10000	0	-0.28	81	81
RAS family/GTP/PI3K	0.014	0.08	-10000	0	-0.42	15	15
FRS2 family/SHP2/GRB2/SOS1	0.029	0.047	-10000	0	-0.36	8	8
NRAS	0.002	0.076	-10000	0	-0.58	10	10
GRB2/SOS1	0.016	0.018	-10000	0	-0.42	1	1
PRKCI	0.008	0.042	-10000	0	-0.58	3	3
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
RAC1	0.011	0	-10000	0	-10000	0	0
PRKCZ	0.01	0.031	-10000	0	-0.52	2	2
MAPKKK cascade	-0.09	0.19	-10000	0	-0.63	59	59
RASA1	0.009	0.034	-10000	0	-0.58	2	2
TRKA/c-Abl	-0.019	0.11	-10000	0	-0.38	54	54
SQSTM1	0.011	0	-10000	0	-10000	0	0
BDNF (dimer)/TRKB/GIPC	-0.096	0.16	-10000	0	-0.36	102	102
NGF (dimer)/TRKA/p62/Atypical PKCs	-0.018	0.12	-10000	0	-0.33	65	65
MATK	-0.069	0.19	-10000	0	-0.52	91	91
NEDD4L	0.01	0.024	-10000	0	-0.58	1	1
RAS family/GDP	-0.02	0.048	-10000	0	-0.27	8	8
NGF (dimer)/TRKA	-0.076	0.14	-10000	0	-0.33	114	114
Rac1/GTP	-0.079	0.11	-10000	0	-0.34	57	57
FRS2 family/SHP2/CRK family	0.029	0.049	-10000	0	-0.4	7	7

×

Caspase cascade in apoptosis

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
TOP1	-0.029	0.13	0.19	2	-0.34	65	67
ACTA1	-0.052	0.16	0.22	3	-0.42	70	73
NUMA1	-0.029	0.13	0.19	2	-0.33	65	67
SPTAN1	-0.043	0.15	0.23	2	-0.42	65	67
LIMK1	-0.043	0.15	0.23	2	-0.42	65	67
BIRC3	-0.016	0.12	-10000	0	-0.53	31	31
BIRC2	-0.001	0.086	-10000	0	-0.59	13	13
BAX	0.01	0.024	-10000	0	-0.58	1	1
CASP10	-0.058	0.16	-10000	0	-0.34	136	136
CRMA	0	0	-10000	0	-10000	0	0
XIAP	0.01	0.024	-10000	0	-0.58	1	1
PTK2	-0.029	0.13	0.19	2	-0.34	64	66
DIABLO	0.011	0	-10000	0	-10000	0	0
apoptotic nuclear changes	-0.042	0.15	0.23	2	-0.41	65	67
response to UV	0	0	-10000	0	-10000	0	0
CRADD	0.01	0.024	-10000	0	-0.58	1	1
GSN	-0.049	0.16	0.23	2	-0.43	66	68
MADD	0.011	0	-10000	0	-10000	0	0
TFAP2A	-0.084	0.2	-10000	0	-0.56	83	83
BID	-0.024	0.087	-10000	0	-0.23	68	68
MAP3K1	-0.014	0.07	-10000	0	-0.31	14	14
TRADD	0.011	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0.014	0.036	-10000	0	-0.42	4	4
mol:Activated DNA	0	0	-10000	0	-10000	0	0
ARHGDIB	-0.045	0.16	0.23	2	-0.42	66	68
CASP9	0.011	0.024	-10000	0	-0.58	1	1
DNA repair	0.004	0.049	-10000	0	-0.2	7	7
neuron apoptosis	0.012	0.036	-10000	0	-0.5	2	2
mol:NAD	0	0	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	-0.035	0.15	0.22	2	-0.4	62	64
APAF1	0.009	0.042	-10000	0	-0.58	3	3
CASP6	-0.006	0.086	-10000	0	-0.52	5	5
TRAF2	0.01	0.024	-10000	0	-0.58	1	1
ICAD/CAD	-0.036	0.15	0.22	2	-0.4	62	64
CASP7	0.009	0.059	0.28	18	-10000	0	18
KRT18	0.006	0.033	-10000	0	-0.55	1	1
apoptosis	-0.04	0.15	0.25	2	-0.37	71	73
DFFA	-0.043	0.15	0.23	2	-0.42	63	65
DFFB	-0.043	0.15	0.23	2	-0.42	64	66
PARP1	-0.005	0.05	0.2	7	-10000	0	7
actin filament polymerization	0.044	0.15	0.38	71	-0.22	2	73
TNF	-0.017	0.12	-10000	0	-0.54	31	31
CYCS	-0.023	0.086	-10000	0	-0.27	36	36
SATB1	-0.02	0.11	-10000	0	-0.41	20	20
SLK	-0.054	0.16	0.23	2	-0.42	79	81
p15 BID/BAX	-0.016	0.079	-10000	0	-0.29	14	14
CASP2	0.022	0.061	-10000	0	-0.4	2	2
JNK cascade	0.014	0.07	0.31	14	-10000	0	14
CASP3	-0.051	0.16	0.23	3	-0.44	66	69
LMNB2	0.016	0.061	-10000	0	-0.36	6	6
RIPK1	0.011	0	-10000	0	-10000	0	0
CASP4	0.008	0.046	-10000	0	-0.55	4	4
Mammalian IAPs/DIABLO	0.006	0.1	-10000	0	-0.45	22	22
negative regulation of DNA binding	-0.083	0.2	-10000	0	-0.56	83	83
stress fiber formation	-0.053	0.16	0.23	2	-0.41	79	81
GZMB	-0.076	0.19	-10000	0	-0.41	135	135
CASP1	-0.007	0.086	-10000	0	-0.31	40	40
LMNB1	0.017	0.054	-10000	0	-0.27	5	5
APP	0.012	0.037	-10000	0	-0.5	2	2
TNFRSF1A	0.011	0	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
CASP8	0.009	0.018	-10000	0	-0.43	1	1
VIM	-0.034	0.14	0.22	6	-0.36	65	71
LMNA	0.016	0.059	-10000	0	-0.35	5	5
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD	0.017	0.064	-10000	0	-0.43	2	2
LRDD	0.008	0.042	-10000	0	-0.58	3	3
SREBF1	-0.044	0.16	0.23	2	-0.42	65	67
APAF-1/Caspase 9	-0.003	0.065	0.4	7	-0.76	1	8
nuclear fragmentation during apoptosis	-0.028	0.12	0.19	2	-0.33	65	67
CFL2	-0.045	0.15	0.22	2	-0.39	71	73
GAS2	-0.074	0.18	0.23	1	-0.41	98	99
positive regulation of apoptosis	0.019	0.059	-10000	0	-0.33	5	5
PRF1	-0.041	0.16	-10000	0	-0.51	61	61

×

JNK signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1	-0.047	0.19	-9999	-0.49	75	75
MAP4K1	-0.045	0.17	-9999	-0.56	60	60
MAP3K8	0.01	0.031	-9999	-0.52	2	2
PRKCB	-0.044	0.17	-9999	-0.55	60	60
DBNL	0.01	0.024	-9999	-0.58	1	1
CRKL	0.011	0	-9999	-10000	0	0
MAP3K1	-0.02	0.15	-9999	-0.52	39	39
JUN	-0.034	0.2	-9999	-0.72	44	44
MAP3K7	-0.017	0.15	-9999	-0.54	33	33
GRAP2	-0.023	0.14	-9999	-0.55	37	37
CRK	0.011	0.019	-9999	-0.46	1	1
MAP2K4	-0.013	0.15	-9999	-0.52	36	36
LAT	-0.009	0.1	-9999	-0.51	24	24
LCP2	-0.015	0.12	-9999	-0.55	29	29
MAPK8	-0.04	0.21	-9999	-0.76	43	43
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family	-0.024	0.16	-9999	-0.58	33	33
LAT/GRAP2/SLP76/HPK1/HIP-55	-0.039	0.18	-9999	-0.47	75	75

×

Canonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.015	0.026	-10000	0	-10000	0	0
AES	0.013	0.033	-10000	0	-0.58	1	1
FBXW11	0.011	0	-10000	0	-10000	0	0
mol:GTP	0	0.001	-10000	0	-10000	0	0
LRP6/FZD1	0.014	0.039	-10000	0	-0.4	5	5
SMAD4	0.004	0.068	-10000	0	-0.58	8	8
DKK2	-0.087	0.21	-10000	0	-0.54	108	108
TLE1	0.01	0.053	-10000	0	-0.59	4	4
MACF1	0.012	0	-10000	0	-10000	0	0
CTNNB1	0.05	0.098	0.25	13	-0.95	2	15
WIF1	-0.18	0.25	-10000	0	-0.5	221	221
beta catenin/RanBP3	0.025	0.13	0.39	58	-0.7	2	60
KREMEN2	-0.038	0.15	-10000	0	-0.48	61	61
DKK1	-0.16	0.24	-10000	0	-0.51	192	192
beta catenin/beta TrCP1	0.054	0.09	0.25	10	-0.8	2	12
FZD1	0.009	0.039	-10000	0	-0.54	3	3
AXIN2	-0.11	0.42	-10000	0	-1.4	55	55
AXIN1	0.011	0.024	-10000	0	-0.59	1	1
RAN	0.012	0.001	-10000	0	-10000	0	0
Axin1/APC/GSK3/beta catenin	0.014	0.081	-10000	0	-0.95	3	3
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4	0.049	0.1	-10000	0	-0.62	7	7
Axin1/APC/GSK3	0.046	0.078	0.22	15	-0.78	2	17
Axin1/APC/GSK3/beta catenin/Macf1	0.037	0.093	-10000	0	-0.71	4	4
HNF1A	0.009	0.059	-10000	0	-0.53	6	6
CTBP1	0.013	0.034	-10000	0	-0.59	1	1
MYC	-0.013	0.16	-10000	0	-1.6	5	5
RANBP3	0.011	0.024	-10000	0	-0.58	1	1
DKK2/LRP6/Kremen 2	-0.07	0.16	-10000	0	-0.32	162	162
NKD1	-0.13	0.24	-10000	0	-0.53	162	162
TCF4	0.001	0.088	-10000	0	-0.52	15	15
TCF3	0.013	0.033	-10000	0	-0.59	1	1
WNT1/LRP6/FZD1/Axin1	0.017	0.059	-10000	0	-0.37	5	5
Ran/GTP	0.009	0.002	-10000	0	-10000	0	0
CtBP/CBP/TCF/TLE1/AES	0.028	0.16	0.46	51	-0.62	6	57
LEF1	-0.01	0.11	-10000	0	-0.52	27	27
DVL1	0.046	0.06	0.21	1	-0.5	4	5
CSNK2A1	0.012	0	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES	0.042	0.11	-10000	0	-0.51	12	12
DKK1/LRP6/Kremen 2	-0.11	0.18	-10000	0	-0.32	234	234
LRP6	0.01	0.034	-10000	0	-0.59	2	2
CSNK1A1	0.013	0.043	-10000	0	-0.59	2	2
NLK	0.011	0.004	-10000	0	-10000	0	0
CCND1	-0.007	0.11	-10000	0	-0.88	5	5
WNT1	-0.007	0.083	-10000	0	-0.46	20	20
GSK3A	0.012	0.001	-10000	0	-10000	0	0
GSK3B	0.01	0.034	-10000	0	-0.59	2	2
FRAT1	0.01	0.024	-10000	0	-0.58	1	1
PPP2R5D	0.089	0.11	0.27	158	-10000	0	158
APC	0.011	0.082	-10000	0	-0.38	12	12
WNT1/LRP6/FZD1	0.07	0.1	0.23	78	-0.69	3	81
CREBBP	0.014	0.023	-10000	0	-10000	0	0

×

Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved)	-0.017	0.091	-10000	0	-0.64	10	10
HDAC1	0.008	0.004	-10000	0	-10000	0	0
AES	0.01	0.024	-10000	0	-0.58	1	1
FBXW11	0.011	0	-10000	0	-10000	0	0
DTX1	-0.011	0.11	-10000	0	-0.54	25	25
LRP6/FZD1	0.014	0.038	-10000	0	-0.4	5	5
TLE1	0.007	0.048	-10000	0	-0.59	4	4
AP1	-0.061	0.13	-10000	0	-0.3	115	115
NCSTN	0.011	0	-10000	0	-10000	0	0
ADAM10	0.006	0.054	-10000	0	-0.58	5	5
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4	0.036	0.068	-10000	0	-1.3	1	1
NICD/RBPSUH	0.016	0.085	-10000	0	-0.65	9	9
WIF1	-0.18	0.25	-10000	0	-0.5	221	221
NOTCH1	-0.011	0.078	-10000	0	-0.63	9	9
PSENEN	0.01	0.024	-10000	0	-0.58	1	1
KREMEN2	-0.038	0.15	-10000	0	-0.48	61	61
DKK1	-0.16	0.24	-10000	0	-0.51	192	192
beta catenin/beta TrCP1	0.051	0.068	0.25	3	-10000	0	3
APH1B	0.006	0.059	-10000	0	-0.58	6	6
APH1A	0.011	0	-10000	0	-10000	0	0
AXIN1	-0.013	0.047	-10000	0	-0.3	8	8
CtBP/CBP/TCF1/TLE1/AES	0.013	0.053	-10000	0	-0.34	9	9
PSEN1	0.011	0	-10000	0	-10000	0	0
FOS	-0.026	0.14	-10000	0	-0.54	41	41
JUN	0.007	0.052	-10000	0	-0.56	5	5
MAP3K7	0.01	0.002	-10000	0	-10000	0	0
CTNNB1	0.048	0.073	0.2	62	-10000	0	62
MAPK3	0.01	0.024	-10000	0	-0.58	1	1
DKK2/LRP6/Kremen 2	-0.069	0.16	-10000	0	-0.32	162	162
HNF1A	0.005	0.057	-10000	0	-0.56	6	6
CTBP1	0.01	0.024	-10000	0	-0.58	1	1
MYC	0.01	0.13	-10000	0	-1.4	5	5
NKD1	-0.13	0.24	-10000	0	-0.53	162	162
FZD1	0.009	0.039	-10000	0	-0.54	3	3
NOTCH1 precursor/Deltex homolog 1	0.005	0.098	-10000	0	-0.59	10	10
apoptosis	-0.061	0.13	-10000	0	-0.3	115	115
Delta 1/NOTCHprecursor	0.01	0.095	-10000	0	-0.63	10	10
DLL1	-0.003	0.086	-10000	0	-0.52	16	16
PPARD	0.019	0.057	-10000	0	-1.4	1	1
Gamma Secretase	0.031	0.035	-10000	0	-0.3	7	7
APC	-0.028	0.1	-10000	0	-0.49	22	22
DVL1	-0.009	0.051	-10000	0	-0.5	4	4
CSNK2A1	0.012	0.001	-10000	0	-10000	0	0
MAP3K7IP1	-0.002	0.002	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	-0.11	0.18	-10000	0	-0.32	234	234
LRP6	0.01	0.034	-10000	0	-0.58	2	2
CSNK1A1	0.01	0.034	-10000	0	-0.58	2	2
NLK	0.011	0.005	-10000	0	-10000	0	0
CCND1	0.017	0.081	-10000	0	-1.4	2	2
WNT1	-0.008	0.083	-10000	0	-0.46	20	20
Axin1/APC/beta catenin	0.026	0.077	-10000	0	-0.36	12	12
DKK2	-0.087	0.21	-10000	0	-0.54	108	108
NOTCH1 precursor/DVL1	-0.016	0.088	-10000	0	-0.66	10	10
GSK3B	0.009	0.034	-10000	0	-0.58	2	2
FRAT1	0.01	0.024	-10000	0	-0.58	1	1
NOTCH/Deltex homolog 1	-0.022	0.093	-10000	0	-0.6	10	10
PPP2R5D	0.061	0.12	0.25	158	-10000	0	158
MAPK1	0.01	0.024	-10000	0	-0.58	1	1
WNT1/LRP6/FZD1	-0.092	0.15	-10000	0	-0.34	88	88
RBPJ	0.01	0.031	-10000	0	-0.52	2	2
CREBBP	0.014	0.002	-10000	0	-10000	0	0

×

Glypican 2 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MDK	-0.009	0.1	-9999	-0.51	24	24
GPC2	-0.007	0.1	-9999	-0.55	20	20
GPC2/Midkine	-0.012	0.1	-9999	-0.39	43	43
neuron projection morphogenesis	-0.012	0.1	-9999	-0.38	43	43

×

Angiopoietin receptor Tie2-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	0.024	0.26	-10000	0	-0.88	39	39
NCK1/PAK1/Dok-R	-0.039	0.11	-10000	0	-0.42	42	42
NCK1/Dok-R	-0.028	0.3	-10000	0	-1.1	39	39
PIK3CA	0.009	0.034	-10000	0	-0.58	2	2
mol:beta2-estradiol	0.006	0.057	0.24	31	-10000	0	31
RELA	0.011	0	-10000	0	-10000	0	0
SHC1	0.012	0.001	-10000	0	-10000	0	0
Rac/GDP	0.009	0	-10000	0	-10000	0	0
F2	-0.11	0.23	0.24	26	-0.5	147	173
TNIP2	0.01	0.024	-10000	0	-0.58	1	1
NF kappa B/RelA	-0.043	0.26	-10000	0	-1	39	39
FN1	-0.088	0.21	-10000	0	-0.52	112	112
PLD2	-0.008	0.31	-10000	0	-1.1	39	39
PTPN11	0.007	0.054	-10000	0	-0.58	5	5
GRB14	-0.12	0.24	-10000	0	-0.54	144	144
ELK1	0.004	0.27	-10000	0	-0.99	39	39
GRB7	0.002	0.065	-10000	0	-0.46	12	12
PAK1	0.011	0	-10000	0	-10000	0	0
Tie2/Ang1/alpha5/beta1 Integrin	-0.087	0.3	-10000	0	-1.1	43	43
CDKN1A	0.041	0.2	-10000	0	-0.6	39	39
ITGA5	-0.006	0.093	-10000	0	-0.49	21	21
mol:GTP	0	0	-10000	0	-10000	0	0
RasGAP/Dok-R	-0.028	0.3	-10000	0	-1.1	39	39
CRK	0.011	0.019	-10000	0	-0.46	1	1
mol:NO	0.033	0.21	-10000	0	-0.64	43	43
PLG	-0.035	0.31	-10000	0	-1.1	41	41
mol:GDP	0	0	-10000	0	-10000	0	0
chemokinesis	0.02	0.25	-10000	0	-0.84	39	39
GRB2	0.011	0	-10000	0	-10000	0	0
PIK3R1	0.009	0.042	-10000	0	-0.58	3	3
ANGPT2	0.018	0.2	-10000	0	-0.64	22	22
BMX	-0.054	0.33	-10000	0	-1.2	41	41
ANGPT1	-0.019	0.31	-10000	0	-1.2	33	33
tube development	0.035	0.22	-10000	0	-0.65	41	41
ANGPT4	0.001	0.042	-10000	0	-0.46	5	5
response to hypoxia	-0.001	0.019	-10000	0	-10000	0	0
Tie2/Ang1/GRB14	-0.079	0.33	-10000	0	-1.2	40	40
alpha5/beta1 Integrin	0.004	0.067	-10000	0	-0.35	21	21
FGF2	-0.04	0.16	-10000	0	-0.52	57	57
STAT5A (dimer)	0.036	0.24	-10000	0	-0.74	39	39
mol:L-citrulline	0.033	0.21	-10000	0	-0.64	43	43
AGTR1	-0.096	0.21	-10000	0	-0.51	123	123
MAPK14	0	0.3	-10000	0	-1.1	39	39
Tie2/SHP2	-0.042	0.19	-10000	0	-0.99	20	20
TEK	-0.018	0.22	-10000	0	-1.2	16	16
RPS6KB1	0.024	0.25	-10000	0	-0.86	39	39
Angiotensin II/AT1	-0.068	0.16	-10000	0	-0.37	123	123
Tie2/Ang1/GRB2	-0.012	0.32	-10000	0	-1.2	39	39
MAPK3	0.001	0.28	-10000	0	-1	39	39
MAPK1	0.001	0.28	-10000	0	-1	39	39
Tie2/Ang1/GRB7	-0.016	0.32	-10000	0	-1.2	39	39
NFKB1	0.01	0.024	-10000	0	-0.58	1	1
MAPK8	-0.008	0.31	-10000	0	-1.1	39	39
PI3K	0.012	0.29	-10000	0	-1	39	39
FES	-0.006	0.32	-10000	0	-1.1	40	40
Crk/Dok-R	-0.027	0.3	-10000	0	-1.1	39	39
Tie2/Ang1/ABIN2	-0.013	0.32	-10000	0	-1.2	39	39
blood circulation	0	0	-10000	0	-10000	0	0
negative regulation of caspase activity	0.03	0.24	-10000	0	-0.78	39	39
STAT5A	0.012	0.001	-10000	0	-10000	0	0
mol:ROS	0	0	-10000	0	-10000	0	0
PTK2	0.026	0.25	-10000	0	-0.84	39	39
Tie2/Ang2	0.02	0.28	-10000	0	-0.89	40	40
Tie2/Ang1	-0.017	0.34	-10000	0	-1.2	39	39
FOXO1	0.032	0.24	-10000	0	-0.77	42	42
ELF1	0.013	0.046	-10000	0	-0.59	3	3
ELF2	-0.009	0.31	-10000	0	-1.1	39	39
mol:Choline	-0.004	0.29	-10000	0	-1.1	39	39
cell migration	-0.03	0.068	-10000	0	-0.23	45	45
FYN	0.03	0.24	-10000	0	-0.76	40	40
DOK2	-0.012	0.11	-10000	0	-0.55	25	25
negative regulation of cell cycle	0.044	0.19	-10000	0	-0.55	39	39
ETS1	-0.003	0.088	-10000	0	-0.46	14	14
PXN	0.037	0.21	-10000	0	-0.69	39	39
ITGB1	0.011	0	-10000	0	-10000	0	0
NOS3	0.027	0.23	-10000	0	-0.74	43	43
RAC1	0.011	0	-10000	0	-10000	0	0
TNF	-0.023	0.14	-10000	0	-0.53	35	35
MAPKKK cascade	-0.004	0.29	-10000	0	-1.1	39	39
RASA1	0.009	0.034	-10000	0	-0.58	2	2
Tie2/Ang1/Shc	-0.011	0.32	-10000	0	-1.2	39	39
NCK1	0.009	0.034	-10000	0	-0.58	2	2
vasculogenesis	0.036	0.19	-10000	0	-0.57	43	43
mol:Phosphatidic acid	-0.004	0.29	-10000	0	-1.1	39	39
mol:Angiotensin II	0.001	0.004	-10000	0	-10000	0	0
mol:NADP	0.033	0.21	-10000	0	-0.64	43	43
Rac1/GTP	-0.061	0.2	-10000	0	-0.78	40	40
MMP2	-0.028	0.33	-10000	0	-1.2	40	40

×

Visual signal transduction: Rods

Figure S43. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S43. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:K +	0.009	0.034	-9999	-0.58	2	2
GNAT1/GTP	0	0.023	-9999	-0.32	3	3
Metarhodopsin II/Arrestin	0	0.022	-9999	-0.27	4	4
PDE6G/GNAT1/GTP	-0.016	0.091	-9999	-0.33	45	45
mol:GTP	0	0	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
GNAT1	0	0.033	-9999	-0.46	3	3
GRK1	-0.003	0.046	-9999	-0.46	6	6
CNG Channel	-0.12	0.18	-9999	-0.37	162	162
mol:Na +	-0.066	0.13	-9999	-0.5	23	23
mol:ADP	-0.003	0.046	-9999	-0.46	6	6
RGS9-1/Gbeta5/R9AP	-0.021	0.12	-9999	-0.33	75	75
mol:GDP	0	0	-9999	-10000	0	0
cGMP/CNG Channel	-0.068	0.13	-9999	-0.51	23	23
CNGB1	-0.004	0.067	-9999	-0.46	13	13
RDH5	0	0.078	-9999	-0.53	13	13
SAG	0.002	0.019	-9999	-0.46	1	1
mol:Ca2+	-0.043	0.14	-9999	-0.48	23	23
Na + (4 Units)	-0.063	0.12	-9999	-0.46	23	23
RGS9	-0.034	0.15	-9999	-0.52	51	51
GNB1/GNGT1	-0.023	0.12	-9999	-0.38	58	58
GNAT1/GDP	-0.017	0.1	-9999	-0.32	45	45
GUCY2D	-0.015	0.1	-9999	-0.46	30	30
GNGT1	-0.043	0.16	-9999	-0.52	58	58
GUCY2F	0	0.019	-9999	-0.46	1	1
GNB5	0.007	0.048	-9999	-0.58	4	4
mol:GMP (4 units)	-0.087	0.18	-9999	-0.37	130	130
mol:11-cis-retinal	0	0.078	-9999	-0.52	13	13
mol:cGMP	-0.025	0.11	-9999	-0.34	33	33
GNB1	0.011	0	-9999	-10000	0	0
Rhodopsin	-0.001	0.061	-9999	-0.37	16	16
SLC24A1	0.009	0.034	-9999	-0.58	2	2
CNGA1	-0.05	0.17	-9999	-0.53	69	69
Metarhodopsin II	-0.002	0.033	-9999	-0.28	8	8
mol:Ca ++	0	0	-9999	-10000	0	0
GC1/GCAP Family	-0.027	0.11	-9999	-0.36	35	35
RGS9BP	-0.01	0.1	-9999	-0.54	22	22
Metarhodopsin II/Transducin	-0.012	0.071	-9999	-0.28	33	33
GCAP Family/Ca ++	-0.019	0.094	-9999	-0.34	30	30
PDE6A/B	-0.1	0.2	-9999	-0.42	164	164
mol:Pi	-0.021	0.12	-9999	-0.32	75	75
mol:all-trans-retinal	0	0	-9999	-10000	0	0
Transducin	-0.016	0.092	-9999	-0.33	32	32
PDE6B	-0.033	0.15	-9999	-0.53	49	49
PDE6A	-0.11	0.23	-9999	-0.54	130	130
PDE6G	-0.027	0.14	-9999	-0.55	42	42
RHO	-0.001	0.032	-9999	-0.46	3	3
PDE6	-0.12	0.18	-9999	-0.56	53	53
GUCA1A	-0.02	0.12	-9999	-0.49	34	34
GC2/GCAP Family	-0.019	0.095	-9999	-0.34	31	31
GUCA1C	-0.001	0.026	-9999	-0.46	2	2
GUCA1B	-0.016	0.12	-9999	-0.54	30	30

×

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

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
MAP4K1	-0.032	0.14	-10000	0	-0.41	47	47
CRKL	-0.011	0.12	-10000	0	-0.42	38	38
HRAS	-0.025	0.15	-10000	0	-0.49	31	31
mol:PIP3	-0.021	0.12	-10000	0	-0.41	39	39
SPRED1	0.006	0.059	-10000	0	-0.58	6	6
SPRED2	0.008	0.042	-10000	0	-0.58	3	3
GAB1	-0.018	0.13	-10000	0	-0.44	39	39
FOXO3	-0.006	0.12	-10000	0	-0.38	40	40
AKT1	-0.014	0.13	-10000	0	-0.42	40	40
BAD	-0.007	0.12	-10000	0	-0.39	40	40
megakaryocyte differentiation	-0.082	0.18	-10000	0	-0.36	137	137
GSK3B	-0.007	0.12	-10000	0	-0.39	41	41
RAF1	-0.012	0.13	-10000	0	-0.4	28	28
SHC1	0.011	0	-10000	0	-10000	0	0
STAT3	-0.018	0.13	-10000	0	-0.44	39	39
STAT1	-0.062	0.32	-10000	0	-1.1	41	41
HRAS/SPRED1	-0.015	0.13	-10000	0	-0.41	33	33
cell proliferation	-0.018	0.13	-10000	0	-0.44	39	39
PIK3CA	0.009	0.034	-10000	0	-0.59	2	2
TEC	0.011	0.019	-10000	0	-0.46	1	1
RPS6KB1	-0.02	0.14	-10000	0	-0.46	40	40
HRAS/SPRED2	-0.015	0.13	-10000	0	-0.4	32	32
LYN/TEC/p62DOK	-0.006	0.12	-10000	0	-0.41	38	38
MAPK3	0.002	0.095	-10000	0	-0.29	20	20
STAP1	-0.05	0.17	-10000	0	-0.5	54	54
GRAP2	-0.023	0.14	-10000	0	-0.55	37	37
JAK2	-0.054	0.28	-10000	0	-0.97	42	42
STAT1 (dimer)	-0.059	0.31	-10000	0	-1.1	41	41
mol:Gleevec	0	0.005	-10000	0	-10000	0	0
GRB2/SOCS1/VAV1	-0.043	0.17	-10000	0	-0.48	53	53
actin filament polymerization	-0.03	0.14	-10000	0	-0.46	41	41
LYN	0.011	0	-10000	0	-10000	0	0
STAP1/STAT5A (dimer)	-0.057	0.22	-10000	0	-0.65	55	55
PIK3R1	0.008	0.042	-10000	0	-0.58	3	3
CBL/CRKL/GRB2	0.002	0.12	-10000	0	-0.38	37	37
PI3K	-0.01	0.14	-10000	0	-0.45	40	40
PTEN	0.006	0.059	-10000	0	-0.58	6	6
SCF/KIT/EPO/EPOR	-0.064	0.34	-10000	0	-1.3	37	37
MAPK8	-0.018	0.13	-10000	0	-0.44	39	39
STAT3 (dimer)	-0.017	0.13	-10000	0	-0.44	39	39
positive regulation of transcription	0.005	0.08	-10000	0	-0.24	15	15
mol:GDP	-0.035	0.16	-10000	0	-0.49	41	41
PIK3C2B	-0.018	0.13	-10000	0	-0.44	39	39
CBL/CRKL	-0.004	0.12	-10000	0	-0.39	38	38
FER	-0.022	0.14	-10000	0	-0.46	40	40
SH2B3	-0.018	0.13	-10000	0	-0.44	39	39
PDPK1	-0.014	0.11	-10000	0	-0.38	38	38
SNAI2	-0.027	0.14	-10000	0	-0.45	45	45
positive regulation of cell proliferation	-0.039	0.23	-10000	0	-0.78	42	42
KITLG	-0.003	0.099	-10000	0	-0.6	16	16
cell motility	-0.039	0.23	-10000	0	-0.78	42	42
PTPN6	0.011	0.007	-10000	0	-10000	0	0
EPOR	-0.001	0.14	-10000	0	-1.2	4	4
STAT5A (dimer)	-0.03	0.19	-10000	0	-0.64	43	43
SOCS1	-0.028	0.14	-10000	0	-0.5	47	47
cell migration	0.057	0.16	0.42	70	-10000	0	70
SOS1	0.01	0.024	-10000	0	-0.58	1	1
EPO	0.001	0.054	-10000	0	-0.46	8	8
VAV1	-0.028	0.15	-10000	0	-0.58	40	40
GRB10	-0.02	0.13	-10000	0	-0.45	41	41
PTPN11	0.007	0.053	-10000	0	-0.58	5	5
SCF/KIT	-0.025	0.14	-10000	0	-0.45	44	44
GO:0007205	0	0.007	-10000	0	-10000	0	0
MAP2K1	-0.002	0.1	-10000	0	-0.31	29	29
CBL	0.011	0	-10000	0	-10000	0	0
KIT	-0.065	0.33	-10000	0	-1.4	33	33
MAP2K2	-0.002	0.1	-10000	0	-0.31	26	26
SHC/Grb2/SOS1	-0.006	0.12	-10000	0	-0.42	38	38
STAT5A	-0.032	0.2	-10000	0	-0.66	43	43
GRB2	0.011	0	-10000	0	-10000	0	0
response to radiation	-0.026	0.14	-10000	0	-0.44	45	45
SHC/GRAP2	-0.008	0.1	-10000	0	-0.4	37	37
PTPRO	-0.084	0.18	-10000	0	-0.36	137	137
SH2B2	-0.031	0.14	-10000	0	-0.47	41	41
DOK1	0.011	0	-10000	0	-10000	0	0
MATK	-0.058	0.17	-10000	0	-0.43	70	70
CREBBP	0.022	0.031	-10000	0	-10000	0	0
BCL2	-0.019	0.23	-10000	0	-1.3	16	16

×

Cellular roles of Anthrax toxin

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ANTXR1	-0.045	0.17	-10000	0	-0.54	63	63
ANTXR2	0.005	0.058	-10000	0	-0.53	7	7
negative regulation of myeloid dendritic cell antigen processing and presentation	-0.008	0.022	-10000	0	-0.069	69	69
monocyte activation	-0.026	0.14	-10000	0	-0.49	40	40
MAP2K2	-0.004	0.032	-10000	0	-0.77	1	1
MAP2K1	-0.008	0.027	-10000	0	-0.35	2	2
MAP2K7	-0.007	0.022	-10000	0	-0.32	1	1
MAP2K6	-0.012	0.046	-10000	0	-0.32	11	11
CYAA	-0.021	0.094	-10000	0	-0.28	69	69
MAP2K4	-0.008	0.029	-10000	0	-0.32	3	3
IL1B	-0.039	0.11	-10000	0	-0.28	89	89
Channel	-0.021	0.1	-10000	0	-0.3	69	69
NLRP1	-0.02	0.065	-10000	0	-0.28	31	31
CALM1	0.011	0	-10000	0	-10000	0	0
negative regulation of phagocytosis	-0.009	0.025	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
regulation of endothelial cell proliferation	0.008	0.022	0.069	69	-10000	0	69
MAPK3	-0.007	0.022	-10000	0	-0.32	1	1
MAPK1	-0.007	0.024	-10000	0	-0.38	1	1
PGR	-0.041	0.099	-10000	0	-0.29	78	78
PA/Cellular Receptors	-0.024	0.11	-10000	0	-0.33	69	69
apoptosis	-0.008	0.022	-10000	0	-0.069	69	69
LOC728358	0	0	-10000	0	-10000	0	0
Lethal toxin (unfolded)	-0.019	0.094	-10000	0	-0.28	69	69
macrophage activation	0.007	0.028	-10000	0	-0.33	2	2
TNF	-0.017	0.12	-10000	0	-0.54	31	31
VCAM1	-0.026	0.14	-10000	0	-0.5	40	40
platelet activation	-0.009	0.025	-10000	0	-10000	0	0
MAPKKK cascade	-0.002	0.027	0.14	4	-10000	0	4
IL18	-0.007	0.055	-10000	0	-0.26	17	17
negative regulation of macrophage activation	-0.008	0.022	-10000	0	-0.069	69	69
LEF	-0.008	0.022	-10000	0	-0.069	69	69
CASP1	-0.017	0.041	-10000	0	-0.16	33	33
mol:cAMP	-0.009	0.025	-10000	0	-10000	0	0
necrosis	-0.008	0.022	-10000	0	-0.069	69	69
intracellular pH reduction	0	0	-10000	0	-10000	0	0
PAGA	0	0	-10000	0	-10000	0	0
Edema toxin (unfolded)	-0.019	0.096	-10000	0	-0.28	69	69
mol:Epigallocatechin-3-gallate (EGCG)	0	0	-10000	0	-10000	0	0

×

Arf6 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CENTA1/KIF3B	0.013	0.034	-9999	-0.44	3	3
ARNO/beta Arrestin1-2	-0.004	0.07	-9999	-10000	0	0
EGFR	0.005	0.058	-9999	-0.53	7	7
EPHA2	0.006	0.055	-9999	-0.54	6	6
USP6	0.008	0.041	-9999	-0.49	4	4
IQSEC1	0.011	0	-9999	-10000	0	0
EGFR/EGFR/EGF/EGF	-0.13	0.19	-9999	-0.36	228	228
ARRB2	0.007	0.008	-9999	-0.19	1	1
mol:GTP	0.004	0.046	-9999	-0.26	12	12
ARRB1	0.009	0.034	-9999	-0.58	2	2
FBXO8	0.009	0.034	-9999	-0.58	2	2
TSHR	-0.011	0.093	-9999	-0.46	25	25
EGF	-0.18	0.25	-9999	-0.51	222	222
somatostatin receptor activity	0	0	-9999	-0.001	47	47
ARAP2	-0.005	0.098	-9999	-0.58	17	17
mol:GDP	-0.033	0.085	-9999	-0.26	44	44
mol:PI-3-4-5-P3	0	0	-9999	-0.001	19	19
ITGA2B	-0.043	0.16	-9999	-0.5	63	63
ARF6	0.01	0.024	-9999	-0.58	1	1
Ephrin A1/EPHA2/NCK1/GIT1	0.024	0.045	-9999	-0.37	6	6
ADAP1	0.01	0.031	-9999	-0.52	2	2
KIF13B	0.009	0.034	-9999	-0.58	2	2
HGF/MET	-0.021	0.12	-9999	-0.39	57	57
PXN	0.011	0	-9999	-10000	0	0
ARF6/GTP	-0.038	0.092	-9999	-0.26	44	44
EGFR/EGFR/EGF/EGF/ARFGEP100	-0.099	0.16	-9999	-0.3	228	228
ADRB2	-0.029	0.15	-9999	-0.55	44	44
receptor agonist activity	0	0	-9999	0	44	44
actin filament binding	0	0	-9999	0	45	45
SRC	0.01	0.024	-9999	-0.58	1	1
ITGB3	-0.008	0.1	-9999	-0.55	21	21
GNAQ	0.005	0.059	-9999	-0.59	6	6
EFA6/PI-4-5-P2	0	0	-9999	-0.001	35	35
ARF6/GDP	-0.002	0.1	-9999	-0.36	33	33
ARF6/GDP/GULP/ACAP1	-0.06	0.14	-9999	-0.38	68	68
alphaIIb/beta3 Integrin/paxillin/GIT1	-0.013	0.11	-9999	-0.32	40	40
ACAP1	-0.026	0.14	-9999	-0.54	41	41
ACAP2	0.002	0.076	-9999	-0.58	10	10
LHCGR/beta Arrestin2	0.001	0.011	-9999	-0.26	1	1
EFNA1	0.011	0.019	-9999	-0.46	1	1
HGF	-0.039	0.16	-9999	-0.55	55	55
CYTH3	0.007	0.029	-9999	-0.4	3	3
CYTH2	0.008	0.002	-9999	-10000	0	0
NCK1	0.009	0.034	-9999	-0.58	2	2
fibronectin binding	0	0	-9999	0	31	31
endosomal lumen acidification	0	0	-9999	0	35	35
microtubule-based process	0	0	-9999	-10000	0	0
GULP1	-0.051	0.18	-9999	-0.54	69	69
GNAQ/ARNO	0.011	0.031	-9999	-0.3	6	6
mol:Phosphatidic acid	0	0	-9999	-10000	0	0
PIP3-E	0	0	-9999	0	21	21
MET	0.01	0.031	-9999	-0.52	2	2
GNA14	-0.007	0.1	-9999	-0.56	19	19
GNA15	-0.009	0.1	-9999	-0.54	22	22
GIT1	0.01	0.024	-9999	-0.58	1	1
mol:PI-4-5-P2	0	0	-9999	-0.001	36	36
GNA11	0.007	0.05	-9999	-0.53	5	5
LHCGR	0	0.019	-9999	-0.46	1	1
AGTR1	-0.097	0.21	-9999	-0.51	123	123
desensitization of G-protein coupled receptor protein signaling pathway	0.001	0.011	-9999	-0.26	1	1
IPCEF1/ARNO	-0.074	0.12	-9999	-0.48	1	1
alphaIIb/beta3 Integrin	-0.037	0.14	-9999	-0.37	83	83

×

IL1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
UBC13/UEV1A	-0.035	0.12	-10000	0	-0.33	84	84
PRKCZ	0.01	0.031	-10000	0	-0.52	2	2
MAP3K7IP2	0	0	-10000	0	-10000	0	0
ERC1	0.009	0.033	-10000	0	-0.46	3	3
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4	-0.033	0.072	-10000	0	-0.32	12	12
IRAK/TOLLIP	-0.014	0.096	-10000	0	-0.42	7	7
IKBKB	0.011	0.019	-10000	0	-0.46	1	1
IKBKG	0.01	0.024	-10000	0	-0.58	1	1
IL1 alpha/IL1R2	-0.1	0.2	-10000	0	-0.41	171	171
IL1A	-0.09	0.21	-10000	0	-0.52	116	116
IL1B	-0.056	0.17	-10000	0	-0.4	108	108
IRAK/TRAF6/p62/Atypical PKCs	0.003	0.095	-10000	0	-0.58	5	5
IL1R2	-0.055	0.18	-10000	0	-0.52	76	76
IL1R1	-0.006	0.095	-10000	0	-0.51	20	20
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.008	0.09	0.2	9	-0.36	11	20
TOLLIP	0.01	0.024	-10000	0	-0.58	1	1
TICAM2	-0.009	0.11	-10000	0	-0.58	20	20
MAP3K3	0.009	0.034	-10000	0	-0.58	2	2
TAK1/TAB1/TAB2	0.008	0	-10000	0	-10000	0	0
IKK complex/ELKS	0.021	0.086	-10000	0	-0.62	4	4
JUN	-0.001	0.089	-10000	0	-0.55	4	4
MAP3K7	0.011	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/PI3K	-0.031	0.14	-10000	0	-0.55	17	17
IL1 alpha/IL1R1/IL1RAP/MYD88	-0.043	0.14	-10000	0	-0.35	71	71
PIK3R1	0.008	0.042	-10000	0	-0.58	3	3
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4	-0.035	0.13	-10000	0	-0.32	71	71
IL1 beta fragment/IL1R1/IL1RAP	-0.045	0.15	-10000	0	-0.37	74	74
NFKB1	0.01	0.024	-10000	0	-0.58	1	1
MAPK8	-0.005	0.089	-10000	0	-0.53	4	4
IRAK1	-0.022	0.1	-10000	0	-0.41	7	7
IL1RN/IL1R1	-0.04	0.15	-10000	0	-0.39	84	84
IRAK4	0.011	0	-10000	0	-10000	0	0
PRKCI	0.008	0.042	-10000	0	-0.58	3	3
TRAF6	0.01	0.024	-10000	0	-0.58	1	1
PI3K	0.013	0.04	-10000	0	-0.43	5	5
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.013	0.096	-10000	0	-0.33	22	22
CHUK	0.007	0.048	-10000	0	-0.58	4	4
IL1 beta fragment/IL1R1/IL1RAP/MYD88s	-0.045	0.15	-10000	0	-0.37	74	74
IL1 beta/IL1R2	-0.081	0.19	-10000	0	-0.37	159	159
IRAK/TRAF6/TAK1/TAB1/TAB2	-0.017	0.081	-10000	0	-0.58	2	2
NF kappa B1 p50/RelA	-0.055	0.11	-10000	0	-0.5	18	18
IRAK3	-0.026	0.14	-10000	0	-0.54	41	41
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4	-0.039	0.15	-10000	0	-0.55	18	18
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.022	0.11	-10000	0	-0.4	12	12
IL1 alpha/IL1R1/IL1RAP	-0.056	0.15	-10000	0	-0.33	138	138
RELA	0.011	0	-10000	0	-10000	0	0
MAP3K7IP1	0	0	-10000	0	-10000	0	0
SQSTM1	0.011	0	-10000	0	-10000	0	0
MYD88	0.011	0	-10000	0	-10000	0	0
IRAK/TRAF6/MEKK3	-0.006	0.093	-10000	0	-0.46	4	4
IL1RAP	0.002	0.076	-10000	0	-0.58	10	10
UBE2N	0.01	0.024	-10000	0	-0.58	1	1
IRAK/TRAF6	-0.08	0.14	-10000	0	-0.45	45	45
CASP1	-0.022	0.13	-10000	0	-0.54	37	37
IL1RN/IL1R2	-0.074	0.19	-10000	0	-0.43	123	123
IL1 beta fragment/IL1R1/IL1RAP/MYD88	-0.035	0.14	-10000	0	-0.34	74	74
TMEM189-UBE2V1	-0.06	0.16	-10000	0	-0.46	84	84
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.025	0.11	-10000	0	-0.41	22	22
PIK3CA	0.009	0.034	-10000	0	-0.58	2	2
IL1RN	-0.05	0.17	-10000	0	-0.52	70	70
TRAF6/TAK1/TAB1/TAB2	-0.03	0.078	-10000	0	-0.39	5	5
MAP2K6	-0.011	0.092	-10000	0	-0.37	10	10

