Ovarian Serous Cystadenocarcinoma: PARADIGM pathway analysis of mRNA expression data

Pathway.Name	Avg.Num.Perturbations
FOXM1 transcription factor network	145
HIF-1-alpha transcription factor network	119
LPA receptor mediated events	101
TCGA08_retinoblastoma	98
Syndecan-1-mediated signaling events	91
Osteopontin-mediated events	90
Endothelins	88
PDGFR-alpha signaling pathway	84
Nectin adhesion pathway	74
TCGA08_p53	74

Pathway.Name	Avg.Num.Perturbations	Total.Perturbations	Num.Entities	Min.Mean.Truth	Max.Mean.Truth	Min.Mean.Within	Max.Mean.Within	Min.Mean.Any	Max.Mean.Within.1
FOXM1 transcription factor network	145	7417	51	-0.66	0.022	1000	-1000	-0.021	-1000
HIF-1-alpha transcription factor network	119	9094	76	-0.16	0.034	1000	-1000	-0.015	-1000
LPA receptor mediated events	101	10390	102	-0.086	0.023	1000	-1000	-0.021	-1000
TCGA08_retinoblastoma	98	784	8	-0.023	0.022	1000	-1000	-0.003	-1000
Syndecan-1-mediated signaling events	91	3115	34	-0.087	0.023	1000	-1000	0	-1000
Osteopontin-mediated events	90	3420	38	-0.22	0.023	1000	-1000	0	-1000
Endothelins	88	8468	96	-0.21	0.023	1000	-1000	-0.013	-1000
PDGFR-alpha signaling pathway	84	3718	44	-0.15	0.031	1000	-1000	0	-1000
Nectin adhesion pathway	74	4718	63	-0.081	0.033	1000	-1000	-0.025	-1000
TCGA08_p53	74	523	7	-0.069	0.019	1000	-1000	0	-1000
Ephrin B reverse signaling	72	3461	48	-0.2	0.051	1000	-1000	-0.03	-1000
Fc-epsilon receptor I signaling in mast cells	71	6917	97	-0.088	0.026	1000	-1000	-0.017	-1000
Thromboxane A2 receptor signaling	69	7296	105	-0.21	0.052	1000	-1000	-0.031	-1000
PLK2 and PLK4 events	68	204	3	-0.002	0.016	1000	-1000	0.018	-1000
amb2 Integrin signaling	68	5628	82	-0.13	0.034	1000	-1000	0	-1000
TRAIL signaling pathway	67	3238	48	-0.038	0.023	1000	-1000	-0.005	-1000
Cellular roles of Anthrax toxin	66	2582	39	-0.1	0.022	1000	-1000	-0.004	-1000
Syndecan-4-mediated signaling events	65	4370	67	-0.11	0.027	1000	-1000	-0.008	-1000
IL4-mediated signaling events	63	5793	91	-0.33	0.17	1000	-1000	-0.097	-1000
Noncanonical Wnt signaling pathway	60	1565	26	-0.033	0.026	1000	-1000	-0.007	-1000
BARD1 signaling events	59	3416	57	-0.035	0.027	1000	-1000	-0.035	-1000
IL1-mediated signaling events	59	3683	62	-0.074	0.045	1000	-1000	0	-1000
Nongenotropic Androgen signaling	59	3068	52	-0.13	0.066	1000	-1000	-0.014	-1000
IL23-mediated signaling events	58	3500	60	-0.27	0.025	1000	-1000	-0.011	-1000
IL6-mediated signaling events	57	4340	75	-0.12	0.025	1000	-1000	-0.019	-1000
Integrins in angiogenesis	54	4555	84	-0.056	0.033	1000	-1000	0	-1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)	53	4581	85	-0.17	0.023	1000	-1000	-0.018	-1000
a4b1 and a4b7 Integrin signaling	50	252	5	0.004	0.019	1000	-1000	0.018	-1000
Caspase cascade in apoptosis	49	3685	74	-0.064	0.044	1000	-1000	-0.009	-1000
IFN-gamma pathway	49	3398	68	-0.053	0.034	1000	-1000	-0.02	-1000
IGF1 pathway	48	2758	57	-0.021	0.035	1000	-1000	-0.014	-1000
Signaling events mediated by the Hedgehog family	47	2489	52	-0.083	0.034	1000	-1000	-0.018	-1000
PLK1 signaling events	47	4053	85	-0.063	0.025	1000	-1000	-0.006	-1000
Ras signaling in the CD4+ TCR pathway	46	792	17	-0.026	0.024	1000	-1000	0	-1000
Signaling events mediated by PTP1B	45	3469	76	-0.094	0.075	1000	-1000	-0.012	-1000
BMP receptor signaling	45	3648	81	-0.074	0.049	1000	-1000	-0.024	-1000
Paxillin-independent events mediated by a4b1 and a4b7	45	1683	37	-0.041	0.033	1000	-1000	0	-1000
Canonical Wnt signaling pathway	45	2306	51	-0.19	0.084	1000	-1000	-0.017	-1000
EPHB forward signaling	45	3846	85	-0.028	0.036	1000	-1000	-0.019	-1000
Wnt signaling	45	319	7	-0.033	0.022	1000	-1000	0.011	-1000
IL12-mediated signaling events	43	3824	87	-0.26	0.026	1000	-1000	-0.054	-1000
TCR signaling in naïve CD8+ T cells	43	4033	93	-0.05	0.033	1000	-1000	-0.022	-1000
Stabilization and expansion of the E-cadherin adherens junction	43	3192	74	-0.059	0.035	1000	-1000	-0.028	-1000
E-cadherin signaling in keratinocytes	43	1882	43	-0.012	0.026	1000	-1000	-0.009	-1000
Syndecan-2-mediated signaling events	42	2956	69	-0.018	0.027	1000	-1000	0	-1000
BCR signaling pathway	42	4255	99	-0.057	0.032	1000	-1000	-0.017	-1000
Circadian rhythm pathway	41	910	22	-0.08	0.024	1000	-1000	-0.017	-1000
Aurora A signaling	41	2485	60	-0.064	0.037	1000	-1000	0	-1000
Reelin signaling pathway	41	2297	56	-0.018	0.055	1000	-1000	0	-1000
Paxillin-dependent events mediated by a4b1	41	1501	36	-0.032	0.035	1000	-1000	-0.03	-1000
IL2 signaling events mediated by PI3K	41	2435	58	-0.11	0.023	1000	-1000	-0.008	-1000
HIF-2-alpha transcription factor network	40	1749	43	-0.098	0.041	1000	-1000	-0.098	-1000
Ephrin A reverse signaling	39	276	7	0	0.023	1000	-1000	0	-1000
FOXA2 and FOXA3 transcription factor networks	39	1805	46	-0.17	0.042	1000	-1000	-0.002	-1000
Retinoic acid receptors-mediated signaling	39	2309	58	-0.098	0.029	1000	-1000	-0.006	-1000
ErbB2/ErbB3 signaling events	38	2483	65	-0.072	0.023	1000	-1000	-0.023	-1000
Arf6 downstream pathway	38	1668	43	-0.027	0.031	1000	-1000	-0.025	-1000
FoxO family signaling	38	2470	64	-0.27	0.041	1000	-1000	-0.006	-1000
ceramide signaling pathway	37	1819	49	-0.014	0.038	1000	-1000	-0.003	-1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha	37	1672	45	-0.06	0.038	1000	-1000	-0.006	-1000
E-cadherin signaling in the nascent adherens junction	37	2847	76	-0.059	0.041	1000	-1000	-0.026	-1000
Signaling events mediated by PRL	36	1244	34	-0.014	0.023	1000	-1000	-0.001	-1000
Aurora B signaling	35	2362	67	-0.065	0.033	1000	-1000	-0.012	-1000
FAS signaling pathway (CD95)	33	1582	47	-0.054	0.042	1000	-1000	-0.014	-1000
Plasma membrane estrogen receptor signaling	33	2845	86	-0.055	0.051	1000	-1000	-0.027	-1000
p75(NTR)-mediated signaling	32	4008	125	-0.039	0.055	1000	-1000	-0.016	-1000
TCGA08_rtk_signaling	32	848	26	-0.014	0.028	1000	-1000	-0.018	-1000
ErbB4 signaling events	31	2207	69	-0.068	0.046	1000	-1000	-0.013	-1000
Class I PI3K signaling events	30	2205	73	-0.008	0.041	1000	-1000	-0.003	-1000
Signaling mediated by p38-gamma and p38-delta	28	430	15	-0.05	0.023	1000	-1000	0	-1000
Lissencephaly gene (LIS1) in neuronal migration and development	27	1487	54	-0.015	0.029	1000	-1000	0	-1000
E-cadherin signaling events	27	136	5	0.018	0.025	1000	-1000	0.019	-1000
Regulation of Androgen receptor activity	27	1949	70	-0.095	0.033	1000	-1000	-0.017	-1000
RXR and RAR heterodimerization with other nuclear receptor	26	1360	52	-0.029	0.06	1000	-1000	-0.003	-1000
Regulation of Telomerase	25	2595	102	-0.13	0.046	1000	-1000	-0.003	-1000
S1P3 pathway	25	1064	42	-0.054	0.03	1000	-1000	-0.004	-1000
Nephrin/Neph1 signaling in the kidney podocyte	24	840	34	-0.023	0.049	1000	-1000	-0.022	-1000
Canonical NF-kappaB pathway	24	965	39	0	0.037	1000	-1000	0	-1000
Atypical NF-kappaB pathway	24	753	31	0	0.023	1000	-1000	0	-1000
IL2 signaling events mediated by STAT5	24	542	22	-0.077	0.032	1000	-1000	0.001	-1000
PDGFR-beta signaling pathway	24	2384	97	-0.059	0.046	1000	-1000	-0.017	-1000
S1P4 pathway	24	615	25	-0.003	0.03	1000	-1000	0	-1000
Presenilin action in Notch and Wnt signaling	23	1442	61	-0.18	0.042	1000	-1000	-0.014	-1000
LPA4-mediated signaling events	22	266	12	0	0.014	1000	-1000	0	-1000
Coregulation of Androgen receptor activity	22	1691	76	-0.01	0.033	1000	-1000	-0.019	-1000
Glucocorticoid receptor regulatory network	22	2550	114	-0.13	0.046	1000	-1000	-0.02	-1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	22	1514	68	-0.08	0.092	1000	-1000	-0.032	-1000
Arf6 signaling events	21	1336	62	-0.017	0.036	1000	-1000	0	-1000
EPO signaling pathway	21	1188	55	-0.006	0.058	1000	-1000	0	-1000
Neurotrophic factor-mediated Trk receptor signaling	21	2579	120	-0.058	0.056	1000	-1000	-0.021	-1000
Regulation of nuclear SMAD2/3 signaling	20	2810	136	-0.13	0.071	1000	-1000	-0.036	-1000
Glypican 1 network	20	992	48	-0.021	0.039	1000	-1000	-0.02	-1000
EGFR-dependent Endothelin signaling events	19	417	21	0	0.041	1000	-1000	0	-1000
p38 MAPK signaling pathway	19	854	44	-0.012	0.043	1000	-1000	0	-1000
S1P5 pathway	18	319	17	-0.007	0.023	1000	-1000	-0.011	-1000
Regulation of p38-alpha and p38-beta	18	977	54	-0.007	0.057	1000	-1000	0	-1000
Signaling events mediated by VEGFR1 and VEGFR2	18	2359	125	-0.019	0.055	1000	-1000	-0.026	-1000
mTOR signaling pathway	17	908	53	-0.015	0.032	1000	-1000	-0.015	-1000
Ceramide signaling pathway	17	1365	76	-0.012	0.044	1000	-1000	0	-1000
Signaling events mediated by HDAC Class III	17	687	40	-0.036	0.042	1000	-1000	-0.028	-1000
Signaling events regulated by Ret tyrosine kinase	17	1411	82	-0.008	0.056	1000	-1000	-0.022	-1000
Signaling events mediated by HDAC Class I	17	1858	104	-0.036	0.052	1000	-1000	-0.029	-1000
Syndecan-3-mediated signaling events	17	612	35	-0.009	0.034	1000	-1000	0	-1000
Signaling mediated by p38-alpha and p38-beta	17	757	44	-0.008	0.033	1000	-1000	0	-1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha	17	563	33	-0.002	0.053	1000	-1000	0	-1000
Class IB PI3K non-lipid kinase events	17	51	3	-0.019	0.019	1000	-1000	-0.019	-1000
Arf6 trafficking events	16	1205	71	-0.025	0.033	1000	-1000	-0.018	-1000
Class I PI3K signaling events mediated by Akt	15	1030	68	-0.026	0.047	1000	-1000	-0.014	-1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes	14	1219	83	-0.006	0.048	1000	-1000	-0.017	-1000
Hedgehog signaling events mediated by Gli proteins	13	896	65	-0.005	0.053	1000	-1000	-0.01	-1000
S1P1 pathway	13	485	36	-0.001	0.028	1000	-1000	-0.016	-1000
Calcium signaling in the CD4+ TCR pathway	13	432	31	-0.002	0.089	1000	-1000	-0.017	-1000
VEGFR1 specific signals	13	738	56	0	0.039	1000	-1000	0	-1000
JNK signaling in the CD4+ TCR pathway	12	207	17	-0.002	0.044	1000	-1000	0	-1000
Insulin-mediated glucose transport	12	389	32	0	0.033	1000	-1000	0	-1000
Effects of Botulinum toxin	12	320	26	0	0.041	1000	-1000	0	-1000
Insulin Pathway	12	890	74	-0.012	0.063	1000	-1000	-0.017	-1000
Alternative NF-kappaB pathway	12	165	13	0	0.055	1000	-1000	0	-1000
Signaling events mediated by HDAC Class II	11	886	75	-0.034	0.059	1000	-1000	-0.013	-1000
Sphingosine 1-phosphate (S1P) pathway	11	329	28	0	0.037	1000	-1000	0	-1000
Sumoylation by RanBP2 regulates transcriptional repression	11	313	27	-0.013	0.047	1000	-1000	-0.014	-1000
Angiopoietin receptor Tie2-mediated signaling	11	989	88	-0.029	0.057	1000	-1000	-0.044	-1000
Aurora C signaling	10	70	7	0	0.033	1000	-1000	0	-1000
IL27-mediated signaling events	10	540	51	-0.006	0.034	1000	-1000	-0.027	-1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling	9	226	23	-0.013	0.043	1000	-1000	-0.001	-1000
Glypican 2 network	9	39	4	0.021	0.029	1000	-1000	0.019	-1000
Arf1 pathway	9	488	54	-0.01	0.032	1000	-1000	-0.001	-1000
Signaling events mediated by Stem cell factor receptor (c-Kit)	8	664	78	-0.013	0.037	1000	-1000	-0.009	-1000
Visual signal transduction: Rods	7	390	52	0	0.065	1000	-1000	0	-1000
Rapid glucocorticoid signaling	6	136	20	0	0.025	1000	-1000	0	-1000
Visual signal transduction: Cones	1	73	38	0	0.064	1000	-1000	0	-1000
Total	4801	276456	7203	-8.1	5.2	131000	-131000	-1.5	-131000

FOXM1 transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC3	-0.43	0.59	-10000	0	-1.2	187	187
PLK1	-0.062	0.29	-10000	0	-1.3	30	30
BIRC5	-0.061	0.29	-10000	0	-1.3	29	29
HSPA1B	-0.44	0.59	-10000	0	-1.1	206	206
MAP2K1	0.001	0.044	-10000	0	-0.16	3	3
BRCA2	-0.44	0.6	-10000	0	-1.2	194	194
FOXM1	-0.66	0.96	-10000	0	-1.7	203	203
XRCC1	-0.43	0.59	-10000	0	-1.2	192	192
FOXM1B/p19	-0.54	0.66	-10000	0	-1.3	210	210
Cyclin D1/CDK4	-0.44	0.55	-10000	0	-1	218	218
CDC2	-0.5	0.67	-10000	0	-1.3	199	199
TGFA	-0.39	0.52	-10000	0	-0.97	205	205
SKP2	-0.44	0.6	-10000	0	-1.2	188	188
CCNE1	-0.001	0.049	-10000	0	-0.13	70	70
CKS1B	-0.44	0.6	-10000	0	-1.2	194	194
RB1	-0.36	0.45	-10000	0	-0.91	190	190
FOXM1C/SP1	-0.53	0.71	-10000	0	-1.4	208	208
AURKB	-0.069	0.3	-10000	0	-1.3	32	32
CENPF	-0.48	0.62	-10000	0	-1.2	216	216
CDK4	0.008	0.027	-10000	0	-0.14	9	9
MYC	-0.39	0.52	-10000	0	-0.98	212	212
CHEK2	-0.003	0.051	-10000	0	-0.14	26	26
ONECUT1	-0.44	0.57	-10000	0	-1.1	208	208
CDKN2A	0.013	0.023	0.093	1	-0.13	12	13
LAMA4	-0.48	0.62	-10000	0	-1.2	210	210
FOXM1B/HNF6	-0.55	0.72	-10000	0	-1.4	208	208
FOS	-0.52	0.64	-10000	0	-1.2	230	230
SP1	0.021	0.011	-10000	0	-0.036	14	14
CDC25B	-0.44	0.59	-10000	0	-1.1	194	194
response to radiation	-0.012	0.032	-10000	0	-10000	0	0
CENPB	-0.43	0.59	-10000	0	-1.2	188	188
CENPA	-0.43	0.59	-10000	0	-1.1	194	194
NEK2	-0.44	0.61	-10000	0	-1.2	194	194
HIST1H2BA	-0.43	0.59	-10000	0	-1.1	191	191
CCNA2	0.01	0.034	-10000	0	-0.13	29	29
EP300	0.022	0.01	-10000	0	-0.12	2	2
CCNB1/CDK1	-0.58	0.78	-10000	0	-1.5	195	195
CCNB2	-0.46	0.62	-10000	0	-1.2	205	205
CCNB1	-0.48	0.65	-10000	0	-1.3	193	193
ETV5	-0.49	0.63	-10000	0	-1.2	220	220
ESR1	-0.47	0.61	-10000	0	-1.2	213	213
CCND1	-0.44	0.56	-10000	0	-1	220	220
GSK3A	0.003	0.042	-10000	0	-0.16	10	10
Cyclin A-E1/CDK1-2	-0.037	0.1	-10000	0	-0.16	184	184
CDK2	0.015	0.025	-10000	0	-0.13	14	14
G2/M transition of mitotic cell cycle	-0.015	0.038	-10000	0	-10000	0	0
FOXM1B/Cbp/p300	-0.49	0.66	-10000	0	-1.3	203	203
GAS1	-0.44	0.6	-10000	0	-1.2	195	195
MMP2	-0.53	0.64	-10000	0	-1.2	240	240
RB1/FOXM1C	-0.49	0.58	-10000	0	-1.1	223	223
CREBBP	0.021	0.015	-10000	0	-0.12	6	6

×

HIF-1-alpha transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PKM2	-0.13	0.34	-9999	-0.55	166	166
HDAC7	-0.001	0.006	-9999	-10000	0	0
HIF1A/ARNT/Cbp/p300/Src-1	-0.067	0.34	-9999	-0.59	107	107
SMAD4	0.023	0.007	-9999	-0.12	1	1
ID2	-0.13	0.34	-9999	-0.55	165	165
AP1	-0.03	0.087	-9999	-0.15	161	161
ABCG2	-0.13	0.34	-9999	-0.56	165	165
HIF1A	-0.017	0.091	-9999	-0.13	147	147
TFF3	-0.13	0.34	-9999	-0.55	173	173
GATA2	0.019	0.023	-9999	-0.1	17	17
AKT1	-0.005	0.073	-9999	-0.11	100	100
response to hypoxia	-0.021	0.064	-9999	-0.11	125	125
MCL1	-0.13	0.34	-9999	-0.55	164	164
NDRG1	-0.14	0.35	-9999	-0.58	166	166
SERPINE1	-0.14	0.33	-9999	-0.56	165	165
FECH	-0.13	0.34	-9999	-0.56	164	164
FURIN	-0.13	0.34	-9999	-0.55	164	164
NCOA2	0.023	0.013	-9999	-0.1	5	5
EP300	0	0.089	-9999	-0.22	28	28
HMOX1	-0.13	0.35	-9999	-0.57	167	167
BHLHE40	-0.14	0.33	-9999	-0.56	164	164
BHLHE41	-0.14	0.33	-9999	-0.56	164	164
HIF1A/ARNT/SMAD3/SMAD4/SP1	0.034	0.12	-9999	-0.19	52	52
ENG	0.005	0.089	-9999	-0.19	42	42
JUN	0.014	0.033	-9999	-0.12	30	30
RORA	-0.13	0.34	-9999	-0.55	164	164
ABCB1	-0.026	0.11	-9999	-0.78	4	4
TFRC	-0.14	0.35	-9999	-0.57	175	175
CXCR4	-0.14	0.35	-9999	-0.56	179	179
TF	-0.13	0.34	-9999	-0.55	166	166
CITED2	-0.13	0.34	-9999	-0.55	165	165
HIF1A/ARNT	-0.084	0.44	-9999	-0.71	121	121
LDHA	-0.09	0.3	-9999	-0.99	54	54
ETS1	-0.13	0.35	-9999	-0.57	165	165
PGK1	-0.13	0.35	-9999	-0.56	171	171
NOS2	-0.14	0.33	-9999	-0.56	164	164
ITGB2	-0.14	0.35	-9999	-0.57	171	171
ALDOA	-0.13	0.34	-9999	-0.55	165	165
Cbp/p300/CITED2	-0.12	0.36	-9999	-0.64	131	131
FOS	-0.006	0.054	-9999	-0.12	96	96
HK2	-0.13	0.34	-9999	-0.55	169	169
SP1	0.031	0.009	-9999	-0.11	1	1
GCK	0.002	0.12	-9999	-0.42	1	1
HK1	-0.13	0.34	-9999	-0.55	164	164
NPM1	-0.13	0.34	-9999	-0.55	165	165
EGLN1	-0.12	0.34	-9999	-0.55	165	165
CREB1	0.023	0.028	-9999	-0.075	42	42
PGM1	-0.13	0.34	-9999	-0.56	169	169
SMAD3	0.022	0.016	-9999	-0.12	7	7
EDN1	-0.037	0.19	-9999	-1.1	13	13
IGFBP1	-0.12	0.34	-9999	-0.55	164	164
VEGFA	-0.093	0.29	-9999	-0.51	137	137
HIF1A/JAB1	-0.005	0.085	-9999	-0.18	72	72
CP	-0.15	0.36	-9999	-0.58	176	176
CXCL12	-0.15	0.35	-9999	-0.57	177	177
COPS5	0.02	0.022	-9999	-0.11	13	13
SMAD3/SMAD4	0.029	0.032	-9999	-0.12	25	25
BNIP3	-0.14	0.34	-9999	-0.56	173	173
EGLN3	-0.15	0.35	-9999	-0.57	179	179
CA9	-0.15	0.34	-9999	-0.55	182	182
TERT	-0.12	0.34	-9999	-0.55	164	164
ENO1	-0.13	0.34	-9999	-0.56	164	164
PFKL	-0.13	0.34	-9999	-0.55	164	164
NCOA1	0.023	0.009	-9999	-0.12	2	2
ADM	-0.14	0.34	-9999	-0.56	168	168
ARNT	-0.009	0.07	-9999	-0.096	157	157
HNF4A	0.027	0.009	-9999	-0.12	2	2
ADFP	-0.14	0.35	-9999	-0.57	178	178
SLC2A1	-0.097	0.29	-9999	-0.52	136	136
LEP	-0.12	0.34	-9999	-0.55	164	164
HIF1A/ARNT/Cbp/p300	-0.077	0.34	-9999	-0.58	119	119
EPO	-0.076	0.28	-9999	-0.57	91	91
CREBBP	-0.002	0.09	-9999	-0.22	32	32
HIF1A/ARNT/Cbp/p300/HDAC7	-0.08	0.35	-9999	-0.6	117	117
PFKFB3	-0.13	0.34	-9999	-0.56	167	167
NT5E	-0.16	0.36	-9999	-0.58	182	182

×

LPA receptor mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.021	0.074	-10000	0	-0.13	138	138
NF kappa B1 p50/RelA/I kappa B alpha	-0.015	0.092	-10000	0	-0.19	88	88
AP1	-0.058	0.074	-10000	0	-0.13	250	250
mol:PIP3	-0.051	0.063	-10000	0	-0.14	156	156
AKT1	-0.015	0.07	-10000	0	-0.16	54	54
PTK2B	-0.028	0.066	-10000	0	-0.14	123	123
RHOA	-0.009	0.054	-10000	0	-0.35	6	6
PIK3CB	0.015	0.03	-10000	0	-0.12	24	24
mol:Ca2+	-0.004	0.039	-10000	0	-0.12	31	31
MAGI3	0.018	0.026	-10000	0	-0.12	18	18
RELA	0.023	0.009	-10000	0	-0.12	2	2
apoptosis	-0.035	0.07	-10000	0	-0.15	124	124
HRAS/GDP	0.017	0.008	-10000	0	-0.11	2	2
positive regulation of microtubule depolymerization	-0.019	0.06	-10000	0	-0.12	125	125
NF kappa B1 p50/RelA	-0.04	0.062	-10000	0	-0.13	141	141
endothelial cell migration	-0.086	0.14	-10000	0	-0.23	247	247
ADCY4	-0.043	0.097	-10000	0	-0.2	135	135
ADCY5	-0.045	0.098	-10000	0	-0.2	141	141
ADCY6	-0.043	0.098	-10000	0	-0.2	134	134
ADCY7	-0.042	0.097	-10000	0	-0.2	134	134
ADCY1	-0.042	0.097	-10000	0	-0.2	134	134
ADCY2	-0.043	0.097	-10000	0	-0.2	135	135
ADCY3	-0.043	0.098	-10000	0	-0.2	135	135
ADCY8	-0.048	0.098	-10000	0	-0.2	138	138
ADCY9	-0.045	0.1	-10000	0	-0.2	141	141
GSK3B	-0.024	0.064	-10000	0	-0.13	126	126
arachidonic acid secretion	-0.041	0.091	-10000	0	-0.19	129	129
GNG2	0.02	0.018	-10000	0	-0.12	9	9
TRIP6	0.002	0.05	-10000	0	-0.25	19	19
GNAO1	-0.04	0.073	-10000	0	-0.11	248	248
HRAS	0.023	0.006	-10000	0	-0.12	1	1
NFKBIA	-0.03	0.085	-10000	0	-0.21	69	69
GAB1	0.02	0.021	-10000	0	-0.12	12	12
mol:GTP	0	0	-10000	0	-10000	0	0
lamellipodium assembly	-0.023	0.22	-10000	0	-0.87	37	37
JUN	0.014	0.033	-10000	0	-0.12	30	30
LPA/LPA2/NHERF2	-0.01	0.035	-10000	0	-0.062	140	140
TIAM1	-0.041	0.26	-10000	0	-1	37	37
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
mol:IP3	-0.004	0.039	-10000	0	-0.12	31	31
PLCB3	-0.003	0.032	-10000	0	-0.071	37	37
FOS	-0.005	0.053	-10000	0	-0.12	95	95
positive regulation of mitosis	-0.041	0.091	-10000	0	-0.19	129	129
LPA/LPA1-2-3	-0.037	0.061	-10000	0	-0.098	247	247
mol:Ca ++	0	0	-10000	0	-10000	0	0
JNK cascade	0	0	-10000	0	-10000	0	0
BCAR1	0.022	0.011	-10000	0	-0.12	3	3
stress fiber formation	-0.026	0.075	-10000	0	-0.15	109	109
GNAZ	-0.035	0.071	-10000	0	-0.11	247	247
EGFR/PI3K-beta/Gab1	-0.053	0.065	-10000	0	-0.14	155	155
positive regulation of dendritic cell cytokine production	-0.037	0.06	-10000	0	-0.098	247	247
LPA/LPA2/MAGI-3	-0.009	0.036	-10000	0	-0.063	136	136
ARHGEF1	-0.02	0.062	-10000	0	-0.12	128	128
GNAI2	-0.035	0.071	-10000	0	-0.11	247	247
GNAI3	-0.039	0.077	-10000	0	-0.11	248	248
GNAI1	-0.045	0.081	-10000	0	-0.12	247	247
LPA/LPA3	-0.021	0.031	-10000	0	-0.053	247	247
LPA/LPA2	-0.021	0.031	-10000	0	-0.052	247	247
LPA/LPA1	-0.052	0.082	-10000	0	-0.14	247	247
HB-EGF/EGFR	-0.003	0.06	-10000	0	-0.12	88	88
HBEGF	0.004	0.039	-10000	0	-0.078	95	95
mol:DAG	-0.004	0.039	-10000	0	-0.12	31	31
cAMP biosynthetic process	-0.045	0.096	-10000	0	-0.2	135	135
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
SRC	0.023	0.009	-10000	0	-0.12	2	2
GNB1	0.023	0.007	-10000	0	-0.12	1	1
LYN	-0.03	0.089	-10000	0	-0.22	71	71
GNAQ	-0.012	0.038	-10000	0	-0.069	125	125
LPAR2	0	0	-10000	0	-10000	0	0
LPAR3	0	0	-10000	0	-10000	0	0
LPAR1	-0.034	0.049	-10000	0	-0.084	247	247
IL8	-0.083	0.15	-10000	0	-0.36	97	97
PTK2	-0.029	0.063	-10000	0	-0.09	251	251
Rac1/GDP	0.016	0.015	-10000	0	-0.15	5	5
CASP3	-0.035	0.07	-10000	0	-0.15	124	124
EGFR	0.015	0.03	-10000	0	-0.12	25	25
PLCG1	-0.007	0.041	-10000	0	-0.069	122	122
PLD2	-0.026	0.06	-10000	0	-0.087	247	247
G12/G13	-0.019	0.073	-10000	0	-0.14	128	128
PI3K-beta	-0.04	0.06	0.084	1	-0.19	49	50
cell migration	-0.012	0.078	-10000	0	-0.23	50	50
SLC9A3R2	0.017	0.028	-10000	0	-0.12	22	22
PXN	-0.027	0.076	-10000	0	-0.16	80	80
HRAS/GTP	-0.042	0.093	-10000	0	-0.19	129	129
RAC1	0.023	0.002	-10000	0	-10000	0	0
MMP9	0	0.05	-10000	0	-0.12	81	81
PRKCE	0.021	0.017	-10000	0	-0.12	8	8
PRKCD	-0.005	0.045	-10000	0	-0.13	37	37
Gi(beta/gamma)	-0.043	0.096	-10000	0	-0.19	138	138
mol:LPA	-0.034	0.049	-10000	0	-0.084	247	247
TRIP6/p130 Cas/FAK1/Paxillin	-0.022	0.093	-10000	0	-0.16	140	140
MAPKKK cascade	-0.041	0.091	-10000	0	-0.19	129	129
contractile ring contraction involved in cytokinesis	-0.008	0.054	-10000	0	-0.35	6	6
mol:GDP	0	0	-10000	0	-10000	0	0
GNA14	-0.009	0.029	-10000	0	-0.057	128	128
GNA15	-0.011	0.035	-10000	0	-0.064	125	125
GNA12	0.023	0.001	-10000	0	-10000	0	0
GNA13	0.022	0.009	-10000	0	-0.12	2	2
MAPT	-0.019	0.061	-10000	0	-0.12	125	125
GNA11	-0.009	0.028	-10000	0	-0.056	124	124
Rac1/GTP	-0.026	0.24	-10000	0	-0.92	37	37
MMP2	-0.086	0.14	-10000	0	-0.23	247	247

×

TCGA08_retinoblastoma

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2B	0.017	0.017	-10000	0	-0.085	8	8
CDKN2C	0.008	0.044	-10000	0	-0.12	56	56
CDKN2A	0.014	0.023	-10000	0	-0.12	12	12
CCND2	0.015	0.052	0.12	107	-10000	0	107
RB1	-0.023	0.061	0.091	1	-0.12	136	137
CDK4	0.022	0.068	0.13	138	-0.12	17	155
CDK6	0.014	0.073	0.13	131	-0.13	39	170
G1/S progression	0.02	0.065	0.12	138	-0.09	1	139

×

Syndecan-1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.019	0.023	-9999	-0.12	14	14
CCL5	0.005	0.044	-9999	-0.12	60	60
SDCBP	0.021	0.01	-9999	-0.12	2	2
FGFR/FGF2/Syndecan-1	-0.083	0.12	-9999	-0.25	132	132
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
Syndecan-1/Laminin-5	-0.073	0.12	-9999	-0.24	139	139
Syndecan-1/Syntenin	-0.076	0.13	-9999	-0.24	151	151
MAPK3	-0.06	0.12	-9999	-0.21	141	141
HGF/MET	-0.017	0.074	-9999	-0.14	118	118
TGFB1/TGF beta receptor Type II	0.019	0.023	-9999	-0.12	14	14
BSG	0.022	0.013	-9999	-0.12	4	4
keratinocyte migration	-0.072	0.12	-9999	-0.23	139	139
Syndecan-1/RANTES	-0.087	0.14	-9999	-0.25	168	168
Syndecan-1/CD147	-0.062	0.12	-9999	-0.22	138	138
Syndecan-1/Syntenin/PIP2	-0.074	0.12	-9999	-0.23	153	153
LAMA5	0.019	0.025	-9999	-0.12	17	17
positive regulation of cell-cell adhesion	-0.073	0.12	-9999	-0.22	153	153
MMP7	-0.022	0.06	-9999	-0.12	144	144
HGF	0.02	0.023	-9999	-0.12	14	14
Syndecan-1/CASK	-0.079	0.12	-9999	-0.24	132	132
Syndecan-1/HGF/MET	-0.087	0.13	-9999	-0.22	197	197
regulation of cell adhesion	-0.058	0.11	-9999	-0.23	111	111
HPSE	0.014	0.034	-9999	-0.12	33	33
positive regulation of cell migration	-0.083	0.12	-9999	-0.25	132	132
SDC1	-0.084	0.12	-9999	-0.25	132	132
Syndecan-1/Collagen	-0.083	0.12	-9999	-0.25	132	132
PPIB	0.023	0.003	-9999	-10000	0	0
MET	0	0.047	-9999	-0.12	70	70
PRKACA	0.021	0.017	-9999	-0.12	8	8
MMP9	0	0.05	-9999	-0.12	81	81
MAPK1	-0.061	0.12	-9999	-0.21	139	139
homophilic cell adhesion	-0.082	0.12	-9999	-0.25	132	132
MMP1	-0.007	0.058	-9999	-0.12	115	115

×

Osteopontin-mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IKK alpha homodimer	-0.047	0.11	-9999	-0.22	120	120
NF kappa B1 p50/RelA/I kappa B alpha	-0.067	0.17	-9999	-0.31	141	141
alphaV/beta3 Integrin/Osteopontin/Src	-0.038	0.11	-9999	-0.19	164	164
AP1	-0.12	0.16	-9999	-0.3	184	184
ILK	-0.047	0.099	-9999	-0.22	102	102
bone resorption	-0.041	0.11	-9999	-0.19	151	151
PTK2B	0.023	0.009	-9999	-0.12	2	2
PYK2/p130Cas	-0.022	0.11	-9999	-0.19	118	118
ITGAV	0.008	0.035	-9999	-0.12	30	30
mol:GTP	0	0	-9999	-10000	0	0
CD44/Rho Family GTPase/ROCK2	-0.001	0.07	-9999	-0.12	125	125
alphaV/beta3 Integrin/Osteopontin	-0.042	0.12	-9999	-0.22	129	129
MAP3K1	-0.05	0.1	-9999	-0.2	131	131
JUN	0.012	0.033	-9999	-0.12	30	30
MAPK3	-0.064	0.12	-9999	-0.25	139	139
MAPK1	-0.064	0.13	-9999	-0.25	140	140
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
NFKB1	0.021	0.013	-9999	-0.12	4	4
MAPK8	-0.053	0.1	-9999	-0.2	143	143
ITGB3	-0.001	0.048	-9999	-0.12	71	71
NFKBIA	-0.081	0.16	-9999	-0.32	144	144
FOS	-0.007	0.054	-9999	-0.12	95	95
CD44	0.011	0.038	-9999	-0.12	41	41
CHUK	0.021	0.013	-9999	-0.12	4	4
PLAU	-0.22	0.4	-9999	-1	106	106
NF kappa B1 p50/RelA	-0.068	0.17	-9999	-0.36	123	123
BCAR1	0.022	0.011	-9999	-0.12	3	3
RELA	0.023	0.009	-9999	-0.12	2	2
alphaV beta3 Integrin	-0.027	0.088	-9999	-0.17	117	117
mol:GDP	0	0	-9999	-10000	0	0
SYK	-0.047	0.1	-9999	-0.2	130	130
VAV3	-0.055	0.11	-9999	-0.21	148	148
MAP3K14	-0.054	0.11	-9999	-0.21	145	145
ROCK2	0.019	0.021	-9999	-0.12	11	11
SPP1	0.008	0.034	-9999	-0.12	31	31
RAC1	0.023	0.002	-9999	-10000	0	0
Rac1/GTP	-0.05	0.11	-9999	-0.2	147	147
MMP2	-0.13	0.16	-9999	-0.28	244	244

×

Endothelins

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	-0.075	0.13	0.27	6	-0.25	165	171
PTK2B	0.022	0.009	-10000	0	-0.12	2	2
mol:Ca2+	-0.041	0.16	-10000	0	-0.5	37	37
EDN1	-0.057	0.11	0.2	6	-0.19	165	171
EDN3	0.02	0.023	-10000	0	-0.12	14	14
EDN2	0.018	0.027	-10000	0	-0.12	20	20
HRAS/GDP	-0.068	0.14	0.21	2	-0.31	102	104
ETA receptor/Endothelin-1/Gq/GTP/PLC beta	-0.05	0.11	0.2	3	-0.23	106	109
ADCY4	-0.059	0.11	0.2	6	-0.2	164	170
ADCY5	-0.062	0.11	0.2	5	-0.2	169	174
ADCY6	-0.058	0.11	0.2	6	-0.2	161	167
ADCY7	-0.058	0.11	0.2	6	-0.2	161	167
ADCY1	-0.058	0.11	0.2	6	-0.2	161	167
ADCY2	-0.059	0.11	0.2	6	-0.2	163	169
ADCY3	-0.059	0.11	0.2	6	-0.2	162	168
ADCY8	-0.067	0.11	0.2	4	-0.2	174	178
ADCY9	-0.06	0.11	0.2	6	-0.2	162	168
arachidonic acid secretion	-0.13	0.23	-10000	0	-0.45	150	150
ETB receptor/Endothelin-1/Gq/GTP	-0.022	0.082	-10000	0	-0.2	57	57
GNAO1	0.01	0.042	-10000	0	-0.12	51	51
HRAS	0.022	0.006	-10000	0	-0.12	1	1
ETA receptor/Endothelin-1/G12/GTP	-0.053	0.14	0.32	6	-0.23	149	155
ETA receptor/Endothelin-1/Gs/GTP	-0.051	0.13	0.3	6	-0.21	160	166
mol:GTP	-0.001	0.006	-10000	0	-10000	0	0
COL3A1	-0.13	0.19	0.28	6	-0.35	200	206
EDNRB	-0.012	0.054	-10000	0	-0.089	149	149
response to oxidative stress	0	0	-10000	0	-10000	0	0
CYSLTR2	-0.074	0.14	0.28	6	-0.27	139	145
CYSLTR1	-0.084	0.15	0.28	5	-0.28	149	154
SLC9A1	-0.043	0.088	0.19	6	-0.17	130	136
mol:GDP	-0.08	0.15	0.21	2	-0.33	104	106
SLC9A3	-0.059	0.16	-10000	0	-0.47	38	38
RAF1	-0.092	0.18	-10000	0	-0.38	119	119
JUN	-0.081	0.27	-10000	0	-0.84	54	54
JAK2	-0.082	0.14	0.27	6	-0.26	172	178
mol:IP3	-0.053	0.12	0.18	2	-0.26	84	86
ETA receptor/Endothelin-1	-0.086	0.17	0.36	6	-0.3	163	169
PLCB1	0.011	0.034	-10000	0	-0.12	32	32
PLCB2	0.019	0.018	-10000	0	-0.12	8	8
ETA receptor/Endothelin-3	-0.02	0.077	0.16	6	-0.13	136	142
FOS	-0.17	0.34	-10000	0	-0.85	106	106
Gai/GDP	0.013	0.062	-10000	0	-0.47	3	3
CRK	0.021	0.016	-10000	0	-0.12	7	7
mol:Ca ++	-0.1	0.16	0.27	3	-0.32	156	159
BCAR1	0.023	0.011	-10000	0	-0.12	3	3
PRKCB1	-0.053	0.12	-10000	0	-0.26	87	87
GNAQ	0.019	0.017	-10000	0	-0.12	6	6
GNAZ	0.022	0.011	-10000	0	-0.12	3	3
GNAL	0.021	0.018	-10000	0	-0.12	9	9
Gs family/GDP	-0.067	0.14	0.2	2	-0.3	104	106
ETA receptor/Endothelin-1/Gq/GTP	-0.043	0.12	0.21	4	-0.24	96	100
MAPK14	-0.028	0.086	-10000	0	-0.2	70	70
TRPC6	-0.043	0.17	-10000	0	-0.52	36	36
GNAI2	0.022	0.011	-10000	0	-0.12	3	3
GNAI3	0.021	0.008	-10000	0	-0.12	1	1
GNAI1	0.012	0.035	-10000	0	-0.12	35	35
ETB receptor/Endothelin-1/Gq/GTP/PLC beta	-0.032	0.09	-10000	0	-0.21	69	69
ETB receptor/Endothelin-2	0.004	0.048	-10000	0	-0.12	36	36
ETB receptor/Endothelin-3	0.007	0.043	-10000	0	-0.11	25	25
ETB receptor/Endothelin-1	-0.05	0.1	0.17	4	-0.19	158	162
MAPK3	-0.16	0.3	-10000	0	-0.74	111	111
MAPK1	-0.16	0.31	-10000	0	-0.75	111	111
Rac1/GDP	-0.068	0.14	0.21	2	-0.31	103	105
cAMP biosynthetic process	-0.04	0.1	0.21	5	-0.2	104	109
MAPK8	-0.058	0.19	-10000	0	-0.51	69	69
SRC	0.023	0.009	-10000	0	-0.12	2	2
ETB receptor/Endothelin-1/Gi/GTP	-0.034	0.095	-10000	0	-0.25	60	60
p130Cas/CRK/Src/PYK2	-0.055	0.15	-10000	0	-0.38	66	66
mol:K +	0	0	-10000	0	-10000	0	0
G12/GDP	-0.068	0.14	0.21	2	-0.31	102	104
COL1A2	-0.14	0.23	0.28	5	-0.49	148	153
EntrezGene:2778	0	0	-10000	0	-10000	0	0
ETA receptor/Endothelin-2	-0.023	0.08	0.16	6	-0.13	146	152
mol:DAG	-0.053	0.12	0.18	2	-0.26	84	86
MAP2K2	-0.12	0.23	-10000	0	-0.54	117	117
MAP2K1	-0.12	0.23	-10000	0	-0.53	116	116
EDNRA	-0.05	0.1	0.2	6	-0.18	174	180
positive regulation of muscle contraction	-0.06	0.12	0.24	6	-0.21	161	167
Gq family/GDP	-0.046	0.14	-10000	0	-0.3	91	91
HRAS/GTP	-0.07	0.14	-10000	0	-0.31	98	98
PRKCH	-0.053	0.12	-10000	0	-0.26	89	89
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCA	-0.058	0.12	-10000	0	-0.26	96	96
PRKCB	-0.054	0.11	-10000	0	-0.26	89	89
PRKCE	-0.052	0.12	-10000	0	-0.26	87	87
PRKCD	-0.056	0.12	-10000	0	-0.26	94	94
PRKCG	-0.051	0.12	-10000	0	-0.26	85	85
regulation of vascular smooth muscle contraction	-0.21	0.4	-10000	0	-1	106	106
PRKCQ	-0.059	0.12	-10000	0	-0.26	93	93
PLA2G4A	-0.14	0.25	-10000	0	-0.49	149	149
GNA14	0.018	0.022	-10000	0	-0.12	11	11
GNA15	0.019	0.019	-10000	0	-0.12	8	8
GNA12	0.023	0.001	-10000	0	-10000	0	0
GNA11	0.021	0.015	-10000	0	-0.12	5	5
Rac1/GTP	-0.054	0.14	0.32	6	-0.23	151	157
MMP1	0.019	0.14	0.22	6	-0.6	12	18

×

PDGFR-alpha signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.004	0.046	-10000	0	-0.13	59	59
PDGF/PDGFRA/CRKL	-0.009	0.068	-10000	0	-0.13	121	121
positive regulation of JUN kinase activity	0.01	0.068	-10000	0	-0.1	115	115
CRKL	0.023	0.009	-10000	0	-0.12	2	2
PDGF/PDGFRA/Caveolin-3	-0.01	0.068	-10000	0	-0.12	157	157
AP1	-0.15	0.26	-10000	0	-0.66	107	107
mol:IP3	-0.007	0.046	-10000	0	-0.074	139	139
PLCG1	-0.007	0.046	-10000	0	-0.074	139	139
PDGF/PDGFRA/alphaV Integrin	-0.037	0.094	-10000	0	-0.15	193	193
RAPGEF1	0.023	0	-10000	0	-10000	0	0
CRK	0.021	0.016	-10000	0	-0.12	7	7
mol:Ca2+	-0.011	0.053	-10000	0	-0.083	150	150
CAV3	0.022	0.011	-10000	0	-0.12	3	3
CAV1	0.012	0.039	-10000	0	-0.12	43	43
SHC/Grb2/SOS1	0.011	0.069	-10000	0	-0.1	115	115
PDGF/PDGFRA/Shf	-0.009	0.068	-10000	0	-0.13	122	122
FOS	-0.14	0.26	-10000	0	-0.66	107	107
JUN	-0.019	0.045	0.26	4	-0.13	35	39
oligodendrocyte development	-0.037	0.094	-10000	0	-0.15	193	193
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
mol:DAG	-0.007	0.046	-10000	0	-0.074	139	139
PDGF/PDGFRA	-0.004	0.046	-10000	0	-0.13	59	59
actin cytoskeleton reorganization	-0.009	0.068	-10000	0	-0.13	122	122
SRF	0.024	0.022	-10000	0	-0.069	23	23
SHC1	0.023	0.001	-10000	0	-10000	0	0
PI3K	-0.014	0.084	-10000	0	-0.13	153	153
PDGF/PDGFRA/Crk/C3G	0.007	0.061	-10000	0	-0.11	99	99
JAK1	0.003	0.032	-10000	0	-0.076	61	61
ELK1/SRF	-0.011	0.066	-10000	0	-0.13	110	110
SHB	0.023	0.009	-10000	0	-0.12	2	2
SHF	0.023	0.009	-10000	0	-0.12	2	2
CSNK2A1	0.031	0.021	0.066	2	-0.1	6	8
GO:0007205	-0.023	0.072	-10000	0	-0.11	172	172
SOS1	0.017	0.027	-10000	0	-0.12	20	20
Ras protein signal transduction	0.01	0.068	-10000	0	-0.1	115	115
PDGF/PDGFRA/SHB	-0.009	0.068	-10000	0	-0.13	122	122
PDGF/PDGFRA/Caveolin-1	-0.02	0.08	-10000	0	-0.13	181	181
ITGAV	0.013	0.032	-10000	0	-0.12	28	28
ELK1	-0.024	0.07	-10000	0	-0.12	146	146
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PDGF/PDGFRA/Crk	-0.01	0.068	-10000	0	-0.13	127	127
JAK-STAT cascade	0.004	0.032	-10000	0	-0.076	61	61
cell proliferation	-0.009	0.067	-10000	0	-0.13	122	122

×

Nectin adhesion pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.01	0.042	-9999	-0.12	52	52
alphaV beta3 Integrin	-0.018	0.081	-9999	-0.16	107	107
PTK2	-0.073	0.15	-9999	-0.31	140	140
positive regulation of JNK cascade	-0.052	0.11	-9999	-0.26	116	116
CDC42/GDP	-0.044	0.17	-9999	-0.35	116	116
Rac1/GDP	-0.043	0.17	-9999	-0.35	117	117
RAP1B	0.019	0.02	-9999	-0.12	10	10
RAP1A	0.021	0.012	-9999	-0.12	3	3
CTNNB1	0.022	0.008	-9999	-0.12	1	1
CDC42/GTP	-0.044	0.15	-9999	-0.32	116	116
nectin-3/I-afadin	-0.02	0.08	-9999	-0.15	119	119
RAPGEF1	-0.06	0.17	-9999	-0.38	115	115
mol:GTP	0	0	-9999	-10000	0	0
CRK	-0.073	0.19	-9999	-0.43	115	115
PDGFB-D/PDGFRB	0.01	0.042	-9999	-0.12	52	52
TLN1	-0.037	0.097	-9999	-0.16	163	163
Rap1/GTP	-0.063	0.12	-9999	-0.28	116	116
IQGAP1	0.02	0.017	-9999	-0.12	7	7
Rap1/GTP/I-afadin	0.016	0.059	-9999	-0.11	85	85
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin	-0.02	0.08	-9999	-0.15	119	119
PVR	0.022	0.011	-9999	-0.12	3	3
Necl-5(dimer)	0.022	0.011	-9999	-0.12	3	3
mol:GDP	-0.066	0.2	-9999	-0.43	116	116
MLLT4	0.014	0.032	-9999	-0.12	29	29
PIK3CA	0.02	0.017	-9999	-0.12	7	7
PI3K	-0.009	0.085	-9999	-0.11	179	179
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin	0.017	0.048	-9999	-0.14	36	36
positive regulation of lamellipodium assembly	-0.059	0.12	-9999	-0.28	124	124
PVRL1	0.022	0.011	-9999	-0.12	3	3
PVRL3	0.003	0.046	-9999	-0.12	66	66
PVRL2	0.019	0.023	-9999	-0.12	15	15
PIK3R1	0.015	0.031	-9999	-0.12	27	27
CDH1	0.021	0.016	-9999	-0.12	6	6
CLDN1	-0.003	0.051	-9999	-0.12	87	87
JAM-A/CLDN1	-0.029	0.087	-9999	-0.12	216	216
SRC	-0.081	0.21	-9999	-0.48	115	115
ITGB3	0.004	0.047	-9999	-0.12	68	68
nectin-1(dimer)/I-afadin/I-afadin	0.017	0.048	-9999	-0.14	36	36
FARP2	-0.063	0.19	-9999	-0.42	116	116
RAC1	0.023	0.002	-9999	-10000	0	0
CTNNA1	0.022	0.01	-9999	-0.12	2	2
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer)	-0.003	0.072	-9999	-0.12	120	120
nectin-1/I-afadin	0.017	0.048	-9999	-0.14	36	36
nectin-2/I-afadin	0.013	0.054	-9999	-0.15	43	43
RAC1/GTP/IQGAP1/filamentous actin	0.017	0.044	-9999	-0.11	55	55
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin	-0.003	0.072	-9999	-0.12	119	119
CDC42/GTP/IQGAP1/filamentous actin	0.018	0.043	-9999	-0.11	54	54
F11R	0.023	0.007	-9999	-0.12	1	1
positive regulation of filopodium formation	-0.052	0.11	-9999	-0.26	116	116
alphaV/beta3 Integrin/Talin	-0.053	0.11	-9999	-0.21	150	150
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.013	0.054	-9999	-0.15	43	43
nectin-2(dimer)/I-afadin/I-afadin	0.013	0.054	-9999	-0.15	43	43
PIP5K1C	-0.046	0.1	-9999	-0.17	174	174
VAV2	-0.076	0.21	-9999	-0.44	126	126
RAP1/GDP	-0.044	0.16	-9999	-0.33	117	117
ITGAV	0.013	0.032	-9999	-0.12	28	28
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin	-0.007	0.074	-9999	-0.12	128	128
nectin-3(dimer)/I-afadin/I-afadin	-0.02	0.08	-9999	-0.15	119	119
Rac1/GTP	-0.051	0.16	-9999	-0.34	124	124
PTPRM	-0.056	0.11	-9999	-0.2	174	174
E-cadherin/beta catenin/alpha catenin	0.033	0.07	-9999	-0.18	25	25
adherens junction assembly	0	0	-9999	-10000	0	0
CDC42	0.023	0.002	-9999	-10000	0	0

×

TCGA08_p53

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

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

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

×

Ephrin B reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EFNB2	0.007	0.041	-10000	0	-0.12	50	50
EPHB2	0.022	0.021	-10000	0	-0.12	11	11
EFNB1	0.023	0.018	-10000	0	-0.068	19	19
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.045	0.055	-10000	0	-0.15	11	11
Ephrin B2/EPHB1-2	0.011	0.062	-10000	0	-0.1	101	101
neuron projection morphogenesis	0.029	0.046	-10000	0	-0.15	11	11
Ephrin B1/EPHB1-2/Tiam1	0.04	0.056	-10000	0	-0.12	29	29
DNM1	0.022	0.019	-10000	0	-0.12	10	10
cell-cell signaling	0.002	0.004	-10000	0	-10000	0	0
MAP2K4	-0.12	0.21	-10000	0	-0.47	150	150
YES1	-0.19	0.31	-10000	0	-0.71	149	149
Ephrin B1/EPHB1-2/NCK2	0.051	0.043	-10000	0	-0.094	24	24
PI3K	-0.13	0.22	-10000	0	-0.47	156	156
mol:GDP	0.038	0.055	-10000	0	-0.11	29	29
ITGA2B	0.023	0.006	-10000	0	-0.12	1	1
endothelial cell proliferation	0.001	0.058	-10000	0	-0.12	89	89
FYN	-0.2	0.31	-10000	0	-0.7	154	154
MAP3K7	-0.13	0.22	-10000	0	-0.49	152	152
FGR	-0.18	0.31	-10000	0	-0.69	149	149
TIAM1	0.015	0.032	-10000	0	-0.12	28	28
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
RGS3	0.023	0	-10000	0	-10000	0	0
cell adhesion	-0.12	0.2	-10000	0	-0.43	160	160
LYN	-0.2	0.31	-10000	0	-0.71	149	149
Ephrin B1/EPHB1-2/Src Family Kinases	-0.18	0.28	-10000	0	-0.64	149	149
Ephrin B1/EPHB1-2	-0.15	0.24	-10000	0	-0.54	149	149
SRC	-0.18	0.31	-10000	0	-0.69	149	149
ITGB3	0.004	0.047	-10000	0	-0.12	68	68
EPHB1	0.018	0.032	-10000	0	-0.12	28	28
EPHB4	0.022	0.009	-10000	0	-0.12	2	2
RAC1	0.023	0.002	-10000	0	-10000	0	0
Ephrin B2/EPHB4	0.001	0.058	-10000	0	-0.12	89	89
alphaIIb/beta3 Integrin	0.01	0.053	-10000	0	-0.14	38	38
BLK	-0.18	0.31	-10000	0	-0.7	149	149
HCK	-0.19	0.31	-10000	0	-0.69	151	151
regulation of stress fiber formation	-0.049	0.042	0.093	24	-10000	0	24
MAPK8	-0.12	0.2	-10000	0	-0.44	151	151
Ephrin B1/EPHB1-2/RGS3	0.051	0.043	-10000	0	-0.096	21	21
endothelial cell migration	-0.12	0.18	-10000	0	-0.4	160	160
NCK2	0.023	0.006	-10000	0	-0.12	1	1
PTPN13	-0.013	0.058	-10000	0	-0.13	112	112
regulation of focal adhesion formation	-0.049	0.042	0.093	24	-10000	0	24
chemotaxis	-0.049	0.042	0.095	21	-10000	0	21
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
Rac1/GTP	0.038	0.051	-10000	0	-0.15	11	11
angiogenesis	-0.15	0.23	-10000	0	-0.53	149	149
LCK	-0.18	0.31	-10000	0	-0.69	149	149

×

Fc-epsilon receptor I signaling in mast cells

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PPAP2A	0.02	0.019	-9999	-0.12	10	10
LAT2	-0.033	0.11	-9999	-0.2	138	138
AP1	-0.068	0.18	-9999	-0.38	107	107
mol:PIP3	-0.037	0.14	-9999	-0.26	128	128
IKBKB	-0.014	0.082	-9999	-0.15	125	125
AKT1	-0.025	0.071	-9999	-0.14	112	112
IKBKG	-0.013	0.082	-9999	-0.15	126	126
MS4A2	0.026	0.014	-9999	-0.13	3	3
mol:Sphingosine-1-phosphate	0	0	-9999	-10000	0	0
PIK3CA	0.02	0.017	-9999	-0.12	7	7
MAP3K1	-0.038	0.13	-9999	-0.28	98	98
mol:Ca2+	-0.026	0.11	-9999	-0.2	128	128
LYN	0.02	0.014	-9999	-0.12	4	4
CBLB	-0.032	0.1	-9999	-0.2	131	131
SHC1	0.023	0.001	-9999	-10000	0	0
RasGAP/p62DOK	-0.005	0.065	-9999	-0.1	132	132
positive regulation of cell migration	0.011	0.01	-9999	-0.077	7	7
INPP5D	0	0	-9999	-10000	0	0
PLD2	-0.008	0.051	-9999	-0.092	95	95
PTPN13	-0.088	0.2	-9999	-0.44	97	97
PTPN11	0.021	0.013	-9999	-0.12	3	3
GO:0007205	0	0	-9999	-10000	0	0
regulation of mast cell degranulation	-0.035	0.11	-9999	-0.22	98	98
SYK	0.016	0.028	-9999	-0.12	20	20
GRB2	0.023	0.006	-9999	-0.12	1	1
LAT/PLCgamma1/GRB2/SLP76/GADs	-0.062	0.12	-9999	-0.26	130	130
LAT	-0.032	0.1	-9999	-0.19	137	137
PAK2	-0.043	0.14	-9999	-0.29	107	107
NFATC2	-0.003	0.061	-9999	-0.42	10	10
HRAS	-0.047	0.15	-9999	-0.28	132	132
GAB2	0.007	0.041	-9999	-0.12	50	50
PLA2G1B	0.017	0.11	-9999	-0.92	8	8
Fc epsilon R1	0.003	0.062	-9999	-0.094	129	129
Antigen/IgE/Fc epsilon R1	0.006	0.055	-9999	-0.078	135	135
mol:GDP	-0.057	0.17	-9999	-0.32	131	131
JUN	0.014	0.033	-9999	-0.12	30	30
mol:Ca++	0	0	-9999	-10000	0	0
PIK3R1	0.015	0.031	-9999	-0.12	27	27
FOS	-0.005	0.053	-9999	-0.12	95	95
Antigen/IgE/Fc epsilon R1/LYN/SYK	-0.037	0.11	-9999	-0.21	138	138
CHUK	-0.017	0.085	-9999	-0.16	127	127
KLRG1	-0.015	0.088	-9999	-0.18	103	103
VAV1	-0.034	0.11	-9999	-0.2	132	132
calcium-dependent protein kinase C activity	0	0	-9999	-10000	0	0
CBL	-0.032	0.1	-9999	-0.19	137	137
negative regulation of mast cell degranulation	-0.026	0.086	-9999	-0.18	93	93
BTK	-0.064	0.19	-9999	-0.44	84	84
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK	-0.035	0.1	-9999	-0.18	158	158
GAB2/PI3K/SHP2	-0.046	0.06	-9999	-0.14	117	117
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP	0.002	0.073	-9999	-0.23	40	40
RAF1	0.011	0.12	-9999	-0.99	8	8
Fc epsilon R1/FcgammaRIIB/SHIP	-0.008	0.083	-9999	-0.12	182	182
FCER1G	0.002	0.044	-9999	-0.12	62	62
FCER1A	0.018	0.028	-9999	-0.12	20	20
Antigen/IgE/Fc epsilon R1/Fyn	0.002	0.066	-9999	-0.097	109	109
MAPK3	0.015	0.12	-9999	-0.93	8	8
MAPK1	0.014	0.12	-9999	-0.93	8	8
NFKB1	0.021	0.013	-9999	-0.12	4	4
MAPK8	-0.007	0.13	-9999	-0.53	26	26
DUSP1	-0.004	0.052	-9999	-0.12	90	90
NF-kappa-B/RelA	-0.005	0.061	-9999	-0.12	94	94
actin cytoskeleton reorganization	-0.066	0.2	-9999	-0.5	68	68
mol:Glucocorticoid Dexamethasone	0	0	-9999	-10000	0	0
PI3K	-0.037	0.14	-9999	-0.25	137	137
FER	-0.032	0.1	-9999	-0.2	134	134
RELA	0.023	0.009	-9999	-0.12	2	2
ITK	-0.004	0.05	-9999	-0.25	12	12
SOS1	0.017	0.027	-9999	-0.12	20	20
PLCG1	-0.054	0.16	-9999	-0.3	133	133
cytokine secretion	-0.005	0.044	-9999	-0.087	99	99
SPHK1	-0.033	0.1	-9999	-0.19	138	138
PTK2	-0.07	0.21	-9999	-0.53	68	68
NTAL/PLCgamma1/GRB2/SLP76/GADs	-0.062	0.13	-9999	-0.26	132	132
EDG1	0.011	0.01	-9999	-0.077	7	7
mol:DAG	-0.035	0.14	-9999	-0.26	126	126
MAP2K2	0.01	0.12	-9999	-0.94	8	8
MAP2K1	0.013	0.11	-9999	-0.93	8	8
MAP2K7	0.022	0.012	-9999	-0.12	4	4
KLRG1/SHP2	-0.014	0.084	-9999	-0.17	94	94
MAP2K4	0.012	0.12	-9999	-0.84	11	11
Fc epsilon R1/FcgammaRIIB	-0.009	0.09	-9999	-0.13	182	182
mol:Choline	-0.008	0.05	-9999	-0.092	95	95
SHC/Grb2/SOS1	-0.011	0.12	-9999	-0.19	133	133
FYN	0.011	0.037	-9999	-0.12	40	40
DOK1	0.021	0.016	-9999	-0.12	7	7
PXN	-0.06	0.19	-9999	-0.48	68	68
HCLS1	-0.035	0.12	-9999	-0.23	117	117
PRKCB	-0.026	0.11	-9999	-0.2	128	128
FCGR2B	0.004	0.044	-9999	-0.12	60	60
IGHE	-0.001	0.003	-9999	-10000	0	0
KLRG1/SHIP	-0.027	0.087	-9999	-0.18	93	93
LCP2	0.013	0.033	-9999	-0.12	31	31
PLA2G4A	-0.045	0.11	-9999	-0.22	134	134
RASA1	0.021	0.012	-9999	-0.12	3	3
mol:Phosphatidic acid	-0.008	0.05	-9999	-0.092	95	95
IKK complex	-0.006	0.068	-9999	-0.14	88	88
WIPF1	0.02	0.02	-9999	-0.12	11	11