×

Effects of Botulinum toxin

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
STX1A	0.002	0.051	-9999	-0.34	13	13
UniProt:P19321	0	0	-9999	-10000	0	0
RIMS1/UNC13B	-0.032	0.12	-9999	-0.36	73	73
STXBP1	-0.006	0.1	-9999	-0.56	19	19
ACh/CHRNA1	-0.026	0.1	-9999	-0.36	49	49
RAB3GAP2/RIMS1/UNC13B	-0.021	0.11	-9999	-0.36	34	34
mol:Ca2+	0	0	-9999	-10000	0	0
UniProt:P30996	0	0	-9999	-10000	0	0
UniProt:Q60393	0	0	-9999	-10000	0	0
CST086	0	0	-9999	-10000	0	0
RIMS1	-0.054	0.17	-9999	-0.51	72	72
mol:ACh	-0.007	0.036	-9999	-0.13	32	32
RAB3GAP2	0.008	0.042	-9999	-0.58	3	3
STX1A/SNAP25/VAMP2	-0.051	0.1	-9999	-0.46	13	13
UniProt:P10844	0	0	-9999	-10000	0	0
muscle contraction	-0.026	0.1	-9999	-0.36	49	49
UNC13B	0.01	0.031	-9999	-0.52	2	2
CHRNA1	-0.032	0.15	-9999	-0.53	49	49
UniProt:P10845	0	0	-9999	-10000	0	0
ACh/Synaptotagmin 1	-0.083	0.16	-9999	-0.38	134	134
SNAP25	-0.024	0.076	-9999	-0.2	85	85
VAMP2	0.006	0	-9999	-10000	0	0
SYT1	-0.12	0.24	-9999	-0.57	134	134
UniProt:Q00496	0	0	-9999	-10000	0	0
STXIA/STXBP1	-0.002	0.075	-9999	-0.32	32	32
STX1A/SNAP25 fragment 1/VAMP2	-0.051	0.1	-9999	-0.46	13	13

×

Integrins in angiogenesis

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	0.012	0.045	-9999	-0.37	8	8
alphaV beta3 Integrin	-0.026	0.14	-9999	-0.37	76	76
PTK2	-0.027	0.15	-9999	-0.54	29	29
IGF1R	0.01	0.024	-9999	-0.58	1	1
PI4KB	0.011	0	-9999	-10000	0	0
MFGE8	0.001	0.074	-9999	-0.5	13	13
SRC	0.01	0.024	-9999	-0.58	1	1
CDKN1B	-0.038	0.14	-9999	-0.51	32	32
VEGFA	0.011	0.019	-9999	-0.46	1	1
ILK	-0.037	0.13	-9999	-0.5	31	31
ROCK1	0.001	0.08	-9999	-0.58	11	11
AKT1	-0.026	0.13	-9999	-0.46	32	32
PTK2B	0.011	0.081	-9999	-0.59	2	2
alphaV/beta3 Integrin/JAM-A	-0.043	0.15	-9999	-0.37	78	78
CBL	0.011	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
alphaV beta3 Integrin/ANGPTL3	-0.001	0.084	-9999	-0.34	33	33
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.029	0.13	-9999	-0.33	65	65
VEGF/Rho/ROCK/alphaV/beta3 Integrin	-0.006	0.11	-9999	-0.6	12	12
alphaV/beta3 Integrin/Syndecan-1	0.004	0.084	-9999	-0.35	31	31
PI4KA	0.011	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.12	0.2	-9999	-0.59	71	71
PI4 Kinase	0.017	0	-9999	-10000	0	0
PIK3CA	0.009	0.034	-9999	-0.58	2	2
alphaV/beta3 Integrin/Osteopontin	-0.1	0.18	-9999	-0.33	215	215
RPS6KB1	-0.085	0.21	-9999	-0.55	74	74
TLN1	0.01	0.024	-9999	-0.58	1	1
MAPK3	-0.068	0.21	-9999	-0.68	50	50
GPR124	0.003	0.069	-9999	-0.56	9	9
MAPK1	-0.068	0.21	-9999	-0.68	50	50
PXN	0.011	0	-9999	-10000	0	0
PIK3R1	0.008	0.042	-9999	-0.58	3	3
alphaV/beta3 Integrin/Tumstatin	-0.048	0.14	-9999	-0.32	124	124
cell adhesion	0.002	0.093	-9999	-0.37	29	29
ANGPTL3	0.002	0.033	-9999	-0.46	3	3
VEGFR2 homodimer/VEGFA homodimer/Src	0.018	0.041	-9999	-0.31	9	9
IGF-1R heterotetramer	0.01	0.024	-9999	-0.58	1	1
Rac1/GDP	0.009	0	-9999	-10000	0	0
TGFBR2	0.011	0.019	-9999	-0.46	1	1
ITGB3	-0.008	0.1	-9999	-0.55	21	21
IGF1	-0.075	0.2	-9999	-0.52	97	97
RAC1	0.011	0	-9999	-10000	0	0
regulation of cell-matrix adhesion	0	0.096	-9999	-0.37	36	36
apoptosis	0.002	0.076	-9999	-0.58	10	10
CD47	0.009	0.034	-9999	-0.58	2	2
alphaV/beta3 Integrin/CD47	0.004	0.087	-9999	-0.36	31	31
VCL	0.009	0.034	-9999	-0.58	2	2
alphaV/beta3 Integrin/Del1	-0.025	0.15	-9999	-0.43	64	64
CSF1	0.006	0.055	-9999	-0.54	6	6
PIK3C2A	-0.055	0.18	-9999	-0.59	48	48
PI4 Kinase/Pyk2	-0.059	0.12	-9999	-0.47	25	25
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.009	0.084	-9999	-0.34	27	27
FAK1/Vinculin	-0.014	0.13	-9999	-0.43	28	28
alphaV beta3/Integrin/ppsTEM5	0	0.097	-9999	-0.37	36	36
RHOA	0.01	0.024	-9999	-0.58	1	1
VTN	-0.054	0.17	-9999	-0.5	76	76
BCAR1	0.008	0.043	-9999	-0.52	4	4
FGF2	-0.039	0.16	-9999	-0.52	57	57
F11R	-0.018	0.12	-9999	-0.37	57	57
alphaV/beta3 Integrin/Lactadherin	-0.002	0.097	-9999	-0.35	40	40
alphaV/beta3 Integrin/TGFBR2	0.005	0.083	-9999	-0.34	31	31
alphaV/beta3 Integrin/c-FMS/Cbl/Cas	0.019	0.061	-9999	-0.33	16	16
HSP90AA1	0.01	0.024	-9999	-0.58	1	1
alphaV/beta3 Integrin/Talin	0.005	0.076	-9999	-0.34	25	25
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.088	0.21	-9999	-0.52	112	112
alphaV/beta3 Integrin/Pyk2	0.013	0.081	-9999	-0.6	2	2
SDC1	0.01	0.024	-9999	-0.58	1	1
VAV3	-0.02	0.12	-9999	-0.31	90	90
PTPN11	0.007	0.054	-9999	-0.58	5	5
IRS1	0.002	0.076	-9999	-0.58	10	10
FAK1/Paxillin	-0.014	0.12	-9999	-0.42	28	28
cell migration	-0.006	0.12	-9999	-0.4	23	23
ITGAV	0.002	0.076	-9999	-0.58	10	10
PI3K	-0.063	0.13	-9999	-0.52	26	26
SPP1	-0.16	0.25	-9999	-0.52	197	197
KDR	0.005	0.058	-9999	-0.53	7	7
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Caspase 8	0.002	0.076	-9999	-0.58	10	10
COL4A3	-0.074	0.19	-9999	-0.51	98	98
angiogenesis	-0.067	0.21	-9999	-0.68	50	50
Rac1/GTP	-0.013	0.11	-9999	-0.59	3	3
EDIL3	-0.037	0.16	-9999	-0.58	50	50
cell proliferation	0.004	0.083	-9999	-0.34	31	31

×

a4b1 and a4b7 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ITGB1	0.011	0	-9999	-10000	0	0
ITGB7	-0.016	0.12	-9999	-0.53	30	30
ITGA4	-0.019	0.13	-9999	-0.57	32	32
alpha4/beta7 Integrin	-0.024	0.14	-9999	-0.44	55	55
alpha4/beta1 Integrin	-0.006	0.096	-9999	-0.41	32	32

×

Retinoic acid receptors-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.011	0	-10000	0	-10000	0	0
HDAC3	0.011	0	-10000	0	-10000	0	0
VDR	0.01	0.024	-10000	0	-0.58	1	1
Cbp/p300/PCAF	0.01	0.072	-10000	0	-0.37	20	20
EP300	0.007	0.048	-10000	0	-0.58	4	4
RARs/AIB1/Cbp/p300/PCAF/9cRA	-0.003	0.079	-10000	0	-0.35	16	16
KAT2B	-0.005	0.098	-10000	0	-0.58	17	17
MAPK14	0.011	0	-10000	0	-10000	0	0
AKT1	0.003	0.085	0.21	12	-0.3	16	28
RAR alpha/9cRA/Cyclin H	-0.049	0.085	-10000	0	-0.46	5	5
mol:9cRA	0	0	-10000	0	-10000	0	0
RARs/Src-1/Cbp/p300/PCAF/9cRA	-0.007	0.086	-10000	0	-0.38	17	17
CDC2	0	0.002	-10000	0	-10000	0	0
response to UV	0.001	0.003	-10000	0	-10000	0	0
RAR alpha/Jnk1	-0.033	0.083	-10000	0	-0.48	1	1
NCOR2	0.008	0.046	-10000	0	-0.55	4	4
VDR/VDR/Vit D3	0.008	0.018	-10000	0	-0.43	1	1
RXRs/RARs/NRIP1/9cRA	-0.055	0.18	-10000	0	-0.42	98	98
NCOA2	0.004	0.066	-10000	0	-0.57	8	8
NCOA3	0.01	0.024	-10000	0	-0.58	1	1
NCOA1	0.01	0.024	-10000	0	-0.58	1	1
VDR/VDR/DNA	0.01	0.024	-10000	0	-0.58	1	1
RARG	0.006	0.059	-10000	0	-0.58	6	6
RAR gamma1/9cRA	0.012	0.038	-10000	0	-0.36	6	6
MAPK3	0.011	0.024	-10000	0	-0.58	1	1
MAPK1	0.01	0.024	-10000	0	-0.58	1	1
MAPK8	0.011	0.024	-10000	0	-0.58	1	1
mol:Vit D3	0	0	-10000	0	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.063	0.17	-10000	0	-0.43	92	92
RARA	-0.042	0.1	-10000	0	-0.25	94	94
negative regulation of phosphoinositide 3-kinase cascade	0	0	-10000	0	-10000	0	0
RARs/TIF2/Cbp/p300/PCAF/9cRA	-0.01	0.094	-10000	0	-0.4	19	19
PRKCA	0.012	0.031	-10000	0	-0.52	2	2
RXRs/RARs/NRIP1/9cRA/HDAC1	-0.063	0.18	-10000	0	-0.43	97	97
RXRG	-0.076	0.14	-10000	0	-0.35	93	93
RXRA	-0.031	0.094	-10000	0	-0.26	5	5
RXRB	-0.065	0.14	-10000	0	-0.34	91	91
VDR/Vit D3/DNA	0.008	0.018	-10000	0	-0.43	1	1
RBP1	-0.083	0.2	-10000	0	-0.49	115	115
CRBP1/9-cic-RA	-0.059	0.14	-10000	0	-0.35	115	115
RARB	-0.004	0.098	-10000	0	-0.54	19	19
PRKCG	-0.15	0.25	-10000	0	-0.52	190	190
MNAT1	0.008	0.046	-10000	0	-0.55	4	4
RAR alpha/RXRs	-0.049	0.18	-10000	0	-0.43	95	95
RXRs/RARs/SMRT(N-CoR2)/9cRA	-0.045	0.16	-10000	0	-0.37	93	93
proteasomal ubiquitin-dependent protein catabolic process	-0.02	0.097	-10000	0	-0.36	18	18
RXRs/RARs/NRIP1/9cRA/HDAC3	-0.063	0.18	-10000	0	-0.43	97	97
positive regulation of DNA binding	-0.046	0.081	-10000	0	-0.43	5	5
NRIP1	-0.064	0.2	-10000	0	-0.91	15	15
RXRs/RARs	-0.066	0.17	-10000	0	-0.42	99	99
RXRs/RXRs/DNA/9cRA	-0.072	0.17	-10000	0	-0.44	97	97
PRKACA	0.011	0	-10000	0	-10000	0	0
CDK7	0.008	0.042	-10000	0	-0.58	3	3
TFIIH	0.019	0.044	-10000	0	-0.4	6	6
RAR alpha/9cRA	-0.035	0.062	-10000	0	-0.37	5	5
CCNH	0.011	0	-10000	0	-10000	0	0
CREBBP	0.011	0	-10000	0	-10000	0	0
RAR gamma2/9cRA	-0.006	0.042	-10000	0	-0.42	2	2

×

Signaling events mediated by PTP1B

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
PDGFRB	-0.006	0.097	-10000	0	-0.54	19	19
Jak2/Leptin Receptor	-0.054	0.13	0.19	2	-0.41	50	52
PTP1B/AKT1	-0.021	0.079	-10000	0	-0.32	16	16
FYN	0.005	0.06	-10000	0	-0.55	7	7
p210 bcr-abl/PTP1B	-0.029	0.084	0.17	1	-0.3	25	26
EGFR	0.002	0.059	-10000	0	-0.54	7	7
EGF/EGFR	-0.11	0.14	-10000	0	-0.34	113	113
CSF1	0.006	0.055	-10000	0	-0.54	6	6
AKT1	0.01	0.025	-10000	0	-0.59	1	1
INSR	0.009	0.034	-10000	0	-0.59	2	2
PTP1B/N-cadherin	-0.071	0.15	-10000	0	-0.35	109	109
Insulin Receptor/Insulin	-0.026	0.061	-10000	0	-0.34	10	10
HCK	-0.017	0.12	-10000	0	-0.54	31	31
CRK	0.011	0.019	-10000	0	-0.46	1	1
TYK2	-0.022	0.083	-10000	0	-0.33	18	18
EGF	-0.18	0.25	-10000	0	-0.51	222	222
YES1	0.005	0.064	-10000	0	-0.58	7	7
CAV1	-0.042	0.1	-10000	0	-0.37	21	21
TXN	0.009	0.004	-10000	0	-10000	0	0
PTP1B/IRS1/GRB2	-0.02	0.088	-10000	0	-0.35	19	19
cell migration	0.029	0.084	0.3	25	-0.17	1	26
STAT3	0.011	0.001	-10000	0	-10000	0	0
PRLR	-0.042	0.17	-10000	0	-0.58	54	54
ITGA2B	-0.044	0.16	-10000	0	-0.5	63	63
CSF1R	-0.03	0.15	-10000	0	-0.54	46	46
Prolactin Receptor/Prolactin	-0.043	0.14	-10000	0	-0.42	71	71
FGR	-0.026	0.14	-10000	0	-0.54	41	41
PTP1B/p130 Cas	-0.024	0.085	-10000	0	-0.32	22	22
Crk/p130 Cas	-0.017	0.084	-10000	0	-0.34	18	18
DOK1	-0.019	0.092	-10000	0	-0.37	22	22
JAK2	-0.046	0.13	-10000	0	-0.42	48	48
Jak2/Leptin Receptor/Leptin	-0.054	0.12	-10000	0	-0.47	26	26
PIK3R1	0.008	0.042	-10000	0	-0.58	3	3
PTPN1	-0.029	0.085	0.17	1	-0.3	25	26
LYN	0.011	0	-10000	0	-10000	0	0
CDH2	-0.084	0.21	-10000	0	-0.53	106	106
SRC	0	0.059	-10000	0	-1.2	1	1
ITGB3	-0.009	0.1	-10000	0	-0.55	21	21
CAT1/PTP1B	-0.08	0.16	-10000	0	-0.47	57	57
CAPN1	0.01	0.025	-10000	0	-0.6	1	1
CSK	0.01	0.024	-10000	0	-0.58	1	1
PI3K	-0.022	0.066	-10000	0	-0.44	7	7
mol:H2O2	-0.001	0.004	-10000	0	-10000	0	0
STAT3 (dimer)	-0.049	0.11	-10000	0	-0.46	24	24
negative regulation of transcription	-0.045	0.13	-10000	0	-0.41	48	48
FCGR2A	-0.022	0.13	-10000	0	-0.54	37	37
FER	0	0.07	-10000	0	-0.54	10	10
alphaIIb/beta3 Integrin	-0.039	0.13	-10000	0	-0.37	83	83
BLK	-0.11	0.23	-10000	0	-0.53	138	138
Insulin Receptor/Insulin/Shc	0.013	0.031	-10000	0	-0.32	5	5
RHOA	0.01	0.025	-10000	0	-0.59	1	1
LEPR	0	0.079	-10000	0	-0.55	12	12
BCAR1	0.008	0.043	-10000	0	-0.52	4	4
p210 bcr-abl/Grb2	0.011	0	-10000	0	-10000	0	0
mol:NADPH	-0.002	0.003	-10000	0	-10000	0	0
TRPV6	-0.082	0.18	-10000	0	-0.51	62	62
PRL	-0.013	0.088	-10000	0	-0.46	23	23
SOCS3	-0.003	0.13	-10000	0	-1.3	5	5
SPRY2	0.008	0.042	-10000	0	-0.59	3	3
Insulin Receptor/Insulin/IRS1	0.007	0.06	-10000	0	-0.37	14	14
CSF1/CSF1R	-0.038	0.13	-10000	0	-0.39	47	47
Ras protein signal transduction	0.021	0.025	-10000	0	-10000	0	0
IRS1	0.002	0.076	-10000	0	-0.58	10	10
INS	-0.002	0.035	-10000	0	-0.5	3	3
LEP	-0.025	0.12	-10000	0	-0.46	40	40
STAT5B	-0.032	0.09	-10000	0	-0.29	35	35
STAT5A	-0.032	0.09	-10000	0	-0.29	35	35
GRB2	0.011	0	-10000	0	-10000	0	0
PDGFB-D/PDGFRB	-0.031	0.11	-10000	0	-0.41	30	30
CSN2	-0.008	0.06	-10000	0	-10000	0	0
PIK3CA	0.009	0.034	-10000	0	-0.58	2	2
LAT	-0.033	0.14	-10000	0	-0.57	33	33
YBX1	0.016	0.016	-10000	0	-0.36	1	1
LCK	-0.031	0.14	-10000	0	-0.51	49	49
SHC1	0.011	0	-10000	0	-10000	0	0
NOX4	-0.073	0.2	-10000	0	-0.53	93	93

×

FAS signaling pathway (CD95)

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
SPTAN1	0.011	0.057	0.26	15	-0.3	4	19
RFC1	0.01	0.061	0.24	21	-0.38	4	25
PRKDC	0.01	0.06	0.23	25	-0.3	6	31
RIPK1	0.013	0.003	-10000	0	-10000	0	0
CASP7	-0.01	0.051	0.24	5	-0.43	1	6
FASLG/FAS/FADD/FAF1	0.002	0.12	0.22	65	-0.3	34	99
MAP2K4	-0.029	0.13	-10000	0	-0.43	25	25
mol:ceramide	-0.028	0.12	-10000	0	-0.39	46	46
GSN	0.005	0.069	0.26	15	-0.3	13	28
FASLG/FAS/FADD/FAF1/Caspase 8	-0.001	0.12	-10000	0	-0.36	36	36
FAS	-0.003	0.085	-10000	0	-0.57	13	13
BID	0.008	0.05	0.29	13	-0.32	2	15
MAP3K1	-0.006	0.089	0.22	5	-0.3	15	20
MAP3K7	0.01	0.004	-10000	0	-10000	0	0
RB1	0	0.084	0.26	14	-0.35	21	35
CFLAR	0.013	0.003	-10000	0	-10000	0	0
HGF/MET	-0.066	0.17	-10000	0	-0.37	138	138
ARHGDIB	0.009	0.059	0.24	23	-0.31	5	28
FADD	0.009	0.005	-10000	0	-10000	0	0
actin filament polymerization	-0.005	0.069	0.3	13	-0.26	15	28
NFKB1	-0.044	0.086	-10000	0	-1.2	1	1
MAPK8	-0.047	0.18	-10000	0	-0.46	72	72
DFFA	0.012	0.055	0.24	21	-0.29	3	24
DNA fragmentation during apoptosis	0.012	0.055	0.24	21	-0.28	3	24
FAS/FADD/MET	0.01	0.058	-10000	0	-0.35	15	15
CFLAR/RIP1	0.013	0.007	-10000	0	-10000	0	0
FAIM3	-0.011	0.11	-10000	0	-0.52	27	27
FAF1	0.009	0.008	-10000	0	-10000	0	0
PARP1	0.012	0.055	0.26	15	-0.29	3	18
DFFB	0.012	0.055	0.24	21	-0.29	3	24
CHUK	-0.04	0.081	-10000	0	-0.77	2	2
FASLG	-0.054	0.18	-10000	0	-0.54	70	70
FAS/FADD	0.004	0.064	-10000	0	-0.42	13	13
HGF	-0.039	0.16	-10000	0	-0.55	55	55
LMNA	0.009	0.051	0.23	14	-0.3	3	17
CASP6	0.011	0.053	0.23	21	-0.29	3	24
CASP10	0.008	0.025	-10000	0	-0.58	1	1
CASP3	0.014	0.066	0.28	26	-0.33	3	29
PTPN13	-0.08	0.21	-10000	0	-0.56	97	97
CASP8	0.012	0.066	0.3	27	-0.44	1	28
IL6	-0.17	0.41	-10000	0	-1.2	70	70
MET	0.01	0.031	-10000	0	-0.52	2	2
ICAD/CAD	0.011	0.051	0.24	15	-0.29	2	17
FASLG/FAS/FADD/FAF1/Caspase 10	-0.029	0.13	-10000	0	-0.39	46	46
activation of caspase activity by cytochrome c	0.008	0.05	0.29	13	-0.32	2	15
PAK2	0.011	0.059	0.24	21	-0.4	3	24
BCL2	-0.007	0.1	-10000	0	-0.55	20	20

×

IL27-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	-0.044	0.14	-10000	0	-0.42	63	63
CD4-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
cytokine production during immune response	0.024	0.12	0.49	15	-10000	0	15
IL27/IL27R/JAK1	-0.025	0.16	-10000	0	-0.62	17	17
TBX21	-0.047	0.23	-10000	0	-0.55	75	75
IL12B	-0.004	0.07	-10000	0	-0.46	14	14
IL12A	-0.026	0.12	-10000	0	-0.42	48	48
IL6ST	-0.004	0.093	-10000	0	-0.59	15	15
IL27RA/JAK1	0.006	0.095	-10000	0	-1.2	3	3
IL27	-0.007	0.082	-10000	0	-0.46	19	19
TYK2	0.01	0.025	-10000	0	-0.59	1	1
T-helper cell lineage commitment	-0.19	0.41	-10000	0	-1.3	64	64
T-helper 2 cell differentiation	0.024	0.12	0.49	15	-10000	0	15
T cell proliferation during immune response	0.024	0.12	0.49	15	-10000	0	15
MAPKKK cascade	-0.024	0.12	-10000	0	-0.49	15	15
STAT3	0.011	0	-10000	0	-10000	0	0
STAT2	0.011	0.019	-10000	0	-0.46	1	1
STAT1	0.006	0.055	-10000	0	-0.5	7	7
IL12RB1	-0.036	0.15	-10000	0	-0.55	50	50
positive regulation of tyrosine phosphorylation of STAT protein	0	0	-10000	0	-10000	0	0
IL12RB2	-0.043	0.22	-10000	0	-0.59	52	52
IL27/IL27R/JAK2/TYK2	-0.024	0.13	-10000	0	-0.49	15	15
positive regulation of T cell mediated cytotoxicity	-0.024	0.12	-10000	0	-0.49	15	15
STAT1 (dimer)	-0.058	0.24	0.4	21	-0.74	33	54
JAK2	-0.008	0.1	-10000	0	-0.55	21	21
JAK1	0.009	0.042	-10000	0	-0.59	3	3
STAT2 (dimer)	-0.018	0.12	-10000	0	-0.49	13	13
T cell proliferation	-0.1	0.18	-10000	0	-0.5	60	60
IL12/IL12R/TYK2/JAK2	-0.044	0.14	-10000	0	-0.55	15	15
IL17A	-0.2	0.41	-10000	0	-1.3	64	64
mast cell activation	0.024	0.12	0.49	15	-10000	0	15
IFNG	-0.011	0.043	-10000	0	-0.11	61	61
T cell differentiation	-0.004	0.007	0.014	2	-0.022	65	67
STAT3 (dimer)	-0.018	0.12	-10000	0	-0.5	12	12
STAT5A (dimer)	-0.018	0.12	-10000	0	-0.5	12	12
STAT4 (dimer)	-0.039	0.16	-10000	0	-0.52	37	37
STAT4	-0.029	0.15	-10000	0	-0.56	43	43
T cell activation	-0.006	0.01	0.12	3	-10000	0	3
IL27R/JAK2/TYK2	-0.013	0.12	-10000	0	-0.85	6	6
GATA3	-0.028	0.23	-10000	0	-1.3	17	17
IL18	0.003	0.049	-10000	0	-0.4	9	9
positive regulation of mast cell cytokine production	-0.018	0.12	-10000	0	-0.49	12	12
IL27/EBI3	-0.028	0.13	-10000	0	-0.4	63	63
IL27RA	-0.002	0.096	-10000	0	-1.3	3	3
IL6	-0.16	0.26	-10000	0	-0.54	174	174
STAT5A	0.011	0	-10000	0	-10000	0	0
monocyte differentiation	-0.001	0.002	-10000	0	-10000	0	0
IL2	0.005	0.039	0.47	3	-10000	0	3
IL1B	-0.041	0.13	-10000	0	-0.38	79	79
EBI3	-0.032	0.15	-10000	0	-0.56	46	46
TNF	-0.012	0.09	-10000	0	-0.4	31	31

×

Ras signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ERK1-2/ELK1	-0.022	0.17	-9999	-0.51	45	45
MAP3K8	0.009	0.031	-9999	-0.52	2	2
FOS	-0.023	0.15	-9999	-0.58	30	30
PRKCA	0.01	0.031	-9999	-0.52	2	2
PTPN7	-0.048	0.16	-9999	-0.5	72	72
HRAS	0.008	0.041	-9999	-0.49	4	4
PRKCB	-0.044	0.17	-9999	-0.55	60	60
NRAS	0.002	0.076	-9999	-0.58	10	10
RAS family/GTP	0.011	0.069	-9999	-0.38	16	16
MAPK3	-0.019	0.14	-9999	-0.58	26	26
MAP2K1	-0.009	0.12	-9999	-0.42	45	45
ELK1	0.01	0.025	-9999	-0.58	1	1
BRAF	-0.015	0.12	-9999	-0.43	44	44
mol:GTP	0	0.001	-9999	-0.005	40	40
MAPK1	-0.019	0.14	-9999	-0.63	22	22
RAF1	-0.014	0.12	-9999	-0.42	43	43
KRAS	0.006	0.057	-9999	-0.56	6	6

×

Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
DYNC1H1	0.011	0	-9999	-10000	0	0
VLDLR	-0.041	0.16	-9999	-0.55	57	57
LRPAP1	0.01	0.024	-9999	-0.58	1	1
NUDC	0.011	0.019	-9999	-0.46	1	1
RELN/LRP8	-0.046	0.14	-9999	-0.31	125	125
CaM/Ca2+	0.009	0	-9999	-10000	0	0
KATNA1	0.01	0.024	-9999	-0.58	1	1
GO:0030286	0	0	-9999	-10000	0	0
ABL1	-0.036	0.12	-9999	-0.32	65	65
IQGAP1/CaM	0.015	0.029	-9999	-0.39	3	3
DAB1	-0.081	0.2	-9999	-0.52	104	104
IQGAP1	0.009	0.039	-9999	-0.54	3	3
PLA2G7	-0.023	0.14	-9999	-0.56	36	36
CALM1	0.011	0	-9999	-10000	0	0
DYNLT1	0.011	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
LRPAP1/LRP8	0.014	0.036	-9999	-0.42	4	4
UniProt:Q4QZ09	0	0	-9999	-10000	0	0
CLIP1	0.009	0.034	-9999	-0.58	2	2
CDK5R1	0.009	0.033	-9999	-0.46	3	3
LIS1/Poliovirus Protein 3A	0.014	0	-9999	-10000	0	0
CDK5R2	-0.052	0.17	-9999	-0.5	73	73
mol:PP1	0	0	-9999	-10000	0	0
RELN/VLDLR/DAB1	-0.13	0.21	-9999	-0.37	235	235
YWHAE	0.011	0	-9999	-10000	0	0
NDEL1/14-3-3 E	-0.026	0.12	-9999	-0.43	16	16
MAP1B	-0.012	0.05	-9999	-0.31	10	10
RAC1	0.017	0.012	-9999	-10000	0	0
p35/CDK5	-0.021	0.11	-9999	-0.49	3	3
RELN	-0.096	0.22	-9999	-0.52	121	121
PAFAH/LIS1	0.001	0.086	-9999	-0.34	36	36
LIS1/CLIP170	0.021	0.022	-9999	-0.36	2	2
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain	-0.046	0.082	-9999	-0.37	9	9
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3	-0.073	0.16	-9999	-0.32	133	133
GO:0005869	0	0	-9999	-10000	0	0
NDEL1	-0.034	0.13	-9999	-0.41	25	25
LIS1/IQGAP1	0.021	0.025	-9999	-0.32	3	3
RHOA	0.016	0.035	-9999	-0.81	1	1
PAFAH1B1	0.019	0	-9999	-10000	0	0
PAFAH1B3	0.008	0.043	-9999	-0.52	4	4
PAFAH1B2	0.007	0.048	-9999	-0.58	4	4
MAP1B/LIS1/Dynein heavy chain	0.013	0.035	-9999	-10000	0	0
NDEL1/Katanin 60/Dynein heavy chain	-0.021	0.12	-9999	-0.41	17	17
LRP8	0.008	0.042	-9999	-0.58	3	3
NDEL1/Katanin 60	-0.027	0.12	-9999	-0.43	17	17
P39/CDK5	-0.051	0.15	-9999	-0.48	25	25
LIS1/NudC/Dynein intermediate chain/microtubule organizing center	0.022	0.011	-9999	-0.26	1	1
CDK5	-0.027	0.12	-9999	-0.3	65	65
PPP2R5D	0.011	0	-9999	-10000	0	0
LIS1/CLIP170/Dynein Complex/Dynactin Complex	0.018	0.019	-9999	-0.31	2	2
CSNK2A1	0.011	0	-9999	-10000	0	0
RELN/VLDLR/DAB1/LIS1	-0.1	0.18	-9999	-0.37	141	141
RELN/VLDLR	-0.063	0.16	-9999	-0.35	99	99
CDC42	0.013	0.057	-9999	-0.58	5	5

×

Plasma membrane estrogen receptor signaling

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
GNB1/GNG2	-0.012	0.11	-10000	0	-0.33	50	50
ER alpha/Gai/GDP/Gbeta gamma	-0.023	0.14	-10000	0	-0.47	36	36
AKT1	-0.021	0.18	-10000	0	-0.74	33	33
PIK3CA	0.009	0.034	-10000	0	-0.58	2	2
E2/ER alpha (dimer)/PELP1/Src/PI3K	-0.023	0.18	-10000	0	-0.78	31	31
mol:Ca2+	-0.023	0.13	-10000	0	-0.43	31	31
IGF1R	0.01	0.024	-10000	0	-0.58	1	1
E2/ER alpha (dimer)/Striatin	-0.017	0.1	-10000	0	-0.32	58	58
SHC1	0.011	0	-10000	0	-10000	0	0
apoptosis	0.019	0.17	0.71	33	-10000	0	33
RhoA/GTP	-0.029	0.088	-10000	0	-0.58	5	5
E2/ER alpha (dimer)/PELP1/Src/p130 Cas	-0.048	0.12	-10000	0	-0.47	35	35
regulation of stress fiber formation	-0.009	0.095	0.48	10	-10000	0	10
E2/ERA-ERB (dimer)	-0.025	0.11	-10000	0	-0.34	69	69
KRAS	0.006	0.057	-10000	0	-0.56	6	6
G13/GTP	-0.013	0.088	-10000	0	-0.29	54	54
pseudopodium formation	0.009	0.095	-10000	0	-0.48	10	10
E2/ER alpha (dimer)/PELP1	-0.014	0.096	-10000	0	-0.32	53	53
GRB2	0.011	0	-10000	0	-10000	0	0
GNG2	0.003	0.067	-10000	0	-0.54	9	9
GNAO1	-0.045	0.16	-10000	0	-0.49	68	68
HRAS	0.008	0.041	-10000	0	-0.49	4	4
mol:GTP	0	0	-10000	0	-10000	0	0
mol:NO	-0.02	0.14	-10000	0	-0.52	34	34
E2/ER beta (dimer)	-0.005	0.073	-10000	0	-0.4	20	20
mol:GDP	-0.04	0.11	-10000	0	-0.38	48	48
mol:NADP	-0.02	0.14	-10000	0	-0.52	34	34
PIK3R1	0.008	0.042	-10000	0	-0.58	3	3
mol:IP3	-0.025	0.13	-10000	0	-0.45	31	31
IGF-1R heterotetramer	0.01	0.024	-10000	0	-0.58	1	1
PLCB1	-0.028	0.13	-10000	0	-0.46	31	31
PLCB2	-0.01	0.11	-10000	0	-0.45	26	26
IGF1	-0.075	0.2	-10000	0	-0.52	97	97
mol:L-citrulline	-0.02	0.14	-10000	0	-0.52	34	34
RHOA	0.01	0.024	-10000	0	-0.58	1	1
Gai/GDP	-0.022	0.15	-10000	0	-0.77	19	19
JNK cascade	-0.005	0.073	-10000	0	-0.4	20	20
BCAR1	0.008	0.043	-10000	0	-0.52	4	4
ESR2	-0.007	0.1	-10000	0	-0.55	20	20
GNAQ	0.006	0.059	-10000	0	-0.58	6	6
ESR1	-0.035	0.15	-10000	0	-0.53	52	52
Gq family/GDP/Gbeta gamma	0.002	0.11	-10000	0	-0.51	21	21
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1	0.008	0.071	-10000	0	-0.32	2	2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC	-0.047	0.12	-10000	0	-0.47	34	34
GNAZ	-0.013	0.11	-10000	0	-0.55	26	26
E2/ER alpha (dimer)	-0.026	0.11	-10000	0	-0.38	52	52
STRN	0.006	0.059	-10000	0	-0.58	6	6
GNAL	-0.018	0.12	-10000	0	-0.51	34	34
PELP1	0.01	0.024	-10000	0	-0.58	1	1
MAPK11	-0.004	0.081	-10000	0	-0.33	34	34
GNAI2	0.011	0	-10000	0	-10000	0	0
GNAI3	0.011	0	-10000	0	-10000	0	0
GNAI1	-0.003	0.089	-10000	0	-0.56	15	15
HBEGF	-0.038	0.16	-10000	0	-0.51	36	36
cAMP biosynthetic process	-0.044	0.11	-10000	0	-0.27	97	97
SRC	-0.016	0.14	-10000	0	-0.45	33	33
PI3K	0.013	0.04	-10000	0	-0.43	5	5
GNB1	0.011	0	-10000	0	-10000	0	0
G13/GDP/Gbeta gamma	-0.038	0.1	-10000	0	-0.38	35	35
SOS1	0.01	0.024	-10000	0	-0.58	1	1
IGF-1R heterotetramer/IGF1	-0.067	0.13	-10000	0	-0.43	54	54
Gs family/GTP	-0.045	0.11	-10000	0	-0.28	97	97
EntrezGene:2778	0	0	-10000	0	-10000	0	0
RAS family/GTP	0.012	0.069	-10000	0	-0.38	16	16
vasodilation	-0.019	0.14	-10000	0	-0.5	34	34
mol:DAG	-0.025	0.13	-10000	0	-0.45	31	31
Gs family/GDP/Gbeta gamma	-0.046	0.11	-10000	0	-0.38	38	38
MSN	0.008	0.1	-10000	0	-0.53	10	10
Gq family/GTP	-0.013	0.11	-10000	0	-0.49	24	24
mol:PI-3-4-5-P3	-0.022	0.18	-10000	0	-0.75	31	31
NRAS	0.002	0.076	-10000	0	-0.58	10	10
mol:E2	0	0	-10000	0	-10000	0	0
cell adhesion	0.019	0.14	0.5	34	-10000	0	34
GRB2/SOS1	0.016	0.018	-10000	0	-0.42	1	1
RhoA/GDP	-0.038	0.1	-10000	0	-0.37	46	46
NOS3	-0.022	0.15	-10000	0	-0.55	34	34
GNA11	0.007	0.05	-10000	0	-0.53	5	5
MAPKKK cascade	-0.007	0.15	-10000	0	-0.57	35	35
E2/ER alpha (dimer)/PELP1/Src	-0.05	0.13	-10000	0	-0.5	34	34
ruffle organization	0.009	0.095	-10000	0	-0.48	10	10
ROCK2	0.002	0.11	-10000	0	-0.62	9	9
GNA14	-0.007	0.1	-10000	0	-0.56	19	19
GNA15	-0.009	0.1	-10000	0	-0.54	22	22
GNA13	0.009	0.034	-10000	0	-0.58	2	2
MMP9	-0.044	0.16	-10000	0	-0.56	30	30
MMP2	-0.03	0.16	-10000	0	-0.58	26	26

×

LPA4-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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ADCY4	0.011	0.04	-9999	-0.31	9	9
ADCY5	-0.058	0.14	-9999	-0.32	134	134
ADCY6	0.016	0	-9999	-10000	0	0
ADCY7	0.014	0.022	-9999	-0.3	3	3
ADCY1	-0.019	0.097	-9999	-0.29	69	69
ADCY2	-0.017	0.1	-9999	-0.34	55	55
ADCY3	0.015	0.015	-9999	-0.36	1	1
ADCY8	0.003	0.042	-9999	-0.27	14	14
PRKCE	0.009	0	-9999	-10000	0	0
ADCY9	0.014	0.025	-9999	-0.33	3	3
mol:DAG	0	0	-9999	-10000	0	0
cAMP biosynthetic process	-0.014	0.068	-9999	-0.34	5	5

×

ErbB4 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF	0.014	0.1	-10000	0	-0.98	4	4
epithelial cell differentiation	-0.048	0.12	-10000	0	-0.46	26	26
ITCH	0.008	0.056	-10000	0	-0.6	5	5
WWP1	0.017	0.11	-10000	0	-1.1	5	5
FYN	0.005	0.06	-10000	0	-0.55	7	7
EGFR	0.005	0.058	-10000	0	-0.53	7	7
PRL	-0.013	0.088	-10000	0	-0.46	23	23
neuron projection morphogenesis	0.006	0.12	-10000	0	-0.79	4	4
PTPRZ1	-0.078	0.19	-10000	0	-0.51	102	102
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC	-0.005	0.13	-10000	0	-1.1	3	3
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta	-0.025	0.14	-10000	0	-0.36	58	58
ADAM17	0.011	0.038	-10000	0	-0.63	2	2
ErbB4/ErbB4	0.018	0.1	-10000	0	-0.9	5	5
ErbB4/ErbB4/neuregulin 3/neuregulin 3	0.001	0.1	-10000	0	-1	4	4
NCOR1	0.01	0.024	-10000	0	-0.58	1	1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn	-0.021	0.14	-10000	0	-1	4	4
GRIN2B	-0.038	0.16	-10000	0	-0.66	17	17
ErbB4/ErbB2/betacellulin	0.013	0.11	-10000	0	-0.44	18	18
STAT1	0.006	0.054	-10000	0	-0.49	7	7
HBEGF	0.001	0.068	-10000	0	-0.46	13	13
PRLR	-0.041	0.17	-10000	0	-0.58	54	54
E4ICDs/ETO2	-0.036	0.15	-10000	0	-0.38	55	55
axon guidance	0.015	0.13	-10000	0	-0.67	9	9
NEDD4	0.008	0.048	-10000	0	-0.58	4	4
Prolactin receptor/Prolactin receptor/Prolactin	-0.039	0.14	-10000	0	-0.42	71	71
CBFA2T3	-0.084	0.2	-10000	0	-0.51	112	112
ErbB4/ErbB2/HBEGF	0.016	0.1	-10000	0	-0.78	5	5
MAPK3	0	0.12	-10000	0	-0.84	4	4
STAT1 (dimer)	0.016	0.11	-10000	0	-1.1	4	4
MAPK1	0	0.12	-10000	0	-0.94	3	3
JAK2	-0.008	0.1	-10000	0	-0.55	21	21
ErbB4/ErbB2/neuregulin 1 beta	-0.023	0.14	-10000	0	-0.34	57	57
NRG1	-0.043	0.15	-10000	0	-0.39	92	92
NRG3	-0.003	0.065	-10000	0	-0.46	12	12
NRG2	-0.016	0.1	-10000	0	-0.46	32	32
NRG4	-0.022	0.12	-10000	0	-0.47	39	39
heart development	0.015	0.13	-10000	0	-0.67	9	9
neural crest cell migration	-0.023	0.14	-10000	0	-0.34	57	57
ERBB2	0.01	0.059	-10000	0	-0.35	16	16
WWOX/E4ICDs	0.018	0.095	-10000	0	-0.76	6	6
SHC1	0.011	0	-10000	0	-10000	0	0
ErbB4/EGFR/neuregulin 4	0.004	0.12	-10000	0	-0.56	13	13
apoptosis	0.036	0.096	0.85	5	-10000	0	5
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta	-0.002	0.12	-10000	0	-0.79	7	7
ErbB4/ErbB2/epiregulin	-0.075	0.17	-10000	0	-0.32	147	147
ErbB4/ErbB4/betacellulin/betacellulin	0.011	0.11	-10000	0	-0.48	18	18
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2	-0.018	0.16	-10000	0	-0.57	23	23
MDM2	0.02	0.1	-10000	0	-0.9	5	5
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta	-0.023	0.14	-10000	0	-0.35	59	59
STAT5A	0.019	0.12	-10000	0	-0.82	6	6
ErbB4/EGFR/neuregulin 1 beta	-0.02	0.14	-10000	0	-0.35	58	58
DLG4	0.007	0.047	-10000	0	-0.51	5	5
GRB2/SHC	0.017	0	-10000	0	-10000	0	0
E4ICDs/TAB2/NCoR1	0.017	0.089	-10000	0	-0.81	5	5
STAT5A (dimer)	-0.052	0.13	-10000	0	-0.52	25	25
MAP3K7IP2	0	0	-10000	0	-10000	0	0
STAT5B (dimer)	0.018	0.12	-10000	0	-0.82	6	6
LRIG1	-0.001	0.086	-10000	0	-0.58	13	13
EREG	-0.17	0.26	-10000	0	-0.55	191	191
BTC	-0.002	0.09	-10000	0	-0.58	14	14
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta	0.014	0.13	-10000	0	-0.7	9	9
ERBB4	0.018	0.1	-10000	0	-0.91	5	5
STAT5B	0.011	0	-10000	0	-10000	0	0
YAP1	-0.006	0.085	-10000	0	-1.1	3	3
GRB2	0.011	0	-10000	0	-10000	0	0
ErbB4/ErbB2/neuregulin 4	0.002	0.11	-10000	0	-0.51	12	12
glial cell differentiation	-0.007	0.086	0.79	5	-10000	0	5
WWOX	0.009	0.034	-10000	0	-0.58	2	2
cell proliferation	-0.017	0.15	-10000	0	-0.61	12	12

×

Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.01	0.12	-9999	-0.42	41	41
CRKL	0.011	0	-9999	-10000	0	0
Rac1/GDP	0.009	0	-9999	-10000	0	0
DOCK1	0.01	0.024	-9999	-0.58	1	1
ITGA4	-0.019	0.13	-9999	-0.57	32	32
alpha4/beta7 Integrin/MAdCAM1	-0.081	0.17	-9999	-0.37	117	117
EPO	0	0.053	-9999	-0.46	8	8
alpha4/beta7 Integrin	-0.024	0.14	-9999	-0.44	55	55
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.011	0.019	-9999	-0.46	1	1
alpha4/beta1 Integrin	-0.006	0.096	-9999	-0.41	32	32
EPO/EPOR (dimer)	0.002	0.063	-9999	-0.35	18	18
lamellipodium assembly	0.026	0.049	-9999	-0.44	5	5
PIK3CA	0.009	0.034	-9999	-0.58	2	2
PI3K	0.013	0.04	-9999	-0.43	5	5
ARF6	0.01	0.024	-9999	-0.58	1	1
JAK2	-0.007	0.11	-9999	-0.49	18	18
PXN	0.011	0	-9999	-10000	0	0
PIK3R1	0.008	0.042	-9999	-0.58	3	3
MADCAM1	-0.13	0.23	-9999	-0.52	156	156
cell adhesion	-0.081	0.17	-9999	-0.36	117	117
CRKL/CBL	0.017	0	-9999	-10000	0	0
ITGB1	0.011	0	-9999	-10000	0	0
SRC	-0.009	0.13	-9999	-0.44	41	41
ITGB7	-0.016	0.12	-9999	-0.53	30	30
RAC1	0.011	0	-9999	-10000	0	0
alpha4/beta1 Integrin/VCAM1	-0.016	0.14	-9999	-0.44	51	51
p130Cas/Crk/Dock1	0.008	0.12	-9999	-0.52	20	20
VCAM1	-0.022	0.13	-9999	-0.53	37	37
RHOA	0.01	0.024	-9999	-0.58	1	1
alpha4/beta1 Integrin/Paxillin/GIT1	0.011	0.077	-9999	-0.32	29	29
BCAR1	-0.004	0.12	-9999	-0.41	42	42
EPOR	0.002	0.068	-9999	-0.49	11	11
mol:GDP	0	0	-9999	-10000	0	0
CBL	0.011	0	-9999	-10000	0	0
GIT1	0.01	0.024	-9999	-0.58	1	1
Rac1/GTP	-0.002	0.051	-9999	-0.46	5	5

×

S1P1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	0.01	0.045	-9999	-0.37	8	8
PDGFRB	-0.007	0.098	-9999	-0.55	19	19
SPHK1	-0.046	0.15	-9999	-0.8	22	22
mol:S1P	-0.045	0.14	-9999	-0.69	23	23
S1P1/S1P/Gi	-0.047	0.16	-9999	-0.4	64	64
GNAO1	-0.047	0.16	-9999	-0.49	68	68
PDGFB-D/PDGFRB/PLCgamma1	-0.043	0.15	-9999	-0.48	27	27
PLCG1	-0.042	0.15	-9999	-0.38	65	65
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	-0.007	0.098	-9999	-0.55	19	19
GNAI2	0.01	0.005	-9999	-10000	0	0
GNAI3	0.01	0.005	-9999	-10000	0	0
GNAI1	-0.004	0.089	-9999	-0.56	15	15
mol:GDP	0	0	-9999	-10000	0	0
EDG1	0.008	0.039	-9999	-0.32	8	8
S1P1/S1P	-0.021	0.12	-9999	-0.49	27	27
negative regulation of cAMP metabolic process	-0.046	0.15	-9999	-0.38	64	64
MAPK3	-0.061	0.2	-9999	-0.56	59	59
calcium-dependent phospholipase C activity	-0.001	0.003	-9999	-10000	0	0
Rac1/GDP	0.009	0	-9999	-10000	0	0
RhoA/GDP	0.008	0.018	-9999	-0.43	1	1
KDR	0.004	0.058	-9999	-0.53	7	7
PLCB2	-0.015	0.11	-9999	-0.42	30	30
RAC1	0.011	0	-9999	-10000	0	0
RhoA/GTP	-0.038	0.092	-9999	-0.41	27	27
receptor internalization	-0.041	0.1	-9999	-0.45	27	27
PTGS2	-0.1	0.31	-9999	-0.98	57	57
Rac1/GTP	-0.037	0.092	-9999	-0.41	27	27
RHOA	0.01	0.024	-9999	-0.58	1	1
VEGFA	0.01	0.019	-9999	-0.46	1	1
negative regulation of T cell proliferation	-0.046	0.15	-9999	-0.38	64	64
GO:0007205	0	0	-9999	-10000	0	0
GNAZ	-0.014	0.12	-9999	-0.55	26	26
MAPK1	-0.061	0.2	-9999	-0.56	59	59
S1P1/S1P/PDGFB-D/PDGFRB	-0.022	0.13	-9999	-0.45	31	31
ABCC1	0.01	0.024	-9999	-0.59	1	1

×

Nongenotropic Androgen signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.009	0.018	-10000	0	-0.43	1	1
GNB1/GNG2	-0.017	0.1	-10000	0	-0.35	29	29
regulation of S phase of mitotic cell cycle	-0.001	0.073	-10000	0	-0.27	28	28
GNAO1	-0.045	0.16	-10000	0	-0.49	68	68
HRAS	0.008	0.041	-10000	0	-0.49	4	4
SHBG/T-DHT	-0.008	0.061	-10000	0	-0.27	30	30
PELP1	0.01	0.024	-10000	0	-0.58	1	1
AKT1	0.009	0.018	-10000	0	-0.43	1	1
MAP2K1	0.001	0.089	-10000	0	-0.42	5	5
T-DHT/AR	-0.036	0.12	-10000	0	-0.36	71	71
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
mol:GTP	0	0.002	-10000	0	-0.006	40	40
GNAI2	0.011	0	-10000	0	-10000	0	0
GNAI3	0.011	0	-10000	0	-10000	0	0
GNAI1	-0.003	0.089	-10000	0	-0.56	15	15
mol:GDP	-0.033	0.098	-10000	0	-0.44	24	24
cell proliferation	0.001	0.12	-10000	0	-0.38	30	30
PIK3CA	0.009	0.034	-10000	0	-0.58	2	2
FOS	-0.014	0.18	-10000	0	-0.76	29	29
mol:Ca2+	-0.011	0.021	-10000	0	-0.062	67	67
MAPK3	0.002	0.1	-10000	0	-0.48	5	5
MAPK1	0.005	0.062	-10000	0	-0.31	4	4
PIK3R1	0.008	0.042	-10000	0	-0.58	3	3
mol:IP3	0	0.001	-10000	0	-0.004	41	41
cAMP biosynthetic process	-0.003	0.061	-10000	0	-0.26	30	30
GNG2	0.003	0.067	-10000	0	-0.54	9	9
potassium channel inhibitor activity	0	0.001	-10000	0	-0.004	41	41
HRAS/GTP	-0.031	0.083	-10000	0	-0.3	27	27
actin cytoskeleton reorganization	-0.005	0.046	-10000	0	-0.41	7	7
SRC	0.01	0.024	-10000	0	-0.58	1	1
voltage-gated calcium channel activity	0	0.001	-10000	0	-0.004	41	41
PI3K	0.012	0.034	-10000	0	-0.36	5	5
apoptosis	-0.001	0.11	0.39	31	-10000	0	31
T-DHT/AR/PELP1	-0.023	0.1	-10000	0	-0.3	72	72
HRAS/GDP	-0.032	0.094	-10000	0	-0.42	25	25
CREB1	0	0.11	-10000	0	-0.42	31	31
RAC1-CDC42/GTP	-0.004	0.047	-10000	0	-0.42	7	7
AR	-0.05	0.16	-10000	0	-0.5	71	71
GNB1	0.011	0	-10000	0	-10000	0	0
RAF1	-0.003	0.089	-10000	0	-0.29	25	25
RAC1-CDC42/GDP	-0.03	0.093	-10000	0	-0.4	27	27
T-DHT/AR/PELP1/Src	-0.014	0.096	-10000	0	-0.27	72	72
MAP2K2	0.001	0.091	-10000	0	-0.47	4	4
T-DHT/AR/PELP1/Src/PI3K	-0.001	0.074	-10000	0	-0.27	28	28
GNAZ	-0.013	0.11	-10000	0	-0.55	26	26
SHBG	-0.014	0.1	-10000	0	-0.46	30	30
Gi family/GNB1/GNG2/GDP	-0.008	0.1	-10000	0	-0.39	20	20
mol:T-DHT	0	0.001	-10000	0	-0.002	34	34
RAC1	0.011	0	-10000	0	-10000	0	0
GNRH1	0	0.062	-10000	0	-0.42	13	13
Gi family/GTP	-0.022	0.089	-10000	0	-0.23	67	67
CDC42	0.007	0.054	-10000	0	-0.58	5	5

×

IL6-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.021	0.2	-10000	0	-0.72	12	12
CRP	-0.029	0.2	-10000	0	-0.7	17	17
cell cycle arrest	-0.036	0.22	-10000	0	-0.7	26	26
TIMP1	-0.01	0.18	-10000	0	-0.62	12	12
IL6ST	-0.001	0.093	-10000	0	-0.58	15	15
Rac1/GDP	-0.041	0.18	-10000	0	-0.54	40	40
AP1	0.002	0.12	-10000	0	-0.55	10	10
GAB2	0.01	0.034	-10000	0	-0.58	2	2
TNFSF11	-0.076	0.33	-10000	0	-1	54	54
HSP90B1	0.009	0.14	-10000	0	-1.3	6	6
GAB1	0.012	0.001	-10000	0	-10000	0	0
MAPK14	-0.03	0.16	-10000	0	-0.55	30	30
AKT1	0.038	0.071	-10000	0	-0.73	4	4
FOXO1	0.041	0.069	-10000	0	-0.68	4	4
MAP2K6	-0.037	0.16	-10000	0	-0.53	34	34
mol:GTP	0	0.002	-10000	0	-10000	0	0
MAP2K4	-0.031	0.18	-10000	0	-0.57	35	35
MITF	-0.049	0.17	-10000	0	-0.5	47	47
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TYK2	0.01	0.024	-10000	0	-0.58	1	1
A2M	0.009	0.09	-10000	0	-1.4	2	2
CEBPB	0.013	0.041	-10000	0	-0.49	4	4
GRB2/SOS1/GAB family/SHP2	0.001	0.089	0.22	1	-0.6	5	6
STAT3	-0.04	0.23	-10000	0	-0.73	28	28
STAT1	-0.009	0.066	-10000	0	-1.1	2	2
CEBPD	-0.023	0.2	-10000	0	-0.8	12	12
PIK3CA	0.011	0.034	-10000	0	-0.58	2	2
PI3K	0.016	0.04	-10000	0	-0.42	5	5
JUN	0.007	0.052	-10000	0	-0.56	5	5
PIAS3/MITF	-0.042	0.17	-10000	0	-0.53	35	35
MAPK11	-0.037	0.17	-10000	0	-0.6	32	32
STAT3 (dimer)/FOXO1	0.01	0.19	-10000	0	-0.62	14	14
GRB2/SOS1/GAB family	-0.058	0.13	-10000	0	-0.54	29	29
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK	-0.047	0.17	-10000	0	-0.47	54	54
GRB2	0.012	0.001	-10000	0	-10000	0	0
JAK2	-0.008	0.1	-10000	0	-0.55	21	21
LBP	-0.094	0.32	-10000	0	-0.86	67	67
PIK3R1	0.009	0.042	-10000	0	-0.58	3	3
JAK1	0.01	0.042	-10000	0	-0.58	3	3
MYC	-0.026	0.21	-10000	0	-0.84	15	15
FGG	-0.038	0.22	-10000	0	-0.72	20	20
macrophage differentiation	-0.036	0.22	-10000	0	-0.7	26	26
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4	-0.069	0.17	-10000	0	-0.44	59	59
JUNB	-0.024	0.2	-10000	0	-0.77	14	14
FOS	-0.026	0.14	-10000	0	-0.54	41	41
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4	-0.039	0.16	-10000	0	-0.45	49	49
STAT1/PIAS1	-0.029	0.16	-10000	0	-0.47	36	36
GRB2/SOS1/GAB family/SHP2/PI3K	0.028	0.074	-10000	0	-0.56	7	7
STAT3 (dimer)	-0.038	0.23	-10000	0	-0.73	26	26
PRKCD	-0.022	0.2	-10000	0	-0.61	28	28
IL6R	-0.005	0.1	-10000	0	-0.56	19	19
SOCS3	-0.034	0.18	-10000	0	-0.82	16	16
gp130 (dimer)/JAK1/JAK1/LMO4	0.013	0.078	-10000	0	-0.33	27	27
Rac1/GTP	-0.04	0.18	-10000	0	-0.53	44	44
HCK	-0.017	0.12	-10000	0	-0.54	31	31
MAPKKK cascade	0.013	0.093	-10000	0	-0.8	5	5
bone resorption	-0.067	0.31	-10000	0	-0.93	54	54
IRF1	-0.022	0.2	-10000	0	-0.72	12	12
mol:GDP	-0.05	0.18	-10000	0	-0.52	50	50
SOS1	0.011	0.024	-10000	0	-0.58	1	1
VAV1	-0.051	0.19	-10000	0	-0.53	50	50
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3	-0.04	0.17	-10000	0	-0.56	37	37
PTPN11	-0.011	0.084	-10000	0	-0.9	5	5
IL6/IL6RA	-0.082	0.18	-10000	0	-0.38	156	156
gp130 (dimer)/TYK2/TYK2/LMO4	0.011	0.073	-10000	0	-0.34	22	22
gp130 (dimer)/JAK2/JAK2/LMO4	0	0.1	-10000	0	-0.35	42	42
IL6	-0.11	0.23	-10000	0	-0.52	142	142
PIAS3	0.01	0.031	-10000	0	-0.52	2	2
PTPRE	0.007	0.026	-10000	0	-0.57	1	1
PIAS1	0.011	0	-10000	0	-10000	0	0
RAC1	0.012	0.001	-10000	0	-10000	0	0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4	-0.043	0.14	-10000	0	-0.41	48	48
LMO4	0.006	0.062	-10000	0	-0.49	9	9
STAT3 (dimer)/PIAS3	-0.035	0.22	-10000	0	-0.7	28	28
MCL1	0.043	0.062	-10000	0	-0.7	3	3

×

Coregulation of Androgen receptor activity

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
NRIP1	-0.006	0.071	-10000	0	-0.59	8	8
SVIL	0	0.045	-10000	0	-0.49	4	4
ZNF318	0.033	0.05	-10000	0	-10000	0	0
JMJD2C	0.003	0.02	-10000	0	-0.077	29	29
T-DHT/AR/Ubc9	-0.023	0.11	-10000	0	-0.3	71	71
CARM1	0.009	0.024	-10000	0	-0.58	1	1
PRDX1	0.012	0.025	-10000	0	-0.58	1	1
PELP1	0.014	0.026	-10000	0	-0.58	1	1
CTNNB1	0.005	0.016	-10000	0	-10000	0	0
AKT1	0.016	0.028	-10000	0	-0.59	1	1
PTK2B	0.004	0.037	-10000	0	-0.58	2	2
MED1	0.015	0.046	-10000	0	-0.51	4	4
MAK	0.007	0.12	-10000	0	-0.47	31	31
response to oxidative stress	0.001	0.004	-10000	0	-10000	0	0
HIP1	-0.003	0.063	-10000	0	-0.6	6	6
GSN	-0.009	0.08	-10000	0	-0.52	13	13
NCOA2	0.003	0.067	-10000	0	-0.57	8	8
NCOA6	0.004	0.031	-10000	0	-0.58	1	1
DNA-PK	0.041	0.058	-10000	0	-0.48	2	2
NCOA4	0.008	0.034	-10000	0	-0.58	2	2
PIAS3	0.004	0.034	-10000	0	-0.52	2	2
cell proliferation	-0.004	0.11	-10000	0	-0.5	16	16
XRCC5	0.015	0.027	-10000	0	-0.58	1	1
UBE3A	-0.006	0.057	-10000	0	-0.58	4	4
T-DHT/AR/SNURF	-0.077	0.16	-10000	0	-0.34	154	154
FHL2	0.022	0.098	-10000	0	-1.1	3	3
RANBP9	0.004	0.031	-10000	0	-0.58	1	1
JMJD1A	-0.006	0.044	-10000	0	-0.11	80	80
CDK6	0.012	0.002	-10000	0	-10000	0	0
TGFB1I1	-0.002	0.056	-10000	0	-0.52	6	6
T-DHT/AR/CyclinD1	-0.031	0.11	-10000	0	-0.31	73	73
XRCC6	0.016	0.011	-10000	0	-10000	0	0
T-DHT/AR	-0.019	0.12	-10000	0	-0.3	77	77
CTDSP1	0.007	0.025	-10000	0	-0.58	1	1
CTDSP2	0.026	0.033	-10000	0	-10000	0	0
BRCA1	0.002	0.031	-10000	0	-0.58	1	1
TCF4	0.008	0.09	-10000	0	-0.53	15	15
CDKN2A	-0.064	0.19	-10000	0	-0.5	96	96
SRF	0.022	0.033	-10000	0	-0.45	2	2
NKX3-1	-0.076	0.25	-10000	0	-0.63	81	81
KLK3	-0.17	0.43	-10000	0	-1.4	59	59
TMF1	0.003	0.059	-10000	0	-0.58	6	6
HNRNPA1	0.019	0.018	-10000	0	-10000	0	0
AOF2	-0.009	0.022	-10000	0	-0.069	59	59
APPL1	0.023	0.07	-10000	0	-0.42	12	12
T-DHT/AR/Caspase 8	-0.015	0.11	-10000	0	-0.3	71	71
AR	-0.053	0.17	-10000	0	-0.5	71	71
UBA3	0.007	0.025	-10000	0	-0.58	1	1
PATZ1	0.019	0.018	-10000	0	-10000	0	0
PAWR	0.008	0.025	-10000	0	-0.58	1	1
PRKDC	0.013	0.04	-10000	0	-0.52	3	3
PA2G4	0.021	0.022	-10000	0	-10000	0	0
UBE2I	0.011	0	-10000	0	-10000	0	0
T-DHT/AR/Cyclin D3/CDK11 p58	-0.016	0.1	-10000	0	-0.27	75	75
RPS6KA3	-0.002	0.054	-10000	0	-0.6	4	4
T-DHT/AR/ARA70	-0.029	0.11	-10000	0	-0.31	72	72
LATS2	0.018	0.024	-10000	0	-0.4	1	1
T-DHT/AR/PRX1	-0.01	0.11	0.17	1	-0.27	71	72
Cyclin D3/CDK11 p58	0.007	0.031	-10000	0	-0.32	5	5
VAV3	-0.071	0.2	-10000	0	-0.59	78	78
KLK2	-0.027	0.095	-10000	0	-0.4	29	29
CASP8	0.013	0.025	-10000	0	-0.58	1	1
T-DHT/AR/TIF2/CARM1	-0.025	0.11	-10000	0	-0.32	48	48
TMPRSS2	-0.019	0.11	-10000	0	-0.95	4	4
CCND1	0.006	0.036	-10000	0	-0.59	2	2
PIAS1	-0.002	0.032	-10000	0	-10000	0	0
mol:T-DHT	-0.003	0.024	-10000	0	-0.072	39	39
CDC2L1	0.001	0.002	-10000	0	-10000	0	0
PIAS4	-0.01	0.054	-10000	0	-0.58	1	1
T-DHT/AR/CDK6	-0.02	0.11	-10000	0	-0.3	71	71
CMTM2	-0.028	0.14	-10000	0	-0.52	47	47
SNURF	-0.077	0.2	-10000	0	-0.54	93	93
ZMIZ1	0.008	0.028	-10000	0	-0.45	1	1
CCND3	0.008	0.042	-10000	0	-0.46	5	5
TGIF1	0.019	0.018	-10000	0	-10000	0	0
FKBP4	0.002	0.038	-10000	0	-0.46	3	3

×

IGF1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NCK2	0.01	0.024	-10000	0	-0.58	1	1
PTK2	0.01	0.024	-10000	0	-0.58	1	1
CRKL	-0.023	0.1	-10000	0	-0.3	52	52
GRB2/SOS1/SHC	0.023	0.015	-10000	0	-0.36	1	1
HRAS	0.008	0.041	-10000	0	-0.49	4	4
IRS1/Crk	-0.023	0.1	-10000	0	-0.3	53	53
IGF-1R heterotetramer/IGF1/PTP1B	-0.029	0.12	-10000	0	-0.34	53	53
AKT1	-0.006	0.094	-10000	0	-0.48	3	3
BAD	-0.001	0.092	-10000	0	-0.46	5	5
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	-0.023	0.1	-10000	0	-0.3	53	53
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.026	0.11	-10000	0	-0.31	57	57
RAF1	0.005	0.087	-10000	0	-0.42	3	3
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos	-0.014	0.1	-10000	0	-0.29	53	53
YWHAZ	0.008	0.042	-10000	0	-0.58	3	3
IGF-1R heterotetramer/IGF1/IRS1	-0.032	0.11	-10000	0	-0.32	60	60
PIK3CA	0.009	0.034	-10000	0	-0.58	2	2
RPS6KB1	-0.008	0.1	-10000	0	-0.51	6	6
GNB2L1	0.011	0.019	-10000	0	-0.46	1	1
positive regulation of MAPKKK cascade	0.003	0.077	-10000	0	-0.36	3	3
PXN	0.011	0	-10000	0	-10000	0	0
PIK3R1	0.008	0.042	-10000	0	-0.58	3	3
cell adhesion	0	0	-10000	0	-10000	0	0
GRB2/SOS1	0.016	0.018	-10000	0	-0.42	1	1
HRAS/GTP	-0.035	0.08	-10000	0	-0.48	3	3
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc	-0.008	0.096	-10000	0	-0.38	4	4
IGF-1R heterotetramer	-0.001	0.038	-10000	0	-0.67	1	1
IGF-1R heterotetramer/IGF1/IRS/Nck	-0.022	0.11	-10000	0	-0.31	53	53
Crk/p130 Cas/Paxillin	-0.01	0.098	-10000	0	-0.42	5	5
IGF1R	-0.001	0.038	-10000	0	-0.67	1	1
IGF1	-0.076	0.2	-10000	0	-0.53	97	97
IRS2/Crk	-0.02	0.1	-10000	0	-0.29	57	57
PI3K	-0.016	0.1	-10000	0	-0.28	57	57
apoptosis	-0.005	0.088	0.42	8	-10000	0	8
HRAS/GDP	0.006	0.029	-10000	0	-0.35	4	4
PRKCD	-0.015	0.12	-10000	0	-0.39	52	52
RAF1/14-3-3 E	0.012	0.078	-10000	0	-0.36	3	3
BAD/14-3-3	0.005	0.093	-10000	0	-0.45	8	8
PRKCZ	-0.006	0.095	-10000	0	-0.47	4	4
Crk/p130 Cas/Paxillin/FAK1	-0.032	0.077	-10000	0	-0.44	8	8
PTPN1	0.01	0.024	-10000	0	-0.58	1	1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1	-0.022	0.13	-10000	0	-0.41	52	52
BCAR1	0.008	0.043	-10000	0	-0.52	4	4
IGF-1R heterotetramer/IGF1/SHC/GRB10	-0.018	0.11	-10000	0	-0.3	55	55
mol:GDP	0	0	-10000	0	-10000	0	0
SOS1	0.01	0.024	-10000	0	-0.58	1	1
IRS1/NCK2	-0.023	0.1	-10000	0	-0.3	53	53
GRB10	0.007	0.048	-10000	0	-0.58	4	4
PTPN11	-0.026	0.11	-10000	0	-0.31	57	57
IRS1	-0.032	0.11	-10000	0	-0.32	60	60
IRS2	-0.027	0.11	-10000	0	-0.31	60	60
IGF-1R heterotetramer/IGF1	-0.049	0.15	-10000	0	-0.39	97	97
GRB2	0.011	0	-10000	0	-10000	0	0
PDPK1	-0.012	0.097	-10000	0	-0.42	5	5
YWHAE	0.011	0	-10000	0	-10000	0	0
PRKD1	-0.037	0.16	-10000	0	-0.43	75	75
SHC1	0.011	0	-10000	0	-10000	0	0

×

EPHB forward signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Ephrin A5/EPHB2	-0.06	0.15	-10000	0	-0.33	133	133
cell-cell adhesion	0.06	0.1	0.43	15	-10000	0	15
Ephrin B/EPHB2/RasGAP	0.008	0.09	-10000	0	-0.57	3	3
ITSN1	0.01	0.024	-10000	0	-0.58	1	1
PIK3CA	0.009	0.034	-10000	0	-0.58	2	2
SHC1	0.011	0	-10000	0	-10000	0	0
Ephrin B1/EPHB3	-0.004	0.083	-10000	0	-0.34	33	33
Ephrin B1/EPHB1	-0.056	0.13	-10000	0	-0.29	140	140
HRAS/GDP	-0.058	0.1	-10000	0	-0.43	13	13
Ephrin B/EPHB1/GRB7	-0.05	0.14	-10000	0	-0.49	17	17
Endophilin/SYNJ1	0.006	0.083	-10000	0	-0.53	3	3
KRAS	0.006	0.057	-10000	0	-0.56	6	6
Ephrin B/EPHB1/Src	-0.046	0.14	-10000	0	-0.53	11	11
endothelial cell migration	-0.003	0.035	-10000	0	-0.36	5	5
GRB2	0.011	0	-10000	0	-10000	0	0
GRB7	0.002	0.065	-10000	0	-0.46	12	12
PAK1	0.01	0.093	-10000	0	-0.6	5	5
HRAS	0.008	0.041	-10000	0	-0.49	4	4
RRAS	0.006	0.087	-10000	0	-0.64	3	3
DNM1	-0.007	0.096	-10000	0	-0.5	22	22
cell-cell signaling	0	0	-10000	0	-10000	0	0
CRK	-0.045	0.13	-10000	0	-0.48	11	11
lamellipodium assembly	-0.06	0.1	-10000	0	-0.43	15	15
Ephrin B/EPHB1/Src/p52 SHC/GRB2	-0.022	0.1	-10000	0	-0.42	8	8
PIK3R1	0.008	0.042	-10000	0	-0.58	3	3
EPHB2	0	0.079	-10000	0	-0.55	12	12
EPHB3	-0.019	0.13	-10000	0	-0.55	33	33
EPHB1	-0.1	0.21	-10000	0	-0.49	139	139
EPHB4	0.011	0	-10000	0	-10000	0	0
mol:GDP	-0.023	0.11	-10000	0	-0.42	12	12
Ephrin B/EPHB2	0.002	0.088	-10000	0	-0.33	28	28
Ephrin B/EPHB3	-0.008	0.1	-10000	0	-0.34	40	40
JNK cascade	-0.036	0.12	-10000	0	-0.3	51	51
Ephrin B/EPHB1	-0.052	0.14	-10000	0	-0.34	60	60
RAP1/GDP	-0.01	0.1	-10000	0	-0.41	8	8
EFNB2	0.01	0.031	-10000	0	-0.52	2	2
EFNB3	-0.021	0.13	-10000	0	-0.52	37	37
EFNB1	0.01	0.024	-10000	0	-0.58	1	1
Ephrin B2/EPHB1-2	-0.05	0.13	-10000	0	-0.27	150	150
RAP1B	0.011	0	-10000	0	-10000	0	0
RAP1A	0.01	0.024	-10000	0	-0.58	1	1
CDC42/GTP	-0.065	0.12	-10000	0	-0.48	19	19
Rap1/GTP	-0.06	0.1	-10000	0	-0.43	17	17
axon guidance	-0.06	0.15	-10000	0	-0.33	133	133
MAPK3	-0.01	0.093	-10000	0	-0.39	9	9
MAPK1	-0.01	0.094	-10000	0	-0.46	6	6
Rac1/GDP	-0.015	0.11	-10000	0	-0.44	7	7
actin cytoskeleton reorganization	-0.052	0.091	-10000	0	-0.4	16	16
CDC42/GDP	-0.017	0.11	-10000	0	-0.42	11	11
PI3K	0.024	0.038	-10000	0	-0.36	5	5
EFNA5	-0.1	0.22	-10000	0	-0.52	127	127
Ephrin B2/EPHB4	0.014	0.019	-10000	0	-0.32	2	2
Ephrin B/EPHB2/Intersectin/N-WASP	0.011	0.073	-10000	0	-0.49	4	4
CDC42	0.007	0.054	-10000	0	-0.58	5	5
RAS family/GTP	-0.066	0.12	-10000	0	-0.46	23	23
PTK2	0.016	0.038	-10000	0	-0.58	1	1
MAP4K4	-0.037	0.12	-10000	0	-0.31	51	51
SRC	0.01	0.024	-10000	0	-0.58	1	1
KALRN	0.007	0.054	-10000	0	-0.58	5	5
Intersectin/N-WASP	0.016	0.018	-10000	0	-0.42	1	1
neuron projection morphogenesis	-0.008	0.11	-10000	0	-0.41	14	14
MAP2K1	-0.016	0.097	-10000	0	-0.4	10	10
WASL	0.011	0	-10000	0	-10000	0	0
Ephrin B1/EPHB1-2/NCK1	-0.044	0.13	-10000	0	-0.33	50	50
cell migration	-0.013	0.11	-10000	0	-0.44	10	10
NRAS	0.002	0.076	-10000	0	-0.58	10	10
SYNJ1	0.006	0.085	-10000	0	-0.55	3	3
PXN	0.011	0	-10000	0	-10000	0	0
TF	-0.047	0.13	-10000	0	-0.45	19	19
HRAS/GTP	-0.066	0.11	-10000	0	-0.47	17	17
Ephrin B1/EPHB1-2	-0.049	0.13	-10000	0	-0.34	48	48
cell adhesion mediated by integrin	0.011	0.081	0.32	23	-10000	0	23
RAC1	0.011	0	-10000	0	-10000	0	0
mol:GTP	-0.044	0.13	-10000	0	-0.49	15	15
RAC1-CDC42/GTP	-0.073	0.12	-10000	0	-0.47	29	29
RASA1	0.009	0.034	-10000	0	-0.58	2	2
RAC1-CDC42/GDP	-0.012	0.11	-10000	0	-0.42	9	9
ruffle organization	-0.025	0.12	-10000	0	-0.46	12	12
NCK1	0.009	0.034	-10000	0	-0.58	2	2
receptor internalization	0.003	0.097	-10000	0	-0.49	8	8
Ephrin B/EPHB2/KALRN	0.007	0.098	-10000	0	-0.64	5	5
ROCK1	-0.003	0.094	-10000	0	-0.34	40	40
RAS family/GDP	-0.048	0.088	-10000	0	-0.4	16	16
Rac1/GTP	-0.063	0.11	-10000	0	-0.45	15	15
Ephrin B/EPHB1/Src/Paxillin	-0.027	0.1	-10000	0	-0.46	8	8

×

Class I PI3K signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ARF5/GTP	-0.01	0.07	0.25	6	-0.56	4	10
DAPP1	-0.065	0.19	-10000	0	-0.51	68	68
Src family/SYK family/BLNK-LAT/BTK-ITK	-0.068	0.22	-10000	0	-0.61	63	63
mol:DAG	-0.015	0.1	0.18	2	-0.28	53	55
HRAS	0.008	0.041	-10000	0	-0.49	4	4
RAP1A	0.01	0.026	-10000	0	-0.62	1	1
ARF5/GDP	0	0.11	-10000	0	-0.44	25	25
PLCG2	-0.01	0.11	-10000	0	-0.55	23	23
PLCG1	0.01	0.024	-10000	0	-0.58	1	1
ARF5	0.011	0	-10000	0	-10000	0	0
mol:GTP	-0.01	0.072	0.23	6	-0.32	22	28
ARF1/GTP	-0.01	0.069	0.24	6	-0.57	4	10
RHOA	0.01	0.024	-10000	0	-0.58	1	1
YES1	0.005	0.064	-10000	0	-0.58	7	7
RAP1A/GTP	0.011	0.074	0.22	6	-0.32	22	28
ADAP1	-0.01	0.07	0.22	6	-0.56	5	11
ARAP3	-0.01	0.07	0.23	6	-0.32	22	28
INPPL1	0.01	0.024	-10000	0	-0.58	1	1
PREX1	0.005	0.06	-10000	0	-0.55	7	7
ARHGEF6	-0.006	0.097	-10000	0	-0.54	19	19
ARHGEF7	0.011	0	-10000	0	-10000	0	0
ARF1	0.011	0.019	-10000	0	-0.46	1	1
NRAS	0.002	0.077	-10000	0	-0.6	10	10
FYN	0.005	0.06	-10000	0	-0.55	7	7
ARF6	0.01	0.024	-10000	0	-0.58	1	1
FGR	-0.026	0.14	-10000	0	-0.54	41	41
mol:Ca2+	0	0.055	-10000	0	-0.21	1	1
mol:IP4	0	0	-10000	0	-10000	0	0
TIAM1	-0.044	0.16	-10000	0	-0.52	63	63
ZAP70	-0.035	0.15	-10000	0	-0.53	52	52
mol:IP3	-0.005	0.076	-10000	0	-0.23	18	18
LYN	0.011	0	-10000	0	-10000	0	0
ARF1/GDP	-0.001	0.11	-10000	0	-0.45	24	24
RhoA/GDP	-0.021	0.082	0.24	3	-0.41	15	18
PDK1/Src/Hsp90	0.022	0.022	-10000	0	-0.36	2	2
BLNK	-0.01	0.11	-10000	0	-0.58	22	22
actin cytoskeleton reorganization	0.013	0.11	0.23	3	-0.47	17	20
SRC	0.01	0.024	-10000	0	-0.58	1	1
PLEKHA2	0.002	0.09	-10000	0	-0.36	34	34
RAC1	0.011	0	-10000	0	-10000	0	0
PTEN	0.004	0.057	-10000	0	-0.56	6	6
HSP90AA1	0.01	0.024	-10000	0	-0.58	1	1
ARF6/GTP	-0.01	0.072	0.25	6	-0.63	4	10
RhoA/GTP	0.016	0.075	0.22	6	-0.37	13	19
Src family/SYK family/BLNK-LAT	-0.064	0.2	-10000	0	-0.56	62	62
BLK	-0.11	0.23	-10000	0	-0.53	138	138
PDPK1	0.011	0	-10000	0	-10000	0	0
CYTH1	-0.01	0.067	0.22	6	-0.56	4	10
HCK	-0.017	0.12	-10000	0	-0.54	31	31
CYTH3	-0.011	0.069	0.22	6	-0.47	6	12
CYTH2	-0.01	0.067	0.22	6	-0.56	4	10
KRAS	0.006	0.059	-10000	0	-0.58	6	6
GO:0030676	0	0	-10000	0	-10000	0	0
FOXO3	0.024	0.068	-10000	0	-0.54	5	5
SGK1	-0.01	0.071	0.19	6	-0.6	5	11
INPP5D	-0.018	0.13	-10000	0	-0.58	30	30
mol:GDP	-0.007	0.11	-10000	0	-0.46	26	26
SOS1	0.01	0.024	-10000	0	-0.58	1	1
SYK	0.011	0.019	-10000	0	-0.46	1	1
ARF6/GDP	-0.021	0.081	0.24	3	-0.41	15	18
mol:PI-3-4-5-P3	-0.01	0.074	0.29	6	-0.37	13	19
ARAP3/RAP1A/GTP	0.011	0.075	0.22	6	-0.32	22	28
VAV1	-0.028	0.15	-10000	0	-0.58	40	40
mol:PI-3-4-P2	-0.004	0.1	-10000	0	-0.44	30	30
RAS family/GTP/PI3K Class I	0.012	0.073	-10000	0	-0.33	22	22
PLEKHA1	0.002	0.089	-10000	0	-0.36	33	33
Rac1/GDP	0	0.11	-10000	0	-0.44	24	24
LAT	-0.009	0.1	-10000	0	-0.51	24	24
Rac1/GTP	-0.015	0.14	-10000	0	-0.57	27	27
ITK	-0.031	0.097	0.22	5	-0.32	40	45
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma	-0.028	0.14	0.21	2	-0.4	54	56
LCK	-0.031	0.14	-10000	0	-0.51	49	49
BTK	-0.03	0.094	0.22	3	-0.32	37	40

×

PDGFR-alpha 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.012	0.11	-9999	-0.58	23	23
PDGF/PDGFRA/CRKL	0.001	0.081	-9999	-0.41	23	23
positive regulation of JUN kinase activity	0.015	0.064	-9999	-0.3	22	22
CRKL	0.011	0	-9999	-10000	0	0
PDGF/PDGFRA/Caveolin-3	-0.01	0.088	-9999	-0.41	28	28
AP1	-0.062	0.21	-9999	-0.9	30	30
mol:IP3	0	0.087	-9999	-0.42	24	24
PLCG1	0	0.088	-9999	-0.42	24	24
PDGF/PDGFRA/alphaV Integrin	-0.007	0.1	-9999	-0.42	32	32
RAPGEF1	0.01	0.024	-9999	-0.58	1	1
CRK	0.011	0.019	-9999	-0.46	1	1
mol:Ca2+	0	0.087	-9999	-0.42	24	24
CAV3	-0.003	0.046	-9999	-0.46	6	6
CAV1	-0.002	0.082	-9999	-0.5	16	16
SHC/Grb2/SOS1	0.016	0.064	-9999	-0.31	22	22
PDGF/PDGFRA/Shf	-0.033	0.14	-9999	-0.38	75	75
FOS	-0.029	0.22	-9999	-0.89	30	30
JUN	-0.008	0.042	-9999	-0.44	5	5
oligodendrocyte development	-0.007	0.1	-9999	-0.42	32	32
GRB2	0.011	0	-9999	-10000	0	0
PIK3R1	0.008	0.042	-9999	-0.58	3	3
mol:DAG	0	0.087	-9999	-0.42	24	24
PDGF/PDGFRA	-0.012	0.11	-9999	-0.58	23	23
actin cytoskeleton reorganization	0	0.082	-9999	-0.4	24	24
SRF	0.017	0.02	-9999	-0.31	2	2
SHC1	0.011	0	-9999	-10000	0	0
PI3K	0.006	0.077	-9999	-0.35	26	26
PDGF/PDGFRA/Crk/C3G	0.008	0.072	-9999	-0.34	23	23
JAK1	0	0.087	-9999	-0.41	26	26
ELK1/SRF	0.015	0.07	-9999	-0.32	23	23
SHB	0.011	0.019	-9999	-0.46	1	1
SHF	-0.034	0.14	-9999	-0.48	56	56
CSNK2A1	0.005	0.014	-9999	-10000	0	0
GO:0007205	0	0.091	-9999	-0.44	24	24
SOS1	0.01	0.024	-9999	-0.58	1	1
Ras protein signal transduction	0.015	0.064	-9999	-0.3	22	22
PDGF/PDGFRA/SHB	0	0.082	-9999	-0.4	24	24
PDGF/PDGFRA/Caveolin-1	-0.009	0.11	-9999	-0.42	35	35
ITGAV	0.002	0.076	-9999	-0.58	10	10
ELK1	0.005	0.083	-9999	-0.39	23	23
PIK3CA	0.009	0.034	-9999	-0.58	2	2
PDGF/PDGFRA/Crk	0	0.082	-9999	-0.4	24	24
JAK-STAT cascade	0	0.087	-9999	-0.41	26	26
cell proliferation	-0.033	0.13	-9999	-0.38	75	75

×

RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	-0.024	0.17	-10000	0	-1.2	11	11
VDR	0.01	0.024	-10000	0	-0.58	1	1
FAM120B	0.01	0.024	-10000	0	-0.58	1	1
RXRs/LXRs/DNA/9cRA	0.026	0.083	-10000	0	-0.66	2	2
RXRs/LXRs/DNA/Oxysterols	0.026	0.11	-10000	0	-0.41	29	29
MED1	0.008	0.043	-10000	0	-0.52	4	4
mol:9cRA	0.003	0.013	-10000	0	-10000	0	0
RARs/THRs/DNA/Src-1	-0.021	0.12	-10000	0	-0.28	92	92
RXRs/NUR77	0.009	0.089	-10000	0	-0.42	6	6
RXRs/PPAR	0.021	0.059	-10000	0	-0.52	2	2
NCOR2	0.008	0.046	-10000	0	-0.55	4	4
VDR/VDR/Vit D3	0.008	0.018	-10000	0	-0.43	1	1
RARs/VDR/DNA/Vit D3	0.012	0.071	-10000	0	-0.33	19	19
RARA	0.007	0.045	-10000	0	-0.48	5	5
NCOA1	0.01	0.024	-10000	0	-0.58	1	1
VDR/VDR/DNA	0.01	0.024	-10000	0	-0.58	1	1
RARs/RARs/DNA/9cRA	0.008	0.068	-10000	0	-0.29	29	29
RARG	0.006	0.059	-10000	0	-0.58	6	6
RPS6KB1	-0.008	0.081	-10000	0	-0.46	17	17
RARs/THRs/DNA/SMRT	-0.022	0.12	-10000	0	-0.28	93	93
THRA	0.008	0.041	-10000	0	-0.49	4	4
mol:Bile acids	0	0	-10000	0	-10000	0	0
VDR/Vit D3/DNA	0.008	0.018	-10000	0	-0.43	1	1
RXRs/PPAR/9cRA/PGJ2/DNA	0.021	0.072	0.28	7	-0.32	4	11
NR1H4	-0.12	0.23	-10000	0	-0.5	156	156
RXRs/LXRs/DNA	0.034	0.077	-10000	0	-0.73	1	1
NR1H2	0.013	0.027	-10000	0	-0.61	1	1
NR1H3	0.014	0.024	-10000	0	-0.49	1	1
RXRs/VDR/DNA/Vit D3	0.022	0.058	-10000	0	-0.3	3	3
NR4A1	-0.017	0.11	-10000	0	-0.46	36	36
mol:ATRA	0	0	-10000	0	-10000	0	0
RXRs/FXR/9cRA/MED1	-0.032	0.1	-10000	0	-0.26	62	62
RXRG	-0.01	0.096	-10000	0	-0.46	26	26
RXR alpha/CCPG	0.018	0.027	-10000	0	-0.43	2	2
RXRA	0.013	0.027	-10000	0	-0.6	1	1
RXRB	0.014	0.012	-10000	0	-10000	0	0
THRB	-0.072	0.2	-10000	0	-0.56	88	88
PPARG	0.004	0.068	-10000	0	-0.58	8	8
PPARD	0.01	0.024	-10000	0	-0.58	1	1
TNF	0.004	0.22	-10000	0	-1.1	22	22
mol:Oxysterols	0.003	0.011	-10000	0	-10000	0	0
cholesterol transport	0.026	0.11	-10000	0	-0.41	29	29
PPARA	0.009	0.034	-10000	0	-0.58	2	2
mol:Vit D3	0	0	-10000	0	-10000	0	0
RARB	-0.006	0.097	-10000	0	-0.54	19	19
RXRs/NUR77/BCL2	0.002	0.069	-10000	0	-0.31	9	9
SREBF1	0.03	0.11	-10000	0	-1.1	2	2
RXRs/RXRs/DNA/9cRA	0.021	0.072	0.28	7	-0.32	4	11
ABCA1	0.022	0.16	-10000	0	-1.1	9	9
RARs/THRs	-0.028	0.13	-10000	0	-0.32	91	91
RXRs/FXR	-0.053	0.14	-10000	0	-0.34	67	67
BCL2	-0.007	0.1	-10000	0	-0.55	20	20

×

IL2 signaling events mediated by STAT5

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GAB2	0.01	0.034	-9999	-0.58	2	2
ELF1	-0.019	0.11	-9999	-0.36	50	50
CCNA2	0.01	0.024	-9999	-0.58	1	1
PIK3CA	0.01	0.034	-9999	-0.58	2	2
JAK3	0.001	0.076	-9999	-0.53	12	12
PIK3R1	0.009	0.042	-9999	-0.58	3	3
JAK1	0.009	0.042	-9999	-0.58	3	3
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.008	0.14	-9999	-0.46	33	33
SHC1	0.012	0.001	-9999	-10000	0	0
SP1	-0.009	0.097	-9999	-0.35	43	43
IL2RA	-0.052	0.23	-9999	-0.7	66	66
IL2RB	-0.018	0.13	-9999	-0.55	32	32
SOS1	0.011	0.024	-9999	-0.58	1	1
IL2RG	0	0.084	-9999	-0.56	13	13
G1/S transition of mitotic cell cycle	-0.019	0.19	-9999	-0.69	44	44
PTPN11	0.007	0.054	-9999	-0.58	5	5
CCND2	-0.036	0.22	-9999	-0.78	46	46
LCK	-0.03	0.14	-9999	-0.51	49	49
GRB2	0.012	0.001	-9999	-10000	0	0
IL2	0.002	0.027	-9999	-0.46	2	2
CDK6	0.011	0	-9999	-10000	0	0
CCND3	0.015	0.13	-9999	-0.56	12	12