×

Thromboxane A2 receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGM2	0.005	0.046	-10000	0	-0.12	65	65
GNB1/GNG2	-0.069	0.081	-10000	0	-0.18	194	194
AKT1	-0.055	0.11	-10000	0	-0.19	195	195
EGF	0.02	0.021	-10000	0	-0.12	12	12
mol:TXA2	0	0.001	-10000	0	-10000	0	0
FGR	0.026	0.029	-10000	0	-0.11	7	7
mol:Ca2+	-0.096	0.15	-10000	0	-0.29	196	196
LYN	0.024	0.031	-10000	0	-0.13	8	8
RhoA/GTP	-0.036	0.069	-10000	0	-0.12	196	196
mol:PGI2	0	0	-10000	0	-10000	0	0
SYK	-0.12	0.17	-10000	0	-0.34	194	194
GNG2	0.02	0.018	-10000	0	-0.12	9	9
ARRB2	0.022	0.014	-10000	0	-0.12	5	5
TP alpha/Gq family/GDP/G beta5/gamma2	0.028	0.047	-10000	0	-0.24	12	12
G beta5/gamma2	-0.091	0.11	-10000	0	-0.23	194	194
PRKCH	-0.12	0.18	-10000	0	-0.35	196	196
DNM1	0.021	0.019	-10000	0	-0.12	10	10
TXA2/TP beta/beta Arrestin3	0.017	0.014	-10000	0	-10000	0	0
mol:GTP	-0.001	0.001	-10000	0	-10000	0	0
PTGDR	0.023	0.006	-10000	0	-0.12	1	1
G12 family/GTP	-0.12	0.13	-10000	0	-0.29	196	196
ADRBK1	0.023	0.001	-10000	0	-10000	0	0
ADRBK2	0.015	0.032	-10000	0	-0.12	28	28
RhoA/GTP/ROCK1	0.027	0.021	-10000	0	-0.1	14	14
mol:GDP	0.05	0.12	0.23	91	-10000	0	91
mol:NADP	0.023	0	-10000	0	-10000	0	0
RAB11A	0.023	0.007	-10000	0	-0.12	1	1
PRKG1	0.018	0.026	-10000	0	-0.12	19	19
mol:IP3	-0.12	0.19	-10000	0	-0.36	196	196
cell morphogenesis	0.027	0.021	-10000	0	-0.1	14	14
PLCB2	-0.17	0.25	-10000	0	-0.49	196	196
mol:cGMP	0	0.001	-10000	0	-10000	0	0
BLK	0.026	0.029	-10000	0	-0.12	6	6
mol:PDG2	0	0	-10000	0	-10000	0	0
HCK	0.024	0.032	-10000	0	-0.14	7	7
RHOA	0.023	0.006	-10000	0	-0.12	1	1
PTGIR	0.023	0.002	-10000	0	-10000	0	0
PRKCB1	-0.13	0.19	-10000	0	-0.37	196	196
GNAQ	0.021	0.016	-10000	0	-0.12	6	6
mol:L-citrulline	0.023	0	-10000	0	-10000	0	0
TXA2/TXA2-R family	-0.18	0.26	-10000	0	-0.51	194	194
LCK	0.026	0.029	-10000	0	-0.11	6	6
TXA2/TP beta/beta Arrestin3/RAB11/GDP	0.042	0.026	-10000	0	-0.12	7	7
TXA2-R family/G12 family/GDP/G beta/gamma	0.028	0.061	-10000	0	-0.43	8	8
TXA2/TP beta/beta Arrestin2/RAB11/GDP	0.041	0.028	-10000	0	-0.12	7	7
MAPK14	-0.073	0.12	-10000	0	-0.22	195	195
TGM2/GTP	-0.14	0.21	-10000	0	-0.4	200	200
MAPK11	-0.072	0.12	-10000	0	-0.22	194	194
ARHGEF1	-0.053	0.094	-10000	0	-0.17	196	196
GNAI2	0.022	0.011	-10000	0	-0.12	3	3
JNK cascade	-0.13	0.19	-10000	0	-0.38	195	195
RAB11/GDP	0.023	0.007	-10000	0	-0.12	1	1
ICAM1	-0.11	0.16	-10000	0	-0.32	195	195
cAMP biosynthetic process	-0.11	0.17	-10000	0	-0.33	198	198
Gq family/GTP/EBP50	0.017	0.042	-10000	0	-0.14	29	29
actin cytoskeleton reorganization	0.027	0.021	-10000	0	-0.1	14	14
SRC	0.026	0.029	-10000	0	-0.11	6	6
GNB5	0.023	0.009	-10000	0	-0.12	2	2
GNB1	0.023	0.007	-10000	0	-0.12	1	1
EGF/EGFR	0.018	0.057	-10000	0	-0.13	38	38
VCAM1	-0.12	0.17	-10000	0	-0.34	195	195
TP beta/Gq family/GDP/G beta5/gamma2	0.028	0.047	-10000	0	-0.24	12	12
platelet activation	-0.094	0.16	-10000	0	-0.29	195	195
PGI2/IP	0.015	0.017	-10000	0	-0.15	6	6
PRKACA	0.021	0.023	-10000	0	-0.15	8	8
Gq family/GDP/G beta5/gamma2	0.027	0.046	-10000	0	-0.22	12	12
TXA2/TP beta/beta Arrestin2	0.016	0.033	-10000	0	-0.26	5	5
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TBXA2R	0.021	0.021	-10000	0	-0.14	8	8
mol:DAG	-0.14	0.21	-10000	0	-0.41	196	196
EGFR	0.015	0.03	-10000	0	-0.12	25	25
TXA2/TP alpha	-0.15	0.23	-10000	0	-0.45	197	197
Gq family/GTP	0.014	0.037	-10000	0	-0.14	25	25
YES1	0.024	0.032	-10000	0	-0.14	8	8
GNAI2/GTP	0.02	0.029	-10000	0	-0.12	6	6
PGD2/DP	0.017	0.004	-10000	0	-0.078	1	1
SLC9A3R1	0.016	0.031	-10000	0	-0.12	26	26
FYN	0.02	0.035	-10000	0	-0.13	13	13
mol:NO	0.023	0	-10000	0	-10000	0	0
GNA15	0.021	0.017	-10000	0	-0.12	8	8
PGK/cGMP	0.028	0.016	-10000	0	-10000	0	0
RhoA/GDP	0.023	0.006	-10000	0	-0.12	1	1
TP alpha/TGM2/GDP/G beta/gamma	0.04	0.045	-10000	0	-0.15	7	7
NOS3	0.023	0	-10000	0	-10000	0	0
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCA	-0.12	0.18	-10000	0	-0.35	197	197
PRKCB	-0.12	0.18	-10000	0	-0.34	196	196
PRKCE	-0.12	0.18	-10000	0	-0.36	195	195
PRKCD	-0.13	0.19	-10000	0	-0.37	195	195
PRKCG	-0.13	0.19	-10000	0	-0.37	196	196
muscle contraction	-0.16	0.24	-10000	0	-0.47	195	195
PRKCZ	-0.11	0.17	-10000	0	-0.33	195	195
ARR3	0.023	0.006	-10000	0	-0.12	1	1
TXA2/TP beta	0.033	0.035	-10000	0	-0.12	11	11
PRKCQ	-0.12	0.18	-10000	0	-0.35	196	196
MAPKKK cascade	-0.15	0.22	-10000	0	-0.43	196	196
SELE	-0.094	0.15	-10000	0	-0.28	194	194
TP beta/GNAI2/GDP/G beta/gamma	0.052	0.035	-10000	0	-0.2	2	2
ROCK1	0.022	0.009	-10000	0	-0.12	2	2
GNA14	0.02	0.02	-10000	0	-0.12	11	11
chemotaxis	-0.21	0.3	-10000	0	-0.6	194	194
GNA12	0.023	0.001	-10000	0	-10000	0	0
GNA13	0.022	0.009	-10000	0	-0.12	2	2
GNA11	0.022	0.014	-10000	0	-0.12	5	5
Rac1/GTP	0.015	0.015	-10000	0	-0.15	5	5

×

PLK2 and PLK4 events

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

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

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

×

amb2 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2	-0.03	0.083	-9999	-0.13	180	180
alphaM/beta2 Integrin/GPIbA	0.022	0.059	-9999	-0.11	77	77
alphaM/beta2 Integrin/proMMP-9	-0.005	0.081	-9999	-0.13	128	128
PLAUR	0.018	0.024	-9999	-0.12	15	15
HMGB1	0.023	0.008	-9999	-0.041	1	1
alphaM/beta2 Integrin/Talin	0.015	0.069	-9999	-0.12	95	95
AGER	0.022	0.017	-9999	-0.11	7	7
RAP1A	0.021	0.012	-9999	-0.12	3	3
SELPLG	0.02	0.021	-9999	-0.12	12	12
mol:LDL	0	0	-9999	-10000	0	0
alphaM/beta2 Integrin/RAGE/HMGB1	0.034	0.07	-9999	-0.15	22	22
mol:GTP	0	0	-9999	-10000	0	0
MMP9	0	0.05	-9999	-0.12	81	81
CYR61	0.002	0.047	-9999	-0.12	70	70
TLN1	0.021	0.012	-9999	-0.12	3	3
Rap1/GTP	-0.099	0.15	-9999	-0.3	162	162
RHOA	0.023	0.006	-9999	-0.12	1	1
P-selectin oligomer	0.018	0.027	-9999	-0.12	21	21
MYH2	-0.12	0.15	-9999	-0.28	208	208
MST1R	0.017	0.029	-9999	-0.12	23	23
leukocyte activation during inflammatory response	0.027	0.052	-9999	-0.1	37	37
APOB	0.022	0.011	-9999	-0.12	3	3
mol:GDP	0	0	-9999	-10000	0	0
complement component iC3b receptor activity	0	0	-9999	-10000	0	0
MMP2	-0.015	0.059	-9999	-0.12	128	128
JAM3	0.02	0.02	-9999	-0.12	11	11
GP1BA	0.022	0.012	-9999	-0.12	4	4
alphaM/beta2 Integrin/CTGF	0.003	0.073	-9999	-0.12	118	118
alphaM/beta2 Integrin	-0.12	0.16	-9999	-0.33	157	157
JAM3 homodimer	0.02	0.02	-9999	-0.12	11	11
ICAM2	0.017	0.029	-9999	-0.12	23	23
ICAM1	0	0.048	-9999	-0.12	74	74
phagocytosis triggered by activation of immune response cell surface activating receptor	-0.12	0.16	-9999	-0.33	157	157
cell adhesion	0.021	0.059	-9999	-0.11	77	77
NFKB1	0.021	0.072	-9999	-0.25	14	14
THY1	-0.003	0.049	-9999	-0.12	79	79
RhoA/GDP	0.016	0.016	-9999	-0.14	6	6
Lipoprotein(a)	0.03	0.014	-9999	-0.062	12	12
alphaM/beta2 Integrin/LRP/tPA	-0.016	0.087	-9999	-0.15	94	94
IL6	0.007	0.094	-9999	-0.44	10	10
ITGB2	0.013	0.032	-9999	-0.098	37	37
elevation of cytosolic calcium ion concentration	-0.016	0.1	-9999	-0.15	153	153
alphaM/beta2 Integrin/JAM2/JAM3	0.027	0.063	-9999	-0.1	83	83
JAM2	0.014	0.035	-9999	-0.12	35	35
alphaM/beta2 Integrin/ICAM1	0.004	0.088	-9999	-0.17	66	66
alphaM/beta2 Integrin/uPA/Plg	-0.006	0.088	-9999	-0.14	132	132
RhoA/GTP	-0.13	0.16	-9999	-0.3	216	216
positive regulation of phagocytosis	-0.078	0.14	-9999	-0.29	135	135
Ron/MSP	0.027	0.031	-9999	-0.088	36	36
alphaM/beta2 Integrin/uPAR/uPA	-0.015	0.1	-9999	-0.15	153	153
alphaM/beta2 Integrin/uPAR	0.012	0.077	-9999	-0.15	88	88
PLAU	-0.007	0.055	-9999	-0.12	102	102
PLAT	-0.001	0.049	-9999	-0.12	76	76
actin filament polymerization	-0.12	0.14	-9999	-0.27	208	208
MST1	0.022	0.012	-9999	-0.12	4	4
alphaM/beta2 Integrin/lipoprotein(a)	0.031	0.054	-9999	-0.1	37	37
TNF	0.015	0.076	-9999	-0.38	5	5
RAP1B	0.019	0.02	-9999	-0.12	10	10
alphaM/beta2 Integrin/uPA	-0.02	0.091	-9999	-0.15	143	143
fibrinolysis	-0.007	0.086	-9999	-0.14	132	132
HCK	0.019	0.024	-9999	-0.12	15	15
dendritic cell antigen processing and presentation	-0.12	0.16	-9999	-0.33	157	157
VTN	0.023	0.009	-9999	-0.12	2	2
alphaM/beta2 Integrin/CYR61	-0.01	0.08	-9999	-0.13	144	144
LPA	0.021	0.019	-9999	-0.12	10	10
LRP1	0.014	0.032	-9999	-0.12	29	29
cell migration	-0.044	0.086	-9999	-0.13	234	234
FN1	-0.013	0.056	-9999	-0.12	114	114
alphaM/beta2 Integrin/Thy1	-0.026	0.085	-9999	-0.13	197	197
MPO	0.023	0.009	-9999	-0.12	2	2
KNG1	0.022	0.011	-9999	-0.12	3	3
RAP1/GDP	0.015	0.05	-9999	-0.12	61	61
ROCK1	-0.12	0.15	-9999	-0.28	208	208
ELA2	0.022	0.011	-9999	-0.12	3	3
PLG	0.023	0.009	-9999	-0.12	2	2
CTGF	0.012	0.036	-9999	-0.12	37	37
alphaM/beta2 Integrin/Hck	0.017	0.07	-9999	-0.14	81	81
ITGAM	0.021	0.019	-9999	-0.11	9	9
alphaM/beta2 Integrin/P-Selectin/PSGL1	0.03	0.066	-9999	-0.11	80	80
HP	-0.035	0.063	-9999	-0.12	193	193
leukocyte adhesion	-0.009	0.088	-9999	-0.18	51	51
SELP	0.018	0.028	-9999	-0.12	21	21

×

TRAIL signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TNFSF10	0.001	0.046	-9999	-0.12	67	67
positive regulation of NF-kappaB transcription factor activity	-0.021	0.079	-9999	-0.12	202	202
MAP2K4	-0.008	0.086	-9999	-0.23	34	34
IKBKB	0.022	0.015	-9999	-0.12	6	6
TNFRSF10B	0.022	0.014	-9999	-0.12	5	5
TNFRSF10A	0.019	0.021	-9999	-0.12	12	12
SMPD1	-0.013	0.053	-9999	-0.16	9	9
IKBKG	0.023	0.009	-9999	-0.12	2	2
mol:GTP	0	0	-9999	-10000	0	0
TNFRSF10D	0.019	0.023	-9999	-0.12	15	15
TRAIL/TRAILR2	-0.02	0.078	-9999	-0.12	197	197
TRAIL/TRAILR3	-0.02	0.075	-9999	-0.12	204	204
TRAIL/TRAILR1	-0.025	0.082	-9999	-0.12	213	213
TRAIL/TRAILR4	-0.021	0.08	-9999	-0.12	202	202
TRAIL/TRAILR1/DAP3/GTP	-0.006	0.069	-9999	-0.11	142	142
IKK complex	0.006	0.079	-9999	-0.28	32	32
RIPK1	0.022	0.011	-9999	-0.12	3	3
response to oxidative stress	0	0	-9999	-10000	0	0
DAP3/GTP	0.014	0.021	-9999	-0.14	10	10
MAPK3	0.006	0.032	-9999	-0.074	71	71
MAP3K1	-0.008	0.087	-9999	-0.16	121	121
TRAILR4 (trimer)	0.019	0.023	-9999	-0.12	15	15
TRADD	0.023	0.006	-9999	-0.12	1	1
TRAILR1 (trimer)	0.019	0.021	-9999	-0.12	12	12
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2	-0.011	0.083	-9999	-0.14	138	138
CFLAR	0.022	0.011	-9999	-0.12	3	3
MAPK1	0.005	0.034	-9999	-0.076	73	73
TRAIL/TRAILR1/FADD/TRADD/RIP	0.015	0.073	-9999	-0.094	140	140
mol:ceramide	-0.013	0.053	-9999	-0.16	9	9
FADD	0.023	0.009	-9999	-0.12	2	2
MAPK8	-0.007	0.084	-9999	-0.22	40	40
TRAF2	0.023	0	-9999	-10000	0	0
TRAILR3 (trimer)	0.019	0.025	-9999	-0.12	18	18
CHUK	0.021	0.013	-9999	-0.12	4	4
TRAIL/TRAILR1/FADD	-0.007	0.074	-9999	-0.12	137	137
DAP3	0.023	0.007	-9999	-0.12	1	1
CASP10	-0.038	0.098	-9999	-0.2	128	128
JNK cascade	-0.021	0.079	-9999	-0.12	202	202
TRAIL (trimer)	0.001	0.046	-9999	-0.12	67	67
TNFRSF10C	0.019	0.026	-9999	-0.12	18	18
TRAIL/TRAILR1/DAP3/GTP/FADD	0.004	0.069	-9999	-0.098	142	142
TRAIL/TRAILR2/FADD	-0.002	0.071	-9999	-0.12	129	129
cell death	-0.013	0.052	-9999	-0.1	129	129
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2	-0.007	0.079	-9999	-0.14	131	131
TRAILR2 (trimer)	0.022	0.014	-9999	-0.12	5	5
CASP8	-0.002	0.11	-9999	-0.66	15	15
negative regulation of caspase activity	0	0	-9999	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP	0.019	0.071	-9999	-0.091	132	132

×

Cellular roles of Anthrax toxin

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
ANTXR1	0.007	0.043	-10000	0	-0.12	54	54
ANTXR2	0.013	0.036	-10000	0	-0.12	36	36
negative regulation of myeloid dendritic cell antigen processing and presentation	-0.007	0.013	-10000	0	-0.034	102	102
monocyte activation	-0.1	0.16	-10000	0	-0.35	156	156
MAP2K2	0.006	0.052	-10000	0	-0.66	3	3
MAP2K1	0	0.015	-10000	0	-0.031	80	80
MAP2K7	0	0.014	-10000	0	-0.03	81	81
MAP2K6	-0.005	0.024	-10000	0	-0.065	55	55
CYAA	-0.016	0.048	-10000	0	-0.11	102	102
MAP2K4	-0.001	0.016	-10000	0	-0.031	81	81
IL1B	-0.009	0.035	-10000	0	-0.075	90	90
Channel	-0.003	0.06	-10000	0	-0.12	102	102
NLRP1	-0.001	0.015	-10000	0	-0.032	81	81
CALM1	0.022	0.014	-10000	0	-0.12	5	5
negative regulation of phagocytosis	0.001	0.054	-10000	0	-0.46	7	7
mol:Ca2+	0	0	-10000	0	-10000	0	0
regulation of endothelial cell proliferation	0.007	0.013	0.034	102	-10000	0	102
MAPK3	-0.001	0.015	-10000	0	-0.052	19	19
MAPK1	-0.001	0.019	-10000	0	-0.036	85	85
PGR	-0.011	0.027	-10000	0	-0.047	173	173
PA/Cellular Receptors	-0.004	0.066	-10000	0	-0.13	102	102
apoptosis	-0.007	0.013	-10000	0	-0.034	102	102
LOC728358	0	0	-10000	0	-10000	0	0
Lethal toxin (unfolded)	-0.002	0.058	-10000	0	-0.12	102	102
macrophage activation	0.003	0.018	-10000	0	-0.053	29	29
TNF	0.02	0.02	-10000	0	-0.12	11	11
VCAM1	-0.1	0.16	-10000	0	-0.36	156	156
platelet activation	0.001	0.054	-10000	0	-0.46	7	7
MAPKKK cascade	0.003	0.02	0.048	52	-10000	0	52
IL18	-0.011	0.039	-10000	0	-0.076	110	110
negative regulation of macrophage activation	-0.007	0.013	-10000	0	-0.034	102	102
LEF	-0.007	0.013	-10000	0	-0.034	102	102
CASP1	-0.005	0.024	-10000	0	-0.05	82	82
mol:cAMP	0.001	0.055	-10000	0	-0.46	7	7
necrosis	-0.007	0.013	-10000	0	-0.034	102	102
intracellular pH reduction	0	0	-10000	0	-10000	0	0
PAGA	0	0	-10000	0	-10000	0	0
Edema toxin (unfolded)	-0.001	0.056	-10000	0	-0.11	102	102
mol:Epigallocatechin-3-gallate (EGCG)	0	0	-10000	0	-10000	0	0

×

Syndecan-4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.11	0.2	-10000	0	-0.37	177	177
Syndecan-4/Syndesmos	-0.08	0.18	-10000	0	-0.4	102	102
positive regulation of JNK cascade	-0.1	0.18	-10000	0	-0.4	114	114
Syndecan-4/ADAM12	-0.094	0.18	-10000	0	-0.41	104	104
CCL5	0.005	0.044	-10000	0	-0.12	60	60
Rac1/GDP	0.016	0.015	-10000	0	-0.15	5	5
DNM2	0.02	0.022	-10000	0	-0.12	13	13
ITGA5	0.013	0.036	-10000	0	-0.12	38	38
SDCBP	0.021	0.01	-10000	0	-0.12	2	2
PLG	0.027	0.011	0.068	1	-0.1	2	3
ADAM12	-0.01	0.06	-10000	0	-0.12	127	127
mol:GTP	0	0	-10000	0	-10000	0	0
NUDT16L1	0.021	0.019	-10000	0	-0.12	10	10
mol:PI-4-5-P2	0	0	-10000	0	-10000	0	0
Syndecan-4/PKC alpha	-0.008	0.009	-10000	0	-0.041	4	4
Syndecan-4/Laminin alpha1	-0.088	0.18	-10000	0	-0.41	103	103
Syndecan-4/CXCL12/CXCR4	-0.11	0.19	-10000	0	-0.42	114	114
Syndecan-4/Laminin alpha3	-0.094	0.18	-10000	0	-0.42	106	106
MDK	0.021	0.014	-10000	0	-0.12	5	5
Syndecan-4/FZD7	-0.086	0.18	-10000	0	-0.41	102	102
Syndecan-4/Midkine	-0.081	0.18	-10000	0	-0.4	102	102
FZD7	0.015	0.031	-10000	0	-0.12	27	27
Syndecan-4/FGFR1/FGF	-0.068	0.17	-10000	0	-0.38	103	103
THBS1	-0.004	0.053	-10000	0	-0.12	92	92
integrin-mediated signaling pathway	-0.098	0.18	-10000	0	-0.41	105	105
positive regulation of MAPKKK cascade	-0.1	0.18	-10000	0	-0.4	114	114
Syndecan-4/TACI	-0.079	0.18	-10000	0	-0.4	102	102
CXCR4	0.012	0.032	-10000	0	-0.12	29	29
cell adhesion	-0.054	0.096	-10000	0	-0.19	166	166
Syndecan-4/Dynamin	-0.081	0.18	-10000	0	-0.41	102	102
Syndecan-4/TSP1	-0.1	0.18	-10000	0	-0.41	110	110
Syndecan-4/GIPC	-0.081	0.18	-10000	0	-0.4	102	102
Syndecan-4/RANTES	-0.096	0.19	-10000	0	-0.42	105	105
ITGB1	0.021	0.015	-10000	0	-0.12	6	6
LAMA1	0	0.053	-10000	0	-0.12	89	89
LAMA3	0.006	0.043	-10000	0	-0.12	55	55
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCA	0.001	0.052	0.079	4	-0.16	40	44
Syndecan-4/alpha-Actinin	-0.082	0.18	-10000	0	-0.41	103	103
TFPI	0.018	0.026	-10000	0	-0.12	19	19
F2	0.02	0.016	-10000	0	-0.12	4	4
alpha5/beta1 Integrin	0.016	0.048	-10000	0	-0.14	34	34
positive regulation of cell adhesion	-0.097	0.18	-10000	0	-0.4	111	111
ACTN1	0.022	0.011	-10000	0	-0.12	3	3
TNC	-0.004	0.053	-10000	0	-0.12	93	93
Syndecan-4/CXCL12	-0.1	0.19	-10000	0	-0.43	103	103
FGF6	0.022	0.012	-10000	0	-0.12	4	4
RHOA	0.023	0.006	-10000	0	-0.12	1	1
CXCL12	-0.003	0.051	-10000	0	-0.12	86	86
TNFRSF13B	0.023	0	-10000	0	-10000	0	0
FGF2	0.023	0.009	-10000	0	-0.12	2	2
FGFR1	0.008	0.043	-10000	0	-0.12	54	54
Syndecan-4/PI-4-5-P2	-0.089	0.17	-10000	0	-0.4	102	102
mol:GDP	0	0	-10000	0	-10000	0	0
FN1	-0.012	0.056	-10000	0	-0.12	114	114
cell migration	-0.005	0.005	-10000	0	-10000	0	0
PRKCD	0.023	0.019	-10000	0	-0.12	8	8
vasculogenesis	-0.099	0.18	-10000	0	-0.4	110	110
SDC4	-0.09	0.18	-10000	0	-0.43	102	102
Syndecan-4/Tenascin C	-0.1	0.18	-10000	0	-0.42	105	105
Syndecan-4/PI-4-5-P2/PKC alpha	-0.006	0.007	-10000	0	-10000	0	0
Syndecan-4/Syntenin	-0.085	0.18	-10000	0	-0.41	102	102
MMP9	0.001	0.051	-10000	0	-0.12	81	81
Rac1/GTP	-0.054	0.098	-10000	0	-0.19	168	168
cytoskeleton organization	-0.077	0.17	-10000	0	-0.39	102	102
GIPC1	0.019	0.023	-10000	0	-0.12	15	15
Syndecan-4/TFPI	-0.081	0.18	-10000	0	-0.4	102	102

×

IL4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.16	0.46	-10000	0	-1	88	88
STAT6 (cleaved dimer)	-0.25	0.38	-10000	0	-0.94	106	106
IGHG1	-0.031	0.2	-10000	0	-0.41	36	36
IGHG3	-0.16	0.42	-10000	0	-0.93	94	94
AKT1	-0.12	0.34	-10000	0	-0.77	84	84
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1	-0.11	0.34	-10000	0	-0.81	77	77
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1	-0.13	0.37	-10000	0	-0.86	81	81
THY1	-0.33	0.62	-10000	0	-1.2	170	170
MYB	0.011	0.038	-10000	0	-0.12	41	41
HMGA1	0.012	0.037	-10000	0	-0.12	40	40
IL4/IL4R/JAK1/IL2R gamma/JAK3	-0.11	0.33	-10000	0	-0.68	99	99
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP	-0.13	0.37	-10000	0	-0.85	82	82
SP1	-0.002	0.049	-10000	0	-0.09	109	109
INPP5D	0	0	-10000	0	-10000	0	0
SOCS5	0.017	0.023	-10000	0	-0.088	3	3
STAT6 (dimer)/ETS1	-0.17	0.45	-10000	0	-0.96	101	101
SOCS1	-0.096	0.32	-10000	0	-0.65	93	93
SOCS3	-0.11	0.34	-10000	0	-0.83	66	66
FCER2	-0.099	0.33	-10000	0	-0.76	49	49
PARP14	0.014	0.032	-10000	0	-0.12	28	28
CCL17	-0.15	0.45	-10000	0	-0.99	85	85
GRB2	0.023	0.006	-10000	0	-0.12	1	1
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP	-0.078	0.27	-10000	0	-0.61	71	71
T cell proliferation	-0.18	0.47	-10000	0	-1	99	99
IL4R/JAK1	-0.17	0.46	-10000	0	-1	96	96
EGR2	-0.15	0.45	-10000	0	-1	86	86
JAK2	0.014	0.05	-10000	0	-0.14	16	16
JAK3	0.023	0.016	-10000	0	-0.12	5	5
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
JAK1	0.024	0.021	-10000	0	-0.13	2	2
COL1A2	-0.24	0.54	-10000	0	-1.3	112	112
CCL26	-0.16	0.46	-10000	0	-1	91	91
IL4R	-0.17	0.49	-10000	0	-1.1	90	90
PTPN6	0.023	0.018	-10000	0	-0.12	2	2
IL13RA2	-0.16	0.45	-10000	0	-1	86	86
IL13RA1	0.015	0.049	-10000	0	-0.13	13	13
IRF4	0.001	0.13	-10000	0	-0.85	2	2
ARG1	-0.001	0.16	-10000	0	-0.72	5	5
CBL	-0.1	0.31	-10000	0	-0.64	99	99
GTF3A	-0.013	0.055	-10000	0	-0.096	144	144
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
IL13RA1/JAK2	0.004	0.092	-10000	0	-0.16	75	75
IRF4/BCL6	-0.004	0.12	-10000	0	-0.84	2	2
CD40LG	0.031	0.012	-10000	0	-0.12	2	2
MAPK14	-0.11	0.33	-10000	0	-0.68	94	94
mitosis	-0.11	0.32	-10000	0	-0.72	84	84
STAT6	-0.18	0.52	-10000	0	-1.1	94	94
SPI1	0.027	0.021	-10000	0	-0.12	12	12
RPS6KB1	-0.1	0.31	-10000	0	-0.69	85	85
STAT6 (dimer)	-0.18	0.51	-10000	0	-1.1	94	94
STAT6 (dimer)/PARP14	-0.19	0.47	-10000	0	-1	96	96
mast cell activation	0.001	0.015	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2	-0.12	0.36	-10000	0	-0.79	88	88
FRAP1	-0.12	0.34	-10000	0	-0.77	84	84
LTA	-0.15	0.45	-10000	0	-0.99	87	87
FES	0.022	0.011	-10000	0	-0.12	3	3
T-helper 1 cell differentiation	0.17	0.5	1.1	94	-10000	0	94
CCL11	-0.18	0.47	-10000	0	-1	98	98
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES	-0.12	0.35	-10000	0	-0.78	88	88
IL2RG	0	0.051	-10000	0	-0.12	82	82
IL10	-0.15	0.44	-10000	0	-0.99	86	86
IRS1	0.019	0.023	-10000	0	-0.12	14	14
IRS2	0.021	0.016	-10000	0	-0.12	7	7
IL4	0.003	0.14	-10000	0	-10000	0	0
IL5	-0.15	0.45	-10000	0	-1	79	79
IL4/IL4R/JAK1/IL13RA1/JAK2	-0.14	0.43	-10000	0	-0.89	94	94
COL1A1	-0.3	0.6	-10000	0	-1.3	139	139
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1	-0.17	0.47	-10000	0	-1	89	89
IL2R gamma/JAK3	-0.008	0.072	-10000	0	-0.13	116	116
TFF3	-0.17	0.47	-10000	0	-1.1	86	86
ALOX15	-0.15	0.45	-10000	0	-0.99	85	85
MYBL1	0.017	0.028	-10000	0	-0.12	22	22
T-helper 2 cell differentiation	-0.15	0.42	-10000	0	-0.88	99	99
SHC1	0.023	0.001	-10000	0	-10000	0	0
CEBPB	0.023	0.032	-10000	0	-0.12	29	29
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2	-0.12	0.37	-10000	0	-0.84	82	82
mol:PI-3-4-5-P3	-0.12	0.34	-10000	0	-0.77	84	84
PI3K	-0.13	0.37	-10000	0	-0.84	84	84
DOK2	0.02	0.021	-10000	0	-0.12	12	12
ETS1	0.012	0.036	-10000	0	-0.12	27	27
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2	-0.074	0.26	-10000	0	-0.6	71	71
ITGB3	-0.2	0.51	-10000	0	-1.1	98	98
PIGR	-0.18	0.46	-10000	0	-1	89	89
IGHE	0.001	0.06	0.16	18	-0.16	11	29
MAPKKK cascade	-0.072	0.26	-10000	0	-0.59	71	71
BCL6	0.018	0.02	-10000	0	-0.12	10	10
OPRM1	-0.15	0.45	-10000	0	-0.99	85	85
RETNLB	-0.15	0.45	-10000	0	-0.99	86	86
SELP	-0.16	0.45	-10000	0	-0.99	86	86
AICDA	-0.15	0.43	-10000	0	-0.96	86	86

×

Noncanonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC2	0.02	0.019	-9999	-0.12	10	10
GNB1/GNG2	-0.012	0.11	-9999	-0.23	68	68
mol:DAG	-0.018	0.095	-9999	-0.21	76	76
PLCG1	-0.019	0.097	-9999	-0.21	76	76
YES1	-0.029	0.1	-9999	-0.17	153	153
FZD3	0.013	0.032	-9999	-0.12	29	29
FZD6	0.017	0.023	-9999	-0.12	13	13
G protein	-0.009	0.1	-9999	-0.22	68	68
MAP3K7	-0.014	0.084	-9999	-0.18	82	82
mol:Ca2+	-0.017	0.093	-9999	-0.2	76	76
mol:IP3	-0.018	0.095	-9999	-0.21	76	76
NLK	0.026	0.045	-9999	-0.98	1	1
GNB1	0.023	0.007	-9999	-0.12	1	1
CAMK2A	-0.015	0.087	-9999	-0.19	76	76
MAP3K7IP1	0.023	0	-9999	-10000	0	0
Noncanonical Wnts/FZD	-0.033	0.1	-9999	-0.18	162	162
CSNK1A1	0.022	0.007	-9999	-0.12	1	1
GNAS	-0.028	0.098	-9999	-0.16	162	162
GO:0007205	-0.021	0.093	-9999	-0.21	76	76
WNT6	0.022	0.011	-9999	-0.12	3	3
WNT4	0.022	0.011	-9999	-0.12	3	3
NFAT1/CK1 alpha	-0.01	0.11	-9999	-0.22	82	82
GNG2	0.02	0.018	-9999	-0.12	9	9
WNT5A	0.014	0.031	-9999	-0.12	27	27
WNT11	0.002	0.051	-9999	-0.12	82	82
CDC42	-0.025	0.096	-9999	-0.16	153	153

×

BARD1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BARD1/CSTF1	0.016	0.052	-10000	0	-0.12	70	70
ATM	0.018	0.022	-10000	0	-0.12	13	13
UBE2D3	0.023	0.001	-10000	0	-10000	0	0
PRKDC	0.021	0.015	-10000	0	-0.12	6	6
ATR	0.02	0.015	-10000	0	-0.12	5	5
UBE2L3	0.022	0.012	-10000	0	-0.12	4	4
FANCD2	-0.008	0.096	-10000	0	-0.24	69	69
protein ubiquitination	-0.016	0.086	-10000	0	-0.11	211	211
XRCC5	0.021	0.01	-10000	0	-0.12	2	2
XRCC6	0.022	0.004	-10000	0	-10000	0	0
M/R/N Complex	0.023	0.065	-10000	0	-0.14	64	64
MRE11A	0.02	0.017	-10000	0	-0.12	7	7
DNA-PK	0.026	0.06	-10000	0	-0.14	60	60
FA complex/FANCD2/Ubiquitin	0.01	0.093	-10000	0	-0.32	27	27
FANCF	0.022	0.011	-10000	0	-0.12	3	3
BRCA1	0.015	0.03	-10000	0	-0.12	24	24
CCNE1	0.002	0.047	-10000	0	-0.12	70	70
CDK2/Cyclin E1	-0.016	0.075	-10000	0	-0.12	190	190
FANCG	0.021	0.016	-10000	0	-0.12	7	7
BRCA1/BACH1/BARD1	-0.001	0.071	-10000	0	-0.13	125	125
FANCE	0.023	0	-10000	0	-10000	0	0
FANCC	0.022	0.014	-10000	0	-0.12	5	5
NBN	0.02	0.015	-10000	0	-0.12	5	5
FANCA	0.021	0.019	-10000	0	-0.12	10	10
DNA repair	-0.014	0.11	-10000	0	-0.3	45	45
BRCA1/BARD1/ubiquitin	-0.001	0.071	-10000	0	-0.13	125	125
BARD1/DNA-PK	0.027	0.076	-10000	0	-0.14	80	80
FANCL	0.018	0.023	-10000	0	-0.12	14	14
mRNA polyadenylation	-0.015	0.052	0.12	70	-10000	0	70
BRCA1/BARD1/CTIP/M/R/N Complex	-0.035	0.14	-10000	0	-0.33	73	73
BRCA1/BACH1/BARD1/TopBP1	0.008	0.072	-10000	0	-0.13	104	104
BRCA1/BARD1/P53	-0.026	0.092	-10000	0	-0.12	252	252
BARD1/CSTF1/BRCA1	0.013	0.065	-10000	0	-0.12	94	94
BRCA1/BACH1	0.015	0.03	-10000	0	-0.12	24	24
BARD1	0.016	0.029	-10000	0	-0.12	23	23
PCNA	0.019	0.018	-10000	0	-0.12	8	8
BRCA1/BARD1/UbcH5C	0.015	0.063	-10000	0	-0.12	88	88
BRCA1/BARD1/UbcH7	0.013	0.065	-10000	0	-0.12	93	93
BRCA1/BARD1/RAD51/PCNA	0	0.085	-10000	0	-0.12	155	155
BARD1/DNA-PK/P53	-0.008	0.096	-10000	0	-0.2	59	59
BRCA1/BARD1/Ubiquitin	-0.001	0.071	-10000	0	-0.13	125	125
BRCA1/BARD1/CTIP	-0.011	0.083	-10000	0	-0.13	157	157
FA complex	0.018	0.074	-10000	0	-0.32	17	17
BARD1/EWS	0.018	0.049	-10000	0	-0.12	63	63
RBBP8	0.011	0.029	-10000	0	-0.077	47	47
TP53	0.011	0.029	-10000	0	-0.12	22	22
TOPBP1	0.021	0.016	-10000	0	-0.12	6	6
G1/S transition of mitotic cell cycle	0.027	0.091	0.12	252	-10000	0	252
BRCA1/BARD1	-0.013	0.09	-10000	0	-0.11	211	211
CSTF1	0.023	0.007	-10000	0	-0.12	1	1
BARD1/EWS-Fli1	0.002	0.045	-10000	0	-0.12	62	62
CDK2	0.018	0.023	-10000	0	-0.12	14	14
UniProt:Q9BZD1	0	0	-10000	0	-10000	0	0
RAD51	0.015	0.03	-10000	0	-0.12	25	25
RAD50	0.021	0.014	-10000	0	-0.12	5	5
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme	-0.001	0.071	-10000	0	-0.13	125	125
EWSR1	0.023	0.001	-10000	0	-10000	0	0

×

IL1-mediated signaling events

Figure S22. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S22. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
UBC13/UEV1A	0.014	0.022	-10000	0	-0.14	11	11
PRKCZ	0.023	0	-10000	0	-10000	0	0
MAP3K7IP2	0.02	0.016	-10000	0	-0.12	6	6
ERC1	0.016	0.029	-10000	0	-0.12	24	24
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4	-0.063	0.15	-10000	0	-0.29	128	128
IRAK/TOLLIP	0.028	0.026	-10000	0	-0.1	15	15
IKBKB	0.022	0.015	-10000	0	-0.12	6	6
IKBKG	0.023	0.009	-10000	0	-0.12	2	2
IL1 alpha/IL1R2	0.014	0.048	-10000	0	-0.15	23	23
IL1A	0.017	0.029	-10000	0	-0.12	24	24
IL1B	0.002	0.039	-10000	0	-0.085	82	82
IRAK/TRAF6/p62/Atypical PKCs	0.036	0.059	-10000	0	-0.16	17	17
IL1R2	0.007	0.045	-10000	0	-0.12	62	62
IL1R1	0.003	0.046	-10000	0	-0.12	66	66
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.063	0.15	0.16	1	-0.28	137	138
TOLLIP	0.022	0.011	-10000	0	-0.12	3	3
TICAM2	0.021	0.014	-10000	0	-0.12	5	5
MAP3K3	0.023	0	-10000	0	-10000	0	0
TAK1/TAB1/TAB2	0.033	0.051	-10000	0	-0.14	37	37
IKK complex/ELKS	0.024	0.092	-10000	0	-0.24	50	50
JUN	0.011	0.048	-10000	0	-0.16	31	31
MAP3K7	0.021	0.014	-10000	0	-0.12	5	5
IL1 beta fragment/IL1R1/IL1RAP/PI3K	-0.051	0.12	-10000	0	-0.21	142	142
IL1 alpha/IL1R1/IL1RAP/MYD88	-0.001	0.077	-10000	0	-0.11	134	134
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4	-0.003	0.087	-10000	0	-0.12	162	162
IL1 beta fragment/IL1R1/IL1RAP	-0.056	0.1	-10000	0	-0.15	243	243
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
MAPK8	0.013	0.051	-10000	0	-0.16	32	32
IRAK1	0.016	0.023	-10000	0	-0.087	23	23
IL1RN/IL1R1	-0.007	0.07	-10000	0	-0.15	89	89
IRAK4	0.019	0.02	-10000	0	-0.12	10	10
PRKCI	0.016	0.028	-10000	0	-0.12	22	22
TRAF6	0.022	0.009	-10000	0	-0.12	2	2
PI3K	0.007	0.065	-10000	0	-0.13	96	96
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.074	0.15	-10000	0	-0.3	138	138
CHUK	0.021	0.013	-10000	0	-0.12	4	4
IL1 beta fragment/IL1R1/IL1RAP/MYD88s	-0.056	0.1	-10000	0	-0.15	243	243
IL1 beta/IL1R2	-0.036	0.089	-10000	0	-0.15	181	181
IRAK/TRAF6/TAK1/TAB1/TAB2	0.045	0.057	-10000	0	-0.19	18	18
NF kappa B1 p50/RelA	-0.05	0.11	-10000	0	-0.2	149	149
IRAK3	0.009	0.042	-10000	0	-0.12	52	52
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4	-0.05	0.12	-10000	0	-0.22	129	129
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.03	0.11	-10000	0	-0.18	154	154
IL1 alpha/IL1R1/IL1RAP	-0.014	0.078	-10000	0	-0.13	131	131
RELA	0.023	0.009	-10000	0	-0.12	2	2
MAP3K7IP1	0.023	0	-10000	0	-10000	0	0
SQSTM1	0.021	0.014	-10000	0	-0.12	5	5
MYD88	0.023	0.006	-10000	0	-0.12	1	1
IRAK/TRAF6/MEKK3	0.039	0.031	-10000	0	-0.095	23	23
IL1RAP	0.009	0.039	-10000	0	-0.12	44	44
UBE2N	0.023	0.007	-10000	0	-0.12	1	1
IRAK/TRAF6	-0.046	0.098	-10000	0	-0.19	140	140
CASP1	0.006	0.04	-10000	0	-0.12	48	48
IL1RN/IL1R2	0.011	0.053	-10000	0	-0.15	33	33
IL1 beta fragment/IL1R1/IL1RAP/MYD88	-0.045	0.1	-10000	0	-0.14	243	243
TMEM189-UBE2V1	0	0	-10000	0	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.037	0.13	-10000	0	-0.27	106	106
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
IL1RN	0.019	0.024	-10000	0	-0.12	16	16
TRAF6/TAK1/TAB1/TAB2	0.041	0.054	-10000	0	-0.12	46	46
MAP2K6	0.014	0.051	-10000	0	-0.13	48	48

×

Nongenotropic Androgen signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.01	0.009	-10000	0	-0.078	6	6
GNB1/GNG2	0.012	0.058	-10000	0	-0.1	94	94
regulation of S phase of mitotic cell cycle	-0.018	0.085	-10000	0	-0.16	130	130
GNAO1	0.01	0.042	-10000	0	-0.12	51	51
HRAS	0.022	0.006	-10000	0	-0.12	1	1
SHBG/T-DHT	0.015	0.005	-10000	0	-0.062	2	2
PELP1	0.022	0.009	-10000	0	-0.12	2	2
AKT1	0.01	0.012	-10000	0	-0.077	10	10
MAP2K1	-0.013	0.061	-10000	0	-0.11	113	113
T-DHT/AR	-0.013	0.059	-10000	0	-0.12	120	120
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
mol:GTP	-0.002	0.003	-10000	0	-0.007	103	103
GNAI2	0.022	0.011	-10000	0	-0.12	3	3
GNAI3	0.021	0.008	-10000	0	-0.12	1	1
GNAI1	0.012	0.035	-10000	0	-0.12	35	35
mol:GDP	-0.047	0.096	-10000	0	-0.25	92	92
cell proliferation	-0.063	0.16	-10000	0	-0.37	107	107
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
FOS	-0.13	0.29	-10000	0	-0.7	107	107
mol:Ca2+	-0.008	0.022	-10000	0	-0.045	107	107
MAPK3	-0.042	0.11	-10000	0	-0.25	110	110
MAPK1	-0.032	0.1	-10000	0	-0.24	63	63
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
mol:IP3	-0.001	0.002	-10000	0	-0.004	103	103
cAMP biosynthetic process	0.01	0.015	0.058	17	-10000	0	17
GNG2	0.02	0.018	-10000	0	-0.12	9	9
potassium channel inhibitor activity	-0.001	0.002	-10000	0	-0.004	103	103
HRAS/GTP	0.006	0.054	-10000	0	-0.092	86	86
actin cytoskeleton reorganization	0.016	0.047	-10000	0	-0.099	66	66
SRC	0.022	0.009	-10000	0	-0.13	2	2
voltage-gated calcium channel activity	-0.001	0.002	-10000	0	-0.004	103	103
PI3K	0.008	0.055	-10000	0	-0.1	96	96
apoptosis	0.066	0.17	0.38	112	-10000	0	112
T-DHT/AR/PELP1	0.002	0.053	-10000	0	-0.11	87	87
HRAS/GDP	-0.027	0.1	-10000	0	-0.23	94	94
CREB1	-0.072	0.18	-10000	0	-0.41	112	112
RAC1-CDC42/GTP	0.023	0.051	-10000	0	-0.1	66	66
AR	0.008	0.039	-10000	0	-0.12	43	43
GNB1	0.023	0.007	-10000	0	-0.12	1	1
RAF1	-0.008	0.053	-10000	0	-0.13	32	32
RAC1-CDC42/GDP	-0.014	0.1	-10000	0	-0.22	95	95
T-DHT/AR/PELP1/Src	0.014	0.053	-10000	0	-0.098	85	85
MAP2K2	-0.015	0.062	-10000	0	-0.12	115	115
T-DHT/AR/PELP1/Src/PI3K	-0.018	0.086	-10000	0	-0.16	130	130
GNAZ	0.022	0.011	-10000	0	-0.12	3	3
SHBG	0.023	0.009	-10000	0	-0.12	2	2
Gi family/GNB1/GNG2/GDP	0.002	0.076	-10000	0	-0.22	38	38
mol:T-DHT	-0.001	0.001	-10000	0	-0.003	81	81
RAC1	0.023	0.002	-10000	0	-10000	0	0
GNRH1	0.011	0.009	-10000	0	-0.077	6	6
Gi family/GTP	-0.018	0.07	-10000	0	-0.15	90	90
CDC42	0.023	0.002	-10000	0	-10000	0	0

×

IL23-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCL2	-0.27	0.57	-9999	-1.2	126	126
IL23A	-0.2	0.5	-9999	-1.2	85	85
NF kappa B1 p50/RelA/I kappa B alpha	-0.19	0.49	-9999	-1.1	92	92
positive regulation of T cell mediated cytotoxicity	-0.22	0.56	-9999	-1.3	91	91
ITGA3	-0.24	0.54	-9999	-1.2	121	121
IL17F	-0.11	0.32	-9999	-0.7	91	91
IL12B	0.016	0.04	-9999	-10000	0	0
STAT1 (dimer)	-0.22	0.53	-9999	-1.3	93	93
CD4	-0.21	0.52	-9999	-1.2	101	101
IL23	-0.18	0.48	-9999	-1.2	85	85
IL23R	0.002	0.089	-9999	-10000	0	0
IL1B	-0.22	0.54	-9999	-1.3	94	94
T-helper cell lineage commitment	0	0	-9999	-10000	0	0
IL24	-0.18	0.46	-9999	-1.1	86	86
TYK2	0.013	0.034	-9999	-0.14	7	7
STAT4	0.02	0.02	-9999	-0.12	11	11
STAT3	0.022	0.011	-9999	-0.12	3	3
IL18RAP	0.022	0.018	-9999	-0.13	8	8
IL12RB1	0.015	0.03	-9999	-0.15	1	1
PIK3CA	0.02	0.017	-9999	-0.12	7	7
IL12Rbeta1/TYK2	0.021	0.04	-9999	-0.11	8	8
IL23R/JAK2	-0.001	0.12	-9999	-10000	0	0
positive regulation of chronic inflammatory response	-0.22	0.56	-9999	-1.3	91	91
natural killer cell activation	0	0.008	-9999	-10000	0	0
JAK2	0.012	0.046	-9999	-0.13	16	16
PIK3R1	0.016	0.031	-9999	-0.12	27	27
NFKB1	0.021	0.013	-9999	-0.12	4	4
RELA	0.022	0.01	-9999	-0.12	2	2
positive regulation of dendritic cell antigen processing and presentation	-0.17	0.45	-9999	-1.1	85	85
ALOX12B	-0.18	0.46	-9999	-1.1	87	87
CXCL1	-0.23	0.52	-9999	-1.1	117	117
T cell proliferation	-0.22	0.56	-9999	-1.3	91	91
NFKBIA	0.016	0.028	-9999	-0.12	21	21
IL17A	-0.073	0.26	-9999	-0.55	84	84
PI3K	-0.2	0.5	-9999	-1.2	94	94
IFNG	-0.005	0.026	-9999	-10000	0	0
STAT3 (dimer)	-0.18	0.48	-9999	-1.1	92	92
IL18R1	0.021	0.022	-9999	-0.12	13	13
IL23/IL23R/JAK2/TYK2/SOCS3	-0.086	0.28	-9999	-0.62	80	80
IL18/IL18R	0.015	0.061	-9999	-0.11	78	78
macrophage activation	-0.009	0.021	-9999	-0.045	78	78
TNF	-0.19	0.5	-9999	-1.2	81	81
STAT3/STAT4	-0.19	0.51	-9999	-1.2	93	93
STAT4 (dimer)	-0.21	0.53	-9999	-1.2	91	91
IL18	0.004	0.046	-9999	-0.12	66	66
IL19	-0.18	0.47	-9999	-1.1	88	88
STAT5A (dimer)	-0.21	0.53	-9999	-1.2	92	92
STAT1	0.014	0.031	-9999	-0.12	26	26
SOCS3	0.015	0.032	-9999	-0.12	28	28
CXCL9	-0.26	0.55	-9999	-1.2	128	128
MPO	-0.18	0.46	-9999	-1.1	86	86
positive regulation of humoral immune response	-0.22	0.56	-9999	-1.3	91	91
IL23/IL23R/JAK2/TYK2	-0.24	0.61	-9999	-1.4	91	91
IL6	-0.2	0.48	-9999	-1.2	88	88
STAT5A	0.022	0.013	-9999	-0.12	4	4
IL2	0.025	0.014	-9999	-0.13	3	3
positive regulation of tyrosine phosphorylation of STAT protein	0	0.008	-9999	-10000	0	0
CD3E	-0.2	0.5	-9999	-1.2	92	92
keratinocyte proliferation	-0.22	0.56	-9999	-1.3	91	91
NOS2	-0.18	0.46	-9999	-1.1	91	91

×

IL6-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.072	0.32	-10000	0	-0.77	71	71
CRP	-0.063	0.3	-10000	0	-0.73	67	67
cell cycle arrest	-0.09	0.36	-10000	0	-0.79	85	85
TIMP1	-0.11	0.35	-10000	0	-0.75	105	105
IL6ST	0.016	0.03	-10000	0	-0.084	33	33
Rac1/GDP	-0.019	0.17	-10000	0	-0.36	77	77
AP1	-0.06	0.21	-10000	0	-0.47	93	93
GAB2	0.01	0.042	-10000	0	-0.12	50	50
TNFSF11	-0.063	0.3	-10000	0	-0.74	65	65
HSP90B1	0.007	0.18	-10000	0	-1.2	11	11
GAB1	0.022	0.022	-10000	0	-0.12	12	12
MAPK14	-0.031	0.17	-10000	0	-0.47	55	55
AKT1	-0.018	0.15	-10000	0	-0.39	53	53
FOXO1	-0.015	0.15	-10000	0	-0.38	49	49
MAP2K6	-0.03	0.16	-10000	0	-0.37	75	75
mol:GTP	0	0.003	-10000	0	-10000	0	0
MAP2K4	-0.028	0.2	-10000	0	-0.4	92	92
MITF	-0.02	0.15	-10000	0	-0.34	74	74
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TYK2	0.021	0.016	-10000	0	-0.12	7	7
A2M	-0.12	0.39	-10000	0	-1.2	63	63
CEBPB	0.023	0.036	-10000	0	-0.11	36	36
GRB2/SOS1/GAB family/SHP2	-0.03	0.18	0.25	5	-0.38	87	92
STAT3	-0.1	0.38	-10000	0	-0.86	85	85
STAT1	-0.088	0.28	-10000	0	-0.84	68	68
CEBPD	-0.071	0.31	-10000	0	-0.74	71	71
PIK3CA	0.021	0.017	-10000	0	-0.12	7	7
PI3K	0.009	0.066	-10000	0	-0.14	81	81
JUN	0.014	0.033	-10000	0	-0.12	30	30
PIAS3/MITF	-0.014	0.15	-10000	0	-0.32	73	73
MAPK11	-0.03	0.17	-10000	0	-0.46	55	55
STAT3 (dimer)/FOXO1	-0.086	0.34	-10000	0	-0.69	99	99
GRB2/SOS1/GAB family	0.003	0.12	0.22	6	-0.25	65	71
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK	-0.01	0.12	-10000	0	-0.27	74	74
GRB2	0.025	0.008	-10000	0	-0.12	1	1
JAK2	0.017	0.025	-10000	0	-0.12	16	16
LBP	-0.038	0.25	-10000	0	-0.57	66	66
PIK3R1	0.016	0.031	-10000	0	-0.12	27	27
JAK1	0.022	0.015	-10000	0	-0.042	19	19
MYC	-0.12	0.4	-10000	0	-0.88	106	106
FGG	-0.063	0.3	-10000	0	-0.72	69	69
macrophage differentiation	-0.09	0.36	-10000	0	-0.79	85	85
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4	0.013	0.094	-10000	0	-0.16	92	92
JUNB	-0.11	0.37	-10000	0	-0.86	89	89
FOS	-0.005	0.053	-10000	0	-0.12	95	95
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4	-0.023	0.16	-10000	0	-0.36	73	73
STAT1/PIAS1	-0.031	0.18	-10000	0	-0.35	94	94
GRB2/SOS1/GAB family/SHP2/PI3K	-0.024	0.16	-10000	0	-0.32	86	86
STAT3 (dimer)	-0.099	0.38	-10000	0	-0.84	85	85
PRKCD	-0.044	0.26	-10000	0	-0.51	95	95
IL6R	0.018	0.025	-10000	0	-0.082	24	24
SOCS3	-0.047	0.22	-10000	0	-0.9	29	29
gp130 (dimer)/JAK1/JAK1/LMO4	0.02	0.08	-10000	0	-0.15	80	80
Rac1/GTP	-0.024	0.18	-10000	0	-0.39	79	79
HCK	0.019	0.024	-10000	0	-0.12	15	15
MAPKKK cascade	-0.049	0.22	-10000	0	-0.5	94	94
bone resorption	-0.057	0.29	-10000	0	-0.69	65	65
IRF1	-0.12	0.41	-10000	0	-0.96	93	93
mol:GDP	-0.025	0.16	-10000	0	-0.36	77	77
SOS1	0.019	0.028	-10000	0	-0.12	20	20
VAV1	-0.025	0.16	-10000	0	-0.36	77	77
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3	-0.03	0.18	-10000	0	-0.46	68	68
PTPN11	-0.007	0.16	-10000	0	-0.83	19	19
IL6/IL6RA	0.007	0.063	-10000	0	-0.14	64	64
gp130 (dimer)/TYK2/TYK2/LMO4	0.025	0.061	-10000	0	-0.12	65	65
gp130 (dimer)/JAK2/JAK2/LMO4	0.014	0.076	-10000	0	-0.14	88	88
IL6	0.005	0.049	-10000	0	-0.1	88	88
PIAS3	0.02	0.022	-10000	0	-0.12	13	13
PTPRE	0.022	0.018	0.08	18	-10000	0	18
PIAS1	0.022	0.009	-10000	0	-0.12	2	2
RAC1	0.023	0.003	-10000	0	-10000	0	0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4	-0.013	0.097	-10000	0	-0.22	73	73
LMO4	0.021	0.023	-10000	0	-0.084	14	14
STAT3 (dimer)/PIAS3	-0.087	0.35	-10000	0	-0.78	84	84
MCL1	-0.014	0.16	-10000	0	-0.71	14	14

×

Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer	0.019	0.049	-9999	-0.15	38	38
alphaV beta3 Integrin	-0.001	0.073	-9999	-0.13	107	107
PTK2	-0.029	0.13	-9999	-0.3	71	71
IGF1R	0.013	0.032	-9999	-0.12	28	28
PI4KB	0.022	0.014	-9999	-0.12	5	5
MFGE8	0.006	0.043	-9999	-0.12	56	56
SRC	0.023	0.009	-9999	-0.12	2	2
CDKN1B	-0.006	0.085	-9999	-0.34	28	28
VEGFA	0.019	0.021	-9999	-0.12	11	11
ILK	0.013	0.04	-9999	-0.31	3	3
ROCK1	0.022	0.009	-9999	-0.12	2	2
AKT1	0.014	0.038	-9999	-0.28	3	3
PTK2B	-0.011	0.063	-9999	-0.11	139	139
alphaV/beta3 Integrin/JAM-A	0.014	0.068	-9999	-0.1	114	114
CBL	0.023	0.006	-9999	-0.12	1	1
mol:GTP	0	0	-9999	-10000	0	0
alphaV beta3 Integrin/ANGPTL3	-0.001	0.073	-9999	-0.13	107	107
IGF-1R heterotetramer/IGF1/IRS1/Shp2	0.013	0.07	-9999	-0.11	107	107
VEGF/Rho/ROCK/alphaV/beta3 Integrin	-0.011	0.095	-9999	-0.25	51	51
alphaV/beta3 Integrin/Syndecan-1	-0.003	0.074	-9999	-0.13	113	113
PI4KA	0.021	0.016	-9999	-0.12	7	7
IGF-1R heterotetramer/IGF1/IRS1	-0.055	0.086	-9999	-0.16	152	152
PI4 Kinase	0.028	0.032	-9999	-0.12	24	24
PIK3CA	0.02	0.017	-9999	-0.12	7	7
alphaV/beta3 Integrin/Osteopontin	-0.03	0.098	-9999	-0.16	164	164
RPS6KB1	-0.056	0.082	-9999	-0.16	163	163
TLN1	0.021	0.012	-9999	-0.12	3	3
MAPK3	-0.054	0.14	-9999	-0.34	102	102
GPR124	0.022	0.011	-9999	-0.12	3	3
MAPK1	-0.055	0.14	-9999	-0.34	102	102
PXN	0.022	0.014	-9999	-0.12	5	5
PIK3R1	0.015	0.031	-9999	-0.12	27	27
alphaV/beta3 Integrin/Tumstatin	-0.001	0.073	-9999	-0.13	107	107
cell adhesion	-0.03	0.097	-9999	-0.18	117	117
ANGPTL3	0.022	0.011	-9999	-0.12	3	3
VEGFR2 homodimer/VEGFA homodimer/Src	0.033	0.044	-9999	-0.11	38	38
IGF-1R heterotetramer	0.013	0.032	-9999	-0.12	28	28
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
TGFBR2	0.02	0.02	-9999	-0.12	11	11
ITGB3	0.004	0.047	-9999	-0.12	68	68
IGF1	0.007	0.045	-9999	-0.12	60	60
RAC1	0.023	0.002	-9999	-10000	0	0
regulation of cell-matrix adhesion	-0.001	0.073	-9999	-0.13	107	107
apoptosis	0.013	0.032	-9999	-0.12	28	28
CD47	0.021	0.012	-9999	-0.12	3	3
alphaV/beta3 Integrin/CD47	-0.009	0.084	-9999	-0.14	124	124
VCL	0.021	0.013	-9999	-0.12	4	4
alphaV/beta3 Integrin/Del1	-0.03	0.083	-9999	-0.14	161	161
CSF1	0.013	0.033	-9999	-0.12	31	31
PIK3C2A	-0.012	0.1	-9999	-0.36	41	41
PI4 Kinase/Pyk2	0.001	0.059	-9999	-0.14	49	49
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.001	0.079	-9999	-0.12	139	139
FAK1/Vinculin	-0.016	0.12	-9999	-0.25	72	72
alphaV beta3/Integrin/ppsTEM5	-0.001	0.073	-9999	-0.13	107	107
RHOA	0.023	0.006	-9999	-0.12	1	1
VTN	0.023	0.009	-9999	-0.12	2	2
BCAR1	0.022	0.011	-9999	-0.12	3	3
FGF2	0.023	0.009	-9999	-0.12	2	2
F11R	0.022	0.012	-9999	-0.12	3	3
alphaV/beta3 Integrin/Lactadherin	-0.028	0.088	-9999	-0.14	170	170
alphaV/beta3 Integrin/TGFBR2	-0.006	0.079	-9999	-0.14	112	112
alphaV/beta3 Integrin/c-FMS/Cbl/Cas	0.015	0.075	-9999	-0.12	112	112
HSP90AA1	0.023	0.003	-9999	-10000	0	0
alphaV/beta3 Integrin/Talin	-0.005	0.074	-9999	-0.12	124	124
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.013	0.056	-9999	-0.12	114	114
alphaV/beta3 Integrin/Pyk2	0	0.072	-9999	-0.16	49	49
SDC1	0.021	0.018	-9999	-0.12	9	9
VAV3	-0.012	0.074	-9999	-0.14	118	118
PTPN11	0.022	0.011	-9999	-0.12	3	3
IRS1	0.019	0.023	-9999	-0.12	14	14
FAK1/Paxillin	-0.014	0.11	-9999	-0.25	66	66
cell migration	-0.011	0.11	-9999	-0.23	71	71
ITGAV	0.013	0.032	-9999	-0.12	28	28
PI3K	0.006	0.083	-9999	-0.17	61	61
SPP1	0.012	0.032	-9999	-0.12	28	28
KDR	0.021	0.019	-9999	-0.12	10	10
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Caspase 8	0.013	0.032	-9999	-0.12	28	28
COL4A3	0.023	0.009	-9999	-0.12	2	2
angiogenesis	-0.056	0.16	-9999	-0.37	102	102
Rac1/GTP	-0.007	0.075	-9999	-0.18	54	54
EDIL3	-0.007	0.057	-9999	-0.12	109	109
cell proliferation	-0.006	0.079	-9999	-0.14	112	112

×

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

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
MET/RANBP9	-0.018	0.078	-10000	0	-0.15	124	124
CRKL	-0.026	0.11	-10000	0	-0.34	32	32
mol:PIP3	-0.002	0.049	0.22	24	-10000	0	24
AKT1	0.004	0.039	0.17	23	-0.1	10	33
PTK2B	0.023	0.009	-10000	0	-0.12	2	2
RAPGEF1	-0.021	0.1	-10000	0	-0.32	31	31
RANBP10	0.023	0.009	-10000	0	-0.12	2	2
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
HGF/MET/SHIP2	-0.002	0.069	-10000	0	-0.11	122	122
MAP3K5	-0.014	0.1	-10000	0	-0.3	37	37
HGF/MET/CIN85/CBL/ENDOPHILINS	0.011	0.067	-10000	0	-0.097	126	126
AP1	-0.04	0.075	-10000	0	-0.14	166	166
mol:SU11274	0	0	-10000	0	-10000	0	0
SHC1	0.023	0.001	-10000	0	-10000	0	0
apoptosis	-0.17	0.32	-10000	0	-0.75	124	124
STAT3 (dimer)	-0.022	0.099	-10000	0	-0.28	38	38
GAB1/CRKL/SHP2/PI3K	-0.015	0.12	-10000	0	-0.29	53	53
INPP5D	0	0	-10000	0	-10000	0	0
CBL/CRK	-0.014	0.11	-10000	0	-0.31	33	33
PTPN11	0.022	0.011	-10000	0	-0.12	3	3
GO:0007205	0	0	-10000	0	-10000	0	0
PLCG1	0.019	0.024	-10000	0	-0.12	16	16
PTEN	0.022	0.008	-10000	0	-0.12	1	1
ELK1	-0.021	0.058	0.25	12	-10000	0	12
mol:SU5416	0	0	-10000	0	-10000	0	0
SHP2/GRB2/SOS1GAB1	-0.016	0.082	-10000	0	-0.2	56	56
PAK1	0.002	0.042	0.16	22	-0.1	18	40
HGF/MET/RANBP10	0	0.067	-10000	0	-0.11	118	118
HRAS	-0.084	0.21	-10000	0	-0.48	122	122
DOCK1	-0.026	0.11	-10000	0	-0.31	41	41
GAB1	-0.031	0.11	-10000	0	-0.34	34	34
CRK	-0.026	0.11	-10000	0	-0.33	33	33
mol:PHA665752	0	0	-10000	0	-10000	0	0
mol:GDP	-0.073	0.19	-10000	0	-0.42	122	122
JUN	0.014	0.033	-10000	0	-0.12	30	30
EntrezGene:200958	0	0	-10000	0	-10000	0	0
HGF/MET	-0.028	0.077	-10000	0	-0.17	119	119
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
cell morphogenesis	-0.028	0.12	-10000	0	-0.27	67	67
GRB2/SHC	-0.006	0.078	-10000	0	-0.14	125	125
FOS	-0.005	0.053	-10000	0	-0.12	95	95
GLMN	0.004	0.013	0.076	7	-0.049	17	24
cell motility	-0.021	0.058	0.25	12	-10000	0	12
HGF/MET/MUC20	-0.011	0.062	-10000	0	-0.12	118	118
cell migration	-0.006	0.077	-10000	0	-0.14	125	125
GRB2	0.023	0.006	-10000	0	-0.12	1	1
CBL	0.023	0.006	-10000	0	-0.12	1	1
MET/RANBP10	-0.015	0.074	-10000	0	-0.12	187	187
HGF/MET/Paxillin/FAK1/FAK12/RasGAP	-0.02	0.092	-10000	0	-0.27	30	30
MET/MUC20	-0.028	0.068	-10000	0	-0.12	186	186
RAP1B	-0.019	0.1	-10000	0	-0.3	35	35
RAP1A	-0.019	0.1	-10000	0	-0.3	37	37
HGF/MET/RANBP9	-0.003	0.071	-10000	0	-0.12	126	126
RAF1	-0.077	0.2	-10000	0	-0.46	122	122
STAT3	-0.02	0.098	-10000	0	-0.3	31	31
cell proliferation	-0.036	0.13	-10000	0	-0.26	123	123
RPS6KB1	-0.018	0.077	-10000	0	-0.27	36	36
MAPK3	-0.025	0.075	0.69	5	-10000	0	5
MAPK1	-0.021	0.092	0.7	8	-10000	0	8
RANBP9	0.021	0.014	-10000	0	-0.12	5	5
MAPK8	-0.015	0.12	-10000	0	-0.35	46	46
SRC	-0.016	0.086	-10000	0	-0.25	30	30
PI3K	-0.022	0.092	-10000	0	-0.16	128	128
MET/Glomulin	-0.003	0.05	-10000	0	-0.097	95	95
SOS1	0.017	0.027	-10000	0	-0.12	20	20
MAP2K1	-0.068	0.19	-10000	0	-0.42	122	122
MET	0	0.047	-10000	0	-0.12	70	70
MAP4K1	-0.014	0.1	-10000	0	-0.33	28	28
PTK2	0.021	0.016	-10000	0	-0.12	6	6
MAP2K2	-0.07	0.19	-10000	0	-0.43	122	122
BAD	0.008	0.037	0.16	23	-0.096	10	33
MAP2K4	-0.011	0.097	-10000	0	-0.26	41	41
SHP2/GRB2/SOS1/GAB1	-0.029	0.12	-10000	0	-0.23	128	128
INPPL1	0.021	0.017	-10000	0	-0.12	8	8
PXN	0.022	0.014	-10000	0	-0.12	5	5
SH3KBP1	0.02	0.019	-10000	0	-0.12	10	10
HGS	-0.022	0.071	-10000	0	-0.15	119	119
PLCgamma1/PKC	0.012	0.026	-10000	0	-0.1	26	26
HGF	0.02	0.023	-10000	0	-0.12	14	14
RASA1	0.021	0.012	-10000	0	-0.12	3	3
NCK1	0.02	0.019	-10000	0	-0.12	9	9
PTPRJ	0.02	0.019	-10000	0	-0.12	9	9
NCK/PLCgamma1	-0.014	0.085	-10000	0	-0.15	131	131
PDPK1	0.001	0.043	0.19	24	-0.11	9	33
HGF/MET/SHIP	-0.011	0.062	-10000	0	-0.12	118	118