×

Nectin adhesion pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	-0.006	0.097	-9999	-0.54	19	19
alphaV beta3 Integrin	-0.004	0.095	-9999	-0.42	30	30
PTK2	-0.029	0.1	-9999	-0.43	31	31
positive regulation of JNK cascade	-0.018	0.069	-9999	-0.3	31	31
CDC42/GDP	0.017	0.11	-9999	-0.42	32	32
Rac1/GDP	0.02	0.11	-9999	-0.42	29	29
RAP1B	0.011	0	-9999	-10000	0	0
RAP1A	0.01	0.024	-9999	-0.58	1	1
CTNNB1	0.011	0	-9999	-10000	0	0
CDC42/GTP	-0.022	0.085	-9999	-0.38	30	30
nectin-3/I-afadin	-0.004	0.094	-9999	-0.42	29	29
RAPGEF1	0.018	0.11	-9999	-0.46	29	29
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.012	0.12	-9999	-0.52	29	29
PDGFB-D/PDGFRB	-0.006	0.097	-9999	-0.54	19	19
TLN1	0.012	0.062	-9999	-0.49	4	4
Rap1/GTP	-0.017	0.07	-9999	-0.32	29	29
IQGAP1	0.009	0.039	-9999	-0.54	3	3
Rap1/GTP/I-afadin	0.02	0.024	-9999	-0.32	3	3
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin	-0.004	0.094	-9999	-0.42	29	29
PVR	0.011	0	-9999	-10000	0	0
Necl-5(dimer)	0.011	0	-9999	-10000	0	0
mol:GDP	0.012	0.13	-9999	-0.53	29	29
MLLT4	0.009	0.034	-9999	-0.58	2	2
PIK3CA	0.009	0.034	-9999	-0.58	2	2
PI3K	0.006	0.093	-9999	-0.31	44	44
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin	0.014	0.036	-9999	-0.42	4	4
positive regulation of lamellipodium assembly	-0.027	0.086	-9999	-0.3	51	51
PVRL1	0.009	0.034	-9999	-0.58	2	2
PVRL3	-0.015	0.12	-9999	-0.58	27	27
PVRL2	0.01	0.031	-9999	-0.52	2	2
PIK3R1	0.008	0.042	-9999	-0.58	3	3
CDH1	0.01	0.024	-9999	-0.58	1	1
CLDN1	-0.014	0.12	-9999	-0.57	27	27
JAM-A/CLDN1	-0.002	0.099	-9999	-0.32	51	51
SRC	0.005	0.13	-9999	-0.57	29	29
ITGB3	-0.008	0.1	-9999	-0.55	21	21
nectin-1(dimer)/I-afadin/I-afadin	0.014	0.036	-9999	-0.42	4	4
FARP2	0.015	0.12	-9999	-0.5	29	29
RAC1	0.011	0	-9999	-10000	0	0
CTNNA1	0.009	0.034	-9999	-0.58	2	2
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer)	0.005	0.08	-9999	-0.35	29	29
nectin-1/I-afadin	0.014	0.036	-9999	-0.42	4	4
nectin-2/I-afadin	0.014	0.034	-9999	-0.4	4	4
RAC1/GTP/IQGAP1/filamentous actin	0.014	0.025	-9999	-0.33	3	3
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin	0.004	0.083	-9999	-0.35	31	31
CDC42/GTP/IQGAP1/filamentous actin	0.011	0.05	-9999	-0.46	6	6
F11R	0.011	0	-9999	-10000	0	0
positive regulation of filopodium formation	-0.018	0.069	-9999	-0.3	31	31
alphaV/beta3 Integrin/Talin	0.01	0.094	-9999	-0.54	8	8
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.014	0.034	-9999	-0.4	4	4
nectin-2(dimer)/I-afadin/I-afadin	0.014	0.034	-9999	-0.4	4	4
PIP5K1C	0.007	0.061	-9999	-0.44	4	4
VAV2	-0.006	0.16	-9999	-0.51	51	51
RAP1/GDP	-0.023	0.085	-9999	-0.39	29	29
ITGAV	0.002	0.076	-9999	-0.58	10	10
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin	0.004	0.082	-9999	-0.35	31	31
nectin-3(dimer)/I-afadin/I-afadin	-0.004	0.094	-9999	-0.42	29	29
Rac1/GTP	-0.033	0.1	-9999	-0.36	51	51
PTPRM	0.001	0.066	-9999	-0.25	30	30
E-cadherin/beta catenin/alpha catenin	-0.004	0.037	-9999	-0.57	1	1
adherens junction assembly	0	0	-9999	-10000	0	0
CDC42	0.007	0.054	-9999	-0.58	5	5

×

Regulation of Telomerase

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Telomerase catalytic core complex	-0.096	0.28	-9999	-1.1	39	39
RAD9A	0.01	0.024	-9999	-0.58	1	1
AP1	-0.013	0.11	-9999	-0.39	45	45
IFNAR2	0.011	0.025	-9999	-0.58	1	1
AKT1	-0.005	0.061	-9999	-0.31	3	3
ER alpha/Oestrogen	-0.026	0.11	-9999	-0.38	52	52
NFX1/SIN3/HDAC complex	0.033	0.029	-9999	-10000	0	0
EGF	-0.18	0.25	-9999	-0.51	222	222
SMG5	0.01	0.024	-9999	-0.58	1	1
SMG6	0.011	0	-9999	-10000	0	0
SP3/HDAC2	0.017	0.02	-9999	-0.42	1	1
TERT/c-Abl	-0.085	0.26	-9999	-0.97	41	41
SAP18	0.011	0.019	-9999	-0.46	1	1
MRN complex	0.008	0.09	-9999	-0.46	19	19
WT1	-0.18	0.26	-9999	-0.53	208	208
WRN	0.005	0.062	-9999	-0.57	7	7
SP1	0.011	0.025	-9999	-0.58	1	1
SP3	0.01	0.024	-9999	-0.58	1	1
TERF2IP	0.01	0.024	-9999	-0.58	1	1
Telomerase/Nucleolin	-0.093	0.22	-9999	-0.88	39	39
Mad/Max	0.015	0.027	-9999	-0.35	3	3
TERT	-0.1	0.3	-9999	-1.1	39	39
CCND1	-0.079	0.25	-9999	-0.99	35	35
MAX	0.011	0.004	-9999	-10000	0	0
RBBP7	0.009	0.034	-9999	-0.58	2	2
RBBP4	0.01	0.024	-9999	-0.58	1	1
TERF2	0.012	0.009	-9999	-10000	0	0
PTGES3	0.009	0.034	-9999	-0.58	2	2
SIN3A	0.01	0.024	-9999	-0.58	1	1
Telomerase/911	0.019	0.047	-9999	-0.7	1	1
CDKN1B	-0.021	0.12	-9999	-0.48	6	6
RAD1	0.011	0.019	-9999	-0.46	1	1
XRCC5	0.01	0.024	-9999	-0.58	1	1
XRCC6	0.011	0	-9999	-10000	0	0
SAP30	0.009	0.034	-9999	-0.58	2	2
TRF2/PARP2	0.017	0.018	-9999	-0.38	1	1
UBE3A	0.007	0.048	-9999	-0.59	4	4
JUN	0.006	0.052	-9999	-0.56	5	5
E6	0	0.004	-9999	-10000	0	0
HPV-16 E6/E6AP	0.006	0.036	-9999	-0.43	4	4
FOS	-0.026	0.14	-9999	-0.54	41	41
IFN-gamma/IRF1	-0.035	0.14	-9999	-0.36	90	90
PARP2	0.01	0.024	-9999	-0.58	1	1
BLM	0.006	0.057	-9999	-0.56	6	6
Telomerase	0.003	0.063	-9999	-0.45	6	6
IRF1	0.012	0.034	-9999	-0.45	3	3
ESR1	-0.036	0.15	-9999	-0.53	52	52
KU/TER	0.016	0.018	-9999	-0.42	1	1
ATM/TRF2	0.012	0.048	-9999	-0.38	9	9
ubiquitin-dependent protein catabolic process	0.035	0.037	-9999	-0.38	2	2
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex	0.036	0.038	-9999	-0.39	2	2
HDAC1	0.011	0.001	-9999	-10000	0	0
HDAC2	0.011	0.008	-9999	-10000	0	0
ATM	-0.007	0.053	-9999	-0.44	9	9
SMAD3	0.003	0.081	-9999	-0.4	23	23
ABL1	0.01	0.024	-9999	-0.58	1	1
MXD1	0.009	0.036	-9999	-0.5	3	3
MRE11A	0.004	0.068	-9999	-0.58	8	8
HUS1	0.011	0	-9999	-10000	0	0
RPS6KB1	0.006	0.057	-9999	-0.56	6	6
TERT/NF kappa B1/14-3-3	-0.089	0.25	-9999	-1	34	34
NR2F2	0.012	0.007	-9999	-10000	0	0
MAPK3	0.01	0.027	-9999	-0.35	3	3
MAPK1	0.01	0.027	-9999	-0.35	3	3
TGFB1/TGF beta receptor Type II	-0.002	0.088	-9999	-0.55	15	15
NFKB1	0.01	0.024	-9999	-0.58	1	1
HNRNPC	0.011	0	-9999	-10000	0	0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis	-0.007	0.053	-9999	-0.44	9	9
NBN	-0.004	0.096	-9999	-0.58	16	16
EGFR	0.005	0.058	-9999	-0.53	7	7
mol:Oestrogen	0	0.002	-9999	-10000	0	0
EGF/EGFR	-0.13	0.19	-9999	-0.36	228	228
MYC	0.005	0.057	-9999	-0.56	6	6
IL2	0.001	0.028	-9999	-0.45	2	2
KU	0.016	0.018	-9999	-0.42	1	1
RAD50	0.01	0.024	-9999	-0.58	1	1
HSP90AA1	0.01	0.024	-9999	-0.58	1	1
TGFB1	-0.002	0.088	-9999	-0.55	15	15
TRF2/BLM	0.014	0.04	-9999	-0.37	6	6
FRAP1	0	0	-9999	-10000	0	0
KU/TERT	-0.079	0.26	-9999	-0.99	39	39
SP1/HDAC2	0.017	0.022	-9999	-0.42	1	1
PINX1	0.005	0.064	-9999	-0.58	7	7
Telomerase/EST1A	-0.093	0.22	-9999	-0.88	39	39
Smad3/Myc	0.006	0.077	-9999	-0.34	28	28
911 complex	0.022	0.019	-9999	-0.36	1	1
IFNG	-0.064	0.19	-9999	-0.51	89	89
Telomerase/PinX1	-0.095	0.22	-9999	-0.87	41	41
Telomerase/AKT1/mTOR/p70S6K	-0.001	0.076	-9999	-0.74	2	2
SIN3B	0.01	0.024	-9999	-0.58	1	1
YWHAE	0.011	0	-9999	-10000	0	0
Telomerase/EST1B	-0.093	0.22	-9999	-0.87	40	40
response to DNA damage stimulus	0.001	0.017	-9999	-10000	0	0
MRN complex/TRF2/Rap1	0.02	0.08	-9999	-0.63	6	6
TRF2/WRN	0.013	0.042	-9999	-0.37	7	7
Telomerase/hnRNP C1/C2	-0.093	0.22	-9999	-0.88	39	39
E2F1	0.009	0.036	-9999	-0.5	3	3
ZNFX1	0.011	0.001	-9999	-10000	0	0
PIF1	0.007	0.052	-9999	-0.56	5	5
NCL	0.011	0	-9999	-10000	0	0
DKC1	0.011	0	-9999	-10000	0	0
telomeric DNA binding	0	0	-9999	-10000	0	0

×

FOXM1 transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC3	0.075	0.32	-9999	-0.99	18	18
PLK1	0.043	0.073	-9999	-1.4	1	1
BIRC5	0.045	0.047	-9999	-10000	0	0
HSPA1B	0.061	0.34	-9999	-1	19	19
MAP2K1	0.028	0.049	-9999	-0.63	2	2
BRCA2	0.058	0.37	-9999	-1.1	30	30
FOXM1	0.063	0.38	-9999	-1.3	19	19
XRCC1	0.074	0.33	-9999	-1	19	19
FOXM1B/p19	-0.12	0.28	-9999	-1.1	26	26
Cyclin D1/CDK4	0.072	0.31	-9999	-0.93	17	17
CDC2	0.07	0.34	-9999	-1	19	19
TGFA	0.073	0.31	-9999	-1	11	11
SKP2	0.074	0.33	-9999	-1	18	18
CCNE1	0.013	0.034	-9999	-0.46	3	3
CKS1B	0.074	0.32	-9999	-0.98	19	19
RB1	-0.063	0.18	-9999	-0.96	18	18
FOXM1C/SP1	0.063	0.34	-9999	-1.1	19	19
AURKB	0.045	0.043	-9999	-10000	0	0
CENPF	0.063	0.36	-9999	-1.1	26	26
CDK4	0.019	0.012	-9999	-10000	0	0
MYC	0.076	0.3	-9999	-0.9	20	20
CHEK2	0.029	0.041	-9999	-0.63	1	1
ONECUT1	0.069	0.32	-9999	-0.98	18	18
CDKN2A	-0.075	0.19	-9999	-0.52	96	96
LAMA4	0.072	0.33	-9999	-1.1	17	17
FOXM1B/HNF6	0.063	0.35	-9999	-1.2	18	18
FOS	0.036	0.39	-9999	-1	41	41
SP1	0.011	0.024	-9999	-0.58	1	1
CDC25B	0.074	0.32	-9999	-0.99	17	17
response to radiation	0.016	0.028	-9999	-10000	0	0
CENPB	0.073	0.33	-9999	-1	20	20
CENPA	0.074	0.33	-9999	-1	18	18
NEK2	0.074	0.32	-9999	-1	18	18
HIST1H2BA	0.068	0.32	-9999	-1	17	17
CCNA2	0.014	0.026	-9999	-0.6	1	1
EP300	0.007	0.048	-9999	-0.58	4	4
CCNB1/CDK1	0.064	0.35	-9999	-1.2	18	18
CCNB2	0.072	0.33	-9999	-1	20	20
CCNB1	0.072	0.34	-9999	-1	18	18
ETV5	0.057	0.36	-9999	-1.1	28	28
ESR1	0.034	0.41	-9999	-1.2	40	40
CCND1	0.075	0.32	-9999	-0.94	18	18
GSK3A	0.029	0.026	-9999	-10000	0	0
Cyclin A-E1/CDK1-2	0.038	0.049	-9999	-0.42	3	3
CDK2	0.014	0.026	-9999	-0.6	1	1
G2/M transition of mitotic cell cycle	0.018	0.033	-9999	-10000	0	0
FOXM1B/Cbp/p300	-0.09	0.25	-9999	-1.1	19	19
GAS1	-0.05	0.51	-9999	-1.1	90	90
MMP2	0.038	0.41	-9999	-1.2	36	36
RB1/FOXM1C	0.07	0.33	-9999	-0.99	24	24
CREBBP	0.011	0	-9999	-10000	0	0

×

Sphingosine 1-phosphate (S1P) pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.009	0.036	-9999	-0.5	3	3
SPHK1	-0.03	0.14	-9999	-0.52	48	48
GNAI2	0.011	0	-9999	-10000	0	0
mol:S1P	-0.001	0.069	-9999	-0.3	24	24
GNAO1	-0.045	0.16	-9999	-0.49	68	68
mol:Sphinganine-1-P	-0.014	0.11	-9999	-0.37	51	51
growth factor activity	0	0	-9999	-10000	0	0
S1P/S1P2/G12/G13	0.018	0.054	-9999	-0.29	2	2
GNAI3	0.011	0	-9999	-10000	0	0
G12/G13	0.016	0.025	-9999	-0.42	2	2
S1PR3	0.004	0.063	-9999	-0.54	8	8
S1PR2	0.011	0	-9999	-10000	0	0
EDG1	0	0	-9999	-10000	0	0
S1P1/S1P	-0.004	0.058	-9999	-0.26	24	24
S1PR5	0.001	0.076	-9999	-0.53	12	12
S1PR4	-0.025	0.14	-9999	-0.53	40	40
GNAI1	-0.003	0.089	-9999	-0.56	15	15
S1P/S1P5/G12	0.006	0.069	-9999	-0.32	9	9
S1P/S1P3/Gq	-0.002	0.11	-9999	-0.4	25	25
S1P/S1P4/Gi	-0.022	0.12	-9999	-0.34	49	49
GNAQ	0.006	0.059	-9999	-0.58	6	6
GNAZ	-0.013	0.11	-9999	-0.55	26	26
GNA14	-0.007	0.1	-9999	-0.56	19	19
GNA15	-0.009	0.1	-9999	-0.54	22	22
GNA12	0.011	0	-9999	-10000	0	0
GNA13	0.009	0.034	-9999	-0.58	2	2
GNA11	0.007	0.05	-9999	-0.53	5	5
ABCC1	0.01	0.024	-9999	-0.58	1	1

×

IFN-gamma pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2	-0.02	0.12	-9999	-0.31	57	57
positive regulation of NF-kappaB transcription factor activity	0	0.002	-9999	-10000	0	0
CRKL	0.011	0	-9999	-10000	0	0
STAT1 (dimer)/Cbp/p300	0.002	0.12	-9999	-0.55	13	13
IFN-gammaR/JAK1/JAK1/JAK2/JAK2	0	0.078	-9999	-0.37	23	23
antigen processing and presentation of peptide antigen via MHC class I	-0.039	0.075	-9999	-0.29	20	20
CaM/Ca2+	-0.018	0.11	-9999	-0.42	11	11
RAP1A	0.01	0.024	-9999	-0.58	1	1
STAT1 (dimer)/SHP2	-0.013	0.12	-9999	-0.51	13	13
AKT1	-0.004	0.11	-9999	-0.46	12	12
MAP2K1	-0.01	0.12	-9999	-0.5	14	14
MAP3K11	-0.014	0.11	-9999	-0.38	16	16
IFNGR1	0.008	0.012	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKII	-0.052	0.12	-9999	-0.47	32	32
Rap1/GTP	-0.031	0.074	-9999	-0.41	6	6
CRKL/C3G	0.016	0.018	-9999	-0.42	1	1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP	-0.022	0.12	-9999	-0.38	22	22
CEBPB	-0.01	0.16	-9999	-0.47	37	37
STAT3	0.011	0	-9999	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1	-0.053	0.22	-9999	-1	19	19
STAT1	-0.014	0.12	-9999	-0.5	13	13
CALM1	0.011	0	-9999	-10000	0	0
IFN-gamma (dimer)	-0.067	0.19	-9999	-0.51	89	89
PIK3CA	0.009	0.034	-9999	-0.58	2	2
STAT1 (dimer)/PIAS1	-0.006	0.12	-9999	-0.49	12	12
CEBPB/PTGES2/Cbp/p300	-0.04	0.086	-9999	-0.41	14	14
mol:Ca2+	-0.021	0.11	-9999	-0.31	57	57
MAPK3	-0.006	0.13	-9999	-0.68	8	8
STAT1 (dimer)	-0.052	0.1	-9999	-0.4	19	19
MAPK1	-0.006	0.12	-9999	-0.66	8	8
JAK2	-0.011	0.1	-9999	-0.56	21	21
PIK3R1	0.008	0.042	-9999	-0.58	3	3
JAK1	0.005	0.044	-9999	-0.6	3	3
CAMK2D	0.008	0.048	-9999	-0.58	4	4
DAPK1	-0.014	0.16	-9999	-0.54	39	39
SMAD7	0.011	0.06	-9999	-0.29	2	2
CBL/CRKL/C3G	-0.002	0.1	-9999	-0.43	8	8
PI3K	-0.042	0.1	-9999	-0.5	12	12
IFNG	-0.067	0.19	-9999	-0.51	89	89
apoptosis	-0.013	0.12	-9999	-0.4	37	37
CAMK2G	0.011	0	-9999	-10000	0	0
STAT3 (dimer)	0.011	0	-9999	-10000	0	0
CAMK2A	-0.02	0.12	-9999	-0.53	34	34
CAMK2B	-0.056	0.17	-9999	-0.5	79	79
FRAP1	-0.003	0.1	-9999	-0.42	12	12
PRKCD	-0.003	0.11	-9999	-0.47	12	12
RAP1B	0.011	0	-9999	-10000	0	0
negative regulation of cell growth	-0.039	0.075	-9999	-0.29	20	20
PTPN2	0.008	0.042	-9999	-0.58	3	3
EP300	0.008	0.048	-9999	-0.58	4	4
IRF1	0	0.13	-9999	-0.51	15	15
STAT1 (dimer)/PIASy	-0.006	0.12	-9999	-0.48	12	12
SOCS1	-0.046	0.22	-9999	-1.4	14	14
mol:GDP	-0.031	0.087	-9999	-0.42	8	8
CASP1	0.002	0.087	-9999	-0.28	37	37
PTGES2	0.007	0.045	-9999	-0.48	5	5
IRF9	0.02	0.054	-9999	-0.23	4	4
mol:PI-3-4-5-P3	-0.041	0.1	-9999	-0.49	12	12
RAP1/GDP	-0.032	0.074	-9999	-0.41	6	6
CBL	-0.013	0.11	-9999	-0.43	11	11
MAP3K1	-0.017	0.12	-9999	-0.49	14	14
PIAS1	0.011	0	-9999	-10000	0	0
PIAS4	0.011	0.024	-9999	-0.57	1	1
antigen processing and presentation of peptide antigen via MHC class II	-0.039	0.075	-9999	-0.29	20	20
PTPN11	-0.02	0.12	-9999	-0.31	57	57
CREBBP	0.012	0.001	-9999	-10000	0	0
RAPGEF1	0.01	0.024	-9999	-0.58	1	1

×

Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HIF3A	-0.08	0.2	-9999	-0.51	106	106
oxygen homeostasis	0	0	-9999	-10000	0	0
TCEB2	0.005	0.055	-9999	-0.47	8	8
TCEB1	0.011	0.019	-9999	-0.46	1	1
HIF1A/p53	-0.009	0.096	-9999	-0.28	57	57
HIF1A	0.013	0.037	-9999	-0.25	9	9
COPS5	0.011	0.019	-9999	-0.46	1	1
VHL/Elongin B/Elongin C/RBX1/CUL2	0.029	0.042	-9999	-0.39	4	4
FIH (dimer)	0.011	0	-9999	-10000	0	0
CDKN2A	-0.071	0.19	-9999	-0.51	96	96
ARNT/IPAS	-0.05	0.15	-9999	-0.36	107	107
HIF1AN	0.011	0	-9999	-10000	0	0
GNB2L1	0.011	0.019	-9999	-0.46	1	1
HIF1A/ARNT	0.019	0.04	-9999	-0.4	2	2
CUL2	0.011	0	-9999	-10000	0	0
OS9	0.011	0	-9999	-10000	0	0
RACK1/Elongin B/Elongin C	0.019	0.04	-9999	-0.43	2	2
response to hypoxia	0	0	-9999	-10000	0	0
HIF1A/Hsp90	0.019	0.04	-9999	-0.4	2	2
PHD1-3/OS9	0.018	0.06	-9999	-0.32	13	13
HIF1A/RACK1/Elongin B/Elongin C	0.025	0.055	-9999	-0.4	8	8
VHL	0.01	0.024	-9999	-0.58	1	1
HSP90AA1	0.01	0.024	-9999	-0.58	1	1
HIF1A/JAB1	0.019	0.036	-9999	-0.29	1	1
EGLN3	-0.007	0.098	-9999	-0.53	20	20
EGLN2	0.009	0.036	-9999	-0.5	3	3
EGLN1	0.011	0	-9999	-10000	0	0
TP53	-0.045	0.17	-9999	-0.58	57	57
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A	0.027	0.045	-9999	-0.86	1	1
ARNT	0.01	0.024	-9999	-0.58	1	1
ARD1A	0	0	-9999	-10000	0	0
RBX1	0.01	0.031	-9999	-0.52	2	2
HIF1A/p19ARF	-0.021	0.1	-9999	-0.29	47	47

×

ErbB2/ErbB3 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
USP8	0.011	0.037	-10000	0	-0.36	6	6
RAS family/GTP	-0.001	0.097	-10000	0	-0.36	12	12
NFATC4	0.003	0.088	-10000	0	-0.42	4	4
ERBB2IP	-0.008	0.11	-10000	0	-0.58	20	20
HSP90 (dimer)	0.01	0.024	-10000	0	-0.58	1	1
mammary gland morphogenesis	-0.011	0.1	0.22	6	-0.32	12	18
JUN	0.005	0.1	0.16	3	-0.28	49	52
HRAS	0.008	0.041	-10000	0	-0.49	4	4
DOCK7	-0.004	0.1	-10000	0	-0.41	4	4
ErbB2/ErbB3/neuregulin 1 beta/SHC	-0.02	0.12	0.23	13	-0.32	54	67
AKT1	0.008	0.018	-10000	0	-0.44	1	1
BAD	0.014	0.031	-10000	0	-0.48	2	2
MAPK10	-0.007	0.082	-10000	0	-0.29	19	19
mol:GTP	0	0.001	-10000	0	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta	-0.01	0.11	0.24	6	-0.35	12	18
RAF1	0.009	0.098	-10000	0	-0.36	11	11
ErbB2/ErbB3/neuregulin 2	0	0.073	0.23	12	-0.25	39	51
STAT3	0	0.044	-10000	0	-1.1	1	1
cell migration	0.008	0.075	0.16	7	-0.25	15	22
mol:PI-3-4-5-P3	0	0.002	-10000	0	-10000	0	0
cell proliferation	-0.002	0.19	-10000	0	-0.59	38	38
FOS	0.003	0.16	-10000	0	-0.42	55	55
NRAS	0.002	0.076	-10000	0	-0.58	10	10
mol:Ca2+	-0.011	0.1	0.22	6	-0.32	12	18
MAPK3	0.003	0.16	-10000	0	-0.5	32	32
MAPK1	0.003	0.15	-10000	0	-0.49	31	31
JAK2	-0.011	0.11	-10000	0	-0.43	10	10
NF2	-0.002	0.009	-10000	0	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1	-0.01	0.094	-10000	0	-0.28	53	53
NRG1	-0.07	0.2	-10000	0	-0.53	91	91
GRB2/SOS1	0.016	0.018	-10000	0	-0.42	1	1
MAPK8	0	0.098	0.2	5	-0.3	13	18
MAPK9	0.008	0.059	-10000	0	-0.25	4	4
ERBB2	0.005	0.085	0.39	19	-0.34	13	32
ERBB3	0.01	0.024	-10000	0	-0.58	1	1
SHC1	0.011	0.001	-10000	0	-10000	0	0
RAC1	0.011	0	-10000	0	-10000	0	0
apoptosis	-0.003	0.035	0.82	1	-10000	0	1
STAT3 (dimer)	0.014	0.043	-10000	0	-1	1	1
RNF41	0.016	0.034	-10000	0	-0.32	6	6
FRAP1	0.007	0.016	-10000	0	-0.37	1	1
RAC1-CDC42/GTP	-0.028	0.066	-10000	0	-0.33	7	7
ErbB2/ErbB2/HSP90 (dimer)	0.008	0.061	0.26	18	-0.28	13	31
CHRNA1	-0.002	0.18	-10000	0	-0.6	36	36
myelination	0.005	0.087	-10000	0	-0.4	4	4
PPP3CB	-0.003	0.095	-10000	0	-0.4	3	3
KRAS	0.006	0.057	-10000	0	-0.56	6	6
RAC1-CDC42/GDP	-0.001	0.085	-10000	0	-0.31	6	6
NRG2	-0.016	0.1	-10000	0	-0.46	32	32
mol:GDP	-0.01	0.094	-10000	0	-0.28	53	53
SOS1	0.01	0.024	-10000	0	-0.58	1	1
MAP2K2	0.013	0.1	-10000	0	-0.38	12	12
SRC	0.01	0.024	-10000	0	-0.58	1	1
mol:cAMP	-0.001	0.001	-10000	0	-10000	0	0
PTPN11	-0.006	0.1	-10000	0	-0.42	5	5
MAP2K1	-0.001	0.15	-10000	0	-0.52	18	18
heart morphogenesis	-0.011	0.1	0.22	6	-0.32	12	18
RAS family/GDP	-0.001	0.097	-10000	0	-0.39	9	9
GRB2	0.011	0.001	-10000	0	-10000	0	0
PRKACA	-0.003	0.006	-10000	0	-10000	0	0
CHRNE	0	0.056	-10000	0	-0.18	50	50
HSP90AA1	0.01	0.024	-10000	0	-0.58	1	1
activation of caspase activity	-0.008	0.018	0.44	1	-10000	0	1
nervous system development	-0.011	0.1	0.22	6	-0.32	12	18
CDC42	0.007	0.054	-10000	0	-0.58	5	5

×

Signaling events mediated by PRL

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
CCNE1	0.009	0.033	-10000	0	-0.46	3	3
mol:Halofuginone	0.004	0.009	-10000	0	-0.23	1	1
ITGA1	0.006	0.059	-10000	0	-0.58	6	6
CDKN1A	0.019	0.047	-10000	0	-0.44	4	4
PRL-3/alpha Tubulin	-0.006	0.093	-10000	0	-0.37	36	36
mol:Ca2+	-0.008	0.12	0.3	35	-0.39	38	73
AGT	-0.024	0.13	-10000	0	-0.53	39	39
CCNA2	0.02	0.067	-10000	0	-0.89	1	1
TUBA1B	0.011	0	-10000	0	-10000	0	0
EGR1	0.004	0.076	-10000	0	-0.35	26	26
CDK2/Cyclin E1	0.028	0.047	-10000	0	-0.39	4	4
MAPK3	-0.005	0.095	-10000	0	-0.37	37	37
PRL-2 /Rab GGTase beta	0.015	0.031	-10000	0	-0.42	3	3
MAPK1	-0.005	0.095	-10000	0	-0.37	37	37
PTP4A1	0.016	0.071	-10000	0	-0.95	1	1
PTP4A3	-0.02	0.13	-10000	0	-0.52	36	36
PTP4A2	0.011	0	-10000	0	-10000	0	0
ITGB1	-0.005	0.093	-10000	0	-0.37	36	36
SRC	0.01	0.024	-10000	0	-0.58	1	1
RAC1	0.005	0.085	-10000	0	-0.43	18	18
Rab GGTase beta/Rab GGTase alpha	0.014	0.036	-10000	0	-0.42	4	4
PRL-1/ATF-5	0.02	0.067	-10000	0	-0.89	1	1
RABGGTA	0.01	0.024	-10000	0	-0.58	1	1
BCAR1	0.015	0.075	0.3	34	-0.27	4	38
RHOC	0.005	0.085	-10000	0	-0.42	19	19
RHOA	0.004	0.087	-10000	0	-0.41	21	21
cell motility	0.005	0.092	-10000	0	-0.42	21	21
PRL-1/alpha Tubulin	0.021	0.066	-10000	0	-0.89	1	1
PRL-3/alpha1 Integrin	-0.01	0.1	-10000	0	-0.39	41	41
ROCK1	0.005	0.092	-10000	0	-0.43	21	21
RABGGTB	0.008	0.042	-10000	0	-0.58	3	3
CDK2	0.01	0.024	-10000	0	-0.58	1	1
mitosis	0.016	0.07	-10000	0	-0.93	1	1
ATF5	0.011	0.019	-10000	0	-0.46	1	1

×

S1P4 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-9999	-10000	0	0
GNAO1	-0.045	0.16	-9999	-0.49	68	68
CDC42/GTP	-0.017	0.11	-9999	-0.42	18	18
PLCG1	-0.015	0.11	-9999	-0.46	14	14
mol:GTP	0	0	-9999	-10000	0	0
GNAI2	0.011	0	-9999	-10000	0	0
GNAI3	0.011	0	-9999	-10000	0	0
G12/G13	0.016	0.025	-9999	-0.42	2	2
cell migration	-0.017	0.1	-9999	-0.4	18	18
S1PR5	0.001	0.076	-9999	-0.53	12	12
S1PR4	-0.025	0.14	-9999	-0.53	40	40
MAPK3	-0.015	0.11	-9999	-0.48	14	14
MAPK1	-0.015	0.11	-9999	-0.48	14	14
S1P/S1P5/Gi	-0.011	0.096	-9999	-0.31	29	29
GNAI1	-0.003	0.089	-9999	-0.56	15	15
CDC42/GDP	0.005	0.04	-9999	-0.43	5	5
S1P/S1P5/G12	0.009	0.048	-9999	-0.32	12	12
RHOA	0.005	0.076	-9999	-0.3	27	27
S1P/S1P4/Gi	-0.022	0.11	-9999	-0.32	49	49
mol:GDP	0	0	-9999	-10000	0	0
GNAZ	-0.013	0.11	-9999	-0.55	26	26
S1P/S1P4/G12/G13	0.001	0.08	-9999	-0.32	26	26
GNA12	0.011	0	-9999	-10000	0	0
GNA13	0.009	0.034	-9999	-0.58	2	2
CDC42	0.007	0.054	-9999	-0.58	5	5

×

Regulation of nuclear SMAD2/3 signaling

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
EP300	0.007	0.048	-10000	0	-0.58	4	4
HSPA8	0.01	0.034	-10000	0	-0.58	2	2
SMAD3/SMAD4/ER alpha	-0.037	0.12	0.2	7	-0.36	49	56
AKT1	0.011	0.027	-10000	0	-0.58	1	1
GSC	-0.016	0.14	-10000	0	-1.4	4	4
NKX2-5	-0.014	0.085	-10000	0	-0.46	21	21
muscle cell differentiation	0.04	0.096	0.47	16	-10000	0	16
SMAD2-3/SMAD4/SP1	0.023	0.1	-10000	0	-0.41	10	10
SMAD4	-0.002	0.081	-10000	0	-0.58	8	8
CBFB	0.007	0.048	-10000	0	-0.58	4	4
SAP18	0.011	0.019	-10000	0	-0.46	1	1
Cbp/p300/MSG1	-0.034	0.12	-10000	0	-0.34	39	39
SMAD3/SMAD4/VDR	-0.009	0.061	-10000	0	-0.39	5	5
MYC	0.006	0.058	-10000	0	-0.56	6	6
CDKN2B	-0.011	0.22	-10000	0	-1.4	14	14
AP1	0.009	0.11	-10000	0	-0.47	15	15
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1	0.038	0.056	-10000	0	-0.44	2	2
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1	0.005	0.088	-10000	0	-0.32	20	20
SP3	0.013	0.024	-10000	0	-0.58	1	1
CREB1	0.009	0.034	-10000	0	-0.58	2	2
FOXH1	-0.053	0.17	-10000	0	-0.5	75	75
SMAD3/SMAD4/GR	-0.015	0.11	-10000	0	-0.38	32	32
GATA3	-0.027	0.13	-10000	0	-0.54	32	32
SKI/SIN3/HDAC complex/NCoR1	0.036	0.025	-10000	0	-10000	0	0
MEF2C/TIF2	-0.019	0.14	-10000	0	-0.54	16	16
endothelial cell migration	0.033	0.19	1.3	10	-10000	0	10
MAX	0.013	0.01	-10000	0	-10000	0	0
RBBP7	0.01	0.034	-10000	0	-0.58	2	2
RBBP4	0.011	0.024	-10000	0	-0.58	1	1
RUNX2	-0.006	0.096	-10000	0	-0.54	19	19
RUNX3	-0.022	0.13	-10000	0	-0.51	39	39
RUNX1	0.011	0	-10000	0	-10000	0	0
CTBP1	0.01	0.024	-10000	0	-0.58	1	1
NR3C1	-0.013	0.12	-10000	0	-0.53	28	28
VDR	0.01	0.024	-10000	0	-0.58	1	1
CDKN1A	0.027	0.13	-10000	0	-1	5	5
KAT2B	-0.006	0.099	-10000	0	-0.59	17	17
SMAD2/SMAD2/SMAD4/FOXH1	-0.022	0.13	-10000	0	-0.38	36	36
DCP1A	0.011	0	-10000	0	-10000	0	0
SKI	0.011	0.001	-10000	0	-10000	0	0
SERPINE1	-0.033	0.2	-10000	0	-1.4	10	10
SMAD3/SMAD4/ATF2	0.01	0.08	-10000	0	-0.35	16	16
SMAD3/SMAD4/ATF3	0.002	0.095	-10000	0	-0.36	20	20
SAP30	0.01	0.034	-10000	0	-0.58	2	2
Cbp/p300/PIAS3	0.02	0.04	-10000	0	-0.34	6	6
JUN	0.008	0.11	-10000	0	-0.47	14	14
SMAD3/SMAD4/IRF7	0.005	0.09	-10000	0	-0.42	12	12
TFE3	0.014	0.012	-10000	0	-10000	0	0
COL1A2	-0.049	0.22	-10000	0	-0.72	48	48
mesenchymal cell differentiation	0.001	0.099	0.36	28	-10000	0	28
DLX1	-0.044	0.15	-10000	0	-0.46	68	68
TCF3	0.01	0.024	-10000	0	-0.58	1	1
FOS	-0.024	0.14	-10000	0	-0.54	41	41
SMAD3/SMAD4/Max	0.002	0.074	-10000	0	-0.34	12	12
Cbp/p300/SNIP1	0.02	0.031	-10000	0	-0.35	4	4
ZBTB17	0.011	0.026	-10000	0	-0.59	1	1
LAMC1	0.022	0.071	-10000	0	-0.44	2	2
TGIF2/HDAC complex/SMAD3/SMAD4	0.008	0.084	-10000	0	-0.35	19	19
IRF7	0.005	0.06	-10000	0	-0.55	7	7
ESR1	-0.033	0.15	-10000	0	-0.52	52	52
HNF4A	0.005	0.064	-10000	0	-0.58	7	7
MEF2C	-0.023	0.14	-10000	0	-0.51	21	21
SMAD2-3/SMAD4	0.012	0.089	-10000	0	-0.37	15	15
Cbp/p300/Src-1	0.02	0.04	-10000	0	-0.43	4	4
IGHV3OR16-13	-0.01	0.05	-10000	0	-0.8	2	2
TGIF2/HDAC complex	0.007	0.054	-10000	0	-0.58	5	5
CREBBP	0.011	0.005	-10000	0	-10000	0	0
SKIL	0.001	0.08	-10000	0	-0.58	11	11
HDAC1	0.011	0.001	-10000	0	-10000	0	0
HDAC2	0.011	0.001	-10000	0	-10000	0	0
SNIP1	0.012	0.002	-10000	0	-10000	0	0
GCN5L2	0	0.007	-10000	0	-10000	0	0
SMAD3/SMAD4/TFE3	0.021	0.08	-10000	0	-0.41	4	4
MSG1/HSC70	-0.049	0.14	-10000	0	-0.34	110	110
SMAD2	0.007	0.052	-10000	0	-0.58	4	4
SMAD3	0	0.079	-10000	0	-0.57	8	8
SMAD3/E2F4-5/DP1/p107/SMAD4	0.018	0.071	-10000	0	-0.34	5	5
SMAD2/SMAD2/SMAD4	-0.005	0.077	-10000	0	-0.35	25	25
NCOR1	0.011	0.024	-10000	0	-0.58	1	1
NCOA2	0.004	0.066	-10000	0	-0.57	8	8
NCOA1	0.01	0.024	-10000	0	-0.58	1	1
MYOD/E2A	0.007	0.026	-10000	0	-0.36	3	3
SMAD2-3/SMAD4/SP1/MIZ-1	0.031	0.1	-10000	0	-0.44	6	6
IFNB1	0.008	0.087	-10000	0	-0.48	8	8
SMAD3/SMAD4/MEF2C	-0.019	0.14	-10000	0	-0.56	16	16
CITED1	-0.078	0.19	-10000	0	-0.49	108	108
SMAD2-3/SMAD4/ARC105	0.02	0.082	-10000	0	-0.38	9	9
RBL1	0.009	0.039	-10000	0	-0.54	3	3
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB	0.024	0.1	-10000	0	-0.48	17	17
RUNX1-3/PEBPB2	0	0.086	-10000	0	-0.31	43	43
SMAD7	0.026	0.12	-10000	0	-0.66	6	6
MYC/MIZ-1	0.012	0.05	-10000	0	-0.4	7	7
SMAD3/SMAD4	-0.016	0.098	0.31	4	-0.43	14	18
IL10	-0.039	0.21	-10000	0	-0.62	53	53
PIASy/HDAC complex	0.011	0.025	-10000	0	-0.58	1	1
PIAS3	0.009	0.031	-10000	0	-0.52	2	2
CDK2	0.01	0.025	-10000	0	-0.58	1	1
IL5	-0.015	0.14	-10000	0	-0.58	12	12
CDK4	0.011	0.006	-10000	0	-10000	0	0
PIAS4	0.011	0.025	-10000	0	-0.58	1	1
ATF3	-0.003	0.083	-10000	0	-0.46	19	19
SMAD3/SMAD4/SP1	0.013	0.1	-10000	0	-0.4	11	11
FOXG1	-0.066	0.17	-10000	0	-0.49	83	83
FOXO3	0.019	0.024	-10000	0	-0.42	1	1
FOXO1	0.017	0.035	-10000	0	-0.42	3	3
FOXO4	0.018	0.03	-10000	0	-0.42	2	2
heart looping	-0.023	0.14	-10000	0	-0.51	21	21
CEBPB	0.008	0.041	-10000	0	-0.49	4	4
SMAD3/SMAD4/DLX1	-0.024	0.12	-10000	0	-0.37	20	20
MYOD1	-0.001	0.026	-10000	0	-0.46	2	2
SMAD3/SMAD4/HNF4	0.007	0.091	-10000	0	-0.39	18	18
SMAD3/SMAD4/GATA3	-0.03	0.14	-10000	0	-0.48	25	25
SnoN/SIN3/HDAC complex/NCoR1	0.001	0.079	-10000	0	-0.58	11	11
SMAD3/SMAD4/RUNX1-3/PEBPB2	0.006	0.1	-10000	0	-0.4	13	13
SMAD3/SMAD4/SP1-3	0.025	0.092	-10000	0	-0.42	4	4
MED15	0.01	0.024	-10000	0	-0.58	1	1
SP1	0.008	0.044	-10000	0	-0.57	1	1
SIN3B	0.011	0.024	-10000	0	-0.58	1	1
SIN3A	0.011	0.024	-10000	0	-0.58	1	1
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5	-0.024	0.13	-10000	0	-0.42	19	19
ITGB5	0.027	0.081	-10000	0	-0.44	2	2
TGIF/SIN3/HDAC complex/CtBP	0.036	0.029	-10000	0	-0.46	1	1
SMAD3/SMAD4/AR	-0.028	0.13	-10000	0	-0.37	52	52
AR	-0.05	0.16	-10000	0	-0.5	71	71
negative regulation of cell growth	0.019	0.084	-10000	0	-0.4	8	8
SMAD3/SMAD4/MYOD	0.003	0.078	-10000	0	-0.34	14	14
E2F5	-0.001	0.086	-10000	0	-0.58	13	13
E2F4	0.011	0	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF	-0.006	0.11	-10000	0	-0.42	12	12
SMAD2-3/SMAD4/FOXO1-3a-4	0.025	0.082	-10000	0	-0.34	18	18
TFDP1	0.011	0	-10000	0	-10000	0	0
SMAD3/SMAD4/AP1	0.011	0.12	-10000	0	-0.48	14	14
SMAD3/SMAD4/RUNX2	0	0.099	-10000	0	-0.36	28	28
TGIF2	0.007	0.054	-10000	0	-0.58	5	5
TGIF1	0.011	0	-10000	0	-10000	0	0
ATF2	0.009	0.034	-10000	0	-0.58	2	2

×

Ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.013	0.046	-10000	0	-0.34	10	10
MAP4K4	0.019	0.066	-10000	0	-0.51	2	2
BAG4	0.008	0.042	-10000	0	-0.58	3	3
PKC zeta/ceramide	-0.024	0.041	0.15	1	-0.2	2	3
NFKBIA	0.011	0	-10000	0	-10000	0	0
BIRC3	-0.016	0.12	-10000	0	-0.53	31	31
BAX	-0.009	0.023	-10000	0	-0.31	1	1
RIPK1	0.011	0	-10000	0	-10000	0	0
AKT1	0.018	0.023	-10000	0	-0.52	1	1
BAD	-0.025	0.041	0.16	1	-0.2	2	3
SMPD1	0.012	0.047	-10000	0	-0.2	22	22
RB1	-0.034	0.067	0.16	2	-0.32	20	22
FADD/Caspase 8	0.028	0.062	-10000	0	-0.4	2	2
MAP2K4	-0.021	0.052	-10000	0	-0.31	9	9
NSMAF	0.011	0	-10000	0	-10000	0	0
response to UV	0	0	-10000	0	-10000	0	0
RAF1	-0.018	0.041	-10000	0	-0.31	2	2
EGF	-0.18	0.25	-10000	0	-0.51	222	222
mol:ceramide	-0.032	0.043	0.14	7	-10000	0	7
MADD	0.011	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
mol:Free Fatty acid	0.015	0.038	-10000	0	-0.33	7	7
ASAH1	0.011	0	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.034	0.066	0.16	2	-0.32	20	22
cell proliferation	-0.037	0.091	-10000	0	-0.26	58	58
BID	0.009	0.047	-10000	0	-0.33	2	2
MAP3K1	-0.027	0.05	0.16	2	-0.33	6	8
EIF2A	-0.021	0.063	-10000	0	-0.32	17	17
TRADD	0.011	0	-10000	0	-10000	0	0
CRADD	0.01	0.024	-10000	0	-0.58	1	1
MAPK3	-0.009	0.039	-10000	0	-0.29	2	2
response to heat	0	0	-10000	0	-10000	0	0
MAPK1	-0.009	0.039	-10000	0	-0.29	2	2
Cathepsin D/ceramide	-0.024	0.041	0.15	1	-0.23	2	3
FADD	0.02	0.063	-10000	0	-0.53	1	1
KSR1	-0.025	0.044	0.14	7	-0.34	2	9
MAPK8	-0.016	0.045	0.16	1	-0.26	5	6
PRKRA	-0.024	0.04	0.16	2	-0.2	1	3
PDGFA	0.006	0.052	-10000	0	-0.48	7	7
TRAF2	0.01	0.024	-10000	0	-0.58	1	1
IGF1	-0.075	0.2	-10000	0	-0.52	97	97
mol:GD3	0	0	-10000	0	-10000	0	0
ganglioside biosynthetic process	-0.032	0.042	0.14	7	-10000	0	7
CTSD	0.009	0.036	-10000	0	-0.5	3	3
regulation of nitric oxide biosynthetic process	0.016	0.018	-10000	0	-0.42	1	1
response to radiation	0	0	-10000	0	-10000	0	0
ERK1/PKC delta	-0.038	0.097	-10000	0	-0.28	58	58
PRKCD	0.011	0	-10000	0	-10000	0	0
PRKCZ	0.01	0.031	-10000	0	-0.52	2	2
mol:GW4869	0	0	-10000	0	-10000	0	0
mol:sphingosine	0.015	0.038	-10000	0	-0.33	7	7
RelA/NF kappa B1	0.016	0.018	-10000	0	-0.42	1	1
mol:glutathione	0	0	-10000	0	-10000	0	0
PAWR	0.01	0.024	-10000	0	-0.58	1	1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD	0.015	0.066	-10000	0	-0.56	1	1
TNFR1A/BAG4/TNF-alpha	0.004	0.082	-10000	0	-0.33	34	34
mol:Sphingosine-1-phosphate	0.013	0.046	-10000	0	-0.34	10	10
MAP2K1	-0.012	0.041	-10000	0	-0.29	3	3
mol:C11AG	0	0	-10000	0	-10000	0	0
RELA	0.011	0	-10000	0	-10000	0	0
CYCS	-0.016	0.047	0.16	7	-0.23	12	19
TNFRSF1A	0.011	0	-10000	0	-10000	0	0
NFKB1	0.01	0.024	-10000	0	-0.58	1	1
TNFR1A/BAG4	0.015	0.031	-10000	0	-0.42	3	3
EIF2AK2	-0.027	0.061	-10000	0	-0.32	16	16
TNF-alpha/TNFR1A/FAN	0.005	0.077	-10000	0	-0.32	31	31
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
CASP8	0.024	0.047	-10000	0	-0.38	3	3
MAP2K2	-0.012	0.04	-10000	0	-0.29	2	2
SMPD3	0.007	0.071	-10000	0	-0.26	34	34
TNF	-0.017	0.12	-10000	0	-0.54	31	31
PKC zeta/PAR4	0.015	0.029	-10000	0	-0.39	3	3
mol:PHOSPHOCHOLINE	0.059	0.095	0.18	214	-10000	0	214
NF kappa B1/RelA/I kappa B alpha	0.032	0.029	-10000	0	-0.52	1	1
AIFM1	-0.01	0.038	0.16	7	-0.26	1	8
BCL2	-0.007	0.1	-10000	0	-0.55	20	20

×

Signaling events mediated by HDAC Class III

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
EP300	0.007	0.048	-10000	0	-0.58	4	4
HDAC4	0.011	0.019	-10000	0	-0.46	1	1
induction of apoptosis	0	0	-10000	0	-10000	0	0
regulation of S phase of mitotic cell cycle	0.006	0.091	0.36	37	-10000	0	37
CDKN1A	0.007	0.068	-10000	0	-0.58	5	5
KAT2B	-0.005	0.098	-10000	0	-0.58	17	17
BAX	0.01	0.024	-10000	0	-0.58	1	1
FOXO3	0.004	0.041	0.49	4	-10000	0	4
FOXO1	0.009	0.034	-10000	0	-0.58	2	2
FOXO4	0.016	0.028	-10000	0	-0.3	5	5
response to UV	0	0	-10000	0	-10000	0	0
XRCC6	0.011	0	-10000	0	-10000	0	0
TAT	-0.018	0.11	-10000	0	-0.46	34	34
mol:Lysophosphatidic acid	0	0	-10000	0	-10000	0	0
MYOD1	-0.004	0.075	-10000	0	-0.42	19	19
PPARGC1A	-0.044	0.17	-10000	0	-0.57	58	58
FHL2	0.008	0.042	-10000	0	-0.58	3	3
response to nutrient levels	0	0	-10000	0	-10000	0	0
KU70/SIRT1	0.011	0.041	-10000	0	-0.42	5	5
HIST2H4A	-0.006	0.091	-10000	0	-0.36	37	37
SIRT1/FOXO3a	0	0.031	0.29	2	-0.36	3	5
SIRT1	0.004	0.055	0.2	2	-0.59	5	7
response to hypoxia	0	0	-10000	0	-10000	0	0
SIRT1/MEF2D/HDAC4	0.017	0.04	-10000	0	-0.34	7	7
SIRT1/Histone H1b	0.003	0.067	-10000	0	-0.3	20	20
apoptosis	-0.017	0.038	0.36	6	-10000	0	6
SIRT1/PGC1A	-0.035	0.11	-10000	0	-0.35	63	63
p53/SIRT1	-0.041	0.13	0.32	4	-0.43	61	65
SIRT1/FOXO4	0.014	0.048	-10000	0	-0.37	8	8
FOXO1/FHL2/SIRT1	0.015	0.045	-10000	0	-0.33	10	10
HIST1H1E	0.003	0.062	-10000	0	-0.31	17	17
SIRT1/p300	0.009	0.061	-10000	0	-0.53	7	7
muscle cell differentiation	0	0.079	0.4	21	-10000	0	21
TP53	-0.047	0.17	-10000	0	-0.58	57	57
KU70/SIRT1/BAX	0.018	0.038	-10000	0	-0.36	6	6
CREBBP	0.011	0	-10000	0	-10000	0	0
MEF2D	0.01	0.024	-10000	0	-0.58	1	1
HIV-1 Tat/SIRT1	-0.011	0.085	-10000	0	-0.33	39	39
ACSS2	0.013	0.044	-10000	0	-0.42	6	6
SIRT1/PCAF/MYOD	0	0.08	-10000	0	-0.4	21	21

×

Syndecan-3-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	0.011	0	-9999	-10000	0	0
Syndecan-3/Src/Cortactin	0.013	0.073	-9999	-0.45	2	2
Syndecan-3/Neurocan	0.004	0.041	-9999	-0.6	1	1
POMC	-0.029	0.14	-9999	-0.52	45	45
EGFR	0.005	0.058	-9999	-0.53	7	7
Syndecan-3/EGFR	0.016	0.04	-9999	-0.36	5	5
AGRP	-0.001	0.05	-9999	-0.46	7	7
NCSTN	0.011	0	-9999	-10000	0	0
PSENEN	0.01	0.024	-9999	-0.58	1	1
RP11-540L11.1	0	0	-9999	-10000	0	0
APH1B	0.006	0.059	-9999	-0.58	6	6
APH1A	0.011	0	-9999	-10000	0	0
NCAN	-0.004	0.065	-9999	-0.46	12	12
long-term memory	0.022	0.041	-9999	-0.42	3	3
Syndecan-3/IL8	-0.042	0.12	-9999	-0.31	69	69
PSEN1	0.011	0	-9999	-10000	0	0
Src/Cortactin	0.016	0.018	-9999	-0.42	1	1
FYN	0.005	0.06	-9999	-0.55	7	7
limb bud formation	-0.002	0.026	-9999	-0.62	1	1
MC4R	-0.004	0.056	-9999	-0.46	9	9
SRC	0.01	0.024	-9999	-0.58	1	1
PTN	-0.025	0.14	-9999	-0.54	40	40
FGFR/FGF/Syndecan-3	-0.002	0.026	-9999	-0.63	1	1
neuron projection morphogenesis	-0.005	0.073	-9999	-0.43	2	2
Syndecan-3/AgRP	0.003	0.036	-9999	-0.6	1	1
Syndecan-3/AgRP/MC4R	-0.004	0.044	-9999	-0.42	3	3
Fyn/Cortactin	0.012	0.044	-9999	-0.39	7	7
SDC3	-0.002	0.027	-9999	-0.64	1	1
GO:0007205	0	0	-9999	-10000	0	0
positive regulation of leukocyte migration	-0.042	0.12	-9999	-0.3	69	69
IL8	-0.11	0.22	-9999	-0.52	137	137
Syndecan-3/Fyn/Cortactin	0.023	0.042	-9999	-0.43	3	3
Syndecan-3/CASK	-0.002	0.025	-9999	-0.61	1	1
alpha-MSH/MC4R	-0.023	0.11	-9999	-0.39	51	51
Gamma Secretase	0.03	0.035	-9999	-0.3	7	7

×

PDGFR-beta signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate	-0.015	0.13	-9999	-0.47	30	30
PDGFB-D/PDGFRB/SLAP	-0.015	0.12	-9999	-0.43	43	43
PDGFB-D/PDGFRB/APS/CBL	-0.004	0.093	-9999	-0.32	44	44
AKT1	0.031	0.068	-9999	-0.48	3	3
mol:PI-4-5-P2	0	0.001	-9999	-10000	0	0
mol:Sphingosine-1-phosphate	-0.016	0.13	-9999	-0.49	30	30
PIK3CA	0.009	0.034	-9999	-0.58	2	2
FGR	-0.043	0.17	-9999	-0.6	40	40
mol:Ca2+	-0.006	0.11	-9999	-0.58	18	18
MYC	0	0.12	-9999	-0.61	15	15
SHC1	0.011	0	-9999	-10000	0	0
HRAS/GDP	0.016	0.068	-9999	-0.33	12	12
LRP1/PDGFRB/PDGFB	0.006	0.083	-9999	-0.41	20	20
GRB10	0.007	0.048	-9999	-0.58	4	4
PTPN11	0.007	0.054	-9999	-0.58	5	5
GO:0007205	-0.007	0.12	-9999	-0.6	18	18
PTEN	0.006	0.059	-9999	-0.58	6	6
GRB2	0.011	0	-9999	-10000	0	0
GRB7	0.002	0.065	-9999	-0.46	12	12
PDGFB-D/PDGFRB/SHP2	0	0.082	-9999	-0.4	24	24
PDGFB-D/PDGFRB/GRB10	0.001	0.08	-9999	-0.4	23	23
cell cycle arrest	-0.015	0.12	-9999	-0.42	43	43
HRAS	0.008	0.041	-9999	-0.49	4	4
HIF1A	0.031	0.079	-9999	-0.5	7	7
GAB1	-0.017	0.13	-9999	-0.6	20	20
mol:GTP	0	0	-9999	-10000	0	0
DNM2	-0.012	0.12	-9999	-0.55	20	20
PDGFB-D/PDGFRB	0.011	0.071	-9999	-0.35	22	22
mol:GDP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/LMW-PTP	0.004	0.072	-9999	-0.39	19	19
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB	-0.04	0.12	-9999	-0.48	31	31
positive regulation of MAPKKK cascade	0	0.082	-9999	-0.4	24	24
PIK3R1	0.008	0.042	-9999	-0.58	3	3
mol:IP3	-0.007	0.12	-9999	-0.6	18	18
E5	0	0.002	-9999	-10000	0	0
CSK	0.01	0.024	-9999	-0.58	1	1
PDGFB-D/PDGFRB/GRB7	-0.003	0.087	-9999	-0.37	30	30
SHB	0.011	0.019	-9999	-0.46	1	1
BLK	-0.096	0.21	-9999	-0.56	89	89
PTPN2	0.008	0.042	-9999	-0.59	3	3
PDGFB-D/PDGFRB/SNX15	0.004	0.072	-9999	-0.39	19	19
BCAR1	0.008	0.043	-9999	-0.52	4	4
VAV2	-0.02	0.15	-9999	-0.61	25	25
CBL	0.011	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/DEP1	0.003	0.074	-9999	-0.39	20	20
LCK	-0.038	0.13	-9999	-0.5	38	38
PDGFRB	-0.006	0.099	-9999	-0.55	19	19
ACP1	0.011	0	-9999	-10000	0	0
HCK	-0.033	0.15	-9999	-0.58	35	35
ABL1	-0.017	0.12	-9999	-0.55	21	21
PDGFB-D/PDGFRB/CBL	-0.019	0.14	-9999	-0.64	21	21
PTPN1	0.01	0.025	-9999	-0.59	1	1
SNX15	0.011	0	-9999	-10000	0	0
STAT3	0.011	0	-9999	-10000	0	0
STAT1	0.006	0.054	-9999	-0.49	7	7
cell proliferation	0.002	0.11	-9999	-0.51	18	18
SLA	-0.015	0.12	-9999	-0.53	29	29
actin cytoskeleton reorganization	0.026	0.069	-9999	-0.5	3	3
SRC	-0.013	0.071	-9999	-0.39	18	18
PI3K	-0.014	0.06	-9999	-0.53	2	2
PDGFB-D/PDGFRB/GRB7/SHC	0.006	0.074	-9999	-0.37	14	14
SH2B2	-0.015	0.12	-9999	-0.52	30	30
PLCgamma1/SPHK1	-0.017	0.14	-9999	-0.51	30	30
LYN	-0.011	0.068	-9999	-0.38	17	17
LRP1	0.006	0.057	-9999	-0.56	6	6
SOS1	0.01	0.024	-9999	-0.58	1	1
STAT5B	0.011	0	-9999	-10000	0	0
STAT5A	0.011	0	-9999	-10000	0	0
NCK1-2/p130 Cas	-0.002	0.066	-9999	-0.55	2	2
SPHK1	-0.03	0.14	-9999	-0.52	48	48
EDG1	0	0.003	-9999	-10000	0	0
mol:DAG	-0.007	0.12	-9999	-0.6	18	18
PLCG1	-0.008	0.12	-9999	-0.62	18	18
NHERF/PDGFRB	0.011	0.063	-9999	-0.33	19	19
YES1	-0.018	0.1	-9999	-0.5	21	21
cell migration	0.011	0.063	-9999	-0.33	19	19
SHC/Grb2/SOS1	0.001	0.057	-9999	-10000	0	0
SLC9A3R2	0.01	0.024	-9999	-0.58	1	1
SLC9A3R1	0.011	0	-9999	-10000	0	0
NHERF1-2/PDGFRB/PTEN	0.016	0.067	-9999	-0.32	20	20
FYN	-0.016	0.089	-9999	-0.44	21	21
DOK1	0.014	0.063	-9999	-0.32	17	17
HRAS/GTP	0.006	0.029	-9999	-0.35	4	4
PDGFB	0.007	0.047	-9999	-0.51	5	5
RAC1	-0.01	0.14	-9999	-0.6	23	23
PRKCD	0.014	0.064	-9999	-0.33	17	17
FER	0.009	0.079	-9999	-0.36	21	21
MAPKKK cascade	-0.009	0.051	-9999	-10000	0	0
RASA1	0.013	0.069	-9999	-0.35	18	18
NCK1	0.009	0.034	-9999	-0.58	2	2
NCK2	0.01	0.024	-9999	-0.58	1	1
p62DOK/Csk	0.02	0.059	-9999	-10000	0	0
PDGFB-D/PDGFRB/SHB	0.003	0.073	-9999	-0.39	20	20
chemotaxis	-0.016	0.12	-9999	-0.53	21	21
STAT1-3-5/STAT1-3-5	-0.011	0.055	-9999	-0.56	1	1
Bovine Papilomavirus E5/PDGFRB	-0.005	0.072	-9999	-0.4	19	19
PTPRJ	0.01	0.024	-9999	-0.58	1	1

×

PLK2 and PLK4 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLK2	-0.003	0.084	-9999	-0.48	18	18
PLK4	0.009	0.034	-9999	-0.58	2	2
regulation of centriole replication	0.007	0.068	-9999	-0.36	19	19

×

Regulation of p38-alpha and p38-beta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
RIP1/MEKK3	0.014	0.022	-9999	-0.36	2	2
response to insulin stimulus	0	0	-9999	-10000	0	0
RIPK1	0.011	0	-9999	-10000	0	0
response to stress	0	0	-9999	-10000	0	0
MAP2K6	0.001	0.08	-9999	-0.58	11	11
mol:GTP	0	0	-9999	-10000	0	0
MAP2K4	0.008	0.042	-9999	-0.58	3	3
RAC1-CDC42/GTP/PAK family	0.016	0.034	-9999	-0.29	5	5
response to UV	0	0	-9999	-10000	0	0
YES1	0.005	0.064	-9999	-0.58	7	7
interleukin-1 receptor activity	0	0	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
MAP3K3	0.009	0.034	-9999	-0.58	2	2
FYN	0.005	0.06	-9999	-0.55	7	7
MAP3K12	0.003	0.067	-9999	-0.54	9	9
FGR	-0.026	0.14	-9999	-0.54	41	41
p38 alpha/TAB1	-0.037	0.084	-9999	-0.35	26	26
PRKG1	-0.025	0.14	-9999	-0.56	38	38
DUSP8	0.007	0.048	-9999	-0.58	4	4
PGK/cGMP/p38 alpha	-0.049	0.11	-9999	-0.36	47	47
apoptosis	-0.035	0.08	-9999	-0.34	25	25
RAL/GTP	0.016	0	-9999	-10000	0	0
LYN	0.011	0	-9999	-10000	0	0
DUSP1	-0.006	0.091	-9999	-0.47	22	22
PAK1	0.011	0	-9999	-10000	0	0
SRC	0.01	0.024	-9999	-0.58	1	1
RAC1/OSM/MEKK3/MKK3	0.027	0.034	-9999	-0.38	4	4
TRAF6	0.01	0.024	-9999	-0.58	1	1
RAC1	0.011	0	-9999	-10000	0	0
epidermal growth factor receptor activity	0	0	-9999	-10000	0	0
mol:LPS	0	0	-9999	-10000	0	0
mol:cGMP	0	0	-9999	-10000	0	0
CCM2	0.01	0.031	-9999	-0.52	2	2
RAC1-CDC42/GTP	0.012	0.034	-9999	-0.36	5	5
MAPK11	-0.023	0.14	-9999	-0.44	36	36
BLK	-0.11	0.23	-9999	-0.53	138	138
HCK	-0.017	0.12	-9999	-0.54	31	31
MAP2K3	0.01	0.024	-9999	-0.58	1	1
DUSP16	0.011	0	-9999	-10000	0	0
DUSP10	0.009	0.039	-9999	-0.54	3	3
TRAF6/MEKK3	0.013	0.024	-9999	-0.33	3	3
MAP3K7IP1	0	0	-9999	-10000	0	0
MAPK14	-0.007	0.11	-9999	-0.38	25	25
positive regulation of innate immune response	-0.019	0.15	-9999	-0.48	33	33
LCK	-0.031	0.14	-9999	-0.51	49	49
p38alpha-beta/MKP7	-0.012	0.14	-9999	-0.51	23	23
p38alpha-beta/MKP5	-0.014	0.14	-9999	-0.52	24	24
PGK/cGMP	-0.018	0.1	-9999	-0.41	38	38
PAK2	0.01	0.024	-9999	-0.58	1	1
p38alpha-beta/MKP1	-0.02	0.15	-9999	-0.49	28	28
CDC42	0.007	0.054	-9999	-0.58	5	5
RALB	0.011	0	-9999	-10000	0	0
RALA	0.011	0	-9999	-10000	0	0
PAK3	0	0.056	-9999	-0.46	9	9

×

S1P3 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	-0.006	0.097	-9999	-0.54	19	19
mol:S1P	0	0.005	-9999	-10000	0	0
S1P1/S1P/Gi	-0.009	0.09	-9999	-0.27	50	50
GNAO1	-0.045	0.16	-9999	-0.5	68	68
S1P/S1P3/G12/G13	0.018	0.044	-9999	-0.32	9	9
AKT1	-0.003	0.11	-9999	-0.62	14	14
AKT3	-0.015	0.21	-9999	-0.95	23	23
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	-0.006	0.097	-9999	-0.54	19	19
GNAI2	0.012	0.004	-9999	-10000	0	0
GNAI3	0.012	0.004	-9999	-10000	0	0
GNAI1	-0.002	0.089	-9999	-0.56	15	15
mol:GDP	0	0	-9999	-10000	0	0
S1PR3	0.005	0.065	-9999	-0.55	8	8
S1PR2	0.011	0	-9999	-10000	0	0
EDG1	0	0	-9999	-10000	0	0
mol:Ca2+	-0.01	0.12	-9999	-0.36	32	32
MAPK3	-0.004	0.11	-9999	-0.49	15	15
MAPK1	-0.004	0.11	-9999	-0.49	15	15
JAK2	-0.012	0.13	-9999	-0.46	28	28
CXCR4	-0.017	0.14	-9999	-0.49	28	28
FLT1	0.008	0.053	-9999	-0.57	5	5
RhoA/GDP	0.008	0.018	-9999	-0.43	1	1
Rac1/GDP	0.009	0	-9999	-10000	0	0
SRC	-0.004	0.11	-9999	-0.48	15	15
S1P/S1P3/Gi	-0.01	0.12	-9999	-0.37	32	32
RAC1	0.011	0	-9999	-10000	0	0
RhoA/GTP	-0.004	0.11	-9999	-0.46	15	15
VEGFA	0.012	0.02	-9999	-0.46	1	1
S1P/S1P2/Gi	-0.006	0.092	-9999	-0.32	21	21
VEGFR1 homodimer/VEGFA homodimer	0.018	0.043	-9999	-0.4	6	6
RHOA	0.01	0.024	-9999	-0.58	1	1
S1P/S1P3/Gq	0	0.098	-9999	-0.33	38	38
GNAQ	0.006	0.059	-9999	-0.58	6	6
GNAZ	-0.012	0.11	-9999	-0.55	26	26
G12/G13	0.016	0.025	-9999	-0.42	2	2
GNA14	-0.007	0.1	-9999	-0.56	19	19
GNA15	-0.009	0.1	-9999	-0.54	22	22
GNA12	0.011	0	-9999	-10000	0	0
GNA13	0.009	0.034	-9999	-0.58	2	2
GNA11	0.007	0.05	-9999	-0.53	5	5
Rac1/GTP	-0.004	0.11	-9999	-0.48	14	14

×

Regulation of Androgen receptor activity

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.016	0.018	-9999	-0.42	1	1
SMARCC1	0.002	0.018	-9999	-10000	0	0
REL	0.011	0.043	-9999	-0.58	3	3
HDAC7	0.028	0.093	-9999	-0.52	8	8
JUN	0.004	0.052	-9999	-0.56	5	5
EP300	0.007	0.048	-9999	-0.58	4	4
KAT2B	-0.006	0.098	-9999	-0.58	17	17
KAT5	0.011	0.024	-9999	-0.58	1	1
MAPK14	0.011	0.062	-9999	-0.44	11	11
FOXO1	0.009	0.034	-9999	-0.59	2	2
T-DHT/AR	0.024	0.098	-9999	-0.53	9	9
MAP2K6	0.001	0.081	-9999	-0.6	11	11
BRM/BAF57	0.009	0.041	-9999	-0.43	5	5
MAP2K4	0.009	0.042	-9999	-0.58	3	3
SMARCA2	0.005	0.049	-9999	-0.59	4	4
PDE9A	-0.082	0.28	-9999	-1.1	44	44
NCOA2	0.004	0.066	-9999	-0.57	8	8
CEBPA	-0.005	0.097	-9999	-0.58	17	17
EHMT2	0.007	0.031	-9999	-0.52	2	2
cell proliferation	0.021	0.13	-9999	-0.48	18	18
NR0B1	-0.001	0.05	-9999	-0.46	7	7
EGR1	-0.012	0.1	-9999	-0.5	25	25
RXRs/9cRA	0.004	0.055	-9999	-0.33	2	2
AR/RACK1/Src	0.016	0.076	-9999	-0.41	9	9
AR/GR	-0.01	0.1	-9999	-0.35	33	33
GNB2L1	0.011	0.019	-9999	-0.46	1	1
PKN1	0.008	0.042	-9999	-0.58	3	3
RCHY1	0.01	0.024	-9999	-0.58	1	1
epidermal growth factor receptor activity	0	0.002	-9999	-10000	0	0
MAPK8	0.016	0.037	-9999	-0.42	4	4
T-DHT/AR/TIF2/CARM1	0.02	0.086	-9999	-0.43	11	11
SRC	0.023	0.062	-9999	-0.34	15	15
NR3C1	-0.014	0.12	-9999	-0.54	28	28
KLK3	-0.2	0.38	-9999	-1	82	82
APPBP2	0.008	0.048	-9999	-0.58	4	4
TRIM24	0.009	0.005	-9999	-10000	0	0
T-DHT/AR/TIP60	0.018	0.078	-9999	-0.4	14	14
TMPRSS2	-0.026	0.14	-9999	-0.88	9	9
RXRG	-0.013	0.095	-9999	-0.46	26	26
mol:9cRA	-0.001	0.002	-9999	-10000	0	0
RXRA	0.01	0.024	-9999	-0.58	1	1
RXRB	0.011	0.001	-9999	-10000	0	0
CARM1	0.011	0.024	-9999	-0.59	1	1
NR2C2	0.01	0.024	-9999	-0.58	1	1
KLK2	0.015	0.11	-9999	-0.44	13	13
AR	0	0.084	-9999	-0.29	31	31
SENP1	0.01	0.024	-9999	-0.58	1	1
HSP90AA1	0.01	0.024	-9999	-0.58	1	1
MDM2	0.012	0.045	-9999	-0.52	4	4
SRY	0.002	0.038	-9999	-0.45	4	4
GATA2	-0.021	0.13	-9999	-0.56	34	34
MYST2	0.011	0.024	-9999	-0.58	1	1
HOXB13	-0.097	0.21	-9999	-0.5	125	125
T-DHT/AR/RACK1/Src	0.022	0.074	-9999	-0.43	8	8
positive regulation of transcription	-0.021	0.13	-9999	-0.56	34	34
DNAJA1	0.012	0.004	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.022	0.041	-9999	-0.48	3	3
NCOA1	0.011	0.026	-9999	-0.61	1	1
SPDEF	-0.15	0.25	-9999	-0.54	181	181
T-DHT/AR/TIF2	0.014	0.11	-9999	-0.63	8	8
T-DHT/AR/Hsp90	0.017	0.075	-9999	-0.41	12	12
GSK3B	0.009	0.034	-9999	-0.59	2	2
NR2C1	0.011	0.024	-9999	-0.58	1	1
mol:T-DHT	0.02	0.064	-9999	-0.37	14	14
SIRT1	0.006	0.054	-9999	-0.58	5	5
ZMIZ2	0.015	0.027	-9999	-0.59	1	1
POU2F1	0.011	0.076	-9999	-0.55	10	10
T-DHT/AR/DAX-1	0.009	0.076	-9999	-0.39	14	14
CREBBP	0.011	0.001	-9999	-10000	0	0
SMARCE1	0.008	0.025	-9999	-0.58	1	1

×

S1P5 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	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	0.005	0.087	0.46	7	-10000	0	7
GNAI2	0.011	0	-10000	0	-10000	0	0
S1P/S1P5/G12	0.009	0.048	-10000	0	-0.32	12	12
mol:GDP	0	0	-10000	0	-10000	0	0
GNAO1	-0.045	0.16	-10000	0	-0.49	68	68
RhoA/GTP	-0.005	0.089	-10000	0	-0.47	7	7
negative regulation of cAMP metabolic process	-0.011	0.096	-10000	0	-0.31	29	29
GNAZ	-0.013	0.11	-10000	0	-0.55	26	26
GNAI3	0.011	0	-10000	0	-10000	0	0
GNA12	0.011	0	-10000	0	-10000	0	0
S1PR5	0.001	0.076	-10000	0	-0.53	12	12
mol:GTP	0	0	-10000	0	-10000	0	0
S1P/S1P5/Gi	-0.011	0.096	-10000	0	-0.31	29	29
RhoA/GDP	0.008	0.018	-10000	0	-0.43	1	1
RHOA	0.01	0.024	-10000	0	-0.58	1	1
GNAI1	-0.003	0.089	-10000	0	-0.56	15	15

×

Class IB PI3K non-lipid kinase events

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

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

Entity	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	0.083	0.58	12	-10000	0	12
PI3K Class IB/PDE3B	0.083	-10000	0	-0.58	12	12
PDE3B	0.083	-10000	0	-0.58	12	12

×

Hedgehog signaling events mediated by Gli proteins

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.011	0	-9999	-10000	0	0
HDAC2	0.011	0.001	-9999	-10000	0	0
GNB1/GNG2	0	0.093	-9999	-0.38	30	30
forebrain development	-0.003	0.15	-9999	-0.51	36	36
GNAO1	-0.045	0.16	-9999	-0.49	68	68
SMO/beta Arrestin2	-0.002	0.094	-9999	-0.4	31	31
SMO	-0.017	0.13	-9999	-0.56	31	31
ARRB2	0.012	0.002	-9999	-10000	0	0
GLI3/SPOP	0.014	0.099	-9999	-0.67	5	5
mol:GTP	0	0.001	-9999	-10000	0	0
GSK3B	0.009	0.034	-9999	-0.58	2	2
GNAI2	0.012	0.002	-9999	-10000	0	0
SIN3/HDAC complex	0.026	0.03	-9999	-0.32	4	4
GNAI1	-0.002	0.089	-9999	-0.56	15	15
XPO1	0.003	0.08	-9999	-0.58	11	11
GLI1/Su(fu)	-0.039	0.13	-9999	-0.57	21	21
SAP30	0.009	0.034	-9999	-0.58	2	2
mol:GDP	-0.017	0.13	-9999	-0.56	31	31
MIM/GLI2A	0.002	0.092	-9999	-0.55	16	16
IFT88	0.007	0.048	-9999	-0.58	4	4
GNAI3	0.012	0.002	-9999	-10000	0	0
GLI2	0.022	0.06	-9999	-0.57	2	2
GLI3	0.008	0.1	-9999	-0.32	37	37
CSNK1D	0.011	0	-9999	-10000	0	0
CSNK1E	0.011	0	-9999	-10000	0	0
SAP18	0.011	0.019	-9999	-0.46	1	1
embryonic digit morphogenesis	0.007	0.048	-9999	-0.58	4	4
GNG2	0.003	0.067	-9999	-0.54	9	9
Gi family/GTP	-0.017	0.12	-9999	-0.34	44	44
SIN3B	0.01	0.024	-9999	-0.58	1	1
SIN3A	0.01	0.024	-9999	-0.58	1	1
GLI3/Su(fu)	0.024	0.082	-9999	-0.55	5	5
GLI2/Su(fu)	0.029	0.07	-9999	-0.35	9	9
FOXA2	-0.036	0.18	-9999	-0.94	22	22
neural tube patterning	-0.003	0.15	-9999	-0.51	36	36
SPOP	0.011	0	-9999	-10000	0	0
Su(fu)/PIAS1	0.018	0.044	-9999	-10000	0	0
GNB1	0.011	0	-9999	-10000	0	0
CSNK1G2	0.009	0.034	-9999	-0.58	2	2
CSNK1G3	0.01	0.024	-9999	-0.58	1	1
MTSS1	0.002	0.092	-9999	-0.55	16	16
embryonic limb morphogenesis	-0.003	0.15	-9999	-0.51	36	36
SUFU	0.014	0.049	-9999	-10000	0	0
LGALS3	0.008	0.043	-9999	-0.52	4	4
catabolic process	0.026	0.11	-9999	-0.41	20	20
GLI3A/CBP	0.006	0.067	-9999	-0.35	19	19
KIF3A	0.001	0.08	-9999	-0.58	11	11
GLI1	-0.004	0.16	-9999	-0.53	36	36
RAB23	0.006	0.055	-9999	-0.54	6	6
CSNK1A1	0.009	0.034	-9999	-0.58	2	2
IFT172	0.011	0	-9999	-10000	0	0
RBBP7	0.009	0.034	-9999	-0.58	2	2
Su(fu)/Galectin3	0.016	0.052	-9999	-0.35	3	3
GNAZ	-0.012	0.12	-9999	-0.55	26	26
RBBP4	0.01	0.024	-9999	-0.58	1	1
CSNK1G1	0.01	0.024	-9999	-0.58	1	1
PIAS1	0.011	0	-9999	-10000	0	0
PRKACA	0.011	0	-9999	-10000	0	0
GLI2/SPOP	0.027	0.057	-9999	-0.54	2	2
STK36	0.014	0.003	-9999	-10000	0	0
Gi family/GNB1/GNG2/GDP	-0.009	0.11	-9999	-0.46	15	15
PTCH1	-0.003	0.17	-9999	-0.83	16	16
MIM/GLI1	-0.002	0.17	-9999	-0.59	31	31
CREBBP	0.006	0.067	-9999	-0.35	19	19
Su(fu)/SIN3/HDAC complex	0.035	0.028	-9999	-10000	0	0

×

Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1	0.011	0	-10000	0	-10000	0	0
NFATC1	0.031	0.06	-10000	0	-0.32	3	3
NFATC2	0.016	0.056	-10000	0	-0.24	12	12
NFATC3	0.018	0.02	-10000	0	-0.41	1	1
YWHAE	0.011	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/CABIN1	-0.061	0.14	-10000	0	-0.47	42	42
Exportin 1/Ran/NUP214	0.016	0.051	-10000	0	-0.36	11	11
mol:DAG	0	0.001	-10000	0	-10000	0	0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV	-0.074	0.14	-10000	0	-0.48	45	45
BCL2/BAX	0.003	0.076	-10000	0	-0.39	21	21
CaM/Ca2+/Calcineurin A alpha-beta B1	0.009	0.004	-10000	0	-10000	0	0
CaM/Ca2+	0.009	0.004	-10000	0	-10000	0	0
BAX	0.01	0.024	-10000	0	-0.58	1	1
MAPK14	0.011	0.003	-10000	0	-10000	0	0
BAD	0.01	0.031	-10000	0	-0.52	2	2
CABIN1/MEF2D	-0.053	0.14	-10000	0	-0.45	43	43
Calcineurin A alpha-beta B1/BCL2	-0.007	0.1	-10000	0	-0.55	20	20
FKBP8	0.009	0.034	-10000	0	-0.58	2	2
activation-induced cell death of T cells	0.052	0.14	0.44	43	-10000	0	43
KPNB1	0.011	0	-10000	0	-10000	0	0
KPNA2	0.011	0	-10000	0	-10000	0	0
XPO1	0.001	0.08	-10000	0	-0.58	11	11
SFN	0.005	0.055	-10000	0	-0.47	8	8
MAP3K8	0.009	0.031	-10000	0	-0.52	2	2
NFAT4/CK1 alpha	0.023	0.046	-10000	0	-0.39	6	6
MEF2D/NFAT1/Cbp/p300	0.027	0.093	-10000	0	-0.42	12	12
CABIN1	-0.062	0.15	-10000	0	-0.48	42	42
CALM1	0.011	0.002	-10000	0	-10000	0	0
RAN	0.011	0	-10000	0	-10000	0	0
MAP3K1	0.006	0.059	-10000	0	-0.58	6	6
CAMK4	-0.014	0.12	-10000	0	-0.55	27	27
mol:Ca2+	0	0.003	-10000	0	-10000	0	0
MAPK3	0.01	0.024	-10000	0	-0.58	1	1
YWHAH	0.011	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/AKAP79/PKA	-0.006	0.092	-10000	0	-0.38	35	35
YWHAB	0.011	0	-10000	0	-10000	0	0
MAPK8	0.01	0.024	-10000	0	-0.58	1	1
MAPK9	0.011	0	-10000	0	-10000	0	0
YWHAG	0.011	0	-10000	0	-10000	0	0
FKBP1A	0.011	0	-10000	0	-10000	0	0
NFAT1-c-4/YWHAQ	0.042	0.059	-10000	0	-0.36	3	3
PRKCH	0.006	0.059	-10000	0	-0.58	6	6
CABIN1/Cbp/p300	0.014	0.036	-10000	0	-0.42	4	4
CASP3	0.009	0.034	-10000	0	-0.58	2	2
PIM1	0.011	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0.008	0.002	-10000	0	-10000	0	0
apoptosis	-0.005	0.037	0.23	1	-0.66	1	2
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1	0.032	0.03	-10000	0	-0.38	2	2
PRKCB	-0.044	0.17	-10000	0	-0.55	60	60
PRKCE	0.011	0	-10000	0	-10000	0	0
JNK2/NFAT4	0.023	0.018	-10000	0	-0.37	1	1
BAD/BCL-XL	0.016	0.022	-10000	0	-0.37	2	2
PRKCD	0.011	0	-10000	0	-10000	0	0
NUP214	0.011	0	-10000	0	-10000	0	0
PRKCZ	0.009	0.031	-10000	0	-0.52	2	2
PRKCA	0.01	0.031	-10000	0	-0.52	2	2
PRKCG	-0.16	0.25	-10000	0	-0.52	190	190
PRKCQ	-0.049	0.18	-10000	0	-0.58	62	62
FKBP38/BCL2	0.002	0.078	-10000	0	-0.4	22	22
EP300	0.008	0.048	-10000	0	-0.58	4	4
PRKCB1	0	0	-10000	0	-10000	0	0
CSNK2A1	0.011	0	-10000	0	-10000	0	0
NFATc/JNK1	0.035	0.06	-10000	0	-0.32	3	3
CaM/Ca2+/FKBP38	0.015	0.022	-10000	0	-0.36	2	2
FKBP12/FK506	0.009	0	-10000	0	-10000	0	0
CSNK1A1	0.014	0.022	-10000	0	-0.36	2	2
CaM/Ca2+/CAMK IV	0	0.074	-10000	0	-0.34	27	27
NFATc/ERK1	0.036	0.059	-10000	0	-0.31	2	2
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV	-0.073	0.14	-10000	0	-0.48	44	44
NR4A1	0.018	0.12	-10000	0	-0.42	39	39
GSK3B	0.009	0.034	-10000	0	-0.58	2	2
positive T cell selection	0.018	0.02	-10000	0	-0.41	1	1
NFAT1/CK1 alpha	-0.011	0.044	-10000	0	-0.42	4	4
RCH1/ KPNB1	0.017	0	-10000	0	-10000	0	0
YWHAQ	0.011	0	-10000	0	-10000	0	0
PRKACA	0.011	0.003	-10000	0	-10000	0	0
AKAP5	-0.02	0.13	-10000	0	-0.53	35	35
MEF2D	0.01	0.025	-10000	0	-0.6	1	1
mol:FK506	0	0	-10000	0	-10000	0	0
YWHAZ	0.008	0.042	-10000	0	-0.58	3	3
NFATc/p38 alpha	0.035	0.058	-10000	0	-0.31	2	2
CREBBP	0.011	0.002	-10000	0	-10000	0	0
BCL2	-0.007	0.1	-10000	0	-0.55	20	20

×

Signaling mediated by p38-gamma and p38-delta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EEF2K	0.022	0.022	-9999	-0.36	2	2
SNTA1	0.006	0.055	-9999	-0.54	6	6
response to hypoxia	0	0	-9999	-10000	0	0
STMN1	0.013	0.066	-9999	-0.38	16	16
MAPK12	-0.004	0.096	-9999	-0.38	24	24
CCND1	0.005	0.046	-9999	-0.25	8	8
p38 gamma/SNTA1	0	0.096	-9999	-0.38	23	23
MAP2K3	0.01	0.024	-9999	-0.58	1	1
PKN1	0.008	0.042	-9999	-0.58	3	3
G2/M transition checkpoint	-0.004	0.095	-9999	-0.37	24	24
MAP2K6	0.009	0.061	-9999	-0.33	19	19
MAPT	-0.024	0.11	-9999	-0.35	43	43
MAPK13	0.017	0.025	-9999	-0.42	2	2
hyperosmotic response	0	0	-9999	-10000	0	0
ZAK	0.009	0.042	-9999	-0.35	8	8

×

IL2 signaling events mediated by PI3K

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.015	0.1	-10000	0	-0.52	12	12
UGCG	0.01	0.068	-10000	0	-0.84	3	3
AKT1/mTOR/p70S6K/Hsp90/TERT	0.01	0.13	-10000	0	-0.42	25	25
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucosylceramide	0.01	0.067	-10000	0	-0.82	3	3
mol:DAG	-0.001	0.009	-10000	0	-10000	0	0
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.038	0.11	-10000	0	-0.46	27	27
FRAP1	0.018	0.15	-10000	0	-0.53	27	27
FOXO3	0.024	0.13	-10000	0	-0.48	21	21
AKT1	0.018	0.14	-10000	0	-0.49	26	26
GAB2	0.01	0.034	-10000	0	-0.58	2	2
SMPD1	0.013	0.038	-10000	0	-0.6	1	1
SGMS1	0.014	0.028	-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	0.015	0.035	-10000	0	-0.36	5	5
CALM1	0.011	0	-10000	0	-10000	0	0
cell proliferation	0.019	0.08	-10000	0	-0.64	3	3
EIF3A	0.01	0.024	-10000	0	-0.58	1	1
PI3K	0.018	0.041	-10000	0	-0.43	5	5
RPS6KB1	0.008	0.095	-10000	0	-0.96	5	5
mol:sphingomyelin	-0.001	0.009	-10000	0	-10000	0	0
natural killer cell activation	0.001	0.001	-10000	0	-0.012	4	4
JAK3	0.003	0.076	-10000	0	-0.53	12	12
PIK3R1	0.011	0.042	-10000	0	-0.59	3	3
JAK1	0.011	0.042	-10000	0	-0.58	3	3
NFKB1	0.01	0.024	-10000	0	-0.58	1	1
MYC	0.022	0.15	-10000	0	-0.69	12	12
MYB	0.007	0.16	-10000	0	-1.2	10	10
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.012	0.14	-10000	0	-0.47	26	26
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.018	0.091	-10000	0	-0.87	5	5
mol:PI-3-4-5-P3	0.012	0.13	-10000	0	-0.46	26	26
Rac1/GDP	0.021	0.032	-10000	0	-0.32	5	5
T cell proliferation	0.017	0.13	-10000	0	-0.49	18	18
SHC1	0.012	0.002	-10000	0	-10000	0	0
RAC1	0.012	0	-10000	0	-10000	0	0
positive regulation of cyclin-dependent protein kinase activity	0.004	0.008	-10000	0	-0.065	9	9
PRKCZ	0.017	0.13	-10000	0	-0.51	18	18
NF kappa B1 p50/RelA	-0.037	0.11	-10000	0	-0.49	22	22
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K	0.008	0.11	-10000	0	-0.5	18	18
HSP90AA1	0.01	0.024	-10000	0	-0.58	1	1
RELA	0.011	0	-10000	0	-10000	0	0
IL2RA	-0.047	0.17	-10000	0	-0.55	63	63
IL2RB	-0.016	0.13	-10000	0	-0.55	32	32
TERT	-0.047	0.17	-10000	0	-0.52	67	67
E2F1	0.015	0.065	-10000	0	-0.44	11	11
SOS1	0.011	0.024	-10000	0	-0.58	1	1
RPS6	0.007	0.045	-10000	0	-0.48	5	5
mol:cAMP	-0.002	0.004	0.031	9	-10000	0	9
PTPN11	0.007	0.054	-10000	0	-0.58	5	5
IL2RG	0.001	0.084	-10000	0	-0.56	13	13
actin cytoskeleton organization	0.017	0.13	-10000	0	-0.49	18	18
GRB2	0.012	0.002	-10000	0	-10000	0	0
IL2	0.004	0.027	-10000	0	-0.45	2	2
PIK3CA	0.012	0.034	-10000	0	-0.58	2	2
Rac1/GTP	0.027	0.031	-10000	0	-0.31	5	5
LCK	-0.028	0.14	-10000	0	-0.51	49	49
BCL2	0.015	0.18	-10000	0	-0.84	17	17

×

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BAG4	0.008	0.042	-9999	-0.58	3	3
Caspase 8 (4 units)	0.006	0.087	-9999	-0.52	5	5
NEF	-0.013	0.05	-9999	-10000	0	0
NFKBIA	0.009	0.023	-9999	-10000	0	0
BIRC3	0.007	0.12	-9999	-0.52	31	31
CYCS	0	0.11	-9999	-0.54	8	8
RIPK1	0.011	0	-9999	-10000	0	0
CD247	-0.031	0.15	-9999	-0.65	30	30
MAP2K7	0.013	0.083	-9999	-0.46	6	6
protein ubiquitination	0.039	0.057	-9999	-0.4	3	3
CRADD	0.01	0.024	-9999	-0.58	1	1
DAXX	0.011	0	-9999	-10000	0	0
FAS	-0.001	0.084	-9999	-0.56	13	13
BID	0.001	0.097	-9999	-0.53	5	5
NF-kappa-B/RelA/I kappa B alpha	0.017	0.066	-9999	-0.34	1	1
TRADD	0.011	0	-9999	-10000	0	0
MAP3K5	0.009	0.034	-9999	-0.58	2	2
CFLAR	0.011	0	-9999	-10000	0	0
FADD	0.011	0	-9999	-10000	0	0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin	0.017	0.066	-9999	-0.34	1	1
MAPK8	0.018	0.082	-9999	-0.51	5	5
APAF1	0.008	0.042	-9999	-0.58	3	3
TRAF1	0.008	0.038	-9999	-0.46	4	4
TRAF2	0.01	0.024	-9999	-0.58	1	1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG	-0.005	0.1	-9999	-0.3	50	50
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD	0.033	0.057	-9999	-0.32	1	1
CHUK	0.039	0.061	-9999	-0.44	3	3
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8	0.026	0.054	-9999	-0.32	13	13
TCRz/NEF	-0.037	0.15	-9999	-0.39	80	80
TNF	-0.017	0.12	-9999	-0.54	31	31
FASLG	-0.06	0.23	-9999	-0.62	78	78
NFKB1	0.008	0.033	-9999	-0.58	1	1
TNFR1A/BAG4/TNF-alpha	0.004	0.082	-9999	-0.33	34	34
CASP6	-0.018	0.058	-9999	-0.51	4	4
CASP7	0.022	0.13	-9999	-0.56	19	19
RELA	0.009	0.023	-9999	-10000	0	0
CASP2	0.011	0	-9999	-10000	0	0
CASP3	0.021	0.13	-9999	-0.56	20	20
TNFRSF1A	0.011	0	-9999	-10000	0	0
TNFR1A/BAG4	0.015	0.031	-9999	-0.42	3	3
CASP8	0.01	0.024	-9999	-0.58	1	1
CASP9	0.01	0.024	-9999	-0.58	1	1
MAP3K14	0.037	0.057	-9999	-0.42	1	1
APAF-1/Caspase 9	-0.038	0.1	-9999	-0.46	24	24
BCL2	0.015	0.094	-9999	-0.46	9	9