×

a4b1 and a4b7 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ITGB1	0.021	0.015	-9999	-0.12	6	6
ITGB7	0.019	0.024	-9999	-0.12	15	15
ITGA4	0.015	0.03	-9999	-0.12	24	24
alpha4/beta7 Integrin	0.004	0.065	-9999	-0.13	106	106
alpha4/beta1 Integrin	0.006	0.063	-9999	-0.12	101	101

×

Caspase cascade in apoptosis

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
TOP1	0.004	0.11	0.16	17	-0.24	59	76
ACTA1	0.023	0.073	0.15	59	-0.19	21	80
NUMA1	0.001	0.11	0.16	16	-0.25	66	82
SPTAN1	0.019	0.077	0.15	60	-0.18	28	88
LIMK1	0.025	0.072	0.15	62	-0.19	19	81
BIRC3	-0.005	0.053	-10000	0	-0.12	94	94
BIRC2	0.021	0.013	-10000	0	-0.12	4	4
BAX	0.023	0	-10000	0	-10000	0	0
CASP10	0.005	0.036	-10000	0	-0.072	89	89
CRMA	0	0	-10000	0	-10000	0	0
XIAP	0	0	-10000	0	-10000	0	0
PTK2	-0.008	0.14	0.15	30	-0.3	72	102
DIABLO	0.02	0.016	-10000	0	-0.12	6	6
apoptotic nuclear changes	0.019	0.076	0.15	60	-0.18	28	88
response to UV	0	0	-10000	0	-10000	0	0
CRADD	0.023	0.009	-10000	0	-0.12	2	2
GSN	0.021	0.074	0.15	57	-0.19	23	80
MADD	0.023	0.006	-10000	0	-0.12	1	1
TFAP2A	-0.03	0.15	-10000	0	-0.48	48	48
BID	0.01	0.037	-10000	0	-0.22	5	5
MAP3K1	0.009	0.08	-10000	0	-0.36	20	20
TRADD	0.023	0.006	-10000	0	-0.12	1	1
mol:Ca2+	0	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0.025	0.041	-10000	0	-0.13	33	33
mol:Activated DNA	0	0	-10000	0	-10000	0	0
ARHGDIB	0.006	0.076	0.14	36	-0.2	29	65
CASP9	0.021	0.014	-10000	0	-0.12	5	5
DNA repair	-0.023	0.074	0.26	22	-0.13	74	96
neuron apoptosis	-0.026	0.16	-10000	0	-0.58	39	39
mol:NAD	0	0	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	0.01	0.1	0.17	34	-0.22	52	86
APAF1	0.021	0.014	-10000	0	-0.12	5	5
CASP6	-0.055	0.25	-10000	0	-0.78	58	58
TRAF2	0.023	0	-10000	0	-10000	0	0
ICAD/CAD	0.028	0.069	0.15	60	-0.21	13	73
CASP7	0.044	0.077	0.19	104	-0.2	5	109
KRT18	-0.014	0.12	-10000	0	-0.56	22	22
apoptosis	-0.006	0.13	0.18	30	-0.31	59	89
DFFA	0.025	0.072	0.15	60	-0.19	18	78
DFFB	0.025	0.072	0.15	62	-0.19	19	81
PARP1	0.024	0.074	0.13	74	-0.26	22	96
actin filament polymerization	-0.025	0.069	0.18	18	-0.15	60	78
TNF	0.02	0.02	-10000	0	-0.12	11	11
CYCS	-0.005	0.049	-10000	0	-0.19	25	25
SATB1	-0.064	0.24	-10000	0	-0.75	59	59
SLK	0.018	0.077	0.15	60	-0.18	25	85
p15 BID/BAX	0.016	0.044	-10000	0	-0.1	34	34
CASP2	0.008	0.066	-10000	0	-0.23	18	18
JNK cascade	-0.009	0.079	0.36	20	-10000	0	20
CASP3	0.023	0.077	0.16	62	-0.2	19	81
LMNB2	-0.002	0.099	-10000	0	-0.26	62	62
RIPK1	0.022	0.011	-10000	0	-0.12	3	3
CASP4	0.015	0.029	-10000	0	-0.12	23	23
Mammalian IAPs/DIABLO	-0.019	0.084	-10000	0	-0.13	157	157
negative regulation of DNA binding	-0.03	0.15	-10000	0	-0.47	48	48
stress fiber formation	0.018	0.076	0.15	60	-0.18	25	85
GZMB	0.005	0.045	-10000	0	-0.1	79	79
CASP1	-0.064	0.14	-10000	0	-0.28	148	148
LMNB1	-0.028	0.14	-10000	0	-0.28	103	103
APP	-0.026	0.16	-10000	0	-0.59	39	39
TNFRSF1A	0.021	0.016	-10000	0	-0.12	7	7
response to stress	0	0	-10000	0	-10000	0	0
CASP8	0.011	0.002	-10000	0	-10000	0	0
VIM	-0.003	0.13	0.18	31	-0.31	59	90
LMNA	-0.008	0.11	-10000	0	-0.27	71	71
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD	0.006	0.07	-10000	0	-0.23	21	21
LRDD	0.022	0.015	-10000	0	-0.12	6	6
SREBF1	0.024	0.074	0.15	62	-0.19	20	82
APAF-1/Caspase 9	0.027	0.11	0.26	16	-0.75	8	24
nuclear fragmentation during apoptosis	0.001	0.11	0.16	16	-0.24	66	82
CFL2	0.025	0.07	0.15	60	-0.18	18	78
GAS2	0.023	0.072	0.15	61	-0.19	20	81
positive regulation of apoptosis	-0.014	0.12	-10000	0	-0.3	66	66
PRF1	0.013	0.036	-10000	0	-0.12	37	37

×

IFN-gamma pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2	0.007	0.08	-10000	0	-0.13	107	107
positive regulation of NF-kappaB transcription factor activity	0	0.001	-10000	0	-10000	0	0
CRKL	0.023	0.009	-10000	0	-0.12	2	2
STAT1 (dimer)/Cbp/p300	-0.019	0.13	-10000	0	-0.22	123	123
IFN-gammaR/JAK1/JAK1/JAK2/JAK2	0.007	0.081	-10000	0	-0.15	100	100
antigen processing and presentation of peptide antigen via MHC class I	-0.053	0.093	-10000	0	-0.2	131	131
CaM/Ca2+	0.01	0.077	-10000	0	-0.15	72	72
RAP1A	0.021	0.012	-10000	0	-0.12	3	3
STAT1 (dimer)/SHP2	-0.018	0.093	-10000	0	-0.18	96	96
AKT1	-0.014	0.081	-10000	0	-0.18	85	85
MAP2K1	-0.007	0.068	-10000	0	-0.15	76	76
MAP3K11	-0.007	0.067	-10000	0	-0.15	72	72
IFNGR1	0.016	0.026	-10000	0	-0.12	17	17
mol:GTP	0	0	-10000	0	-10000	0	0
CaM/Ca2+/CAMKII	0.014	0.082	-10000	0	-0.28	28	28
Rap1/GTP	-0.023	0.056	-10000	0	-0.17	54	54
CRKL/C3G	0.034	0.01	-10000	0	-0.14	1	1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP	0.023	0.079	-10000	0	-0.13	83	83
CEBPB	-0.014	0.15	-10000	0	-0.41	52	52
STAT3	0.022	0.011	-10000	0	-0.12	3	3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1	0.018	0.11	-10000	0	-0.99	3	3
STAT1	-0.019	0.087	-10000	0	-0.19	83	83
CALM1	0.022	0.014	-10000	0	-0.12	5	5
IFN-gamma (dimer)	0.01	0.039	-10000	0	-0.12	42	42
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
STAT1 (dimer)/PIAS1	-0.015	0.091	-10000	0	-0.18	95	95
CEBPB/PTGES2/Cbp/p300	-0.036	0.11	-10000	0	-0.3	63	63
mol:Ca2+	0.005	0.078	-10000	0	-0.13	102	102
MAPK3	-0.009	0.11	-10000	0	-0.53	13	13
STAT1 (dimer)	-0.041	0.15	-10000	0	-0.28	129	129
MAPK1	-0.013	0.13	-10000	0	-0.59	16	16
JAK2	0.016	0.026	-10000	0	-0.13	16	16
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
JAK1	0.02	0.012	-10000	0	-0.12	2	2
CAMK2D	0.018	0.024	-10000	0	-0.12	16	16
DAPK1	-0.015	0.16	-10000	0	-0.5	45	45
SMAD7	-0.009	0.064	-10000	0	-0.13	88	88
CBL/CRKL/C3G	0.017	0.068	-10000	0	-0.15	46	46
PI3K	-0.004	0.092	-10000	0	-0.18	91	91
IFNG	0.01	0.039	-10000	0	-0.12	42	42
apoptosis	-0.018	0.13	0.22	1	-0.39	47	48
CAMK2G	0.023	0.006	-10000	0	-0.12	1	1
STAT3 (dimer)	0.022	0.011	-10000	0	-0.12	3	3
CAMK2A	0.023	0.006	-10000	0	-0.12	1	1
CAMK2B	0.023	0.009	-10000	0	-0.12	2	2
FRAP1	-0.012	0.077	-10000	0	-0.17	81	81
PRKCD	-0.016	0.086	-10000	0	-0.19	88	88
RAP1B	0.019	0.02	-10000	0	-0.12	10	10
negative regulation of cell growth	-0.053	0.093	-10000	0	-0.2	131	131
PTPN2	0.023	0.007	-10000	0	-0.12	1	1
EP300	0.022	0.01	-10000	0	-0.12	2	2
IRF1	-0.038	0.13	-10000	0	-0.28	102	102
STAT1 (dimer)/PIASy	-0.015	0.089	0.19	3	-0.18	85	88
SOCS1	0.007	0.096	-10000	0	-1.2	3	3
mol:GDP	0.015	0.065	-10000	0	-0.15	46	46
CASP1	-0.031	0.095	-10000	0	-0.18	143	143
PTGES2	0.023	0.009	-10000	0	-0.12	2	2
IRF9	0.004	0.071	-10000	0	-0.15	72	72
mol:PI-3-4-5-P3	-0.013	0.085	-10000	0	-0.18	91	91
RAP1/GDP	0.006	0.073	-10000	0	-0.18	52	52
CBL	-0.006	0.066	-10000	0	-0.14	78	78
MAP3K1	-0.008	0.071	-10000	0	-0.16	76	76
PIAS1	0.022	0.009	-10000	0	-0.12	2	2
PIAS4	0.023	0.001	-10000	0	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class II	-0.053	0.093	-10000	0	-0.2	131	131
PTPN11	-0.01	0.067	-10000	0	-0.13	102	102
CREBBP	0.02	0.016	-10000	0	-0.12	6	6
RAPGEF1	0.023	0	-10000	0	-10000	0	0

×

IGF1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NCK2	0.023	0.006	-10000	0	-0.12	1	1
PTK2	0.021	0.016	-10000	0	-0.12	6	6
CRKL	-0.005	0.054	-10000	0	-0.12	91	91
GRB2/SOS1/SHC	0.035	0.041	-10000	0	-0.12	30	30
HRAS	0.023	0.006	-10000	0	-0.12	1	1
IRS1/Crk	-0.001	0.057	-10000	0	-0.12	88	88
IGF-1R heterotetramer/IGF1/PTP1B	0.008	0.062	-10000	0	-0.12	89	89
AKT1	-0.01	0.06	-10000	0	-0.11	108	108
BAD	-0.007	0.057	-10000	0	-0.1	108	108
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	-0.005	0.054	-10000	0	-0.12	91	91
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.003	0.062	-10000	0	-0.12	102	102
RAF1	-0.004	0.092	-10000	0	-0.5	11	11
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos	0.01	0.07	-10000	0	-0.12	88	88
YWHAZ	0.023	0.003	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.004	0.063	-10000	0	-0.13	91	91
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
RPS6KB1	-0.011	0.063	-10000	0	-0.12	110	110
GNB2L1	0.023	0.003	-10000	0	-10000	0	0
positive regulation of MAPKKK cascade	-0.007	0.079	0.2	6	-0.4	11	17
PXN	0.022	0.014	-10000	0	-0.12	5	5
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
cell adhesion	0	0	-10000	0	-10000	0	0
GRB2/SOS1	0.021	0.045	-10000	0	-0.15	29	29
HRAS/GTP	-0.002	0.052	-10000	0	-0.15	24	24
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc	0.022	0.068	-10000	0	-0.15	22	22
IGF-1R heterotetramer	0.012	0.033	-10000	0	-0.12	29	29
IGF-1R heterotetramer/IGF1/IRS/Nck	0.008	0.062	-10000	0	-0.12	91	91
Crk/p130 Cas/Paxillin	0.021	0.06	-10000	0	-0.099	86	86
IGF1R	0.012	0.033	-10000	0	-0.12	29	29
IGF1	0.001	0.047	-10000	0	-0.12	62	62
IRS2/Crk	0.004	0.054	-10000	0	-0.11	86	86
PI3K	0	0.076	-10000	0	-0.12	141	141
apoptosis	-0.003	0.057	0.12	57	-10000	0	57
HRAS/GDP	0.017	0.008	-10000	0	-0.11	2	2
PRKCD	-0.015	0.093	-10000	0	-0.26	39	39
RAF1/14-3-3 E	0.007	0.084	-10000	0	-0.43	11	11
BAD/14-3-3	0.003	0.06	-10000	0	-0.12	57	57
PRKCZ	-0.009	0.059	-10000	0	-0.11	107	107
Crk/p130 Cas/Paxillin/FAK1	0.004	0.069	-10000	0	-0.15	55	55
PTPN1	0.023	0.006	-10000	0	-0.12	1	1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1	-0.016	0.095	-10000	0	-0.21	89	89
BCAR1	0.022	0.011	-10000	0	-0.12	3	3
IGF-1R heterotetramer/IGF1/SHC/GRB10	0.019	0.061	-10000	0	-0.13	21	21
mol:GDP	0	0	-10000	0	-10000	0	0
SOS1	0.017	0.027	-10000	0	-0.12	20	20
IRS1/NCK2	0.002	0.058	-10000	0	-0.12	91	91
GRB10	0.022	0.014	-10000	0	-0.12	5	5
PTPN11	-0.006	0.057	-10000	0	-0.12	92	92
IRS1	-0.011	0.058	-10000	0	-0.13	91	91
IRS2	-0.005	0.054	-10000	0	-0.12	92	92
IGF-1R heterotetramer/IGF1	-0.012	0.076	-10000	0	-0.16	91	91
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PDPK1	-0.011	0.064	-10000	0	-0.12	107	107
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
PRKD1	-0.021	0.097	-10000	0	-0.26	51	51
SHC1	0.023	0.001	-10000	0	-10000	0	0

×

Signaling events mediated by the Hedgehog family

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
TGFB2	-0.083	0.19	-10000	0	-0.4	135	135
IHH	-0.002	0.048	-10000	0	-0.076	141	141
SHH Np/Cholesterol/GAS1	0.023	0.028	-10000	0	-0.098	16	16
LRPAP1	0.018	0.024	-10000	0	-0.12	15	15
dorsoventral neural tube patterning	-0.022	0.028	0.097	16	-10000	0	16
SMO/beta Arrestin2	-0.01	0.11	-10000	0	-0.27	12	12
SMO	-0.018	0.11	-10000	0	-0.3	9	9
AKT1	-0.017	0.11	-10000	0	-0.33	40	40
ARRB2	0.022	0.014	-10000	0	-0.12	5	5
BOC	0.011	0.039	-10000	0	-0.12	44	44
ADRBK1	0.023	0.001	-10000	0	-10000	0	0
heart looping	-0.018	0.11	-10000	0	-0.3	9	9
STIL	-0.016	0.082	-10000	0	-0.15	135	135
DHH N/PTCH2	0.034	0.011	-10000	0	-0.09	4	4
DHH N/PTCH1	-0.019	0.099	-10000	0	-0.18	135	135
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
DHH	0.022	0.011	-10000	0	-0.12	3	3
PTHLH	-0.072	0.18	-10000	0	-0.38	135	135
determination of left/right symmetry	-0.018	0.11	-10000	0	-0.3	9	9
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
skeletal system development	-0.072	0.18	-10000	0	-0.37	135	135
IHH N/Hhip	0.016	0.039	-10000	0	-0.098	27	27
DHH N/Hhip	0.029	0.024	-10000	0	-0.14	1	1
mol:Cholesterol	0	0	-10000	0	-10000	0	0
heart development	-0.018	0.11	-10000	0	-0.3	9	9
pancreas development	0.017	0.029	-10000	0	-0.12	24	24
HHAT	0.022	0.011	-10000	0	-0.12	3	3
PI3K	0.007	0.065	-10000	0	-0.13	96	96
EntrezGene:84976	0	0	-10000	0	-10000	0	0
GAS1	0.014	0.035	-10000	0	-0.12	35	35
somite specification	-0.018	0.11	-10000	0	-0.3	9	9
SHH Np/Cholesterol/PTCH1	-0.013	0.087	-10000	0	-0.15	135	135
SHH Np/Cholesterol/PTCH2	0.03	0.012	-10000	0	-0.1	3	3
SHH Np/Cholesterol/Megalin	0.007	0.039	-10000	0	-0.098	20	20
SHH	0.022	0.011	-10000	0	-0.086	5	5
catabolic process	-0.033	0.11	-10000	0	-0.21	135	135
SMO/Vitamin D3	-0.01	0.097	-10000	0	-0.24	9	9
SHH Np/Cholesterol/Hhip	0.027	0.019	-10000	0	-0.099	3	3
LRP2	-0.016	0.064	-10000	0	-0.12	148	148
receptor-mediated endocytosis	-0.02	0.098	-10000	0	-0.21	57	57
SHH Np/Cholesterol/BOC	0.02	0.033	-10000	0	-0.1	23	23
SHH Np/Cholesterol/CDO	0.018	0.036	-10000	0	-0.098	36	36
mesenchymal cell differentiation	-0.027	0.019	0.099	3	-10000	0	3
mol:Vitamin D3	-0.011	0.088	-10000	0	-0.15	135	135
IHH N/PTCH2	0.021	0.032	-10000	0	-0.13	4	4
CDON	0.013	0.035	-10000	0	-0.12	35	35
IHH N/PTCH1	-0.028	0.11	-10000	0	-0.21	135	135
Megalin/LRPAP1	-0.011	0.065	-10000	0	-0.093	200	200
PTCH2	0.023	0.009	-10000	0	-0.12	2	2
SHH Np/Cholesterol	0.018	0.009	-10000	0	-0.068	6	6
PTCH1	-0.033	0.11	-10000	0	-0.21	135	135
HHIP	0.017	0.029	-10000	0	-0.12	24	24

×

PLK1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
regulation of centriole-centriole cohesion	0.012	0.057	0.18	50	-10000	0	50
BUB1B	-0.028	0.1	-10000	0	-0.23	87	87
PLK1	-0.009	0.049	-10000	0	-0.1	93	93
PLK1S1	-0.003	0.022	-10000	0	-0.05	78	78
KIF2A	-0.006	0.047	-10000	0	-0.11	72	72
regulation of mitotic centrosome separation	-0.009	0.048	-10000	0	-0.1	93	93
GOLGA2	0.023	0.006	-10000	0	-0.12	1	1
Hec1/SPC24	-0.015	0.088	-10000	0	-0.15	134	134
WEE1	-0.014	0.076	-10000	0	-0.23	34	34
cytokinesis	-0.053	0.14	-10000	0	-0.29	125	125
PP2A-alpha B56	-0.036	0.24	-10000	0	-0.7	61	61
AURKA	-0.025	0.09	-10000	0	-0.26	70	70
PICH/PLK1	-0.024	0.1	-10000	0	-0.18	138	138
CENPE	-0.005	0.046	-10000	0	-0.11	70	70
RhoA/GTP	0.016	0.016	-10000	0	-0.14	6	6
positive regulation of microtubule depolymerization	-0.006	0.047	-10000	0	-0.11	72	72
PPP2CA	0.023	0.003	-10000	0	-10000	0	0
FZR1	0.023	0	-10000	0	-10000	0	0
TPX2	-0.034	0.099	-10000	0	-0.26	90	90
PAK1	0.016	0.029	-10000	0	-0.12	23	23
SPC24	0.016	0.029	-10000	0	-0.12	24	24
FBXW11	0.023	0.003	-10000	0	-10000	0	0
CLSPN	0	0.035	-10000	0	-0.16	9	9
GORASP1	0.023	0.006	-10000	0	-0.12	1	1
metaphase	-0.001	0.004	-10000	0	-0.014	31	31
mol:GTP	0	0	-10000	0	-10000	0	0
NLP	-0.003	0.022	-10000	0	-0.05	78	78
G2 phase of mitotic cell cycle	-0.001	0.003	-10000	0	-0.009	51	51
STAG2	0.02	0.02	-10000	0	-0.12	10	10
GRASP65/GM130/RAB1/GTP	0.017	0.031	-10000	0	-10000	0	0
spindle elongation	-0.009	0.048	-10000	0	-0.1	93	93
ODF2	0.021	0.014	-10000	0	-0.12	5	5
BUB1	-0.063	0.25	-10000	0	-0.77	61	61
TPT1	0.001	0.035	-10000	0	-0.16	17	17
CDC25C	-0.016	0.096	-10000	0	-0.39	32	32
CDC25B	0.015	0.025	-10000	0	-0.13	14	14
SGOL1	-0.012	0.057	-10000	0	-0.19	50	50
RHOA	0.023	0.006	-10000	0	-0.12	1	1
CCNB1/CDK1	-0.028	0.13	-10000	0	-0.24	134	134
CDC14B	0.011	0.004	-10000	0	-0.085	1	1
CDC20	0.016	0.027	-10000	0	-0.12	19	19
PLK1/PBIP1	-0.003	0.042	-10000	0	-0.096	72	72
mitosis	0.003	0.009	0.025	67	-0.011	1	68
FBXO5	-0.019	0.07	-10000	0	-0.17	78	78
CDC2	0.007	0.04	-10000	0	-0.12	46	46
NDC80	0.008	0.038	-10000	0	-0.12	43	43
metaphase plate congression	0	0.042	-10000	0	-0.17	19	19
ERCC6L	-0.033	0.12	-10000	0	-0.23	132	132
NLP/gamma Tubulin	-0.002	0.029	-10000	0	-0.088	39	39
microtubule cytoskeleton organization	0.001	0.035	-10000	0	-0.16	17	17
G2/M transition DNA damage checkpoint	0	0.002	0.01	16	-10000	0	16
PPP1R12A	0.022	0.008	-10000	0	-0.12	1	1
interphase	0	0.002	0.01	16	-10000	0	16
PLK1/PRC1-2	-0.015	0.095	-10000	0	-0.17	122	122
GRASP65/GM130/RAB1/GTP/PLK1	0.024	0.053	-10000	0	-0.12	49	49
RAB1A	0.023	0.004	-10000	0	-10000	0	0
prophase	0	0	-10000	0	-10000	0	0
Aurora A/BORA	-0.011	0.051	-10000	0	-0.12	86	86
mitotic prometaphase	-0.001	0.003	0.02	6	-0.01	23	29
proteasomal ubiquitin-dependent protein catabolic process	0.013	0.058	-10000	0	-0.25	15	15
microtubule-based process	-0.01	0.072	-10000	0	-0.14	100	100
Golgi organization	-0.009	0.048	-10000	0	-0.1	93	93
Cohesin/SA2	-0.003	0.054	-10000	0	-0.12	80	80
PPP1CB/MYPT1	0.024	0.039	-10000	0	-0.15	27	27
KIF20A	0.009	0.038	-10000	0	-0.12	43	43
APC/C/CDC20	-0.005	0.069	-10000	0	-0.15	79	79
PPP2R1A	0.022	0.009	-10000	0	-0.12	2	2
chromosome segregation	-0.003	0.042	-10000	0	-0.095	72	72
PRC1	0.015	0.03	-10000	0	-0.12	25	25
ECT2	-0.021	0.072	-10000	0	-0.15	102	102
C13orf34	-0.01	0.05	-10000	0	-0.11	80	80
NUDC	0	0.042	-10000	0	-0.17	19	19
regulation of attachment of spindle microtubules to kinetochore	-0.028	0.099	-10000	0	-0.23	87	87
spindle assembly	-0.005	0.037	-10000	0	-0.087	72	72
spindle stabilization	-0.003	0.022	-10000	0	-0.05	78	78
APC/C/HCDH1	0.025	0.007	-10000	0	-0.089	2	2
MKLP2/PLK1	-0.01	0.073	-10000	0	-0.14	100	100
CCNB1	0.014	0.028	-10000	0	-0.12	21	21
PPP1CB	0.022	0.003	-10000	0	-10000	0	0
BTRC	0.023	0.002	-10000	0	-10000	0	0
ROCK2	-0.016	0.095	-10000	0	-0.33	42	42
TUBG1	0	0.039	-10000	0	-0.23	11	11
G2/M transition of mitotic cell cycle	-0.043	0.12	-10000	0	-0.24	132	132
MLF1IP	0.01	0.011	-10000	0	-0.079	8	8
INCENP	0.022	0.009	-10000	0	-0.12	2	2

×

Ras signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ERK1-2/ELK1	-0.026	0.13	-9999	-0.25	110	110
MAP3K8	0.021	0.009	-9999	-0.12	2	2
FOS	-0.014	0.093	-9999	-0.29	25	25
PRKCA	0.008	0.037	-9999	-0.12	40	40
PTPN7	0.017	0.013	-9999	-10000	0	0
HRAS	0.022	0.006	-9999	-0.12	1	1
PRKCB	-0.003	0.006	-9999	-0.01	193	193
NRAS	0.021	0.012	-9999	-0.12	3	3
RAS family/GTP	0.024	0.043	-9999	-0.1	46	46
MAPK3	0.002	0.068	-9999	-0.49	5	5
MAP2K1	-0.017	0.091	-9999	-0.29	46	46
ELK1	0.015	0.02	-9999	-0.13	6	6
BRAF	-0.016	0.086	-9999	-0.3	42	42
mol:GTP	-0.001	0.002	-9999	-0.003	185	185
MAPK1	0	0.076	-9999	-0.47	8	8
RAF1	-0.017	0.085	-9999	-0.29	47	47
KRAS	0.013	0.034	-9999	-0.12	33	33

×

Signaling events mediated by PTP1B

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.01	0.042	-10000	0	-0.12	52	52
Jak2/Leptin Receptor	-0.043	0.13	0.21	1	-0.37	57	58
PTP1B/AKT1	-0.06	0.1	-10000	0	-0.23	97	97
FYN	0.011	0.037	-10000	0	-0.12	40	40
p210 bcr-abl/PTP1B	-0.075	0.1	-10000	0	-0.26	96	96
EGFR	0.014	0.031	-10000	0	-0.13	25	25
EGF/EGFR	-0.058	0.1	-10000	0	-0.23	103	103
CSF1	0.013	0.033	-10000	0	-0.12	31	31
AKT1	0.02	0.019	-10000	0	-0.12	10	10
INSR	0.021	0.017	-10000	0	-0.12	8	8
PTP1B/N-cadherin	-0.094	0.12	-10000	0	-0.24	187	187
Insulin Receptor/Insulin	-0.031	0.091	-10000	0	-0.21	75	75
HCK	0.019	0.024	-10000	0	-0.12	15	15
CRK	0.021	0.016	-10000	0	-0.12	7	7
TYK2	-0.068	0.1	-10000	0	-0.25	96	96
EGF	0.018	0.022	-10000	0	-0.13	12	12
YES1	0.02	0.018	-10000	0	-0.12	8	8
CAV1	-0.056	0.096	-10000	0	-0.24	89	89
TXN	0.019	0.015	-10000	0	-0.12	5	5
PTP1B/IRS1/GRB2	-0.055	0.11	-10000	0	-0.23	104	104
cell migration	0.075	0.1	0.26	96	-10000	0	96
STAT3	0.021	0.011	-10000	0	-0.12	3	3
PRLR	0.014	0.042	-10000	0	-0.12	53	53
ITGA2B	0.022	0.006	-10000	0	-0.13	1	1
CSF1R	0.014	0.031	-10000	0	-0.12	27	27
Prolactin Receptor/Prolactin	0.035	0.035	-10000	0	-0.18	2	2
FGR	0.023	0.006	-10000	0	-0.12	1	1
PTP1B/p130 Cas	-0.063	0.1	-10000	0	-0.24	96	96
Crk/p130 Cas	-0.052	0.1	-10000	0	-0.23	96	96
DOK1	-0.056	0.094	-10000	0	-0.23	84	84
JAK2	-0.052	0.13	-10000	0	-0.42	50	50
Jak2/Leptin Receptor/Leptin	-0.056	0.12	-10000	0	-0.25	116	116
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
PTPN1	-0.075	0.1	-10000	0	-0.26	98	98
LYN	0.021	0.013	-10000	0	-0.12	4	4
CDH2	-0.015	0.057	-10000	0	-0.12	120	120
SRC	-0.008	0.054	-10000	0	-0.61	2	2
ITGB3	0.003	0.047	-10000	0	-0.12	68	68
CAT1/PTP1B	-0.058	0.12	-10000	0	-0.26	103	103
CAPN1	0.02	0.013	-10000	0	-0.12	4	4
CSK	0.023	0.009	-10000	0	-0.12	2	2
PI3K	-0.033	0.1	-10000	0	-0.21	95	95
mol:H2O2	0.002	0.004	-10000	0	-10000	0	0
STAT3 (dimer)	-0.05	0.12	-10000	0	-0.24	116	116
negative regulation of transcription	-0.05	0.13	-10000	0	-0.4	54	54
FCGR2A	0.013	0.031	-10000	0	-0.12	26	26
FER	0.019	0.018	-10000	0	-0.12	8	8
alphaIIb/beta3 Integrin	0.008	0.053	-10000	0	-0.14	38	38
BLK	0.022	0.015	-10000	0	-0.12	6	6
Insulin Receptor/Insulin/Shc	0.043	0.022	-10000	0	-0.11	7	7
RHOA	0.021	0.007	-10000	0	-0.13	1	1
LEPR	0.018	0.028	-10000	0	-0.12	21	21
BCAR1	0.022	0.011	-10000	0	-0.12	3	3
p210 bcr-abl/Grb2	0.023	0.006	-10000	0	-0.12	1	1
mol:NADPH	-0.001	0.002	-10000	0	-10000	0	0
TRPV6	0	0.087	-10000	0	-0.21	48	48
PRL	0.027	0.013	-10000	0	-0.13	3	3
SOCS3	-0.031	0.23	-10000	0	-1.2	22	22
SPRY2	-0.009	0.055	-10000	0	-0.12	103	103
Insulin Receptor/Insulin/IRS1	0.039	0.03	-10000	0	-0.11	12	12
CSF1/CSF1R	-0.077	0.13	-10000	0	-0.26	129	129
Ras protein signal transduction	0.029	0.034	0.099	29	-0.16	5	34
IRS1	0.019	0.023	-10000	0	-0.12	14	14
INS	0.022	0.011	-10000	0	-0.13	3	3
LEP	0.022	0.006	-10000	0	-0.12	1	1
STAT5B	-0.06	0.1	-10000	0	-0.25	89	89
STAT5A	-0.062	0.1	-10000	0	-0.24	102	102
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PDGFB-D/PDGFRB	-0.069	0.1	-10000	0	-0.24	107	107
CSN2	0.04	0.027	-10000	0	-10000	0	0
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
LAT	-0.083	0.19	-10000	0	-0.5	87	87
YBX1	0.033	0.015	-10000	0	-0.18	2	2
LCK	0.022	0.015	-10000	0	-0.12	6	6
SHC1	0.023	0.001	-10000	0	-10000	0	0
NOX4	-0.021	0.062	-10000	0	-0.12	152	152

×

BMP 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS	-0.035	0.091	-9999	-0.12	243	243
SMAD6-7/SMURF1	0.042	0.029	-9999	-0.13	11	11
NOG	0.017	0.029	-9999	-0.12	23	23
SMAD9	0.02	0.05	-9999	-0.54	2	2
SMAD4	0.022	0.007	-9999	-0.12	1	1
SMAD5	0	0.094	-9999	-0.29	32	32
BMP7/USAG1	-0.074	0.094	-9999	-0.13	369	369
SMAD5/SKI	0.011	0.094	-9999	-0.28	32	32
SMAD1	0.021	0.073	-9999	-0.28	26	26
BMP2	0.022	0.014	-9999	-0.12	5	5
SMAD1/SMAD1/SMAD4	-0.003	0.065	-9999	-0.29	18	18
BMPR1A	0.02	0.014	-9999	-0.12	4	4
BMPR1B	0.008	0.04	-9999	-0.12	48	48
BMPR1A-1B/BAMBI	-0.026	0.087	-9999	-0.14	161	161
AHSG	0.023	0.009	-9999	-0.12	2	2
CER1	0.022	0.012	-9999	-0.12	4	4
BMP2-4/CER1	0.033	0.039	-9999	-0.12	16	16
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA	0.003	0.1	-9999	-0.25	54	54
BMP2-4 (homodimer)	0.02	0.041	-9999	-0.087	69	69
RGMB	0.023	0.009	-9999	-0.12	2	2
BMP6/BMPR2/BMPR1A-1B	0.013	0.076	-9999	-0.12	114	114
RGMA	0.021	0.017	-9999	-0.12	8	8
SMURF1	0.023	0.009	-9999	-0.12	2	2
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP	0.004	0.077	-9999	-0.17	74	74
BMP2-4/USAG1	-0.014	0.07	-9999	-0.12	118	118
SMAD6/SMURF1/SMAD5	0.011	0.094	-9999	-0.27	33	33
SOSTDC1	-0.018	0.062	-9999	-0.12	146	146
BMP7/BMPR2/BMPR1A-1B	-0.033	0.093	-9999	-0.13	219	219
SKI	0.022	0.011	-9999	-0.12	3	3
BMP6 (homodimer)	0.02	0.023	-9999	-0.12	14	14
HFE2	0.023	0.009	-9999	-0.12	2	2
ZFYVE16	0.02	0.018	-9999	-0.12	8	8
MAP3K7	0.021	0.014	-9999	-0.12	5	5
BMP2-4/CHRD	0.033	0.038	-9999	-0.11	16	16
SMAD5/SMAD5/SMAD4	0.009	0.096	-9999	-0.28	36	36
MAPK1	0.021	0.016	-9999	-0.12	7	7
TAK1/TAB family	0.022	0.096	-9999	-0.22	50	50
BMP7 (homodimer)	-0.009	0.055	-9999	-0.12	106	106
NUP214	0.023	0.007	-9999	-0.12	1	1
BMP6/FETUA	0.032	0.017	-9999	-0.071	16	16
SMAD1/SKI	0.033	0.072	-9999	-0.26	26	26
SMAD6	0.02	0.02	-9999	-0.12	11	11
CTDSP2	0.022	0.01	-9999	-0.12	2	2
BMP2-4/FETUA	0.033	0.039	-9999	-0.066	70	70
MAP3K7IP1	0.023	0	-9999	-10000	0	0
GREM1	0.008	0.044	-9999	-0.12	58	58
BMPR2 (homodimer)	0.021	0.014	-9999	-0.12	5	5
GADD34/PP1CA	0.03	0.047	-9999	-0.12	46	46
BMPR1A-1B (homodimer)	-0.011	0.081	-9999	-0.13	154	154
CHRDL1	-0.008	0.055	-9999	-0.12	103	103
ENDOFIN/SMAD1	0.03	0.076	-9999	-0.27	27	27
SMAD6-7/SMURF1/SMAD1	0.049	0.076	-9999	-0.25	26	26
SMAD6/SMURF1	0.023	0.009	-9999	-0.12	2	2
BAMBI	-0.004	0.054	-9999	-0.12	95	95
SMURF2	0.022	0.013	-9999	-0.12	4	4
BMP2-4/CHRDL1	-0.014	0.072	-9999	-0.12	135	135
BMP2-4/GREM1	0.023	0.049	-9999	-0.12	30	30
SMAD7	0.023	0.003	-9999	-10000	0	0
SMAD8A/SMAD8A/SMAD4	0.028	0.052	-9999	-0.41	3	3
SMAD1/SMAD6	0.033	0.073	-9999	-0.26	26	26
TAK1/SMAD6	0.027	0.035	-9999	-0.14	21	21
BMP7	-0.009	0.055	-9999	-0.12	106	106
BMP6	0.02	0.023	-9999	-0.12	14	14
MAP3K7IP2	0.02	0.016	-9999	-0.12	6	6
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1	0.003	0.083	-9999	-0.22	44	44
PPM1A	0.023	0.001	-9999	-10000	0	0
SMAD1/SMURF2	0.031	0.075	-9999	-0.27	26	26
SMAD7/SMURF1	0.031	0.023	-9999	-0.14	9	9
CTDSPL	0.023	0.006	-9999	-0.12	1	1
PPP1CA	0.023	0.002	-9999	-10000	0	0
XIAP	0	0	-9999	-10000	0	0
CTDSP1	0.022	0.011	-9999	-0.12	3	3
PPP1R15A	0.019	0.025	-9999	-0.12	17	17
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS	0.002	0.08	-9999	-0.21	51	51
CHRD	0.023	0.006	-9999	-0.12	1	1
BMPR2	0.021	0.014	-9999	-0.12	5	5
BMP2-4/BMPR2/BMPR1A-1B/RGM	-0.005	0.088	-9999	-0.24	43	43
BMP4	0.009	0.042	-9999	-0.12	52	52
FST	0.004	0.049	-9999	-0.12	73	73
BMP2-4/NOG	0.027	0.047	-9999	-0.12	33	33
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1	-0.023	0.091	-9999	-0.12	220	220

×

Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.003	0.076	-9999	-0.17	89	89
CRKL	0.023	0.009	-9999	-0.12	2	2
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
DOCK1	0.019	0.02	-9999	-0.12	10	10
ITGA4	0.015	0.03	-9999	-0.12	24	24
alpha4/beta7 Integrin/MAdCAM1	0.032	0.059	-9999	-0.1	78	78
EPO	0.023	0.006	-9999	-0.12	1	1
alpha4/beta7 Integrin	0.004	0.065	-9999	-0.13	106	106
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.021	0.016	-9999	-0.12	7	7
alpha4/beta1 Integrin	0.006	0.063	-9999	-0.12	101	101
EPO/EPOR (dimer)	0.032	0.019	-9999	-0.08	15	15
lamellipodium assembly	0.004	0.087	-9999	-0.25	35	35
PIK3CA	0.02	0.017	-9999	-0.12	7	7
PI3K	0.007	0.065	-9999	-0.13	96	96
ARF6	0.023	0.003	-9999	-10000	0	0
JAK2	0.003	0.081	-9999	-0.18	73	73
PXN	0.022	0.014	-9999	-0.12	5	5
PIK3R1	0.015	0.031	-9999	-0.12	27	27
MADCAM1	0.023	0.006	-9999	-0.12	1	1
cell adhesion	0.03	0.058	-9999	-0.1	78	78
CRKL/CBL	0.033	0.013	-9999	-0.14	2	2
ITGB1	0.021	0.015	-9999	-0.12	6	6
SRC	-0.038	0.074	-9999	-0.13	186	186
ITGB7	0.019	0.024	-9999	-0.12	15	15
RAC1	0.023	0.002	-9999	-10000	0	0
alpha4/beta1 Integrin/VCAM1	-0.041	0.09	-9999	-0.15	186	186
p130Cas/Crk/Dock1	-0.021	0.075	-9999	-0.16	77	77
VCAM1	-0.019	0.06	-9999	-0.12	139	139
RHOA	0.023	0.006	-9999	-0.12	1	1
alpha4/beta1 Integrin/Paxillin/GIT1	0.033	0.057	-9999	-0.098	74	74
BCAR1	-0.033	0.068	-9999	-0.11	186	186
EPOR	0.02	0.021	-9999	-0.12	12	12
mol:GDP	0	0	-9999	-10000	0	0
CBL	0.023	0.006	-9999	-0.12	1	1
GIT1	0.022	0.012	-9999	-0.12	4	4
Rac1/GTP	0.004	0.09	-9999	-0.26	34	34

×

Canonical Wnt signaling 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.037	0.047	0.11	128	-0.089	10	138
AES	0.036	0.042	0.099	124	-0.11	10	134
FBXW11	0.023	0.003	-10000	0	-10000	0	0
mol:GTP	0.001	0.002	-10000	0	-10000	0	0
LRP6/FZD1	0.018	0.047	-10000	0	-0.11	66	66
SMAD4	0.022	0.007	-10000	0	-0.12	1	1
DKK2	0.023	0.011	-10000	0	-0.12	3	3
TLE1	0.033	0.038	0.097	100	-0.11	8	108
MACF1	0.016	0.026	-10000	0	-0.12	18	18
CTNNB1	0.021	0.098	0.18	8	-0.34	23	31
WIF1	0.02	0.022	-10000	0	-0.12	13	13
beta catenin/RanBP3	0.084	0.19	0.38	135	-0.35	13	148
KREMEN2	0.022	0.012	-10000	0	-0.12	4	4
DKK1	0.015	0.034	-10000	0	-0.12	33	33
beta catenin/beta TrCP1	0.033	0.096	0.19	8	-0.35	20	28
FZD1	0.023	0.006	-10000	0	-0.12	1	1
AXIN2	-0.037	0.16	-10000	0	-0.77	13	13
AXIN1	0.023	0.011	-10000	0	-0.12	3	3
RAN	0.024	0.002	-10000	0	-10000	0	0
Axin1/APC/GSK3/beta catenin	0.036	0.083	-10000	0	-0.5	9	9
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4	0.024	0.11	0.23	9	-0.28	42	51
Axin1/APC/GSK3	0.027	0.06	-10000	0	-0.25	16	16
Axin1/APC/GSK3/beta catenin/Macf1	0.03	0.068	-10000	0	-0.26	16	16
HNF1A	0.037	0.038	0.1	112	-0.12	3	115
CTBP1	0.037	0.04	0.1	107	-0.11	7	114
MYC	-0.17	0.44	-10000	0	-1.3	74	74
RANBP3	0.023	0.009	-10000	0	-0.12	2	2
DKK2/LRP6/Kremen 2	0.032	0.043	-10000	0	-0.11	32	32
NKD1	0.022	0.012	-10000	0	-0.12	4	4
TCF4	0.036	0.042	0.1	120	-0.093	8	128
TCF3	0.037	0.039	0.1	108	-0.12	5	113
WNT1/LRP6/FZD1/Axin1	0.044	0.044	-10000	0	-0.097	36	36
Ran/GTP	0.018	0.012	-10000	0	-0.14	3	3
CtBP/CBP/TCF/TLE1/AES	0.08	0.23	0.45	128	-0.36	12	140
LEF1	0.011	0.057	0.097	78	-0.11	75	153
DVL1	0.027	0.076	-10000	0	-0.33	18	18
CSNK2A1	0.022	0.015	-10000	0	-0.12	6	6
beta catenin/TCF/CtBP/CBP/TLE1/AES	-0.025	0.14	-10000	0	-0.3	74	74
DKK1/LRP6/Kremen 2	0.027	0.047	-10000	0	-0.11	34	34
LRP6	0.014	0.034	-10000	0	-0.12	32	32
CSNK1A1	0.04	0.044	0.11	125	-0.13	1	126
NLK	0.017	0.022	-10000	0	-0.13	11	11
CCND1	-0.19	0.45	-10000	0	-1.3	83	83
WNT1	0.023	0.009	-10000	0	-0.12	2	2
GSK3A	0.021	0.019	-10000	0	-0.12	10	10
GSK3B	0.022	0.011	-10000	0	-0.12	3	3
FRAT1	0.023	0.006	-10000	0	-0.12	1	1
PPP2R5D	0.018	0.044	-10000	0	-0.2	16	16
APC	0.022	0.033	-10000	0	-0.085	38	38
WNT1/LRP6/FZD1	0.018	0.056	-10000	0	-0.24	10	10
CREBBP	0.035	0.037	0.1	89	-0.1	5	94

×

EPHB forward signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Ephrin A5/EPHB2	0.011	0.049	-10000	0	-0.12	54	54
cell-cell adhesion	0.023	0.039	0.14	38	-10000	0	38
Ephrin B/EPHB2/RasGAP	0.016	0.076	-10000	0	-0.15	36	36
ITSN1	0.022	0.011	-10000	0	-0.12	3	3
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
SHC1	0.023	0.001	-10000	0	-10000	0	0
Ephrin B1/EPHB3	0.022	0.034	-10000	0	-0.12	24	24
Ephrin B1/EPHB1	0.024	0.027	-10000	0	-0.068	43	43
HRAS/GDP	-0.002	0.07	-10000	0	-0.14	85	85
Ephrin B/EPHB1/GRB7	0.018	0.071	-10000	0	-0.14	29	29
Endophilin/SYNJ1	-0.001	0.052	-10000	0	-0.087	124	124
KRAS	0.014	0.034	-10000	0	-0.12	33	33
Ephrin B/EPHB1/Src	0.024	0.067	-10000	0	-0.091	108	108
endothelial cell migration	0.001	0.071	-10000	0	-0.11	145	145
GRB2	0.023	0.006	-10000	0	-0.12	1	1
GRB7	0.018	0.026	-10000	0	-0.12	18	18
PAK1	-0.003	0.057	-10000	0	-0.16	28	28
HRAS	0.023	0.006	-10000	0	-0.12	1	1
RRAS	-0.006	0.056	-10000	0	-0.095	127	127
DNM1	0.021	0.019	-10000	0	-0.12	10	10
cell-cell signaling	0	0	-10000	0	-10000	0	0
CRK	0	0.049	-10000	0	-0.087	109	109
lamellipodium assembly	-0.023	0.039	-10000	0	-0.14	38	38
Ephrin B/EPHB1/Src/p52 SHC/GRB2	0.019	0.051	-10000	0	-0.22	13	13
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
EPHB2	0.02	0.02	-10000	0	-0.12	11	11
EPHB3	0.019	0.024	-10000	0	-0.12	15	15
EPHB1	0.016	0.032	-10000	0	-0.12	28	28
EPHB4	0.022	0.009	-10000	0	-0.12	2	2
mol:GDP	-0.01	0.079	-10000	0	-0.17	97	97
Ephrin B/EPHB2	0.012	0.066	-10000	0	-0.097	123	123
Ephrin B/EPHB3	0.011	0.065	-10000	0	-0.095	123	123
JNK cascade	0.015	0.045	-10000	0	-0.1	56	56
Ephrin B/EPHB1	0.013	0.063	-10000	0	-0.095	108	108
RAP1/GDP	0.001	0.084	-10000	0	-0.16	97	97
EFNB2	0.007	0.041	-10000	0	-0.12	50	50
EFNB3	0.018	0.026	-10000	0	-0.12	19	19
EFNB1	0.021	0.018	-10000	0	-0.12	9	9
Ephrin B2/EPHB1-2	0.006	0.061	-10000	0	-0.1	101	101
RAP1B	0.019	0.02	-10000	0	-0.12	10	10
RAP1A	0.021	0.012	-10000	0	-0.12	3	3
CDC42/GTP	0.008	0.077	-10000	0	-0.18	30	30
Rap1/GTP	-0.028	0.045	-10000	0	-0.14	59	59
axon guidance	0.011	0.049	-10000	0	-0.12	54	54
MAPK3	0.008	0.063	-10000	0	-0.19	17	17
MAPK1	0.008	0.063	-10000	0	-0.19	18	18
Rac1/GDP	0.001	0.079	-10000	0	-0.16	85	85
actin cytoskeleton reorganization	-0.025	0.045	-10000	0	-0.14	43	43
CDC42/GDP	0.001	0.079	-10000	0	-0.16	85	85
PI3K	0.004	0.074	-10000	0	-0.11	145	145
EFNA5	0.014	0.033	-10000	0	-0.12	30	30
Ephrin B2/EPHB4	0	0.058	-10000	0	-0.12	89	89
Ephrin B/EPHB2/Intersectin/N-WASP	-0.005	0.08	-10000	0	-0.26	17	17
CDC42	0.023	0.002	-10000	0	-10000	0	0
RAS family/GTP	-0.026	0.042	-10000	0	-0.13	53	53
PTK2	-0.001	0.051	-10000	0	-0.2	33	33
MAP4K4	0.015	0.045	-10000	0	-0.1	56	56
SRC	0.023	0.009	-10000	0	-0.12	2	2
KALRN	0.015	0.033	-10000	0	-0.12	30	30
Intersectin/N-WASP	0.031	0.022	-10000	0	-0.11	12	12
neuron projection morphogenesis	0.005	0.07	-10000	0	-0.16	42	42
MAP2K1	0.005	0.066	-10000	0	-0.2	15	15
WASL	0.023	0.009	-10000	0	-0.12	2	2
Ephrin B1/EPHB1-2/NCK1	0.036	0.056	-10000	0	-0.11	55	55
cell migration	0.002	0.077	-10000	0	-0.2	27	27
NRAS	0.022	0.011	-10000	0	-0.12	3	3
SYNJ1	-0.001	0.052	-10000	0	-0.088	124	124
PXN	0.022	0.014	-10000	0	-0.12	5	5
TF	-0.001	0.049	-10000	0	-0.12	33	33
HRAS/GTP	0.01	0.063	-10000	0	-0.15	29	29
Ephrin B1/EPHB1-2	0.032	0.039	-10000	0	-0.11	26	26
cell adhesion mediated by integrin	0.014	0.047	0.1	100	-10000	0	100
RAC1	0.023	0.002	-10000	0	-10000	0	0
mol:GTP	0.011	0.069	-10000	0	-0.16	29	29
RAC1-CDC42/GTP	-0.024	0.039	-10000	0	-0.13	39	39
RASA1	0.021	0.012	-10000	0	-0.12	3	3
RAC1-CDC42/GDP	0.009	0.08	-10000	0	-0.15	85	85
ruffle organization	0.004	0.057	-10000	0	-0.14	40	40
NCK1	0.02	0.019	-10000	0	-0.12	9	9
receptor internalization	0	0.049	-10000	0	-0.082	125	125
Ephrin B/EPHB2/KALRN	0.019	0.073	-10000	0	-0.13	39	39
ROCK1	0.017	0.028	-10000	0	-0.097	24	24
RAS family/GDP	-0.028	0.049	-10000	0	-0.16	43	43
Rac1/GTP	-0.024	0.041	-10000	0	-0.14	38	38
Ephrin B/EPHB1/Src/Paxillin	0	0.071	-10000	0	-0.14	100	100

×

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

×

IL12-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1	-0.001	0.094	-10000	0	-0.22	49	49
TBX21	-0.081	0.27	-10000	0	-0.71	60	60
B2M	0.024	0.006	-10000	0	-10000	0	0
TYK2	0.015	0.029	-10000	0	-0.088	13	13
IL12RB1	0.017	0.024	-10000	0	-0.12	1	1
GADD45B	-0.09	0.32	-10000	0	-0.84	62	62
IL12RB2	0.014	0.033	-10000	0	-0.12	16	16
GADD45G	-0.079	0.28	-10000	0	-0.78	50	50
natural killer cell activation	-0.003	0.018	-10000	0	-0.039	46	46
RELB	0.022	0.011	-10000	0	-0.12	3	3
RELA	0.023	0.009	-10000	0	-0.12	2	2
IL18	0.004	0.047	-10000	0	-0.12	66	66
IL2RA	0.021	0.017	-10000	0	-0.12	8	8
IFNG	0.013	0.038	-10000	0	-0.12	41	41
STAT3 (dimer)	-0.073	0.27	-10000	0	-0.58	88	88
HLA-DRB5	-0.014	0.058	-10000	0	-0.12	119	119
FASLG	-0.083	0.28	-10000	0	-0.71	61	61
NF kappa B2 p52/RelB	-0.077	0.27	-10000	0	-0.6	89	89
CD4	0.012	0.029	-10000	0	-0.13	21	21
SOCS1	0.016	0.031	-10000	0	-0.12	27	27
EntrezGene:6955	-0.002	0.008	-10000	0	-10000	0	0
CD3D	0.004	0.045	-10000	0	-0.13	56	56
CD3E	0.012	0.034	-10000	0	-0.12	29	29
CD3G	-0.001	0.051	-10000	0	-0.13	78	78
IL12Rbeta2/JAK2	0.009	0.063	-10000	0	-0.15	52	52
CCL3	-0.1	0.32	-10000	0	-0.86	62	62
CCL4	-0.09	0.27	-10000	0	-0.61	89	89
HLA-A	0.021	0.018	-10000	0	-0.12	8	8
IL18/IL18R	0.025	0.076	-10000	0	-0.12	81	81
NOS2	-0.082	0.26	-10000	0	-0.56	93	93
IL12/IL12R/TYK2/JAK2/SPHK2	0.002	0.091	-10000	0	-0.23	41	41
IL1R1	-0.17	0.42	-10000	0	-1	98	98
IL4	0.026	0.021	0.073	3	-0.11	3	6
JAK2	0.012	0.033	-10000	0	-0.12	17	17
EntrezGene:6957	-0.001	0.007	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.01	0.12	-10000	0	-0.4	32	32
RAB7A	-0.063	0.26	-10000	0	-0.7	52	52
lysosomal transport	-0.058	0.25	-10000	0	-0.66	54	54
FOS	-0.26	0.48	-10000	0	-1.1	125	125
STAT4 (dimer)	-0.073	0.28	-10000	0	-0.62	84	84
STAT5A (dimer)	-0.082	0.28	-10000	0	-0.6	93	93
GZMA	-0.11	0.34	-10000	0	-0.87	70	70
GZMB	-0.1	0.31	-10000	0	-0.77	69	69
HLX	0.023	0.006	-10000	0	-0.12	1	1
LCK	-0.092	0.29	-10000	0	-0.64	88	88
TCR/CD3/MHC II/CD4	-0.11	0.21	-10000	0	-0.35	193	193
IL2/IL2R	0.013	0.068	-10000	0	-0.1	114	114
MAPK14	-0.084	0.3	-10000	0	-0.72	73	73
CCR5	-0.063	0.25	-10000	0	-0.65	51	51
IL1B	0.005	0.044	-10000	0	-0.12	45	45
STAT6	-0.025	0.14	-10000	0	-0.36	41	41
STAT4	0.02	0.02	-10000	0	-0.12	11	11
STAT3	0.022	0.011	-10000	0	-0.12	3	3
STAT1	0.014	0.031	-10000	0	-0.12	26	26
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
NFKB2	0.023	0.009	-10000	0	-0.12	2	2
IL12B	0.018	0.023	-10000	0	-0.038	2	2
CD8A	0.024	0.011	-10000	0	-0.12	3	3
CD8B	0.024	0.015	-10000	0	-0.12	6	6
T-helper 1 cell differentiation	0	0	-10000	0	-10000	0	0
natural killer cell mediated cytotoxicity	0.001	0.093	0.22	49	-10000	0	49
IL2RB	0.019	0.024	-10000	0	-0.12	16	16
proteasomal ubiquitin-dependent protein catabolic process	-0.065	0.26	-10000	0	-0.57	84	84
IL2RG	-0.002	0.05	-10000	0	-0.12	82	82
IL12	0.004	0.063	-10000	0	-0.14	48	48
STAT5A	0.022	0.013	-10000	0	-0.12	4	4
CD247	0.021	0.01	-10000	0	-10000	0	0
IL2	0.022	0.011	-10000	0	-0.12	3	3
SPHK2	0.022	0.011	-10000	0	-0.12	3	3
FRAP1	0.022	0.013	-10000	0	-0.12	4	4
IL12A	-0.001	0.051	-10000	0	-0.12	70	70
IL12/IL12R/TYK2/JAK2	-0.099	0.3	-10000	0	-0.68	89	89
MAP2K3	-0.078	0.29	-10000	0	-0.67	81	81
RIPK2	0.013	0.034	-10000	0	-0.12	32	32
MAP2K6	-0.096	0.3	-10000	0	-0.67	86	86
regulation of dendritic cell antigen processing and presentation	0	0	-10000	0	-10000	0	0
HLA-DRA	0.008	0.032	-10000	0	-0.13	24	24
IL18RAP	0.022	0.02	-10000	0	-0.12	8	8
IL12Rbeta1/TYK2	0.024	0.037	-10000	0	-0.15	3	3
EOMES	0.018	0.031	-10000	0	-10000	0	0
STAT1 (dimer)	-0.097	0.28	-10000	0	-0.58	103	103
T cell proliferation	-0.06	0.22	-10000	0	-0.49	85	85
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
IL18R1	0.021	0.024	-10000	0	-0.12	13	13
CD8-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.11	0.2	-10000	0	-0.52	87	87
ATF2	-0.076	0.28	-10000	0	-0.66	76	76

×

TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC	-0.004	0.14	-10000	0	-0.34	60	60
FYN	-0.047	0.18	-10000	0	-0.4	86	86
LAT/GRAP2/SLP76	-0.009	0.15	-10000	0	-0.34	72	72
IKBKB	0.022	0.015	-10000	0	-0.12	6	6
AKT1	-0.009	0.13	-10000	0	-0.3	75	75
B2M	0.022	0.007	-10000	0	-10000	0	0
IKBKG	0.008	0.044	-10000	0	-0.092	63	63
MAP3K8	0.023	0.009	-10000	0	-0.12	2	2
mol:Ca2+	-0.004	0.011	-10000	0	-0.034	45	45
integrin-mediated signaling pathway	0.021	0.035	-10000	0	-0.096	44	44
LAT/GRAP2/SLP76/VAV1/PI3K Class IA	-0.023	0.18	-10000	0	-0.42	75	75
TRPV6	0.003	0.017	-10000	0	-0.13	6	6
CD28	0.022	0.011	-10000	0	-0.12	3	3
SHC1	-0.019	0.16	-10000	0	-0.4	62	62
receptor internalization	-0.014	0.14	-10000	0	-0.35	63	63
PRF1	-0.019	0.18	-10000	0	-0.81	19	19
KRAS	0.014	0.034	-10000	0	-0.12	33	33
GRB2	0.023	0.006	-10000	0	-0.12	1	1
COT/AKT1	0.004	0.11	-10000	0	-0.24	74	74
LAT	-0.019	0.16	-10000	0	-0.4	62	62
EntrezGene:6955	0	0.003	-10000	0	-0.022	3	3
CD3D	0.008	0.044	-10000	0	-0.12	56	56
CD3E	0.015	0.033	-10000	0	-0.13	29	29
CD3G	0.002	0.051	-10000	0	-0.12	78	78
RASGRP2	0.007	0.015	-10000	0	-0.049	1	1
RASGRP1	-0.017	0.14	-10000	0	-0.29	87	87
HLA-A	0.02	0.019	-10000	0	-0.13	8	8
RASSF5	0.02	0.022	-10000	0	-0.12	13	13
RAP1A/GTP/RAPL	0.022	0.035	-10000	0	-0.096	44	44
mol:GTP	0	0	-10000	0	-10000	0	0
mol:GDP	0.009	0.05	-10000	0	-0.094	66	66
PDK1/CARD11/BCL10/MALT1/TRAF6	-0.026	0.054	-10000	0	-0.15	78	78
PRKCA	-0.005	0.08	-10000	0	-0.18	72	72
GRAP2	0.022	0.012	-10000	0	-0.12	4	4
mol:IP3	-0.044	0.098	0.098	3	-0.27	73	76
EntrezGene:6957	0	0.004	-10000	0	-0.023	2	2
TCR/CD3/MHC I/CD8	-0.014	0.13	-10000	0	-0.36	50	50
ORAI1	0	0.023	0.091	6	-0.15	7	13
CSK	-0.019	0.16	-10000	0	-0.4	63	63
B7 family/CD28	-0.007	0.16	-10000	0	-0.35	73	73
CHUK	0.021	0.013	-10000	0	-0.12	4	4
TCR/CD3/MHC I/CD8/LCK/ZAP-70	-0.026	0.17	-10000	0	-0.45	62	62
PTPN6	-0.023	0.16	-10000	0	-0.4	64	64
VAV1	-0.023	0.16	-10000	0	-0.4	68	68
Monovalent TCR/CD3	-0.015	0.095	-10000	0	-0.2	96	96
CBL	0.023	0.006	-10000	0	-0.12	1	1
LCK	-0.036	0.17	-10000	0	-0.4	78	78
PAG1	-0.019	0.16	-10000	0	-0.4	62	62
RAP1A	0.021	0.012	-10000	0	-0.12	3	3
TCR/CD3/MHC I/CD8/LCK	-0.028	0.17	-10000	0	-0.42	68	68
CD80	0.019	0.024	-10000	0	-0.12	15	15
CD86	0.013	0.034	-10000	0	-0.12	32	32
PDK1/CARD11/BCL10/MALT1	-0.027	0.066	-10000	0	-0.18	73	73
HRAS	0.023	0.006	-10000	0	-0.12	1	1
GO:0035030	-0.016	0.13	-10000	0	-0.3	73	73
CD8A	0.022	0.012	-10000	0	-0.13	3	3
CD8B	0.021	0.016	-10000	0	-0.13	6	6
PTPRC	-0.004	0.051	-10000	0	-0.12	86	86
PDK1/PKC theta	-0.016	0.15	-10000	0	-0.35	74	74
CSK/PAG1	-0.014	0.15	-10000	0	-0.39	62	62
SOS1	0.017	0.027	-10000	0	-0.12	20	20
peptide-MHC class I	0.012	0.073	-10000	0	-0.19	59	59
GRAP2/SLP76	-0.015	0.17	-10000	0	-0.38	76	76
STIM1	-0.002	0.032	-10000	0	-0.17	18	18
RAS family/GTP	0.007	0.07	-10000	0	-0.14	73	73
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin	-0.014	0.15	-10000	0	-0.37	63	63
mol:DAG	-0.041	0.088	-10000	0	-0.24	76	76
RAP1A/GDP	0.005	0.026	-10000	0	-0.053	54	54
PLCG1	0.019	0.024	-10000	0	-0.12	16	16
CD247	0.023	0.004	-10000	0	-10000	0	0
cytotoxic T cell degranulation	-0.017	0.18	-10000	0	-0.72	22	22
RAP1A/GTP	-0.002	0.009	-10000	0	-0.037	25	25
mol:PI-3-4-5-P3	-0.015	0.15	-10000	0	-0.35	75	75
LAT/GRAP2/SLP76/VAV1/PLCgamma1	-0.05	0.12	-10000	0	-0.34	70	70
NRAS	0.022	0.011	-10000	0	-0.12	3	3
ZAP70	0.023	0.006	-10000	0	-0.12	1	1
GRB2/SOS1	0.021	0.045	-10000	0	-0.15	29	29
LAT/GRAP2/SLP76/VAV1	-0.013	0.14	-10000	0	-0.33	75	75
MALT1	0.017	0.026	-10000	0	-0.12	19	19
TRAF6	0.022	0.009	-10000	0	-0.12	2	2
CD8 heterodimer	0.033	0.016	-10000	0	-0.083	6	6
CARD11	0.017	0.028	-10000	0	-0.12	22	22
PRKCB	-0.03	0.063	-10000	0	-0.17	76	76
PRKCE	0	0.079	-10000	0	-0.18	71	71
PRKCQ	-0.023	0.17	-10000	0	-0.39	75	75
LCP2	0.013	0.033	-10000	0	-0.12	31	31
BCL10	0.023	0.001	-10000	0	-10000	0	0
regulation of survival gene product expression	-0.005	0.11	-10000	0	-0.26	75	75
IKK complex	0.007	0.044	-10000	0	-0.083	53	53
RAS family/GDP	-0.006	0.01	-10000	0	-0.034	40	40
MAP3K14	0.008	0.087	-10000	0	-0.19	71	71
PDPK1	-0.007	0.12	-10000	0	-0.29	74	74
TCR/CD3/MHC I/CD8/Fyn	-0.03	0.19	-10000	0	-0.48	65	65