×

Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5	0.023	0.048	-10000	0	-0.36	7	7
HDAC3	0.011	0	-10000	0	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	-0.013	0.075	-10000	0	-0.4	19	19
GATA1/HDAC4	0.005	0.053	-10000	0	-0.32	16	16
GATA1/HDAC5	0.005	0.055	-10000	0	-0.32	16	16
GATA2/HDAC5	-0.007	0.1	-10000	0	-0.41	34	34
HDAC5/BCL6/BCoR	0.021	0.028	-10000	0	-0.28	5	5
HDAC9	-0.038	0.16	-10000	0	-0.55	54	54
Glucocorticoid receptor/Hsp90/HDAC6	0.007	0.075	-10000	0	-0.32	29	29
HDAC4/ANKRA2	0.016	0.022	-10000	0	-0.37	2	2
HDAC5/YWHAB	0.016	0.018	-10000	0	-0.42	1	1
NPC/RanGAP1/SUMO1/Ubc9	0	0.095	-10000	0	-0.43	24	24
GATA2	-0.021	0.13	-10000	0	-0.56	34	34
HDAC4/RFXANK	0.014	0.032	-10000	0	-0.37	4	4
BCOR	0.011	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
HDAC10	0.008	0.046	-10000	0	-0.55	4	4
HDAC5	0.01	0.024	-10000	0	-0.58	1	1
GNB1/GNG2	0.011	0.049	-10000	0	-0.39	9	9
Histones	0.011	0.081	-10000	0	-0.73	2	2
ADRBK1	0.01	0.031	-10000	0	-0.52	2	2
HDAC4	0.011	0.019	-10000	0	-0.46	1	1
XPO1	0.001	0.08	-10000	0	-0.58	11	11
HDAC5/ANKRA2	0.016	0.025	-10000	0	-0.42	2	2
HDAC4/Ubc9	0.016	0.014	-10000	0	-0.32	1	1
HDAC7	0.01	0.024	-10000	0	-0.58	1	1
HDAC5/14-3-3 E	0.016	0.018	-10000	0	-0.42	1	1
TUBA1B	0.011	0	-10000	0	-10000	0	0
HDAC6	0.011	0	-10000	0	-10000	0	0
HDAC5/RFXANK	0.014	0.039	-10000	0	-0.51	3	3
CAMK4	-0.014	0.12	-10000	0	-0.55	27	27
Tubulin/HDAC6	0.004	0.076	-10000	0	-0.29	37	37
SUMO1	-0.007	0.1	-10000	0	-0.58	19	19
EntrezGene:9972	0	0	-10000	0	-10000	0	0
YWHAB	0.011	0	-10000	0	-10000	0	0
GATA1	-0.004	0.072	-10000	0	-0.46	15	15
EntrezGene:8021	0	0	-10000	0	-10000	0	0
YWHAE	0.011	0	-10000	0	-10000	0	0
NR3C1	-0.014	0.12	-10000	0	-0.54	28	28
SUMO1/HDAC4	0.005	0.1	-10000	0	-0.55	19	19
SRF	0.01	0.027	-10000	0	-0.46	2	2
HDAC4/YWHAB	0.016	0.014	-10000	0	-0.32	1	1
Tubulin	-0.006	0.089	-10000	0	-0.35	37	37
HDAC4/14-3-3 E	0.016	0.014	-10000	0	-0.32	1	1
GNB1	0.011	0	-10000	0	-10000	0	0
RANGAP1	0.01	0.031	-10000	0	-0.52	2	2
BCL6/BCoR	0.015	0.027	-10000	0	-0.32	4	4
HDAC4/HDAC3/SMRT (N-CoR2)	0.021	0.031	-10000	0	-0.32	5	5
HDAC4/SRF	0.006	0.078	-10000	0	-0.37	20	20
HDAC4/ER alpha	-0.018	0.11	-10000	0	-0.38	53	53
EntrezGene:23225	0	0	-10000	0	-10000	0	0
positive regulation of chromatin silencing	0.011	0.08	-10000	0	-0.72	2	2
cell motility	0.004	0.076	-10000	0	-0.29	37	37
EntrezGene:23636	0	0	-10000	0	-10000	0	0
UBE2I	0.011	0	-10000	0	-10000	0	0
HDAC7/HDAC3	0.016	0.018	-10000	0	-0.42	1	1
BCL6	0.008	0.038	-10000	0	-0.46	4	4
HDAC4/CaMK II delta B	0.011	0.019	-10000	0	-0.46	1	1
Hsp90/HDAC6	0.016	0.018	-10000	0	-0.42	1	1
ESR1	-0.035	0.15	-10000	0	-0.53	52	52
HDAC6/HDAC11	0.016	0.025	-10000	0	-0.42	2	2
Ran/GTP/Exportin 1	0.007	0.12	-10000	0	-0.69	15	15
NPC	-0.003	0.056	-10000	0	-0.31	19	19
MEF2C	0	0.08	-10000	0	-0.54	13	13
RAN	0.011	0	-10000	0	-10000	0	0
HDAC4/MEF2C	0.025	0.051	-10000	0	-10000	0	0
GNG2	0.003	0.067	-10000	0	-0.54	9	9
NCOR2	0.008	0.046	-10000	0	-0.55	4	4
TUBB2A	-0.02	0.12	-10000	0	-0.5	37	37
HDAC11	0.009	0.034	-10000	0	-0.58	2	2
HSP90AA1	0.01	0.024	-10000	0	-0.58	1	1
RANBP2	-0.007	0.1	-10000	0	-0.58	19	19
ANKRA2	0.01	0.024	-10000	0	-0.58	1	1
RFXANK	0.009	0.039	-10000	0	-0.54	3	3
nuclear import	-0.024	0.016	0.32	1	-10000	0	1

×

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

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
MET/RANBP9	0.015	0.035	-10000	0	-0.55	2	2
CRKL	0.013	0.062	-10000	0	-0.26	2	2
mol:PIP3	-0.011	0.054	0.52	6	-10000	0	6
AKT1	0.004	0.038	0.36	6	-0.31	1	7
PTK2B	0.009	0.034	-10000	0	-0.58	2	2
RAPGEF1	0.018	0.061	-10000	0	-0.37	1	1
RANBP10	0.011	0	-10000	0	-10000	0	0
PIK3CA	0.009	0.034	-10000	0	-0.58	2	2
HGF/MET/SHIP2	-0.01	0.1	-10000	0	-0.33	58	58
MAP3K5	0.003	0.1	-10000	0	-0.41	16	16
HGF/MET/CIN85/CBL/ENDOPHILINS	-0.001	0.095	-10000	0	-0.32	40	40
AP1	-0.011	0.095	-10000	0	-0.34	45	45
mol:SU11274	0	0	-10000	0	-10000	0	0
SHC1	0.011	0	-10000	0	-10000	0	0
apoptosis	-0.023	0.16	-10000	0	-0.74	29	29
STAT3 (dimer)	0.011	0.076	-10000	0	-0.41	1	1
GAB1/CRKL/SHP2/PI3K	-0.017	0.066	-10000	0	-0.69	3	3
INPP5D	-0.018	0.13	-10000	0	-0.58	30	30
CBL/CRK	0.019	0.062	-10000	0	-0.45	1	1
PTPN11	0.007	0.054	-10000	0	-0.58	5	5
GO:0007205	0	0	-10000	0	-10000	0	0
PLCG1	0.01	0.024	-10000	0	-0.58	1	1
PTEN	0.006	0.059	-10000	0	-0.58	6	6
ELK1	-0.001	0.025	0.23	2	-0.32	2	4
mol:SU5416	0	0	-10000	0	-10000	0	0
SHP2/GRB2/SOS1GAB1	-0.014	0.046	-10000	0	-0.36	3	3
PAK1	0.009	0.035	0.34	6	-0.28	1	7
HGF/MET/RANBP10	-0.01	0.1	-10000	0	-0.33	57	57
HRAS	0.004	0.097	-10000	0	-1.1	1	1
DOCK1	0.018	0.063	-10000	0	-0.53	1	1
GAB1	0.008	0.065	-10000	0	-0.28	2	2
CRK	0.013	0.064	-10000	0	-0.37	2	2
mol:PHA665752	0	0	-10000	0	-10000	0	0
mol:GDP	-0.009	0.13	-10000	0	-0.49	39	39
JUN	0.007	0.052	-10000	0	-0.56	5	5
EntrezGene:200958	0	0	-10000	0	-10000	0	0
HGF/MET	-0.005	0.058	-10000	0	-0.21	40	40
PIK3R1	0.008	0.042	-10000	0	-0.58	3	3
cell morphogenesis	0.028	0.092	-10000	0	-0.59	4	4
GRB2/SHC	0.009	0.052	-10000	0	-0.24	2	2
FOS	-0.026	0.14	-10000	0	-0.54	41	41
GLMN	-0.008	0.046	-10000	0	-0.27	18	18
cell motility	-0.001	0.025	0.23	2	-0.32	2	4
HGF/MET/MUC20	-0.017	0.1	-10000	0	-0.33	57	57
cell migration	0.009	0.051	-10000	0	-0.24	2	2
GRB2	0.011	0	-10000	0	-10000	0	0
CBL	0.011	0	-10000	0	-10000	0	0
MET/RANBP10	0.016	0.022	-10000	0	-0.37	2	2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP	0.006	0.077	-10000	0	-10000	0	0
MET/MUC20	0.007	0.022	-10000	0	-0.38	2	2
RAP1B	0.023	0.059	-10000	0	-0.34	1	1
RAP1A	0.023	0.06	-10000	0	-0.34	1	1
HGF/MET/RANBP9	-0.01	0.11	-10000	0	-0.36	39	39
RAF1	0.01	0.091	-10000	0	-1	1	1
STAT3	0.01	0.077	-10000	0	-0.42	1	1
cell proliferation	0.014	0.098	-10000	0	-0.34	40	40
RPS6KB1	-0.001	0.043	-10000	0	-0.33	5	5
MAPK3	-0.004	0.03	0.67	1	-0.24	1	2
MAPK1	-0.004	0.03	0.67	1	-0.24	1	2
RANBP9	0.01	0.024	-10000	0	-0.58	1	1
MAPK8	0.019	0.09	-10000	0	-0.36	15	15
SRC	0.011	0.075	-10000	0	-0.54	1	1
PI3K	0.007	0.063	-10000	0	-0.39	5	5
MET/Glomulin	0.003	0.042	-10000	0	-0.22	20	20
SOS1	0.01	0.024	-10000	0	-0.58	1	1
MAP2K1	0.014	0.09	-10000	0	-1.1	1	1
MET	0.01	0.031	-10000	0	-0.52	2	2
MAP4K1	-0.002	0.1	-10000	0	-0.43	15	15
PTK2	0.01	0.024	-10000	0	-0.58	1	1
MAP2K2	0.015	0.087	-10000	0	-0.7	2	2
BAD	0.008	0.042	0.34	6	-0.58	1	7
MAP2K4	0.008	0.096	-10000	0	-0.38	14	14
SHP2/GRB2/SOS1/GAB1	-0.017	0.057	-10000	0	-0.47	3	3
INPPL1	0.01	0.024	-10000	0	-0.58	1	1
PXN	0.011	0	-10000	0	-10000	0	0
SH3KBP1	0.01	0.024	-10000	0	-0.58	1	1
HGS	0.001	0.055	-10000	0	-0.25	3	3
PLCgamma1/PKC	0.008	0.018	-10000	0	-0.43	1	1
HGF	-0.039	0.16	-10000	0	-0.55	55	55
RASA1	0.009	0.034	-10000	0	-0.58	2	2
NCK1	0.009	0.034	-10000	0	-0.58	2	2
PTPRJ	0.01	0.024	-10000	0	-0.58	1	1
NCK/PLCgamma1	0.008	0.063	-10000	0	-0.36	3	3
PDPK1	-0.003	0.042	0.41	6	-10000	0	6
HGF/MET/SHIP	-0.028	0.13	-10000	0	-0.34	85	85

×

Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.011	0	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	-0.017	0.093	-9999	-0.5	19	19
MDM2/SUMO1	0.004	0.11	-9999	-0.58	19	19
HDAC4	0.011	0.019	-9999	-0.46	1	1
Ran/GTP/Exportin 1/HDAC1	-0.017	0.092	-9999	-0.5	19	19
SUMO1	-0.007	0.1	-9999	-0.58	19	19
NPC/RanGAP1/SUMO1	-0.004	0.095	-9999	-0.44	24	24
mol:GTP	0	0	-9999	-10000	0	0
XPO1	0	0.12	-9999	-0.74	15	15
EntrezGene:23636	0	0	-9999	-10000	0	0
RAN	0.011	0	-9999	-10000	0	0
EntrezGene:8021	0	0	-9999	-10000	0	0
RANBP2	-0.007	0.1	-9999	-0.58	19	19
SUMO1/HDAC4	0.005	0.1	-9999	-0.55	19	19
SUMO1/HDAC1	0.006	0.1	-9999	-0.55	19	19
RANGAP1	0.01	0.031	-9999	-0.52	2	2
MDM2/SUMO1/SUMO1	0.016	0.072	-9999	-0.35	19	19
NPC/RanGAP1/SUMO1/RanBP2/Ubc9	0	0.095	-9999	-0.43	24	24
Ran/GTP	0.006	0.087	-9999	-0.39	24	24
EntrezGene:23225	0	0	-9999	-10000	0	0
MDM2	0.008	0.043	-9999	-0.52	4	4
UBE2I	0.011	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.006	0.12	-9999	-0.69	15	15
NPC	-0.003	0.056	-9999	-0.31	19	19
PIAS2	0.01	0.027	-9999	-0.46	2	2
PIAS1	0.011	0	-9999	-10000	0	0
EntrezGene:9972	0	0	-9999	-10000	0	0

×

Insulin Pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CBL/APS/CAP	-0.029	0.084	-9999	-0.48	5	5
TC10/GTP	-0.022	0.071	-9999	-0.48	2	2
Insulin Receptor/Insulin/IRS1/Shp2	0.014	0.063	-9999	-0.34	18	18
HRAS	0.008	0.041	-9999	-0.49	4	4
APS homodimer	-0.015	0.12	-9999	-0.52	30	30
GRB14	-0.12	0.24	-9999	-0.54	144	144
FOXO3	0.002	0.057	-9999	-0.67	3	3
AKT1	-0.031	0.12	-9999	-0.42	3	3
INSR	0.011	0.034	-9999	-0.58	2	2
Insulin Receptor/Insulin	0.027	0.035	-9999	-0.6	1	1
mol:GTP	0	0	-9999	-10000	0	0
GRB10	0.007	0.048	-9999	-0.58	4	4
SORBS1	-0.013	0.11	-9999	-0.52	28	28
CRK	0.011	0.019	-9999	-0.46	1	1
PTPN1	0.024	0.035	-9999	-0.59	1	1
CAV1	0.007	0.068	-9999	-0.33	18	18
CBL/APS/CAP/Crk-II/C3G	0.006	0.088	-9999	-0.31	28	28
Insulin Receptor/Insulin/IRS1/NCK2	0.016	0.056	-9999	-0.34	14	14
mol:GDP	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.009	0.051	-9999	-0.3	15	15
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B	0.025	0.048	-9999	-0.46	3	3
RPS6KB1	-0.025	0.12	-9999	-0.47	4	4
PARD6A	0.006	0.051	-9999	-0.5	6	6
CBL	0.011	0	-9999	-10000	0	0
tumor necrosis factor-mediated signaling pathway	0	0	-9999	-10000	0	0
DOK1	0.001	0.008	-9999	-10000	0	0
PIK3R1	0.008	0.042	-9999	-0.58	3	3
Insulin Receptor/Insuli/IRS1/GRB2/Shc	-0.055	0.094	-9999	-0.46	4	4
HRAS/GTP	-0.019	0.069	-9999	-0.47	3	3
Insulin Receptor	0.011	0.034	-9999	-0.58	2	2
Insulin Receptor/Insuli/IRS1/GRB2/SHC	0.022	0.051	-9999	-0.32	10	10
PRKCI	-0.019	0.054	-9999	-0.59	4	4
Insulin Receptor/Insulin/GRB14/PDK1	-0.064	0.11	-9999	-0.45	3	3
SHC1	0.011	0	-9999	-10000	0	0
negative regulation of MAPKKK cascade	0.02	0.027	-9999	-10000	0	0
PI3K	-0.009	0.052	-9999	-0.3	15	15
NCK2	0.01	0.024	-9999	-0.58	1	1
RHOQ	0.011	0	-9999	-10000	0	0
mol:H2O2	0	0.004	-9999	-10000	0	0
HRAS/GDP	0.006	0.029	-9999	-0.35	4	4
AKT2	-0.031	0.12	-9999	-0.41	5	5
PRKCZ	-0.017	0.041	-9999	-0.78	1	1
SH2B2	-0.015	0.12	-9999	-0.52	30	30
SHC/SHIP	0.005	0.084	-9999	-0.3	39	39
F2RL2	-0.036	0.16	-9999	-0.56	50	50
TRIP10	0.01	0.024	-9999	-0.58	1	1
Insulin Receptor/Insulin/Shc	0.015	0.026	-9999	-0.31	3	3
TC10/GTP/CIP4/Exocyst	0.015	0.015	-9999	-0.36	1	1
Insulin Receptor/Insulin/SHC/GRB2/Sos1	0.027	0.028	-9999	-0.3	1	1
RAPGEF1	0.01	0.024	-9999	-0.58	1	1
RASA1	0.009	0.034	-9999	-0.58	2	2
NCK1	0.009	0.034	-9999	-0.58	2	2
CBL/APS/CAP/Crk-II	0	0.093	-9999	-0.34	27	27
TC10/GDP	0.009	0	-9999	-10000	0	0
Insulin Receptor/Insulin/SHC/GRB10	0.02	0.039	-9999	-0.32	7	7
INPP5D	-0.002	0.088	-9999	-0.32	42	42
SOS1	0.01	0.024	-9999	-0.58	1	1
SGK1	-0.012	0.068	-9999	-0.93	3	3
mol:cAMP	0	0	-9999	-10000	0	0
PTPN11	0.007	0.054	-9999	-0.58	5	5
IRS1	0.002	0.076	-9999	-0.58	10	10
p62DOK/RasGAP	0.02	0.028	-9999	-10000	0	0
INS	0	0.035	-9999	-0.5	3	3
mol:PI-3-4-P2	-0.002	0.088	-9999	-0.32	42	42
GRB2	0.011	0	-9999	-10000	0	0
EIF4EBP1	-0.024	0.12	-9999	-0.45	5	5
PTPRA	0.012	0.003	-9999	-10000	0	0
PIK3CA	0.009	0.034	-9999	-0.58	2	2
TC10/GTP/CIP4	0.015	0.015	-9999	-0.36	1	1
PDPK1	0.011	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos	0.021	0.045	-9999	-0.26	14	14
Insulin Receptor/Insulin/IRS1	0.009	0.054	-9999	-0.35	13	13
Insulin Receptor/Insulin/IRS3	0.008	0.036	-9999	-0.38	5	5
Par3/Par6	-0.002	0.094	-9999	-0.31	44	44

×

Aurora B 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Condensin I complex	0.017	0.087	-9999	-0.47	15	15
STMN1	0.009	0.07	-9999	-0.43	15	15
Aurora B/RasGAP/Survivin	0.025	0.031	-9999	-0.48	2	2
Chromosomal passenger complex/Cul3 protein complex	-0.012	0.079	-9999	-0.22	34	34
BIRC5	0.012	0.019	-9999	-0.46	1	1
DES	-0.11	0.2	-9999	-0.55	98	98
Aurora C/Aurora B/INCENP	0.013	0.063	-9999	-0.3	23	23
Aurora B/TACC1	0.012	0.047	-9999	-0.35	10	10
Aurora B/PP2A	0.019	0.004	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CBX5	0.013	0.012	-9999	-0.28	1	1
mitotic metaphase/anaphase transition	0	0.001	-9999	-10000	0	0
NDC80	0.01	0.068	-9999	-0.43	14	14
Cul3 protein complex	-0.057	0.14	-9999	-0.3	152	152
KIF2C	0.02	0.02	-9999	-0.42	1	1
PEBP1	0.012	0	-9999	-10000	0	0
KIF20A	0.009	0.034	-9999	-0.59	2	2
mol:GDP	0	0	-9999	-10000	0	0
Aurora B/RasGAP	0.018	0.026	-9999	-0.43	2	2
SEPT1	-0.008	0.1	-9999	-0.53	22	22
SMC2	0.003	0.072	-9999	-0.58	9	9
SMC4	-0.003	0.093	-9999	-0.58	15	15
NSUN2/NPM1/Nucleolin	0.024	0.03	-9999	-0.28	3	3
PSMA3	0.011	0	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	0	0.001	-9999	-10000	0	0
H3F3B	0.016	0.002	-9999	-10000	0	0
AURKB	0.015	0.006	-9999	-10000	0	0
AURKC	-0.01	0.11	-9999	-0.55	23	23
CDCA8	0.012	0.001	-9999	-10000	0	0
cytokinesis	0.014	0.038	-9999	-10000	0	0
Aurora B/Septin1	0.006	0.057	-9999	-0.36	2	2
AURKA	0.011	0.001	-9999	-10000	0	0
INCENP	0.012	0.001	-9999	-10000	0	0
KLHL13	-0.12	0.22	-9999	-0.5	151	151
BUB1	0.01	0.024	-9999	-0.59	1	1
hSgo1/Aurora B/Survivin	0.022	0.035	-9999	-0.32	6	6
EVI5	0.005	0.064	-9999	-0.59	7	7
RhoA/GTP	-0.001	0.018	-9999	-0.34	1	1
SGOL1	0.006	0.054	-9999	-0.58	5	5
CENPA	0.023	0.02	-9999	-0.25	3	3
NCAPG	0.008	0.042	-9999	-0.58	3	3
Aurora B/HC8 Proteasome	0.019	0.004	-9999	-10000	0	0
NCAPD2	0.011	0	-9999	-10000	0	0
Aurora B/PP1-gamma	0.019	0.019	-9999	-0.43	1	1
RHOA	0.01	0.024	-9999	-0.58	1	1
NCAPH	0.01	0.024	-9999	-0.58	1	1
NPM1	0.012	0.053	-9999	-0.48	7	7
RASA1	0.009	0.034	-9999	-0.58	2	2
KLHL9	0.01	0.024	-9999	-0.58	1	1
mitotic prometaphase	0.001	0.001	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.019	0.004	-9999	-10000	0	0
PPP1CC	0.01	0.024	-9999	-0.58	1	1
Centraspindlin	0.028	0.02	-9999	-10000	0	0
RhoA/GDP	0.008	0.018	-9999	-0.43	1	1
NSUN2	0.017	0.003	-9999	-10000	0	0
MYLK	-0.005	0.073	-9999	-0.24	49	49
KIF23	0.012	0.001	-9999	-10000	0	0
VIM	0.014	0.051	-9999	-0.38	10	10
RACGAP1	0.012	0.001	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
NCL	0.017	0.003	-9999	-10000	0	0
Chromosomal passenger complex	0.029	0.016	-9999	-0.21	2	2
Chromosomal passenger complex/EVI5	0.022	0.051	-9999	-0.3	7	7
TACC1	0.002	0.073	-9999	-0.56	10	10
PPP2R5D	0.011	0	-9999	-10000	0	0
CUL3	0.009	0.034	-9999	-0.58	2	2
response to DNA damage stimulus	0	0	-9999	-10000	0	0

×

BARD1 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BARD1/CSTF1	0.012	0.047	-10000	0	-0.42	7	7
ATM	0.003	0.072	-10000	0	-0.58	9	9
UBE2D3	0.011	0	-10000	0	-10000	0	0
PRKDC	0.009	0.039	-10000	0	-0.54	3	3
ATR	0.009	0.034	-10000	0	-0.58	2	2
UBE2L3	0.011	0	-10000	0	-10000	0	0
FANCD2	0.014	0.064	-10000	0	-0.44	10	10
protein ubiquitination	0.02	0.062	-10000	0	-0.33	16	16
XRCC5	0.01	0.024	-10000	0	-0.58	1	1
XRCC6	0.011	0	-10000	0	-10000	0	0
M/R/N Complex	0.008	0.09	-10000	0	-0.46	19	19
MRE11A	0.004	0.068	-10000	0	-0.58	8	8
DNA-PK	0.021	0.035	-10000	0	-0.43	3	3
FA complex/FANCD2/Ubiquitin	0.035	0.058	-10000	0	-0.62	3	3
FANCF	0.006	0.059	-10000	0	-0.58	6	6
BRCA1	0.01	0.024	-10000	0	-0.58	1	1
CCNE1	0.009	0.033	-10000	0	-0.46	3	3
CDK2/Cyclin E1	0.015	0.03	-10000	0	-0.34	4	4
FANCG	0.011	0.019	-10000	0	-0.46	1	1
BRCA1/BACH1/BARD1	0.011	0.05	-10000	0	-0.42	8	8
FANCE	0.011	0	-10000	0	-10000	0	0
FANCC	0.011	0	-10000	0	-10000	0	0
NBN	-0.004	0.096	-10000	0	-0.58	16	16
FANCA	0.011	0	-10000	0	-10000	0	0
DNA repair	0.049	0.066	-10000	0	-0.58	4	4
BRCA1/BARD1/ubiquitin	0.011	0.05	-10000	0	-0.42	8	8
BARD1/DNA-PK	0.023	0.049	-10000	0	-0.35	9	9
FANCL	0.008	0.042	-10000	0	-0.58	3	3
mRNA polyadenylation	-0.012	0.047	0.42	7	-10000	0	7
BRCA1/BARD1/CTIP/M/R/N Complex	0.006	0.15	-10000	0	-0.74	18	18
BRCA1/BACH1/BARD1/TopBP1	0.018	0.046	-10000	0	-0.36	9	9
BRCA1/BARD1/P53	-0.009	0.12	-10000	0	-0.33	64	64
BARD1/CSTF1/BRCA1	0.018	0.043	-10000	0	-0.36	8	8
BRCA1/BACH1	0.01	0.024	-10000	0	-0.58	1	1
BARD1	0.005	0.064	-10000	0	-0.58	7	7
PCNA	0.011	0	-10000	0	-10000	0	0
BRCA1/BARD1/UbcH5C	0.018	0.043	-10000	0	-0.36	8	8
BRCA1/BARD1/UbcH7	0.018	0.043	-10000	0	-0.36	8	8
BRCA1/BARD1/RAD51/PCNA	0.025	0.04	-10000	0	-0.32	8	8
BARD1/DNA-PK/P53	-0.002	0.11	-10000	0	-0.31	64	64
BRCA1/BARD1/Ubiquitin	0.011	0.05	-10000	0	-0.42	8	8
BRCA1/BARD1/CTIP	0.01	0.097	-10000	0	-0.42	25	25
FA complex	0.028	0.052	-10000	0	-1	1	1
BARD1/EWS	0.012	0.047	-10000	0	-0.42	7	7
RBBP8	0.001	0.1	-10000	0	-0.54	19	19
TP53	-0.045	0.17	-10000	0	-0.58	57	57
TOPBP1	0.01	0.024	-10000	0	-0.58	1	1
G1/S transition of mitotic cell cycle	0.009	0.11	0.33	64	-10000	0	64
BRCA1/BARD1	0.023	0.063	-10000	0	-0.33	16	16
CSTF1	0.011	0	-10000	0	-10000	0	0
BARD1/EWS-Fli1	0.003	0.047	-10000	0	-0.43	7	7
CDK2	0.01	0.024	-10000	0	-0.58	1	1
UniProt:Q9BZD1	0	0	-10000	0	-10000	0	0
RAD51	0.011	0	-10000	0	-10000	0	0
RAD50	0.01	0.024	-10000	0	-0.58	1	1
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme	0.011	0.05	-10000	0	-0.42	8	8
EWSR1	0.011	0	-10000	0	-10000	0	0

×

Paxillin-dependent events mediated by a4b1

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.011	0	-9999	-10000	0	0
Rac1/GDP	0.003	0.012	-9999	-10000	0	0
DOCK1	0.01	0.024	-9999	-0.58	1	1
ITGA4	-0.019	0.13	-9999	-0.57	32	32
RAC1	0.011	0	-9999	-10000	0	0
alpha4/beta7 Integrin	-0.024	0.14	-9999	-0.44	55	55
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.011	0.019	-9999	-0.46	1	1
alpha4/beta1 Integrin	0.004	0.083	-9999	-0.36	28	28
alpha4/beta7 Integrin/Paxillin	-0.005	0.11	-9999	-0.37	41	41
lamellipodium assembly	-0.003	0.051	-9999	-0.5	5	5
PIK3CA	0.009	0.034	-9999	-0.58	2	2
PI3K	0.013	0.04	-9999	-0.43	5	5
ARF6	0.01	0.024	-9999	-0.58	1	1
TLN1	0.01	0.024	-9999	-0.58	1	1
PXN	0.019	0	-9999	-10000	0	0
PIK3R1	0.008	0.042	-9999	-0.58	3	3
ARF6/GTP	-0.014	0.059	-9999	-10000	0	0
cell adhesion	0.016	0.072	-9999	-10000	0	0
CRKL/CBL	0.017	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin	0.011	0.075	-9999	-0.32	28	28
ITGB1	0.011	0	-9999	-10000	0	0
ITGB7	-0.016	0.12	-9999	-0.53	30	30
ARF6/GDP	0.002	0.026	-9999	-0.58	1	1
alpha4/beta1 Integrin/Paxillin/VCAM1	0	0.12	-9999	-0.42	40	40
p130Cas/Crk/Dock1	0.02	0.037	-9999	-0.37	5	5
VCAM1	-0.022	0.13	-9999	-0.53	37	37
alpha4/beta1 Integrin/Paxillin/Talin	0.017	0.072	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/GIT1	0.017	0.072	-9999	-10000	0	0
BCAR1	0.008	0.043	-9999	-0.52	4	4
mol:GDP	-0.016	0.072	-9999	-10000	0	0
CBL	0.011	0	-9999	-10000	0	0
PRKACA	0.011	0	-9999	-10000	0	0
GIT1	0.01	0.024	-9999	-0.58	1	1
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton	0.017	0.072	-9999	-10000	0	0
Rac1/GTP	-0.003	0.058	-9999	-0.57	5	5

×

TCGA08_rtk_signaling

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
PDGFRA	-0.011	0.11	-10000	0	-0.57	23	23
HRAS	0.008	0.041	-10000	0	-0.49	4	4
EGFR	0.005	0.058	-10000	0	-0.53	7	7
AKT	0.017	0.079	-10000	0	-0.34	21	21
FOXO3	0.011	0	-10000	0	-10000	0	0
AKT1	0.01	0.024	-10000	0	-0.58	1	1
FOXO1	0.009	0.034	-10000	0	-0.58	2	2
AKT3	-0.013	0.11	-10000	0	-0.52	28	28
FOXO4	0.01	0.024	-10000	0	-0.58	1	1
MET	0.01	0.031	-10000	0	-0.52	2	2
PIK3CA	0.009	0.034	-10000	0	-0.58	2	2
PIK3CB	0.008	0.046	-10000	0	-0.55	4	4
NRAS	0.002	0.076	-10000	0	-0.58	10	10
PIK3CG	-0.044	0.17	-10000	0	-0.56	59	59
PIK3R3	0.008	0.042	-10000	0	-0.58	3	3
PIK3R2	0.01	0.024	-10000	0	-0.58	1	1
NF1	0.008	0.042	-10000	0	-0.58	3	3
RAS	0.008	0.054	0.21	1	-0.32	7	8
ERBB2	0	0.072	-10000	0	-0.47	14	14
proliferation/survival/translation	-0.019	0.046	0.25	8	-0.14	3	11
PI3K	0.01	0.062	0.18	2	-0.25	19	21
PIK3R1	0.008	0.042	-10000	0	-0.58	3	3
KRAS	0.006	0.057	-10000	0	-0.56	6	6
FOXO	0.036	0.026	0.16	2	-10000	0	2
AKT2	0.009	0.036	-10000	0	-0.5	3	3
PTEN	0.006	0.059	-10000	0	-0.58	6	6

×

Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization	0.021	0.036	-10000	0	-0.26	10	10
epithelial cell differentiation	0.023	0.023	-10000	0	-0.3	3	3
CYFIP2	0.001	0.08	-10000	0	-0.58	11	11
ENAH	0.037	0.067	-10000	0	-0.43	6	6
EGFR	0.005	0.058	-10000	0	-0.53	7	7
EPHA2	0.006	0.055	-10000	0	-0.54	6	6
MYO6	0.029	0.022	-10000	0	-0.28	3	3
CTNNB1	0.011	0	-10000	0	-10000	0	0
ABI1/Sra1/Nap1	0.015	0.06	-10000	0	-0.38	13	13
AQP5	-0.038	0.1	-10000	0	-0.47	26	26
CTNND1	0.011	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.028	0.025	-10000	0	-0.28	4	4
regulation of calcium-dependent cell-cell adhesion	-0.003	0.093	-10000	0	-0.28	47	47
EGF	-0.18	0.25	-10000	0	-0.51	222	222
NCKAP1	0.009	0.034	-10000	0	-0.58	2	2
AQP3	-0.022	0.066	-10000	0	-0.47	8	8
cortical microtubule organization	0.023	0.023	-10000	0	-0.3	3	3
GO:0000145	0.026	0.024	-10000	0	-0.26	4	4
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.026	0.023	-10000	0	-0.3	3	3
MLLT4	0.009	0.034	-10000	0	-0.58	2	2
ARF6/GDP	-0.005	0.039	-10000	0	-0.49	2	2
ARF6	0.01	0.024	-10000	0	-0.58	1	1
Ephrin A1/EPHA2/NCK1/GIT1	0.024	0.045	-10000	0	-0.37	6	6
mol:Ca2+	0	0	-10000	0	-10000	0	0
VASP	0.036	0.025	-10000	0	-10000	0	0
PVRL2	0.01	0.031	-10000	0	-0.52	2	2
ZYX	0.028	0.025	-10000	0	-0.28	4	4
ARF6/GTP	0.027	0.047	-10000	0	-0.39	6	6
CDH1	0.01	0.024	-10000	0	-0.58	1	1
EGFR/EGFR/EGF/EGF	-0.085	0.11	-10000	0	-0.48	1	1
RhoA/GDP	-0.002	0.023	-10000	0	-0.28	4	4
actin cytoskeleton organization	0.032	0.027	-10000	0	-10000	0	0
IGF-1R heterotetramer	0.01	0.024	-10000	0	-0.58	1	1
GIT1	0.01	0.024	-10000	0	-0.58	1	1
IGF1R	0.01	0.024	-10000	0	-0.58	1	1
IGF1	-0.075	0.2	-10000	0	-0.52	97	97
DIAPH1	-0.013	0.091	-10000	0	-0.62	13	13
Wnt receptor signaling pathway	-0.023	0.023	0.3	3	-10000	0	3
RHOA	0.01	0.024	-10000	0	-0.58	1	1
RhoA/GTP	-0.005	0.038	-10000	0	-0.49	2	2
CTNNA1	0.009	0.034	-10000	0	-0.58	2	2
VCL	0.032	0.027	-10000	0	-10000	0	0
EFNA1	0.011	0.019	-10000	0	-0.46	1	1
LPP	0.033	0.026	-10000	0	-10000	0	0
Ephrin A1/EPHA2	-0.004	0.031	-10000	0	-10000	0	0
SEC6/SEC8	-0.003	0.025	-10000	0	-10000	0	0
MGAT3	-0.003	0.095	-10000	0	-0.29	47	47
HGF/MET	-0.024	0.074	-10000	0	-10000	0	0
HGF	-0.039	0.16	-10000	0	-0.55	55	55
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN	0.021	0.036	-10000	0	-0.26	10	10
actin cable formation	0.052	0.057	-10000	0	-0.35	5	5
KIAA1543	0.031	0.034	-10000	0	-10000	0	0
KIFC3	0.024	0.043	-10000	0	-0.28	10	10
NCK1	0.009	0.034	-10000	0	-0.58	2	2
EXOC3	0.011	0	-10000	0	-10000	0	0
ACTN1	0.029	0.022	-10000	0	-0.28	3	3
NCK1/GIT1	0.015	0.031	-10000	0	-0.42	3	3
mol:GDP	0.023	0.023	-10000	0	-0.3	3	3
EXOC4	0.011	0	-10000	0	-10000	0	0
STX4	0.029	0.022	-10000	0	-0.28	3	3
PIP5K1C	0.028	0.025	-10000	0	-0.28	4	4
LIMA1	0.005	0.064	-10000	0	-0.58	7	7
ABI1	0.01	0.024	-10000	0	-0.58	1	1
ROCK1	0.039	0.059	-10000	0	-0.48	4	4
adherens junction assembly	0.037	0.068	-10000	0	-0.44	7	7
IGF-1R heterotetramer/IGF1	-0.039	0.09	-10000	0	-0.56	1	1
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.014	0.034	-10000	0	-0.4	4	4
MET	0.01	0.031	-10000	0	-0.52	2	2
PLEKHA7	0.028	0.025	-10000	0	-0.28	4	4
mol:GTP	0.023	0.045	-10000	0	-0.37	6	6
establishment of epithelial cell apical/basal polarity	0.046	0.029	-10000	0	-10000	0	0
cortical actin cytoskeleton stabilization	0.021	0.036	-10000	0	-0.26	10	10
regulation of cell-cell adhesion	0.032	0.027	-10000	0	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton	0.021	0.036	-10000	0	-0.26	10	10

×

p38 MAPK signaling pathway

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
TRAF6/ASK1	0.01	0.027	-10000	0	-0.44	2	2
TRAF2/ASK1	0.014	0.027	-10000	0	-0.36	3	3
ATM	0.003	0.072	-10000	0	-0.58	9	9
MAP2K3	0.013	0.095	-10000	0	-0.59	12	12
response to stress	0	0	-10000	0	-10000	0	0
MAP2K6	0.016	0.092	-10000	0	-0.54	12	12
hyperosmotic response	0	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
GADD45G	-0.003	0.083	-10000	0	-0.46	19	19
TXN	0.007	0	-10000	0	-10000	0	0
CALM1	0.011	0	-10000	0	-10000	0	0
GADD45A	0.009	0.034	-10000	0	-0.58	2	2
GADD45B	0.008	0.038	-10000	0	-0.46	4	4
MAP3K1	0.006	0.059	-10000	0	-0.58	6	6
MAP3K6	0.005	0.064	-10000	0	-0.58	7	7
MAP3K7	0.011	0	-10000	0	-10000	0	0
MAP3K4	0.011	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
ASK1/ASK2	0.01	0.053	-10000	0	-0.42	9	9
TAK1/TAB family	0.003	0.021	0.18	3	-10000	0	3
RAC1/OSM/MEKK3	0.02	0.031	-10000	0	-0.4	3	3
TRAF2	0.01	0.024	-10000	0	-0.58	1	1
RAC1/OSM/MEKK3/MKK3	-0.012	0.068	-10000	0	-0.48	11	11
TRAF6	0.007	0.015	-10000	0	-0.36	1	1
RAC1	0.011	0	-10000	0	-10000	0	0
mol:LPS	0	0	-10000	0	-10000	0	0
CAMK2B	-0.056	0.17	-10000	0	-0.5	79	79
CCM2	0.01	0.031	-10000	0	-0.52	2	2
CaM/Ca2+/CAMKIIB	-0.026	0.11	-10000	0	-0.3	79	79
MAPK11	-0.002	0.079	-10000	0	-0.48	16	16
response to DNA damage stimulus	0	0	-10000	0	-10000	0	0
CaM/Ca2+/CAMKIIB/ASK1	-0.017	0.099	-10000	0	-0.27	80	80
OSM/MEKK3	0.014	0.038	-10000	0	-0.51	3	3
TAOK1	0.003	0.077	-10000	0	-0.46	14	14
TAOK2	0.008	0.047	-10000	0	-0.35	10	10
TAOK3	0.009	0.044	-10000	0	-0.35	9	9
MAP3K7IP1	0	0	-10000	0	-10000	0	0
MAPK14	0.011	0	-10000	0	-10000	0	0
MAP3K7IP2	0	0	-10000	0	-10000	0	0
MAP3K5	0.009	0.034	-10000	0	-0.58	2	2
MAP3K10	0.007	0.05	-10000	0	-0.53	5	5
MAP3K3	0.009	0.034	-10000	0	-0.58	2	2
TRX/ASK1	0.013	0.021	-10000	0	-0.36	2	2
GADD45/MTK1/MTK1	0.017	0.053	-10000	0	-0.38	3	3

×

VEGFR1 specific signals

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer	0.017	0.079	-9999	-0.48	13	13
VEGFR1 homodimer/NRP1	0.008	0.078	-9999	-0.48	13	13
mol:DAG	0.015	0.089	-9999	-0.64	7	7
VEGFR1 homodimer/NRP1/VEGFR 121	0.015	0.074	-9999	-0.44	13	13
CaM/Ca2+	0.02	0.084	-9999	-0.61	7	7
HIF1A	0.007	0.081	-9999	-0.54	12	12
GAB1	0.011	0	-9999	-10000	0	0
AKT1	0.03	0.094	-9999	-0.62	10	10
PLCG1	0.015	0.089	-9999	-0.65	7	7
NOS3	0.026	0.11	-9999	-0.59	11	11
CBL	0.011	0	-9999	-10000	0	0
mol:NO	0.026	0.1	-9999	-0.56	11	11
FLT1	0.013	0.09	-9999	-0.55	13	13
PGF	-0.001	0.078	-9999	-0.47	16	16
VEGFR1 homodimer/NRP2/VEGFR121	0.009	0.098	-9999	-0.79	4	4
CALM1	0.011	0	-9999	-10000	0	0
PIK3CA	0.009	0.034	-9999	-0.58	2	2
eNOS/Hsp90	0.031	0.1	-9999	-0.59	10	10
endothelial cell proliferation	0.003	0.12	-9999	-0.73	7	7
mol:Ca2+	0.015	0.088	-9999	-0.64	7	7
MAPK3	0.024	0.081	-9999	-0.56	7	7
MAPK1	0.024	0.081	-9999	-0.56	7	7
PIK3R1	0.008	0.042	-9999	-0.58	3	3
PLGF homodimer	-0.001	0.078	-9999	-0.47	16	16
PRKACA	0.011	0	-9999	-10000	0	0
RP11-342D11.1	0	0	-9999	-10000	0	0
CAV1	-0.002	0.082	-9999	-0.5	16	16
VEGFA homodimer	0.011	0.019	-9999	-0.46	1	1
VEGFR1 homodimer/VEGFA homodimer	0.016	0.079	-9999	-0.48	13	13
platelet activating factor biosynthetic process	0.028	0.08	-9999	-0.54	7	7
PI3K	0.02	0.098	-9999	-0.68	9	9
PRKCA	0.019	0.084	-9999	-0.6	7	7
PRKCB	-0.009	0.13	-9999	-0.6	10	10
VEGFR1 homodimer/PLGF homodimer	0.009	0.094	-9999	-0.49	15	15
VEGFA	0.011	0.019	-9999	-0.46	1	1
VEGFB	0.011	0	-9999	-10000	0	0
mol:IP3	0.015	0.089	-9999	-0.64	7	7
RASA1	0.021	0.077	-9999	-0.63	6	6
NRP2	-0.012	0.11	-9999	-0.5	28	28
VEGFR1 homodimer	0.013	0.089	-9999	-0.55	13	13
VEGFB homodimer	0.011	0	-9999	-10000	0	0
NCK1	0.009	0.034	-9999	-0.58	2	2
eNOS/Caveolin-1	0.026	0.11	-9999	-0.57	11	11
PTPN11	0.007	0.054	-9999	-0.58	5	5
mol:PI-3-4-5-P3	0.019	0.096	-9999	-0.66	9	9
mol:L-citrulline	0.026	0.1	-9999	-0.56	11	11
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP	0.014	0.12	-9999	-0.68	12	12
VEGFR1 homodimer/VEGFA homodimer/NCK1	0.021	0.081	-9999	-0.69	6	6
CD2AP	-0.016	0.12	-9999	-0.58	28	28
PI3K/GAB1	0.025	0.093	-9999	-0.64	9	9
PDPK1	0.023	0.091	-9999	-0.63	9	9
VEGFR1 homodimer/VEGFA homodimer/SHP2	0.02	0.09	-9999	-0.72	7	7
mol:NADP	0.026	0.1	-9999	-0.56	11	11
HSP90AA1	0.01	0.024	-9999	-0.58	1	1
ubiquitin-dependent protein catabolic process	0.013	0.12	-9999	-0.67	12	12
VEGFR1 homodimer/NRP2	0.002	0.1	-9999	-0.44	22	22

×

Rapid glucocorticoid signaling

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
Gs family/GDP/Gbeta gamma	0.001	0.076	-10000	0	-0.33	19	19
MAPK9	0.007	0	-10000	0	-10000	0	0
adrenocorticotropin secretion	-0.001	0.019	-10000	0	-0.32	2	2
GNB1/GNG2	0.01	0.042	-10000	0	-0.33	9	9
GNB1	0.011	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	0.007	0	-10000	0	-10000	0	0
Gs family/GTP	-0.009	0.067	-10000	0	-0.28	34	34
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	0.004	0.017	0.075	34	-10000	0	34
GNAL	-0.018	0.12	-10000	0	-0.51	34	34
GNG2	0.003	0.067	-10000	0	-0.54	9	9
CRH	-0.001	0.026	-10000	0	-0.46	2	2
mol:cortisol	0	0	-10000	0	-10000	0	0
MAPK8	0.007	0.015	-10000	0	-0.36	1	1
MAPK11	0.001	0.039	-10000	0	-0.22	16	16

×

Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaV beta3 Integrin	-0.004	0.095	-9999	-0.42	30	30
AKT1	0.054	0.088	-9999	-0.54	9	9
PTK2B	0.023	0.096	-9999	-0.65	6	6
VEGFR2 homodimer/Frs2	0.022	0.078	-9999	-0.66	6	6
CAV1	-0.002	0.082	-9999	-0.5	16	16
CALM1	0.011	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2	0.029	0.076	-9999	-0.78	4	4
endothelial cell proliferation	0.045	0.098	-9999	-0.51	8	8
mol:Ca2+	0.035	0.073	-9999	-0.67	4	4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac	0.035	0.073	-9999	-0.74	4	4
RP11-342D11.1	0.028	0.072	-9999	-0.67	4	4
CDH5	0.006	0.054	-9999	-0.49	7	7
VEGFA homodimer	0.024	0.054	-9999	-0.39	9	9
SHC1	0.011	0	-9999	-10000	0	0
SHC2	-0.041	0.16	-9999	-0.54	58	58
HRAS/GDP	-0.01	0.061	-9999	-0.53	6	6
SH2D2A	0.011	0.019	-9999	-0.46	1	1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS	-0.017	0.078	-9999	-0.59	5	5
VEGFR2 homodimer/VEGFA homodimer/TsAd	0.03	0.068	-9999	-0.7	4	4
VEGFR1 homodimer	0.007	0.052	-9999	-0.56	5	5
SHC/GRB2/SOS1	-0.009	0.064	-9999	-0.62	5	5
GRB10	0.033	0.088	-9999	-0.68	7	7
PTPN11	0.007	0.054	-9999	-0.58	5	5
GRB2	0.011	0	-9999	-10000	0	0
PAK1	0.011	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin	0.036	0.083	-9999	-0.64	7	7
HRAS	0.008	0.041	-9999	-0.49	4	4
VEGF/Rho/ROCK1/Integrin Complex	0.018	0.12	-9999	-0.78	10	10
HIF1A	0.003	0.072	-9999	-0.58	9	9
FRS2	0.009	0.034	-9999	-0.58	2	2
oxygen and reactive oxygen species metabolic process	0.033	0.072	-9999	-0.72	4	4
mol:GTP	0	0	-9999	-10000	0	0
FLT4	-0.006	0.095	-9999	-0.53	19	19
Nck/Pak	0.016	0.025	-9999	-0.42	2	2
VEGFR2 homodimer/VEGFA homodimer/Fyn	0.027	0.077	-9999	-0.66	5	5
mol:GDP	-0.009	0.062	-9999	-0.6	5	5
mol:NADP	0.042	0.087	-9999	-0.4	17	17
eNOS/Hsp90	0.045	0.084	-9999	-0.48	5	5
PIK3R1	0.008	0.042	-9999	-0.58	3	3
mol:IP3	0.035	0.074	-9999	-0.68	4	4
HIF1A/ARNT	0.01	0.06	-9999	-0.46	9	9
SHB	0.011	0.019	-9999	-0.46	1	1
VEGFA	0.012	0.02	-9999	-0.45	1	1
VEGFC	-0.013	0.12	-9999	-0.55	27	27
FAK1/Vinculin	0.036	0.11	-9999	-0.68	10	10
mol:Ca ++	0	0	-9999	-10000	0	0
RHOA	0.01	0.024	-9999	-0.58	1	1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.02	0.1	-9999	-0.69	6	6
PTPN6	0.011	0	-9999	-10000	0	0
EPAS1	0.015	0.042	-9999	-0.4	5	5
mol:L-citrulline	0.042	0.087	-9999	-0.4	17	17
ITGAV	0.002	0.076	-9999	-0.58	10	10
PIK3CA	0.009	0.034	-9999	-0.58	2	2
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2	0.035	0.072	-9999	-0.74	4	4
VEGFR2 homodimer/VEGFA homodimer	0.032	0.078	-9999	-0.74	4	4
VEGFR2/3 heterodimer	0.013	0.1	-9999	-0.52	17	17
VEGFB	0.011	0	-9999	-10000	0	0
MAPK11	0.034	0.084	-9999	-0.61	7	7
VEGFR2 homodimer	0.021	0.078	-9999	-0.61	8	8
FLT1	0.007	0.052	-9999	-0.56	5	5
NEDD4	0.009	0.048	-9999	-0.58	4	4
MAPK3	0.027	0.076	-9999	-0.52	6	6
MAPK1	0.027	0.076	-9999	-0.52	6	6
VEGFA145/NRP2	0	0.08	-9999	-0.35	29	29
VEGFR1/2 heterodimer	0.02	0.079	-9999	-0.54	10	10
KDR	0.021	0.079	-9999	-0.62	8	8
VEGFA165/NRP1/VEGFR2 homodimer	0.024	0.096	-9999	-0.64	7	7
SRC	0.01	0.024	-9999	-0.58	1	1
platelet activating factor biosynthetic process	0.029	0.078	-9999	-0.63	4	4
PI3K	0.045	0.097	-9999	-0.64	8	8
VEGFR2 homodimer/VEGFA homodimer/NCK1	0.029	0.07	-9999	-0.7	4	4
FES	0.029	0.087	-9999	-0.67	5	5
GAB1	-0.011	0.07	-9999	-0.66	5	5
VEGFR2 homodimer/VEGFA homodimer/Src	0.03	0.069	-9999	-0.7	4	4
CTNNB1	0.011	0	-9999	-10000	0	0
SOS1	0.01	0.024	-9999	-0.58	1	1
ARNT	0.01	0.024	-9999	-0.58	1	1
eNOS/Caveolin-1	0.04	0.093	-9999	-0.39	18	18
VEGFR2 homodimer/VEGFA homodimer/Yes	0.026	0.082	-9999	-0.78	4	4
PI3K/GAB1	0.056	0.086	-9999	-0.58	7	7
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak	0.038	0.074	-9999	-0.68	5	5
PRKACA	0.011	0	-9999	-10000	0	0
VEGFR2/3 heterodimer/VEGFC homodimer	0.005	0.13	-9999	-0.68	13	13
HSP90AA1	0.01	0.024	-9999	-0.58	1	1
CDC42	0.033	0.086	-9999	-0.72	5	5
actin cytoskeleton reorganization	0.029	0.068	-9999	-0.7	4	4
PTK2	0.031	0.12	-9999	-0.71	10	10
EDG1	0.028	0.072	-9999	-0.67	4	4
mol:DAG	0.035	0.074	-9999	-0.68	4	4
CaM/Ca2+	0.037	0.068	-9999	-0.62	4	4
MAP2K3	0.039	0.074	-9999	-0.63	5	5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4	0.035	0.091	-9999	-0.7	7	7
PLCG1	0.035	0.075	-9999	-0.69	4	4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb	0.035	0.067	-9999	-0.67	4	4
IQGAP1	0.009	0.039	-9999	-0.54	3	3
YES1	0.005	0.064	-9999	-0.58	7	7
VEGFR2 homodimer/VEGFA homodimer/SHP2	0.028	0.079	-9999	-0.78	4	4
VEGFR2 homodimer/VEGFA homodimer/SHP1	0.03	0.068	-9999	-0.7	4	4
cell migration	0.053	0.098	-9999	-0.64	7	7
mol:PI-3-4-5-P3	0.044	0.09	-9999	-0.58	8	8
FYN	0.005	0.06	-9999	-0.55	7	7
VEGFB/NRP1	0.033	0.068	-9999	-0.63	4	4
mol:NO	0.042	0.087	-9999	-0.4	17	17
PXN	0.011	0	-9999	-10000	0	0
HRAS/GTP	-0.01	0.061	-9999	-0.53	6	6
VEGFR2 homodimer/VEGFA homodimer/GRB10	0.035	0.091	-9999	-0.7	7	7
VHL	0.01	0.024	-9999	-0.58	1	1
ITGB3	-0.008	0.1	-9999	-0.55	21	21
NOS3	0.042	0.097	-9999	-0.46	17	17
VEGFR2 homodimer/VEGFA homodimer/Sck	0	0.11	-9999	-0.67	5	5
RAC1	0.011	0	-9999	-10000	0	0
PRKCA	0.038	0.071	-9999	-0.63	4	4
PRKCB	0.011	0.11	-9999	-0.59	7	7
VCL	0.009	0.034	-9999	-0.58	2	2
VEGFA165/NRP1	0.029	0.072	-9999	-0.67	4	4
VEGFR1/2 heterodimer/VEGFA homodimer	0.028	0.076	-9999	-0.63	6	6
VEGFA165/NRP2	0	0.08	-9999	-0.35	29	29
MAPKKK cascade	0.05	0.081	-9999	-0.54	9	9
NRP2	-0.012	0.11	-9999	-0.5	28	28
VEGFC homodimer	-0.013	0.12	-9999	-0.55	27	27
NCK1	0.009	0.034	-9999	-0.58	2	2
ROCK1	0.001	0.08	-9999	-0.58	11	11
FAK1/Paxillin	0.037	0.11	-9999	-0.64	10	10
MAP3K13	0.035	0.077	-9999	-0.67	5	5
PDPK1	0.048	0.081	-9999	-0.51	8	8

×

Canonical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FBXW11	0.014	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.055	0.057	-9999	-0.38	3	3
ERC1	0.009	0.033	-9999	-0.46	3	3
RIP2/NOD2	0	0.082	-9999	-0.4	24	24
NFKBIA	0.036	0.014	-9999	-10000	0	0
BIRC2	-0.001	0.086	-9999	-0.58	13	13
IKBKB	0.011	0.019	-9999	-0.46	1	1
RIPK2	0.011	0	-9999	-10000	0	0
IKBKG	0.021	0.071	-9999	-0.46	5	5
IKK complex/A20	0.021	0.088	-9999	-0.48	5	5
NEMO/A20/RIP2	0.011	0	-9999	-10000	0	0
XPO1	0.001	0.08	-9999	-0.58	11	11
NEMO/ATM	0.022	0.09	-9999	-0.53	11	11
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
RAN	0.011	0	-9999	-10000	0	0
Exportin 1/RanGTP	0.009	0.051	-9999	-0.36	11	11
IKK complex/ELKS	-0.015	0.064	-9999	-0.52	5	5
BCL10/MALT1/TRAF6	0.017	0.061	-9999	-0.5	7	7
NOD2	-0.011	0.11	-9999	-0.56	24	24
NFKB1	0.013	0.024	-9999	-0.58	1	1
RELA	0.014	0	-9999	-10000	0	0
MALT1	0.007	0.054	-9999	-0.58	5	5
cIAP1/UbcH5C	0.008	0.064	-9999	-0.42	13	13
ATM	0.003	0.072	-9999	-0.58	9	9
TNF/TNFR1A	-0.004	0.09	-9999	-0.39	31	31
TRAF6	0.01	0.024	-9999	-0.58	1	1
PRKCA	0.01	0.031	-9999	-0.52	2	2
CHUK	0.007	0.048	-9999	-0.58	4	4
UBE2D3	0.011	0	-9999	-10000	0	0
TNF	-0.017	0.12	-9999	-0.54	31	31
NF kappa B1 p50/RelA	0.032	0.015	-9999	-0.34	1	1
BCL10	0.007	0.048	-9999	-0.58	4	4
proteasomal ubiquitin-dependent protein catabolic process	0.036	0.014	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.014	0	-9999	-10000	0	0
TNFRSF1A	0.011	0	-9999	-10000	0	0
IKK complex	0.029	0.078	-9999	-0.56	5	5
CYLD	0.01	0.024	-9999	-0.58	1	1
IKK complex/PKC alpha	0.032	0.076	-9999	-0.59	4	4

×

Aurora A signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Aurora A/GADD45A	0.02	0.025	-9999	-0.36	2	2
BIRC5	0.011	0.019	-9999	-0.46	1	1
NFKBIA	0.023	0.013	-9999	-10000	0	0
CPEB1	-0.054	0.18	-9999	-0.54	70	70
AKT1	0.022	0.02	-9999	-0.36	1	1
NDEL1	0.011	0	-9999	-10000	0	0
Aurora A/BRCA1	0.019	0.023	-9999	-0.5	1	1
NDEL1/TACC3	0.025	0.014	-9999	-10000	0	0
GADD45A	0.009	0.034	-9999	-0.58	2	2
GSK3B	0.009	0.033	-9999	-0.56	2	2
PAK1/Aurora A	0.021	0.013	-9999	-10000	0	0
MDM2	0.008	0.043	-9999	-0.52	4	4
JUB	0.011	0	-9999	-10000	0	0
TPX2	0.017	0.025	-9999	-0.42	2	2
TP53	-0.01	0.11	-9999	-0.33	58	58
DLG7	0.015	0.013	-9999	-0.2	2	2
AURKAIP1	0.01	0.031	-9999	-0.52	2	2
ARHGEF7	0.011	0	-9999	-10000	0	0
G2 phase of mitotic cell cycle	0	0	-9999	-10000	0	0
Aurora A/NDEL1/TACC3	0.027	0.015	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	0.018	0.022	-9999	-0.49	1	1
AURKA	0.019	0.016	-9999	-0.24	2	2
AURKB	0.012	0.018	-9999	-0.24	3	3
CDC25B	0.023	0.015	-9999	-10000	0	0
G2/M transition checkpoint	0.019	0.011	-9999	-10000	0	0
mRNA polyadenylation	-0.02	0.1	-9999	-0.29	70	70
Aurora A/CPEB	-0.021	0.1	-9999	-0.29	70	70
Aurora A/TACC1/TRAP/chTOG	0.028	0.043	-9999	-0.32	8	8
BRCA1	0.01	0.024	-9999	-0.58	1	1
centrosome duplication	0.021	0.013	-9999	-10000	0	0
regulation of centrosome cycle	0.024	0.014	-9999	-10000	0	0
spindle assembly	0.027	0.043	-9999	-0.31	8	8
TDRD7	0.011	0	-9999	-10000	0	0
Aurora A/RasGAP/Survivin	0.029	0.032	-9999	-0.41	3	3
CENPA	0.014	0.032	-9999	-0.42	3	3
Aurora A/PP2A	0.021	0.013	-9999	-10000	0	0
meiosis	0	0	-9999	-10000	0	0
protein catabolic process	0.013	0.049	-9999	-0.57	1	1
negative regulation of DNA binding	-0.01	0.11	-9999	-0.33	58	58
prophase	0	0	-9999	-10000	0	0
GIT1/beta-PIX	0.016	0.018	-9999	-0.42	1	1
RASA1	0.009	0.034	-9999	-0.58	2	2
Ajuba/Aurora A	0.019	0.011	-9999	-10000	0	0
mitotic prometaphase	0	0.002	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.018	0.016	-9999	-0.24	2	2
TACC1	0.002	0.073	-9999	-0.56	10	10
TACC3	0.011	0.019	-9999	-0.46	1	1
Aurora A/Antizyme1	0.026	0.021	-9999	-0.32	1	1
Aurora A/RasGAP	0.02	0.025	-9999	-0.36	2	2
OAZ1	0.011	0	-9999	-10000	0	0
RAN	0.011	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
PRKACA	0.011	0.004	-9999	-10000	0	0
GIT1	0.01	0.024	-9999	-0.58	1	1
GIT1/beta-PIX/PAK1	0.023	0.015	-9999	-0.36	1	1
Importin alpha/Importin beta/TPX2	0.017	0.025	-9999	-0.42	2	2
PPP2R5D	0.011	0	-9999	-10000	0	0
Aurora A/TPX2	0.026	0.021	-9999	-0.29	2	2
PAK1	0.011	0	-9999	-10000	0	0
CKAP5	0.011	0	-9999	-10000	0	0

×

Arf6 downstream pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLAUR	0.025	0.071	-10000	0	-1.1	2	2
regulation of axonogenesis	-0.02	0.045	0.6	2	-10000	0	2
myoblast fusion	-0.016	0.036	0.4	3	-10000	0	3
mol:GTP	0.007	0.024	-10000	0	-0.3	3	3
regulation of calcium-dependent cell-cell adhesion	0.005	0.1	0.29	65	-10000	0	65
ARF1/GTP	-0.002	0.021	-10000	0	-0.32	2	2
mol:GM1	0.007	0.019	-10000	0	-0.23	3	3
mol:Choline	0.02	0.035	-10000	0	-0.43	3	3
lamellipodium assembly	0.006	0.045	-10000	0	-0.45	3	3
MAPK3	0.019	0.032	-10000	0	-0.34	4	4
ARF6/GTP/NME1/Tiam1	-0.005	0.1	-10000	0	-0.29	65	65
ARF1	0.011	0.019	-10000	0	-0.46	1	1
ARF6/GDP	0.016	0.037	-10000	0	-0.41	3	3
ARF1/GDP	0.025	0.036	-10000	0	-0.37	3	3
ARF6	0.01	0.029	-10000	0	-0.68	1	1
RAB11A	0.011	0	-10000	0	-10000	0	0
TIAM1	-0.042	0.16	-10000	0	-0.52	63	63
fibronectin binding	0	0	-10000	0	-10000	0	0
MAPK1	0.019	0.032	-10000	0	-0.34	4	4
actin filament bundle formation	-0.016	0.039	0.47	3	-10000	0	3
KALRN	0.002	0.044	-10000	0	-0.33	8	8
RAB11FIP3/RAB11A	0.016	0.022	-10000	0	-0.37	2	2
RhoA/GDP	0.017	0.039	-10000	0	-0.47	3	3
NME1	0.012	0.019	-10000	0	-0.45	1	1
Rac1/GDP	0.017	0.031	-10000	0	-0.37	3	3
substrate adhesion-dependent cell spreading	0.007	0.024	-10000	0	-0.3	3	3
cortical actin cytoskeleton organization	0.006	0.045	-10000	0	-0.46	3	3
RAC1	0.011	0	-10000	0	-10000	0	0
liver development	0.007	0.024	-10000	0	-0.3	3	3
ARF6/GTP	0.007	0.024	-10000	0	-0.3	3	3
RhoA/GTP	-0.002	0.03	-10000	0	-0.69	1	1
mol:GDP	0.005	0.041	-10000	0	-0.41	3	3
ARF6/GTP/RAB11FIP3/RAB11A	0.018	0.025	-10000	0	-0.29	3	3
RHOA	0.01	0.024	-10000	0	-0.58	1	1
PLD1	0.014	0.039	-10000	0	-0.49	3	3
RAB11FIP3	0.01	0.031	-10000	0	-0.52	2	2
tube morphogenesis	0.006	0.045	-10000	0	-0.45	3	3
ruffle organization	0.02	0.045	-10000	0	-0.6	2	2
regulation of epithelial cell migration	0.007	0.024	-10000	0	-0.3	3	3
PLD2	0.016	0.019	-10000	0	-0.34	1	1
PIP5K1A	0.02	0.046	-10000	0	-0.61	2	2
mol:Phosphatidic acid	0.02	0.035	-10000	0	-0.43	3	3
Rac1/GTP	0.006	0.045	-10000	0	-0.46	3	3

×

Aurora C signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
INCENP	0.011	0	-9999	-10000	0	0
Aurora C/Aurora B/INCENP	0.01	0.062	-9999	-0.3	23	23
metaphase	0	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
H3F3B	-0.003	0.017	-9999	-10000	0	0
AURKB	0.011	0	-9999	-10000	0	0
AURKC	-0.01	0.11	-9999	-0.55	23	23

×

EPO signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.041	0.082	-9999	-0.45	2	2
CRKL	0.02	0.068	-9999	-0.45	3	3
mol:DAG	0.026	0.062	-9999	-0.39	2	2
HRAS	0.036	0.065	-9999	-0.42	4	4
MAPK8	0.019	0.049	-9999	-0.34	5	5
RAP1A	0.02	0.071	-9999	-0.48	4	4
GAB1	0.02	0.068	-9999	-0.45	3	3
MAPK14	0.019	0.047	-9999	-0.34	4	4
EPO	0.001	0.054	-9999	-0.46	8	8
PLCG1	0.026	0.063	-9999	-0.4	2	2
EPOR/TRPC2/IP3 Receptors	0.003	0.068	-9999	-0.49	11	11
RAPGEF1	0.01	0.024	-9999	-0.58	1	1
EPO/EPOR (dimer)/SOCS3	0.005	0.077	-9999	-0.37	16	16
GAB1/SHC/GRB2/SOS1	-0.013	0.052	-9999	-0.45	3	3
EPO/EPOR (dimer)	0.006	0.065	-9999	-0.35	18	18
IRS2	0.016	0.076	-9999	-0.43	4	4
STAT1	0.029	0.08	-9999	-0.49	4	4
STAT5B	0.029	0.066	-9999	-0.39	3	3
cell proliferation	0.024	0.046	-9999	-0.36	2	2
GAB1/SHIP/PIK3R1/SHP2/SHC	-0.026	0.082	-9999	-0.51	8	8
TEC	0.02	0.068	-9999	-0.45	3	3
SOCS3	-0.002	0.082	-9999	-0.5	16	16
STAT1 (dimer)	0.029	0.078	-9999	-0.47	4	4
JAK2	-0.007	0.1	-9999	-0.55	21	21
PIK3R1	0.008	0.042	-9999	-0.58	3	3
EPO/EPOR (dimer)/JAK2	0.026	0.074	-9999	-0.48	3	3
EPO/EPOR	0.006	0.065	-9999	-0.35	18	18
LYN	0.013	0.003	-9999	-10000	0	0
TEC/VAV2	0.013	0.092	-9999	-0.49	4	4
elevation of cytosolic calcium ion concentration	0.003	0.068	-9999	-0.49	11	11
SHC1	0.011	0	-9999	-10000	0	0
EPO/EPOR (dimer)/LYN	0.019	0.054	-9999	-0.37	5	5
mol:IP3	0.026	0.062	-9999	-0.39	2	2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP	0.01	0.099	-9999	-0.52	5	5
SH2B3	0.011	0.007	-9999	-10000	0	0
NFKB1	0.019	0.049	-9999	-0.34	5	5
EPO/EPOR (dimer)/JAK2/SOCS3	-0.016	0.061	-9999	-0.29	21	21
PTPN6	0.014	0.07	-9999	-0.48	3	3
TEC/VAV2/GRB2	0.018	0.089	-9999	-0.47	4	4
EPOR	0.003	0.068	-9999	-0.5	11	11
INPP5D	-0.018	0.13	-9999	-0.58	30	30
mol:GDP	-0.013	0.053	-9999	-0.46	3	3
SOS1	0.01	0.024	-9999	-0.58	1	1
PLCG2	-0.01	0.11	-9999	-0.55	23	23
CRKL/CBL/C3G	0.031	0.066	-9999	-0.47	2	2
VAV2	0.006	0.094	-9999	-0.45	6	6
CBL	0.02	0.068	-9999	-0.45	3	3
SHC/Grb2/SOS1	-0.014	0.055	-9999	-0.48	3	3
STAT5A	0.029	0.066	-9999	-0.39	3	3
GRB2	0.011	0	-9999	-10000	0	0
STAT5 (dimer)	0.041	0.08	-9999	-0.47	2	2
LYN/PLCgamma2	0.002	0.079	-9999	-0.39	23	23
PTPN11	0.007	0.054	-9999	-0.58	5	5
BTK	-0.003	0.11	-9999	-0.44	13	13
BCL2	0.026	0.16	-9999	-0.88	14	14

×

Signaling events mediated by HDAC Class I

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
NF kappa B/RelA	-0.016	0.069	-10000	0	-0.35	22	22
Ran/GTP/Exportin 1/HDAC1	-0.013	0.075	-10000	0	-0.4	19	19
NF kappa B1 p50/RelA/I kappa B alpha	0.023	0.071	-10000	0	-0.32	22	22
SUMO1	-0.007	0.1	-10000	0	-0.58	19	19
ZFPM1	-0.003	0.084	-10000	0	-0.5	17	17
NPC/RanGAP1/SUMO1/Ubc9	0	0.095	-10000	0	-0.43	24	24
FKBP3	-0.002	0.09	-10000	0	-0.58	14	14
Histones	0.03	0.038	-10000	0	-10000	0	0
YY1/LSF	0.016	0.059	-10000	0	-0.28	21	21
SMG5	0.01	0.024	-10000	0	-0.58	1	1
RAN	0.011	0	-10000	0	-10000	0	0
I kappa B alpha/HDAC3	0.015	0.058	-10000	0	-0.27	21	21
I kappa B alpha/HDAC1	0.018	0.042	-10000	0	-10000	0	0
SAP18	0.011	0.019	-10000	0	-0.46	1	1
RELA	0.018	0.057	-10000	0	-0.24	25	25
HDAC1/Smad7	0.022	0.022	-10000	0	-0.36	2	2
RANGAP1	0.01	0.031	-10000	0	-0.52	2	2
HDAC3/TR2	0.017	0.044	-10000	0	-0.32	1	1
NuRD/MBD3 Complex	0.036	0.032	-10000	0	-0.38	2	2
NF kappa B1 p50/RelA	0.021	0.056	-10000	0	-0.52	1	1
EntrezGene:23225	0	0	-10000	0	-10000	0	0
GATA2	-0.021	0.13	-10000	0	-0.56	34	34
GATA1	-0.004	0.072	-10000	0	-0.46	15	15
Mad/Max	0.015	0.026	-10000	0	-0.35	3	3
NuRD/MBD3 Complex/GATA1/Fog1	0.037	0.05	-10000	0	-0.41	4	4
RBBP7	0.009	0.034	-10000	0	-0.58	2	2
NPC	-0.003	0.056	-10000	0	-0.31	19	19
RBBP4	0.01	0.024	-10000	0	-0.58	1	1
MAX	0.011	0	-10000	0	-10000	0	0
EntrezGene:9972	0	0	-10000	0	-10000	0	0
FBXW11	0.011	0	-10000	0	-10000	0	0
NFKBIA	0.013	0.047	-10000	0	-10000	0	0
KAT2B	-0.005	0.098	-10000	0	-0.58	17	17
mol:GTP	0	0	-10000	0	-10000	0	0
SIN3/HDAC complex	0.033	0.026	-10000	0	-10000	0	0
SIN3 complex	0.027	0.03	-10000	0	-0.32	4	4
SMURF1	0.011	0	-10000	0	-10000	0	0
CHD3	0.009	0.034	-10000	0	-0.58	2	2
SAP30	0.009	0.034	-10000	0	-0.58	2	2
EntrezGene:23636	0	0	-10000	0	-10000	0	0
NCOR1	0.01	0.024	-10000	0	-0.58	1	1
YY1/HDAC3	0.019	0.059	-10000	0	-0.54	1	1
YY1/HDAC2	0.017	0.053	-10000	0	-0.26	20	20
YY1/HDAC1	0.017	0.053	-10000	0	-0.26	20	20
NuRD/MBD2 Complex (MeCP1)	0.036	0.03	-10000	0	-0.37	1	1
PPARG	0.011	0.081	-10000	0	-0.32	30	30
HDAC8/hEST1B	0.023	0.015	-10000	0	-0.36	1	1
UBE2I	0.011	0	-10000	0	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.011	0	-10000	0	-10000	0	0
TNFRSF1A	0.011	0	-10000	0	-10000	0	0
HDAC3/SMRT (N-CoR2)	0.016	0.049	-10000	0	-0.32	3	3
MBD3L2	-0.001	0.019	-10000	0	-0.46	1	1
ubiquitin-dependent protein catabolic process	0.022	0.022	-10000	0	-0.36	2	2
CREBBP	0.011	0	-10000	0	-10000	0	0
NuRD/MBD3/MBD3L2 Complex	0.038	0.033	-10000	0	-0.37	2	2
HDAC1	0.011	0	-10000	0	-10000	0	0
HDAC3	0.013	0.047	-10000	0	-10000	0	0
HDAC2	0.011	0	-10000	0	-10000	0	0
YY1	0.014	0.062	-10000	0	-0.31	20	20
HDAC8	0.011	0	-10000	0	-10000	0	0
SMAD7	0.009	0.034	-10000	0	-0.58	2	2
NCOR2	0.008	0.046	-10000	0	-0.55	4	4
MXD1	0.009	0.036	-10000	0	-0.5	3	3
STAT3	0.019	0.03	-10000	0	-0.34	4	4
NFKB1	0.01	0.024	-10000	0	-0.58	1	1
EntrezGene:8021	0	0	-10000	0	-10000	0	0
RANBP2	-0.007	0.1	-10000	0	-0.58	19	19
YY1/LSF/HDAC1	0.022	0.055	-10000	0	-0.47	3	3
YY1/SAP30/HDAC1	0.022	0.053	-10000	0	-0.4	3	3
EP300	0.007	0.048	-10000	0	-0.58	4	4
STAT3 (dimer non-phopshorylated)	0.019	0.03	-10000	0	-0.34	4	4
proteasomal ubiquitin-dependent protein catabolic process	0.013	0.046	-10000	0	-10000	0	0
histone deacetylation	0.035	0.03	-10000	0	-0.36	1	1
STAT3 (dimer non-phopshorylated)/HDAC3	0.024	0.044	-10000	0	-10000	0	0
nuclear export	-0.022	0.015	0.36	1	-10000	0	1
PRKACA	0.011	0	-10000	0	-10000	0	0
GATAD2B	0.011	0	-10000	0	-10000	0	0
GATAD2A	0.01	0.024	-10000	0	-0.58	1	1
GATA2/HDAC3	0	0.087	-10000	0	-0.33	28	28
GATA1/HDAC1	0.006	0.052	-10000	0	-0.32	15	15
GATA1/HDAC3	0.003	0.057	-10000	0	-0.35	2	2
CHD4	0.011	0	-10000	0	-10000	0	0
TNF-alpha/TNFR1A	-0.004	0.09	-10000	0	-0.39	31	31
SIN3/HDAC complex/Mad/Max	0.036	0.027	-10000	0	-0.37	1	1
NuRD Complex	0.041	0.039	-10000	0	-0.36	3	3
positive regulation of chromatin silencing	0.029	0.037	-10000	0	-10000	0	0
SIN3B	0.01	0.024	-10000	0	-0.58	1	1
MTA2	0.011	0	-10000	0	-10000	0	0
SIN3A	0.01	0.024	-10000	0	-0.58	1	1
XPO1	0.001	0.08	-10000	0	-0.58	11	11
SUMO1/HDAC1	0.006	0.1	-10000	0	-0.55	19	19
HDAC complex	0.028	0.024	-10000	0	-0.32	3	3
GATA1/Fog1	-0.004	0.08	-10000	0	-0.35	31	31
FKBP25/HDAC1/HDAC2	0.015	0.057	-10000	0	-0.36	14	14
TNF	-0.017	0.12	-10000	0	-0.54	31	31
negative regulation of cell growth	0.036	0.027	-10000	0	-0.36	1	1
NuRD/MBD2/PRMT5 Complex	0.036	0.03	-10000	0	-0.37	1	1
Ran/GTP/Exportin 1	0.007	0.12	-10000	0	-0.69	15	15
NF kappa B/RelA/I kappa B alpha	0.018	0.071	-10000	0	-0.33	21	21
SIN3/HDAC complex/NCoR1	0.034	0.025	-10000	0	-10000	0	0
TFCP2	0.009	0.034	-10000	0	-0.58	2	2
NR2C1	0.01	0.024	-10000	0	-0.58	1	1
MBD3	0.008	0.046	-10000	0	-0.55	4	4
MBD2	0.007	0.054	-10000	0	-0.58	5	5

×

TRAIL signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TNFSF10	0.007	0.054	-9999	-0.58	5	5
positive regulation of NF-kappaB transcription factor activity	0.011	0.05	-9999	-0.37	10	10
MAP2K4	0.033	0.038	-9999	-0.28	3	3
IKBKB	0.011	0.019	-9999	-0.46	1	1
TNFRSF10B	0.01	0.024	-9999	-0.58	1	1
TNFRSF10A	0.011	0	-9999	-10000	0	0
SMPD1	0.013	0.03	-9999	-0.25	7	7
IKBKG	0.01	0.024	-9999	-0.58	1	1
mol:GTP	0	0	-9999	-10000	0	0
TNFRSF10D	0.008	0.042	-9999	-0.46	5	5
TRAIL/TRAILR2	0.013	0.044	-9999	-0.42	6	6
TRAIL/TRAILR3	-0.005	0.09	-9999	-0.36	36	36
TRAIL/TRAILR1	0.013	0.04	-9999	-0.42	5	5
TRAIL/TRAILR4	0.011	0.05	-9999	-0.37	10	10
TRAIL/TRAILR1/DAP3/GTP	0.019	0.031	-9999	-0.32	5	5
IKK complex	-0.005	0.038	-9999	-0.4	5	5
RIPK1	0.011	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
DAP3/GTP	0.009	0	-9999	-10000	0	0
MAPK3	0.014	0.044	-9999	-0.42	6	6
MAP3K1	0.03	0.032	-9999	-0.25	6	6
TRAILR4 (trimer)	0.008	0.042	-9999	-0.46	5	5
TRADD	0.011	0	-9999	-10000	0	0
TRAILR1 (trimer)	0.011	0	-9999	-10000	0	0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2	0.028	0.028	-9999	-0.25	6	6
CFLAR	0.011	0	-9999	-10000	0	0
MAPK1	0.014	0.044	-9999	-0.42	6	6
TRAIL/TRAILR1/FADD/TRADD/RIP	0.031	0.03	-9999	-0.29	5	5
mol:ceramide	0.013	0.03	-9999	-0.24	8	8
FADD	0.011	0	-9999	-10000	0	0
MAPK8	0.037	0.04	-9999	-0.39	1	1
TRAF2	0.01	0.024	-9999	-0.58	1	1
TRAILR3 (trimer)	-0.014	0.11	-9999	-0.49	31	31
CHUK	0.007	0.048	-9999	-0.58	4	4
TRAIL/TRAILR1/FADD	0.02	0.034	-9999	-0.36	5	5
DAP3	0.011	0	-9999	-10000	0	0
CASP10	-0.002	0.039	-9999	-0.35	6	6
JNK cascade	0.011	0.05	-9999	-0.37	10	10
TRAIL (trimer)	0.007	0.054	-9999	-0.58	5	5
TNFRSF10C	-0.014	0.11	-9999	-0.49	31	31
TRAIL/TRAILR1/DAP3/GTP/FADD	0.025	0.03	-9999	-0.3	5	5
TRAIL/TRAILR2/FADD	0.02	0.038	-9999	-0.36	6	6
cell death	0.013	0.03	-9999	-0.24	7	7
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2	0.028	0.03	-9999	-0.25	7	7
TRAILR2 (trimer)	0.01	0.024	-9999	-0.58	1	1
CASP8	0	0.035	-9999	-0.8	1	1
negative regulation of caspase activity	0	0	-9999	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP	0.031	0.033	-9999	-0.29	6	6

×

ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K4	0.022	0.073	-10000	0	-0.41	4	4
BAG4	0.008	0.042	-10000	0	-0.58	3	3
BAD	0.018	0.036	-10000	0	-0.4	2	2
NFKBIA	0.011	0	-10000	0	-10000	0	0
BIRC3	-0.016	0.12	-10000	0	-0.53	31	31
BAX	0.019	0.034	-10000	0	-0.52	1	1
EnzymeConsortium:3.1.4.12	0.008	0.019	-10000	0	-0.079	7	7
IKBKB	0.027	0.07	-10000	0	-0.48	2	2
MAP2K2	0.027	0.036	-10000	0	-0.3	3	3
MAP2K1	0.026	0.037	-10000	0	-0.27	4	4
SMPD1	0.012	0.025	-10000	0	-0.24	2	2
GO:0005551	0	0	-10000	0	-10000	0	0
FADD/Caspase 8	0.028	0.068	-10000	0	-0.37	2	2
MAP2K4	0.02	0.048	-10000	0	-0.29	10	10
protein ubiquitination	0.027	0.072	-10000	0	-0.44	4	4
EnzymeConsortium:2.7.1.37	0.029	0.041	-10000	0	-0.26	5	5
response to UV	0	0	-10000	0	-0.002	1	1
RAF1	0.023	0.033	-10000	0	-0.24	3	3
CRADD	0.011	0.024	-10000	0	-0.59	1	1
mol:ceramide	0.014	0.029	-10000	0	-0.17	3	3
I-kappa-B-alpha/RELA/p50/ubiquitin	0.016	0	-10000	0	-10000	0	0
MADD	0.012	0	-10000	0	-10000	0	0
MAP3K1	0.016	0.045	-10000	0	-0.32	7	7
TRADD	0.012	0	-10000	0	-10000	0	0
RELA/p50	0.011	0	-10000	0	-10000	0	0
MAPK3	0.029	0.036	-10000	0	-0.25	4	4
MAPK1	0.029	0.036	-10000	0	-0.25	4	4
p50/RELA/I-kappa-B-alpha	0.017	0	-10000	0	-10000	0	0
FADD	0.022	0.07	-10000	0	-0.36	3	3
KSR1	0.018	0.033	-10000	0	-0.26	3	3
MAPK8	0.024	0.047	-10000	0	-0.28	10	10
TRAF2	0.01	0.024	-10000	0	-0.58	1	1
response to radiation	0	0	-10000	0	-10000	0	0
CHUK	0.025	0.075	-10000	0	-0.51	3	3
TNF R/SODD	0.015	0.031	-10000	0	-0.42	3	3
TNF	-0.017	0.12	-10000	0	-0.54	31	31
CYCS	0.019	0.046	0.13	11	-0.25	8	19
IKBKG	0.026	0.072	-10000	0	-0.51	3	3
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD	0.017	0.073	-10000	0	-0.3	18	18
RELA	0.011	0	-10000	0	-10000	0	0
RIPK1	0.011	0	-10000	0	-10000	0	0
AIFM1	0.022	0.038	0.13	11	-0.36	2	13
TNF/TNF R/SODD	0.004	0.082	-10000	0	-0.33	34	34
TNFRSF1A	0.011	0	-10000	0	-10000	0	0
response to heat	0	0	-10000	0	-10000	0	0
CASP8	0.02	0.031	-10000	0	-0.58	1	1
NSMAF	0.022	0.069	-10000	0	-0.36	3	3
response to hydrogen peroxide	0	0	-10000	0	-0.002	1	1
BCL2	-0.007	0.1	-10000	0	-0.55	20	20

×

HIF-2-alpha transcription factor network

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
MMP14	-0.009	0.064	-10000	0	-0.58	3	3
oxygen homeostasis	0.006	0.014	-10000	0	-10000	0	0
TCEB2	0.005	0.055	-10000	0	-0.47	8	8
TCEB1	0.011	0.019	-10000	0	-0.46	1	1
VHL/Elongin B/Elongin C/HIF2A	-0.015	0.056	-10000	0	-0.46	4	4
EPO	0.078	0.18	-10000	0	-0.6	8	8
FIH (dimer)	0.018	0.012	-10000	0	-10000	0	0
APEX1	0.017	0.014	-10000	0	-10000	0	0
SERPINE1	0.059	0.23	-10000	0	-0.74	15	15
FLT1	-0.014	0.11	-10000	0	-0.89	8	8
ADORA2A	0.072	0.2	-10000	0	-0.73	7	7
germ cell development	0.068	0.21	-10000	0	-0.7	11	11
SLC11A2	0.078	0.19	-10000	0	-0.71	5	5
BHLHE40	0.078	0.19	-10000	0	-0.72	6	6
HIF1AN	0.018	0.012	-10000	0	-10000	0	0
HIF2A/ARNT/SIRT1	0.022	0.12	-10000	0	-0.44	6	6
ETS1	0.015	0.067	-10000	0	-0.5	10	10
CITED2	-0.006	0.066	-10000	0	-1.1	2	2
KDR	-0.014	0.11	-10000	0	-0.9	8	8
PGK1	0.078	0.19	-10000	0	-0.71	5	5
SIRT1	0.007	0.054	-10000	0	-0.58	5	5
response to hypoxia	0	0.001	-10000	0	-10000	0	0
HIF2A/ARNT	0.085	0.22	-10000	0	-0.77	8	8
EPAS1	0.05	0.094	-10000	0	-0.37	5	5
SP1	0.017	0.025	-10000	0	-0.58	1	1
ABCG2	0.047	0.24	-10000	0	-0.79	13	13
EFNA1	0.078	0.19	-10000	0	-0.69	6	6
FXN	0.075	0.19	-10000	0	-0.69	6	6
POU5F1	0.068	0.22	-10000	0	-0.74	11	11
neuron apoptosis	-0.083	0.21	0.74	8	-10000	0	8
EP300	0.007	0.048	-10000	0	-0.58	4	4
EGLN3	0	0.099	-10000	0	-0.53	20	20
EGLN2	0.015	0.038	-10000	0	-0.49	3	3
EGLN1	0.018	0.012	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C	0.018	0.042	-10000	0	-0.31	9	9
VHL	0.01	0.024	-10000	0	-0.58	1	1
ARNT	0.016	0.029	-10000	0	-0.6	1	1
SLC2A1	0.07	0.2	-10000	0	-0.78	6	6
TWIST1	0.049	0.24	-10000	0	-0.72	19	19
ELK1	0.017	0.025	-10000	0	-0.58	1	1
HIF2A/ARNT/Cbp/p300	0.068	0.12	-10000	0	-0.43	4	4
VEGFA	0.078	0.19	-10000	0	-0.71	5	5
CREBBP	0.011	0	-10000	0	-10000	0	0

×

Atypical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL3/RelA	0.015	0.029	-9999	-0.39	3	3
FBXW11	0.011	0	-9999	-10000	0	0
NF kappa B1 p50/c-Rel	0.019	0.033	-9999	-0.34	5	5
NF kappa B1 p50/RelA/I kappa B alpha	0.026	0.048	-9999	-10000	0	0
NFKBIA	0.009	0.051	-9999	-0.22	21	21
MAPK14	0.011	0	-9999	-10000	0	0
NF kappa B1 p105/p50	0.021	0.019	-9999	-0.36	1	1
ARRB2	0.014	0	-9999	-10000	0	0
REL	0.008	0.042	-9999	-0.58	3	3
response to oxidative stress	0	0	-9999	-10000	0	0
BCL3/NF kappa B1 p50	0.02	0.031	-9999	-0.32	5	5
response to UV	0	0	-9999	-10000	0	0
NF kappa B1 p105/RelA	0.021	0.019	-9999	-0.36	1	1
PIK3CA	0.009	0.034	-9999	-0.58	2	2
NF kappa B1 p50 dimer	0.016	0.022	-9999	-0.37	2	2
PIK3R1	0.008	0.042	-9999	-0.58	3	3
NFKB1	0.017	0.023	-9999	-0.37	2	2
RELA	0.011	0	-9999	-10000	0	0
positive regulation of anti-apoptosis	0.014	0.052	-9999	-0.22	21	21
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2	0.029	0.046	-9999	-10000	0	0
SRC	0.01	0.024	-9999	-0.58	1	1
PI3K	0.013	0.04	-9999	-0.43	5	5
NF kappa B1 p50/RelA	0.014	0.052	-9999	-0.22	21	21
IKBKB	0.011	0.019	-9999	-0.46	1	1
beta TrCP1/SCF ubiquitin ligase complex	0.011	0	-9999	-10000	0	0
SYK	0.011	0.019	-9999	-0.46	1	1
I kappa B alpha/PIK3R1	0.014	0.053	-9999	-0.28	4	4
cell death	0.028	0.045	-9999	-10000	0	0
NF kappa B1 p105/c-Rel	0.019	0.033	-9999	-0.34	5	5
LCK	-0.031	0.14	-9999	-0.51	49	49
BCL3	0.009	0.039	-9999	-0.54	3	3