×

Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
adherens junction organization	0	0.088	-10000	0	-0.18	86	86
epithelial cell differentiation	0.029	0.059	-10000	0	-0.12	67	67
CYFIP2	0.02	0.018	-10000	0	-0.12	8	8
ENAH	0.009	0.056	-10000	0	-0.13	51	51
EGFR	0.015	0.03	-10000	0	-0.12	25	25
EPHA2	0.02	0.022	-10000	0	-0.12	13	13
MYO6	0.01	0.057	-10000	0	-0.12	67	67
CTNNB1	0.022	0.008	-10000	0	-0.12	1	1
ABI1/Sra1/Nap1	0.03	0.05	-10000	0	-0.11	62	62
AQP5	-0.059	0.15	-10000	0	-0.32	119	119
CTNND1	0.023	0.004	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.015	0.049	-10000	0	-0.11	67	67
regulation of calcium-dependent cell-cell adhesion	0.014	0.05	-10000	0	-0.11	67	67
EGF	0.02	0.021	-10000	0	-0.12	12	12
NCKAP1	0.023	0.004	-10000	0	-10000	0	0
AQP3	0.012	0.076	-10000	0	-0.3	21	21
cortical microtubule organization	0.029	0.059	-10000	0	-0.12	67	67
GO:0000145	0.008	0.045	-10000	0	-0.1	67	67
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.033	0.061	-10000	0	-0.12	67	67
MLLT4	0.014	0.032	-10000	0	-0.12	29	29
ARF6/GDP	-0.022	0.05	-10000	0	-0.17	43	43
ARF6	0.023	0.003	-10000	0	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	0.029	0.062	-10000	0	-0.11	75	75
mol:Ca2+	0	0	-10000	0	-10000	0	0
VASP	0.015	0.058	-10000	0	-0.18	30	30
PVRL2	0.019	0.023	-10000	0	-0.12	15	15
ZYX	0.011	0.054	-10000	0	-0.12	67	67
ARF6/GTP	0.035	0.063	-10000	0	-0.17	18	18
CDH1	0.021	0.016	-10000	0	-0.12	6	6
EGFR/EGFR/EGF/EGF	0.015	0.062	-10000	0	-0.19	24	24
RhoA/GDP	0.03	0.058	-10000	0	-0.11	71	71
actin cytoskeleton organization	0.009	0.059	-10000	0	-0.13	67	67
IGF-1R heterotetramer	0.013	0.032	-10000	0	-0.12	28	28
GIT1	0.022	0.012	-10000	0	-0.12	4	4
IGF1R	0.013	0.032	-10000	0	-0.12	28	28
IGF1	0.007	0.045	-10000	0	-0.12	60	60
DIAPH1	-0.022	0.2	-10000	0	-0.56	70	70
Wnt receptor signaling pathway	-0.029	0.059	0.12	67	-10000	0	67
RHOA	0.023	0.006	-10000	0	-0.12	1	1
RhoA/GTP	-0.022	0.049	-10000	0	-0.17	42	42
CTNNA1	0.022	0.01	-10000	0	-0.12	2	2
VCL	0.009	0.061	-10000	0	-0.13	67	67
EFNA1	0.014	0.031	-10000	0	-0.12	26	26
LPP	0.012	0.054	-10000	0	-0.11	69	69
Ephrin A1/EPHA2	0.012	0.064	-10000	0	-0.19	28	28
SEC6/SEC8	-0.02	0.049	-10000	0	-0.19	32	32
MGAT3	0.014	0.051	-10000	0	-0.11	67	67
HGF/MET	-0.006	0.071	-10000	0	-0.18	45	45
HGF	0.02	0.023	-10000	0	-0.12	14	14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN	0	0.089	-10000	0	-0.18	86	86
actin cable formation	0.012	0.08	-10000	0	-0.2	48	48
KIAA1543	0.013	0.05	-10000	0	-0.11	67	67
KIFC3	0.015	0.05	-10000	0	-0.11	67	67
NCK1	0.02	0.019	-10000	0	-0.12	9	9
EXOC3	0.023	0.009	-10000	0	-0.12	2	2
ACTN1	0.013	0.057	-10000	0	-0.12	67	67
NCK1/GIT1	0.022	0.043	-10000	0	-0.14	32	32
mol:GDP	0.029	0.059	-10000	0	-0.12	67	67
EXOC4	0.022	0.007	-10000	0	-0.12	1	1
STX4	0.014	0.052	-10000	0	-0.11	67	67
PIP5K1C	0.015	0.05	-10000	0	-0.11	67	67
LIMA1	0.019	0.023	-10000	0	-0.12	14	14
ABI1	0.022	0.009	-10000	0	-0.12	2	2
ROCK1	0.011	0.06	-10000	0	-0.16	39	39
adherens junction assembly	0.022	0.059	-10000	0	-0.2	20	20
IGF-1R heterotetramer/IGF1	0	0.071	-10000	0	-0.17	47	47
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.013	0.054	-10000	0	-0.15	43	43
MET	0	0.047	-10000	0	-0.12	70	70
PLEKHA7	0.013	0.052	-10000	0	-0.11	67	67
mol:GTP	0.028	0.061	-10000	0	-0.11	75	75
establishment of epithelial cell apical/basal polarity	0.013	0.062	-10000	0	-0.18	34	34
cortical actin cytoskeleton stabilization	0	0.088	-10000	0	-0.18	86	86
regulation of cell-cell adhesion	0.009	0.059	-10000	0	-0.13	67	67
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton	0	0.089	-10000	0	-0.18	86	86

×

E-cadherin signaling in keratinocytes

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
keratinocyte differentiation	-0.005	0.1	-10000	0	-0.27	51	51
adherens junction organization	-0.007	0.12	-10000	0	-0.26	68	68
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.002	0.098	-10000	0	-0.25	49	49
FMN1	-0.002	0.11	-10000	0	-0.24	69	69
mol:IP3	-0.002	0.092	-10000	0	-0.21	63	63
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin	-0.004	0.11	-10000	0	-0.26	67	67
CTNNB1	0.022	0.008	-10000	0	-0.12	1	1
AKT1	0.001	0.097	-10000	0	-0.25	48	48
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.007	0.13	-10000	0	-0.36	47	47
CTNND1	0.023	0.004	-10000	0	-10000	0	0
mol:PI-4-5-P2	-0.001	0.1	-10000	0	-0.24	68	68
VASP	-0.001	0.11	-10000	0	-0.25	68	68
ZYX	-0.004	0.11	-10000	0	-0.25	69	69
JUB	-0.005	0.11	-10000	0	-0.25	69	69
EGFR(dimer)	-0.001	0.11	-10000	0	-0.25	71	71
E-cadherin/beta catenin-gamma catenin	0.026	0.052	-10000	0	-0.11	63	63
mol:PI-3-4-5-P3	0.003	0.1	-10000	0	-0.26	50	50
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PI3K	0.004	0.11	-10000	0	-0.26	50	50
FYN	-0.012	0.11	-10000	0	-0.27	69	69
mol:Ca2+	-0.002	0.09	-10000	0	-0.21	63	63
JUP	0.019	0.021	-10000	0	-0.12	12	12
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
mol:DAG	-0.002	0.092	-10000	0	-0.21	63	63
CDH1	0.02	0.016	-10000	0	-0.12	6	6
RhoA/GDP	0.002	0.097	-10000	0	-0.24	49	49
establishment of polarity of embryonic epithelium	-0.001	0.1	-10000	0	-0.24	68	68
SRC	0.023	0.009	-10000	0	-0.12	2	2
RAC1	0.023	0.002	-10000	0	-10000	0	0
RHOA	0.023	0.006	-10000	0	-0.12	1	1
EGFR	0.015	0.03	-10000	0	-0.12	25	25
CASR	0.001	0.086	-10000	0	-0.24	42	42
RhoA/GTP	0.006	0.089	-10000	0	-0.25	40	40
AKT2	0	0.097	-10000	0	-0.24	52	52
actin cable formation	0.001	0.1	-10000	0	-0.24	68	68
apoptosis	0.004	0.099	0.24	57	-10000	0	57
CTNNA1	0.022	0.01	-10000	0	-0.12	2	2
mol:GDP	-0.006	0.097	-10000	0	-0.24	57	57
PIP5K1A	-0.001	0.11	-10000	0	-0.25	68	68
PLCG1	-0.003	0.094	-10000	0	-0.21	63	63
Rac1/GTP	0.004	0.11	-10000	0	-0.24	70	70
homophilic cell adhesion	0	0.003	-10000	0	-10000	0	0

×

Syndecan-2-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Syndecan-2/Fibronectin	-0.018	0.069	-9999	-0.16	81	81
EPHB2	0.02	0.02	-9999	-0.12	11	11
Syndecan-2/TACI	0.014	0.043	-9999	-0.11	47	47
LAMA1	0	0.053	-9999	-0.12	89	89
Syndecan-2/alpha2 ITGB1	-0.007	0.08	-9999	-0.15	76	76
HRAS	0.023	0.006	-9999	-0.12	1	1
Syndecan-2/CASK	-0.001	0.039	-9999	-0.11	47	47
ITGA5	0.013	0.036	-9999	-0.12	38	38
BAX	0.025	0.021	-9999	-10000	0	0
EPB41	0.02	0.019	-9999	-0.12	9	9
positive regulation of cell-cell adhesion	0.004	0.05	-9999	-0.1	84	84
LAMA3	0.006	0.043	-9999	-0.12	55	55
EZR	0	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
CAV2	0.01	0.039	-9999	-0.12	45	45
Syndecan-2/MMP2	-0.016	0.066	-9999	-0.16	68	68
RP11-540L11.1	0	0	-9999	-10000	0	0
alpha2 ITGB1	0.007	0.061	-9999	-0.15	60	60
dendrite morphogenesis	0.01	0.049	-9999	-0.12	49	49
Syndecan-2/GM-CSF	0.014	0.043	-9999	-0.11	48	48
determination of left/right symmetry	0.011	0.025	-9999	-0.067	50	50
Syndecan-2/PKC delta	0.01	0.049	-9999	-0.12	54	54
GNB2L1	0.023	0.003	-9999	-10000	0	0
MAPK3	0.014	0.039	-9999	-0.094	48	48
MAPK1	0.013	0.039	-9999	-0.096	48	48
Syndecan-2/RACK1	0.024	0.043	-9999	-0.087	54	54
NF1	0.018	0.02	-9999	-0.12	10	10
FGFR/FGF/Syndecan-2	0.011	0.025	-9999	-0.067	50	50
ITGA2	0.011	0.038	-9999	-0.12	41	41
MAPK8	0.02	0.023	-9999	-0.11	1	1
Syndecan-2/alpha2/beta1 Integrin	0.005	0.07	-9999	-0.11	121	121
Syndecan-2/Kininogen	0.014	0.043	-9999	-0.11	47	47
ITGB1	0.021	0.015	-9999	-0.12	6	6
SRC	0.017	0.036	-9999	-0.078	54	54
Syndecan-2/CASK/Protein 4.1	0.009	0.045	-9999	-0.1	61	61
extracellular matrix organization	0.01	0.049	-9999	-0.12	53	53
actin cytoskeleton reorganization	-0.018	0.069	-9999	-0.16	81	81
Syndecan-2/Caveolin-2/Ras	0.009	0.062	-9999	-0.11	95	95
Syndecan-2/Laminin alpha3	-0.001	0.06	-9999	-0.14	62	62
Syndecan-2/RasGAP	0.027	0.051	-9999	-0.082	80	80
alpha5/beta1 Integrin	0.016	0.048	-9999	-0.14	34	34
PRKCD	0.02	0.018	-9999	-0.12	8	8
Syndecan-2 dimer	0.011	0.049	-9999	-0.12	49	49
GO:0007205	0.004	0	-9999	-10000	0	0
DNA mediated transformation	0	0	-9999	-10000	0	0
Syndecan-2/RasGAP/Src	0.026	0.047	-9999	-0.14	7	7
RHOA	0.023	0.006	-9999	-0.12	1	1
SDCBP	0.021	0.01	-9999	-0.12	2	2
TNFRSF13B	0.023	0	-9999	-10000	0	0
RASA1	0.021	0.012	-9999	-0.12	3	3
alpha2/beta1 Integrin	0.007	0.061	-9999	-0.15	60	60
Syndecan-2/Synbindin	0.006	0.05	-9999	-0.12	56	56
TGFB1	0.019	0.023	-9999	-0.12	14	14
CASP3	0.01	0.043	-9999	-0.1	54	54
FN1	-0.013	0.056	-9999	-0.12	114	114
Syndecan-2/IL8	0.001	0.055	-9999	-0.13	61	61
SDC2	0.011	0.025	-9999	-0.067	50	50
KNG1	0.022	0.011	-9999	-0.12	3	3
Syndecan-2/Neurofibromin	0.007	0.051	-9999	-0.13	52	52
TRAPPC4	0.016	0.025	-9999	-0.12	16	16
CSF2	0.023	0.009	-9999	-0.12	2	2
Syndecan-2/TGFB1	0.01	0.049	-9999	-0.12	53	53
Syndecan-2/Syntenin/PI-4-5-P2	0.004	0.05	-9999	-0.1	84	84
Syndecan-2/Ezrin	0.012	0.04	-9999	-0.097	51	51
PRKACA	0.008	0.045	-9999	-0.11	53	53
angiogenesis	0.001	0.055	-9999	-0.13	61	61
MMP2	-0.015	0.059	-9999	-0.12	128	128
IL8	0.004	0.047	-9999	-0.12	69	69
calcineurin-NFAT signaling pathway	0.014	0.043	-9999	-0.11	47	47

×

BCR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
JUN	-0.024	0.11	-10000	0	-0.25	76	76
IKBKB	0.013	0.077	0.19	14	-0.23	27	41
AKT1	-0.008	0.06	0.14	12	-0.15	49	61
IKBKG	0.012	0.068	0.16	1	-0.22	26	27
CALM1	-0.008	0.1	0.16	4	-0.28	52	56
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
MAP3K1	-0.029	0.13	-10000	0	-0.33	63	63
MAP3K7	0.021	0.014	-10000	0	-0.12	5	5
mol:Ca2+	-0.012	0.11	0.16	4	-0.29	53	57
DOK1	0.021	0.016	-10000	0	-0.12	7	7
AP-1	-0.014	0.077	0.14	1	-0.18	73	74
LYN	0.02	0.013	-10000	0	-0.12	4	4
BLNK	0.014	0.033	-10000	0	-0.12	31	31
SHC1	0.023	0.001	-10000	0	-10000	0	0
BCR complex	0.028	0.026	-10000	0	-0.077	32	32
CD22	-0.04	0.1	-10000	0	-0.21	108	108
CAMK2G	-0.003	0.099	0.15	4	-0.26	50	54
CSNK2A1	0.021	0.015	-10000	0	-0.12	6	6
INPP5D	0	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1	0.001	0.052	-10000	0	-0.14	37	37
GO:0007205	-0.012	0.11	0.16	4	-0.3	53	57
SYK	0.016	0.027	-10000	0	-0.12	20	20
ELK1	-0.008	0.1	0.16	4	-0.28	51	55
NFATC1	-0.014	0.084	0.16	1	-0.22	58	59
B-cell antigen/BCR complex	0.028	0.026	-10000	0	-0.077	32	32
PAG1/CSK	0.032	0.02	-10000	0	-0.1	12	12
NFKBIB	0.008	0.045	-10000	0	-0.13	46	46
HRAS	-0.001	0.087	0.13	3	-0.25	44	47
NFKBIA	0.011	0.041	-10000	0	-0.12	36	36
NF-kappa-B/RelA/I kappa B beta	0.014	0.043	-10000	0	-0.12	41	41
RasGAP/Csk	0.023	0.067	-10000	0	-0.087	127	127
mol:GDP	-0.011	0.11	0.15	4	-0.29	52	56
PTEN	0.022	0.008	-10000	0	-0.12	1	1
CD79B	0.023	0.006	-10000	0	-0.12	1	1
NF-kappa-B/RelA/I kappa B alpha	0.014	0.04	-10000	0	-0.11	41	41
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PI3K/BCAP/CD19	-0.029	0.13	-10000	0	-0.36	60	60
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
mol:IP3	-0.012	0.11	0.16	4	-0.3	53	57
CSK	0.023	0.009	-10000	0	-0.12	2	2
FOS	-0.023	0.11	0.15	2	-0.29	56	58
CHUK	-0.004	0.096	0.16	1	-0.26	55	56
IBTK	0.02	0.016	-10000	0	-0.12	6	6
CARD11/BCL10/MALT1/TAK1	0.006	0.1	0.19	1	-0.24	54	55
PTPN6	-0.036	0.095	-10000	0	-0.2	108	108
RELA	0.023	0.009	-10000	0	-0.12	2	2
BCL2A1	0.009	0.034	-10000	0	-0.079	53	53
VAV2	-0.031	0.11	-10000	0	-0.31	56	56
ubiquitin-dependent protein catabolic process	0.012	0.045	-10000	0	-0.12	46	46
BTK	-0.05	0.25	-10000	0	-1.1	32	32
CD19	-0.032	0.095	-10000	0	-0.21	94	94
MAP4K1	0.02	0.023	-10000	0	-0.12	14	14
CD72	0.023	0.006	-10000	0	-0.12	1	1
PAG1	0.022	0.014	-10000	0	-0.12	5	5
MAPK14	-0.021	0.11	-10000	0	-0.28	63	63
SH3BP5	0.021	0.015	-10000	0	-0.12	6	6
PIK3AP1	-0.009	0.11	0.17	4	-0.33	46	50
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72	-0.012	0.13	-10000	0	-0.29	85	85
RAF1	0.002	0.083	0.13	3	-0.24	42	45
RasGAP/p62DOK/SHIP	0.015	0.062	-10000	0	-0.084	131	131
CD79A	0.016	0.032	-10000	0	-0.12	28	28
re-entry into mitotic cell cycle	-0.014	0.076	0.14	1	-0.18	73	74
RASA1	0.021	0.012	-10000	0	-0.12	3	3
MAPK3	0.009	0.074	0.13	3	-0.21	36	39
MAPK1	0.008	0.074	0.13	3	-0.22	36	39
CD72/SHP1	-0.026	0.095	-10000	0	-0.22	71	71
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
MAPK8	-0.022	0.11	-10000	0	-0.29	63	63
actin cytoskeleton organization	-0.024	0.098	-10000	0	-0.28	56	56
NF-kappa-B/RelA	0.022	0.096	-10000	0	-0.23	54	54
Calcineurin	0.014	0.098	-10000	0	-0.25	48	48
PI3K	-0.038	0.075	-10000	0	-0.22	60	60
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2	-0.012	0.11	0.17	4	-0.34	42	46
SOS1	0.017	0.027	-10000	0	-0.12	20	20
Bam32/HPK1	-0.042	0.18	-10000	0	-0.55	46	46
DAPP1	-0.057	0.19	-10000	0	-0.61	46	46
cytokine secretion	-0.012	0.08	0.16	1	-0.21	58	59
mol:DAG	-0.012	0.11	0.16	4	-0.3	53	57
PLCG2	0.02	0.02	-10000	0	-0.12	11	11
MAP2K1	0.006	0.079	0.13	3	-0.22	39	42
B-cell antigen/BCR complex/FcgammaRIIB	0.009	0.063	-10000	0	-0.11	99	99
mol:PI-3-4-5-P3	-0.034	0.057	0.095	1	-0.17	56	57
ETS1	-0.006	0.098	0.15	2	-0.27	50	52
B-cell antigen/BCR complex/LYN/SYK/BLNK	0.029	0.069	-10000	0	-0.1	96	96
B-cell antigen/BCR complex/LYN	-0.037	0.1	-10000	0	-0.22	94	94
MALT1	0.017	0.026	-10000	0	-0.12	19	19
TRAF6	0.022	0.009	-10000	0	-0.12	2	2
RAC1	-0.026	0.1	-10000	0	-0.29	56	56
B-cell antigen/BCR complex/LYN/SYK	-0.004	0.091	-10000	0	-0.22	54	54
CARD11	-0.009	0.11	0.16	4	-0.28	52	56
FCGR2B	0.004	0.044	-10000	0	-0.12	60	60
PPP3CA	0.021	0.014	-10000	0	-0.12	5	5
BCL10	0.023	0.001	-10000	0	-10000	0	0
IKK complex	0.012	0.039	0.1	16	-0.096	26	42
PTPRC	-0.004	0.051	-10000	0	-0.12	86	86
PDPK1	-0.01	0.054	0.13	13	-0.13	52	65
PPP3CB	0.023	0.003	-10000	0	-10000	0	0
PPP3CC	0.022	0.011	-10000	0	-0.12	3	3
POU2F2	0.012	0.033	-10000	0	-0.075	53	53

×

Circadian rhythm pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
chromatin modification	-0.068	0.31	-10000	0	-1	50	50
CLOCK	0.017	0.024	-10000	0	-0.056	40	40
TIMELESS/CRY2	-0.064	0.31	-10000	0	-1	50	50
DEC1/BMAL1	0.024	0.039	-10000	0	-0.13	30	30
ATR	0.02	0.015	-10000	0	-0.12	5	5
NR1D1	-0.01	0.11	-10000	0	-0.53	2	2
ARNTL	0.018	0.023	-10000	0	-0.051	37	37
TIMELESS	-0.08	0.33	-10000	0	-1.1	50	50
NPAS2	0.002	0.049	-10000	0	-0.097	94	94
CRY2	0.023	0	-10000	0	-10000	0	0
mol:CO	0.001	0.042	0.13	50	-10000	0	50
CHEK1	0.012	0.035	-10000	0	-0.12	34	34
mol:HEME	-0.001	0.042	-10000	0	-0.13	50	50
PER1	0.022	0.014	-10000	0	-0.12	5	5
BMAL/CLOCK/NPAS2	0	0.087	-10000	0	-0.12	155	155
BMAL1/CLOCK	-0.033	0.19	-10000	0	-0.56	55	55
S phase of mitotic cell cycle	-0.068	0.31	-10000	0	-1	50	50
TIMELESS/CHEK1/ATR	-0.071	0.32	-10000	0	-1.1	50	50
mol:NADPH	-0.001	0.042	-10000	0	-0.13	50	50
PER1/TIMELESS	-0.064	0.31	-10000	0	-1.1	50	50
PER1-2 / CRY1-2	0	0	-10000	0	-10000	0	0
DEC1	0.022	0.011	-10000	0	-0.12	3	3

×

Aurora A signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Aurora A/GADD45A	0.001	0.074	-10000	0	-0.18	70	70
BIRC5	0.018	0.023	-10000	0	-0.12	14	14
NFKBIA	0.013	0.039	0.11	8	-0.13	24	32
CPEB1	0.02	0.023	-10000	0	-0.12	14	14
AKT1	0.018	0.027	0.11	8	-0.1	12	20
NDEL1	0.023	0.006	-10000	0	-0.12	1	1
Aurora A/BRCA1	-0.006	0.069	-10000	0	-0.16	69	69
NDEL1/TACC3	0.006	0.075	-10000	0	-0.16	74	74
GADD45A	0.014	0.032	-10000	0	-0.12	29	29
GSK3B	0.021	0.013	0.071	9	-0.12	3	12
PAK1/Aurora A	0.003	0.071	-10000	0	-0.17	67	67
MDM2	0.02	0.02	-10000	0	-0.12	11	11
JUB	0.018	0.024	-10000	0	-0.12	15	15
TPX2	0.017	0.017	-10000	0	-0.071	16	16
TP53	-0.064	0.13	-10000	0	-0.25	179	179
DLG7	0.012	0.026	0.11	2	-0.059	40	42
AURKAIP1	0.02	0.021	-10000	0	-0.12	12	12
ARHGEF7	0.023	0.006	-10000	0	-0.12	1	1
G2 phase of mitotic cell cycle	0	0	-10000	0	-10000	0	0
Aurora A/NDEL1/TACC3	0.006	0.08	-10000	0	-0.17	74	74
G2/M transition of mitotic cell cycle	-0.006	0.069	-10000	0	-0.15	69	69
AURKA	-0.004	0.078	0.14	8	-0.2	67	75
AURKB	0.003	0.064	-10000	0	-0.27	23	23
CDC25B	0.006	0.067	-10000	0	-0.25	29	29
G2/M transition checkpoint	-0.001	0.067	-10000	0	-0.15	75	75
mRNA polyadenylation	0.006	0.061	-10000	0	-0.15	67	67
Aurora A/CPEB	0.006	0.061	-10000	0	-0.15	67	67
Aurora A/TACC1/TRAP/chTOG	0.006	0.091	-10000	0	-0.18	76	76
BRCA1	0.015	0.03	-10000	0	-0.12	24	24
centrosome duplication	0.003	0.071	-10000	0	-0.17	67	67
regulation of centrosome cycle	0.005	0.074	-10000	0	-0.16	74	74
spindle assembly	0.005	0.09	-10000	0	-0.18	76	76
TDRD7	0.014	0.031	-10000	0	-0.12	27	27
Aurora A/RasGAP/Survivin	0.005	0.082	-10000	0	-0.16	81	81
CENPA	0.012	0.044	-10000	0	-0.24	13	13
Aurora A/PP2A	0.007	0.068	-10000	0	-0.16	67	67
meiosis	0	0	-10000	0	-10000	0	0
protein catabolic process	-0.025	0.096	-10000	0	-0.25	67	67
negative regulation of DNA binding	-0.063	0.13	-10000	0	-0.25	179	179
prophase	0	0	-10000	0	-10000	0	0
GIT1/beta-PIX	0.034	0.01	-10000	0	-0.071	5	5
RASA1	0.021	0.012	-10000	0	-0.12	3	3
Ajuba/Aurora A	-0.001	0.068	-10000	0	-0.15	75	75
mitotic prometaphase	0.002	0.018	0.073	32	-10000	0	32
proteasomal ubiquitin-dependent protein catabolic process	-0.004	0.077	0.14	8	-0.2	67	75
TACC1	0.014	0.035	-10000	0	-0.12	34	34
TACC3	0.014	0.032	-10000	0	-0.12	29	29
Aurora A/Antizyme1	0.005	0.077	-10000	0	-0.16	76	76
Aurora A/RasGAP	0.005	0.073	-10000	0	-0.18	67	67
OAZ1	0.017	0.025	-10000	0	-0.12	17	17
RAN	0.023	0.002	-10000	0	-10000	0	0
mitosis	0	0	-10000	0	-10000	0	0
PRKACA	0.02	0.019	0.071	9	-0.12	8	17
GIT1	0.022	0.012	-10000	0	-0.12	4	4
GIT1/beta-PIX/PAK1	0.037	0.036	-10000	0	-0.11	21	21
Importin alpha/Importin beta/TPX2	0.017	0.017	-10000	0	-0.071	16	16
PPP2R5D	0.022	0.014	-10000	0	-0.12	5	5
Aurora A/TPX2	-0.003	0.082	-10000	0	-0.2	74	74
PAK1	0.016	0.029	-10000	0	-0.12	23	23
CKAP5	0.021	0.013	-10000	0	-0.12	4	4

×

Reelin signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDK5R1/CDK5	0.022	0.042	-9999	-0.1	52	52
VLDLR	0.01	0.038	-9999	-0.12	41	41
CRKL	0.023	0.009	-9999	-0.12	2	2
LRPAP1	0.018	0.024	-9999	-0.12	15	15
FYN	0.011	0.037	-9999	-0.12	40	40
ITGA3	0.012	0.034	-9999	-0.12	33	33
RELN/VLDLR/Fyn	-0.006	0.073	-9999	-0.13	102	102
MAPK8IP1/MKK7/MAP3K11/JNK1	0.055	0.042	-9999	-0.093	31	31
AKT1	-0.015	0.078	-9999	-0.15	112	112
MAP2K7	0.022	0.012	-9999	-0.12	4	4
RAPGEF1	0.023	0	-9999	-10000	0	0
DAB1	0.022	0.011	-9999	-0.12	3	3
RELN/LRP8/DAB1	0.025	0.042	-9999	-0.11	21	21
LRPAP1/LRP8	0.015	0.054	-9999	-0.12	72	72
RELN/LRP8/DAB1/Fyn	0.02	0.056	-9999	-0.096	63	63
DAB1/alpha3/beta1 Integrin	-0.006	0.069	-9999	-0.14	60	60
long-term memory	0.016	0.062	-9999	-0.13	20	20
DAB1/LIS1	0.016	0.067	-9999	-0.14	25	25
DAB1/CRLK/C3G	0.012	0.057	-9999	-0.13	21	21
PIK3CA	0.02	0.017	-9999	-0.12	7	7
DAB1/NCK2	0.019	0.067	-9999	-0.14	22	22
ARHGEF2	0.022	0.009	-9999	-0.12	2	2
mol:Src family inhibitors PP1 and PP2	0	0	-9999	-10000	0	0
GRIN2A	0.001	0.052	-9999	-0.12	86	86
CDK5R1	0.023	0.006	-9999	-0.12	1	1
RELN	0.001	0.053	-9999	-0.12	88	88
PIK3R1	0.015	0.031	-9999	-0.12	27	27
RELN/LRP8/Fyn	0.009	0.061	-9999	-0.12	62	62
GRIN2A/RELN/LRP8/DAB1/Fyn	0.015	0.066	-9999	-0.096	89	89
MAPK8	0.021	0.015	-9999	-0.12	6	6
RELN/VLDLR/DAB1	0.011	0.055	-9999	-0.1	69	69
ITGB1	0.021	0.015	-9999	-0.12	6	6
MAP1B	-0.006	0.056	-9999	-0.11	96	96
RELN/LRP8	0.015	0.058	-9999	-0.12	53	53
GRIN2B/RELN/LRP8/DAB1/Fyn	0.029	0.061	-9999	-0.093	65	65
PI3K	0.007	0.065	-9999	-0.13	96	96
mol:PP2	0	0	-9999	-10000	0	0
alpha3/beta1 Integrin	0.004	0.063	-9999	-0.14	72	72
RAP1A	0.005	0.05	-9999	-0.13	26	26
PAFAH1B1	0.021	0.018	-9999	-0.12	9	9
MAPK8IP1	0.017	0.029	-9999	-0.12	24	24
CRLK/C3G	0.034	0.01	-9999	-0.14	1	1
GRIN2B	0.021	0.019	-9999	-0.12	10	10
NCK2	0.023	0.006	-9999	-0.12	1	1
neuron differentiation	0.017	0.057	-9999	-0.18	23	23
neuron adhesion	-0.004	0.061	-9999	-0.13	67	67
LRP8	0.02	0.021	-9999	-0.12	12	12
GSK3B	-0.011	0.074	-9999	-0.14	113	113
RELN/VLDLR/DAB1/Fyn	0.006	0.066	-9999	-0.1	103	103
MAP3K11	0.022	0.014	-9999	-0.12	5	5
RELN/VLDLR/DAB1/P13K	-0.018	0.083	-9999	-0.16	112	112
CDK5	0.015	0.032	-9999	-0.12	28	28
MAPT	0.01	0.016	-9999	-0.094	5	5
neuron migration	-0.014	0.079	-9999	-0.19	52	52
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1	0.017	0.057	-9999	-0.18	23	23
RELN/VLDLR	0.007	0.071	-9999	-0.11	119	119

×

Paxillin-dependent events mediated by a4b1

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.023	0.009	-10000	0	-0.12	2	2
Rac1/GDP	0.021	0.007	-10000	0	-10000	0	0
DOCK1	0.019	0.02	-10000	0	-0.12	10	10
ITGA4	0.015	0.03	-10000	0	-0.12	24	24
RAC1	0.023	0.002	-10000	0	-10000	0	0
alpha4/beta7 Integrin	0.004	0.065	-10000	0	-0.13	106	106
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.021	0.016	-10000	0	-0.12	7	7
alpha4/beta1 Integrin	0.02	0.059	-10000	0	-0.12	75	75
alpha4/beta7 Integrin/Paxillin	0.021	0.055	-10000	0	-0.1	79	79
lamellipodium assembly	0.001	0.12	-10000	0	-0.3	63	63
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PI3K	0.007	0.065	-10000	0	-0.13	96	96
ARF6	0.023	0.003	-10000	0	-10000	0	0
TLN1	0.021	0.012	-10000	0	-0.12	3	3
PXN	0.021	0.014	-10000	0	-0.071	13	13
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
ARF6/GTP	0.031	0.051	-10000	0	-0.13	11	11
cell adhesion	0.026	0.062	-10000	0	-0.098	96	96
CRKL/CBL	0.033	0.013	-10000	0	-0.14	2	2
alpha4/beta1 Integrin/Paxillin	0.022	0.053	-10000	0	-0.1	76	76
ITGB1	0.021	0.015	-10000	0	-0.12	6	6
ITGB7	0.019	0.024	-10000	0	-0.12	15	15
ARF6/GDP	0.02	0.008	-10000	0	-10000	0	0
alpha4/beta1 Integrin/Paxillin/VCAM1	-0.022	0.082	-10000	0	-0.12	187	187
p130Cas/Crk/Dock1	0.035	0.04	-10000	0	-0.11	34	34
VCAM1	-0.019	0.06	-10000	0	-0.12	139	139
alpha4/beta1 Integrin/Paxillin/Talin	0.027	0.063	-10000	0	-0.098	96	96
alpha4/beta1 Integrin/Paxillin/GIT1	0.034	0.055	-10000	0	-0.09	76	76
BCAR1	0.022	0.011	-10000	0	-0.12	3	3
mol:GDP	-0.032	0.054	0.09	76	-10000	0	76
CBL	0.023	0.006	-10000	0	-0.12	1	1
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
GIT1	0.022	0.012	-10000	0	-0.12	4	4
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton	0.027	0.063	-10000	0	-0.098	96	96
Rac1/GTP	-0.001	0.13	-10000	0	-0.33	63	63

×

IL2 signaling events mediated by PI3K

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
BCL2L1	-0.02	0.16	-10000	0	-0.69	21	21
UGCG	-0.001	0.079	-10000	0	-0.73	5	5
AKT1/mTOR/p70S6K/Hsp90/TERT	-0.031	0.16	-10000	0	-0.31	104	104
mol:GTP	0	0.001	-10000	0	-10000	0	0
mol:glucosylceramide	-0.001	0.078	-10000	0	-0.71	5	5
mol:DAG	-0.043	0.2	-10000	0	-0.89	29	29
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.04	0.18	-10000	0	-0.37	104	104
FRAP1	-0.053	0.2	-10000	0	-0.42	104	104
FOXO3	-0.053	0.2	-10000	0	-0.41	108	108
AKT1	-0.058	0.21	-10000	0	-0.44	106	106
GAB2	0.007	0.041	-10000	0	-0.12	50	50
SMPD1	0.006	0.042	-10000	0	-0.52	1	1
SGMS1	-0.029	0.16	-10000	0	-0.68	29	29
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
mol:GDP	-0.005	0.05	-10000	0	-0.13	67	67
CALM1	0.022	0.014	-10000	0	-0.12	5	5
cell proliferation	-0.039	0.16	-10000	0	-0.32	96	96
EIF3A	0.022	0.004	-10000	0	-10000	0	0
PI3K	0.008	0.067	-10000	0	-0.15	67	67
RPS6KB1	-0.031	0.18	-10000	0	-0.85	22	22
mol:sphingomyelin	-0.043	0.2	-10000	0	-0.89	29	29
natural killer cell activation	-0.001	0.003	-10000	0	-0.011	30	30
JAK3	0.022	0.016	-10000	0	-0.066	13	13
PIK3R1	0.015	0.033	-10000	0	-0.12	27	27
JAK1	0.022	0.013	-10000	0	-0.05	10	10
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
MYC	-0.11	0.32	-10000	0	-0.83	84	84
MYB	-0.064	0.29	-10000	0	-1.1	42	42
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	-0.039	0.16	-10000	0	-0.32	104	104
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	-0.008	0.17	-10000	0	-0.78	22	22
mol:PI-3-4-5-P3	-0.037	0.15	-10000	0	-0.31	104	104
Rac1/GDP	0.008	0.051	-10000	0	-0.12	66	66
T cell proliferation	-0.032	0.14	-10000	0	-0.29	104	104
SHC1	0.022	0.004	-10000	0	-10000	0	0
RAC1	0.023	0.002	-10000	0	-10000	0	0
positive regulation of cyclin-dependent protein kinase activity	-0.001	0.019	-10000	0	-0.042	80	80
PRKCZ	-0.033	0.15	-10000	0	-0.3	104	104
NF kappa B1 p50/RelA	-0.035	0.19	-10000	0	-0.37	109	109
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K	-0.016	0.12	-10000	0	-0.33	50	50
HSP90AA1	0.023	0.003	-10000	0	-10000	0	0
RELA	0.023	0.009	-10000	0	-0.12	2	2
IL2RA	0.02	0.018	-10000	0	-0.12	8	8
IL2RB	0.019	0.025	-10000	0	-0.091	24	24
TERT	0.023	0	-10000	0	-10000	0	0
E2F1	-0.016	0.13	-10000	0	-0.42	44	44
SOS1	0.016	0.027	-10000	0	-0.12	20	20
RPS6	0.023	0.002	-10000	0	-10000	0	0
mol:cAMP	0	0.009	0.02	77	-10000	0	77
PTPN11	0.021	0.012	-10000	0	-0.12	3	3
IL2RG	-0.002	0.051	-10000	0	-0.12	82	82
actin cytoskeleton organization	-0.032	0.14	-10000	0	-0.29	104	104
GRB2	0.022	0.007	-10000	0	-0.12	1	1
IL2	0.023	0.014	-10000	0	-0.054	13	13
PIK3CA	0.02	0.019	-10000	0	-0.068	17	17
Rac1/GTP	0.02	0.057	-10000	0	-0.11	66	66
LCK	0.022	0.017	-10000	0	-0.091	9	9
BCL2	-0.033	0.17	-10000	0	-0.41	60	60

×

HIF-2-alpha transcription factor network

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
MMP14	-0.098	0.3	-10000	0	-0.93	63	63
oxygen homeostasis	0.001	0.01	-10000	0	-10000	0	0
TCEB2	0.023	0.006	-10000	0	-0.12	1	1
TCEB1	0.022	0.011	-10000	0	-0.12	3	3
VHL/Elongin B/Elongin C/HIF2A	0.008	0.11	-10000	0	-0.2	68	68
EPO	0.004	0.19	-10000	0	-0.37	53	53
FIH (dimer)	0.023	0.013	-10000	0	-0.12	1	1
APEX1	0.02	0.026	-10000	0	-0.12	11	11
SERPINE1	-0.015	0.19	-10000	0	-0.38	57	57
FLT1	-0.027	0.23	-10000	0	-0.76	46	46
ADORA2A	-0.01	0.17	-10000	0	-0.37	55	55
germ cell development	-0.018	0.2	-10000	0	-0.36	83	83
SLC11A2	-0.011	0.19	-10000	0	-0.38	66	66
BHLHE40	-0.013	0.18	-10000	0	-0.36	68	68
HIF1AN	0.023	0.013	-10000	0	-0.12	1	1
HIF2A/ARNT/SIRT1	0.012	0.14	-10000	0	-0.26	57	57
ETS1	0.027	0.037	-10000	0	-0.11	33	33
CITED2	0.025	0.079	-10000	0	-0.86	3	3
KDR	-0.027	0.22	-10000	0	-0.74	46	46
PGK1	-0.013	0.2	-10000	0	-0.38	77	77
SIRT1	0.023	0.003	-10000	0	-10000	0	0
response to hypoxia	0	0	-10000	0	-10000	0	0
HIF2A/ARNT	0.022	0.23	-10000	0	-0.4	66	66
EPAS1	-0.009	0.11	-10000	0	-0.21	91	91
SP1	0.016	0.034	-10000	0	-0.077	59	59
ABCG2	-0.007	0.19	-10000	0	-0.39	58	58
EFNA1	-0.019	0.2	-10000	0	-0.4	79	79
FXN	-0.011	0.17	-10000	0	-0.37	55	55
POU5F1	-0.02	0.2	-10000	0	-0.37	83	83
neuron apoptosis	-0.021	0.23	0.4	66	-10000	0	66
EP300	0.022	0.01	-10000	0	-0.12	2	2
EGLN3	-0.001	0.051	-10000	0	-0.12	84	84
EGLN2	0.023	0.014	-10000	0	-0.12	2	2
EGLN1	0.023	0.014	-10000	0	-0.12	2	2
VHL/Elongin B/Elongin C	0.041	0.029	-10000	0	-0.12	15	15
VHL	0.021	0.016	-10000	0	-0.12	7	7
ARNT	0.023	0.021	-10000	0	-0.12	4	4
SLC2A1	-0.024	0.19	-10000	0	-0.38	77	77
TWIST1	-0.011	0.17	-10000	0	-0.35	67	67
ELK1	0.028	0.019	-10000	0	-0.1	9	9
HIF2A/ARNT/Cbp/p300	0.008	0.15	-10000	0	-0.28	59	59
VEGFA	-0.013	0.2	-10000	0	-0.4	66	66
CREBBP	0.021	0.015	-10000	0	-0.12	6	6

×

Ephrin A reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAPKKK cascade	0.017	0.04	-9999	-0.089	68	68
EFNA5	0.014	0.033	-9999	-0.12	30	30
FYN	0.007	0.043	-9999	-0.12	40	40
neuron projection morphogenesis	0.017	0.04	-9999	-0.089	68	68
cell-cell signaling	0	0	-9999	-10000	0	0
Ephrin A5/EPHA5	0.017	0.041	-9999	-0.089	68	68
EPHA5	0.023	0.009	-9999	-0.12	2	2

×

FOXA2 and FOXA3 transcription factor networks

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
ACADVL	-0.056	0.28	-10000	0	-0.62	64	64
PCK1	-0.16	0.41	-10000	0	-1	85	85
HNF4A	-0.11	0.36	-10000	0	-0.73	112	112
KCNJ11	-0.012	0.27	-10000	0	-0.6	47	47
AKT1	-0.004	0.16	-10000	0	-0.31	51	51
response to starvation	-0.019	0.045	-10000	0	-0.13	69	69
DLK1	-0.028	0.28	-10000	0	-0.63	52	52
NKX2-1	-0.01	0.15	-10000	0	-0.54	1	1
ACADM	-0.069	0.3	-10000	0	-0.66	75	75
TAT	-0.025	0.2	-10000	0	-0.6	14	14
CEBPB	0.021	0.032	-10000	0	-0.12	29	29
CEBPA	0.029	0.015	-10000	0	-0.12	5	5
TTR	0.011	0.16	-10000	0	-0.83	4	4
PKLR	-0.045	0.27	-10000	0	-0.62	51	51
APOA1	-0.17	0.49	-10000	0	-1	115	115
CPT1C	-0.052	0.27	-10000	0	-0.61	58	58
ALAS1	-0.012	0.19	-10000	0	-0.62	14	14
TFRC	-0.1	0.4	-10000	0	-0.94	85	85
FOXF1	0.015	0.012	-10000	0	-0.11	5	5
NF1	0.024	0.026	-10000	0	-0.13	12	12
HNF1A (dimer)	0.042	0.019	-10000	0	-0.13	5	5
CPT1A	-0.064	0.29	-10000	0	-0.63	77	77
HMGCS1	-0.059	0.29	-10000	0	-0.64	64	64
NR3C1	0.035	0.017	-10000	0	-0.11	5	5
CPT1B	-0.047	0.27	-10000	0	-0.61	56	56
chromatin remodeling	0	0	-10000	0	-10000	0	0
SP1	0.029	0.013	-10000	0	-0.14	2	2
GCK	-0.045	0.27	-10000	0	-0.6	54	54
CREB1	-0.009	0.07	-10000	0	-0.17	76	76
IGFBP1	-0.014	0.16	-10000	0	-0.52	8	8
PDX1	0.028	0.17	-10000	0	-0.7	5	5
UCP2	-0.093	0.33	-10000	0	-0.68	95	95
ALDOB	-0.012	0.27	-10000	0	-0.61	44	44
AFP	0.017	0.051	-10000	0	-0.34	1	1
BDH1	-0.07	0.3	-10000	0	-0.64	77	77
HADH	-0.021	0.28	-10000	0	-0.63	49	49
F2	-0.066	0.34	-10000	0	-0.8	49	49
HNF1A	0.042	0.019	-10000	0	-0.13	5	5
G6PC	0.025	0.076	-10000	0	-0.42	1	1
SLC2A2	0.021	0.18	-10000	0	-0.66	2	2
INS	0.009	0.012	0.16	1	-0.14	2	3
FOXA1	0.035	0.03	-10000	0	-0.21	2	2
FOXA3	0.002	0.097	-10000	0	-0.19	76	76
FOXA2	-0.008	0.32	-10000	0	-0.67	54	54
ABCC8	-0.012	0.27	-10000	0	-0.61	44	44
ALB	0.017	0.051	-10000	0	-0.3	3	3

×

Retinoic acid receptors-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.019	0.02	-10000	0	-0.12	10	10
HDAC3	0.023	0.002	-10000	0	-10000	0	0
VDR	0.019	0.022	-10000	0	-0.12	13	13
Cbp/p300/PCAF	0.02	0.043	-10000	0	-0.13	41	41
EP300	0.022	0.01	-10000	0	-0.12	2	2
RARs/AIB1/Cbp/p300/PCAF/9cRA	-0.001	0.095	-10000	0	-0.26	48	48
KAT2B	0	0	-10000	0	-10000	0	0
MAPK14	0.023	0.007	-10000	0	-0.12	1	1
AKT1	0.019	0.089	0.17	78	-0.18	45	123
RAR alpha/9cRA/Cyclin H	-0.016	0.12	-10000	0	-0.22	106	106
mol:9cRA	0	0	-10000	0	-10000	0	0
RARs/Src-1/Cbp/p300/PCAF/9cRA	0.002	0.081	-10000	0	-0.2	55	55
CDC2	0.006	0.04	-10000	0	-0.12	46	46
response to UV	-0.001	0.008	-10000	0	-10000	0	0
RAR alpha/Jnk1	0.006	0.062	-10000	0	-0.15	52	52
NCOR2	0.019	0.023	-10000	0	-0.12	15	15
VDR/VDR/Vit D3	0.008	0.035	-10000	0	-0.12	36	36
RXRs/RARs/NRIP1/9cRA	-0.044	0.19	-10000	0	-0.48	72	72
NCOA2	0.021	0.013	-10000	0	-0.12	4	4
NCOA3	0.021	0.012	-10000	0	-0.12	3	3
NCOA1	0.022	0.009	-10000	0	-0.12	2	2
VDR/VDR/DNA	0.019	0.022	-10000	0	-0.12	13	13
RARG	0.02	0.016	-10000	0	-0.12	6	6
RAR gamma1/9cRA	0.024	0.028	-10000	0	-0.11	18	18
MAPK3	0.02	0.015	-10000	0	-0.12	5	5
MAPK1	0.021	0.016	-10000	0	-0.12	7	7
MAPK8	0.019	0.018	-10000	0	-0.12	6	6
mol:Vit D3	0	0	-10000	0	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.036	0.14	-10000	0	-0.31	96	96
RARA	0.01	0.056	-10000	0	-0.12	63	63
negative regulation of phosphoinositide 3-kinase cascade	0	0	-10000	0	-10000	0	0
RARs/TIF2/Cbp/p300/PCAF/9cRA	0	0.086	-10000	0	-0.21	56	56
PRKCA	0.008	0.043	-10000	0	-0.088	78	78
RXRs/RARs/NRIP1/9cRA/HDAC1	-0.063	0.21	-10000	0	-0.54	74	74
RXRG	-0.006	0.07	-10000	0	-0.19	56	56
RXRA	-0.034	0.11	-10000	0	-0.21	98	98
RXRB	0.003	0.064	-10000	0	-0.19	43	43
VDR/Vit D3/DNA	0.008	0.035	-10000	0	-0.12	36	36
RBP1	0.01	0.035	-10000	0	-0.12	35	35
CRBP1/9-cic-RA	-0.019	0.065	-10000	0	-0.13	138	138
RARB	0.012	0.036	-10000	0	-0.12	33	33
PRKCG	0.018	0.025	-10000	0	-0.052	52	52
MNAT1	0.023	0.007	-10000	0	-0.12	1	1
RAR alpha/RXRs	-0.021	0.16	-10000	0	-0.36	81	81
RXRs/RARs/SMRT(N-CoR2)/9cRA	-0.016	0.13	-10000	0	-0.28	79	79
proteasomal ubiquitin-dependent protein catabolic process	-0.01	0.099	-10000	0	-0.25	51	51
RXRs/RARs/NRIP1/9cRA/HDAC3	-0.06	0.21	-10000	0	-0.54	73	73
positive regulation of DNA binding	-0.02	0.11	-10000	0	-0.2	106	106
NRIP1	-0.098	0.32	-10000	0	-0.98	59	59
RXRs/RARs	-0.048	0.17	-10000	0	-0.4	93	93
RXRs/RXRs/DNA/9cRA	-0.042	0.14	-10000	0	-0.32	95	95
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
CDK7	0.018	0.023	-10000	0	-0.12	14	14
TFIIH	0.029	0.053	-10000	0	-0.13	46	46
RAR alpha/9cRA	0.023	0.071	-10000	0	-0.2	26	26
CCNH	0.02	0.022	-10000	0	-0.12	13	13
CREBBP	0.021	0.015	-10000	0	-0.12	6	6
RAR gamma2/9cRA	0.025	0.05	-10000	0	-0.18	16	16

×

ErbB2/ErbB3 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
USP8	0.012	0.012	-10000	0	-0.057	15	15
RAS family/GTP	0.004	0.084	-10000	0	-0.18	52	52
NFATC4	0.001	0.053	0.18	6	-0.12	40	46
ERBB2IP	0.021	0.019	-10000	0	-0.12	9	9
HSP90 (dimer)	0.023	0.003	-10000	0	-10000	0	0
mammary gland morphogenesis	0	0.066	0.19	7	-0.12	85	92
JUN	0.004	0.07	-10000	0	-10000	0	0
HRAS	0.023	0.006	-10000	0	-0.12	1	1
DOCK7	-0.005	0.066	0.19	6	-0.13	91	97
ErbB2/ErbB3/neuregulin 1 beta/SHC	0.017	0.061	0.21	7	-0.1	88	95
AKT1	0.01	0.012	-10000	0	-0.078	10	10
BAD	0.013	0.011	-10000	0	-0.057	13	13
MAPK10	0.002	0.045	0.14	6	-0.1	43	49
mol:GTP	-0.001	0.001	-10000	0	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta	0.001	0.071	0.2	7	-0.13	85	92
RAF1	-0.005	0.085	-10000	0	-0.18	57	57
ErbB2/ErbB3/neuregulin 2	0.004	0.054	-10000	0	-0.11	88	88
STAT3	-0.003	0.17	-10000	0	-0.93	19	19
cell migration	0.001	0.053	0.16	5	-0.12	43	48
mol:PI-3-4-5-P3	0	0.001	-10000	0	-10000	0	0
cell proliferation	-0.063	0.21	-10000	0	-0.52	66	66
FOS	-0.072	0.2	-10000	0	-0.41	127	127
NRAS	0.021	0.011	-10000	0	-0.12	3	3
mol:Ca2+	0	0.066	0.19	7	-0.12	85	92
MAPK3	-0.04	0.17	-10000	0	-0.47	47	47
MAPK1	-0.042	0.17	-10000	0	-0.47	50	50
JAK2	-0.005	0.065	0.19	6	-0.13	88	94
NF2	0.013	0.046	-10000	0	-0.73	2	2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1	0.012	0.051	0.13	8	-0.16	28	36
NRG1	0.02	0.017	-10000	0	-0.12	8	8
GRB2/SOS1	0.021	0.045	-10000	0	-0.15	29	29
MAPK8	-0.012	0.092	0.18	6	-0.19	98	104
MAPK9	0.003	0.044	0.14	5	-0.11	36	41
ERBB2	0	0.048	0.27	15	-10000	0	15
ERBB3	0.013	0.031	-10000	0	-0.12	26	26
SHC1	0.023	0.001	-10000	0	-10000	0	0
RAC1	0.023	0.002	-10000	0	-10000	0	0
apoptosis	-0.009	0.017	0.084	12	-10000	0	12
STAT3 (dimer)	-0.002	0.17	-10000	0	-0.91	19	19
RNF41	0.013	0.012	-10000	0	-0.047	17	17
FRAP1	0.013	0.011	-10000	0	-0.057	14	14
RAC1-CDC42/GTP	-0.006	0.05	-10000	0	-0.11	57	57
ErbB2/ErbB2/HSP90 (dimer)	0.012	0.028	-10000	0	-0.1	25	25
CHRNA1	-0.025	0.14	-10000	0	-0.34	50	50
myelination	0	0.053	0.18	6	-0.14	22	28
PPP3CB	-0.001	0.058	0.18	6	-0.11	86	92
KRAS	0.014	0.034	-10000	0	-0.12	33	33
RAC1-CDC42/GDP	0.017	0.074	-10000	0	-0.13	83	83
NRG2	0.023	0.006	-10000	0	-0.12	1	1
mol:GDP	0.012	0.051	0.13	8	-0.16	28	36
SOS1	0.017	0.027	-10000	0	-0.12	20	20
MAP2K2	-0.01	0.09	-10000	0	-0.18	75	75
SRC	0.023	0.009	-10000	0	-0.12	2	2
mol:cAMP	0	0.001	-10000	0	-10000	0	0
PTPN11	-0.002	0.063	0.19	5	-0.12	86	91
MAP2K1	-0.043	0.16	-10000	0	-0.39	60	60
heart morphogenesis	0	0.066	0.19	7	-0.12	85	92
RAS family/GDP	0.012	0.085	-10000	0	-0.18	48	48
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PRKACA	0.01	0.048	-10000	0	-0.77	2	2
CHRNE	0.01	0.019	-10000	0	-10000	0	0
HSP90AA1	0.023	0.003	-10000	0	-10000	0	0
activation of caspase activity	-0.01	0.012	0.078	10	-10000	0	10
nervous system development	0	0.066	0.19	7	-0.12	85	92
CDC42	0.023	0.002	-10000	0	-10000	0	0

×

Arf6 downstream pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLAUR	-0.027	0.22	-10000	0	-0.83	37	37
regulation of axonogenesis	-0.005	0.059	0.18	43	-10000	0	43
myoblast fusion	0	0.1	0.38	37	-10000	0	37
mol:GTP	0	0.065	-10000	0	-0.22	44	44
regulation of calcium-dependent cell-cell adhesion	-0.007	0.087	0.16	100	-10000	0	100
ARF1/GTP	0.013	0.055	-10000	0	-0.16	45	45
mol:GM1	-0.002	0.048	-10000	0	-0.16	44	44
mol:Choline	0.004	0.051	-10000	0	-0.15	45	45
lamellipodium assembly	-0.006	0.12	-10000	0	-0.41	44	44
MAPK3	0.005	0.085	-10000	0	-0.28	44	44
ARF6/GTP/NME1/Tiam1	0.008	0.088	-10000	0	-0.16	100	100
ARF1	0.018	0.028	-10000	0	-0.12	21	21
ARF6/GDP	0	0.1	-10000	0	-0.38	37	37
ARF1/GDP	0.005	0.1	-10000	0	-0.33	44	44
ARF6	0.016	0.035	-10000	0	-0.12	35	35
RAB11A	0.023	0.007	-10000	0	-0.12	1	1
TIAM1	0.014	0.034	-10000	0	-0.13	28	28
fibronectin binding	0	0	-10000	0	-10000	0	0
MAPK1	0.004	0.087	-10000	0	-0.28	45	45
actin filament bundle formation	-0.007	0.1	0.34	44	-10000	0	44
KALRN	0.002	0.08	-10000	0	-0.29	37	37
RAB11FIP3/RAB11A	0.031	0.023	-10000	0	-0.13	11	11
RhoA/GDP	0.007	0.1	-10000	0	-0.34	44	44
NME1	0.014	0.031	-10000	0	-0.12	24	24
Rac1/GDP	0.007	0.1	-10000	0	-0.34	44	44
substrate adhesion-dependent cell spreading	0	0.065	-10000	0	-0.22	44	44
cortical actin cytoskeleton organization	-0.007	0.12	-10000	0	-0.41	44	44
RAC1	0.023	0.002	-10000	0	-10000	0	0
liver development	0	0.065	-10000	0	-0.22	44	44
ARF6/GTP	0	0.065	-10000	0	-0.22	44	44
RhoA/GTP	0.016	0.056	-10000	0	-0.17	44	44
mol:GDP	-0.005	0.11	-10000	0	-0.36	44	44
ARF6/GTP/RAB11FIP3/RAB11A	0.029	0.052	-10000	0	-0.13	50	50
RHOA	0.023	0.006	-10000	0	-0.12	1	1
PLD1	0	0.059	-10000	0	-0.18	44	44
RAB11FIP3	0.022	0.011	-10000	0	-0.12	3	3
tube morphogenesis	-0.006	0.12	-10000	0	-0.41	44	44
ruffle organization	0.005	0.059	-10000	0	-0.18	43	43
regulation of epithelial cell migration	0	0.065	-10000	0	-0.22	44	44
PLD2	0.01	0.05	-10000	0	-0.16	45	45
PIP5K1A	0.005	0.059	-10000	0	-0.18	43	43
mol:Phosphatidic acid	0.004	0.051	-10000	0	-0.15	45	45
Rac1/GTP	-0.007	0.12	-10000	0	-0.41	44	44

×

FoxO family signaling

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
G6PC	0.023	0.06	-9999	-0.41	1	1
PLK1	-0.15	0.36	-9999	-0.85	85	85
CDKN1B	-0.05	0.19	-9999	-0.35	111	111
FOXO3	-0.13	0.32	-9999	-0.6	133	133
KAT2B	-0.011	0.027	-9999	-0.045	193	193
FOXO1/SIRT1	0.025	0.065	-9999	-0.24	15	15
CAT	-0.16	0.38	-9999	-0.92	82	82
CTNNB1	0.022	0.008	-9999	-0.12	1	1
AKT1	0.009	0.038	-9999	-0.072	39	39
FOXO1	0.016	0.066	-9999	-0.27	11	11
MAPK10	0.013	0.042	-9999	-0.1	39	39
mol:GTP	0	0.003	-9999	-10000	0	0
FOXO4	0.011	0.13	-9999	-0.34	41	41
response to oxidative stress	-0.008	0.029	-9999	-0.052	106	106
FOXO3A/SIRT1	-0.14	0.3	-9999	-0.48	202	202
XPO1	0.022	0.01	-9999	-0.12	2	2
EP300	0.024	0.01	-9999	-0.12	2	2
BCL2L11	0.005	0.086	-9999	-1.3	2	2
FOXO1/SKP2	0.022	0.069	-9999	-0.25	17	17
mol:GDP	-0.008	0.029	-9999	-0.052	106	106
RAN	0.024	0.003	-9999	-10000	0	0
GADD45A	-0.081	0.27	-9999	-0.72	61	61
YWHAQ	0.023	0.003	-9999	-10000	0	0
FOXO1/14-3-3 family	0.041	0.086	-9999	-0.27	21	21
MST1	0.007	0.034	-9999	-0.068	19	19
CSNK1D	0.023	0.001	-9999	-10000	0	0
CSNK1E	0.022	0.015	-9999	-0.12	6	6
FOXO4/14-3-3 family	0.013	0.12	-9999	-0.35	29	29
YWHAB	0.023	0.007	-9999	-0.12	1	1
MAPK8	0.016	0.042	-9999	-0.11	31	31
MAPK9	0.015	0.042	-9999	-0.12	28	28
YWHAG	0.02	0.022	-9999	-0.12	13	13
YWHAE	0.022	0.014	-9999	-0.12	5	5
YWHAZ	0.023	0.003	-9999	-10000	0	0
SIRT1	0.02	0.008	-9999	-10000	0	0
SOD2	-0.092	0.3	-9999	-0.69	84	84
RBL2	-0.083	0.27	-9999	-0.69	54	54
RAL/GDP	0.019	0.043	-9999	-0.13	26	26
CHUK	0.007	0.034	-9999	-0.056	50	50
Ran/GTP	0.017	0.014	-9999	-0.14	3	3
CSNK1G2	0.022	0.011	-9999	-0.12	3	3
RAL/GTP	0.022	0.044	-9999	-0.12	26	26
CSNK1G1	0.023	0.009	-9999	-0.12	2	2
FASLG	0.007	0.068	-9999	-1.2	1	1
SKP2	0.018	0.024	-9999	-0.12	16	16
USP7	0.02	0.02	-9999	-0.12	10	10
IKBKB	0.007	0.036	-9999	-0.06	48	48
CCNB1	-0.18	0.42	-9999	-0.98	97	97
FOXO1-3a-4/beta catenin	-0.036	0.21	-9999	-0.39	95	95
proteasomal ubiquitin-dependent protein catabolic process	0.022	0.068	-9999	-0.25	17	17
CSNK1A1	0.022	0.007	-9999	-0.12	1	1
SGK1	-0.011	0.027	-9999	-0.045	193	193
CSNK1G3	0.022	0.007	-9999	-0.12	1	1
Ran/GTP/Exportin 1	0.027	0.032	-9999	-0.12	25	25
ZFAND5	0.019	0.12	-9999	-0.54	9	9
SFN	0.014	0.032	-9999	-0.12	29	29
CDK2	0.022	0.023	-9999	-0.12	14	14
FOXO3A/14-3-3	-0.005	0.13	-9999	-0.33	47	47
CREBBP	0.025	0.016	-9999	-0.12	6	6
FBXO32	-0.27	0.5	-9999	-1.1	148	148
BCL6	-0.12	0.34	-9999	-0.96	55	55
RALB	0.023	0.008	-9999	-0.12	1	1
RALA	0.023	0.009	-9999	-0.12	2	2
YWHAH	0.021	0.014	-9999	-0.12	5	5