×

E-cadherin signaling in the nascent adherens junction

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	0.033	0.026	-9999	-0.46	1	1
KLHL20	-0.019	0.054	-9999	-0.23	29	29
CYFIP2	0.001	0.08	-9999	-0.58	11	11
Rac1/GDP	0.044	0.04	-9999	-0.49	1	1
ENAH	0.026	0.052	-9999	-0.48	2	2
AP1M1	0.01	0.024	-9999	-0.58	1	1
RAP1B	0.011	0	-9999	-10000	0	0
RAP1A	0.01	0.024	-9999	-0.58	1	1
CTNNB1	0.011	0	-9999	-10000	0	0
CDC42/GTP	-0.004	0.032	-9999	-0.41	2	2
ABI1/Sra1/Nap1	-0.015	0.041	-9999	-0.21	11	11
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin	0.013	0.072	-9999	-0.33	20	20
RAPGEF1	0.04	0.033	-9999	-0.45	2	2
CTNND1	0.011	0	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	0.027	0.026	-9999	-0.48	1	1
CRK	0.037	0.028	-9999	-0.43	1	1
E-cadherin/gamma catenin/alpha catenin	0.021	0.031	-9999	-0.36	4	4
alphaE/beta7 Integrin	-0.003	0.09	-9999	-0.39	30	30
IQGAP1	0.009	0.039	-9999	-0.54	3	3
NCKAP1	0.009	0.034	-9999	-0.58	2	2
Rap1/GTP/I-afadin	0.021	0.024	-9999	-0.32	3	3
DLG1	0.031	0.033	-9999	-0.46	1	1
ChemicalAbstracts:7440-70-2	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.003	0.026	-9999	-0.26	5	5
MLLT4	0.009	0.034	-9999	-0.58	2	2
ARF6/GTP/NME1/Tiam1	-0.01	0.094	-9999	-0.32	32	32
PI3K	-0.004	0.034	-9999	-0.34	5	5
ARF6	0.01	0.024	-9999	-0.58	1	1
mol:Ca2+	0	0	-9999	-10000	0	0
E-cadherin/gamma catenin	0.016	0.025	-9999	-0.42	2	2
TIAM1	-0.044	0.16	-9999	-0.52	63	63
E-cadherin(dimer)/Ca2+	0.026	0.023	-9999	-0.3	3	3
AKT1	-0.003	0.023	-9999	-0.23	4	4
PIK3R1	0.008	0.042	-9999	-0.58	3	3
CDH1	0.01	0.024	-9999	-0.58	1	1
RhoA/GDP	0.043	0.041	-9999	-0.49	1	1
actin cytoskeleton organization	0.017	0.051	-9999	-0.2	7	7
CDC42/GDP	0.041	0.047	-9999	-0.43	2	2
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin	0.019	0.023	-9999	-0.26	4	4
ITGB7	-0.016	0.12	-9999	-0.53	30	30
RAC1	0.011	0	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/p120 catenin	0.028	0.024	-9999	-0.32	3	3
E-cadherin/Ca2+/beta catenin/alpha catenin	0.019	0.023	-9999	-0.31	3	3
mol:GDP	0.041	0.045	-9999	-0.46	2	2
CDC42/GTP/IQGAP1	0.011	0.05	-9999	-0.46	6	6
JUP	0.01	0.024	-9999	-0.58	1	1
p120 catenin/RhoA/GDP	0.035	0.041	-9999	-0.5	1	1
RAC1/GTP/IQGAP1	0.014	0.025	-9999	-0.33	3	3
PIP5K1C/AP1M1	0.016	0.032	-9999	-0.78	1	1
RHOA	0.01	0.024	-9999	-0.58	1	1
CDC42	0.007	0.054	-9999	-0.58	5	5
CTNNA1	0.009	0.034	-9999	-0.58	2	2
positive regulation of S phase of mitotic cell cycle	0.016	0.036	-9999	-0.26	2	2
NME1	0.011	0.019	-9999	-0.46	1	1
clathrin coat assembly	0	0	-9999	-10000	0	0
TJP1	0.032	0.028	-9999	-0.46	1	1
regulation of cell-cell adhesion	-0.004	0.028	-9999	-0.35	2	2
WASF2	-0.007	0.021	-9999	-10000	0	0
Rap1/GTP	-0.003	0.026	-9999	-0.45	1	1
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin	0.017	0.071	-9999	-0.44	1	1
CCND1	0.018	0.044	-9999	-0.33	2	2
VAV2	0.009	0.15	-9999	-0.69	28	28
RAP1/GDP	0.036	0.036	-9999	-0.49	1	1
adherens junction assembly	0.032	0.028	-9999	-0.45	1	1
homophilic cell adhesion	0	0	-9999	-10000	0	0
ABI1	0.01	0.024	-9999	-0.58	1	1
PIP5K1C	0.01	0.024	-9999	-0.58	1	1
regulation of heterotypic cell-cell adhesion	0.022	0.068	-9999	-0.42	1	1
E-cadherin/beta catenin	0	0.022	-9999	-0.36	2	2
mol:GTP	0	0	-9999	-10000	0	0
SRC	0.032	0.028	-9999	-0.46	1	1
PIK3CA	0.009	0.034	-9999	-0.58	2	2
Rac1/GTP	-0.03	0.087	-9999	-0.38	28	28
E-cadherin/beta catenin/alpha catenin	0.022	0.027	-9999	-0.36	3	3
ITGAE	0.011	0.019	-9999	-0.46	1	1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.027	0.027	-9999	-0.49	1	1

×

mTOR signaling 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
GBL	0	0	-10000	0	-10000	0	0
MKNK1	0.011	0	-10000	0	-10000	0	0
mol:PIP3	-0.005	0.051	0.28	5	-0.29	14	19
FRAP1	0.012	0.017	-10000	0	-10000	0	0
AKT1	0.017	0.049	0.22	5	-0.26	15	20
INSR	0.009	0.034	-10000	0	-0.58	2	2
Insulin Receptor/Insulin	0.005	0.031	-10000	0	-0.33	5	5
mol:GTP	-0.006	0.038	-10000	0	-0.55	1	1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit	-0.004	0.026	-10000	0	-0.3	3	3
TSC2	0.01	0.031	-10000	0	-0.52	2	2
RHEB/GDP	-0.005	0.034	-10000	0	-0.49	1	1
TSC1	0.011	0	-10000	0	-10000	0	0
Insulin Receptor/IRS1	0.007	0.05	-10000	0	-0.34	12	12
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA	-0.004	0.03	-10000	0	-0.35	3	3
mol:GDP	0	0	-10000	0	-10000	0	0
EIF3A	0.01	0.024	-10000	0	-0.58	1	1
RPS6KB1	0.017	0.048	-10000	0	-0.4	5	5
MAP3K5	0.007	0.022	-10000	0	-0.38	2	2
PIK3R1	0.009	0.042	-10000	0	-0.58	3	3
apoptosis	0.007	0.022	-10000	0	-0.38	2	2
mol:LY294002	0	0	0.001	1	-0.002	10	11
EIF4B	0.022	0.042	-10000	0	-0.34	5	5
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.022	0.043	-10000	0	-0.34	4	4
eIF4E/eIF4G1/eIF4A1	-0.001	0.016	-10000	0	-0.25	2	2
KIAA1303	0	0	-10000	0	-10000	0	0
PI3K	0.013	0.051	-10000	0	-0.31	15	15
mTOR/RHEB/GTP/Raptor/GBL	0.023	0.024	0.16	5	-0.2	1	6
FKBP1A	0.012	0	-10000	0	-10000	0	0
RHEB/GTP	-0.005	0.033	-10000	0	-0.48	1	1
mol:Amino Acids	0	0	0.001	1	-0.002	10	11
FKBP12/Rapamycin	0.009	0.001	-10000	0	-10000	0	0
PDPK1	-0.004	0.045	0.23	5	-0.26	14	19
EIF4E	0.009	0.039	-10000	0	-0.54	3	3
ASK1/PP5C	0.017	0.039	-10000	0	-0.62	2	2
mTOR/RHEB/GTP/Raptor/GBL/eIF4E	0.012	0.031	-10000	0	-0.51	2	2
TSC1/TSC2	0.025	0.046	-10000	0	-0.6	1	1
tumor necrosis factor receptor activity	0	0	0.002	10	-0.001	1	11
RPS6	0.007	0.045	-10000	0	-0.48	5	5
PPP5C	0.011	0	-10000	0	-10000	0	0
EIF4G1	0.011	0	-10000	0	-10000	0	0
IRS1	0.001	0.049	-10000	0	-0.38	10	10
INS	-0.002	0.035	-10000	0	-0.5	3	3
PTEN	0.005	0.059	-10000	0	-0.58	6	6
PDK2	-0.005	0.048	0.23	5	-0.27	16	21
EIF4EBP1	0.009	0.044	-10000	0	-1	1	1
PIK3CA	0.01	0.034	-10000	0	-0.58	2	2
PPP2R5D	0.017	0.016	-10000	0	-10000	0	0
peptide biosynthetic process	0.01	0.036	-10000	0	-0.29	7	7
RHEB	0.011	0	-10000	0	-10000	0	0
EIF4A1	0.011	0	-10000	0	-10000	0	0
mol:Rapamycin	0	0	0.003	6	-0.003	1	7
EEF2	0.01	0.036	-10000	0	-0.29	7	7
eIF4E/4E-BP1	0.013	0.046	-10000	0	-0.96	1	1

×

Class I PI3K signaling events mediated by Akt

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
BCL2L1	0.019	0	-10000	0	-10000	0	0
BAD/BCL-XL/YWHAZ	0.026	0.03	-10000	0	-0.32	4	4
CDKN1B	0.024	0.048	-10000	0	-0.53	4	4
CDKN1A	0.022	0.05	-10000	0	-0.41	6	6
FRAP1	0	0	-10000	0	-10000	0	0
PRKDC	0.009	0.039	-10000	0	-0.54	3	3
FOXO3	0.024	0.044	-10000	0	-0.54	3	3
AKT1	-0.005	0.043	-10000	0	-0.57	3	3
BAD	0.01	0.031	-10000	0	-0.52	2	2
AKT3	0.001	0.062	-10000	0	-0.27	28	28
mol:GTP	0	0	-10000	0	-10000	0	0
FOXO4	0.024	0.045	-10000	0	-0.47	4	4
AKT1/ASK1	0.023	0.053	-10000	0	-0.58	4	4
BAD/YWHAZ	0.02	0.033	-10000	0	-0.36	4	4
RICTOR	-0.008	0.11	-10000	0	-0.58	20	20
RAF1	0.011	0	-10000	0	-10000	0	0
JNK cascade	-0.022	0.05	0.56	4	-10000	0	4
TSC1	0.024	0.044	-10000	0	-0.54	3	3
YWHAZ	0.008	0.042	-10000	0	-0.58	3	3
AKT1/RAF1	0.025	0.044	-10000	0	-0.54	3	3
EP300	0.007	0.048	-10000	0	-0.58	4	4
mol:GDP	0.019	0.045	-10000	0	-0.56	3	3
mol:PI-3-4-5-P3	0	0	-10000	0	-10000	0	0
TSC2	0.024	0.053	-10000	0	-0.54	4	4
YWHAQ	0.011	0	-10000	0	-10000	0	0
TBC1D4	0.015	0.04	-10000	0	-0.34	7	7
MAP3K5	0.009	0.034	-10000	0	-0.58	2	2
MAPKAP1	0.011	0	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.032	0.03	0.32	3	-10000	0	3
YWHAH	0.011	0	-10000	0	-10000	0	0
AKT1S1	0.024	0.051	-10000	0	-0.63	3	3
CASP9	0.024	0.045	-10000	0	-0.47	4	4
YWHAB	0.011	0	-10000	0	-10000	0	0
p27Kip1/KPNA1	0.029	0.057	-10000	0	-0.63	4	4
GBL	0	0	-10000	0	-10000	0	0
PDK1/Src/Hsp90	0.022	0.022	-10000	0	-0.36	2	2
YWHAE	0.011	0	-10000	0	-10000	0	0
SRC	0.01	0.024	-10000	0	-0.58	1	1
AKT2/p21CIP1	0.026	0.051	-10000	0	-0.47	4	4
KIAA1303	0	0	-10000	0	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL	0.013	0.014	-10000	0	-10000	0	0
CHUK	0.023	0.058	-10000	0	-0.5	6	6
BAD/BCL-XL	0.035	0.049	-10000	0	-0.58	3	3
mTORC2	0.003	0.062	-10000	0	-0.33	20	20
AKT2	0.013	0.019	-10000	0	-0.24	3	3
FOXO1-3a-4/14-3-3 family	0.042	0.046	-10000	0	-0.52	3	3
PDPK1	0.011	0	-10000	0	-10000	0	0
MDM2	0.023	0.051	-10000	0	-0.49	5	5
MAPKKK cascade	-0.025	0.043	0.52	3	-10000	0	3
MDM2/Cbp/p300	0.032	0.057	-10000	0	-0.5	5	5
TSC1/TSC2	0.029	0.051	-10000	0	-0.61	3	3
proteasomal ubiquitin-dependent protein catabolic process	0.03	0.054	-10000	0	-0.47	5	5
glucose import	0.005	0.072	-10000	0	-0.27	38	38
mTOR/RHEB/GDP/Raptor/GBL/PRAS40	0.021	0.031	-10000	0	-0.34	3	3
response to stress	0	0	-10000	0	-10000	0	0
SLC2A4	0.005	0.073	-10000	0	-0.27	38	38
GSK3A	0.024	0.044	-10000	0	-0.54	3	3
FOXO1	0.023	0.047	-10000	0	-0.43	5	5
GSK3B	0.024	0.054	-10000	0	-0.6	4	4
SFN	0.005	0.055	-10000	0	-0.47	8	8
G1/S transition of mitotic cell cycle	0.029	0.053	-10000	0	-0.57	4	4
p27Kip1/14-3-3 family	0.036	0.029	-10000	0	-0.39	1	1
PRKACA	0.011	0	-10000	0	-10000	0	0
KPNA1	0.009	0.034	-10000	0	-0.58	2	2
HSP90AA1	0.01	0.024	-10000	0	-0.58	1	1
YWHAG	0.011	0	-10000	0	-10000	0	0
RHEB	0.011	0	-10000	0	-10000	0	0
CREBBP	0.011	0	-10000	0	-10000	0	0

×

FoxO family signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G6PC	0.015	0.072	-9999	-10000	0	0
PLK1	0.056	0.12	-9999	-0.89	3	3
CDKN1B	0.096	0.073	-9999	-0.41	5	5
FOXO3	0.054	0.12	-9999	-0.65	4	4
KAT2B	0.003	0.1	-9999	-0.58	17	17
FOXO1/SIRT1	0.001	0.054	-9999	-0.35	5	5
CAT	0.057	0.12	-9999	-0.74	2	2
CTNNB1	0.011	0	-9999	-10000	0	0
AKT1	0.02	0.027	-9999	-0.58	1	1
FOXO1	0.022	0.048	-9999	-0.28	3	3
MAPK10	0.009	0.083	-9999	-0.29	38	38
mol:GTP	0.002	0.001	-9999	-10000	0	0
FOXO4	0.068	0.065	-9999	-0.58	2	2
response to oxidative stress	0.009	0.013	-9999	-10000	0	0
FOXO3A/SIRT1	-0.001	0.088	-9999	-0.6	5	5
XPO1	0.001	0.08	-9999	-0.58	11	11
EP300	0.008	0.049	-9999	-0.59	4	4
BCL2L11	0.026	0.027	-9999	-10000	0	0
FOXO1/SKP2	0.024	0.053	-9999	-0.43	3	3
mol:GDP	0.009	0.013	-9999	-10000	0	0
RAN	0.013	0.001	-9999	-10000	0	0
GADD45A	0.081	0.088	-9999	-0.89	3	3
YWHAQ	0.011	0	-9999	-10000	0	0
FOXO1/14-3-3 family	0.054	0.052	-9999	-0.59	3	3
MST1	-0.025	0.15	-9999	-0.5	51	51
CSNK1D	0.011	0	-9999	-10000	0	0
CSNK1E	0.011	0	-9999	-10000	0	0
FOXO4/14-3-3 family	0.043	0.043	-9999	-0.46	3	3
YWHAB	0.011	0	-9999	-10000	0	0
MAPK8	0.032	0.017	-9999	-0.34	1	1
MAPK9	0.032	0.007	-9999	-10000	0	0
YWHAG	0.011	0	-9999	-10000	0	0
YWHAE	0.011	0	-9999	-10000	0	0
YWHAZ	0.008	0.042	-9999	-0.58	3	3
SIRT1	0.009	0.056	-9999	-0.58	5	5
SOD2	0.096	0.086	-9999	-0.64	2	2
RBL2	0.066	0.12	-9999	-1.4	2	2
RAL/GDP	0.026	0.01	-9999	-10000	0	0
CHUK	0.016	0.049	-9999	-0.58	4	4
Ran/GTP	0.012	0.002	-9999	-10000	0	0
CSNK1G2	0.009	0.034	-9999	-0.58	2	2
RAL/GTP	0.032	0.01	-9999	-10000	0	0
CSNK1G1	0.01	0.024	-9999	-0.58	1	1
FASLG	-0.081	0.36	-9999	-1.4	42	42
SKP2	0.008	0.042	-9999	-0.58	3	3
USP7	0.013	0.001	-9999	-10000	0	0
IKBKB	0.019	0.021	-9999	-0.44	1	1
CCNB1	0.057	0.12	-9999	-0.74	2	2
FOXO1-3a-4/beta catenin	0.1	0.089	-9999	-0.44	2	2
proteasomal ubiquitin-dependent protein catabolic process	0.023	0.053	-9999	-0.43	3	3
CSNK1A1	0.009	0.034	-9999	-0.58	2	2
SGK1	0.008	0.076	-9999	-0.48	14	14
CSNK1G3	0.01	0.024	-9999	-0.58	1	1
Ran/GTP/Exportin 1	0.014	0.051	-9999	-0.36	11	11
ZFAND5	0.069	0.067	-9999	-0.72	2	2
SFN	0.005	0.055	-9999	-0.47	8	8
CDK2	0.009	0.026	-9999	-0.58	1	1
FOXO3A/14-3-3	0.049	0.051	-9999	-0.42	4	4
CREBBP	0.01	0.009	-9999	-10000	0	0
FBXO32	0.055	0.12	-9999	-0.74	2	2
BCL6	0.066	0.099	-9999	-0.65	2	2
RALB	0.013	0.001	-9999	-10000	0	0
RALA	0.013	0.001	-9999	-10000	0	0
YWHAH	0.011	0	-9999	-10000	0	0

×

Arf6 trafficking events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SLC2A4	-0.015	0.12	-10000	0	-0.51	31	31
CLTC	0.025	0.032	-10000	0	-0.71	1	1
calcium ion-dependent exocytosis	0.021	0.022	-10000	0	-0.46	1	1
Dynamin 2/GTP	0.019	0.022	-10000	0	-0.29	3	3
EXOC4	0.011	0	-10000	0	-10000	0	0
CD59	0.022	0.031	-10000	0	-0.7	1	1
CPE	-0.037	0.12	-10000	0	-0.32	94	94
CTNNB1	0.011	0	-10000	0	-10000	0	0
membrane fusion	0.02	0.022	-10000	0	-0.45	1	1
CTNND1	0.024	0.021	-10000	0	-0.3	2	2
DNM2	0.01	0.024	-10000	0	-0.58	1	1
mol:PI-4-5-P2	0.024	0.031	-10000	0	-0.51	2	2
TSHR	0.001	0.06	-10000	0	-0.28	25	25
INS	0.008	0.024	-10000	0	-0.52	1	1
BIN1	0.007	0.054	-10000	0	-0.58	5	5
mol:Choline	0.02	0.022	-10000	0	-0.45	1	1
growth hormone secretagogue receptor activity	0	0	-10000	0	-10000	0	0
mol:GDP	0.014	0.019	-10000	0	-0.31	2	2
membrane depolarization	0	0	-10000	0	-10000	0	0
ARF6	0.01	0.024	-10000	0	-0.58	1	1
mol:Ca2+	0.019	0.022	-10000	0	-0.29	3	3
JUP	0.022	0.031	-10000	0	-0.7	1	1
ASAP2/amphiphysin II	0.017	0.042	-10000	0	-0.32	9	9
ARF6/GTP	0.008	0.018	-10000	0	-0.43	1	1
CDH1	0.022	0.031	-10000	0	-0.7	1	1
clathrin-independent pinocytosis	0.008	0.018	-10000	0	-0.43	1	1
MAPK8IP3	0.005	0.056	-10000	0	-0.51	7	7
positive regulation of endocytosis	0.008	0.018	-10000	0	-0.43	1	1
EXOC2	0.01	0.024	-10000	0	-0.58	1	1
substrate adhesion-dependent cell spreading	0.026	0.064	-10000	0	-0.61	4	4
insulin receptor binding	0	0	-10000	0	-10000	0	0
SPAG9	0.01	0.024	-10000	0	-0.58	1	1
regulation of calcium-dependent cell-cell adhesion	0.002	0.029	0.62	1	-10000	0	1
positive regulation of phagocytosis	0.015	0.015	-10000	0	-0.36	1	1
ARF6/GTP/JIP3	0.011	0.038	-10000	0	-0.32	8	8
ACAP1	0.014	0.032	-10000	0	-0.36	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
CHRM2	-0.009	0.072	-10000	0	-0.71	1	1
clathrin heavy chain/ACAP1	0.027	0.032	-10000	0	-0.46	2	2
JIP4/KLC1	0.021	0.02	-10000	0	-0.32	2	2
EXOC1	0.01	0.024	-10000	0	-0.58	1	1
exocyst	0.026	0.066	-10000	0	-0.62	4	4
RALA/GTP	0.009	0	-10000	0	-10000	0	0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex	0.014	0.022	-10000	0	-0.36	2	2
receptor recycling	0.008	0.018	-10000	0	-0.43	1	1
CTNNA1	0.023	0.028	-10000	0	-0.3	4	4
NME1	0.014	0.019	-10000	0	-0.32	2	2
clathrin coat assembly	0.024	0.031	-10000	0	-0.69	1	1
IL2RA	0.001	0.071	-10000	0	-0.5	2	2
VAMP3	0.015	0.015	-10000	0	-0.36	1	1
GLUT4/clathrin heavy chain/ACAP1	-0.013	0.054	-10000	0	-0.45	2	2
EXOC6	0.008	0.042	-10000	0	-0.58	3	3
PLD1	0.016	0.029	-10000	0	-0.38	3	3
PLD2	0.018	0.008	-10000	0	-0.17	1	1
EXOC5	-0.005	0.098	-10000	0	-0.58	17	17
PIP5K1C	0.024	0.032	-10000	0	-0.52	2	2
SDC1	0.022	0.031	-10000	0	-0.7	1	1
ARF6/GDP	0.014	0.019	-10000	0	-0.32	2	2
EXOC7	0.011	0	-10000	0	-10000	0	0
E-cadherin/beta catenin	-0.002	0.03	-10000	0	-0.65	1	1
mol:Phosphatidic acid	0.02	0.022	-10000	0	-0.45	1	1
endocytosis	-0.016	0.042	0.32	9	-10000	0	9
SCAMP2	0.011	0	-10000	0	-10000	0	0
ADRB2	0.009	0.079	-10000	0	-0.29	32	32
EXOC3	0.011	0	-10000	0	-10000	0	0
ASAP2	0.008	0.042	-10000	0	-0.58	3	3
Dynamin 2/GDP	0.02	0.022	-10000	0	-0.29	3	3
KLC1	0.011	0	-10000	0	-10000	0	0
AVPR2	0.002	0.084	-10000	0	-0.29	26	26
RALA	0.011	0	-10000	0	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.003	0.03	-10000	0	-0.6	1	1

×

PLK1 signaling events

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
regulation of centriole-centriole cohesion	-0.007	0.025	0.26	5	-10000	0	5
BUB1B	0.017	0.033	-10000	0	-0.34	5	5
PLK1	0.016	0.006	-10000	0	-10000	0	0
PLK1S1	0.011	0.019	-10000	0	-0.27	2	2
KIF2A	0.02	0.015	-10000	0	-0.32	1	1
regulation of mitotic centrosome separation	0.015	0.006	-10000	0	-10000	0	0
GOLGA2	0.009	0.034	-10000	0	-0.58	2	2
Hec1/SPC24	0.012	0.068	-10000	0	-0.29	29	29
WEE1	0.018	0.044	-10000	0	-0.51	4	4
cytokinesis	0.022	0.048	-10000	0	-0.34	7	7
PP2A-alpha B56	0.029	0.036	-10000	0	-0.78	1	1
AURKA	0.014	0.004	-10000	0	-10000	0	0
PICH/PLK1	0.022	0.058	-10000	0	-0.3	16	16
CENPE	0.01	0.059	-10000	0	-0.32	18	18
RhoA/GTP	0.008	0.018	-10000	0	-0.43	1	1
positive regulation of microtubule depolymerization	0.02	0.015	-10000	0	-0.32	1	1
PPP2CA	0.011	0	-10000	0	-10000	0	0
FZR1	0.01	0.024	-10000	0	-0.58	1	1
TPX2	0.012	0.016	-10000	0	-0.26	2	2
PAK1	0.011	0	-10000	0	-10000	0	0
SPC24	-0.003	0.089	-10000	0	-0.56	15	15
FBXW11	0.011	0	-10000	0	-10000	0	0
CLSPN	0.013	0.018	-10000	0	-0.3	2	2
GORASP1	0.011	0	-10000	0	-10000	0	0
metaphase	0	0.001	-10000	0	-0.016	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
NLP	0.009	0.003	-10000	0	-10000	0	0
G2 phase of mitotic cell cycle	0	0.001	0.011	1	-10000	0	1
STAG2	0.007	0.048	-10000	0	-0.58	4	4
GRASP65/GM130/RAB1/GTP	-0.001	0.018	-10000	0	-0.25	3	3
spindle elongation	0.015	0.006	-10000	0	-10000	0	0
ODF2	0.011	0.001	-10000	0	-10000	0	0
BUB1	-0.001	0.035	-10000	0	-0.86	1	1
TPT1	0.013	0.005	-10000	0	-10000	0	0
CDC25C	0.015	0.004	-10000	0	-10000	0	0
CDC25B	0.01	0.027	-10000	0	-0.45	2	2
SGOL1	0.007	0.025	-10000	0	-0.26	5	5
RHOA	0.01	0.024	-10000	0	-0.58	1	1
CCNB1/CDK1	-0.003	0.025	-10000	0	-0.28	4	4
CDC14B	0.007	0.031	-10000	0	-0.44	3	3
CDC20	0.011	0	-10000	0	-10000	0	0
PLK1/PBIP1	0.01	0.046	-10000	0	-0.3	13	13
mitosis	0	0	-10000	0	-10000	0	0
FBXO5	0.016	0.027	-10000	0	-0.31	4	4
CDC2	0.001	0.001	-10000	0	-10000	0	0
NDC80	-0.002	0.09	-10000	0	-0.58	14	14
metaphase plate congression	0.014	0.006	-10000	0	-10000	0	0
ERCC6L	0.019	0.061	-10000	0	-0.32	17	17
NLP/gamma Tubulin	0.012	0.004	-10000	0	-10000	0	0
microtubule cytoskeleton organization	0.013	0.005	-10000	0	-10000	0	0
G2/M transition DNA damage checkpoint	0	0	-10000	0	-10000	0	0
PPP1R12A	0.007	0.049	-10000	0	-0.59	4	4
interphase	0	0	-10000	0	-10000	0	0
PLK1/PRC1-2	0.026	0.02	-10000	0	-0.3	2	2
GRASP65/GM130/RAB1/GTP/PLK1	0.028	0.023	-10000	0	-0.29	3	3
RAB1A	0.01	0.024	-10000	0	-0.58	1	1
prophase	0	0	-10000	0	-10000	0	0
Aurora A/BORA	0.017	0.005	-10000	0	-10000	0	0
mitotic prometaphase	0	0.001	0.012	1	-10000	0	1
proteasomal ubiquitin-dependent protein catabolic process	0.028	0.025	-10000	0	-0.4	1	1
microtubule-based process	0.019	0.021	-10000	0	-0.32	2	2
Golgi organization	0.015	0.006	-10000	0	-10000	0	0
Cohesin/SA2	0.016	0.027	-10000	0	-0.31	4	4
PPP1CB/MYPT1	0.012	0.051	-10000	0	-0.49	6	6
KIF20A	0.009	0.034	-10000	0	-0.58	2	2
APC/C/CDC20	0.021	0.006	-10000	0	-10000	0	0
PPP2R1A	0.01	0.024	-10000	0	-0.58	1	1
chromosome segregation	0.01	0.046	-10000	0	-0.3	13	13
PRC1	0.011	0	-10000	0	-10000	0	0
ECT2	0.013	0.051	-10000	0	-0.33	13	13
C13orf34	0.018	0.005	-10000	0	-10000	0	0
NUDC	0.014	0.006	-10000	0	-10000	0	0
regulation of attachment of spindle microtubules to kinetochore	0.017	0.033	-10000	0	-0.33	5	5
spindle assembly	0.015	0.005	-10000	0	-10000	0	0
spindle stabilization	0.011	0.019	-10000	0	-0.27	2	2
APC/C/HCDH1	0.013	0.031	-10000	0	-0.36	4	4
MKLP2/PLK1	0.02	0.021	-10000	0	-0.33	2	2
CCNB1	0.012	0.001	-10000	0	-10000	0	0
PPP1CB	0.008	0.042	-10000	0	-0.59	3	3
BTRC	0.01	0.024	-10000	0	-0.58	1	1
ROCK2	0.012	0.069	-10000	0	-0.48	11	11
TUBG1	0.013	0.003	-10000	0	-10000	0	0
G2/M transition of mitotic cell cycle	-0.002	0.025	-10000	0	-0.27	4	4
MLF1IP	0	0.065	-10000	0	-0.44	13	13
INCENP	0.011	0.001	-10000	0	-10000	0	0

×

Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4	0.004	0.068	-10000	0	-0.58	8	8
SMAD2	0.013	0.023	0.24	1	-0.25	2	3
SMAD3	0.029	0.032	-10000	0	-10000	0	0
SMAD3/SMAD4	0.034	0.032	-10000	0	-10000	0	0
SMAD4/Ubc9/PIASy	0.018	0.046	-10000	0	-0.36	9	9
SMAD2/SMAD2/SMAD4	0.028	0.037	-10000	0	-10000	0	0
PPM1A	0.011	0	-10000	0	-10000	0	0
CALM1	0.011	0	-10000	0	-10000	0	0
SMAD2/SMAD4	0.014	0.043	-10000	0	-0.32	8	8
MAP3K1	0.006	0.059	-10000	0	-0.58	6	6
TRAP-1/SMAD4	0.01	0.056	-10000	0	-0.42	10	10
MAPK3	0.01	0.024	-10000	0	-0.58	1	1
MAPK1	0.01	0.024	-10000	0	-0.58	1	1
NUP214	0.011	0	-10000	0	-10000	0	0
CTDSP1	0.01	0.024	-10000	0	-0.58	1	1
CTDSP2	0.011	0	-10000	0	-10000	0	0
CTDSPL	0.011	0	-10000	0	-10000	0	0
KPNB1	0.011	0	-10000	0	-10000	0	0
TGFBRAP1	0.009	0.034	-10000	0	-0.58	2	2
UBE2I	0.011	0	-10000	0	-10000	0	0
NUP153	0.011	0	-10000	0	-10000	0	0
KPNA2	0.011	0	-10000	0	-10000	0	0
PIAS4	0.01	0.024	-10000	0	-0.58	1	1

×

Circadian rhythm pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
chromatin modification	0.036	0.056	-10000	0	-1.1	1	1
CLOCK	0.013	0.024	-10000	0	-0.58	1	1
TIMELESS/CRY2	0.033	0.054	-10000	0	-1.2	1	1
DEC1/BMAL1	0.007	0.046	-10000	0	-0.33	11	11
ATR	0.009	0.034	-10000	0	-0.58	2	2
NR1D1	0.031	0.059	-10000	0	-1.3	1	1
ARNTL	0.013	0.024	-10000	0	-0.58	1	1
TIMELESS	0.032	0.058	-10000	0	-1.3	1	1
NPAS2	0.012	0.031	-10000	0	-0.52	2	2
CRY2	0.011	0	-10000	0	-10000	0	0
mol:CO	-0.011	0.009	0.12	3	-10000	0	3
CHEK1	0.01	0.024	-10000	0	-0.58	1	1
mol:HEME	0.011	0.009	-10000	0	-0.12	3	3
PER1	0.005	0.059	-10000	0	-0.5	8	8
BMAL/CLOCK/NPAS2	0.034	0.031	-10000	0	-0.32	4	4
BMAL1/CLOCK	0.036	0.064	-10000	0	-0.88	2	2
S phase of mitotic cell cycle	0.036	0.056	-10000	0	-1.1	1	1
TIMELESS/CHEK1/ATR	0.037	0.057	-10000	0	-1.2	1	1
mol:NADPH	0.011	0.009	-10000	0	-0.12	3	3
PER1/TIMELESS	0.03	0.066	-10000	0	-0.93	2	2
PER1-2 / CRY1-2	0	0	-10000	0	-10000	0	0
DEC1	-0.004	0.059	-10000	0	-0.46	10	10

×

Insulin-mediated glucose transport

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
Insulin responsive Vesicles	0.01	0.059	-10000	0	-0.37	5	5
CaM/Ca2+	0.009	0	-10000	0	-10000	0	0
AKT1	0.01	0.024	-10000	0	-0.58	1	1
AKT2	0.009	0.036	-10000	0	-0.5	3	3
STXBP4	0.006	0.059	-10000	0	-0.58	6	6
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucose	0.029	0.056	0.2	6	-0.36	4	10
YWHAZ	0.008	0.042	-10000	0	-0.58	3	3
CALM1	0.011	0	-10000	0	-10000	0	0
YWHAQ	0.011	0	-10000	0	-10000	0	0
TBC1D4	0.013	0.047	-10000	0	-0.42	7	7
mol:Ca2+	0	0	-10000	0	-10000	0	0
YWHAH	0.011	0	-10000	0	-10000	0	0
YWHAB	0.011	0	-10000	0	-10000	0	0
SNARE/Synip	0.02	0.038	-10000	0	-0.36	6	6
YWHAG	0.011	0	-10000	0	-10000	0	0
ASIP	0	0.053	-10000	0	-0.46	8	8
PRKCI	0.008	0.042	-10000	0	-0.58	3	3
AS160/CaM/Ca2+	0.009	0	-10000	0	-10000	0	0
RHOQ	0.011	0	-10000	0	-10000	0	0
GYS1	0.022	0.043	-10000	0	-0.47	4	4
PRKCZ	0.01	0.031	-10000	0	-0.52	2	2
TRIP10	0.01	0.024	-10000	0	-0.58	1	1
TC10/GTP/CIP4/Exocyst	0.015	0.015	-10000	0	-0.36	1	1
AS160/14-3-3	0.033	0.034	-10000	0	-0.35	2	2
VAMP2	0.011	0	-10000	0	-10000	0	0
SLC2A4	0.029	0.061	0.2	6	-0.4	4	10
STX4	0.011	0	-10000	0	-10000	0	0
GSK3B	0.018	0.045	-10000	0	-0.58	3	3
SFN	0.005	0.055	-10000	0	-0.47	8	8
LNPEP	0.004	0.068	-10000	0	-0.58	8	8
YWHAE	0.011	0	-10000	0	-10000	0	0

×

E-cadherin signaling in keratinocytes

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
keratinocyte differentiation	0.035	0.051	-10000	0	-0.41	6	6
adherens junction organization	0.033	0.033	-10000	0	-0.47	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.038	0.049	-10000	0	-0.48	3	3
FMN1	0.028	0.049	-10000	0	-0.42	2	2
mol:IP3	0.03	0.038	-10000	0	-0.3	6	6
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.028	0.03	-10000	0	-0.37	2	2
CTNNB1	0.011	0.001	-10000	0	-10000	0	0
AKT1	0.035	0.043	-10000	0	-0.7	1	1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.032	0.039	-10000	0	-0.56	2	2
CTNND1	0.012	0.001	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.032	0.036	-10000	0	-0.39	3	3
VASP	0.033	0.029	-10000	0	-0.46	1	1
ZYX	0.032	0.038	-10000	0	-0.74	1	1
JUB	0.033	0.029	-10000	0	-0.46	1	1
EGFR(dimer)	0.03	0.043	-10000	0	-0.4	3	3
E-cadherin/beta catenin-gamma catenin	0.021	0.021	-10000	0	-0.34	2	2
mol:PI-3-4-5-P3	0.03	0.038	-10000	0	-0.3	6	6
PIK3CA	0.01	0.034	-10000	0	-0.58	2	2
PI3K	0.031	0.038	-10000	0	-0.31	6	6
FYN	0.032	0.053	-10000	0	-0.33	7	7
mol:Ca2+	0.03	0.037	-10000	0	-0.3	6	6
JUP	0.01	0.024	-10000	0	-0.59	1	1
PIK3R1	0.009	0.042	-10000	0	-0.58	3	3
mol:DAG	0.03	0.038	-10000	0	-0.3	6	6
CDH1	0.01	0.024	-10000	0	-0.58	1	1
RhoA/GDP	0.038	0.053	-10000	0	-0.49	4	4
establishment of polarity of embryonic epithelium	0.033	0.028	-10000	0	-0.45	1	1
SRC	0.01	0.024	-10000	0	-0.58	1	1
RAC1	0.011	0	-10000	0	-10000	0	0
RHOA	0.01	0.024	-10000	0	-0.58	1	1
EGFR	0.005	0.058	-10000	0	-0.53	7	7
CASR	0.029	0.044	-10000	0	-0.45	1	1
RhoA/GTP	-0.004	0.035	-10000	0	-0.48	2	2
AKT2	0.034	0.047	-10000	0	-0.58	2	2
actin cable formation	0.033	0.048	-10000	0	-0.4	2	2
apoptosis	-0.033	0.047	0.37	6	-10000	0	6
CTNNA1	0.01	0.034	-10000	0	-0.59	2	2
mol:GDP	0.033	0.052	-10000	0	-0.52	3	3
PIP5K1A	0.032	0.037	-10000	0	-0.4	3	3
PLCG1	0.03	0.038	-10000	0	-0.31	6	6
Rac1/GTP	-0.005	0.035	-10000	0	-0.37	3	3
homophilic cell adhesion	0.001	0.001	-10000	0	-10000	0	0

×

Arf1 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
coatomer protein complex	-0.002	0.029	-9999	-0.34	3	3
EntrezGene:79658	0	0	-9999	-10000	0	0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A	0.015	0.021	-9999	-0.26	2	2
AP2	0.015	0.03	-9999	-0.34	4	4
mol:DAG	0	0	-9999	-10000	0	0
Arfaptin 2/Rac/GTP	0.016	0.002	-9999	-10000	0	0
CLTB	0.01	0.031	-9999	-0.52	2	2
coatomer protein complex/ARF1/GTP/ER cargo protein	0.02	0.014	-9999	-0.26	1	1
CD4	-0.013	0.12	-9999	-0.56	26	26
CLTA	0.011	0	-9999	-10000	0	0
mol:GTP	0.001	0.001	-9999	-10000	0	0
ARFGAP1	0.007	0.026	-9999	-0.36	3	3
mol:PI-4-5-P2	-0.001	0.019	-9999	-0.33	2	2
ARF1/GTP	-0.001	0.012	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein	0.02	0.025	-9999	-0.3	3	3
mol:Choline	-0.001	0.019	-9999	-0.32	2	2
mol:GDP	0	0	-9999	-10000	0	0
ARF1	0.011	0.019	-9999	-0.45	1	1
DDEF1	-0.001	0.019	-9999	-0.33	2	2
ARF1/GDP	0.005	0.02	-9999	-0.27	3	3
AP2M1	0.011	0	-9999	-10000	0	0
EntrezGene:1313	0	0	-9999	-10000	0	0
actin filament polymerization	0.014	0.01	-9999	-0.22	1	1
Rac/GTP	0.01	0.001	-9999	-10000	0	0
ARF1/GTP/GGA3/ARF-GAP1	0.02	0.021	-9999	-0.25	3	3
ARFIP2	0.01	0.003	-9999	-10000	0	0
COPA	0.011	0	-9999	-10000	0	0
RAC1	0.011	0	-9999	-10000	0	0
ARF1/GTP/coatomer protein complex	0.02	0.01	-9999	-10000	0	0
ARF1/GTP/ARHGAP10	0.008	0.011	-9999	-0.26	1	1
GGA3	0.011	0	-9999	-10000	0	0
ARF1/GTP/Membrin	0.015	0.011	-9999	-10000	0	0
AP2A1	0.008	0.041	-9999	-0.49	4	4
coatomer protein complex/ARF1/GTP/ARF-GAP1	0.021	0.028	-9999	-0.61	1	1
ARF1/GDP/Membrin	0.015	0.011	-9999	-10000	0	0
Arfaptin 2/Rac/GDP	0.015	0.002	-9999	-10000	0	0
CYTH2	0.012	0.001	-9999	-10000	0	0
ARF1/GTP/GGA3	0.016	0.011	-9999	-0.25	1	1
mol:ATP	0	0	-9999	-10000	0	0
Rac/GDP	0.009	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	0.018	0.049	-9999	-0.4	1	1
PLD2	-0.001	0.019	-9999	-0.32	2	2
ARF-GAP1/v-SNARE	0.007	0.026	-9999	-0.36	3	3
PIP5K1A	-0.001	0.019	-9999	-0.33	2	2
ARF1/GTP/Membrin/GBF1/p115	-0.002	0.019	-9999	-0.28	2	2
mol:Phosphatic acid	0	0	-9999	-10000	0	0
mol:Phosphatidic acid	-0.001	0.019	-9999	-0.32	2	2
KDEL Receptor/Ligand/ARF-GAP1	0.007	0.026	-9999	-0.36	3	3
GOSR2	-0.001	0.008	-9999	-10000	0	0
USO1	-0.005	0.049	-9999	-0.48	6	6
GBF1	-0.001	0.019	-9999	-0.42	1	1
ARF1/GTP/Arfaptin 2	0.016	0.011	-9999	-0.25	1	1
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex	0.006	0.077	-9999	-0.33	30	30

×

Alternative NF-kappaB 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
IKK alpha homodimer	0.013	0.04	-9999	-0.42	5	5
FBXW11	0.011	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.011	0	-9999	-10000	0	0
CHUK	0.007	0.048	-9999	-0.58	4	4
NF kappa B2 p100/RelB	0.029	0.051	-9999	-0.42	6	6
NFKB1	0.01	0.024	-9999	-0.58	1	1
MAP3K14	0.01	0.024	-9999	-0.58	1	1
NF kappa B1 p50/RelB	0.014	0.032	-9999	-0.37	4	4
RELB	0.009	0.036	-9999	-0.5	3	3
NFKB2	0.01	0.031	-9999	-0.52	2	2
NF kappa B2 p52/RelB	0.013	0.038	-9999	-0.49	3	3
regulation of B cell activation	0.013	0.038	-9999	-0.49	3	3

×

E-cadherin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin	0.022	0.022	-9999	-0.36	2	2
E-cadherin/beta catenin	0.016	0.018	-9999	-0.42	1	1
CTNNB1	0.011	0	-9999	-10000	0	0
JUP	0.01	0.024	-9999	-0.58	1	1
CDH1	0.01	0.024	-9999	-0.58	1	1

pid_entity	TCGA.T9.A92H	TCGA.SS.A7HO	TCGA.RU.A8FL	TCGA.QG.A5Z2
109_MAP3K5	0.044	0.044	-0.42	0.044
47_PPARGC1A	0.011	0.011	0.011	0.011
105_BMP4	0.011	0.011	0.011	0.011
105_BMP6	0.011	0.011	0.011	0.011
105_BMP7	-0.58	0.011	-0.46	0.011
105_BMP2	0.011	0.011	-0.58	0.011
131_RELN/VLDLR	0.03	0.022	0.03	0.03
30_TGFB1/TGF beta receptor Type II	0.011	0.011	-0.58	0.011
84_STAT5B	-0.0062	0.039	-0.28	-0.14
84_STAT5A	-0.0062	0.039	-0.28	-0.14