×

ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K4	-0.012	0.11	-10000	0	-0.21	118	118
BAG4	0.022	0.012	-10000	0	-0.12	4	4
BAD	0.007	0.036	-10000	0	-0.11	20	20
NFKBIA	0.016	0.028	-10000	0	-0.12	21	21
BIRC3	-0.005	0.053	-10000	0	-0.12	94	94
BAX	0.007	0.036	-10000	0	-0.11	19	19
EnzymeConsortium:3.1.4.12	0	0.027	-10000	0	-0.063	41	41
IKBKB	-0.009	0.11	-10000	0	-0.2	119	119
MAP2K2	0.013	0.036	-10000	0	-0.1	23	23
MAP2K1	0.015	0.033	-10000	0	-0.099	20	20
SMPD1	0.005	0.028	-10000	0	-0.094	16	16
GO:0005551	0	0	-10000	0	-10000	0	0
FADD/Caspase 8	-0.005	0.12	-10000	0	-0.2	119	119
MAP2K4	0.008	0.039	-10000	0	-0.11	30	30
protein ubiquitination	-0.012	0.11	-10000	0	-0.2	119	119
EnzymeConsortium:2.7.1.37	0.017	0.034	-10000	0	-0.11	12	12
response to UV	0	0	-10000	0	-0.001	8	8
RAF1	0.011	0.035	-10000	0	-0.11	21	21
CRADD	0.023	0.009	-10000	0	-0.12	2	2
mol:ceramide	0.003	0.038	-10000	0	-0.12	20	20
I-kappa-B-alpha/RELA/p50/ubiquitin	0.018	0.041	-10000	0	-0.097	61	61
MADD	0.023	0.006	-10000	0	-0.12	1	1
MAP3K1	0.004	0.04	-10000	0	-0.12	30	30
TRADD	0.023	0.006	-10000	0	-0.12	1	1
RELA/p50	0.023	0.009	-10000	0	-0.12	2	2
MAPK3	0.017	0.035	-10000	0	-0.12	11	11
MAPK1	0.016	0.037	-10000	0	-0.12	16	16
p50/RELA/I-kappa-B-alpha	0.018	0.049	-10000	0	-0.14	40	40
FADD	-0.01	0.11	-10000	0	-0.2	118	118
KSR1	0.008	0.036	-10000	0	-0.11	20	20
MAPK8	0.008	0.042	-10000	0	-0.11	35	35
TRAF2	0.024	0.001	-10000	0	-10000	0	0
response to radiation	0	0	-10000	0	-10000	0	0
CHUK	-0.013	0.11	-10000	0	-0.2	119	119
TNF R/SODD	0.027	0.034	-10000	0	-0.11	29	29
TNF	0.02	0.02	-10000	0	-0.12	11	11
CYCS	0.006	0.038	0.097	1	-0.11	22	23
IKBKG	-0.009	0.11	-10000	0	-0.19	119	119
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD	-0.014	0.12	-10000	0	-0.22	118	118
RELA	0.023	0.009	-10000	0	-0.12	2	2
RIPK1	0.022	0.011	-10000	0	-0.12	3	3
AIFM1	0.001	0.044	0.097	1	-0.12	36	37
TNF/TNF R/SODD	0.038	0.034	-10000	0	-0.11	20	20
TNFRSF1A	0.021	0.016	-10000	0	-0.12	7	7
response to heat	0	0	-10000	0	-10000	0	0
CASP8	0.005	0.13	-10000	0	-0.67	17	17
NSMAF	-0.011	0.11	-10000	0	-0.21	118	118
response to hydrogen peroxide	0	0	-10000	0	-0.001	8	8
BCL2	0.016	0.031	-10000	0	-0.12	27	27

×

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

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
BAG4	0.022	0.012	-9999	-0.12	4	4
Caspase 8 (4 units)	0.023	0.084	-9999	-0.25	33	33
NEF	0.005	0.007	-9999	-0.066	5	5
NFKBIA	-0.001	0.039	-9999	-0.074	88	88
BIRC3	-0.058	0.13	-9999	-0.21	206	206
CYCS	0.013	0.071	-9999	-0.23	29	29
RIPK1	0.022	0.011	-9999	-0.12	3	3
CD247	0.028	0.008	-9999	-0.11	1	1
MAP2K7	0.018	0.091	-9999	-0.36	19	19
protein ubiquitination	0.021	0.067	-9999	-0.19	28	28
CRADD	0.023	0.009	-9999	-0.12	2	2
DAXX	0.022	0.012	-9999	-0.12	4	4
FAS	0.016	0.025	-9999	-0.12	17	17
BID	0.021	0.065	-9999	-0.24	28	28
NF-kappa-B/RelA/I kappa B alpha	-0.021	0.11	-9999	-0.18	146	146
TRADD	0.023	0.006	-9999	-0.12	1	1
MAP3K5	0.018	0.025	-9999	-0.12	17	17
CFLAR	0.022	0.011	-9999	-0.12	3	3
FADD	0.023	0.009	-9999	-0.12	2	2
NF-kappa-B/RelA/I kappa B alpha/ubiquitin	-0.021	0.11	-9999	-0.18	146	146
MAPK8	0.02	0.09	-9999	-0.35	19	19
APAF1	0.021	0.014	-9999	-0.12	5	5
TRAF1	0.023	0.001	-9999	-10000	0	0
TRAF2	0.023	0	-9999	-10000	0	0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG	0.019	0.068	-9999	-0.26	27	27
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD	0.019	0.075	-9999	-0.22	29	29
CHUK	0.021	0.071	-9999	-0.2	28	28
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8	0.038	0.068	-9999	-0.18	27	27
TCRz/NEF	0.028	0.014	-9999	-0.16	2	2
TNF	0.02	0.02	-9999	-0.12	11	11
FASLG	0.029	0.021	-9999	-0.16	5	5
NFKB1	0.004	0.031	-9999	-0.055	86	86
TNFR1A/BAG4/TNF-alpha	0.038	0.034	-9999	-0.11	20	20
CASP6	-0.041	0.21	-9999	-0.53	78	78
CASP7	-0.058	0.19	-9999	-0.41	117	117
RELA	0.003	0.032	-9999	-0.05	102	102
CASP2	0.022	0.009	-9999	-0.12	2	2
CASP3	-0.06	0.2	-9999	-0.41	118	118
TNFRSF1A	0.021	0.016	-9999	-0.12	7	7
TNFR1A/BAG4	0.027	0.034	-9999	-0.11	29	29
CASP8	0.023	0.004	-9999	-10000	0	0
CASP9	0.022	0.014	-9999	-0.12	5	5
MAP3K14	0.022	0.071	-9999	-0.2	28	28
APAF-1/Caspase 9	-0.028	0.12	-9999	-0.22	123	123
BCL2	0.02	0.087	-9999	-0.31	22	22

×

E-cadherin signaling in the nascent adherens junction

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
CTTN	-0.009	0.13	-9999	-0.41	49	49
KLHL20	-0.012	0.085	-9999	-0.19	68	68
CYFIP2	0.02	0.018	-9999	-0.12	8	8
Rac1/GDP	0.012	0.091	-9999	-0.22	55	55
ENAH	-0.01	0.13	-9999	-0.4	50	50
AP1M1	0.021	0.017	-9999	-0.12	8	8
RAP1B	0.019	0.02	-9999	-0.12	10	10
RAP1A	0.021	0.012	-9999	-0.12	3	3
CTNNB1	0.022	0.008	-9999	-0.12	1	1
CDC42/GTP	0.011	0.07	-9999	-0.2	34	34
ABI1/Sra1/Nap1	-0.028	0.049	-9999	-0.14	74	74
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin	0.038	0.055	-9999	-0.1	63	63
RAPGEF1	0	0.11	-9999	-0.34	49	49
CTNND1	0.023	0.004	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.01	0.13	-9999	-0.41	49	49
CRK	-0.005	0.12	-9999	-0.37	49	49
E-cadherin/gamma catenin/alpha catenin	0.025	0.06	-9999	-0.13	61	61
alphaE/beta7 Integrin	0.026	0.035	-9999	-0.11	33	33
IQGAP1	0.02	0.017	-9999	-0.12	7	7
NCKAP1	0.023	0.004	-9999	-10000	0	0
Rap1/GTP/I-afadin	0.015	0.059	-9999	-0.11	85	85
DLG1	-0.01	0.13	-9999	-0.41	49	49
ChemicalAbstracts:7440-70-2	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.022	0.05	-9999	-0.16	53	53
MLLT4	0.014	0.032	-9999	-0.12	29	29
ARF6/GTP/NME1/Tiam1	0.018	0.056	-9999	-0.11	71	71
PI3K	-0.028	0.065	-9999	-0.2	53	53
ARF6	0.023	0.003	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
E-cadherin/gamma catenin	0.017	0.054	-9999	-0.13	61	61
TIAM1	0.015	0.032	-9999	-0.12	28	28
E-cadherin(dimer)/Ca2+	0.033	0.061	-9999	-0.12	67	67
AKT1	0.005	0.049	-9999	-0.12	50	50
PIK3R1	0.015	0.031	-9999	-0.12	27	27
CDH1	0.02	0.016	-9999	-0.12	6	6
RhoA/GDP	0.013	0.091	-9999	-0.22	55	55
actin cytoskeleton organization	-0.007	0.064	-9999	-0.14	69	69
CDC42/GDP	0.013	0.091	-9999	-0.22	54	54
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin	0.001	0.08	-9999	-0.19	66	66
ITGB7	0.019	0.024	-9999	-0.12	15	15
RAC1	0.023	0.002	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/p120 catenin	0.036	0.065	-9999	-0.13	67	67
E-cadherin/Ca2+/beta catenin/alpha catenin	0.023	0.049	-9999	-0.11	64	64
mol:GDP	0.001	0.1	-9999	-0.26	54	54
CDC42/GTP/IQGAP1	0.018	0.043	-9999	-0.11	54	54
JUP	0.019	0.021	-9999	-0.12	12	12
p120 catenin/RhoA/GDP	0.017	0.094	-9999	-0.23	53	53
RAC1/GTP/IQGAP1	0.017	0.044	-9999	-0.11	55	55
PIP5K1C/AP1M1	0.033	0.014	-9999	-0.14	1	1
RHOA	0.023	0.006	-9999	-0.12	1	1
CDC42	0.023	0.002	-9999	-10000	0	0
CTNNA1	0.022	0.01	-9999	-0.12	2	2
positive regulation of S phase of mitotic cell cycle	-0.014	0.063	-9999	-0.12	119	119
NME1	0.015	0.03	-9999	-0.12	24	24
clathrin coat assembly	0	0	-9999	-10000	0	0
TJP1	-0.011	0.14	-9999	-0.42	51	51
regulation of cell-cell adhesion	-0.018	0.05	-9999	-0.18	34	34
WASF2	-0.002	0.036	-9999	-0.073	79	79
Rap1/GTP	0.013	0.08	-9999	-0.23	33	33
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin	0.041	0.064	-9999	-0.1	76	76
CCND1	-0.018	0.076	-9999	-0.15	119	119
VAV2	-0.019	0.17	-9999	-0.46	65	65
RAP1/GDP	0.016	0.087	-9999	-0.24	36	36
adherens junction assembly	-0.01	0.13	-9999	-0.4	51	51
homophilic cell adhesion	0	0	-9999	-10000	0	0
ABI1	0.022	0.009	-9999	-0.12	2	2
PIP5K1C	0.023	0	-9999	-10000	0	0
regulation of heterotypic cell-cell adhesion	0.033	0.064	-9999	-0.17	23	23
E-cadherin/beta catenin	0.008	0.056	-9999	-0.23	28	28
mol:GTP	0	0	-9999	-10000	0	0
SRC	-0.008	0.13	-9999	-0.4	49	49
PIK3CA	0.02	0.017	-9999	-0.12	7	7
Rac1/GTP	-0.059	0.11	-9999	-0.32	66	66
E-cadherin/beta catenin/alpha catenin	0.026	0.058	-9999	-0.13	64	64
ITGAE	0.023	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.011	0.14	-9999	-0.42	49	49

×

Signaling events mediated by PRL

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
CCNE1	0.002	0.047	-10000	0	-0.12	70	70
mol:Halofuginone	0.003	0.025	-10000	0	-0.18	10	10
ITGA1	0.014	0.03	-10000	0	-0.12	24	24
CDKN1A	0.014	0.059	-10000	0	-0.29	18	18
PRL-3/alpha Tubulin	0.014	0.051	-10000	0	-0.1	83	83
mol:Ca2+	0.018	0.076	0.28	41	-0.09	9	50
AGT	0.02	0.02	-10000	0	-0.12	11	11
CCNA2	-0.001	0.094	-10000	0	-0.59	12	12
TUBA1B	0.023	0	-10000	0	-10000	0	0
EGR1	-0.002	0.06	-10000	0	-0.34	12	12
CDK2/Cyclin E1	0.006	0.074	-10000	0	-0.26	23	23
MAPK3	0.014	0.027	-10000	0	-0.072	46	46
PRL-2 /Rab GGTase beta	0.009	0.063	-10000	0	-0.13	87	87
MAPK1	0.013	0.031	-10000	0	-0.083	47	47
PTP4A1	0.001	0.092	-10000	0	-0.57	12	12
PTP4A3	0.011	0.038	-10000	0	-0.12	42	42
PTP4A2	0.022	0.009	-10000	0	-0.12	2	2
ITGB1	0.013	0.028	-10000	0	-0.074	48	48
SRC	0.023	0.009	-10000	0	-0.12	2	2
RAC1	-0.014	0.11	-10000	0	-0.34	54	54
Rab GGTase beta/Rab GGTase alpha	0.012	0.058	-10000	0	-0.13	79	79
PRL-1/ATF-5	-0.003	0.095	-10000	0	-0.54	12	12
RABGGTA	0.023	0.006	-10000	0	-0.12	1	1
BCAR1	0.02	0.076	0.28	41	-0.09	2	43
RHOC	-0.013	0.11	-10000	0	-0.35	51	51
RHOA	-0.014	0.11	-10000	0	-0.34	54	54
cell motility	-0.011	0.11	-10000	0	-0.31	60	60
PRL-1/alpha Tubulin	0	0.094	-10000	0	-0.54	12	12
PRL-3/alpha1 Integrin	-0.012	0.08	-10000	0	-0.13	161	161
ROCK1	-0.012	0.11	-10000	0	-0.31	60	60
RABGGTB	0.017	0.022	-10000	0	-0.12	12	12
CDK2	0.018	0.023	-10000	0	-0.12	14	14
mitosis	0.001	0.091	-10000	0	-0.57	12	12
ATF5	0.018	0.027	-10000	0	-0.12	20	20

×

Aurora B signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Condensin I complex	-0.05	0.17	-9999	-0.35	99	99
STMN1	0.019	0.019	-9999	-0.069	23	23
Aurora B/RasGAP/Survivin	0.018	0.072	-9999	-0.16	70	70
Chromosomal passenger complex/Cul3 protein complex	-0.001	0.087	-9999	-0.23	53	53
BIRC5	0.018	0.023	-9999	-0.12	14	14
DES	-0.029	0.23	-9999	-0.95	32	32
Aurora C/Aurora B/INCENP	0.033	0.039	-9999	-0.11	32	32
Aurora B/TACC1	0.014	0.048	-9999	-0.13	45	45
Aurora B/PP2A	0.02	0.048	-9999	-0.12	51	51
mol:GTP	0	0	-9999	-10000	0	0
CBX5	-0.005	0.061	-9999	-0.2	49	49
mitotic metaphase/anaphase transition	0.002	0.005	-9999	-10000	0	0
NDC80	0.009	0.032	-9999	-0.081	55	55
Cul3 protein complex	0.016	0.056	-9999	-0.11	58	58
KIF2C	-0.065	0.21	-9999	-0.5	87	87
PEBP1	0.022	0.008	-9999	-0.12	1	1
KIF20A	0.009	0.038	-9999	-0.12	43	43
mol:GDP	0	0	-9999	-10000	0	0
Aurora B/RasGAP	0.012	0.058	-9999	-0.14	69	69
SEPT1	0.022	0.014	-9999	-0.12	5	5
SMC2	0.015	0.03	-9999	-0.12	25	25
SMC4	0.018	0.025	-9999	-0.12	17	17
NSUN2/NPM1/Nucleolin	-0.024	0.17	-9999	-0.66	33	33
PSMA3	0.019	0.021	-9999	-0.12	11	11
G2/M transition of mitotic cell cycle	0	0.003	-9999	-10000	0	0
H3F3B	-0.001	0.065	-9999	-0.21	47	47
AURKB	0.018	0.027	-9999	-0.12	19	19
AURKC	0.023	0.006	-9999	-0.12	1	1
CDCA8	0.019	0.021	-9999	-0.11	12	12
cytokinesis	-0.04	0.2	-9999	-0.45	76	76
Aurora B/Septin1	-0.022	0.19	-9999	-0.43	73	73
AURKA	0.015	0.028	-9999	-0.12	21	21
INCENP	0.021	0.011	-9999	-0.12	2	2
KLHL13	-0.001	0.053	-9999	-0.12	89	89
BUB1	0.017	0.026	-9999	-0.12	17	17
hSgo1/Aurora B/Survivin	0.011	0.078	-9999	-0.16	77	77
EVI5	0.021	0.016	-9999	-0.12	6	6
RhoA/GTP	-0.022	0.18	-9999	-0.36	86	86
SGOL1	0.016	0.028	-9999	-0.12	22	22
CENPA	-0.036	0.17	-9999	-0.35	88	88
NCAPG	0.01	0.037	-9999	-0.12	39	39
Aurora B/HC8 Proteasome	0.009	0.063	-9999	-0.14	75	75
NCAPD2	0.015	0.03	-9999	-0.12	25	25
Aurora B/PP1-gamma	0.012	0.059	-9999	-0.15	61	61
RHOA	0.023	0.006	-9999	-0.12	1	1
NCAPH	0.019	0.02	-9999	-0.12	10	10
NPM1	-0.01	0.12	-9999	-0.41	39	39
RASA1	0.021	0.012	-9999	-0.12	3	3
KLHL9	0.023	0.007	-9999	-0.12	1	1
mitotic prometaphase	-0.001	0.004	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.008	0.063	-9999	-0.14	75	75
PPP1CC	0.022	0.005	-9999	-10000	0	0
Centraspindlin	-0.032	0.19	-9999	-0.38	90	90
RhoA/GDP	0.016	0.016	-9999	-0.14	6	6
NSUN2	-0.01	0.11	-9999	-0.39	40	40
MYLK	-0.005	0.066	-9999	-0.21	50	50
KIF23	0.013	0.034	-9999	-0.12	32	32
VIM	0.016	0.028	-9999	-0.09	28	28
RACGAP1	0.017	0.025	-9999	-0.12	16	16
mitosis	0	0	-9999	-10000	0	0
NCL	-0.02	0.12	-9999	-0.37	57	57
Chromosomal passenger complex	-0.035	0.17	-9999	-0.33	94	94
Chromosomal passenger complex/EVI5	0.032	0.084	-9999	-0.16	73	73
TACC1	0.014	0.035	-9999	-0.12	34	34
PPP2R5D	0.022	0.014	-9999	-0.12	5	5
CUL3	0.023	0.004	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0

×

FAS signaling pathway (CD95)

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
SPTAN1	0.003	0.039	0.15	3	-0.26	10	13
RFC1	0.003	0.04	0.16	4	-0.26	10	14
PRKDC	0.003	0.039	0.16	4	-0.25	10	14
RIPK1	0.022	0.011	-10000	0	-0.12	3	3
CASP7	0.002	0.091	-10000	0	-0.45	16	16
FASLG/FAS/FADD/FAF1	0.036	0.085	0.16	118	-0.17	42	160
MAP2K4	-0.001	0.11	-10000	0	-0.31	37	37
mol:ceramide	0.005	0.094	-10000	0	-0.28	33	33
GSN	0.002	0.038	0.16	1	-0.26	10	11
FASLG/FAS/FADD/FAF1/Caspase 8	0.042	0.09	0.16	111	-0.25	18	129
FAS	0.016	0.026	-10000	0	-0.12	17	17
BID	0.005	0.017	0.25	2	-10000	0	2
MAP3K1	0.001	0.093	0.17	2	-0.33	26	28
MAP3K7	0.021	0.014	-10000	0	-0.12	5	5
RB1	0.001	0.041	0.16	4	-0.25	11	15
CFLAR	0.022	0.011	-10000	0	-0.12	3	3
HGF/MET	-0.054	0.089	-10000	0	-0.14	247	247
ARHGDIB	-0.002	0.043	0.16	3	-0.28	10	13
FADD	0.022	0.01	-10000	0	-0.12	2	2
actin filament polymerization	-0.002	0.038	0.25	10	-0.16	1	11
NFKB1	-0.037	0.2	-10000	0	-0.74	38	38
MAPK8	-0.001	0.12	-10000	0	-0.36	34	34
DFFA	0.003	0.04	0.16	4	-0.25	11	15
DNA fragmentation during apoptosis	0.003	0.04	0.16	4	-0.25	11	15
FAS/FADD/MET	-0.014	0.082	-10000	0	-0.13	163	163
CFLAR/RIP1	0.03	0.027	-10000	0	-0.12	16	16
FAIM3	0.022	0.012	-10000	0	-0.12	4	4
FAF1	0.021	0.015	-10000	0	-0.12	5	5
PARP1	0.004	0.037	0.16	4	-0.24	10	14
DFFB	0.003	0.04	0.16	4	-0.25	11	15
CHUK	-0.034	0.19	-10000	0	-0.71	38	38
FASLG	0.022	0.014	-10000	0	-0.13	4	4
FAS/FADD	0.012	0.056	-10000	0	-0.13	67	67
HGF	0.02	0.023	-10000	0	-0.12	14	14
LMNA	0	0.047	0.14	4	-0.25	14	18
CASP6	-0.003	0.05	0.16	4	-0.29	12	16
CASP10	0.018	0.02	-10000	0	-0.12	10	10
CASP3	-0.002	0.046	0.18	4	-0.28	11	15
PTPN13	-0.012	0.056	-10000	0	-0.12	112	112
CASP8	-0.005	0.018	0.28	2	-10000	0	2
IL6	-0.038	0.21	-10000	0	-0.77	33	33
MET	0	0.047	-10000	0	-0.12	70	70
ICAD/CAD	0.007	0.038	0.15	2	-0.22	12	14
FASLG/FAS/FADD/FAF1/Caspase 10	0.005	0.095	-10000	0	-0.28	33	33
activation of caspase activity by cytochrome c	0.005	0.017	0.25	2	-10000	0	2
PAK2	0.003	0.04	0.16	4	-0.25	11	15
BCL2	0.016	0.031	-10000	0	-0.12	27	27

×

Plasma membrane estrogen receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	0.036	0.049	-10000	0	-0.094	62	62
ER alpha/Gai/GDP/Gbeta gamma	0.006	0.094	-10000	0	-0.26	53	53
AKT1	-0.054	0.23	-10000	0	-0.6	78	78
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
E2/ER alpha (dimer)/PELP1/Src/PI3K	-0.055	0.23	-10000	0	-0.61	78	78
mol:Ca2+	0.011	0.069	-10000	0	-0.25	30	30
IGF1R	0.013	0.032	-10000	0	-0.12	28	28
E2/ER alpha (dimer)/Striatin	0.014	0.047	-10000	0	-0.12	54	54
SHC1	0.023	0.001	-10000	0	-10000	0	0
apoptosis	0.051	0.22	0.57	78	-10000	0	78
RhoA/GTP	-0.016	0.034	-10000	0	-0.15	17	17
E2/ER alpha (dimer)/PELP1/Src/p130 Cas	0.008	0.1	-10000	0	-0.26	58	58
regulation of stress fiber formation	-0.007	0.049	0.14	38	-10000	0	38
E2/ERA-ERB (dimer)	0.018	0.041	-10000	0	-0.099	59	59
KRAS	0.014	0.034	-10000	0	-0.12	33	33
G13/GTP	0.014	0.041	-10000	0	-0.1	55	55
pseudopodium formation	0.007	0.049	-10000	0	-0.14	38	38
E2/ER alpha (dimer)/PELP1	0.018	0.041	-10000	0	-0.12	43	43
GRB2	0.023	0.006	-10000	0	-0.12	1	1
GNG2	0.02	0.018	-10000	0	-0.12	9	9
GNAO1	0.01	0.042	-10000	0	-0.12	51	51
HRAS	0.023	0.006	-10000	0	-0.12	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
mol:NO	-0.012	0.13	-10000	0	-0.33	66	66
E2/ER beta (dimer)	0.017	0.004	-10000	0	-0.077	1	1
mol:GDP	0.002	0.075	-10000	0	-0.24	44	44
mol:NADP	-0.012	0.13	-10000	0	-0.33	66	66
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
mol:IP3	0.01	0.071	-10000	0	-0.26	30	30
IGF-1R heterotetramer	0.013	0.032	-10000	0	-0.12	28	28
PLCB1	0.009	0.072	-10000	0	-0.26	30	30
PLCB2	0.016	0.069	-10000	0	-0.26	28	28
IGF1	0.007	0.045	-10000	0	-0.12	60	60
mol:L-citrulline	-0.012	0.13	-10000	0	-0.33	66	66
RHOA	0.023	0.006	-10000	0	-0.12	1	1
Gai/GDP	0.023	0.057	-10000	0	-0.53	2	2
JNK cascade	0.017	0.004	-10000	0	-0.077	1	1
BCAR1	0.022	0.011	-10000	0	-0.12	3	3
ESR2	0.023	0.006	-10000	0	-0.12	1	1
GNAQ	0.021	0.016	-10000	0	-0.12	6	6
ESR1	0.018	0.024	-10000	0	-0.12	15	15
Gq family/GDP/Gbeta gamma	0.031	0.062	-10000	0	-0.3	16	16
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1	0.017	0.086	-10000	0	-0.51	8	8
E2/ER alpha (dimer)/PELP1/Src/p52 SHC	0.008	0.1	-10000	0	-0.25	58	58
GNAZ	0.022	0.011	-10000	0	-0.12	3	3
E2/ER alpha (dimer)	0.002	0.045	-10000	0	-0.13	58	58
STRN	0.022	0.013	-10000	0	-0.12	4	4
GNAL	0.021	0.018	-10000	0	-0.12	9	9
PELP1	0.023	0.009	-10000	0	-0.12	2	2
MAPK11	0.021	0.003	-10000	0	-0.057	1	1
GNAI2	0.022	0.011	-10000	0	-0.12	3	3
GNAI3	0.021	0.008	-10000	0	-0.12	1	1
GNAI1	0.012	0.035	-10000	0	-0.12	35	35
HBEGF	-0.025	0.1	-10000	0	-0.25	65	65
cAMP biosynthetic process	0.016	0.032	-10000	0	-0.086	44	44
SRC	0.004	0.096	-10000	0	-0.25	62	62
PI3K	0.007	0.065	-10000	0	-0.13	96	96
GNB1	0.023	0.007	-10000	0	-0.12	1	1
G13/GDP/Gbeta gamma	0.023	0.076	-10000	0	-0.2	46	46
SOS1	0.017	0.027	-10000	0	-0.12	20	20
IGF-1R heterotetramer/IGF1	-0.038	0.072	-10000	0	-0.22	62	62
Gs family/GTP	0.022	0.035	-10000	0	-0.087	44	44
EntrezGene:2778	0	0	-10000	0	-10000	0	0
RAS family/GTP	0.03	0.043	-10000	0	-0.11	38	38
vasodilation	-0.011	0.12	-10000	0	-0.31	68	68
mol:DAG	0.01	0.071	-10000	0	-0.26	30	30
Gs family/GDP/Gbeta gamma	0.005	0.068	-10000	0	-0.2	45	45
MSN	0.007	0.051	-10000	0	-0.15	38	38
Gq family/GTP	0.015	0.073	-10000	0	-0.27	28	28
mol:PI-3-4-5-P3	-0.053	0.22	-10000	0	-0.59	78	78
NRAS	0.022	0.011	-10000	0	-0.12	3	3
mol:E2	0	0	-10000	0	-10000	0	0
cell adhesion	0.011	0.12	0.31	68	-10000	0	68
GRB2/SOS1	0.021	0.045	-10000	0	-0.15	29	29
RhoA/GDP	0.014	0.076	-10000	0	-0.22	46	46
NOS3	-0.013	0.13	-10000	0	-0.34	66	66
GNA11	0.022	0.014	-10000	0	-0.12	5	5
MAPKKK cascade	-0.005	0.15	-10000	0	-0.44	53	53
E2/ER alpha (dimer)/PELP1/Src	0.003	0.1	-10000	0	-0.26	59	59
ruffle organization	0.007	0.049	-10000	0	-0.14	38	38
ROCK2	0.01	0.049	-10000	0	-0.15	23	23
GNA14	0.02	0.02	-10000	0	-0.12	11	11
GNA15	0.021	0.017	-10000	0	-0.12	8	8
GNA13	0.022	0.009	-10000	0	-0.12	2	2
MMP9	-0.012	0.099	-10000	0	-0.26	60	60
MMP2	-0.018	0.1	-10000	0	-0.26	65	65

×

p75(NTR)-mediated 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
Sortilin/TRAF6	0.02	0.048	-10000	0	-0.13	49	49
Necdin/E2F1	0.016	0.046	-10000	0	-0.15	20	20
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E	0.039	0.048	-10000	0	-0.098	51	51
NGF (dimer)/p75(NTR)/BEX1	-0.008	0.054	-10000	0	-0.075	210	210
NT-4/5 (dimer)/p75(NTR)	0.016	0.013	-10000	0	-0.085	9	9
IKBKB	0.022	0.015	-10000	0	-0.12	6	6
AKT1	0.009	0.045	-10000	0	-0.1	63	63
IKBKG	0.023	0.009	-10000	0	-0.12	2	2
BDNF	0.022	0.011	-10000	0	-0.12	3	3
MGDIs/NGR/p75(NTR)/LINGO1	0.04	0.031	-10000	0	-0.12	13	13
FURIN	0.02	0.02	-10000	0	-0.12	11	11
proBDNF (dimer)/p75(NTR)/Sortilin	0.035	0.042	-10000	0	-0.12	33	33
LINGO1	0.018	0.026	-10000	0	-0.12	19	19
Sortilin/TRAF6/NRIF	0.003	0.054	-10000	0	-0.17	24	24
proBDNF (dimer)	0.022	0.011	-10000	0	-0.12	3	3
NTRK1	0.023	0.006	-10000	0	-0.12	1	1
RTN4R	0.021	0.018	-10000	0	-0.12	9	9
neuron apoptosis	-0.039	0.12	-10000	0	-0.36	34	34
IRAK1	0.019	0.023	-10000	0	-0.12	14	14
SHC1	0.019	0.011	-10000	0	-0.063	9	9
ARHGDIA	0.016	0.032	-10000	0	-0.12	29	29
RhoA/GTP	0.016	0.016	-10000	0	-0.14	6	6
Gamma Secretase	0.034	0.067	-10000	0	-0.097	89	89
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1	0.025	0.05	-10000	0	-0.11	59	59
MAGEH1	0.018	0.024	-10000	0	-0.12	16	16
proNGF (dimer)/p75(NTR)/Sortilin/Necdin	0.021	0.051	-10000	0	-0.11	53	53
Mammalian IAPs/DIABLO	-0.019	0.083	-10000	0	-0.13	157	157
proNGF (dimer)	0	0	-10000	0	-10000	0	0
MAGED1	0.02	0.019	-10000	0	-0.12	10	10
APP	0.022	0.008	-10000	0	-0.12	1	1
NT-4/5 (dimer)	0	0	-10000	0	-10000	0	0
ZNF274	0.023	0	-10000	0	-10000	0	0
RhoA/GDP/RHOGDI	0.029	0.028	-10000	0	-0.1	12	12
NGF	0	0	-10000	0	-10000	0	0
cell cycle arrest	0.023	0.042	0.098	60	-0.091	39	99
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK	0.01	0.063	-10000	0	-0.16	60	60
NT-4/5 (dimer)/p75(NTR)/TRAF6	0.027	0.023	-10000	0	-0.091	19	19
NCSTN	0.022	0.012	-10000	0	-0.12	4	4
mol:GTP	0.022	0.034	-10000	0	-0.094	42	42
PSENEN	0.016	0.03	-10000	0	-0.12	24	24
mol:ceramide	0.016	0.034	-10000	0	-0.11	33	33
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs	-0.004	0.091	-10000	0	-0.3	31	31
p75(NTR)/beta APP	0.023	0.043	-10000	0	-0.13	41	41
BEX1	-0.017	0.062	-10000	0	-0.12	145	145
mol:GDP	0.006	0.01	-10000	0	-0.068	9	9
NGF (dimer)	-0.028	0.064	-10000	0	-0.1	197	197
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI	0.046	0.041	-10000	0	-0.11	21	21
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
RAC1/GTP	0.025	0.016	-10000	0	-0.073	13	13
MYD88	0.023	0.006	-10000	0	-0.12	1	1
CHUK	0.021	0.013	-10000	0	-0.12	4	4
NGF (dimer)/p75(NTR)/PKA	0.022	0.034	-10000	0	-0.094	42	42
RHOB	0.022	0.014	-10000	0	-0.12	5	5
RHOA	0.023	0.006	-10000	0	-0.12	1	1
MAGE-G1/E2F1	0.032	0.018	-10000	0	-0.088	12	12
NT3 (dimer)	-0.003	0.056	-10000	0	-0.12	101	101
TP53	0.011	0.047	-10000	0	-0.18	23	23
PRDM4	0.017	0.032	-10000	0	-0.1	33	33
BDNF (dimer)	-0.021	0.069	-10000	0	-0.096	203	203
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
SORT1	0.02	0.018	-10000	0	-0.12	8	8
activation of caspase activity	0.034	0.046	-10000	0	-0.098	51	51
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6	0.032	0.042	-10000	0	-0.11	40	40
RHOC	0.023	0.002	-10000	0	-10000	0	0
XIAP	0	0	-10000	0	-10000	0	0
MAPK10	0.022	0.054	-10000	0	-0.18	20	20
DIABLO	0.02	0.016	-10000	0	-0.12	6	6
SMPD2	0.016	0.034	-10000	0	-0.11	33	33
APH1B	0.014	0.032	-10000	0	-0.12	29	29
APH1A	0.023	0.009	-10000	0	-0.12	2	2
proNGF (dimer)/p75(NTR)/Sortilin	0.021	0.038	-10000	0	-0.1	45	45
PSEN1	0.022	0.008	-10000	0	-0.12	1	1
APAF-1/Pro-Caspase 9	0.025	0.041	-10000	0	-0.13	33	33
NT3 (dimer)/p75(NTR)	0.011	0.048	-10000	0	-0.078	118	118
MAPK8	0.022	0.058	-10000	0	-0.2	21	21
MAPK9	0.022	0.054	-10000	0	-0.18	20	20
APAF1	0.021	0.014	-10000	0	-0.12	5	5
NTF3	-0.003	0.056	-10000	0	-0.12	101	101
NTF4	0	0	-10000	0	-10000	0	0
NDN	0.007	0.044	-10000	0	-0.12	59	59
RAC1/GDP	0.016	0.015	-10000	0	-0.15	5	5
RhoA-B-C/GDP	0.04	0.035	-10000	0	-0.084	34	34
p75 CTF/Sortilin/TRAF6/NRIF	0.037	0.059	-10000	0	-0.12	62	62
RhoA-B-C/GTP	0.022	0.034	-10000	0	-0.094	42	42
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	0.055	0.045	-10000	0	-0.18	5	5
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6	0.045	0.046	-10000	0	-0.1	40	40
PRKACB	0.019	0.02	-10000	0	-0.12	11	11
proBDNF (dimer)/p75 ECD	0.022	0.045	-10000	0	-0.15	33	33
ChemicalAbstracts:86-01-1	0	0	-10000	0	-10000	0	0
BIRC3	-0.005	0.053	-10000	0	-0.12	94	94
BIRC2	0.021	0.013	-10000	0	-0.12	4	4
neuron projection morphogenesis	0.003	0.055	0.099	47	-0.13	45	92
BAD	0.021	0.06	-10000	0	-0.2	20	20
RIPK2	0.013	0.034	-10000	0	-0.12	32	32
NGFR	0.021	0.017	-10000	0	-0.12	8	8
CYCS	0.015	0.042	-10000	0	-0.11	47	47
ADAM17	0.019	0.021	-10000	0	-0.12	11	11
NGF (dimer)/p75(NTR)/TRAF6/RIP2	0.024	0.05	-10000	0	-0.11	54	54
BCL2L11	0.021	0.06	-10000	0	-0.19	21	21
BDNF (dimer)/p75(NTR)	0.032	0.017	-10000	0	-0.14	2	2
PI3K	0.021	0.054	-10000	0	-0.11	63	63
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1	0.033	0.038	-10000	0	-0.1	35	35
NDNL2	0.023	0.009	-10000	0	-0.12	2	2
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
PRKCI	0.016	0.028	-10000	0	-0.12	22	22
NGF (dimer)/p75(NTR)	0.016	0.013	-10000	0	-0.085	9	9
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE	0.029	0.046	-10000	0	-0.11	47	47
TRAF6	0.022	0.009	-10000	0	-0.12	2	2
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCZ	0.023	0	-10000	0	-10000	0	0
PLG	0.023	0.009	-10000	0	-0.12	2	2
oligodendrocyte cell fate commitment	0	0	-10000	0	-10000	0	0
CASP6	0.013	0.05	-10000	0	-0.16	33	33
SQSTM1	0.021	0.014	-10000	0	-0.12	5	5
NGFRAP1	0.022	0.009	-10000	0	-0.12	2	2
CASP3	0.021	0.059	-10000	0	-0.19	20	20
E2F1	0.021	0.016	-10000	0	-0.12	7	7
CASP9	0.022	0.014	-10000	0	-0.12	5	5
IKK complex	0.021	0.08	-10000	0	-0.22	34	34
NGF (dimer)/TRKA	0.017	0.004	-10000	0	-0.077	1	1
MMP7	-0.022	0.06	-10000	0	-0.12	144	144
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	0.042	0.042	-10000	0	-0.097	40	40
MMP3	0.017	0.029	-10000	0	-0.12	23	23
APAF-1/Caspase 9	-0.037	0.061	-10000	0	-0.16	86	86

×

TCGA08_rtk_signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	0.004	0.044	-10000	0	-0.12	59	59
HRAS	0.023	0.006	-10000	0	-0.12	1	1
EGFR	0.015	0.03	-10000	0	-0.12	25	25
AKT	0	0.065	0.14	5	-0.12	83	88
FOXO3	0.021	0.017	-10000	0	-0.12	8	8
AKT1	0.021	0.019	-10000	0	-0.12	10	10
FOXO1	0.023	0.009	-10000	0	-0.12	2	2
AKT3	-0.004	0.056	-10000	0	-0.12	102	102
FOXO4	0.023	0	-10000	0	-10000	0	0
MET	0	0.047	-10000	0	-0.12	70	70
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PIK3CB	0.015	0.03	-10000	0	-0.12	24	24
NRAS	0.022	0.011	-10000	0	-0.12	3	3
PIK3CG	0.011	0.037	-10000	0	-0.12	39	39
PIK3R3	0.012	0.036	-10000	0	-0.12	37	37
PIK3R2	0.017	0.03	-10000	0	-0.12	25	25
NF1	0.018	0.02	-10000	0	-0.12	10	10
RAS	0.005	0.061	0.15	33	-0.15	43	76
ERBB2	0.02	0.021	-10000	0	-0.12	12	12
proliferation/survival/translation	0.002	0.074	0.23	36	-10000	0	36
PI3K	-0.014	0.075	0.13	9	-0.14	105	114
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
KRAS	0.014	0.034	-10000	0	-0.12	33	33
FOXO	0.028	0.037	0.14	9	-0.033	13	22
AKT2	0.019	0.025	-10000	0	-0.12	17	17
PTEN	0.022	0.008	-10000	0	-0.12	1	1

×

ErbB4 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF	-0.046	0.2	-10000	0	-0.79	33	33
epithelial cell differentiation	-0.037	0.19	-10000	0	-0.65	40	40
ITCH	0.027	0.027	0.085	4	-0.072	28	32
WWP1	-0.051	0.28	-10000	0	-1.2	33	33
FYN	0.011	0.037	-10000	0	-0.12	40	40
EGFR	0.015	0.03	-10000	0	-0.12	25	25
PRL	0.022	0.011	-10000	0	-0.12	3	3
neuron projection morphogenesis	-0.015	0.16	-10000	0	-0.57	35	35
PTPRZ1	0.021	0.018	-10000	0	-0.12	9	9
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC	-0.007	0.18	-10000	0	-0.59	39	39
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta	-0.035	0.18	-10000	0	-0.66	39	39
ADAM17	0.023	0.031	0.085	1	-0.087	33	34
ErbB4/ErbB4	-0.035	0.21	-10000	0	-0.8	37	37
ErbB4/ErbB4/neuregulin 3/neuregulin 3	-0.053	0.2	-10000	0	-0.8	33	33
NCOR1	0.022	0.009	-10000	0	-0.12	2	2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn	-0.037	0.18	-10000	0	-0.62	42	42
GRIN2B	-0.035	0.17	-10000	0	-0.59	42	42
ErbB4/ErbB2/betacellulin	-0.04	0.18	-10000	0	-0.64	40	40
STAT1	0.014	0.031	-10000	0	-0.12	26	26
HBEGF	0.018	0.026	-10000	0	-0.12	19	19
PRLR	0.01	0.042	-10000	0	-0.12	53	53
E4ICDs/ETO2	-0.044	0.2	-10000	0	-0.79	33	33
axon guidance	-0.06	0.23	-10000	0	-0.81	40	40
NEDD4	0.024	0.034	0.085	6	-0.082	41	47
Prolactin receptor/Prolactin receptor/Prolactin	0.024	0.032	-10000	0	-0.074	54	54
CBFA2T3	0.023	0.006	-10000	0	-0.12	1	1
ErbB4/ErbB2/HBEGF	-0.031	0.18	-10000	0	-0.64	38	38
MAPK3	-0.016	0.16	-10000	0	-0.55	39	39
STAT1 (dimer)	-0.056	0.21	-10000	0	-0.75	38	38
MAPK1	-0.016	0.16	-10000	0	-0.55	39	39
JAK2	0.017	0.025	-10000	0	-0.12	16	16
ErbB4/ErbB2/neuregulin 1 beta	-0.03	0.18	-10000	0	-0.64	39	39
NRG1	0.021	0.027	-10000	0	-0.07	30	30
NRG3	0.005	0.048	-10000	0	-0.12	72	72
NRG2	0.023	0.006	-10000	0	-0.12	1	1
NRG4	0.001	0.047	-10000	0	-0.12	70	70
heart development	-0.06	0.23	-10000	0	-0.81	40	40
neural crest cell migration	-0.03	0.18	-10000	0	-0.62	39	39
ERBB2	0.021	0.027	-10000	0	-0.059	41	41
WWOX/E4ICDs	-0.044	0.2	-10000	0	-0.79	33	33
SHC1	0.023	0.001	-10000	0	-10000	0	0
ErbB4/EGFR/neuregulin 4	-0.068	0.2	-10000	0	-0.63	46	46
apoptosis	0.046	0.19	0.7	38	-10000	0	38
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta	-0.044	0.2	-10000	0	-0.79	33	33
ErbB4/ErbB2/epiregulin	-0.03	0.18	-10000	0	-0.64	39	39
ErbB4/ErbB4/betacellulin/betacellulin	-0.054	0.2	-10000	0	-0.79	34	34
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2	-0.027	0.19	-10000	0	-0.64	39	39
MDM2	-0.032	0.2	-10000	0	-0.8	33	33
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta	-0.024	0.17	-10000	0	-0.59	39	39
STAT5A	-0.055	0.22	-10000	0	-0.78	40	40
ErbB4/EGFR/neuregulin 1 beta	-0.035	0.18	-10000	0	-0.65	38	38
DLG4	0.023	0.009	-10000	0	-0.12	2	2
GRB2/SHC	0.033	0.019	-10000	0	-0.14	6	6
E4ICDs/TAB2/NCoR1	-0.04	0.2	-10000	0	-0.72	37	37
STAT5A (dimer)	-0.037	0.21	-10000	0	-0.73	40	40
MAP3K7IP2	0.02	0.016	-10000	0	-0.12	6	6
STAT5B (dimer)	-0.05	0.22	-10000	0	-0.78	40	40
LRIG1	0.01	0.037	-10000	0	-0.12	40	40
EREG	0.021	0.017	-10000	0	-0.12	8	8
BTC	0.01	0.039	-10000	0	-0.12	43	43
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta	-0.06	0.23	-10000	0	-0.82	40	40
ERBB4	-0.033	0.21	-10000	0	-0.8	37	37
STAT5B	0.023	0.006	-10000	0	-0.12	1	1
YAP1	0.002	0.077	-10000	0	-0.5	11	11
GRB2	0.023	0.006	-10000	0	-0.12	1	1
ErbB4/ErbB2/neuregulin 4	-0.049	0.18	-10000	0	-0.55	51	51
glial cell differentiation	0.039	0.2	0.71	37	-10000	0	37
WWOX	0.023	0.006	-10000	0	-0.12	1	1
cell proliferation	-0.068	0.21	-10000	0	-0.58	61	61

×

Class I PI3K signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ARF5/GTP	0.005	0.042	-10000	0	-0.11	49	49
DAPP1	0.005	0.08	-10000	0	-0.25	27	27
Src family/SYK family/BLNK-LAT/BTK-ITK	0	0.12	-10000	0	-0.3	53	53
mol:DAG	0.015	0.066	0.16	14	-0.14	44	58
HRAS	0.023	0.008	-10000	0	-0.13	1	1
RAP1A	0.022	0.012	-10000	0	-0.12	3	3
ARF5/GDP	0.003	0.086	-10000	0	-0.2	62	62
PLCG2	0.02	0.02	-10000	0	-0.12	11	11
PLCG1	0.019	0.024	-10000	0	-0.12	16	16
ARF5	0.02	0.018	-10000	0	-0.12	9	9
mol:GTP	-0.006	0.038	-10000	0	-0.11	54	54
ARF1/GTP	0.003	0.05	0.16	21	-0.12	41	62
RHOA	0.023	0.006	-10000	0	-0.12	1	1
YES1	0.02	0.018	-10000	0	-0.12	8	8
RAP1A/GTP	0.012	0.05	0.17	22	-0.12	38	60
ADAP1	-0.005	0.036	-10000	0	-0.1	54	54
ARAP3	-0.006	0.038	-10000	0	-0.11	54	54
INPPL1	0.021	0.017	-10000	0	-0.12	8	8
PREX1	0.021	0.017	-10000	0	-0.12	8	8
ARHGEF6	0.014	0.032	-10000	0	-0.12	28	28
ARHGEF7	0.023	0.006	-10000	0	-0.12	1	1
ARF1	0.018	0.028	-10000	0	-0.12	21	21
NRAS	0.022	0.012	-10000	0	-0.12	3	3
FYN	0.011	0.037	-10000	0	-0.12	40	40
ARF6	0.023	0.003	-10000	0	-10000	0	0
FGR	0.023	0.006	-10000	0	-0.12	1	1
mol:Ca2+	0.012	0.038	0.092	14	-0.077	38	52
mol:IP4	0	0	-10000	0	-10000	0	0
TIAM1	0.015	0.032	-10000	0	-0.12	28	28
ZAP70	0.023	0.006	-10000	0	-0.12	1	1
mol:IP3	0.013	0.05	0.11	14	-0.1	42	56
LYN	0.021	0.013	-10000	0	-0.12	4	4
ARF1/GDP	0.002	0.088	-10000	0	-0.21	59	59
RhoA/GDP	0.014	0.067	0.17	19	-0.15	46	65
PDK1/Src/Hsp90	0.041	0.032	-10000	0	-0.12	19	19
BLNK	0.014	0.033	-10000	0	-0.12	31	31
actin cytoskeleton reorganization	0.005	0.087	0.19	17	-0.22	45	62
SRC	0.023	0.009	-10000	0	-0.12	2	2
PLEKHA2	0.013	0.011	-10000	0	-0.057	12	12
RAC1	0.023	0.002	-10000	0	-10000	0	0
PTEN	0.022	0.009	-10000	0	-0.12	1	1
HSP90AA1	0.023	0.003	-10000	0	-10000	0	0
ARF6/GTP	0.006	0.042	-10000	0	-0.11	47	47
RhoA/GTP	0.013	0.052	0.17	22	-0.11	41	63
Src family/SYK family/BLNK-LAT	0.006	0.097	-10000	0	-0.27	37	37
BLK	0.022	0.015	-10000	0	-0.12	6	6
PDPK1	0.023	0.007	-10000	0	-0.12	1	1
CYTH1	-0.005	0.036	-10000	0	-0.1	54	54
HCK	0.019	0.024	-10000	0	-0.12	15	15
CYTH3	-0.005	0.036	-10000	0	-0.1	54	54
CYTH2	-0.005	0.036	-10000	0	-0.1	54	54
KRAS	0.014	0.035	-10000	0	-0.12	33	33
GO:0030676	0	0	-10000	0	-10000	0	0
FOXO3	0.015	0.054	0.13	22	-0.21	20	42
SGK1	0.008	0.05	-10000	0	-0.22	19	19
INPP5D	0	0	-10000	0	-10000	0	0
mol:GDP	-0.008	0.086	-10000	0	-0.22	58	58
SOS1	0.017	0.027	-10000	0	-0.12	20	20
SYK	0.016	0.027	-10000	0	-0.12	20	20
ARF6/GDP	0.008	0.064	0.17	19	-0.15	47	66
mol:PI-3-4-5-P3	-0.004	0.039	0.085	1	-0.11	54	55
ARAP3/RAP1A/GTP	0.012	0.05	0.17	22	-0.12	38	60
VAV1	0.02	0.02	-10000	0	-0.12	10	10
mol:PI-3-4-P2	0.01	0.011	-10000	0	-0.077	8	8
RAS family/GTP/PI3K Class I	0.026	0.058	0.19	22	-0.11	54	76
PLEKHA1	0.013	0.012	-10000	0	-0.057	15	15
Rac1/GDP	0.004	0.087	-10000	0	-0.2	60	60
LAT	0.022	0.011	-10000	0	-0.12	3	3
Rac1/GTP	-0.001	0.1	-10000	0	-0.25	67	67
ITK	-0.002	0.04	-10000	0	-0.1	58	58
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma	0.014	0.083	0.19	14	-0.19	44	58
LCK	0.022	0.015	-10000	0	-0.12	6	6
BTK	-0.003	0.043	-10000	0	-0.11	56	56

×

Signaling mediated by p38-gamma and p38-delta

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
EEF2K	0.019	0.016	-9999	-0.058	18	18
SNTA1	0.023	0.009	-9999	-0.12	2	2
response to hypoxia	0	0	-9999	-10000	0	0
STMN1	0.017	0.021	-9999	-0.074	21	21
MAPK12	0.01	0.027	-9999	-0.059	36	36
CCND1	-0.05	0.14	-9999	-0.36	89	89
p38 gamma/SNTA1	0.005	0.057	-9999	-0.16	40	40
MAP2K3	0.023	0.006	-9999	-0.12	1	1
PKN1	0.016	0.031	-9999	-0.12	26	26
G2/M transition checkpoint	0.003	0.044	-9999	-0.15	36	36
MAP2K6	0.008	0.028	-9999	-0.05	79	79
MAPT	0.007	0.039	-9999	-0.13	28	28
MAPK13	0.019	0.019	-9999	-0.079	17	17
hyperosmotic response	0	0	-9999	-10000	0	0
ZAK	-0.001	0.058	-9999	-0.21	37	37

×

Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
DYNC1H1	0.021	0.014	-10000	0	-0.12	5	5
VLDLR	0.01	0.038	-10000	0	-0.12	41	41
LRPAP1	0.018	0.024	-10000	0	-0.12	15	15
NUDC	0.022	0.011	-10000	0	-0.12	3	3
RELN/LRP8	0.015	0.058	-10000	0	-0.12	53	53
CaM/Ca2+	0.014	0.02	-10000	0	-0.12	12	12
KATNA1	0.02	0.02	-10000	0	-0.12	10	10
GO:0030286	0	0	-10000	0	-10000	0	0
ABL1	0.006	0.047	-10000	0	-0.11	53	53
IQGAP1/CaM	0.016	0.054	-10000	0	-0.13	63	63
DAB1	0.022	0.011	-10000	0	-0.12	3	3
IQGAP1	0.02	0.017	-10000	0	-0.12	7	7
PLA2G7	0.004	0.045	-10000	0	-0.12	61	61
CALM1	0.022	0.014	-10000	0	-0.12	5	5
DYNLT1	0.018	0.023	-10000	0	-0.12	14	14
mol:Ca2+	0	0	-10000	0	-10000	0	0
LRPAP1/LRP8	0.015	0.054	-10000	0	-0.12	72	72
UniProt:Q4QZ09	0	0	-10000	0	-10000	0	0
CLIP1	0.023	0.009	-10000	0	-0.12	2	2
CDK5R1	0.023	0.006	-10000	0	-0.12	1	1
LIS1/Poliovirus Protein 3A	0.012	0.023	-10000	0	-0.086	26	26
CDK5R2	0.022	0.011	-10000	0	-0.12	3	3
mol:PP1	0	0	-10000	0	-10000	0	0
RELN/VLDLR/DAB1	0.01	0.06	-10000	0	-0.12	69	69
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
NDEL1/14-3-3 E	0.023	0.055	-10000	0	-0.15	24	24
MAP1B	-0.015	0.059	0.2	3	-0.19	47	50
RAC1	0.014	0.048	-10000	0	-0.36	7	7
p35/CDK5	0.008	0.054	-10000	0	-0.12	33	33
RELN	0.001	0.053	-10000	0	-0.12	88	88
PAFAH/LIS1	0.015	0.038	-10000	0	-0.13	14	14
LIS1/CLIP170	0.029	0.028	-10000	0	-0.13	11	11
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain	0.016	0.063	-10000	0	-0.15	39	39
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3	-0.014	0.098	-10000	0	-0.21	93	93
GO:0005869	0	0	-10000	0	-10000	0	0
NDEL1	0.011	0.052	-10000	0	-0.15	22	22
LIS1/IQGAP1	0.025	0.034	-10000	0	-0.16	13	13
RHOA	0.014	0.048	-10000	0	-0.3	9	9
PAFAH1B1	0.02	0.015	-10000	0	-0.071	15	15
PAFAH1B3	0.014	0.032	-10000	0	-0.12	29	29
PAFAH1B2	0.022	0.013	-10000	0	-0.12	4	4
MAP1B/LIS1/Dynein heavy chain	0.009	0.054	0.13	3	-0.13	53	56
NDEL1/Katanin 60/Dynein heavy chain	0.025	0.065	-10000	0	-0.17	25	25
LRP8	0.02	0.021	-10000	0	-0.12	12	12
NDEL1/Katanin 60	0.021	0.056	-10000	0	-0.14	30	30
P39/CDK5	0.008	0.053	-10000	0	-0.09	94	94
LIS1/NudC/Dynein intermediate chain/microtubule organizing center	0.028	0.029	-10000	0	-0.13	11	11
CDK5	0.004	0.043	-10000	0	-0.099	56	56
PPP2R5D	0.022	0.014	-10000	0	-0.12	5	5
LIS1/CLIP170/Dynein Complex/Dynactin Complex	0.025	0.023	-10000	0	-0.11	11	11
CSNK2A1	0.021	0.015	-10000	0	-0.12	6	6
RELN/VLDLR/DAB1/LIS1	0.021	0.059	-10000	0	-0.092	81	81
RELN/VLDLR	0.007	0.071	-10000	0	-0.11	119	119
CDC42	0.015	0.04	-10000	0	-0.27	7	7

×

E-cadherin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin	0.025	0.057	-9999	-0.12	63	63
E-cadherin/beta catenin	0.018	0.053	-9999	-0.14	54	54
CTNNB1	0.022	0.008	-9999	-0.12	1	1
JUP	0.019	0.021	-9999	-0.12	12	12
CDH1	0.021	0.016	-9999	-0.12	6	6

×

Regulation of Androgen receptor activity

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
HDAC1	0.02	0.015	-9999	-0.07	13	13
SMARCC1	0	0.17	-9999	-1.1	13	13
REL	0.021	0.014	-9999	-0.12	5	5
HDAC7	-0.018	0.096	-9999	-0.17	120	120
JUN	0.014	0.033	-9999	-0.12	30	30
EP300	0.022	0.01	-9999	-0.12	2	2
KAT2B	0	0	-9999	-10000	0	0
KAT5	0	0	-9999	-10000	0	0
MAPK14	0.013	0.025	-9999	-0.071	34	34
FOXO1	0.023	0.009	-9999	-0.12	2	2
T-DHT/AR	-0.001	0.11	-9999	-0.18	119	119
MAP2K6	0.012	0.035	-9999	-0.12	33	33
BRM/BAF57	0.007	0.062	-9999	-0.12	110	110
MAP2K4	0.022	0.012	-9999	-0.12	3	3
SMARCA2	0.012	0.036	-9999	-0.12	36	36
PDE9A	-0.095	0.31	-9999	-0.86	79	79
NCOA2	0.022	0.013	-9999	-0.12	4	4
CEBPA	0.022	0.014	-9999	-0.12	5	5
EHMT2	0.023	0.009	-9999	-0.12	2	2
cell proliferation	-0.011	0.11	-9999	-0.25	60	60
NR0B1	0.013	0.038	-9999	-0.12	41	41
EGR1	-0.005	0.054	-9999	-0.12	99	99
RXRs/9cRA	0.033	0.033	-9999	-0.096	4	4
AR/RACK1/Src	0.011	0.073	-9999	-0.17	47	47
AR/GR	-0.013	0.085	-9999	-0.17	101	101
GNB2L1	0.023	0.003	-9999	-10000	0	0
PKN1	0.016	0.031	-9999	-0.12	26	26
RCHY1	0.018	0.022	-9999	-0.12	13	13
epidermal growth factor receptor activity	0	0	-9999	-10000	0	0
MAPK8	0.018	0.018	-9999	-0.074	9	9
T-DHT/AR/TIF2/CARM1	0.01	0.084	-9999	-0.16	66	66
SRC	0.015	0.027	-9999	-0.066	16	16
NR3C1	0.021	0.015	-9999	-0.12	5	5
KLK3	0.004	0.047	-9999	-10000	0	0
APPBP2	0.019	0.017	-9999	-0.12	6	6
TRIM24	0.023	0.014	-9999	-0.12	5	5
T-DHT/AR/TIP60	-0.014	0.071	-9999	-0.15	87	87
TMPRSS2	0.002	0.092	-9999	-0.68	4	4
RXRG	0.006	0.047	-9999	-0.12	68	68
mol:9cRA	0	0	-9999	-10000	0	0
RXRA	0.021	0.017	-9999	-0.12	8	8
RXRB	0.023	0	-9999	-10000	0	0
CARM1	0.019	0.026	-9999	-0.12	19	19
NR2C2	0.023	0.006	-9999	-0.12	1	1
KLK2	0.019	0.072	-9999	-0.25	13	13
AR	-0.01	0.074	-9999	-0.16	94	94
SENP1	0.022	0.011	-9999	-0.12	3	3
HSP90AA1	0.023	0.003	-9999	-10000	0	0
MDM2	0.018	0.02	-9999	-0.12	11	11
SRY	0.021	0.008	-9999	-0.11	2	2
GATA2	0.02	0.022	-9999	-0.12	13	13
MYST2	0.022	0.011	-9999	-0.12	3	3
HOXB13	0.02	0.026	-9999	-0.12	19	19
T-DHT/AR/RACK1/Src	0.006	0.074	-9999	-0.17	52	52
positive regulation of transcription	0.02	0.022	-9999	-0.12	13	13
DNAJA1	0.02	0.012	-9999	-0.13	2	2
proteasomal ubiquitin-dependent protein catabolic process	-0.001	0.09	-9999	-0.28	48	48
NCOA1	0.025	0.032	-9999	-0.16	15	15
SPDEF	0.012	0.042	-9999	-0.12	50	50
T-DHT/AR/TIF2	-0.006	0.088	-9999	-0.22	57	57
T-DHT/AR/Hsp90	-0.003	0.078	-9999	-0.18	60	60
GSK3B	0.022	0.011	-9999	-0.12	3	3
NR2C1	0.021	0.01	-9999	-0.12	2	2
mol:T-DHT	0.013	0.028	-9999	-0.07	16	16
SIRT1	0.023	0.003	-9999	-10000	0	0
ZMIZ2	0.02	0.014	-9999	-0.12	5	5
POU2F1	0.017	0.041	-9999	-0.077	78	78
T-DHT/AR/DAX-1	-0.007	0.077	-9999	-0.15	86	86
CREBBP	0.021	0.015	-9999	-0.12	6	6
SMARCE1	0.023	0.011	-9999	-0.12	3	3

×

RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	-0.021	0.2	-10000	0	-0.97	24	24
VDR	0.019	0.022	-10000	0	-0.12	13	13
FAM120B	0.022	0.011	-10000	0	-0.12	3	3
RXRs/LXRs/DNA/9cRA	0.025	0.095	-10000	0	-0.24	54	54
RXRs/LXRs/DNA/Oxysterols	0.019	0.13	-10000	0	-0.35	59	59
MED1	0.021	0.014	-10000	0	-0.12	5	5
mol:9cRA	0.002	0.016	-10000	0	-0.047	49	49
RARs/THRs/DNA/Src-1	-0.003	0.087	-10000	0	-0.29	24	24
RXRs/NUR77	0.033	0.067	0.18	8	-0.13	27	35
RXRs/PPAR	0.032	0.039	-10000	0	-0.16	5	5
NCOR2	0.019	0.023	-10000	0	-0.12	15	15
VDR/VDR/Vit D3	0.008	0.035	-10000	0	-0.12	36	36
RARs/VDR/DNA/Vit D3	0.029	0.056	-10000	0	-0.1	66	66
RARA	0.023	0	-10000	0	-10000	0	0
NCOA1	0.022	0.009	-10000	0	-0.12	2	2
VDR/VDR/DNA	0.019	0.022	-10000	0	-0.12	13	13
RARs/RARs/DNA/9cRA	0.025	0.045	-10000	0	-0.097	52	52
RARG	0.021	0.015	-10000	0	-0.12	6	6
RPS6KB1	-0.004	0.091	-10000	0	-0.32	39	39
RARs/THRs/DNA/SMRT	-0.002	0.083	-10000	0	-0.27	24	24
THRA	0.022	0.015	-10000	0	-0.12	6	6
mol:Bile acids	0	0	-10000	0	-10000	0	0
VDR/Vit D3/DNA	0.008	0.035	-10000	0	-0.12	36	36
RXRs/PPAR/9cRA/PGJ2/DNA	0.041	0.074	0.27	14	-0.16	15	29
NR1H4	0.021	0.017	-10000	0	-0.12	8	8
RXRs/LXRs/DNA	0.06	0.085	-10000	0	-0.16	53	53
NR1H2	0.021	0.027	-10000	0	-0.12	11	11
NR1H3	0.02	0.029	-10000	0	-0.052	64	64
RXRs/VDR/DNA/Vit D3	0.039	0.059	0.17	6	-0.13	23	29
NR4A1	0.003	0.049	-10000	0	-0.12	74	74
mol:ATRA	0	0	-10000	0	-10000	0	0
RXRs/FXR/9cRA/MED1	0.022	0.049	-10000	0	-0.17	15	15
RXRG	0.006	0.05	-10000	0	-0.12	68	68
RXR alpha/CCPG	0.031	0.026	-10000	0	-0.12	9	9
RXRA	0.021	0.025	-10000	0	-0.11	10	10
RXRB	0.024	0.02	-10000	0	-0.045	2	2
THRB	0.011	0.036	-10000	0	-0.12	36	36
PPARG	0.018	0.028	-10000	0	-0.12	22	22
PPARD	0.023	0.009	-10000	0	-0.12	2	2
TNF	0.022	0.13	-10000	0	-0.59	5	5
mol:Oxysterols	0.001	0.015	-10000	0	-0.041	56	56
cholesterol transport	0.02	0.13	-10000	0	-0.34	59	59
PPARA	0.022	0.012	-10000	0	-0.12	4	4
mol:Vit D3	0	0	-10000	0	-10000	0	0
RARB	0.013	0.034	-10000	0	-0.12	33	33
RXRs/NUR77/BCL2	0.013	0.045	-10000	0	-0.15	23	23
SREBF1	0.022	0.13	-10000	0	-0.41	20	20
RXRs/RXRs/DNA/9cRA	0.041	0.073	0.26	14	-0.16	15	29
ABCA1	-0.029	0.27	-10000	0	-0.84	55	55
RARs/THRs	0.027	0.072	-10000	0	-0.16	28	28
RXRs/FXR	0.049	0.057	0.18	8	-0.12	15	23
BCL2	0.016	0.031	-10000	0	-0.12	27	27

×

Regulation of Telomerase

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Telomerase catalytic core complex	-0.047	0.18	-10000	0	-0.45	59	59
RAD9A	0.023	0	-10000	0	-10000	0	0
AP1	-0.031	0.087	-10000	0	-0.16	150	150
IFNAR2	0.018	0.02	-10000	0	-0.13	8	8
AKT1	0.012	0.041	-10000	0	-0.17	7	7
ER alpha/Oestrogen	0.002	0.046	-10000	0	-0.13	58	58
NFX1/SIN3/HDAC complex	0.009	0.089	-10000	0	-0.27	35	35
EGF	0.02	0.022	-10000	0	-0.13	12	12
SMG5	0.022	0.011	-10000	0	-0.12	3	3
SMG6	0.022	0.011	-10000	0	-0.12	3	3
SP3/HDAC2	0.026	0.031	-10000	0	-0.13	13	13
TERT/c-Abl	-0.042	0.17	-10000	0	-0.42	60	60
SAP18	0.023	0.003	-10000	0	-10000	0	0
MRN complex	0.023	0.065	-10000	0	-0.14	64	64
WT1	0.019	0.016	-10000	0	-0.12	5	5
WRN	0.019	0.02	-10000	0	-0.12	10	10
SP1	0.02	0.015	-10000	0	-0.14	1	1
SP3	0.023	0.003	-10000	0	-10000	0	0
TERF2IP	0.023	0.009	-10000	0	-0.12	2	2
Telomerase/Nucleolin	-0.033	0.17	-10000	0	-0.39	66	66
Mad/Max	0.032	0.015	-10000	0	-0.079	4	4
TERT	-0.048	0.18	-10000	0	-0.46	58	58
CCND1	-0.13	0.37	-10000	0	-0.98	83	83
MAX	0.023	0.004	-10000	0	-10000	0	0
RBBP7	0.021	0.012	-10000	0	-0.12	3	3
RBBP4	0.021	0.014	-10000	0	-0.12	5	5
TERF2	0.025	0.017	0.082	38	-0.12	1	39
PTGES3	0.014	0.036	-10000	0	-0.12	36	36
SIN3A	0.021	0.014	-10000	0	-0.12	5	5
Telomerase/911	0.017	0.096	-10000	0	-0.34	27	27
CDKN1B	-0.015	0.095	-10000	0	-0.25	51	51
RAD1	0.02	0.021	-10000	0	-0.12	12	12
XRCC5	0.021	0.01	-10000	0	-0.12	2	2
XRCC6	0.022	0.004	-10000	0	-10000	0	0
SAP30	0.023	0.001	-10000	0	-10000	0	0
TRF2/PARP2	0.03	0.032	-10000	0	-0.09	30	30
UBE3A	0.023	0.004	-10000	0	-10000	0	0
JUN	0.014	0.033	-10000	0	-0.12	30	30
E6	-0.001	0.003	-10000	0	-10000	0	0
HPV-16 E6/E6AP	0.013	0.021	-10000	0	-0.15	8	8
FOS	-0.006	0.053	-10000	0	-0.12	95	95
IFN-gamma/IRF1	-0.007	0.086	-10000	0	-0.16	112	112
PARP2	0.018	0.026	-10000	0	-0.12	18	18
BLM	0.015	0.032	-10000	0	-0.12	28	28
Telomerase	0.013	0.1	-10000	0	-0.41	23	23
IRF1	0.004	0.058	-10000	0	-0.13	70	70
ESR1	0.017	0.024	-10000	0	-0.12	15	15
KU/TER	0.018	0.058	-10000	0	-0.17	44	44
ATM/TRF2	0.02	0.049	-10000	0	-0.13	51	51
ubiquitin-dependent protein catabolic process	0.013	0.088	-10000	0	-0.26	33	33
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex	0.013	0.09	-10000	0	-0.26	33	33
HDAC1	0.019	0.02	-10000	0	-0.12	10	10
HDAC2	0.017	0.024	-10000	0	-0.12	12	12
ATM	-0.012	0.067	0.14	1	-0.26	38	39
SMAD3	0.019	0.019	-10000	0	-0.072	21	21
ABL1	0.022	0.007	-10000	0	-0.12	1	1
MXD1	0.021	0.018	-10000	0	-0.12	8	8
MRE11A	0.02	0.017	-10000	0	-0.12	7	7
HUS1	0.023	0	-10000	0	-10000	0	0
RPS6KB1	0.021	0.014	-10000	0	-0.12	5	5
TERT/NF kappa B1/14-3-3	-0.024	0.17	-10000	0	-0.4	53	53
NR2F2	0.023	0.014	-10000	0	-0.12	4	4
MAPK3	0.021	0.016	-10000	0	-0.091	8	8
MAPK1	0.02	0.017	-10000	0	-0.087	10	10
TGFB1/TGF beta receptor Type II	0.019	0.023	-10000	0	-0.12	14	14
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
HNRNPC	0.022	0.012	-10000	0	-0.12	4	4
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis	-0.012	0.067	0.14	1	-0.26	38	39
NBN	0.02	0.015	-10000	0	-0.12	5	5
EGFR	0.015	0.03	-10000	0	-0.12	25	25
mol:Oestrogen	0	0.002	-10000	0	-10000	0	0
EGF/EGFR	0.015	0.051	-10000	0	-0.14	46	46
MYC	0.015	0.028	-10000	0	-0.12	20	20
IL2	0.02	0.017	-10000	0	-0.12	3	3
KU	0.018	0.058	-10000	0	-0.17	44	44
RAD50	0.021	0.014	-10000	0	-0.12	5	5
HSP90AA1	0.023	0.003	-10000	0	-10000	0	0
TGFB1	0.019	0.023	-10000	0	-0.12	14	14
TRF2/BLM	0.024	0.043	-10000	0	-0.095	57	57
FRAP1	0.022	0.013	-10000	0	-0.12	4	4
KU/TERT	-0.035	0.18	-10000	0	-0.42	62	62
SP1/HDAC2	0.025	0.038	-10000	0	-0.14	19	19
PINX1	0.021	0.017	-10000	0	-0.12	8	8
Telomerase/EST1A	-0.029	0.17	-10000	0	-0.38	64	64
Smad3/Myc	0.016	0.046	-10000	0	-0.15	29	29
911 complex	0.043	0.024	-10000	0	-0.11	9	9
IFNG	0.009	0.047	-10000	0	-0.1	76	76
Telomerase/PinX1	-0.032	0.17	-10000	0	-0.38	65	65
Telomerase/AKT1/mTOR/p70S6K	0.004	0.11	-10000	0	-0.37	26	26
SIN3B	0.022	0.015	-10000	0	-0.12	6	6
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
Telomerase/EST1B	-0.03	0.17	-10000	0	-0.38	65	65
response to DNA damage stimulus	-0.004	0.03	0.052	1	-0.12	38	39
MRN complex/TRF2/Rap1	0.046	0.06	-10000	0	-0.11	54	54
TRF2/WRN	0.024	0.042	-10000	0	-0.11	47	47
Telomerase/hnRNP C1/C2	-0.029	0.17	-10000	0	-0.38	64	64
E2F1	0.02	0.018	-10000	0	-0.12	7	7
ZNFX1	0.018	0.022	-10000	0	-0.12	12	12
PIF1	0.023	0.006	-10000	0	-0.12	1	1
NCL	0.022	0.008	-10000	0	-0.12	1	1
DKC1	0.022	0.011	-10000	0	-0.12	3	3
telomeric DNA binding	0	0	-10000	0	-10000	0	0

×

S1P3 pathway

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
PDGFRB	0.01	0.042	-9999	-0.12	52	52
mol:S1P	-0.002	0.007	-9999	-0.029	24	24
S1P1/S1P/Gi	0.008	0.065	-9999	-0.22	31	31
GNAO1	0.008	0.043	-9999	-0.12	51	51
S1P/S1P3/G12/G13	0.024	0.024	-9999	-0.1	14	14
AKT1	0.006	0.059	-9999	-0.36	7	7
AKT3	-0.054	0.23	-9999	-1	24	24
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.01	0.042	-9999	-0.12	52	52
GNAI2	0.02	0.014	-9999	-0.12	3	3
GNAI3	0.02	0.012	-9999	-0.027	13	13
GNAI1	0.01	0.036	-9999	-0.12	35	35
mol:GDP	0	0	-9999	-10000	0	0
S1PR3	-0.002	0.008	-9999	-0.031	24	24
S1PR2	0	0	-9999	-10000	0	0
EDG1	0.021	0.016	-9999	-0.12	7	7
mol:Ca2+	-0.016	0.088	-9999	-0.25	45	45
MAPK3	-0.012	0.084	-9999	-0.23	48	48
MAPK1	-0.013	0.085	-9999	-0.23	47	47
JAK2	-0.023	0.1	-9999	-0.27	60	60
CXCR4	-0.021	0.092	-9999	-0.24	58	58
FLT1	0.019	0.019	-9999	-0.052	24	24
RhoA/GDP	0.016	0.016	-9999	-0.14	6	6
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
SRC	-0.012	0.083	-9999	-0.23	45	45
S1P/S1P3/Gi	-0.016	0.089	-9999	-0.25	45	45
RAC1	0.023	0.002	-9999	-10000	0	0
RhoA/GTP	-0.005	0.085	-9999	-0.22	46	46
VEGFA	0.017	0.024	-9999	-0.073	24	24
S1P/S1P2/Gi	-0.011	0.076	-9999	-0.15	100	100
VEGFR1 homodimer/VEGFA homodimer	0.016	0.055	-9999	-0.15	44	44
RHOA	0.023	0.006	-9999	-0.12	1	1
S1P/S1P3/Gq	0.014	0.045	-9999	-0.15	34	34
GNAQ	0.021	0.016	-9999	-0.12	6	6
GNAZ	0.02	0.014	-9999	-0.12	3	3
G12/G13	0.03	0.028	-9999	-0.14	14	14
GNA14	0.02	0.02	-9999	-0.12	11	11
GNA15	0.021	0.017	-9999	-0.12	8	8
GNA12	0.023	0.001	-9999	-10000	0	0
GNA13	0.022	0.009	-9999	-0.12	2	2
GNA11	0.022	0.014	-9999	-0.12	5	5
Rac1/GTP	-0.005	0.085	-9999	-0.22	46	46

×

Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity	-0.023	0.042	0.11	47	-10000	0	47
KIRREL	0.018	0.028	-10000	0	-0.12	20	20
Nephrin/NEPH1Par3/Par6/Atypical PKCs	0.023	0.043	-10000	0	-0.11	47	47
PLCG1	0.019	0.024	-10000	0	-0.12	16	16
ARRB2	0.022	0.014	-10000	0	-0.12	5	5
WASL	0.023	0.009	-10000	0	-0.12	2	2
Nephrin/NEPH1/podocin/CD2AP	0.036	0.056	-10000	0	-0.11	64	64
ChemicalAbstracts:57-88-5	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP	0.021	0.053	-10000	0	-0.14	34	34
FYN	0.014	0.034	-10000	0	-0.11	26	26
mol:Ca2+	0.041	0.047	-10000	0	-0.11	38	38
mol:DAG	0.042	0.048	-10000	0	-0.11	38	38
NPHS2	0.022	0.014	-10000	0	-0.12	4	4
mol:IP3	0.042	0.048	-10000	0	-0.11	38	38
regulation of endocytosis	0.031	0.045	-10000	0	-0.098	32	32
Nephrin/NEPH1/podocin/Cholesterol	0.034	0.035	-10000	0	-0.1	27	27
establishment of cell polarity	0.023	0.042	-10000	0	-0.11	47	47
Nephrin/NEPH1/podocin/NCK1-2	0.049	0.054	-10000	0	-0.1	39	39
Nephrin/NEPH1/beta Arrestin2	0.033	0.046	-10000	0	-0.099	32	32
NPHS1	0.021	0.02	-10000	0	-0.1	12	12
Nephrin/NEPH1/podocin	0.025	0.045	-10000	0	-0.11	28	28
TJP1	0.021	0.01	-10000	0	-0.12	2	2
NCK1	0.02	0.019	-10000	0	-0.12	9	9
NCK2	0.023	0.006	-10000	0	-0.12	1	1
heterophilic cell adhesion	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/PLCgamma1	0.043	0.048	-10000	0	-0.11	38	38
CD2AP	0.02	0.017	-10000	0	-0.12	7	7
Nephrin/NEPH1/podocin/GRB2	0.047	0.042	-10000	0	-0.11	28	28
GRB2	0.023	0.006	-10000	0	-0.12	1	1
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
TRPC6	0.019	0.029	-10000	0	-0.089	25	25
cytoskeleton organization	0.022	0.047	-10000	0	-0.13	30	30
Nephrin/NEPH1	0.022	0.029	-10000	0	-0.072	47	47
Nephrin/NEPH1/ZO-1	0.027	0.055	-10000	0	-0.13	56	56

×

Canonical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FBXW11	0.019	0.02	-9999	-0.055	27	27
mol:GTP	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.013	0.11	-9999	-0.26	53	53
ERC1	0.016	0.029	-9999	-0.12	24	24
RIP2/NOD2	0.013	0.053	-9999	-0.11	81	81
NFKBIA	0.001	0.087	-9999	-0.22	60	60
BIRC2	0.021	0.013	-9999	-0.12	4	4
IKBKB	0.022	0.015	-9999	-0.12	6	6
RIPK2	0.013	0.034	-9999	-0.12	32	32
IKBKG	0.012	0.091	-9999	-0.32	29	29
IKK complex/A20	0.037	0.096	-9999	-0.31	26	26
NEMO/A20/RIP2	0.013	0.034	-9999	-0.12	32	32
XPO1	0.022	0.01	-9999	-0.12	2	2
NEMO/ATM	0.017	0.1	-9999	-0.3	39	39
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
RAN	0.023	0.002	-9999	-10000	0	0
Exportin 1/RanGTP	0.025	0.03	-9999	-0.11	26	26
IKK complex/ELKS	0.021	0.094	-9999	-0.33	25	25
BCL10/MALT1/TRAF6	0.034	0.043	-9999	-0.12	31	31
NOD2	0.023	0.006	-9999	-0.12	1	1
NFKB1	0.017	0.023	-9999	-0.062	33	33
RELA	0.019	0.022	-9999	-0.055	37	37
MALT1	0.017	0.026	-9999	-0.12	19	19
cIAP1/UbcH5C	0.021	0.047	-9999	-0.14	45	45
ATM	0.018	0.022	-9999	-0.12	13	13
TNF/TNFR1A	0.025	0.036	-9999	-0.11	37	37
TRAF6	0.022	0.009	-9999	-0.12	2	2
PRKCA	0.011	0.037	-9999	-0.12	40	40
CHUK	0.021	0.013	-9999	-0.12	4	4
UBE2D3	0.023	0.001	-9999	-10000	0	0
TNF	0.02	0.02	-9999	-0.12	11	11
NF kappa B1 p50/RelA	0.029	0.075	-9999	-0.15	75	75
BCL10	0.023	0.001	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.001	0.086	-9999	-0.22	60	60
beta TrCP1/SCF ubiquitin ligase complex	0.019	0.02	-9999	-0.056	27	27
TNFRSF1A	0.021	0.016	-9999	-0.12	7	7
IKK complex	0.029	0.098	-9999	-0.31	30	30
CYLD	0.023	0.007	-9999	-0.12	1	1
IKK complex/PKC alpha	0.024	0.1	-9999	-0.33	26	26

×

Atypical NF-kappaB 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
BCL3/RelA	0.03	0.026	-9999	-0.094	21	21
FBXW11	0.023	0.003	-9999	-10000	0	0
NF kappa B1 p50/c-Rel	0.022	0.04	-9999	-0.11	41	41
NF kappa B1 p50/RelA/I kappa B alpha	0.018	0.073	-9999	-0.21	28	28
NFKBIA	0.001	0.066	-9999	-0.15	78	78
MAPK14	0.023	0.007	-9999	-0.12	1	1
NF kappa B1 p105/p50	0.022	0.042	-9999	-0.12	40	40
ARRB2	0.014	0.035	-9999	-0.2	14	14
REL	0.022	0.014	-9999	-0.12	5	5
response to oxidative stress	0	0	-9999	-10000	0	0
BCL3/NF kappa B1 p50	0.02	0.042	-9999	-0.12	40	40
response to UV	0	0	-9999	-10000	0	0
NF kappa B1 p105/RelA	0.022	0.04	-9999	-0.11	40	40
PIK3CA	0.02	0.017	-9999	-0.12	7	7
NF kappa B1 p50 dimer	0.012	0.044	-9999	-0.13	48	48
PIK3R1	0.015	0.031	-9999	-0.12	27	27
NFKB1	0.02	0.014	-9999	-0.071	10	10
RELA	0.023	0.009	-9999	-0.12	2	2
positive regulation of anti-apoptosis	0.013	0.051	-9999	-0.2	9	9
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2	0.02	0.075	-9999	-0.2	35	35
SRC	0.023	0.009	-9999	-0.12	2	2
PI3K	0.007	0.065	-9999	-0.13	96	96
NF kappa B1 p50/RelA	0.013	0.052	-9999	-0.2	9	9
IKBKB	0.022	0.015	-9999	-0.12	6	6
beta TrCP1/SCF ubiquitin ligase complex	0.023	0.003	-9999	-10000	0	0
SYK	0.016	0.027	-9999	-0.12	20	20
I kappa B alpha/PIK3R1	0.008	0.069	-9999	-0.14	78	78
cell death	0.02	0.072	-9999	-0.19	35	35
NF kappa B1 p105/c-Rel	0.022	0.04	-9999	-0.11	41	41
LCK	0.022	0.015	-9999	-0.12	6	6
BCL3	0.02	0.023	-9999	-0.12	14	14

×

IL2 signaling events mediated by STAT5

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GAB2	0.008	0.041	-9999	-0.12	50	50
ELF1	0.032	0.023	-9999	-0.2	3	3
CCNA2	0.013	0.032	-9999	-0.12	29	29
PIK3CA	0.02	0.017	-9999	-0.12	7	7
JAK3	0.022	0.014	-9999	-0.12	5	5
PIK3R1	0.016	0.031	-9999	-0.12	27	27
JAK1	0.022	0.01	-9999	-0.12	2	2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	-0.006	0.13	-9999	-0.31	53	53
SHC1	0.024	0.002	-9999	-10000	0	0
SP1	0.012	0.055	-9999	-0.25	11	11
IL2RA	0.03	0.037	-9999	-0.49	2	2
IL2RB	0.019	0.024	-9999	-0.12	16	16
SOS1	0.018	0.027	-9999	-0.12	20	20
IL2RG	-0.001	0.05	-9999	-0.12	82	82
G1/S transition of mitotic cell cycle	-0.077	0.17	-9999	-0.31	154	154
PTPN11	0.022	0.011	-9999	-0.12	3	3
CCND2	-0.001	0.088	-9999	-0.48	10	10
LCK	0.022	0.015	-9999	-0.12	6	6
GRB2	0.023	0.007	-9999	-0.12	1	1
IL2	0.023	0.011	-9999	-0.12	3	3
CDK6	0.008	0.04	-9999	-0.12	46	46
CCND3	-0.004	0.14	-9999	-0.6	12	12

×

PDGFR-beta 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate	0.025	0.07	-9999	-0.22	17	17
PDGFB-D/PDGFRB/SLAP	0.02	0.039	-9999	-0.08	72	72
PDGFB-D/PDGFRB/APS/CBL	0.022	0.028	-9999	-0.06	57	57
AKT1	0.008	0.053	-9999	-0.12	45	45
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
mol:Sphingosine-1-phosphate	0.019	0.068	-9999	-0.24	17	17
PIK3CA	0.02	0.017	-9999	-0.12	7	7
FGR	0.014	0.04	-9999	-0.2	2	2
mol:Ca2+	0.011	0.065	-9999	-0.28	13	13
MYC	-0.059	0.26	-9999	-0.7	76	76
SHC1	0.023	0.001	-9999	-10000	0	0
HRAS/GDP	0.026	0.038	-9999	-0.086	38	38
LRP1/PDGFRB/PDGFB	0.024	0.053	-9999	-0.11	57	57
GRB10	0.022	0.014	-9999	-0.12	5	5
PTPN11	0.022	0.011	-9999	-0.12	3	3
GO:0007205	0.011	0.066	-9999	-0.28	13	13
PTEN	0.022	0.008	-9999	-0.12	1	1
GRB2	0.023	0.006	-9999	-0.12	1	1
GRB7	0.018	0.026	-9999	-0.12	18	18
PDGFB-D/PDGFRB/SHP2	0.017	0.045	-9999	-0.091	77	77
PDGFB-D/PDGFRB/GRB10	0.021	0.039	-9999	-0.082	66	66
cell cycle arrest	0.02	0.039	-9999	-0.08	72	72
HRAS	0.023	0.006	-9999	-0.12	1	1
HIF1A	0.007	0.054	-9999	-0.13	52	52
GAB1	0.006	0.08	-9999	-0.24	24	24
mol:GTP	0	0	-9999	-10000	0	0
DNM2	0.006	0.078	-9999	-0.21	34	34
PDGFB-D/PDGFRB	0.032	0.039	-9999	-0.11	14	14
mol:GDP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/LMW-PTP	0.016	0.047	-9999	-0.097	77	77
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB	0.018	0.086	-9999	-0.2	45	45
positive regulation of MAPKKK cascade	0.017	0.045	-9999	-0.091	77	77
PIK3R1	0.015	0.031	-9999	-0.12	27	27
mol:IP3	0.011	0.066	-9999	-0.29	13	13
E5	0	0.001	-9999	-10000	0	0
CSK	0.023	0.009	-9999	-0.12	2	2
PDGFB-D/PDGFRB/GRB7	0.017	0.046	-9999	-0.088	82	82
SHB	0.023	0.009	-9999	-0.12	2	2
BLK	0.014	0.039	-9999	-0.19	5	5
PTPN2	0.022	0.008	-9999	-0.13	1	1
PDGFB-D/PDGFRB/SNX15	0.024	0.033	-9999	-0.074	55	55
BCAR1	0.022	0.011	-9999	-0.12	3	3
VAV2	-0.004	0.11	-9999	-0.24	80	80
CBL	0.023	0.006	-9999	-0.12	1	1
PDGFB-D/PDGFRB/DEP1	0.017	0.046	-9999	-0.09	81	81
LCK	0.014	0.039	-9999	-0.18	5	5
PDGFRB	0.01	0.043	-9999	-0.12	52	52
ACP1	0.021	0.014	-9999	-0.12	5	5
HCK	-0.001	0.091	-9999	-0.42	19	19
ABL1	0.007	0.068	-9999	-0.21	22	22
PDGFB-D/PDGFRB/CBL	0.007	0.082	-9999	-0.26	20	20
PTPN1	0.022	0.007	-9999	-0.13	1	1
SNX15	0.023	0	-9999	-10000	0	0
STAT3	0.022	0.011	-9999	-0.12	3	3
STAT1	0.014	0.031	-9999	-0.12	26	26
cell proliferation	-0.049	0.23	-9999	-0.61	77	77
SLA	0.02	0.019	-9999	-0.12	10	10
actin cytoskeleton reorganization	0.031	0.041	-9999	-0.15	7	7
SRC	0.015	0.038	-9999	-0.18	5	5
PI3K	-0.021	0.04	-9999	-0.14	43	43
PDGFB-D/PDGFRB/GRB7/SHC	0.03	0.042	-9999	-0.13	17	17
SH2B2	0	0	-9999	-10000	0	0
PLCgamma1/SPHK1	0.019	0.07	-9999	-0.24	17	17
LYN	-0.021	0.13	-9999	-0.44	44	44
LRP1	0.014	0.032	-9999	-0.12	29	29
SOS1	0.017	0.027	-9999	-0.12	20	20
STAT5B	0.023	0.006	-9999	-0.12	1	1
STAT5A	0.022	0.013	-9999	-0.12	4	4
NCK1-2/p130 Cas	0.046	0.052	-9999	-0.12	15	15
SPHK1	0.022	0.015	-9999	-0.12	6	6
EDG1	0.022	0.016	-9999	-0.12	7	7
mol:DAG	0.011	0.066	-9999	-0.29	13	13
PLCG1	0.011	0.068	-9999	-0.29	13	13
NHERF/PDGFRB	0.024	0.049	-9999	-0.12	28	28
YES1	-0.011	0.12	-9999	-0.44	34	34
cell migration	0.024	0.049	-9999	-0.12	28	28
SHC/Grb2/SOS1	0.044	0.051	-9999	-0.16	8	8
SLC9A3R2	0.017	0.028	-9999	-0.12	22	22
SLC9A3R1	0.016	0.031	-9999	-0.12	26	26
NHERF1-2/PDGFRB/PTEN	0.031	0.056	-9999	-0.1	50	50
FYN	-0.021	0.12	-9999	-0.38	46	46
DOK1	0.021	0.029	-9999	-0.11	10	10
HRAS/GTP	0.017	0.008	-9999	-0.11	2	2
PDGFB	0.022	0.011	-9999	-0.12	3	3
RAC1	-0.022	0.16	-9999	-0.4	82	82
PRKCD	0.019	0.031	-9999	-0.12	11	11
FER	0.02	0.03	-9999	-0.11	11	11
MAPKKK cascade	-0.007	0.028	-9999	-0.15	8	8
RASA1	0.02	0.03	-9999	-0.12	10	10
NCK1	0.02	0.019	-9999	-0.12	9	9
NCK2	0.023	0.006	-9999	-0.12	1	1
p62DOK/Csk	0.032	0.033	-9999	-0.093	16	16
PDGFB-D/PDGFRB/SHB	0.023	0.033	-9999	-0.074	57	57
chemotaxis	0.007	0.067	-9999	-0.2	22	22
STAT1-3-5/STAT1-3-5	0.021	0.058	-9999	-0.14	22	22
Bovine Papilomavirus E5/PDGFRB	0.007	0.03	-9999	-0.081	55	55
PTPRJ	0.02	0.019	-9999	-0.12	9	9

×

S1P4 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-9999	-10000	0	0
GNAO1	0.01	0.042	-9999	-0.12	51	51
CDC42/GTP	0.008	0.067	-9999	-0.21	22	22
PLCG1	-0.001	0.065	-9999	-0.14	86	86
mol:GTP	0	0	-9999	-10000	0	0
GNAI2	0.022	0.011	-9999	-0.12	3	3
GNAI3	0.021	0.008	-9999	-0.12	1	1
G12/G13	0.03	0.028	-9999	-0.14	14	14
cell migration	0.007	0.065	-9999	-0.21	22	22
S1PR5	0	0	-9999	-10000	0	0
S1PR4	0	0	-9999	-10000	0	0
MAPK3	0	0.066	-9999	-0.14	86	86
MAPK1	0	0.066	-9999	-0.14	86	86
S1P/S1P5/Gi	-0.003	0.069	-9999	-0.15	86	86
GNAI1	0.012	0.035	-9999	-0.12	35	35
CDC42/GDP	0.016	0.012	-9999	-0.15	3	3
S1P/S1P5/G12	0.016	0.006	-9999	-0.12	1	1
RHOA	0.021	0.02	-9999	-0.1	14	14
S1P/S1P4/Gi	-0.003	0.069	-9999	-0.15	86	86
mol:GDP	0	0	-9999	-10000	0	0
GNAZ	0.022	0.011	-9999	-0.12	3	3
S1P/S1P4/G12/G13	0.026	0.021	-9999	-0.1	14	14
GNA12	0.023	0.001	-9999	-10000	0	0
GNA13	0.022	0.009	-9999	-0.12	2	2
CDC42	0.023	0.002	-9999	-10000	0	0

×

Presenilin action in Notch and Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved)	0.015	0.12	-10000	0	-0.48	29	29
HDAC1	0.027	0.027	0.087	22	-0.1	10	32
AES	0.023	0.021	0.065	1	-0.12	10	11
FBXW11	0.023	0.003	-10000	0	-10000	0	0
DTX1	0.023	0.009	-10000	0	-0.12	2	2
LRP6/FZD1	0.018	0.047	-10000	0	-0.11	66	66
TLE1	0.022	0.02	0.075	1	-0.11	10	11
AP1	-0.004	0.071	-10000	0	-0.2	45	45
NCSTN	0.022	0.012	-10000	0	-0.12	4	4
ADAM10	0.022	0.013	-10000	0	-0.12	4	4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4	-0.056	0.18	-10000	0	-0.48	52	52
NICD/RBPSUH	0.013	0.12	-10000	0	-0.48	29	29
WIF1	0.02	0.022	-10000	0	-0.12	13	13
NOTCH1	0.001	0.12	-10000	0	-0.51	29	29
PSENEN	0.016	0.03	-10000	0	-0.12	24	24
KREMEN2	0.022	0.012	-10000	0	-0.12	4	4
DKK1	0.015	0.034	-10000	0	-0.12	33	33
beta catenin/beta TrCP1	-0.005	0.081	-10000	0	-0.28	30	30
APH1B	0.014	0.032	-10000	0	-0.12	29	29
APH1A	0.023	0.009	-10000	0	-0.12	2	2
AXIN1	-0.001	0.046	0.19	4	-0.2	10	14
CtBP/CBP/TCF1/TLE1/AES	0.038	0.094	0.18	107	-0.2	22	129
PSEN1	0.022	0.008	-10000	0	-0.12	1	1
FOS	-0.005	0.053	-10000	0	-0.12	95	95
JUN	0.014	0.033	-10000	0	-0.12	30	30
MAP3K7	0.024	0.017	-10000	0	-0.12	5	5
CTNNB1	-0.016	0.078	-10000	0	-0.28	29	29
MAPK3	0.022	0.014	-10000	0	-0.12	5	5
DKK2/LRP6/Kremen 2	0.032	0.043	-10000	0	-0.11	32	32
HNF1A	0.024	0.014	0.063	2	-0.12	4	6
CTBP1	0.024	0.018	-10000	0	-0.12	7	7
MYC	-0.15	0.42	-10000	0	-1.2	73	73
NKD1	0.023	0.012	-10000	0	-0.12	4	4
FZD1	0.023	0.006	-10000	0	-0.12	1	1
NOTCH1 precursor/Deltex homolog 1	0.014	0.12	-10000	0	-0.48	29	29
apoptosis	-0.004	0.071	-10000	0	-0.2	45	45
Delta 1/NOTCHprecursor	0.013	0.12	-10000	0	-0.48	29	29
DLL1	0.022	0.012	-10000	0	-0.12	4	4
PPARD	0.001	0.045	-10000	0	-10000	0	0
Gamma Secretase	0.033	0.067	-10000	0	-0.098	89	89
APC	-0.004	0.057	0.19	4	-0.28	11	15
DVL1	0.017	0.066	-10000	0	-0.3	20	20
CSNK2A1	0.021	0.015	-10000	0	-0.12	6	6
MAP3K7IP1	0.026	0.008	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	0.027	0.047	-10000	0	-0.11	34	34
LRP6	0.014	0.034	-10000	0	-0.12	32	32
CSNK1A1	0.022	0.007	-10000	0	-0.12	1	1
NLK	0.029	0.042	-10000	0	-0.22	11	11
CCND1	-0.18	0.43	-10000	0	-1.2	82	82
WNT1	0.023	0.009	-10000	0	-0.12	2	2
Axin1/APC/beta catenin	-0.001	0.086	0.2	3	-0.28	27	30
DKK2	0.022	0.011	-10000	0	-0.12	3	3
NOTCH1 precursor/DVL1	0.014	0.13	-10000	0	-0.44	34	34
GSK3B	0.023	0.011	-10000	0	-0.12	3	3
FRAT1	0.024	0.007	-10000	0	-0.12	1	1
NOTCH/Deltex homolog 1	0.016	0.12	-10000	0	-0.48	29	29
PPP2R5D	0.009	0.041	-10000	0	-0.21	12	12
MAPK1	0.021	0.016	-10000	0	-0.12	7	7
WNT1/LRP6/FZD1	0.042	0.045	-10000	0	-0.096	37	37
RBPJ	0.023	0.006	-10000	0	-0.12	1	1
CREBBP	0.017	0.018	-10000	0	-0.12	6	6

×

LPA4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ADCY4	0.012	0.014	-9999	-0.057	22	22
ADCY5	0.009	0.02	-9999	-0.06	42	42
ADCY6	0.013	0.01	-9999	-0.057	11	11
ADCY7	0.014	0.009	-9999	-0.057	8	8
ADCY1	0.013	0.013	-9999	-0.067	12	12
ADCY2	0.012	0.013	-9999	-0.057	18	18
ADCY3	0.012	0.013	-9999	-0.057	18	18
ADCY8	0.002	0.03	-9999	-0.061	99	99
PRKCE	0.01	0.011	-9999	-0.077	8	8
ADCY9	0.012	0.015	-9999	-0.064	17	17
mol:DAG	0	0	-9999	-10000	0	0
cAMP biosynthetic process	0.012	0.032	-9999	-0.18	11	11

×

Coregulation of Androgen receptor activity

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
NRIP1	0.014	0.035	-9999	-0.12	35	35
SVIL	0.016	0.031	-9999	-0.12	26	26
ZNF318	0.018	0.014	-9999	-0.12	5	5
JMJD2C	0.029	0.016	-9999	-0.12	6	6
T-DHT/AR/Ubc9	0.017	0.057	-9999	-0.11	84	84
CARM1	0.018	0.026	-9999	-0.12	19	19
PRDX1	0.022	0.004	-9999	-10000	0	0
PELP1	0.022	0.009	-9999	-0.12	2	2
CTNNB1	0.023	0.008	-9999	-0.12	1	1
AKT1	0.02	0.019	-9999	-0.12	10	10
PTK2B	0.023	0.009	-9999	-0.12	2	2
MED1	0.02	0.014	-9999	-0.12	5	5
MAK	0.008	0.04	-9999	-0.12	47	47
response to oxidative stress	0	0	-9999	-10000	0	0
HIP1	0.022	0.019	-9999	-0.12	9	9
GSN	0.023	0.012	-9999	-0.12	3	3
NCOA2	0.021	0.013	-9999	-0.12	4	4
NCOA6	0.023	0.014	-9999	-0.12	5	5
DNA-PK	0.023	0.06	-9999	-0.14	60	60
NCOA4	0.023	0.004	-9999	-10000	0	0
PIAS3	0.021	0.022	-9999	-0.12	13	13
cell proliferation	0.004	0.045	-9999	-0.5	2	2
XRCC5	0.021	0.01	-9999	-0.12	2	2
UBE3A	0.025	0.003	-9999	-10000	0	0
T-DHT/AR/SNURF	0.016	0.058	-9999	-0.11	84	84
FHL2	0.018	0.078	-9999	-0.67	5	5
RANBP9	0.023	0.014	-9999	-0.12	5	5
JMJD1A	0.033	0.024	-9999	-0.12	6	6
CDK6	0.008	0.04	-9999	-0.12	46	46
TGFB1I1	0.024	0.012	-9999	-0.12	4	4
T-DHT/AR/CyclinD1	-0.01	0.079	-9999	-0.13	140	140
XRCC6	0.022	0.004	-9999	-10000	0	0
T-DHT/AR	0.027	0.076	-9999	-0.18	20	20
CTDSP1	0.023	0.011	-9999	-0.12	3	3
CTDSP2	0.02	0.009	-9999	-0.12	2	2
BRCA1	0.016	0.03	-9999	-0.12	24	24
TCF4	0.019	0.017	-9999	-0.12	8	8
CDKN2A	0.013	0.022	-9999	-0.12	12	12
SRF	0.024	0.03	-9999	-0.12	23	23
NKX3-1	0.013	0.086	-9999	-0.29	34	34
KLK3	0.013	0.04	-9999	-10000	0	0
TMF1	0.022	0.012	-9999	-0.12	3	3
HNRNPA1	0.022	0.002	-9999	-10000	0	0
AOF2	0.024	0.009	-9999	-0.12	2	2
APPL1	0.019	0.014	-9999	-0.073	12	12
T-DHT/AR/Caspase 8	0.012	0.061	-9999	-0.11	96	96
AR	0.015	0.039	-9999	-0.11	44	44
UBA3	0.001	0	-9999	-10000	0	0
PATZ1	0.021	0.012	-9999	-0.12	4	4
PAWR	0.023	0.009	-9999	-0.12	2	2
PRKDC	0.02	0.015	-9999	-0.12	6	6
PA2G4	0.021	0.009	-9999	-0.12	2	2
UBE2I	0.023	0.001	-9999	-10000	0	0
T-DHT/AR/Cyclin D3/CDK11 p58	0.015	0.054	-9999	-0.1	81	81
RPS6KA3	0.019	0.023	-9999	-0.12	13	13
T-DHT/AR/ARA70	0.014	0.062	-9999	-0.11	99	99
LATS2	0.022	0.006	-9999	-0.12	1	1
T-DHT/AR/PRX1	0.012	0.055	-9999	-0.097	100	100
Cyclin D3/CDK11 p58	0.014	0.019	-9999	-0.1	14	14
VAV3	0.011	0.038	-9999	-0.12	41	41
KLK2	0.016	0.072	-9999	-0.29	23	23
CASP8	0.022	0.004	-9999	-10000	0	0
T-DHT/AR/TIF2/CARM1	0.023	0.065	-9999	-0.1	101	101
TMPRSS2	0.005	0.099	-9999	-0.3	36	36
CCND1	0.006	0.042	-9999	-0.12	54	54
PIAS1	0.025	0.009	-9999	-0.12	2	2
mol:T-DHT	0.006	0.007	-9999	-0.055	2	2
CDC2L1	0	0	-9999	-10000	0	0
PIAS4	0.026	0.002	-9999	-10000	0	0
T-DHT/AR/CDK6	-0.008	0.078	-9999	-0.12	143	143
CMTM2	0.023	0.006	-9999	-0.12	1	1
SNURF	0.021	0.017	-9999	-0.12	8	8
ZMIZ1	0.022	0.031	-9999	-0.11	26	26
CCND3	0.021	0.018	-9999	-0.12	9	9
TGIF1	0.022	0.001	-9999	-10000	0	0
FKBP4	0.022	0.02	-9999	-0.12	10	10

×

Glucocorticoid receptor regulatory network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PCK2	-0.011	0.059	-10000	0	-0.7	2	2
SMARCC2	0.022	0.012	-10000	0	-0.12	4	4
SMARCC1	0.023	0.003	-10000	0	-10000	0	0
TBX21	0.042	0.047	-10000	0	-0.27	2	2
SUMO2	0.021	0.005	-10000	0	-10000	0	0
STAT1 (dimer)	-0.007	0.08	-10000	0	-0.17	92	92
FKBP4	0.02	0.02	-10000	0	-0.12	10	10
FKBP5	0.006	0.043	-10000	0	-0.12	56	56
GR alpha/HSP90/FKBP51/HSP90	-0.013	0.082	0.24	1	-0.2	44	45
PRL	0.045	0.057	-10000	0	-0.5	1	1
cortisol/GR alpha (dimer)/TIF2	-0.02	0.11	0.43	3	-0.33	4	7
RELA	-0.02	0.075	-10000	0	-0.15	116	116
FGG	-0.016	0.1	0.45	1	-0.32	3	4
GR beta/TIF2	-0.006	0.07	0.23	2	-0.2	23	25
IFNG	-0.003	0.12	-10000	0	-0.45	4	4
apoptosis	-0.052	0.16	-10000	0	-0.45	34	34
CREB1	0.033	0.008	-10000	0	-10000	0	0
histone acetylation	0.028	0.081	0.27	8	-0.28	20	28
BGLAP	0.042	0.075	-10000	0	-0.87	2	2
GR/PKAc	0.028	0.063	0.23	2	-0.15	21	23
NF kappa B1 p50/RelA	-0.044	0.14	-10000	0	-0.27	132	132
SMARCD1	0.021	0.018	-10000	0	-0.12	9	9
MDM2	-0.003	0.047	0.14	1	-0.22	9	10
GATA3	0.037	0.022	-10000	0	-0.12	11	11
AKT1	0.015	0.022	0.15	2	-0.13	10	12
CSF2	0.03	0.055	-10000	0	-10000	0	0
GSK3B	0.02	0.012	-10000	0	-0.13	3	3
NR1I3	-0.038	0.15	-10000	0	-0.49	8	8
CSN2	-0.015	0.093	0.32	2	-0.29	3	5
BRG1/BAF155/BAF170/BAF60A	0.041	0.052	-10000	0	-0.11	45	45
NFATC1	0.033	0.013	-10000	0	-10000	0	0
POU2F1	0.031	0.008	-10000	0	-0.11	1	1
CDKN1A	-0.041	0.12	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
response to UV	-0.002	0.004	-10000	0	-10000	0	0
SFN	0.014	0.032	-10000	0	-0.12	29	29
GR alpha/HSP90/FKBP51/HSP90/14-3-3	-0.007	0.086	0.24	1	-0.18	62	63
prolactin receptor activity	0	0	-10000	0	-10000	0	0
EGR1	-0.11	0.28	-10000	0	-0.72	92	92
JUN	0.021	0.089	-10000	0	-0.3	7	7
IL4	0.046	0.048	-10000	0	-10000	0	0
CDK5R1	0.022	0.007	-10000	0	-0.12	1	1
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
cortisol/GR alpha (monomer)/AP-1	-0.043	0.079	0.19	12	-0.2	62	74
GR alpha/HSP90/FKBP51/HSP90/PP5C	0.006	0.079	0.24	1	-0.17	46	47
cortisol/GR alpha (monomer)	-0.039	0.12	0.48	3	-0.38	3	6
NCOA2	0.021	0.013	-10000	0	-0.12	4	4
response to hypoxia	0	0	-10000	0	-10000	0	0
FOS	-0.014	0.079	-10000	0	-0.14	130	130
AP-1/NFAT1-c-4	-0.012	0.15	-10000	0	-0.4	25	25
AFP	0.017	0.083	-10000	0	-0.56	1	1
SUV420H1	0.021	0.015	-10000	0	-0.12	6	6
IRF1	-0.095	0.24	-10000	0	-0.6	86	86
TP53	0.026	0.033	-10000	0	-10000	0	0
PPP5C	0.022	0.014	-10000	0	-0.12	5	5
KRT17	-0.011	0.15	-10000	0	-0.78	10	10
KRT14	-0.006	0.2	0.46	9	-1.1	15	24
TBP	0.031	0.026	-10000	0	-0.2	5	5
CREBBP	0.023	0.052	0.3	15	-0.13	5	20
HDAC1	0.013	0.02	-10000	0	-0.13	10	10
HDAC2	0.018	0.021	-10000	0	-0.12	12	12
AP-1	-0.012	0.15	-10000	0	-0.4	25	25
MAPK14	0.02	0.008	-10000	0	-0.13	1	1
MAPK10	0.011	0.037	-10000	0	-0.13	38	38
MAPK11	0.021	0.004	-10000	0	-10000	0	0
KRT5	-0.07	0.26	-10000	0	-0.89	46	46
interleukin-1 receptor activity	-0.002	0.001	-10000	0	-10000	0	0
NCOA1	0.024	0.01	-10000	0	-0.08	4	4
STAT1	-0.007	0.08	-10000	0	-0.17	92	92
CGA	0.043	0.059	-10000	0	-0.41	2	2
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2	-0.046	0.11	0.27	10	-0.34	37	47
MAPK3	0.019	0.015	-10000	0	-0.13	5	5
MAPK1	0.019	0.017	-10000	0	-0.12	7	7
ICAM1	-0.13	0.32	-10000	0	-0.8	101	101
NFKB1	-0.031	0.097	-10000	0	-0.18	133	133
MAPK8	0.033	0.076	-10000	0	-0.26	6	6
MAPK9	0.019	0.012	-10000	0	-0.12	3	3
cortisol/GR alpha (dimer)	-0.055	0.17	-10000	0	-0.46	35	35
BAX	-0.039	0.12	-10000	0	-10000	0	0
POMC	0.029	0.082	-10000	0	-10000	0	0
EP300	0.023	0.047	0.29	14	-0.13	1	15
cortisol/GR alpha (dimer)/p53	-0.045	0.12	0.5	1	-0.36	5	6
proteasomal ubiquitin-dependent protein catabolic process	-0.006	0.058	0.26	15	-0.2	8	23
SGK1	0.001	0.1	0.34	14	-0.32	31	45
IL13	0.021	0.089	-10000	0	-0.52	1	1
IL6	-0.028	0.15	-10000	0	-0.72	12	12
PRKACG	0.023	0.009	-10000	0	-0.12	2	2
IL5	0.025	0.089	-10000	0	-10000	0	0
IL2	0.004	0.11	-10000	0	-0.46	2	2
CDK5	0.014	0.032	-10000	0	-0.12	28	28
PRKACB	0.019	0.02	-10000	0	-0.12	11	11
HSP90AA1	0.023	0.003	-10000	0	-10000	0	0
IL8	-0.055	0.22	-10000	0	-0.76	40	40
CDK5R1/CDK5	0.019	0.042	-10000	0	-0.11	52	52
NF kappa B1 p50/RelA/PKAc	-0.002	0.12	-10000	0	-0.19	112	112
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90	-0.01	0.11	0.4	2	-0.31	4	6
SMARCA4	0.015	0.031	-10000	0	-0.12	27	27
chromatin remodeling	-0.009	0.092	0.27	2	-0.32	14	16
NF kappa B1 p50/RelA/Cbp	-0.02	0.13	0.34	8	-0.25	80	88
JUN (dimer)	0.021	0.089	-10000	0	-0.3	7	7
YWHAH	0.021	0.014	-10000	0	-0.12	5	5
VIPR1	0.043	0.045	-10000	0	-0.22	2	2
NR3C1	-0.015	0.081	0.32	2	-0.33	10	12
NR4A1	0.01	0.048	-10000	0	-10000	0	0
TIF2/SUV420H1	0.02	0.048	-10000	0	-0.13	50	50
MAPKKK cascade	-0.052	0.16	-10000	0	-0.45	34	34
cortisol/GR alpha (dimer)/Src-1	-0.013	0.11	0.44	3	-0.32	2	5
PBX1	0.029	0.014	-10000	0	-0.11	4	4
POU1F1	0.03	0.014	-10000	0	-0.13	4	4
SELE	-0.006	0.11	-10000	0	-0.41	3	3
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A	-0.009	0.092	0.27	2	-0.32	14	16
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90	-0.01	0.11	0.4	2	-0.31	4	6
mol:cortisol	-0.027	0.065	0.26	3	-10000	0	3
MMP1	-0.038	0.16	-10000	0	-0.95	12	12

×

Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FOXP3	0.028	0.018	-10000	0	-0.1	6	6
NFATC2	0.016	0.19	-10000	0	-0.4	55	55
NFATC3	0.06	0.059	0.26	28	-0.24	2	30
CD40LG	0.043	0.14	-10000	0	-0.53	5	5
ITCH	0.026	0.064	-10000	0	-0.28	17	17
CBLB	0.023	0.073	-10000	0	-0.31	19	19
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment	0.038	0.15	-10000	0	-0.5	12	12
JUNB	0.007	0.042	-10000	0	-0.12	52	52
CaM/Ca2+/Calcineurin A alpha-beta B1	0.034	0.059	-10000	0	-0.19	30	30
T cell anergy	0.012	0.087	-10000	0	-0.31	29	29
TLE4	-0.016	0.18	-10000	0	-0.44	62	62
Jun/NFAT1-c-4/p21SNFT	0.08	0.15	-10000	0	-0.56	4	4
AP-1/NFAT1-c-4	0.08	0.2	-10000	0	-0.62	4	4
IKZF1	0.019	0.13	-10000	0	-0.27	49	49
T-helper 2 cell differentiation	0.023	0.14	-10000	0	-0.49	4	4
AP-1/NFAT1	0.007	0.15	-10000	0	-0.27	68	68
CALM1	0.027	0.037	-10000	0	-0.11	32	32
EGR2	0.067	0.15	0.51	15	-0.76	4	19
EGR3	0.068	0.14	-10000	0	-0.52	1	1
NFAT1/FOXP3	0.038	0.14	-10000	0	-0.27	51	51
EGR1	-0.005	0.054	-10000	0	-0.12	99	99
JUN	0.019	0.035	-10000	0	-0.12	31	31
EGR4	0.023	0.014	-10000	0	-0.13	5	5
mol:Ca2+	0.006	0.03	-10000	0	-0.12	26	26
GBP3	-0.06	0.23	-10000	0	-0.46	123	123
FOSL1	0.021	0.018	-10000	0	-0.12	9	9
NFAT1-c-4/MAF/IRF4	0.092	0.14	-10000	0	-0.53	4	4
DGKA	0.012	0.14	-10000	0	-0.31	56	56
CREM	0.021	0.012	-10000	0	-0.12	4	4
NFAT1-c-4/PPARG	0.081	0.14	-10000	0	-0.57	4	4
CTLA4	0.018	0.11	-10000	0	-0.28	23	23
NFAT1-c-4 (dimer)/EGR1	0.053	0.15	-10000	0	-0.56	5	5
NFAT1-c-4 (dimer)/EGR4	0.088	0.14	-10000	0	-0.56	4	4
FOS	0	0.053	-10000	0	-0.11	96	96
IFNG	0.017	0.14	-10000	0	-0.43	8	8
T cell activation	0.027	0.11	-10000	0	-0.46	1	1
MAF	0.023	0.012	-10000	0	-0.12	4	4
T-helper 2 cell lineage commitment	0	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	-0.07	0.13	0.61	3	-0.49	25	28
TNF	0.037	0.14	-10000	0	-0.51	6	6
FASLG	0.056	0.15	-10000	0	-0.98	3	3
TBX21	0.026	0.018	-10000	0	-0.13	3	3
BATF3	0	0	-10000	0	-10000	0	0
PRKCQ	0.019	0.03	-10000	0	-0.12	25	25
PTPN1	0.019	0.13	-10000	0	-0.31	31	31
NFAT1-c-4/ICER1	0.081	0.14	-10000	0	-0.56	4	4
GATA3	0.024	0.021	-10000	0	-0.12	11	11
T-helper 1 cell differentiation	0.017	0.14	-10000	0	-0.43	8	8
IL2RA	0.04	0.15	-10000	0	-0.44	16	16
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
CASP3	0.015	0.14	-10000	0	-0.35	35	35
E2F1	0.017	0.045	-10000	0	-0.15	36	36
PPARG	0.018	0.028	-10000	0	-0.12	22	22
SLC3A2	0.013	0.14	-10000	0	-0.3	57	57
IRF4	0.019	0.025	-10000	0	-0.12	17	17
PTGS2	0.035	0.15	-10000	0	-0.56	5	5
CSF2	0.043	0.14	-10000	0	-0.53	5	5
JunB/Fra1/NFAT1-c-4	0.071	0.15	-10000	0	-0.5	6	6
IL4	0.022	0.14	-10000	0	-0.52	3	3
IL5	0.042	0.14	-10000	0	-0.53	5	5
IL2	0.027	0.11	-10000	0	-0.47	1	1
IL3	0.012	0.04	-10000	0	-0.38	3	3
RNF128	0.026	0.051	-10000	0	-0.25	7	7
NFATC1	0.071	0.13	0.49	25	-0.62	3	28
CDK4	-0.08	0.28	0.46	1	-1.2	29	30
PTPRK	-0.007	0.18	-10000	0	-0.43	59	59
IL8	0.029	0.15	-10000	0	-0.5	8	8
POU2F1	0.031	0.007	-10000	0	-0.12	1	1

×

Arf6 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CENTA1/KIF3B	0.013	0.017	-9999	-0.078	18	18
ARNO/beta Arrestin1-2	0.029	0.019	-9999	-0.077	11	11
EGFR	0.015	0.03	-9999	-0.12	25	25
EPHA2	0.02	0.022	-9999	-0.12	13	13
USP6	0.023	0.006	-9999	-0.12	1	1
IQSEC1	0.023	0.006	-9999	-0.12	1	1
EGFR/EGFR/EGF/EGF	0.016	0.05	-9999	-0.14	40	40
ARRB2	0.017	0.018	-9999	-0.2	3	3
mol:GTP	0.003	0.006	-9999	-0.04	1	1
ARRB1	0.02	0.022	-9999	-0.12	13	13
FBXO8	0.022	0.011	-9999	-0.12	3	3
TSHR	0.013	0.038	-9999	-0.12	41	41
EGF	0.02	0.021	-9999	-0.12	12	12
somatostatin receptor activity	0	0	-9999	0	27	27
ARAP2	0	0	-9999	0	26	26
mol:GDP	0.015	0.046	-9999	-0.17	22	22
mol:PI-3-4-5-P3	0	0	-9999	0	27	27
ITGA2B	0.023	0.006	-9999	-0.12	1	1
ARF6	0.023	0.003	-9999	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	0.029	0.062	-9999	-0.11	75	75
ADAP1	0	0	-9999	0	26	26
KIF13B	0.02	0.022	-9999	-0.12	13	13
HGF/MET	-0.017	0.074	-9999	-0.14	118	118
PXN	0.022	0.014	-9999	-0.12	5	5
ARF6/GTP	0.022	0.059	-9999	-0.21	26	26
EGFR/EGFR/EGF/EGF/ARFGEP100	0.03	0.046	-9999	-0.11	40	40
ADRB2	0.023	0.006	-9999	-0.12	1	1
receptor agonist activity	0	0	-9999	0	27	27
actin filament binding	0	0	-9999	0	27	27
SRC	0.023	0.009	-9999	-0.12	2	2
ITGB3	0.004	0.047	-9999	-0.12	68	68
GNAQ	0.021	0.016	-9999	-0.12	6	6
EFA6/PI-4-5-P2	0	0	-9999	-0.001	26	26
ARF6/GDP	0.021	0.05	-9999	-0.25	11	11
ARF6/GDP/GULP/ACAP1	0.017	0.061	-9999	-0.16	29	29
alphaIIb/beta3 Integrin/paxillin/GIT1	0.036	0.05	-9999	-0.096	39	39
ACAP1	0	0	-9999	0	4	4
ACAP2	0	0	-9999	0	26	26
LHCGR/beta Arrestin2	0.023	0.016	-9999	-0.14	3	3
EFNA1	0.014	0.031	-9999	-0.12	26	26
HGF	0.02	0.023	-9999	-0.12	14	14
CYTH3	0	0	-9999	-0.001	27	27
CYTH2	0	0.001	-9999	-0.004	27	27
NCK1	0.02	0.019	-9999	-0.12	9	9
fibronectin binding	0	0	-9999	0	28	28
endosomal lumen acidification	0	0	-9999	0	16	16
microtubule-based process	0	0	-9999	-10000	0	0
GULP1	0.005	0.045	-9999	-0.12	63	63
GNAQ/ARNO	0.015	0.007	-9999	-0.047	6	6
mol:Phosphatidic acid	0	0	-9999	0	26	26
PIP3-E	0.018	0.028	-9999	-0.12	22	22
MET	0	0.047	-9999	-0.12	70	70
GNA14	0.02	0.02	-9999	-0.12	11	11
GNA15	0.021	0.017	-9999	-0.12	8	8
GIT1	0.022	0.012	-9999	-0.12	4	4
mol:PI-4-5-P2	0	0	-9999	-0.001	26	26
GNA11	0.022	0.014	-9999	-0.12	5	5
LHCGR	0.022	0.014	-9999	-0.12	5	5
AGTR1	0.022	0.012	-9999	-0.12	4	4
desensitization of G-protein coupled receptor protein signaling pathway	0.023	0.016	-9999	-0.14	3	3
IPCEF1/ARNO	0.026	0.038	-9999	-0.084	41	41
alphaIIb/beta3 Integrin	0.01	0.053	-9999	-0.14	38	38

×

EPO signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.015	0.15	-9999	-0.51	27	27
CRKL	0.029	0.037	-9999	-0.1	8	8
mol:DAG	0.026	0.075	-9999	-0.2	44	44
HRAS	0.032	0.045	-9999	-0.14	10	10
MAPK8	0.021	0.041	-9999	-0.11	43	43
RAP1A	0.026	0.045	-9999	-0.17	14	14
GAB1	0.027	0.038	-9999	-0.11	10	10
MAPK14	0.022	0.041	-9999	-0.11	44	44
EPO	0.025	0.008	-9999	-0.12	1	1
PLCG1	0.026	0.076	-9999	-0.2	44	44
EPOR/TRPC2/IP3 Receptors	0.022	0.022	-9999	-0.12	12	12
RAPGEF1	0.023	0	-9999	-10000	0	0
EPO/EPOR (dimer)/SOCS3	0.035	0.043	-9999	-0.11	32	32
GAB1/SHC/GRB2/SOS1	0.042	0.052	-9999	-0.14	11	11
EPO/EPOR (dimer)	0.034	0.022	-9999	-0.088	11	11
IRS2	0.028	0.038	-9999	-0.11	9	9
STAT1	0.02	0.1	-9999	-0.26	53	53
STAT5B	0.032	0.076	-9999	-0.2	40	40
cell proliferation	0.02	0.038	-9999	-0.1	44	44
GAB1/SHIP/PIK3R1/SHP2/SHC	0.022	0.046	-9999	-0.13	13	13
TEC	0.02	0.045	-9999	-0.13	22	22
SOCS3	0.015	0.032	-9999	-0.12	28	28
STAT1 (dimer)	0.021	0.098	-9999	-0.25	53	53
JAK2	0.019	0.025	-9999	-0.12	16	16
PIK3R1	0.015	0.031	-9999	-0.12	27	27
EPO/EPOR (dimer)/JAK2	0.058	0.054	-9999	-0.12	8	8
EPO/EPOR	0.034	0.022	-9999	-0.088	11	11
LYN	0.022	0.014	-9999	-0.12	4	4
TEC/VAV2	0.021	0.059	-9999	-0.13	29	29
elevation of cytosolic calcium ion concentration	0.022	0.022	-9999	-0.12	12	12
SHC1	0.023	0.001	-9999	-10000	0	0
EPO/EPOR (dimer)/LYN	0.039	0.052	-9999	-0.13	43	43
mol:IP3	0.026	0.075	-9999	-0.2	44	44
PI3K regualtory subunit polypeptide 1/IRS2/SHIP	0.029	0.047	-9999	-0.14	15	15
SH2B3	0.024	0.004	-9999	-10000	0	0
NFKB1	0.018	0.053	-9999	-0.15	43	43
EPO/EPOR (dimer)/JAK2/SOCS3	-0.006	0.06	-9999	-0.17	64	64
PTPN6	0.025	0.038	-9999	-0.11	10	10
TEC/VAV2/GRB2	0.029	0.062	-9999	-0.13	23	23
EPOR	0.022	0.022	-9999	-0.12	12	12
INPP5D	0	0	-9999	-10000	0	0
mol:GDP	0.042	0.053	-9999	-0.14	11	11
SOS1	0.017	0.027	-9999	-0.12	20	20
PLCG2	0.02	0.02	-9999	-0.12	11	11
CRKL/CBL/C3G	0.053	0.042	-9999	-0.13	4	4
VAV2	0.027	0.037	-9999	-0.1	8	8
CBL	0.029	0.038	-9999	-0.12	8	8
SHC/Grb2/SOS1	0.03	0.045	-9999	-0.13	16	16
STAT5A	0.03	0.079	-9999	-0.23	33	33
GRB2	0.023	0.006	-9999	-0.12	1	1
STAT5 (dimer)	0.049	0.088	-9999	-0.24	31	31
LYN/PLCgamma2	0.02	0.05	-9999	-0.13	54	54
PTPN11	0.022	0.011	-9999	-0.12	3	3
BTK	0.022	0.047	-9999	-0.15	20	20
BCL2	0.019	0.12	-9999	-0.37	34	34

×

Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.023	0.009	-10000	0	-0.12	2	2
RAS family/GTP/Tiam1	0	0.066	-10000	0	-0.16	64	64
NT3 (dimer)/TRKC	0.007	0.051	-10000	0	-0.15	19	19
NT3 (dimer)/TRKB	0.023	0.047	-10000	0	-0.12	19	19
SHC/Grb2/SOS1/GAB1/PI3K	0.003	0.087	-10000	0	-0.31	22	22
RAPGEF1	0.023	0	-10000	0	-10000	0	0
BDNF	0.022	0.011	-10000	0	-0.12	3	3
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
DYNLT1	0.018	0.023	-10000	0	-0.12	14	14
NTRK1	0.023	0.006	-10000	0	-0.12	1	1
NTRK2	0.019	0.026	-10000	0	-0.12	18	18
NTRK3	0.015	0.033	-10000	0	-0.12	31	31
NT-4/5 (dimer)/TRKB	0.027	0.02	-10000	0	-0.064	25	25
neuron apoptosis	-0.043	0.036	-10000	0	-10000	0	0
SHC 2-3/Grb2	0.045	0.038	-10000	0	-10000	0	0
SHC1	0.023	0.001	-10000	0	-10000	0	0
SHC2	0.027	0.034	-10000	0	-10000	0	0
SHC3	0.027	0.034	-10000	0	-10000	0	0
STAT3 (dimer)	-0.02	0.1	-10000	0	-0.25	86	86
NT3 (dimer)/TRKA	0.025	0.044	-10000	0	-0.13	11	11
RIN/GDP	0.03	0.061	-10000	0	-0.19	26	26
GIPC1	0.019	0.023	-10000	0	-0.12	15	15
KRAS	0.014	0.034	-10000	0	-0.12	33	33
DNAJA3	0.009	0.042	0.16	13	-0.14	8	21
RIN/GTP	0.017	0.007	-10000	0	-0.077	3	3
CCND1	-0.058	0.18	-10000	0	-0.48	85	85
MAGED1	0.02	0.019	-10000	0	-0.12	10	10
PTPN11	0.022	0.011	-10000	0	-0.12	3	3
RICS	0.017	0.027	-10000	0	-0.12	20	20
NT-4/5 (dimer)	0	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1	0.035	0.041	-10000	0	-0.12	30	30
GRB2	0.023	0.006	-10000	0	-0.12	1	1
NGF (dimer)/TRKA/MATK	0.031	0.01	-10000	0	-0.07	5	5
TRKA/NEDD4-2	0.022	0.043	-10000	0	-0.11	50	50
ELMO1	0.01	0.041	-10000	0	-0.12	49	49
RhoG/GTP/ELMO1/DOCK1	0.009	0.049	-10000	0	-0.088	108	108
NGF	0	0	-10000	0	-10000	0	0
HRAS	0.023	0.006	-10000	0	-0.12	1	1
DOCK1	0.019	0.02	-10000	0	-0.12	10	10
GAB2	0.007	0.041	-10000	0	-0.12	50	50
RIT2	0.022	0.011	-10000	0	-0.12	3	3
RIT1	0.021	0.014	-10000	0	-0.12	5	5
FRS2	0.019	0.024	-10000	0	-0.12	15	15
DNM1	0.021	0.019	-10000	0	-0.12	10	10
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.021	0.016	-10000	0	-0.12	7	7
SH2B1 (homopentamer)	0	0	-10000	0	-10000	0	0
RhoG/GTP	0.006	0.044	0.13	3	-0.14	12	15
mol:GDP	0.027	0.083	-10000	0	-0.28	26	26
NGF (dimer)	0	0	-10000	0	-10000	0	0
RhoG/GDP	0.003	0.039	-10000	0	-0.097	69	69
RIT1/GDP	0.029	0.064	-10000	0	-0.2	26	26
TIAM1	0.015	0.032	-10000	0	-0.12	28	28
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
BDNF (dimer)/TRKB	0.043	0.021	-10000	0	-0.11	3	3
KIDINS220/CRKL/C3G	0.034	0.01	-10000	0	-0.14	1	1
SHC/RasGAP	0.025	0.039	-10000	0	-0.14	29	29
FRS2 family/SHP2	0.035	0.041	-10000	0	-0.12	30	30
SHC/GRB2/SOS1/GAB1	0.043	0.047	-10000	0	-0.1	41	41
RIT1/GTP	0.012	0.028	-10000	0	-0.13	20	20
NT3 (dimer)	-0.003	0.056	-10000	0	-0.12	101	101
RAP1/GDP	0.017	0.056	-10000	0	-0.17	28	28
KIDINS220/CRKL	0.023	0.009	-10000	0	-0.12	2	2
BDNF (dimer)	0.022	0.011	-10000	0	-0.12	3	3
ubiquitin-dependent protein catabolic process	0.02	0.035	-10000	0	-0.09	50	50
Schwann cell development	-0.004	0.009	-10000	0	-0.057	2	2
EHD4	0.023	0.001	-10000	0	-10000	0	0
FRS2 family/GRB2/SOS1	0.042	0.05	-10000	0	-0.11	38	38
FRS2 family/SHP2/CRK family/C3G/GAB2	0.012	0.065	-10000	0	-0.21	19	19
RAP1B	0.019	0.02	-10000	0	-0.12	10	10
RAP1A	0.021	0.012	-10000	0	-0.12	3	3
CDC42/GTP	0.031	0.04	-10000	0	-0.15	4	4
ABL1	0.022	0.007	-10000	0	-0.12	1	1
SH2B family/GRB2/SOS1	0.021	0.045	-10000	0	-0.15	29	29
Rap1/GTP	0.023	0.081	-10000	0	-0.26	34	34
STAT3	-0.02	0.1	-10000	0	-0.25	86	86
axon guidance	0.02	0.034	-10000	0	-0.15	4	4
MAPK3	0.024	0.013	-10000	0	-0.21	1	1
MAPK1	0.024	0.014	-10000	0	-0.21	1	1
CDC42/GDP	0.03	0.062	-10000	0	-0.19	26	26
NTF3	-0.003	0.056	-10000	0	-0.12	101	101
NTF4	0	0	-10000	0	-10000	0	0
NGF (dimer)/TRKA/FAIM	0.03	0.012	-10000	0	-0.073	7	7
PI3K	0.007	0.065	-10000	0	-0.13	96	96
FRS3	0.023	0.009	-10000	0	-0.12	2	2
FAIM	0.022	0.012	-10000	0	-0.12	4	4
GAB1	0.02	0.021	-10000	0	-0.12	12	12
RASGRF1	0.01	0.041	0.16	13	-0.14	8	21
SOS1	0.017	0.027	-10000	0	-0.12	20	20
MCF2L	0.008	0.039	-10000	0	-0.12	19	19
RGS19	0.023	0	-10000	0	-10000	0	0
CDC42	0.023	0.002	-10000	0	-10000	0	0
RAS family/GTP	0.018	0.11	-10000	0	-0.32	46	46
Rac1/GDP	0.03	0.062	-10000	0	-0.19	26	26
NGF (dimer)/TRKA/GRIT	0.022	0.034	-10000	0	-0.12	26	26
neuron projection morphogenesis	-0.04	0.18	-10000	0	-0.82	20	20
NGF (dimer)/TRKA/NEDD4-2	0.021	0.036	-10000	0	-0.09	50	50
MAP2K1	0.022	0.035	-10000	0	-0.089	41	41
NGFR	0.021	0.017	-10000	0	-0.12	8	8
NGF (dimer)/TRKA/GIPC/GAIP	0.019	0.048	-10000	0	-0.14	42	42
RAS family/GTP/PI3K	-0.003	0.084	-10000	0	-0.18	87	87
FRS2 family/SHP2/GRB2/SOS1	0.047	0.058	-10000	0	-0.2	12	12
NRAS	0.022	0.011	-10000	0	-0.12	3	3
GRB2/SOS1	0.021	0.045	-10000	0	-0.15	29	29
PRKCI	0.016	0.028	-10000	0	-0.12	22	22
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCZ	0.023	0	-10000	0	-10000	0	0
MAPKKK cascade	0.027	0.033	-10000	0	-0.4	2	2
RASA1	0.021	0.012	-10000	0	-0.12	3	3
TRKA/c-Abl	0.029	0.031	-10000	0	-0.14	18	18
SQSTM1	0.021	0.014	-10000	0	-0.12	5	5
BDNF (dimer)/TRKB/GIPC	0.041	0.049	-10000	0	-0.1	42	42
NGF (dimer)/TRKA/p62/Atypical PKCs	0.033	0.053	-10000	0	-0.097	67	67
MATK	0.022	0.014	-10000	0	-0.12	5	5
NEDD4L	0.017	0.027	-10000	0	-0.12	20	20
RAS family/GDP	-0.013	0.034	-10000	0	-0.14	28	28
NGF (dimer)/TRKA	0.003	0.036	-10000	0	-0.15	8	8
Rac1/GTP	-0.017	0.041	-10000	0	-0.13	42	42
FRS2 family/SHP2/CRK family	0.056	0.042	-10000	0	-0.13	6	6

×

Regulation of nuclear SMAD2/3 signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EP300	0.02	0.011	-10000	0	-0.12	2	2
HSPA8	0.023	0.003	-10000	0	-10000	0	0
SMAD3/SMAD4/ER alpha	0.061	0.084	0.2	44	-0.14	29	73
AKT1	0.023	0.021	-10000	0	-0.1	15	15
GSC	0.024	0.078	-10000	0	-1.2	2	2
NKX2-5	0.022	0.015	-10000	0	-0.047	19	19
muscle cell differentiation	-0.039	0.08	0.28	19	-10000	0	19
SMAD2-3/SMAD4/SP1	0.048	0.094	-10000	0	-0.23	19	19
SMAD4	0.024	0.039	-10000	0	-0.14	13	13
CBFB	0.022	0.009	-10000	0	-0.12	2	2
SAP18	0.023	0.003	-10000	0	-10000	0	0
Cbp/p300/MSG1	0.026	0.052	-10000	0	-0.14	37	37
SMAD3/SMAD4/VDR	0.047	0.073	-10000	0	-0.16	31	31
MYC	0.013	0.029	0.098	5	-0.13	20	25
CDKN2B	0.03	0.12	-10000	0	-1.2	5	5
AP1	0.005	0.1	-10000	0	-0.22	68	68
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1	0.006	0.12	-10000	0	-0.32	48	48
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1	0.039	0.055	-10000	0	-0.28	10	10
SP3	0.02	0.015	-10000	0	-0.042	8	8
CREB1	0.023	0.003	-10000	0	-10000	0	0
FOXH1	0.024	0.018	-10000	0	-0.11	6	6
SMAD3/SMAD4/GR	0.036	0.07	0.18	1	-0.15	36	37
GATA3	0.026	0.021	-10000	0	-0.12	11	11
SKI/SIN3/HDAC complex/NCoR1	0.02	0.078	-10000	0	-0.25	27	27
MEF2C/TIF2	0.042	0.064	-10000	0	-0.2	24	24
endothelial cell migration	0.014	0.11	1.2	3	-10000	0	3
MAX	0.023	0.006	0.076	2	-10000	0	2
RBBP7	0.022	0.012	-10000	0	-0.12	3	3
RBBP4	0.021	0.014	-10000	0	-0.12	5	5
RUNX2	0.019	0.023	-10000	0	-0.12	15	15
RUNX3	0.018	0.028	-10000	0	-0.12	22	22
RUNX1	0.019	0.022	-10000	0	-0.12	13	13
CTBP1	0.021	0.016	-10000	0	-0.12	7	7
NR3C1	0.021	0.016	0.074	3	-0.13	5	8
VDR	0.019	0.022	-10000	0	-0.12	13	13
CDKN1A	0.017	0.065	-10000	0	-0.53	1	1
KAT2B	-0.001	0.002	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1	0.055	0.053	-10000	0	-0.2	10	10
DCP1A	0.023	0.001	-10000	0	-10000	0	0
SKI	0.023	0.011	-10000	0	-0.12	3	3
SERPINE1	-0.014	0.11	-10000	0	-1.2	3	3
SMAD3/SMAD4/ATF2	0.041	0.064	-10000	0	-0.17	22	22
SMAD3/SMAD4/ATF3	0.035	0.062	-10000	0	-0.13	25	25
SAP30	0.023	0.001	-10000	0	-10000	0	0
Cbp/p300/PIAS3	0.027	0.051	0.14	2	-0.14	38	40
JUN	-0.008	0.098	-10000	0	-0.22	67	67
SMAD3/SMAD4/IRF7	0.051	0.058	-10000	0	-0.17	13	13
TFE3	0.018	0.032	-10000	0	-0.082	44	44
COL1A2	-0.13	0.26	-10000	0	-0.64	112	112
mesenchymal cell differentiation	-0.041	0.057	0.15	15	-10000	0	15
DLX1	0.021	0.017	-10000	0	-0.12	8	8
TCF3	0.022	0.014	-10000	0	-0.12	5	5
FOS	-0.004	0.055	-10000	0	-0.11	105	105
SMAD3/SMAD4/Max	0.046	0.056	0.18	1	-0.16	9	10
Cbp/p300/SNIP1	0.033	0.047	-10000	0	-0.13	36	36
ZBTB17	0.022	0.006	0.081	5	-10000	0	5
LAMC1	0.021	0.083	-10000	0	-0.26	38	38
TGIF2/HDAC complex/SMAD3/SMAD4	0.04	0.061	-10000	0	-0.15	23	23
IRF7	0.024	0.017	-10000	0	-0.12	7	7
ESR1	0.033	0.037	0.099	99	-0.13	10	109
HNF4A	0.023	0.009	-10000	0	-0.12	2	2
MEF2C	0.034	0.061	-10000	0	-0.22	23	23
SMAD2-3/SMAD4	0.05	0.063	-10000	0	-0.19	11	11
Cbp/p300/Src-1	0.029	0.053	-10000	0	-0.14	46	46
IGHV3OR16-13	0.005	0.075	-10000	0	-0.49	12	12
TGIF2/HDAC complex	0.021	0.013	-10000	0	-0.12	4	4
CREBBP	0.02	0.016	-10000	0	-0.13	6	6
SKIL	0.011	0.035	-10000	0	-0.12	35	35
HDAC1	0.02	0.02	-10000	0	-0.12	10	10
HDAC2	0.02	0.021	-10000	0	-0.12	12	12
SNIP1	0.023	0.011	-10000	0	-0.12	3	3
GCN5L2	0.021	0.013	-10000	0	-0.12	4	4
SMAD3/SMAD4/TFE3	0.047	0.072	-10000	0	-0.16	37	37
MSG1/HSC70	0.027	0.032	-10000	0	-0.082	42	42
SMAD2	0.027	0.015	-10000	0	-0.068	7	7
SMAD3	0.022	0.036	-10000	0	-0.1	21	21
SMAD3/E2F4-5/DP1/p107/SMAD4	0.024	0.067	-10000	0	-0.18	33	33
SMAD2/SMAD2/SMAD4	-0.001	0.043	0.12	2	-0.2	16	18
NCOR1	0.022	0.009	-10000	0	-0.12	2	2
NCOA2	0.021	0.013	-10000	0	-0.12	4	4
NCOA1	0.022	0.009	-10000	0	-0.12	2	2
MYOD/E2A	0.032	0.016	-10000	0	-0.077	12	12
SMAD2-3/SMAD4/SP1/MIZ-1	0.061	0.091	-10000	0	-0.22	17	17
IFNB1	0.035	0.044	-10000	0	-0.17	8	8
SMAD3/SMAD4/MEF2C	0.059	0.076	-10000	0	-0.22	20	20
CITED1	0.014	0.035	-10000	0	-0.12	35	35
SMAD2-3/SMAD4/ARC105	0.062	0.061	-10000	0	-0.17	10	10
RBL1	0.019	0.022	-10000	0	-0.12	13	13
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB	0.042	0.067	-10000	0	-0.4	8	8
RUNX1-3/PEBPB2	0.035	0.04	-10000	0	-0.12	27	27
SMAD7	-0.003	0.14	-10000	0	-0.42	28	28
MYC/MIZ-1	0.003	0.063	0.17	5	-0.13	93	98
SMAD3/SMAD4	-0.018	0.098	0.29	2	-0.3	37	39
IL10	0.039	0.044	-10000	0	-0.18	7	7
PIASy/HDAC complex	0.024	0.004	-10000	0	-10000	0	0
PIAS3	0.019	0.022	-10000	0	-0.12	13	13
CDK2	0.017	0.023	-10000	0	-0.12	14	14
IL5	0.039	0.044	-10000	0	-0.2	6	6
CDK4	0.018	0.019	-10000	0	-0.12	9	9
PIAS4	0.024	0.004	-10000	0	-10000	0	0
ATF3	0.011	0.04	-10000	0	-0.12	47	47
SMAD3/SMAD4/SP1	0.027	0.09	-10000	0	-0.21	30	30
FOXG1	0.02	0.019	-10000	0	-0.12	10	10
FOXO3	0.023	0.02	-10000	0	-0.07	23	23
FOXO1	0.025	0.017	-10000	0	-0.071	17	17
FOXO4	0.025	0.016	-10000	0	-0.072	15	15
heart looping	0.034	0.06	-10000	0	-0.22	23	23
CEBPB	0.017	0.033	-10000	0	-0.11	34	34
SMAD3/SMAD4/DLX1	0.044	0.055	-10000	0	-0.16	13	13
MYOD1	0.022	0.015	-10000	0	-0.12	6	6
SMAD3/SMAD4/HNF4	0.045	0.053	-10000	0	-0.14	14	14
SMAD3/SMAD4/GATA3	0.059	0.059	-10000	0	-0.2	7	7
SnoN/SIN3/HDAC complex/NCoR1	0.011	0.035	-10000	0	-0.12	35	35
SMAD3/SMAD4/RUNX1-3/PEBPB2	0.058	0.062	-10000	0	-0.13	18	18
SMAD3/SMAD4/SP1-3	0.042	0.097	-10000	0	-0.21	34	34
MED15	0.022	0.012	-10000	0	-0.12	4	4
SP1	-0.004	0.053	-10000	0	-0.093	113	113
SIN3B	0.022	0.015	-10000	0	-0.12	6	6
SIN3A	0.022	0.014	-10000	0	-0.12	5	5
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5	0.071	0.061	-10000	0	-0.16	21	21
ITGB5	0.007	0.094	-10000	0	-0.28	39	39
TGIF/SIN3/HDAC complex/CtBP	0.022	0.078	-10000	0	-0.27	22	22
SMAD3/SMAD4/AR	0.016	0.077	-10000	0	-0.14	61	61
AR	0.009	0.038	-10000	0	-0.12	43	43
negative regulation of cell growth	0.026	0.073	-10000	0	-0.22	32	32
SMAD3/SMAD4/MYOD	0.044	0.055	-10000	0	-0.17	12	12
E2F5	0.02	0.02	-10000	0	-0.12	11	11
E2F4	0.022	0.012	-10000	0	-0.12	4	4
SMAD2/SMAD2/SMAD4/FOXH1/SMIF	0.069	0.058	-10000	0	-0.16	12	12
SMAD2-3/SMAD4/FOXO1-3a-4	0.041	0.061	-10000	0	-0.31	10	10
TFDP1	0.019	0.023	-10000	0	-0.12	14	14
SMAD3/SMAD4/AP1	0.012	0.11	-10000	0	-0.23	65	65
SMAD3/SMAD4/RUNX2	0.041	0.057	-10000	0	-0.15	15	15
TGIF2	0.021	0.013	-10000	0	-0.12	4	4
TGIF1	0.023	0	-10000	0	-10000	0	0
ATF2	0.022	0.004	-10000	0	-10000	0	0

×

Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer	0.029	0.045	-10000	0	-0.11	31	31
fibroblast growth factor receptor signaling pathway	0.028	0.044	-10000	0	-0.11	31	31
LAMA1	0	0.053	-10000	0	-0.12	89	89
PRNP	0.021	0.015	-10000	0	-0.12	5	5
GPC1/SLIT2	-0.011	0.07	-10000	0	-0.14	101	101
SMAD2	0.024	0.028	-10000	0	-0.1	18	18
GPC1/PrPc/Cu2+	0.021	0.036	-10000	0	-0.12	33	33
GPC1/Laminin alpha1	0.015	0.043	-10000	0	-0.076	101	101
TDGF1	0.022	0.015	-10000	0	-0.12	6	6
CRIPTO/GPC1	0.032	0.017	-10000	0	-0.076	14	14
APP/GPC1	0.023	0.043	-10000	0	-0.13	41	41
mol:NO	0	0	-10000	0	-10000	0	0
YES1	0.024	0.016	-10000	0	-0.11	1	1
FLT1	0.022	0.014	-10000	0	-0.12	5	5
GPC1/TGFB/TGFBR1/TGFBR2	0.039	0.033	-10000	0	-0.11	18	18
SERPINC1	0.023	0.009	-10000	0	-0.12	2	2
FYN	0.019	0.024	-10000	0	-0.11	1	1
FGR	0.026	0.014	-10000	0	-0.11	1	1
positive regulation of MAPKKK cascade	0.016	0.052	-10000	0	-0.18	17	17
SLIT2	0.001	0.047	-10000	0	-0.12	71	71
GPC1/NRG	0.031	0.019	-10000	0	-0.14	2	2
NRG1	0.021	0.017	-10000	0	-0.12	8	8
GPC1/VEGF165 homodimer/VEGFR1 homodimer	0.032	0.046	-10000	0	-0.12	41	41
LYN	0.024	0.015	-10000	0	-0.11	1	1
mol:Spermine	0.011	0.01	-10000	0	-0.077	7	7
cell growth	0.028	0.044	-10000	0	-0.11	31	31
BMP signaling pathway	-0.021	0.016	0.12	7	-10000	0	7
SRC	0.026	0.015	-10000	0	-0.11	2	2
TGFBR1	0.022	0.011	-10000	0	-0.12	3	3
mol:Cu2+	0	0	-10000	0	-10000	0	0
PLA2G2A	0.011	0.041	-10000	0	-0.12	48	48
GPC1	0.021	0.016	-10000	0	-0.12	7	7
TGFBR1 (dimer)	0.022	0.011	-10000	0	-0.12	3	3
VEGFA	0.019	0.021	-10000	0	-0.12	11	11
BLK	0.025	0.016	-10000	0	-0.11	2	2
HCK	0.023	0.019	-10000	0	-0.17	1	1
FGF2	0.023	0.009	-10000	0	-0.12	2	2
FGFR1	0.008	0.043	-10000	0	-0.12	54	54
VEGFR1 homodimer	0.022	0.014	-10000	0	-0.12	5	5
TGFBR2	0.02	0.02	-10000	0	-0.12	11	11
cell death	0.023	0.043	-10000	0	-0.13	41	41
ATIII/GPC1	0.033	0.015	-10000	0	-0.078	10	10
PLA2G2A/GPC1	0.023	0.034	-10000	0	-0.076	57	57
LCK	0.025	0.016	-10000	0	-0.17	1	1
neuron differentiation	0.031	0.019	-10000	0	-0.14	2	2
PrPc/Cu2+	0.007	0.039	-10000	0	-0.14	37	37
APP	0.022	0.008	-10000	0	-0.12	1	1
TGFBR2 (dimer)	0.02	0.02	-10000	0	-0.12	11	11

×

EGFR-dependent Endothelin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HRAS	0.023	0.006	-9999	-0.12	1	1
EGFR	0.015	0.03	-9999	-0.12	25	25
EGF/EGFR	0.013	0.053	-9999	-0.092	80	80
EGF/EGFR dimer/SHC/GRB2/SOS1	0.041	0.058	-9999	-0.17	9	9
mol:GTP	0	0	-9999	-10000	0	0
EDNRA	0.014	0.035	-9999	-0.12	34	34
response to oxidative stress	0	0	-9999	-10000	0	0
EGF	0.02	0.021	-9999	-0.12	12	12
EGF/EGFR dimer/SHC	0.03	0.046	-9999	-0.11	40	40
mol:GDP	0.036	0.056	-9999	-0.17	9	9
mol:Ca2+	0	0	-9999	-10000	0	0
EDN1	0.009	0.043	-9999	-0.12	54	54
GRB2/SOS1	0.021	0.045	-9999	-0.15	29	29
HRAS/GTP	0.023	0.045	-9999	-0.16	9	9
SHC1	0.023	0.001	-9999	-10000	0	0
HRAS/GDP	0.036	0.052	-9999	-0.16	9	9
FRAP1	0.016	0.044	-9999	-0.16	11	11
EGF/EGFR dimer	0.016	0.05	-9999	-0.14	40	40
SOS1	0.017	0.027	-9999	-0.12	20	20
GRB2	0.023	0.006	-9999	-0.12	1	1
ETA receptor/Endothelin-1	0.008	0.056	-9999	-0.16	34	34

×

p38 MAPK signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TRAF6/ASK1	0.008	0.054	-9999	-0.15	53	53
TRAF2/ASK1	0.022	0.033	-9999	-0.091	42	42
ATM	0.018	0.022	-9999	-0.12	13	13
MAP2K3	-0.002	0.12	-9999	-0.32	63	63
response to stress	0	0	-9999	-10000	0	0
MAP2K6	-0.012	0.12	-9999	-0.27	70	70
hyperosmotic response	0	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
GADD45G	0.015	0.033	-9999	-0.12	30	30
TXN	-0.003	0.051	-9999	-0.21	33	33
CALM1	0.022	0.014	-9999	-0.12	5	5
GADD45A	0.014	0.032	-9999	-0.12	29	29
GADD45B	0.016	0.029	-9999	-0.12	24	24
MAP3K1	0.021	0.015	-9999	-0.12	6	6
MAP3K6	0.022	0.012	-9999	-0.12	4	4
MAP3K7	0.021	0.014	-9999	-0.12	5	5
MAP3K4	0.023	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
ASK1/ASK2	0.023	0.041	-9999	-0.14	26	26
TAK1/TAB family	-0.002	0.072	-9999	-0.32	25	25
RAC1/OSM/MEKK3	0.043	0.015	-9999	-0.097	6	6
TRAF2	0.023	0	-9999	-10000	0	0
RAC1/OSM/MEKK3/MKK3	0.016	0.1	-9999	-0.25	63	63
TRAF6	0.004	0.058	-9999	-0.21	36	36
RAC1	0.023	0.002	-9999	-10000	0	0
mol:LPS	0	0	-9999	-10000	0	0
CAMK2B	0.023	0.009	-9999	-0.12	2	2
CCM2	0.023	0.001	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB	0.029	0.019	-9999	-0.093	13	13
MAPK11	0.023	0	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB/ASK1	0.033	0.037	-9999	-0.1	32	32
OSM/MEKK3	0.034	0.007	-9999	-0.14	1	1
TAOK1	-0.001	0.067	-9999	-0.22	43	43
TAOK2	0.003	0.056	-9999	-0.2	38	38
TAOK3	-0.003	0.067	-9999	-0.21	50	50
MAP3K7IP1	0.023	0	-9999	-10000	0	0
MAPK14	0.023	0.007	-9999	-0.12	1	1
MAP3K7IP2	0.02	0.016	-9999	-0.12	6	6
MAP3K5	0.018	0.025	-9999	-0.12	17	17
MAP3K10	0.022	0.015	-9999	-0.12	6	6
MAP3K3	0.023	0	-9999	-10000	0	0
TRX/ASK1	0.009	0.051	-9999	-0.18	33	33
GADD45/MTK1/MTK1	0.025	0.057	-9999	-0.095	79	79

×

S1P5 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-10000	0	-10000	0	0
telencephalon oligodendrocyte cell migration	-0.007	0.066	0.21	23	-10000	0	23
GNAI2	0.022	0.011	-10000	0	-0.12	3	3
S1P/S1P5/G12	0.016	0.006	-10000	0	-0.12	1	1
mol:GDP	0	0	-10000	0	-10000	0	0
GNAO1	0.01	0.042	-10000	0	-0.12	51	51
RhoA/GTP	0.007	0.067	-10000	0	-0.21	23	23
negative regulation of cAMP metabolic process	-0.003	0.068	-10000	0	-0.15	86	86
GNAZ	0.022	0.011	-10000	0	-0.12	3	3
GNAI3	0.021	0.008	-10000	0	-0.12	1	1
GNA12	0.023	0.001	-10000	0	-10000	0	0
S1PR5	0	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
S1P/S1P5/Gi	-0.003	0.069	-10000	0	-0.15	86	86
RhoA/GDP	0.016	0.016	-10000	0	-0.14	6	6
RHOA	0.023	0.006	-10000	0	-0.12	1	1
GNAI1	0.012	0.035	-10000	0	-0.12	35	35

×

Regulation of p38-alpha and p38-beta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
RIP1/MEKK3	0.03	0.016	-9999	-0.095	9	9
response to insulin stimulus	0	0	-9999	-10000	0	0
RIPK1	0.022	0.011	-9999	-0.12	3	3
response to stress	0	0	-9999	-10000	0	0
MAP2K6	0.013	0.034	-9999	-0.12	33	33
mol:GTP	0	0	-9999	-10000	0	0
MAP2K4	0.022	0.011	-9999	-0.12	3	3
RAC1-CDC42/GTP/PAK family	0.007	0.055	-9999	-0.15	50	50
response to UV	0	0	-9999	-10000	0	0
YES1	0.02	0.018	-9999	-0.12	8	8
interleukin-1 receptor activity	0	0	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
MAP3K3	0.023	0	-9999	-10000	0	0
FYN	0.011	0.037	-9999	-0.12	40	40
MAP3K12	0.022	0.011	-9999	-0.12	3	3
FGR	0.023	0.006	-9999	-0.12	1	1
p38 alpha/TAB1	0.019	0.083	-9999	-0.2	45	45
PRKG1	0.018	0.026	-9999	-0.12	19	19
DUSP8	0.023	0.006	-9999	-0.12	1	1
PGK/cGMP/p38 alpha	0.013	0.08	-9999	-0.2	45	45
apoptosis	0.018	0.08	-9999	-0.19	45	45
RAL/GTP	0.024	0.033	-9999	-0.11	29	29
LYN	0.021	0.013	-9999	-0.12	4	4
DUSP1	-0.004	0.052	-9999	-0.12	90	90
PAK1	0.016	0.029	-9999	-0.12	23	23
SRC	0.023	0.009	-9999	-0.12	2	2
RAC1/OSM/MEKK3/MKK3	0.057	0.021	-9999	-0.093	11	11
TRAF6	0.022	0.009	-9999	-0.12	2	2
RAC1	0.023	0.002	-9999	-10000	0	0
epidermal growth factor receptor activity	0	0	-9999	-10000	0	0
mol:LPS	0	0	-9999	-10000	0	0
mol:cGMP	0	0	-9999	-10000	0	0
CCM2	0.023	0.001	-9999	-10000	0	0
RAC1-CDC42/GTP	0.03	0.019	-9999	-0.13	7	7
MAPK11	0.004	0.1	-9999	-0.24	54	54
BLK	0.022	0.015	-9999	-0.12	6	6
HCK	0.019	0.024	-9999	-0.12	15	15
MAP2K3	0.023	0.006	-9999	-0.12	1	1
DUSP16	0.018	0.026	-9999	-0.12	18	18
DUSP10	0.012	0.036	-9999	-0.12	36	36
TRAF6/MEKK3	0.028	0.017	-9999	-0.093	11	11
MAP3K7IP1	0.023	0	-9999	-10000	0	0
MAPK14	0.01	0.087	-9999	-0.22	47	47
positive regulation of innate immune response	0.007	0.11	-9999	-0.27	52	52
LCK	0.022	0.015	-9999	-0.12	6	6
p38alpha-beta/MKP7	0.013	0.11	-9999	-0.27	48	48
p38alpha-beta/MKP5	0.005	0.12	-9999	-0.26	59	59
PGK/cGMP	0.014	0.017	-9999	-0.077	19	19
PAK2	0.022	0.011	-9999	-0.12	3	3
p38alpha-beta/MKP1	-0.007	0.12	-9999	-0.27	67	67
CDC42	0.023	0.002	-9999	-10000	0	0
RALB	0.022	0.007	-9999	-0.12	1	1
RALA	0.022	0.009	-9999	-0.12	2	2
PAK3	0.008	0.044	-9999	-0.12	59	59

×

Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaV beta3 Integrin	-0.018	0.081	-9999	-0.16	107	107
AKT1	0.019	0.12	-9999	-0.32	32	32
PTK2B	-0.005	0.081	-9999	-0.2	49	49
VEGFR2 homodimer/Frs2	0.025	0.058	-9999	-0.29	7	7
CAV1	0.012	0.039	-9999	-0.12	43	43
CALM1	0.022	0.014	-9999	-0.12	5	5
VEGFR2 homodimer/VEGFA homodimer/Frs2	0.03	0.073	-9999	-0.24	17	17
endothelial cell proliferation	0.026	0.1	-9999	-0.31	23	23
mol:Ca2+	0.027	0.068	-9999	-0.23	18	18
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac	0.036	0.083	-9999	-0.22	28	28
RP11-342D11.1	0.019	0.062	-9999	-0.23	17	17
CDH5	0.022	0.014	-9999	-0.12	5	5
VEGFA homodimer	0.038	0.057	-9999	-0.1	69	69
SHC1	0.023	0.001	-9999	-10000	0	0
SHC2	0.023	0.009	-9999	-0.12	2	2
HRAS/GDP	0.03	0.061	-9999	-0.25	11	11
SH2D2A	0.023	0.009	-9999	-0.12	2	2
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS	0.054	0.083	-9999	-0.32	9	9
VEGFR2 homodimer/VEGFA homodimer/TsAd	0.036	0.07	-9999	-0.24	16	16
VEGFR1 homodimer	0.022	0.014	-9999	-0.12	5	5
SHC/GRB2/SOS1	0.055	0.078	-9999	-0.26	12	12
GRB10	0.029	0.073	-9999	-0.34	11	11
PTPN11	0.022	0.011	-9999	-0.12	3	3
GRB2	0.023	0.006	-9999	-0.12	1	1
PAK1	0.016	0.029	-9999	-0.12	23	23
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin	0.04	0.087	-9999	-0.21	31	31
HRAS	0.023	0.006	-9999	-0.12	1	1
VEGF/Rho/ROCK1/Integrin Complex	-0.019	0.12	-9999	-0.3	64	64
HIF1A	0.022	0.01	-9999	-0.12	2	2
FRS2	0.019	0.024	-9999	-0.12	15	15
oxygen and reactive oxygen species metabolic process	0.034	0.081	-9999	-0.22	28	28
mol:GTP	0	0	-9999	-10000	0	0
FLT4	0.023	0.009	-9999	-0.12	2	2
Nck/Pak	0.013	0.056	-9999	-0.15	50	50
VEGFR2 homodimer/VEGFA homodimer/Fyn	0.021	0.08	-9999	-0.22	24	24
mol:GDP	0.041	0.071	-9999	-0.25	12	12
mol:NADP	0.037	0.071	-9999	-0.29	9	9
eNOS/Hsp90	0.045	0.071	-9999	-0.27	9	9
PIK3R1	0.015	0.031	-9999	-0.12	27	27
mol:IP3	0.027	0.068	-9999	-0.24	18	18
HIF1A/ARNT	0.024	0.042	-9999	-0.14	34	34
SHB	0.023	0.009	-9999	-0.12	2	2
VEGFA	0.022	0.021	-9999	-0.099	14	14
VEGFC	0.018	0.028	-9999	-0.12	21	21
FAK1/Vinculin	-0.007	0.13	-9999	-0.39	33	33
mol:Ca ++	0	0	-9999	-10000	0	0
RHOA	0.023	0.006	-9999	-0.12	1	1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.007	0.095	-9999	-0.21	47	47
PTPN6	0.023	0.009	-9999	-0.12	2	2
EPAS1	0.025	0.04	-9999	-0.13	27	27
mol:L-citrulline	0.037	0.071	-9999	-0.29	9	9
ITGAV	0.013	0.032	-9999	-0.12	28	28
PIK3CA	0.02	0.017	-9999	-0.12	7	7
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2	0.042	0.074	-9999	-0.21	20	20
VEGFR2 homodimer/VEGFA homodimer	0.047	0.079	-9999	-0.25	17	17
VEGFR2/3 heterodimer	0.028	0.057	-9999	-0.28	7	7
VEGFB	0.015	0.033	-9999	-0.12	30	30
MAPK11	0.022	0.069	-9999	-0.25	17	17
VEGFR2 homodimer	0.028	0.052	-9999	-0.34	7	7
FLT1	0.022	0.014	-9999	-0.12	5	5
NEDD4	0.023	0.022	-9999	-0.12	12	12
MAPK3	0.014	0.064	-9999	-0.23	17	17
MAPK1	0.013	0.065	-9999	-0.24	17	17
VEGFA145/NRP2	0.001	0.072	-9999	-0.15	85	85
VEGFR1/2 heterodimer	0.027	0.059	-9999	-0.27	9	9
KDR	0.028	0.052	-9999	-0.34	7	7
VEGFA165/NRP1/VEGFR2 homodimer	0.032	0.084	-9999	-0.21	29	29
SRC	0.023	0.009	-9999	-0.12	2	2
platelet activating factor biosynthetic process	0.014	0.066	-9999	-0.24	16	16
PI3K	0.034	0.099	-9999	-0.3	22	22
VEGFR2 homodimer/VEGFA homodimer/NCK1	0.027	0.076	-9999	-0.22	21	21
FES	0.029	0.066	-9999	-0.23	17	17
GAB1	0.026	0.095	-9999	-0.3	25	25
VEGFR2 homodimer/VEGFA homodimer/Src	0.036	0.07	-9999	-0.24	16	16
CTNNB1	0.022	0.008	-9999	-0.12	1	1
SOS1	0.017	0.027	-9999	-0.12	20	20
ARNT	0.022	0.012	-9999	-0.12	4	4
eNOS/Caveolin-1	0.039	0.075	-9999	-0.28	10	10
VEGFR2 homodimer/VEGFA homodimer/Yes	0.028	0.076	-9999	-0.22	22	22
PI3K/GAB1	0.027	0.12	-9999	-0.34	30	30
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak	0.035	0.083	-9999	-0.19	29	29
PRKACA	0.021	0.017	-9999	-0.12	8	8
VEGFR2/3 heterodimer/VEGFC homodimer	0.036	0.06	-9999	-0.32	6	6
HSP90AA1	0.023	0.003	-9999	-10000	0	0
CDC42	0.029	0.066	-9999	-0.23	17	17
actin cytoskeleton reorganization	0.035	0.07	-9999	-0.23	16	16
PTK2	-0.016	0.13	-9999	-0.4	32	32
EDG1	0.03	0.068	-9999	-0.28	11	11
mol:DAG	0.027	0.068	-9999	-0.24	18	18
CaM/Ca2+	0.033	0.068	-9999	-0.26	12	12
MAP2K3	0.023	0.065	-9999	-0.24	14	14
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4	0.052	0.084	-9999	-0.35	11	11
PLCG1	0.027	0.069	-9999	-0.24	18	18
VEGFR2 homodimer/VEGFA homodimer/Src/Shb	0.048	0.069	-9999	-0.22	16	16
IQGAP1	0.02	0.017	-9999	-0.12	7	7
YES1	0.02	0.018	-9999	-0.12	8	8
VEGFR2 homodimer/VEGFA homodimer/SHP2	0.031	0.075	-9999	-0.24	20	20
VEGFR2 homodimer/VEGFA homodimer/SHP1	0.035	0.071	-9999	-0.24	16	16
cell migration	-0.002	0.14	-9999	-0.37	47	47
mol:PI-3-4-5-P3	0.034	0.095	-9999	-0.28	22	22
FYN	0.011	0.037	-9999	-0.12	40	40
VEGFB/NRP1	0.026	0.064	-9999	-0.21	19	19
mol:NO	0.037	0.071	-9999	-0.29	9	9
PXN	0.022	0.014	-9999	-0.12	5	5
HRAS/GTP	-0.013	0.043	-9999	-0.24	11	11
VEGFR2 homodimer/VEGFA homodimer/GRB10	0.048	0.078	-9999	-0.35	11	11
VHL	0.021	0.016	-9999	-0.12	7	7
ITGB3	0.004	0.047	-9999	-0.12	68	68
NOS3	0.037	0.076	-9999	-0.32	9	9
VEGFR2 homodimer/VEGFA homodimer/Sck	0.036	0.07	-9999	-0.24	16	16
RAC1	0.023	0.002	-9999	-10000	0	0
PRKCA	0.02	0.063	-9999	-0.22	20	20
PRKCB	0.02	0.062	-9999	-0.22	18	18
VCL	0.021	0.013	-9999	-0.12	4	4
VEGFA165/NRP1	0.033	0.065	-9999	-0.23	17	17
VEGFR1/2 heterodimer/VEGFA homodimer	0.034	0.073	-9999	-0.24	18	18
VEGFA165/NRP2	0.001	0.072	-9999	-0.15	85	85
MAPKKK cascade	0.048	0.074	-9999	-0.28	13	13
NRP2	0.011	0.036	-9999	-0.12	38	38
VEGFC homodimer	0.018	0.027	-9999	-0.12	21	21
NCK1	0.02	0.019	-9999	-0.12	9	9
ROCK1	0.022	0.009	-9999	-0.12	2	2
FAK1/Paxillin	-0.005	0.13	-9999	-0.38	33	33
MAP3K13	0.024	0.069	-9999	-0.23	19	19
PDPK1	0.029	0.085	-9999	-0.26	22	22

×

mTOR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GBL	0.023	0.009	-10000	0	-0.12	2	2
MKNK1	0.023	0.006	-10000	0	-0.12	1	1
mol:PIP3	-0.005	0.043	-10000	0	-0.14	28	28
FRAP1	0.01	0.072	-10000	0	-0.42	13	13
AKT1	0.006	0.057	0.18	19	-0.14	34	53
INSR	0.021	0.017	-10000	0	-0.12	8	8
Insulin Receptor/Insulin	0.028	0.019	-10000	0	-0.12	6	6
mol:GTP	0.022	0.057	0.18	18	-0.13	26	44
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit	-0.015	0.045	-10000	0	-0.17	33	33
TSC2	0.021	0.017	-10000	0	-0.12	8	8
RHEB/GDP	0.008	0.047	-10000	0	-0.13	33	33
TSC1	0.023	0.006	-10000	0	-0.12	1	1
Insulin Receptor/IRS1	0.02	0.029	-10000	0	-0.22	6	6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA	0.01	0.061	-10000	0	-0.2	31	31
mol:GDP	0	0	-10000	0	-10000	0	0
EIF3A	0.022	0.004	-10000	0	-10000	0	0
RPS6KB1	0.006	0.085	0.16	14	-0.3	29	43
MAP3K5	-0.004	0.058	-10000	0	-0.27	25	25
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
apoptosis	-0.004	0.058	-10000	0	-0.27	25	25
mol:LY294002	0	0	0	6	-0.001	6	12
EIF4B	0.008	0.079	0.16	14	-0.26	31	45
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.021	0.078	0.16	12	-0.24	31	43
eIF4E/eIF4G1/eIF4A1	-0.007	0.042	-10000	0	-0.24	15	15
KIAA1303	0.023	0.009	-10000	0	-0.12	2	2
PI3K	0.016	0.053	-10000	0	-0.16	24	24
mTOR/RHEB/GTP/Raptor/GBL	0.026	0.054	0.16	16	-0.15	26	42
FKBP1A	0.022	0.012	-10000	0	-0.12	4	4
RHEB/GTP	0.019	0.053	0.14	3	-0.13	33	36
mol:Amino Acids	0	0	0	6	-0.001	6	12
FKBP12/Rapamycin	0.016	0.014	-10000	0	-0.11	7	7
PDPK1	0.005	0.052	0.18	17	-0.15	20	37
EIF4E	0.023	0.001	-10000	0	-10000	0	0
ASK1/PP5C	0.005	0.14	-10000	0	-0.49	38	38
mTOR/RHEB/GTP/Raptor/GBL/eIF4E	0.032	0.061	-10000	0	-10000	0	0
TSC1/TSC2	0.025	0.061	0.19	18	-0.14	26	44
tumor necrosis factor receptor activity	0	0	0.001	6	0	6	12
RPS6	0.023	0.002	-10000	0	-10000	0	0
PPP5C	0.022	0.014	-10000	0	-0.12	5	5
EIF4G1	0.023	0.004	-10000	0	-10000	0	0
IRS1	0.006	0.028	-10000	0	-0.27	5	5
INS	0.022	0.011	-10000	0	-0.12	3	3
PTEN	0.022	0.008	-10000	0	-0.12	1	1
PDK2	0.004	0.054	0.18	17	-0.16	24	41
EIF4EBP1	0.011	0.1	-10000	0	-1.1	5	5
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PPP2R5D	0.014	0.066	-10000	0	-0.37	13	13
peptide biosynthetic process	0.022	0.018	-10000	0	-0.11	6	6
RHEB	0.019	0.022	-10000	0	-0.12	13	13
EIF4A1	0.023	0.007	-10000	0	-0.12	1	1
mol:Rapamycin	0	0.001	0.003	20	-0.002	17	37
EEF2	0.023	0.018	-10000	0	-0.12	6	6
eIF4E/4E-BP1	0.023	0.098	-10000	0	-1	5	5

×

Ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.02	0.016	-10000	0	-0.076	15	15
MAP4K4	0.003	0.068	-10000	0	-0.22	21	21
BAG4	0.022	0.012	-10000	0	-0.12	4	4
PKC zeta/ceramide	0.013	0.009	0.075	5	-10000	0	5
NFKBIA	0.016	0.028	-10000	0	-0.12	21	21
BIRC3	-0.005	0.053	-10000	0	-0.12	94	94
BAX	0.01	0.005	-10000	0	-10000	0	0
RIPK1	0.022	0.011	-10000	0	-0.12	3	3
AKT1	0.007	0.021	-10000	0	-0.13	12	12
BAD	0.001	0.01	0.068	5	-0.055	3	8
SMPD1	0.009	0.036	-10000	0	-0.14	17	17
RB1	-0.012	0.033	0.068	3	-0.092	78	81
FADD/Caspase 8	0.003	0.095	-10000	0	-0.3	29	29
MAP2K4	0	0.023	0.069	5	-0.093	27	32
NSMAF	0.021	0.014	-10000	0	-0.12	5	5
response to UV	0	0	-10000	0	-10000	0	0
RAF1	0.004	0.015	0.069	5	-0.097	7	12
EGF	0.02	0.021	-10000	0	-0.12	12	12
mol:ceramide	-0.004	0.01	0.063	7	-10000	0	7
MADD	0.023	0.006	-10000	0	-0.12	1	1
response to oxidative stress	0	0	-10000	0	-10000	0	0
mol:Free Fatty acid	0.018	0.022	-10000	0	-0.085	20	20
ASAH1	0.021	0.017	-10000	0	-0.12	7	7
negative regulation of cell cycle	-0.012	0.033	0.068	3	-0.091	78	81
cell proliferation	0.017	0.041	-10000	0	-0.12	14	14
BID	0.009	0.079	-10000	0	-0.6	4	4
MAP3K1	-0.003	0.021	0.068	5	-0.1	18	23
EIF2A	-0.007	0.043	-10000	0	-0.11	59	59
TRADD	0.023	0.006	-10000	0	-0.12	1	1
CRADD	0.023	0.009	-10000	0	-0.12	2	2
MAPK3	0.009	0.021	-10000	0	-0.1	12	12
response to heat	0	0	-10000	0	-10000	0	0
MAPK1	0.008	0.024	-10000	0	-0.12	13	13
Cathepsin D/ceramide	0.011	0.013	0.076	4	-0.056	9	13
FADD	0.004	0.068	-10000	0	-0.22	20	20
KSR1	0.001	0.01	0.068	5	-10000	0	5
MAPK8	0.005	0.039	-10000	0	-0.19	17	17
PRKRA	-0.002	0.02	0.068	5	-0.099	17	22
PDGFA	0.02	0.022	-10000	0	-0.12	13	13
TRAF2	0.023	0	-10000	0	-10000	0	0
IGF1	0.007	0.045	-10000	0	-0.12	60	60
mol:GD3	0	0	-10000	0	-10000	0	0
ganglioside biosynthetic process	-0.004	0.01	0.063	7	-10000	0	7
CTSD	0.02	0.02	-10000	0	-0.12	11	11
regulation of nitric oxide biosynthetic process	0.021	0.046	-10000	0	-0.13	47	47
response to radiation	0	0	-10000	0	-10000	0	0
ERK1/PKC delta	0.019	0.043	-10000	0	-0.13	14	14
PRKCD	0.02	0.018	-10000	0	-0.12	8	8
PRKCZ	0.023	0	-10000	0	-10000	0	0
mol:GW4869	0	0	-10000	0	-10000	0	0
mol:sphingosine	0.018	0.022	-10000	0	-0.085	20	20
RelA/NF kappa B1	0.021	0.047	-10000	0	-0.13	47	47
mol:glutathione	0	0	-10000	0	-10000	0	0
PAWR	0.023	0.009	-10000	0	-0.12	2	2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD	0.001	0.073	-10000	0	-0.24	19	19
TNFR1A/BAG4/TNF-alpha	0.038	0.034	-10000	0	-0.11	20	20
mol:Sphingosine-1-phosphate	0.02	0.016	-10000	0	-0.076	15	15
MAP2K1	0.007	0.016	0.071	1	-0.094	9	10
mol:C11AG	0	0	-10000	0	-10000	0	0
RELA	0.023	0.009	-10000	0	-0.12	2	2
CYCS	0.004	0.024	0.13	2	-0.12	14	16
TNFRSF1A	0.021	0.016	-10000	0	-0.12	7	7
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
TNFR1A/BAG4	0.027	0.034	-10000	0	-0.11	29	29
EIF2AK2	-0.008	0.036	0.069	5	-0.1	53	58
TNF-alpha/TNFR1A/FAN	0.033	0.047	-10000	0	-0.13	34	34
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
CASP8	-0.003	0.12	-10000	0	-0.4	39	39
MAP2K2	0.005	0.019	0.071	1	-0.094	11	12
SMPD3	0.011	0.041	-10000	0	-0.16	15	15
TNF	0.02	0.02	-10000	0	-0.12	11	11
PKC zeta/PAR4	0.034	0.012	-10000	0	-0.11	4	4
mol:PHOSPHOCHOLINE	-0.008	0.016	0.092	5	-10000	0	5
NF kappa B1/RelA/I kappa B alpha	0.044	0.059	-10000	0	-0.096	72	72
AIFM1	-0.005	0.036	0.13	1	-0.12	44	45
BCL2	0.016	0.031	-10000	0	-0.12	27	27

×

Signaling events mediated by HDAC Class III

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EP300	0.022	0.01	-10000	0	-0.12	2	2
HDAC4	0.023	0	-10000	0	-10000	0	0
induction of apoptosis	0	0	-10000	0	-10000	0	0
regulation of S phase of mitotic cell cycle	-0.008	0.002	-10000	0	-10000	0	0
CDKN1A	0.034	0.04	-10000	0	-10000	0	0
KAT2B	0	0	-10000	0	-10000	0	0
BAX	0.023	0	-10000	0	-10000	0	0
FOXO3	0.003	0.05	0.26	19	-10000	0	19
FOXO1	0.023	0.009	-10000	0	-0.12	2	2
FOXO4	0.009	0.064	-10000	0	-0.22	34	34
response to UV	0	0	-10000	0	-10000	0	0
XRCC6	0.022	0.004	-10000	0	-10000	0	0
TAT	0.023	0.009	-10000	0	-0.12	2	2
mol:Lysophosphatidic acid	0	0	-10000	0	-10000	0	0
MYOD1	0.011	0.009	-10000	0	-0.077	6	6
PPARGC1A	0.014	0.035	-10000	0	-0.12	35	35
FHL2	0.02	0.02	-10000	0	-0.12	11	11
response to nutrient levels	0	0	-10000	0	-10000	0	0
KU70/SIRT1	0.022	0.045	-10000	0	-0.18	25	25
HIST2H4A	0.008	0.002	-10000	0	-10000	0	0
SIRT1/FOXO3a	0.014	0.037	0.2	19	-0.089	5	24
SIRT1	0.019	0.004	-10000	0	-10000	0	0
response to hypoxia	0	0	-10000	0	-10000	0	0
SIRT1/MEF2D/HDAC4	0.042	0.021	-10000	0	-0.11	10	10
SIRT1/Histone H1b	0.005	0.071	-10000	0	-0.17	69	69
apoptosis	-0.036	0.039	0.14	25	-10000	0	25
SIRT1/PGC1A	0.021	0.029	-10000	0	-0.12	10	10
p53/SIRT1	-0.035	0.081	-10000	0	-0.15	173	173
SIRT1/FOXO4	0.017	0.058	-10000	0	-0.19	34	34
FOXO1/FHL2/SIRT1	0.037	0.026	-10000	0	-0.1	14	14
HIST1H1E	-0.005	0.079	-10000	0	-0.2	69	69
SIRT1/p300	0.022	0.04	-10000	0	-0.14	32	32
muscle cell differentiation	-0.014	0.02	0.12	11	-10000	0	11
TP53	0.007	0.029	-10000	0	-0.13	22	22
KU70/SIRT1/BAX	0.036	0.039	-10000	0	-0.14	25	25
CREBBP	0.021	0.015	-10000	0	-0.12	6	6
MEF2D	0.023	0	-10000	0	-10000	0	0
HIV-1 Tat/SIRT1	0.028	0.024	-10000	0	-0.14	10	10
ACSS2	0.018	0.01	-10000	0	-0.074	6	6
SIRT1/PCAF/MYOD	0.014	0.02	-10000	0	-0.12	11	11

×

Signaling events regulated by Ret tyrosine kinase

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.008	0.098	-9999	-0.39	31	31
Crk/p130 Cas/Paxillin	-0.007	0.025	-9999	-0.15	7	7
JUN	0.012	0.06	-9999	-0.21	22	22
HRAS	0.023	0.006	-9999	-0.12	1	1
RET51/GFRalpha1/GDNF/GRB10	0.045	0.039	-9999	-0.1	11	11
RAP1A	0.021	0.012	-9999	-0.12	3	3
FRS2	0.019	0.024	-9999	-0.12	15	15
RAP1A/GDP	0.009	0.034	-9999	-0.14	28	28
RET51/GFRalpha1/GDNF/DOK1	0.045	0.039	-9999	-0.11	9	9
EntrezGene:5979	0	0	-9999	-10000	0	0
PTPN11	0.022	0.011	-9999	-0.12	3	3
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.021	0.016	-9999	-0.12	7	7
RET9/GFRalpha1/GDNF/Enigma	0.034	0.032	-9999	-0.11	7	7
RHOA	0.023	0.006	-9999	-0.12	1	1
RAP1A/GTP	0.039	0.042	-9999	-0.092	30	30
GRB7	0.018	0.026	-9999	-0.12	18	18
RET51/GFRalpha1/GDNF	0.046	0.037	-9999	-0.097	8	8
MAPKKK cascade	0.037	0.037	-9999	-0.18	5	5
BCAR1	0.022	0.011	-9999	-0.12	3	3
RET9/GFRalpha1/GDNF/IRS1	0.033	0.033	-9999	-0.1	10	10
lamellipodium assembly	0.025	0.043	-9999	-0.17	7	7
RET51/GFRalpha1/GDNF/SHC	0.047	0.035	-9999	-0.096	5	5
PIK3CA	0.02	0.017	-9999	-0.12	7	7
RET9/GFRalpha1/GDNF/SHC	0.036	0.027	-9999	-0.099	3	3
RET9/GFRalpha1/GDNF/Shank3	0.036	0.027	-9999	-0.1	3	3
MAPK3	0.022	0.033	-9999	-0.087	30	30
DOK1	0.021	0.016	-9999	-0.12	7	7
DOK6	0.023	0.009	-9999	-0.12	2	2
PXN	0.022	0.014	-9999	-0.12	5	5
neurite development	0.028	0.039	-9999	-0.17	10	10
DOK5	-0.008	0.054	-9999	-0.12	102	102
GFRA1	0.01	0.041	-9999	-0.12	50	50
MAPK8	0.014	0.061	-9999	-0.15	57	57
HRAS/GTP	0.042	0.041	-9999	-0.15	9	9
tube development	0.038	0.03	-9999	-0.12	6	6
MAPK1	0.021	0.033	-9999	-0.087	30	30
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2	0.018	0.055	-9999	-0.17	32	32
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
SRC	0.023	0.009	-9999	-0.12	2	2
PDLIM7	0.02	0.021	-9999	-0.12	12	12
RET51/GFRalpha1/GDNF/Dok6	0.056	0.036	-9999	-0.097	5	5
SHC1	0.023	0.001	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/Dok4	0.047	0.035	-9999	-0.098	7	7
RET51/GFRalpha1/GDNF/Dok5	-0.003	0.072	-9999	-0.1	144	144
PRKCA	0.011	0.037	-9999	-0.12	40	40
HRAS/GDP	0.017	0.008	-9999	-0.11	2	2
CREB1	0.021	0.071	-9999	-0.24	28	28
PIK3R1	0.015	0.031	-9999	-0.12	27	27
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2	0.024	0.034	-9999	-0.14	17	17
RET51/GFRalpha1/GDNF/Grb7	0.041	0.044	-9999	-0.11	18	18
mol:GDP	0	0	-9999	-10000	0	0
RET	0.019	0.026	-9999	-0.12	18	18
DOK4	0.022	0.012	-9999	-0.12	4	4
JNK cascade	0.01	0.063	-9999	-0.2	28	28
RET9/GFRalpha1/GDNF/FRS2	0.031	0.036	-9999	-0.1	17	17
SHANK3	0.023	0.006	-9999	-0.12	1	1
RASA1	0.021	0.012	-9999	-0.12	3	3
NCK1	0.02	0.019	-9999	-0.12	9	9
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1	0.019	0.048	-9999	-0.15	31	31
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2	0.023	0.055	-9999	-0.17	32	32
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK	0.014	0.065	-9999	-0.16	60	60
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1	0.024	0.049	-9999	-0.15	31	31
PI3K	0.035	0.052	-9999	-0.19	11	11
SOS1	0.017	0.027	-9999	-0.12	20	20
RET9/GFRalpha1/GDNF/Shank3/Grb2	0.045	0.032	-9999	-0.12	6	6
GRB10	0.022	0.014	-9999	-0.12	5	5
activation of MAPKK activity	0.022	0.056	-9999	-0.29	9	9
RET51/GFRalpha1/GDNF/FRS2	0.042	0.043	-9999	-0.097	19	19
GAB1	0.02	0.021	-9999	-0.12	12	12
IRS1	0.019	0.023	-9999	-0.12	14	14
IRS2	0.021	0.016	-9999	-0.12	7	7
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2	0.03	0.036	-9999	-0.21	2	2
RET51/GFRalpha1/GDNF/PKC alpha	0.03	0.053	-9999	-0.097	46	46
GRB2	0.023	0.006	-9999	-0.12	1	1
PRKACA	0.021	0.017	-9999	-0.12	8	8
GDNF	0.023	0.009	-9999	-0.12	2	2
RAC1	0.023	0.002	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/IRS1	0.044	0.039	-9999	-0.096	13	13
Rac1/GTP	0.032	0.05	-9999	-0.2	7	7
RET9/GFRalpha1/GDNF	0.023	0.026	-9999	-0.059	52	52
GFRalpha1/GDNF	0.025	0.032	-9999	-0.074	52	52

×

Signaling events mediated by HDAC Class I

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NF kappa B/RelA	0.032	0.075	-10000	0	-0.2	35	35
Ran/GTP/Exportin 1/HDAC1	-0.012	0.04	-10000	0	-0.12	54	54
NF kappa B1 p50/RelA/I kappa B alpha	0.019	0.091	-10000	0	-0.26	40	40
SUMO1	0.023	0.009	-10000	0	-0.12	2	2
ZFPM1	0.022	0.011	-10000	0	-0.12	3	3
NPC/RanGAP1/SUMO1/Ubc9	0.015	0.037	-10000	0	-0.14	30	30
FKBP3	0.021	0.013	-10000	0	-0.12	4	4
Histones	0.04	0.067	-10000	0	-0.2	22	22
YY1/LSF	0.017	0.063	-10000	0	-0.21	34	34
SMG5	0.022	0.011	-10000	0	-0.12	3	3
RAN	0.023	0.002	-10000	0	-10000	0	0
I kappa B alpha/HDAC3	0.016	0.066	-10000	0	-0.17	49	49
I kappa B alpha/HDAC1	0.011	0.084	-10000	0	-0.24	48	48
SAP18	0.023	0.003	-10000	0	-10000	0	0
RELA	0.017	0.076	-10000	0	-0.22	36	36
HDAC1/Smad7	0.034	0.042	-10000	0	-0.11	39	39
RANGAP1	0.023	0.006	-10000	0	-0.12	1	1
HDAC3/TR2	0.031	0.046	-10000	0	-0.24	11	11
NuRD/MBD3 Complex	0.013	0.099	-10000	0	-0.32	32	32
NF kappa B1 p50/RelA	0.022	0.079	-10000	0	-0.21	44	44
EntrezGene:23225	0	0	-10000	0	-10000	0	0
GATA2	0.02	0.022	-10000	0	-0.12	13	13
GATA1	0.023	0.006	-10000	0	-0.12	1	1
Mad/Max	0.033	0.012	-10000	0	-0.071	8	8
NuRD/MBD3 Complex/GATA1/Fog1	0.025	0.094	-10000	0	-0.29	32	32
RBBP7	0.022	0.011	-10000	0	-0.12	3	3
NPC	0.009	0.023	-10000	0	-0.096	27	27
RBBP4	0.021	0.014	-10000	0	-0.12	5	5
MAX	0.023	0	-10000	0	-10000	0	0
EntrezGene:9972	0	0	-10000	0	-10000	0	0
FBXW11	0.023	0.003	-10000	0	-10000	0	0
NFKBIA	0.004	0.083	-10000	0	-0.26	43	43
KAT2B	0	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
SIN3/HDAC complex	0.015	0.082	-10000	0	-0.3	22	22
SIN3 complex	0.052	0.032	-10000	0	-0.098	20	20
SMURF1	0.023	0.009	-10000	0	-0.12	2	2
CHD3	0.021	0.016	-10000	0	-0.12	7	7
SAP30	0.023	0	-10000	0	-10000	0	0
EntrezGene:23636	0	0	-10000	0	-10000	0	0
NCOR1	0.022	0.009	-10000	0	-0.12	2	2
YY1/HDAC3	0.023	0.065	-10000	0	-0.25	19	19
YY1/HDAC2	0.018	0.059	-10000	0	-0.19	35	35
YY1/HDAC1	0.017	0.059	-10000	0	-0.2	34	34
NuRD/MBD2 Complex (MeCP1)	0.013	0.098	-10000	0	-0.31	32	32
PPARG	0.021	0.062	-10000	0	-0.2	35	35
HDAC8/hEST1B	0.037	0.039	-10000	0	-0.12	28	28
UBE2I	0.023	0.001	-10000	0	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.023	0.003	-10000	0	-10000	0	0
TNFRSF1A	0.021	0.016	-10000	0	-0.12	7	7
HDAC3/SMRT (N-CoR2)	0.031	0.046	-10000	0	-0.25	10	10
MBD3L2	0.022	0.011	-10000	0	-0.12	3	3
ubiquitin-dependent protein catabolic process	0.034	0.041	-10000	0	-0.11	39	39
CREBBP	0.021	0.015	-10000	0	-0.12	6	6
NuRD/MBD3/MBD3L2 Complex	0.023	0.095	-10000	0	-0.3	32	32
HDAC1	0.019	0.02	-10000	0	-0.12	10	10
HDAC3	0.023	0.044	-10000	0	-0.26	9	9
HDAC2	0.02	0.021	-10000	0	-0.12	12	12
YY1	0.008	0.064	-10000	0	-0.22	34	34
HDAC8	0.021	0.013	-10000	0	-0.12	4	4
SMAD7	0.023	0.003	-10000	0	-10000	0	0
NCOR2	0.019	0.023	-10000	0	-0.12	15	15
MXD1	0.021	0.017	-10000	0	-0.12	8	8
STAT3	0.006	0.078	-10000	0	-0.23	48	48
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
EntrezGene:8021	0	0	-10000	0	-10000	0	0
RANBP2	0.022	0.01	-10000	0	-0.12	2	2
YY1/LSF/HDAC1	0.019	0.072	-10000	0	-0.19	41	41
YY1/SAP30/HDAC1	0.025	0.062	-10000	0	-0.17	35	35
EP300	0.022	0.01	-10000	0	-0.12	2	2
STAT3 (dimer non-phopshorylated)	0.006	0.078	-10000	0	-0.23	48	48
proteasomal ubiquitin-dependent protein catabolic process	0.004	0.082	-10000	0	-0.26	43	43
histone deacetylation	0.013	0.097	-10000	0	-0.31	32	32
STAT3 (dimer non-phopshorylated)/HDAC3	0.02	0.077	-10000	0	-0.26	24	24
nuclear export	-0.036	0.038	0.12	28	-10000	0	28
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
GATAD2B	0.022	0.009	-10000	0	-0.12	2	2
GATAD2A	0.02	0.022	-10000	0	-0.12	13	13
GATA2/HDAC3	0.032	0.047	-10000	0	-0.25	10	10
GATA1/HDAC1	0.023	0.042	-10000	0	-0.12	40	40
GATA1/HDAC3	0.033	0.044	-10000	0	-0.24	10	10
CHD4	0.022	0.009	-10000	0	-0.12	2	2
TNF-alpha/TNFR1A	0.025	0.036	-10000	0	-0.11	37	37
SIN3/HDAC complex/Mad/Max	0.022	0.077	-10000	0	-0.27	22	22
NuRD Complex	0.024	0.095	-10000	0	-0.3	32	32
positive regulation of chromatin silencing	0.038	0.065	-10000	0	-0.2	22	22
SIN3B	0.022	0.015	-10000	0	-0.12	6	6
MTA2	0.023	0.002	-10000	0	-10000	0	0
SIN3A	0.022	0.014	-10000	0	-0.12	5	5
XPO1	0.022	0.01	-10000	0	-0.12	2	2
SUMO1/HDAC1	0.029	0.048	-10000	0	-0.19	13	13
HDAC complex	0.034	0.064	-10000	0	-0.12	66	66
GATA1/Fog1	0.034	0.01	-10000	0	-0.15	1	1
FKBP25/HDAC1/HDAC2	0.027	0.054	-10000	0	-0.12	54	54
TNF	0.02	0.02	-10000	0	-0.12	11	11
negative regulation of cell growth	0.022	0.077	-10000	0	-0.27	22	22
NuRD/MBD2/PRMT5 Complex	0.013	0.098	-10000	0	-0.31	32	32
Ran/GTP/Exportin 1	0.034	0.049	-10000	0	-0.15	30	30
NF kappa B/RelA/I kappa B alpha	0.018	0.08	-10000	0	-0.28	30	30
SIN3/HDAC complex/NCoR1	0.019	0.079	-10000	0	-0.26	28	28
TFCP2	0.021	0.014	-10000	0	-0.12	5	5
NR2C1	0.022	0.01	-10000	0	-0.12	2	2
MBD3	0.023	0.009	-10000	0	-0.12	2	2
MBD2	0.023	0	-10000	0	-10000	0	0

×

Syndecan-3-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	0.022	0.011	-9999	-0.12	3	3
Syndecan-3/Src/Cortactin	-0.001	0.076	-9999	-0.3	12	12
Syndecan-3/Neurocan	0.02	0.052	-9999	-0.47	5	5
POMC	0.022	0.011	-9999	-0.12	3	3
EGFR	0.015	0.03	-9999	-0.12	25	25
Syndecan-3/EGFR	0.016	0.054	-9999	-0.38	7	7
AGRP	0.023	0	-9999	-10000	0	0
NCSTN	0.022	0.012	-9999	-0.12	4	4
PSENEN	0.016	0.03	-9999	-0.12	24	24
RP11-540L11.1	0	0	-9999	-10000	0	0
APH1B	0.014	0.032	-9999	-0.12	29	29
APH1A	0.023	0.009	-9999	-0.12	2	2
NCAN	0.022	0.011	-9999	-0.12	3	3
long-term memory	0.017	0.065	-9999	-0.3	11	11
Syndecan-3/IL8	0.011	0.056	-9999	-0.43	6	6
PSEN1	0.022	0.008	-9999	-0.12	1	1
Src/Cortactin	0.03	0.027	-9999	-0.12	17	17
FYN	0.011	0.037	-9999	-0.12	40	40
limb bud formation	0.006	0.052	-9999	-0.49	5	5
MC4R	0	0	-9999	-10000	0	0
SRC	0.023	0.009	-9999	-0.12	2	2
PTN	-0.009	0.055	-9999	-0.12	106	106
FGFR/FGF/Syndecan-3	0.006	0.052	-9999	-0.49	5	5
neuron projection morphogenesis	-0.006	0.068	-9999	-0.3	11	11
Syndecan-3/AgRP	0.021	0.051	-9999	-0.47	5	5
Syndecan-3/AgRP/MC4R	0.019	0.049	-9999	-0.45	5	5
Fyn/Cortactin	0.011	0.056	-9999	-0.11	93	93
SDC3	0.006	0.052	-9999	-0.5	5	5
GO:0007205	0	0	-9999	-10000	0	0
positive regulation of leukocyte migration	0.011	0.055	-9999	-0.42	6	6
IL8	0.004	0.047	-9999	-0.12	69	69
Syndecan-3/Fyn/Cortactin	0.018	0.066	-9999	-0.31	11	11
Syndecan-3/CASK	0.005	0.049	-9999	-0.47	5	5
alpha-MSH/MC4R	0.017	0.007	-9999	-0.077	3	3
Gamma Secretase	0.034	0.067	-9999	-0.097	89	89

×

Signaling mediated by p38-alpha and p38-beta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTGS2	0.005	0.12	-9999	-0.82	9	9
MKNK1	0.023	0.006	-9999	-0.12	1	1
MAPK14	0.015	0.049	-9999	-0.2	15	15
ATF2/c-Jun	-0.006	0.11	-9999	-0.33	51	51
MAPK11	0.015	0.049	-9999	-0.21	14	14
MITF	0.018	0.062	-9999	-0.24	19	19
MAPKAPK5	0.02	0.058	-9999	-0.23	19	19
KRT8	0.016	0.065	-9999	-0.24	25	25
MAPKAPK3	0.022	0.012	-9999	-0.12	4	4
MAPKAPK2	0.023	0.009	-9999	-0.12	2	2
p38alpha-beta/CK2	0.019	0.072	-9999	-0.26	18	18
CEBPB	0.016	0.063	-9999	-0.24	20	20
SLC9A1	0.019	0.059	-9999	-0.23	20	20
mol:GDP	0	0	-9999	-10000	0	0
ATF2	0.016	0.07	-9999	-0.27	18	18
p38alpha-beta/MNK1	0.033	0.063	-9999	-0.27	11	11
JUN	-0.008	0.11	-9999	-0.33	51	51
PPARGC1A	0.016	0.06	-9999	-0.29	13	13
USF1	0.019	0.059	-9999	-0.23	21	21
RAB5/GDP/GDI1	0.018	0.052	-9999	-0.17	27	27
NOS2	0.011	0.056	-9999	-0.24	18	18
DDIT3	0.015	0.06	-9999	-0.23	21	21
RAB5A	0.023	0.006	-9999	-0.12	1	1
HSPB1	0.019	0.045	-9999	-0.24	11	11
p38alpha-beta/HBP1	0.025	0.069	-9999	-0.24	16	16
CREB1	0.019	0.071	-9999	-0.3	21	21
RAB5/GDP	0.016	0.014	-9999	-0.13	5	5
EIF4E	0.02	0.049	-9999	-0.23	11	11
RPS6KA4	0.02	0.057	-9999	-0.28	13	13
PLA2G4A	0	0.06	-9999	-0.23	18	18
GDI1	0.017	0.062	-9999	-0.23	24	24
TP53	0.005	0.066	-9999	-0.28	19	19
RPS6KA5	0.018	0.059	-9999	-0.22	22	22
ESR1	0.01	0.076	-9999	-0.29	27	27
HBP1	0.022	0.005	-9999	-10000	0	0
MEF2C	0.016	0.068	-9999	-0.24	24	24
MEF2A	0.019	0.061	-9999	-0.24	20	20
EIF4EBP1	0.019	0.068	-9999	-0.28	21	21
KRT19	0.009	0.075	-9999	-0.25	30	30
ELK4	0.021	0.056	-9999	-0.23	18	18
ATF6	0.018	0.064	-9999	-0.26	19	19
ATF1	0.019	0.07	-9999	-0.3	20	20
p38alpha-beta/MAPKAPK2	0.033	0.061	-9999	-0.27	10	10
p38alpha-beta/MAPKAPK3	0.033	0.061	-9999	-0.27	10	10

×

Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

Figure S105. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S105. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HIF3A	0.016	0.032	-9999	-0.12	28	28
oxygen homeostasis	0	0	-9999	-10000	0	0
TCEB2	0.023	0.006	-9999	-0.12	1	1
TCEB1	0.022	0.011	-9999	-0.12	3	3
HIF1A/p53	0.002	0.061	-9999	-0.2	32	32
HIF1A	0.007	0.047	-9999	-0.19	22	22
COPS5	0.019	0.022	-9999	-0.12	12	12
VHL/Elongin B/Elongin C/RBX1/CUL2	0.053	0.049	-9999	-0.17	8	8
FIH (dimer)	0.023	0.006	-9999	-0.12	1	1
CDKN2A	0.014	0.023	-9999	-0.12	12	12
ARNT/IPAS	0.027	0.028	-9999	-0.079	36	36
HIF1AN	0.023	0.006	-9999	-0.12	1	1
GNB2L1	0.023	0.003	-9999	-10000	0	0
HIF1A/ARNT	0.014	0.055	-9999	-0.18	23	23
CUL2	0.022	0.011	-9999	-0.12	3	3
OS9	0.022	0.009	-9999	-0.12	2	2
RACK1/Elongin B/Elongin C	0.043	0.024	-9999	-0.11	13	13
response to hypoxia	0	0	-9999	-10000	0	0
HIF1A/Hsp90	0.014	0.056	-9999	-0.19	24	24
PHD1-3/OS9	0.014	0.066	-9999	-0.097	112	112
HIF1A/RACK1/Elongin B/Elongin C	0.035	0.057	-9999	-0.18	21	21
VHL	0.021	0.016	-9999	-0.12	7	7
HSP90AA1	0.023	0.003	-9999	-10000	0	0
HIF1A/JAB1	0.011	0.057	-9999	-0.19	25	25
EGLN3	-0.002	0.051	-9999	-0.12	84	84
EGLN2	0.023	0.009	-9999	-0.12	2	2
EGLN1	0.023	0.009	-9999	-0.12	2	2
TP53	0.011	0.029	-9999	-0.12	22	22
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A	0.027	0.091	-9999	-0.52	14	14
ARNT	0.022	0.012	-9999	-0.12	4	4
ARD1A	0.018	0.025	-9999	-0.12	17	17
RBX1	0.022	0.011	-9999	-0.12	3	3
HIF1A/p19ARF	0.004	0.063	-9999	-0.21	29	29

×

Class IB PI3K non-lipid kinase events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
cAMP biosynthetic process	-0.019	0.025	0.12	17	-10000	0	17
PI3K Class IB/PDE3B	0.019	0.025	-10000	0	-0.12	17	17
PDE3B	0.019	0.025	-10000	0	-0.12	17	17

×

Arf6 trafficking events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SLC2A4	0.023	0.006	-10000	0	-0.12	1	1
CLTC	0.005	0.082	-10000	0	-0.35	18	18
calcium ion-dependent exocytosis	0.01	0.043	-10000	0	-0.15	22	22
Dynamin 2/GTP	0.014	0.044	-10000	0	-0.11	53	53
EXOC4	0.022	0.007	-10000	0	-0.12	1	1
CD59	0.009	0.061	-10000	0	-0.35	12	12
CPE	0.009	0.028	-10000	0	-0.066	58	58
CTNNB1	0.022	0.008	-10000	0	-0.12	1	1
membrane fusion	0.015	0.036	-10000	0	-0.15	22	22
CTNND1	0.012	0.041	-10000	0	-0.099	52	52
DNM2	0.02	0.022	-10000	0	-0.12	13	13
mol:PI-4-5-P2	0.015	0.048	-10000	0	-0.26	13	13
TSHR	0.013	0.026	-10000	0	-0.069	49	49
INS	0.018	0.017	-10000	0	-10000	0	0
BIN1	0.022	0.012	-10000	0	-0.12	4	4
mol:Choline	0.015	0.036	-10000	0	-0.15	22	22
growth hormone secretagogue receptor activity	0	0	-10000	0	-10000	0	0
mol:GDP	0.014	0.022	-10000	0	-0.072	30	30
membrane depolarization	0	0	-10000	0	-10000	0	0
ARF6	0.023	0.003	-10000	0	-10000	0	0
mol:Ca2+	0.014	0.043	-10000	0	-0.1	53	53
JUP	0.006	0.066	-10000	0	-0.36	13	13
ASAP2/amphiphysin II	0.027	0.02	-10000	0	-0.089	16	16
ARF6/GTP	0.015	0.021	-10000	0	-0.15	9	9
CDH1	0.005	0.069	-10000	0	-0.35	14	14
clathrin-independent pinocytosis	0.015	0.021	-10000	0	-0.15	9	9
MAPK8IP3	0.023	0.006	-10000	0	-0.12	1	1
positive regulation of endocytosis	0.015	0.021	-10000	0	-0.15	9	9
EXOC2	0.022	0.013	-10000	0	-0.12	4	4
substrate adhesion-dependent cell spreading	0.011	0.1	-10000	0	-0.39	27	27
insulin receptor binding	0	0	-10000	0	-10000	0	0
SPAG9	0.021	0.015	-10000	0	-0.12	6	6
regulation of calcium-dependent cell-cell adhesion	-0.014	0.079	0.27	22	-10000	0	22
positive regulation of phagocytosis	0.018	0.016	-10000	0	-0.11	8	8
ARF6/GTP/JIP3	0.029	0.019	-10000	0	-0.11	10	10
ACAP1	0.014	0.032	-10000	0	-0.13	22	22
mol:GTP	0	0	-10000	0	-10000	0	0
CHRM2	0.01	0.06	-10000	0	-0.37	11	11
clathrin heavy chain/ACAP1	0.011	0.066	-10000	0	-0.27	20	20
JIP4/KLC1	0.033	0.039	-10000	0	-0.11	37	37
EXOC1	0.021	0.012	-10000	0	-0.12	3	3
exocyst	0.011	0.11	-10000	0	-0.4	27	27
RALA/GTP	0.014	0.021	-10000	0	-0.13	11	11
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex	0.025	0.029	-10000	0	-0.1	27	27
receptor recycling	0.015	0.021	-10000	0	-0.15	9	9
CTNNA1	0.012	0.04	-10000	0	-0.098	52	52
NME1	0.014	0.022	-10000	0	-0.072	30	30
clathrin coat assembly	0.005	0.081	-10000	0	-0.34	18	18
IL2RA	0.01	0.06	-10000	0	-0.36	11	11
VAMP3	0.019	0.016	-10000	0	-0.12	8	8
GLUT4/clathrin heavy chain/ACAP1	0.019	0.065	-10000	0	-0.28	16	16
EXOC6	0.021	0.012	-10000	0	-0.12	3	3
PLD1	0.002	0.057	-10000	0	-0.19	40	40
PLD2	0.018	0.028	-10000	0	-0.19	6	6
EXOC5	0.022	0.011	-10000	0	-0.12	3	3
PIP5K1C	0.015	0.048	-10000	0	-0.26	13	13
SDC1	0.009	0.061	-10000	0	-0.35	12	12
ARF6/GDP	0.012	0.041	-10000	0	-0.098	63	63
EXOC7	0.023	0.001	-10000	0	-10000	0	0
E-cadherin/beta catenin	0.016	0.082	-10000	0	-0.28	22	22
mol:Phosphatidic acid	0.015	0.036	-10000	0	-0.15	22	22
endocytosis	-0.025	0.02	0.088	16	-10000	0	16
SCAMP2	0.023	0.009	-10000	0	-0.12	2	2
ADRB2	0.009	0.078	-10000	0	-0.33	18	18
EXOC3	0.023	0.009	-10000	0	-0.12	2	2
ASAP2	0	0	-10000	0	-10000	0	0
Dynamin 2/GDP	0.016	0.044	-10000	0	-0.1	53	53
KLC1	0.021	0.013	-10000	0	-0.12	4	4
AVPR2	0.008	0.079	-10000	0	-0.34	18	18
RALA	0.022	0.009	-10000	0	-0.12	2	2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.015	0.087	-10000	0	-0.25	32	32

×

Class I PI3K signaling events mediated by Akt

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.02	0.016	-10000	0	-0.071	16	16
BAD/BCL-XL/YWHAZ	0.039	0.031	-10000	0	-0.096	22	22
CDKN1B	0.013	0.076	-10000	0	-0.34	22	22
CDKN1A	0.017	0.075	-10000	0	-0.34	22	22
FRAP1	0.022	0.013	-10000	0	-0.12	4	4
PRKDC	0.021	0.015	-10000	0	-0.12	6	6
FOXO3	0.016	0.076	-10000	0	-0.33	23	23
AKT1	0.014	0.077	-10000	0	-0.35	22	22
BAD	0.022	0.011	-10000	0	-0.12	3	3
AKT3	-0.006	0.055	-10000	0	-0.2	32	32
mol:GTP	0	0	-10000	0	-10000	0	0
FOXO4	0.018	0.074	-10000	0	-0.33	22	22
AKT1/ASK1	0.019	0.077	-10000	0	-0.33	22	22
BAD/YWHAZ	0.043	0.025	-10000	0	-0.11	11	11
RICTOR	0.02	0.017	-10000	0	-0.12	7	7
RAF1	0.023	0.003	-10000	0	-10000	0	0
JNK cascade	-0.018	0.075	0.32	22	-10000	0	22
TSC1	0.017	0.074	-10000	0	-0.33	22	22
YWHAZ	0.023	0.003	-10000	0	-10000	0	0
AKT1/RAF1	0.026	0.079	-10000	0	-0.34	23	23
EP300	0.022	0.01	-10000	0	-0.12	2	2
mol:GDP	0.014	0.077	-10000	0	-0.35	22	22
mol:PI-3-4-5-P3	0	0	-10000	0	-10000	0	0
TSC2	0.016	0.074	-10000	0	-0.33	22	22
YWHAQ	0.023	0.003	-10000	0	-10000	0	0
TBC1D4	0.018	0.014	-10000	0	-0.04	28	28
MAP3K5	0.018	0.025	-10000	0	-0.12	17	17
MAPKAP1	0.023	0.002	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.018	0.071	0.23	23	-10000	0	23
YWHAH	0.021	0.014	-10000	0	-0.12	5	5
AKT1S1	0.017	0.074	-10000	0	-0.32	23	23
CASP9	0.016	0.075	-10000	0	-0.34	22	22
YWHAB	0.023	0.007	-10000	0	-0.12	1	1
p27Kip1/KPNA1	0.021	0.081	-10000	0	-0.32	25	25
GBL	0.023	0.009	-10000	0	-0.12	2	2
PDK1/Src/Hsp90	0.041	0.032	-10000	0	-0.12	19	19
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
SRC	0.023	0.009	-10000	0	-0.12	2	2
AKT2/p21CIP1	0.022	0.07	-10000	0	-0.29	23	23
KIAA1303	0.023	0.009	-10000	0	-0.12	2	2
mTOR/RHEB/GTP/Raptor/GBL	0.026	0.072	-10000	0	-0.34	17	17
CHUK	0.014	0.078	-10000	0	-0.34	23	23
BAD/BCL-XL	0.035	0.077	-10000	0	-0.32	22	22
mTORC2	0.047	0.043	-10000	0	-0.1	38	38
AKT2	0.014	0.029	-10000	0	-0.2	8	8
FOXO1-3a-4/14-3-3 family	0.024	0.088	-10000	0	-0.26	32	32
PDPK1	0.023	0.007	-10000	0	-0.12	1	1
MDM2	0.015	0.078	-10000	0	-0.35	22	22
MAPKKK cascade	-0.026	0.077	0.33	23	-10000	0	23
MDM2/Cbp/p300	0.032	0.087	-10000	0	-0.33	23	23
TSC1/TSC2	0.018	0.073	-10000	0	-0.32	22	22
proteasomal ubiquitin-dependent protein catabolic process	0.03	0.083	-10000	0	-0.32	23	23
glucose import	0.018	0.023	-10000	0	-0.14	8	8
mTOR/RHEB/GDP/Raptor/GBL/PRAS40	0.027	0.071	-10000	0	-0.25	21	21
response to stress	0	0	-10000	0	-10000	0	0
SLC2A4	0.02	0.012	-10000	0	-0.031	29	29
GSK3A	0.016	0.076	-10000	0	-0.34	22	22
FOXO1	0.017	0.074	-10000	0	-0.33	22	22
GSK3B	0.017	0.076	-10000	0	-0.34	22	22
SFN	0.014	0.032	-10000	0	-0.12	29	29
G1/S transition of mitotic cell cycle	0.019	0.075	-10000	0	-0.33	22	22
p27Kip1/14-3-3 family	0.029	0.078	-10000	0	-0.33	17	17
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
KPNA1	0.023	0.003	-10000	0	-10000	0	0
HSP90AA1	0.023	0.003	-10000	0	-10000	0	0
YWHAG	0.02	0.022	-10000	0	-0.12	13	13
RHEB	0.019	0.022	-10000	0	-0.12	13	13
CREBBP	0.021	0.015	-10000	0	-0.12	6	6

×

Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.021	0.017	-10000	0	-0.12	8	8
NFATC1	0.03	0.065	-10000	0	-0.25	14	14
NFATC2	0.02	0.048	-10000	0	-0.18	15	15
NFATC3	0.024	0.022	-10000	0	-0.24	2	2
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
Calcineurin A alpha-beta B1/CABIN1	-0.006	0.08	-10000	0	-0.22	37	37
Exportin 1/Ran/NUP214	0.037	0.039	-10000	0	-0.11	34	34
mol:DAG	0	0.001	-10000	0	-10000	0	0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV	0.015	0.079	-10000	0	-0.22	27	27
BCL2/BAX	0.029	0.025	-10000	0	-0.076	29	29
CaM/Ca2+/Calcineurin A alpha-beta B1	0.013	0.021	-10000	0	-0.12	12	12
CaM/Ca2+	0.013	0.021	-10000	0	-0.12	12	12
BAX	0.023	0	-10000	0	-10000	0	0
MAPK14	0.022	0.007	-10000	0	-0.12	1	1
BAD	0.022	0.011	-10000	0	-0.12	3	3
CABIN1/MEF2D	0.006	0.08	-10000	0	-0.21	37	37
Calcineurin A alpha-beta B1/BCL2	0.016	0.031	-10000	0	-0.12	27	27
FKBP8	0.016	0.031	-10000	0	-0.12	27	27
activation-induced cell death of T cells	-0.006	0.079	0.2	37	-10000	0	37
KPNB1	0.022	0.009	-10000	0	-0.12	2	2
KPNA2	0.017	0.024	-10000	0	-0.12	15	15
XPO1	0.022	0.01	-10000	0	-0.12	2	2
SFN	0.014	0.032	-10000	0	-0.12	29	29
MAP3K8	0.022	0.009	-10000	0	-0.12	2	2
NFAT4/CK1 alpha	0.03	0.038	-10000	0	-0.15	13	13
MEF2D/NFAT1/Cbp/p300	0.04	0.079	-10000	0	-0.16	43	43
CABIN1	-0.006	0.081	-10000	0	-0.22	37	37
CALM1	0.021	0.014	-10000	0	-0.12	5	5
RAN	0.023	0.002	-10000	0	-10000	0	0
MAP3K1	0.021	0.015	-10000	0	-0.12	6	6
CAMK4	0.016	0.031	-10000	0	-0.12	27	27
mol:Ca2+	0	0.003	-10000	0	-10000	0	0
MAPK3	0.022	0.014	-10000	0	-0.12	5	5
YWHAH	0.021	0.014	-10000	0	-0.12	5	5
Calcineurin A alpha-beta B1/AKAP79/PKA	0.032	0.017	-10000	0	-0.082	12	12
YWHAB	0.023	0.007	-10000	0	-0.12	1	1
MAPK8	0.021	0.015	-10000	0	-0.12	6	6
MAPK9	0.021	0.012	-10000	0	-0.12	3	3
YWHAG	0.02	0.022	-10000	0	-0.12	13	13
FKBP1A	0.022	0.012	-10000	0	-0.12	4	4
NFAT1-c-4/YWHAQ	0.048	0.071	-10000	0	-0.27	12	12
PRKCH	0.019	0.024	-10000	0	-0.12	15	15
CABIN1/Cbp/p300	0.02	0.052	-10000	0	-0.16	41	41
CASP3	0.022	0.009	-10000	0	-0.12	2	2
PIM1	0.02	0.023	-10000	0	-0.12	14	14
Calcineurin A alpha-beta B1/FKBP12/FK506	0.014	0.012	-10000	0	-0.087	7	7
apoptosis	0.019	0.036	0.14	2	-0.21	11	13
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1	0.017	0.07	-10000	0	-0.27	15	15
PRKCB	0	0	-10000	0	-10000	0	0
PRKCE	0.021	0.017	-10000	0	-0.12	8	8
JNK2/NFAT4	0.034	0.024	-10000	0	-0.2	3	3
BAD/BCL-XL	0.029	0.028	-10000	0	-0.11	22	22
PRKCD	0.02	0.018	-10000	0	-0.12	8	8
NUP214	0.022	0.007	-10000	0	-0.12	1	1
PRKCZ	0.023	0.001	-10000	0	-10000	0	0
PRKCA	0.011	0.037	-10000	0	-0.12	40	40
PRKCG	0.021	0.016	-10000	0	-0.12	7	7
PRKCQ	0.015	0.03	-10000	0	-0.12	24	24
FKBP38/BCL2	0.023	0.035	-10000	0	-0.08	55	55
EP300	0.022	0.01	-10000	0	-0.12	2	2
PRKCB1	0.014	0.035	-10000	0	-0.12	35	35
CSNK2A1	0.021	0.015	-10000	0	-0.12	6	6
NFATc/JNK1	0.039	0.068	-10000	0	-0.24	18	18
CaM/Ca2+/FKBP38	0.024	0.028	-10000	0	-0.074	39	39
FKBP12/FK506	0.016	0.014	-10000	0	-0.11	7	7
CSNK1A1	0.017	0.017	-10000	0	-0.085	12	12
CaM/Ca2+/CAMK IV	0.023	0.028	-10000	0	-0.1	14	14
NFATc/ERK1	0.04	0.066	-10000	0	-0.24	14	14
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV	0.014	0.08	-10000	0	-0.22	28	28
NR4A1	0.017	0.082	-10000	0	-0.21	36	36
GSK3B	0.022	0.011	-10000	0	-0.12	3	3
positive T cell selection	0.024	0.022	-10000	0	-0.24	2	2
NFAT1/CK1 alpha	0.021	0.044	-10000	0	-0.17	17	17
RCH1/ KPNB1	0.01	0.061	-10000	0	-0.13	82	82
YWHAQ	0.023	0.003	-10000	0	-10000	0	0
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
AKAP5	0.023	0.009	-10000	0	-0.12	2	2
MEF2D	0.023	0.002	-10000	0	-10000	0	0
mol:FK506	0	0	-10000	0	-10000	0	0
YWHAZ	0.023	0.003	-10000	0	-10000	0	0
NFATc/p38 alpha	0.041	0.067	-10000	0	-0.24	17	17
CREBBP	0.021	0.016	-10000	0	-0.12	6	6
BCL2	0.016	0.031	-10000	0	-0.12	27	27

×

Hedgehog signaling events mediated by Gli proteins

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
HDAC1	0.019	0.02	-9999	-0.12	10	10
HDAC2	0.019	0.021	-9999	-0.12	12	12
GNB1/GNG2	0.04	0.034	-9999	-0.11	23	23
forebrain development	0.027	0.11	-9999	-0.42	21	21
GNAO1	0.011	0.042	-9999	-0.12	51	51
SMO/beta Arrestin2	0.035	0.021	-9999	-0.097	13	13
SMO	0.024	0.011	-9999	-0.12	3	3
ARRB2	0.023	0.014	-9999	-0.12	5	5
GLI3/SPOP	0.006	0.11	-9999	-0.3	37	37
mol:GTP	0.001	0.001	-9999	-10000	0	0
GSK3B	0.022	0.011	-9999	-0.12	3	3
GNAI2	0.023	0.011	-9999	-0.12	3	3
SIN3/HDAC complex	0.051	0.032	-9999	-0.098	20	20
GNAI1	0.013	0.035	-9999	-0.12	35	35
XPO1	0.025	0.01	-9999	-0.12	2	2
GLI1/Su(fu)	0.034	0.11	-9999	-0.38	27	27
SAP30	0.023	0	-9999	-10000	0	0
mol:GDP	0.024	0.011	-9999	-0.12	3	3
MIM/GLI2A	0.022	0.034	-9999	-0.11	31	31
IFT88	0.016	0.03	-9999	-0.12	25	25
GNAI3	0.022	0.009	-9999	-0.12	1	1
GLI2	0.036	0.043	-9999	-0.23	8	8
GLI3	-0.005	0.11	-9999	-0.32	36	36
CSNK1D	0.023	0.001	-9999	-10000	0	0
CSNK1E	0.022	0.015	-9999	-0.12	6	6
SAP18	0.023	0.003	-9999	-10000	0	0
embryonic digit morphogenesis	0.016	0.03	-9999	-0.12	25	25
GNG2	0.02	0.018	-9999	-0.12	9	9
Gi family/GTP	0.009	0.07	-9999	-0.14	86	86
SIN3B	0.021	0.015	-9999	-0.12	6	6
SIN3A	0.021	0.014	-9999	-0.12	5	5
GLI3/Su(fu)	0.015	0.1	-9999	-0.33	27	27
GLI2/Su(fu)	0.053	0.045	-9999	-0.22	9	9
FOXA2	0.028	0.085	-9999	-0.74	5	5
neural tube patterning	0.027	0.11	-9999	-0.42	21	21
SPOP	0.022	0.011	-9999	-0.12	3	3
Su(fu)/PIAS1	0.036	0.041	-9999	-0.2	13	13
GNB1	0.023	0.007	-9999	-0.12	1	1
CSNK1G2	0.022	0.011	-9999	-0.12	3	3
CSNK1G3	0.022	0.007	-9999	-0.12	1	1
MTSS1	0.022	0.034	-9999	-0.11	31	31
embryonic limb morphogenesis	0.027	0.11	-9999	-0.42	21	21
SUFU	0.026	0.041	-9999	-0.22	12	12
LGALS3	0.018	0.023	-9999	-0.12	14	14
catabolic process	0.032	0.1	-9999	-0.32	25	25
GLI3A/CBP	0.033	0.022	-9999	-0.14	7	7
KIF3A	0.019	0.021	-9999	-0.12	12	12
GLI1	0.027	0.11	-9999	-0.43	21	21
RAB23	0.022	0.011	-9999	-0.12	3	3
CSNK1A1	0.022	0.007	-9999	-0.12	1	1
IFT172	0.021	0.014	-9999	-0.12	5	5
RBBP7	0.021	0.011	-9999	-0.12	3	3
Su(fu)/Galectin3	0.031	0.044	-9999	-0.19	16	16
GNAZ	0.023	0.011	-9999	-0.12	3	3
RBBP4	0.021	0.014	-9999	-0.12	5	5
CSNK1G1	0.023	0.009	-9999	-0.12	2	2
PIAS1	0.022	0.009	-9999	-0.12	2	2
PRKACA	0.021	0.017	-9999	-0.12	8	8
GLI2/SPOP	0.045	0.044	-9999	-0.23	8	8
STK36	0.022	0.022	-9999	-0.12	12	12
Gi family/GNB1/GNG2/GDP	0.009	0.077	-9999	-0.22	31	31
PTCH1	0.033	0.11	-9999	-0.56	7	7
MIM/GLI1	0.043	0.11	-9999	-0.4	23	23
CREBBP	0.033	0.022	-9999	-0.14	7	7
Su(fu)/SIN3/HDAC complex	0.02	0.094	-9999	-0.31	28	28

×

S1P1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	0.029	0.054	-9999	-0.15	39	39
PDGFRB	0.01	0.042	-9999	-0.12	52	52
SPHK1	0.001	0.015	-9999	-10000	0	0
mol:S1P	0.015	0.027	-9999	-10000	0	0
S1P1/S1P/Gi	0.023	0.07	-9999	-0.28	17	17
GNAO1	0.01	0.042	-9999	-0.12	51	51
PDGFB-D/PDGFRB/PLCgamma1	0.009	0.086	-9999	-0.26	26	26
PLCG1	0.021	0.07	-9999	-0.25	21	21
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.01	0.042	-9999	-0.12	52	52
GNAI2	0.022	0.011	-9999	-0.12	3	3
GNAI3	0.022	0.009	-9999	-0.12	1	1
GNAI1	0.012	0.035	-9999	-0.12	35	35
mol:GDP	0	0	-9999	-10000	0	0
EDG1	0.023	0.047	-9999	-0.19	9	9
S1P1/S1P	0.025	0.052	-9999	-0.22	8	8
negative regulation of cAMP metabolic process	0.023	0.069	-9999	-0.27	17	17
MAPK3	0.021	0.09	-9999	-0.42	14	14
calcium-dependent phospholipase C activity	-0.001	0.001	-9999	-10000	0	0
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
RhoA/GDP	0.016	0.016	-9999	-0.14	6	6
KDR	0.025	0.022	-9999	-0.095	16	16
PLCB2	0.026	0.049	-9999	-0.2	8	8
RAC1	0.023	0.002	-9999	-10000	0	0
RhoA/GTP	0.021	0.046	-9999	-0.19	11	11
receptor internalization	0.024	0.05	-9999	-0.2	9	9
PTGS2	0.001	0.14	-9999	-0.92	9	9
Rac1/GTP	0.021	0.045	-9999	-0.19	9	9
RHOA	0.023	0.006	-9999	-0.12	1	1
VEGFA	0.023	0.022	-9999	-0.11	13	13
negative regulation of T cell proliferation	0.023	0.069	-9999	-0.27	17	17
GO:0007205	0	0	-9999	-10000	0	0
GNAZ	0.022	0.011	-9999	-0.12	3	3
MAPK1	0.021	0.091	-9999	-0.42	14	14
S1P1/S1P/PDGFB-D/PDGFRB	0.028	0.065	-9999	-0.24	11	11
ABCC1	0.021	0.018	-9999	-0.12	8	8

×

Calcium signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC1	0.025	0.021	-9999	-0.089	14	14
NFATC2	0.024	0.022	-9999	-0.084	15	15
NFATC3	0.026	0.02	-9999	-0.094	11	11
CD40LG	0.045	0.079	-9999	-0.22	13	13
PTGS2	0.037	0.089	-9999	-0.22	23	23
JUNB	0.007	0.042	-9999	-0.12	52	52
CaM/Ca2+/Calcineurin A alpha-beta B1	0.019	0.021	-9999	-0.12	12	12
CaM/Ca2+	0.019	0.021	-9999	-0.12	12	12
CALM1	0.024	0.014	-9999	-0.12	5	5
JUN	0.017	0.033	-9999	-0.12	30	30
mol:Ca2+	0.002	0.003	-9999	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0.016	0.012	-9999	-0.086	7	7
FOSL1	0.021	0.018	-9999	-0.12	9	9
CREM	0.021	0.012	-9999	-0.12	4	4
Jun/NFAT1-c-4/p21SNFT	0.062	0.06	-9999	-0.17	9	9
FOS	-0.002	0.053	-9999	-0.12	95	95
IFNG	0.041	0.085	-9999	-0.24	14	14
AP-1/NFAT1-c-4	0.089	0.12	-9999	-0.24	13	13
FASLG	0.044	0.08	-9999	-0.22	14	14
NFAT1-c-4/ICER1	0.052	0.038	-9999	-0.13	8	8
IL2RA	0.043	0.081	-9999	-0.21	16	16
FKBP12/FK506	0.016	0.014	-9999	-0.11	7	7
CSF2	0.044	0.079	-9999	-0.22	13	13
JunB/Fra1/NFAT1-c-4	0.046	0.06	-9999	-0.14	17	17
IL4	0.044	0.079	-9999	-0.23	11	11
IL2	0.008	0.015	-9999	-10000	0	0
IL3	0.039	0.05	-9999	-0.61	3	3
FKBP1A	0.022	0.012	-9999	-0.12	4	4
BATF3	0	0	-9999	-10000	0	0
mol:FK506	0	0	-9999	-10000	0	0
POU2F1	0.031	0.007	-9999	-0.12	1	1

×

VEGFR1 specific signals

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer	0.026	0.057	-9999	-0.28	10	10
VEGFR1 homodimer/NRP1	0.014	0.05	-9999	-0.4	5	5
mol:DAG	0.022	0.05	-9999	-0.26	10	10
VEGFR1 homodimer/NRP1/VEGFR 121	0.019	0.06	-9999	-0.29	10	10
CaM/Ca2+	0.032	0.053	-9999	-0.25	10	10
HIF1A	0.029	0.033	-9999	-0.23	7	7
GAB1	0.02	0.021	-9999	-0.12	12	12
AKT1	0.014	0.072	-9999	-0.24	26	26
PLCG1	0.022	0.05	-9999	-0.26	10	10
NOS3	0.029	0.061	-9999	-0.26	12	12
CBL	0.023	0.006	-9999	-0.12	1	1
mol:NO	0.029	0.059	-9999	-0.26	12	12
FLT1	0.027	0.05	-9999	-0.47	5	5
PGF	0.021	0.018	-9999	-0.12	9	9
VEGFR1 homodimer/NRP2/VEGFR121	0.015	0.077	-9999	-0.25	20	20
CALM1	0.022	0.014	-9999	-0.12	5	5
PIK3CA	0.02	0.017	-9999	-0.12	7	7
eNOS/Hsp90	0.039	0.063	-9999	-0.25	13	13
endothelial cell proliferation	0.006	0.068	-9999	-0.31	12	12
mol:Ca2+	0.022	0.05	-9999	-0.26	10	10
MAPK3	0.016	0.045	-9999	-0.24	9	9
MAPK1	0.016	0.046	-9999	-0.23	11	11
PIK3R1	0.015	0.031	-9999	-0.12	27	27
PLGF homodimer	0.021	0.018	-9999	-0.12	9	9
PRKACA	0.021	0.017	-9999	-0.12	8	8
RP11-342D11.1	0	0	-9999	-10000	0	0
CAV1	0.012	0.039	-9999	-0.12	43	43
VEGFA homodimer	0.019	0.021	-9999	-0.12	11	11
VEGFR1 homodimer/VEGFA homodimer	0.026	0.06	-9999	-0.32	10	10
platelet activating factor biosynthetic process	0.017	0.044	-9999	-0.22	10	10
PI3K	0.032	0.074	-9999	-0.23	22	22
PRKCA	0.016	0.047	-9999	-0.23	11	11
PRKCB	0.016	0.045	-9999	-0.24	10	10
VEGFR1 homodimer/PLGF homodimer	0.029	0.054	-9999	-0.36	6	6
VEGFA	0.019	0.021	-9999	-0.12	11	11
VEGFB	0.015	0.033	-9999	-0.12	30	30
mol:IP3	0.022	0.05	-9999	-0.26	10	10
RASA1	0.02	0.052	-9999	-0.24	14	14
NRP2	0.011	0.036	-9999	-0.12	38	38
VEGFR1 homodimer	0.027	0.05	-9999	-0.47	5	5
VEGFB homodimer	0.015	0.033	-9999	-0.12	30	30
NCK1	0.02	0.019	-9999	-0.12	9	9
eNOS/Caveolin-1	0.034	0.064	-9999	-0.27	11	11
PTPN11	0.022	0.011	-9999	-0.12	3	3
mol:PI-3-4-5-P3	0.03	0.073	-9999	-0.23	22	22
mol:L-citrulline	0.029	0.059	-9999	-0.26	12	12
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP	0.034	0.073	-9999	-0.23	18	18
VEGFR1 homodimer/VEGFA homodimer/NCK1	0.024	0.072	-9999	-0.26	16	16
CD2AP	0.02	0.017	-9999	-0.12	7	7
PI3K/GAB1	0.037	0.077	-9999	-0.22	25	25
PDPK1	0.015	0.063	-9999	-0.22	24	24
VEGFR1 homodimer/VEGFA homodimer/SHP2	0.028	0.07	-9999	-0.25	19	19
mol:NADP	0.029	0.059	-9999	-0.26	12	12
HSP90AA1	0.023	0.003	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	0.033	0.071	-9999	-0.23	18	18
VEGFR1 homodimer/NRP2	0.02	0.061	-9999	-0.3	11	11

×

JNK signaling in the CD4+ TCR pathway

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

×

Insulin-mediated glucose transport

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Insulin responsive Vesicles	0.021	0.074	0.18	5	-0.21	24	29
CaM/Ca2+	0.014	0.02	-10000	0	-0.12	12	12
AKT1	0.021	0.019	-10000	0	-0.12	10	10
AKT2	0.019	0.025	-10000	0	-0.12	17	17
STXBP4	0.018	0.026	-10000	0	-0.12	19	19
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucose	0.015	0.067	0.18	7	-0.2	20	27
YWHAZ	0.023	0.003	-10000	0	-10000	0	0
CALM1	0.022	0.014	-10000	0	-0.12	5	5
YWHAQ	0.023	0.003	-10000	0	-10000	0	0
TBC1D4	0.02	0.017	-10000	0	-0.071	20	20
mol:Ca2+	0	0	-10000	0	-10000	0	0
YWHAH	0.021	0.014	-10000	0	-0.12	5	5
YWHAB	0.023	0.007	-10000	0	-0.12	1	1
SNARE/Synip	0.033	0.041	-10000	0	-0.13	19	19
YWHAG	0.02	0.022	-10000	0	-0.12	13	13
ASIP	0.021	0.015	-10000	0	-0.12	6	6
PRKCI	0.016	0.028	-10000	0	-0.12	22	22
AS160/CaM/Ca2+	0.014	0.02	-10000	0	-0.12	12	12
RHOQ	0.021	0.017	-10000	0	-0.12	8	8
GYS1	0.025	0.017	-10000	0	-0.22	1	1
PRKCZ	0.023	0	-10000	0	-10000	0	0
TRIP10	0.021	0.018	-10000	0	-0.12	9	9
TC10/GTP/CIP4/Exocyst	0.026	0.027	-10000	0	-0.12	14	14
AS160/14-3-3	0.024	0.064	-10000	0	-0.25	19	19
VAMP2	0.015	0.033	-10000	0	-0.12	30	30
SLC2A4	0.015	0.072	0.18	6	-0.22	20	26
STX4	0.022	0.012	-10000	0	-0.12	4	4
GSK3B	0.023	0.03	-10000	0	-0.2	7	7
SFN	0.014	0.032	-10000	0	-0.12	29	29
LNPEP	0.016	0.027	-10000	0	-0.12	20	20
YWHAE	0.022	0.014	-10000	0	-0.12	5	5

×

Effects of Botulinum toxin

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
STX1A	0.011	0.006	-9999	-0.077	3	3
UniProt:P19321	0	0	-9999	-10000	0	0
RIMS1/UNC13B	0.032	0.016	-9999	-0.085	10	10
STXBP1	0.02	0.02	-9999	-0.12	11	11
ACh/CHRNA1	0.013	0.025	-9999	-0.063	49	49
RAB3GAP2/RIMS1/UNC13B	0.041	0.029	-9999	-0.091	25	25
mol:Ca2+	0	0	-9999	-10000	0	0
UniProt:P30996	0	0	-9999	-10000	0	0
UniProt:Q60393	0	0	-9999	-10000	0	0
CST086	0	0	-9999	-10000	0	0
RIMS1	0.023	0.006	-9999	-0.12	1	1
mol:ACh	0.005	0.01	-9999	-0.056	6	6
RAB3GAP2	0.022	0.009	-9999	-0.12	2	2
STX1A/SNAP25/VAMP2	0.039	0.031	-9999	-0.098	9	9
UniProt:P10844	0	0	-9999	-10000	0	0
muscle contraction	0.013	0.025	-9999	-0.063	49	49
UNC13B	0.021	0.016	-9999	-0.12	7	7
CHRNA1	0.011	0.04	-9999	-0.12	47	47
UniProt:P10845	0	0	-9999	-10000	0	0
ACh/Synaptotagmin 1	0.015	0.023	-9999	-0.062	39	39
SNAP25	0.004	0.017	-9999	-0.19	1	1
VAMP2	0.004	0.016	-9999	-0.18	2	2
SYT1	0.014	0.036	-9999	-0.12	36	36
UniProt:Q00496	0	0	-9999	-10000	0	0
STXIA/STXBP1	0.024	0.013	-9999	-0.057	14	14
STX1A/SNAP25 fragment 1/VAMP2	0.039	0.031	-9999	-0.098	9	9

×

Insulin Pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CBL/APS/CAP	0.034	0.028	-9999	-0.1	11	11
TC10/GTP	0.031	0.024	-9999	-0.082	15	15
Insulin Receptor/Insulin/IRS1/Shp2	0.049	0.042	-9999	-0.1	29	29
HRAS	0.023	0.006	-9999	-0.12	1	1
APS homodimer	0	0	-9999	-10000	0	0
GRB14	0.013	0.036	-9999	-0.12	38	38
FOXO3	0.009	0.065	-9999	-0.6	6	6
AKT1	0.015	0.048	-9999	-0.13	28	28
INSR	0.023	0.017	-9999	-0.11	9	9
Insulin Receptor/Insulin	0.06	0.028	-9999	-0.19	2	2
mol:GTP	0	0	-9999	-10000	0	0
GRB10	0.022	0.014	-9999	-0.12	5	5
SORBS1	0.02	0.021	-9999	-0.12	12	12
CRK	0.021	0.016	-9999	-0.12	7	7
PTPN1	0.026	0.021	-9999	-0.19	2	2
CAV1	0.02	0.027	-9999	-0.091	13	13
CBL/APS/CAP/Crk-II/C3G	0.051	0.024	-9999	-0.1	7	7
Insulin Receptor/Insulin/IRS1/NCK2	0.055	0.03	-9999	-0.09	13	13
mol:GDP	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	0.025	0.052	-9999	-0.094	69	69
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B	0.038	0.053	-9999	-0.3	12	12
RPS6KB1	0.014	0.05	-9999	-0.14	32	32
PARD6A	0.023	0.009	-9999	-0.12	2	2
CBL	0.023	0.006	-9999	-0.12	1	1
tumor necrosis factor-mediated signaling pathway	0	0	-9999	-10000	0	0
DOK1	0.009	0.074	-9999	-0.68	6	6
PIK3R1	0.015	0.031	-9999	-0.12	27	27
Insulin Receptor/Insuli/IRS1/GRB2/Shc	0.026	0.056	-9999	-0.16	23	23
HRAS/GTP	-0.007	0.02	-9999	-0.12	6	6
Insulin Receptor	0.023	0.017	-9999	-0.11	9	9
Insulin Receptor/Insuli/IRS1/GRB2/SHC	0.063	0.034	-9999	-0.13	2	2
PRKCI	-0.012	0.13	-9999	-0.38	63	63
Insulin Receptor/Insulin/GRB14/PDK1	0.007	0.046	-9999	-0.14	25	25
SHC1	0.023	0.001	-9999	-10000	0	0
negative regulation of MAPKKK cascade	0.021	0.079	-9999	-0.47	9	9
PI3K	0.033	0.057	-9999	-0.095	69	69
NCK2	0.023	0.006	-9999	-0.12	1	1
RHOQ	0.021	0.017	-9999	-0.12	8	8
mol:H2O2	0	0.002	-9999	-10000	0	0
HRAS/GDP	0.017	0.008	-9999	-0.11	2	2
AKT2	0.015	0.049	-9999	-0.13	27	27
PRKCZ	0.028	0.063	-9999	-0.36	13	13
SH2B2	0	0	-9999	-10000	0	0
SHC/SHIP	0.025	0.02	-9999	-0.079	13	13
F2RL2	0.019	0.023	-9999	-0.12	15	15
TRIP10	0.021	0.018	-9999	-0.12	9	9
Insulin Receptor/Insulin/Shc	0.044	0.02	-9999	-0.095	7	7
TC10/GTP/CIP4/Exocyst	0.026	0.027	-9999	-0.12	14	14
Insulin Receptor/Insulin/SHC/GRB2/Sos1	0.057	0.046	-9999	-0.16	5	5
RAPGEF1	0.023	0	-9999	-10000	0	0
RASA1	0.021	0.012	-9999	-0.12	3	3
NCK1	0.02	0.019	-9999	-0.12	9	9
CBL/APS/CAP/Crk-II	0.04	0.024	-9999	-0.11	7	7
TC10/GDP	0.014	0.022	-9999	-0.11	16	16
Insulin Receptor/Insulin/SHC/GRB10	0.056	0.029	-9999	-0.092	15	15
INPP5D	0.012	0.018	-9999	-0.086	12	12
SOS1	0.017	0.027	-9999	-0.12	20	20
SGK1	-0.002	0.004	-9999	-10000	0	0
mol:cAMP	0	0	-9999	-10000	0	0
PTPN11	0.022	0.011	-9999	-0.12	3	3
IRS1	0.019	0.023	-9999	-0.12	14	14
p62DOK/RasGAP	0.021	0.08	-9999	-0.48	9	9
INS	0.024	0.011	-9999	-0.12	3	3
mol:PI-3-4-P2	0.011	0.018	-9999	-0.085	12	12
GRB2	0.023	0.006	-9999	-0.12	1	1
EIF4EBP1	0.015	0.046	-9999	-0.12	31	31
PTPRA	0.024	0.012	-9999	-0.12	4	4
PIK3CA	0.02	0.017	-9999	-0.12	7	7
TC10/GTP/CIP4	0.026	0.027	-9999	-0.12	14	14
PDPK1	0.023	0.007	-9999	-0.12	1	1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos	0.027	0.048	-9999	-0.22	5	5
Insulin Receptor/Insulin/IRS1	0.04	0.027	-9999	-0.094	12	12
Insulin Receptor/Insulin/IRS3	0.034	0.024	-9999	-0.13	7	7
Par3/Par6	0.045	0.032	-9999	-0.089	18	18

×

Alternative 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
IKK alpha homodimer	0.024	0.04	-9999	-0.13	35	35
FBXW11	0.023	0.003	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.023	0.003	-9999	-10000	0	0
CHUK	0.021	0.013	-9999	-0.12	4	4
NF kappa B2 p100/RelB	0.055	0.045	-9999	-0.091	44	44
NFKB1	0.021	0.013	-9999	-0.12	4	4
MAP3K14	0.023	0.006	-9999	-0.12	1	1
NF kappa B1 p50/RelB	0.02	0.048	-9999	-0.13	48	48
RELB	0.022	0.011	-9999	-0.12	3	3
NFKB2	0.023	0.009	-9999	-0.12	2	2
NF kappa B2 p52/RelB	0.029	0.02	-9999	-0.1	12	12
regulation of B cell activation	0.028	0.02	-9999	-0.1	12	12

×

Signaling events mediated by HDAC Class II

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G beta1gamma2/HDAC5	0.052	0.033	-10000	0	-0.098	21	21
HDAC3	0.023	0.002	-10000	0	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	-0.007	0.028	-10000	0	-0.11	36	36
GATA1/HDAC4	0.034	0.004	-10000	0	-0.071	1	1
GATA1/HDAC5	0.034	0.004	-10000	0	-0.071	1	1
GATA2/HDAC5	0.032	0.016	-10000	0	-0.071	13	13
HDAC5/BCL6/BCoR	0.034	0.044	-10000	0	-0.12	41	41
HDAC9	0.015	0.032	-10000	0	-0.12	28	28
Glucocorticoid receptor/Hsp90/HDAC6	0.031	0.047	-10000	0	-0.12	45	45
HDAC4/ANKRA2	0.028	0.031	-10000	0	-0.14	14	14
HDAC5/YWHAB	0.032	0.02	-10000	0	-0.13	8	8
NPC/RanGAP1/SUMO1/Ubc9	0.015	0.037	-10000	0	-0.14	30	30
GATA2	0.02	0.022	-10000	0	-0.12	13	13
HDAC4/RFXANK	0.025	0.037	-10000	0	-0.11	37	37
BCOR	0.023	0.007	-10000	0	-0.12	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
HDAC10	0.023	0	-10000	0	-10000	0	0
HDAC5	0.023	0	-10000	0	-10000	0	0
GNB1/GNG2	0.026	0.035	-10000	0	-0.14	20	20
Histones	0.026	0.035	-10000	0	-0.12	26	26
ADRBK1	0.023	0.001	-10000	0	-10000	0	0
HDAC4	0.023	0	-10000	0	-10000	0	0
XPO1	0.022	0.01	-10000	0	-0.12	2	2
HDAC5/ANKRA2	0.028	0.031	-10000	0	-0.11	26	26
HDAC4/Ubc9	0.034	0.007	-10000	0	-0.14	1	1
HDAC7	0	0	-10000	0	-10000	0	0
HDAC5/14-3-3 E	0.031	0.023	-10000	0	-0.11	13	13
TUBA1B	0.023	0	-10000	0	-10000	0	0
HDAC6	0.019	0.023	-10000	0	-0.12	15	15
HDAC5/RFXANK	0.025	0.037	-10000	0	-0.11	37	37
CAMK4	0.016	0.031	-10000	0	-0.12	27	27
Tubulin/HDAC6	0.043	0.02	-10000	0	-10000	0	0
SUMO1	0.023	0.009	-10000	0	-0.12	2	2
EntrezGene:9972	0	0	-10000	0	-10000	0	0
YWHAB	0.023	0.007	-10000	0	-0.12	1	1
GATA1	0.023	0.006	-10000	0	-0.12	1	1
EntrezGene:8021	0	0	-10000	0	-10000	0	0
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
NR3C1	0.021	0.015	-10000	0	-0.12	5	5
SUMO1/HDAC4	0.036	0.035	-10000	0	-0.17	6	6
SRF	0.018	0.026	-10000	0	-0.12	19	19
HDAC4/YWHAB	0.032	0.02	-10000	0	-0.13	8	8
Tubulin	0.033	0.012	-10000	0	-10000	0	0
HDAC4/14-3-3 E	0.031	0.023	-10000	0	-0.14	8	8
GNB1	0.023	0.007	-10000	0	-0.12	1	1
RANGAP1	0.023	0.006	-10000	0	-0.12	1	1
BCL6/BCoR	0.019	0.05	-10000	0	-0.15	41	41
HDAC4/HDAC3/SMRT (N-CoR2)	0.043	0.022	-10000	0	-0.11	6	6
HDAC4/SRF	0.038	0.03	-10000	0	-0.12	5	5
HDAC4/ER alpha	0.018	0.049	-10000	0	-0.14	43	43
EntrezGene:23225	0	0	-10000	0	-10000	0	0
positive regulation of chromatin silencing	0.026	0.035	-10000	0	-0.12	26	26
cell motility	0.043	0.019	-10000	0	-10000	0	0
EntrezGene:23636	0	0	-10000	0	-10000	0	0
UBE2I	0.023	0.001	-10000	0	-10000	0	0
HDAC7/HDAC3	0.016	0.012	-10000	0	-0.15	3	3
BCL6	0.019	0.02	-10000	0	-0.12	10	10
HDAC4/CaMK II delta B	0.023	0	-10000	0	-10000	0	0
Hsp90/HDAC6	0.028	0.031	-10000	0	-0.1	28	28
ESR1	0.018	0.024	-10000	0	-0.12	15	15
HDAC6/HDAC11	0.029	0.028	-10000	0	-0.095	26	26
Ran/GTP/Exportin 1	0.034	0.049	-10000	0	-0.15	30	30
NPC	0.009	0.023	-10000	0	-0.096	27	27
MEF2C	0.02	0.02	-10000	0	-0.12	11	11
RAN	0.023	0.002	-10000	0	-10000	0	0
HDAC4/MEF2C	0.059	0.037	-10000	0	-0.091	22	22
GNG2	0.02	0.018	-10000	0	-0.12	9	9
NCOR2	0.019	0.023	-10000	0	-0.12	15	15
TUBB2A	0.021	0.017	-10000	0	-0.12	8	8
HDAC11	0.022	0.012	-10000	0	-0.12	4	4
HSP90AA1	0.023	0.003	-10000	0	-10000	0	0
RANBP2	0.022	0.01	-10000	0	-0.12	2	2
ANKRA2	0.02	0.021	-10000	0	-0.12	12	12
RFXANK	0.018	0.024	-10000	0	-0.12	16	16
nuclear import	-0.034	0.033	0.16	14	-10000	0	14

×

Sphingosine 1-phosphate (S1P) 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.022	0.011	-9999	-0.12	3	3
SPHK1	0.022	0.015	-9999	-0.12	6	6
GNAI2	0.022	0.011	-9999	-0.12	3	3
mol:S1P	0.019	0.029	-9999	-0.18	11	11
GNAO1	0.01	0.042	-9999	-0.12	51	51
mol:Sphinganine-1-P	0.022	0.012	-9999	-0.071	9	9
growth factor activity	0	0	-9999	-10000	0	0
S1P/S1P2/G12/G13	0.037	0.033	-9999	-0.14	12	12
GNAI3	0.021	0.008	-9999	-0.12	1	1
G12/G13	0.03	0.028	-9999	-0.14	14	14
S1PR3	0	0	-9999	-10000	0	0
S1PR2	0	0	-9999	-10000	0	0
EDG1	0.021	0.016	-9999	-0.12	7	7
S1P1/S1P	0.028	0.028	-9999	-0.14	11	11
S1PR5	0	0	-9999	-10000	0	0
S1PR4	0	0	-9999	-10000	0	0
GNAI1	0.012	0.035	-9999	-0.12	35	35
S1P/S1P5/G12	0.026	0.024	-9999	-0.13	11	11
S1P/S1P3/Gq	0.022	0.057	-9999	-0.22	26	26
S1P/S1P4/Gi	0.002	0.074	-9999	-0.16	86	86
GNAQ	0.021	0.016	-9999	-0.12	6	6
GNAZ	0.022	0.011	-9999	-0.12	3	3
GNA14	0.02	0.02	-9999	-0.12	11	11
GNA15	0.021	0.017	-9999	-0.12	8	8
GNA12	0.023	0.001	-9999	-10000	0	0
GNA13	0.022	0.009	-9999	-0.12	2	2
GNA11	0.022	0.014	-9999	-0.12	5	5
ABCC1	0.021	0.017	-9999	-0.12	8	8

×

Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.019	0.02	-9999	-0.12	10	10
Ran/GTP/Exportin 1/HDAC4	-0.008	0.033	-9999	-0.15	26	26
MDM2/SUMO1	0.032	0.041	-9999	-0.18	8	8
HDAC4	0.023	0	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC1	-0.013	0.043	-9999	-0.17	30	30
SUMO1	0.023	0.009	-9999	-0.12	2	2
NPC/RanGAP1/SUMO1	0.01	0.036	-9999	-0.14	29	29
mol:GTP	0	0	-9999	-10000	0	0
XPO1	0.02	0.03	-9999	-0.13	17	17
EntrezGene:23636	0	0	-9999	-10000	0	0
RAN	0.023	0.002	-9999	-10000	0	0
EntrezGene:8021	0	0	-9999	-10000	0	0
RANBP2	0.022	0.01	-9999	-0.12	2	2
SUMO1/HDAC4	0.036	0.035	-9999	-0.17	6	6
SUMO1/HDAC1	0.029	0.048	-9999	-0.19	13	13
RANGAP1	0.023	0.006	-9999	-0.12	1	1
MDM2/SUMO1/SUMO1	0.047	0.043	-9999	-0.11	31	31
NPC/RanGAP1/SUMO1/RanBP2/Ubc9	0.015	0.037	-9999	-0.14	30	30
Ran/GTP	0.026	0.036	-9999	-0.12	30	30
EntrezGene:23225	0	0	-9999	-10000	0	0
MDM2	0.02	0.02	-9999	-0.12	11	11
UBE2I	0.023	0.001	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.025	0.047	-9999	-0.15	30	30
NPC	0.009	0.023	-9999	-0.096	27	27
PIAS2	0.021	0.017	-9999	-0.12	8	8
PIAS1	0.022	0.009	-9999	-0.12	2	2
EntrezGene:9972	0	0	-9999	-10000	0	0

×

Angiopoietin receptor Tie2-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	0.022	0.17	-9999	-0.68	14	14
NCK1/PAK1/Dok-R	-0.028	0.072	-9999	-0.32	15	15
NCK1/Dok-R	0.049	0.087	-9999	-0.84	2	2
PIK3CA	0.019	0.017	-9999	-0.12	7	7
mol:beta2-estradiol	-0.008	0.012	-9999	-10000	0	0
RELA	0.023	0.009	-9999	-0.12	2	2
SHC1	0.024	0.002	-9999	-10000	0	0
Rac/GDP	0.016	0.015	-9999	-0.15	5	5
F2	0.014	0.02	-9999	-0.14	4	4
TNIP2	0.021	0.017	-9999	-0.12	8	8
NF kappa B/RelA	0.057	0.087	-9999	-0.79	2	2
FN1	-0.013	0.056	-9999	-0.12	114	114
PLD2	0.041	0.076	-9999	-0.87	2	2
PTPN11	0.022	0.011	-9999	-0.12	3	3
GRB14	0.013	0.036	-9999	-0.12	38	38
ELK1	0.044	0.074	-9999	-0.82	2	2
GRB7	0.018	0.026	-9999	-0.12	18	18
PAK1	0.016	0.029	-9999	-0.12	23	23
Tie2/Ang1/alpha5/beta1 Integrin	0.013	0.1	-9999	-0.82	2	2
CDKN1A	0.027	0.18	-9999	-0.61	41	41
ITGA5	0.013	0.036	-9999	-0.12	38	38
mol:GTP	0	0	-9999	-10000	0	0
RasGAP/Dok-R	0.051	0.084	-9999	-0.84	2	2
CRK	0.021	0.016	-9999	-0.12	7	7
mol:NO	0.03	0.14	-9999	-0.5	17	17
PLG	0.041	0.077	-9999	-0.87	2	2
mol:GDP	0	0	-9999	-10000	0	0
chemokinesis	0.036	0.14	-9999	-0.74	6	6
GRB2	0.023	0.006	-9999	-0.12	1	1
PIK3R1	0.015	0.031	-9999	-0.12	27	27
ANGPT2	-0.029	0.27	-9999	-1	39	39
BMX	0.041	0.077	-9999	-0.87	2	2
ANGPT1	0.022	0.048	-9999	-10000	0	0
tube development	0.009	0.2	-9999	-0.69	41	41
ANGPT4	0.023	0.01	-9999	-0.12	2	2
response to hypoxia	0.002	0.008	-9999	-0.061	2	2
Tie2/Ang1/GRB14	0.043	0.083	-9999	-0.88	2	2
alpha5/beta1 Integrin	0.016	0.048	-9999	-0.14	34	34
FGF2	0.023	0.01	-9999	-0.12	2	2
STAT5A (dimer)	0.024	0.23	-9999	-0.78	41	41
mol:L-citrulline	0.03	0.14	-9999	-0.5	17	17
AGTR1	0.021	0.017	-9999	-0.12	4	4
MAPK14	0.037	0.12	-9999	-1	4	4
Tie2/SHP2	0.036	0.083	-9999	-0.67	4	4
TEK	0.033	0.088	-9999	-0.84	3	3
RPS6KB1	0.025	0.15	-9999	-0.71	9	9
Angiotensin II/AT1	0.016	0.018	-9999	-0.079	4	4
Tie2/Ang1/GRB2	0.048	0.081	-9999	-0.88	2	2
MAPK3	0.042	0.073	-9999	-0.81	2	2
MAPK1	0.041	0.074	-9999	-0.81	2	2
Tie2/Ang1/GRB7	0.045	0.083	-9999	-0.88	2	2
NFKB1	0.021	0.013	-9999	-0.12	4	4
MAPK8	0.039	0.077	-9999	-0.87	2	2
PI3K	0.024	0.16	-9999	-0.92	6	6
FES	0.045	0.097	-9999	-1	2	2
Crk/Dok-R	0.055	0.082	-9999	-0.84	2	2
Tie2/Ang1/ABIN2	0.047	0.081	-9999	-0.88	2	2
blood circulation	0	0	-9999	-10000	0	0
negative regulation of caspase activity	0.024	0.16	-9999	-0.62	14	14
STAT5A	0.022	0.013	-9999	-0.12	4	4
mol:ROS	0	0	-9999	-10000	0	0
PTK2	0.024	0.15	-9999	-0.74	7	7
Tie2/Ang2	0.002	0.27	-9999	-0.93	41	41
Tie2/Ang1	0.04	0.081	-9999	-0.92	2	2
FOXO1	0.02	0.18	-9999	-0.6	41	41
ELF1	0.03	0.014	-9999	-0.098	3	3
ELF2	0.041	0.078	-9999	-0.88	2	2
mol:Choline	0.041	0.075	-9999	-0.84	2	2
cell migration	-0.02	0.045	-9999	-0.19	16	16
FYN	0.003	0.23	-9999	-0.79	41	41
DOK2	0.02	0.021	-9999	-0.12	12	12
negative regulation of cell cycle	0.029	0.17	-9999	-0.55	41	41
ETS1	0.022	0.035	-9999	-0.12	27	27
PXN	0.028	0.14	-9999	-0.62	7	7
ITGB1	0.021	0.015	-9999	-0.12	6	6
NOS3	0.028	0.15	-9999	-0.58	14	14
RAC1	0.023	0.002	-9999	-10000	0	0
TNF	0.028	0.025	-9999	-0.12	11	11
MAPKKK cascade	0.041	0.075	-9999	-0.84	2	2
RASA1	0.021	0.012	-9999	-0.12	3	3
Tie2/Ang1/Shc	0.049	0.082	-9999	-0.88	2	2
NCK1	0.02	0.019	-9999	-0.12	9	9
vasculogenesis	0.031	0.13	-9999	-0.45	17	17
mol:Phosphatidic acid	0.041	0.075	-9999	-0.84	2	2
mol:Angiotensin II	-0.001	0.009	-9999	-10000	0	0
mol:NADP	0.03	0.14	-9999	-0.5	17	17
Rac1/GTP	0.03	0.14	-9999	-0.73	6	6
MMP2	0.015	0.083	-9999	-0.87	2	2

×

Aurora C signaling

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

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

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

×

IL27-mediated 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
TGFB1	0.025	0.035	-10000	0	-0.4	2	2
CD4-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
cytokine production during immune response	-0.002	0.086	0.36	16	-10000	0	16
IL27/IL27R/JAK1	0.029	0.089	-10000	0	-0.95	2	2
TBX21	0	0.077	-10000	0	-0.53	3	3
IL12B	0.024	0.002	-10000	0	-10000	0	0
IL12A	0	0.029	-10000	0	-0.077	70	70
IL6ST	0.016	0.027	-10000	0	-0.12	19	19
IL27RA/JAK1	0.012	0.073	-10000	0	-1.1	2	2
IL27	0.023	0.004	-10000	0	-10000	0	0
TYK2	0.021	0.017	-10000	0	-0.12	7	7
T-helper cell lineage commitment	0.013	0.09	-10000	0	-1.2	2	2
T-helper 2 cell differentiation	-0.002	0.086	0.36	16	-10000	0	16
T cell proliferation during immune response	-0.002	0.086	0.36	16	-10000	0	16
MAPKKK cascade	0.002	0.086	-10000	0	-0.36	16	16
STAT3	0.022	0.011	-10000	0	-0.12	3	3
STAT2	0.02	0.019	-10000	0	-0.12	9	9
STAT1	0.014	0.031	-10000	0	-0.12	26	26
IL12RB1	0.023	0.006	-10000	0	-0.12	1	1
positive regulation of tyrosine phosphorylation of STAT protein	0	0	-10000	0	-10000	0	0
IL12RB2	0	0.08	-10000	0	-0.48	4	4
IL27/IL27R/JAK2/TYK2	0.002	0.086	-10000	0	-0.37	16	16
positive regulation of T cell mediated cytotoxicity	0.002	0.086	-10000	0	-0.36	16	16
STAT1 (dimer)	0.015	0.11	-10000	0	-0.74	3	3
JAK2	0.016	0.025	-10000	0	-0.12	16	16
JAK1	0.022	0.01	-10000	0	-0.12	2	2
STAT2 (dimer)	0.004	0.094	-10000	0	-0.36	17	17
T cell proliferation	0	0.084	-10000	0	-0.34	17	17
IL12/IL12R/TYK2/JAK2	0.026	0.066	-10000	0	-0.72	1	1
IL17A	0.013	0.09	-10000	0	-1.2	2	2
mast cell activation	-0.002	0.086	0.36	16	-10000	0	16
IFNG	0.003	0.021	-10000	0	-0.07	4	4
T cell differentiation	-0.001	0.003	-10000	0	-0.02	3	3
STAT3 (dimer)	0.004	0.094	-10000	0	-0.36	16	16
STAT5A (dimer)	0.006	0.091	-10000	0	-0.35	16	16
STAT4 (dimer)	0.006	0.091	-10000	0	-0.35	16	16
STAT4	0.02	0.02	-10000	0	-0.12	11	11
T cell activation	-0.006	0.011	0.12	2	-10000	0	2
IL27R/JAK2/TYK2	0.009	0.094	-10000	0	-0.98	2	2
GATA3	0.014	0.029	-10000	0	-10000	0	0
IL18	0	0.028	-10000	0	-0.077	66	66
positive regulation of mast cell cytokine production	0.004	0.092	-10000	0	-0.36	16	16
IL27/EBI3	0.034	0.009	-10000	0	-10000	0	0
IL27RA	-0.001	0.076	-10000	0	-1.1	2	2
IL6	0.012	0.054	-10000	0	-0.33	3	3
STAT5A	0.022	0.013	-10000	0	-0.12	4	4
monocyte differentiation	0	0.001	-10000	0	-10000	0	0
IL2	0.005	0.041	0.46	2	-10000	0	2
IL1B	0.003	0.024	-10000	0	-0.077	45	45
EBI3	0.023	0.008	-10000	0	-0.12	1	1
TNF	0.01	0.012	-10000	0	-0.077	11	11

×

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	0.022	0.007	-10000	0	-0.12	1	1
SMAD2	0.015	0.036	0.19	2	-0.16	8	10
SMAD3	0.027	0.046	-10000	0	-0.29	4	4
SMAD3/SMAD4	-0.013	0.16	-10000	0	-0.37	81	81
SMAD4/Ubc9/PIASy	0.043	0.027	-10000	0	-0.12	15	15
SMAD2/SMAD2/SMAD4	0.034	0.063	-10000	0	-0.17	18	18
PPM1A	0.023	0.001	-10000	0	-10000	0	0
CALM1	0.022	0.014	-10000	0	-0.12	5	5
SMAD2/SMAD4	0.027	0.032	0.16	2	-0.14	8	10
MAP3K1	0.021	0.015	-10000	0	-0.12	6	6
TRAP-1/SMAD4	0.025	0.041	-10000	0	-0.14	30	30
MAPK3	0.022	0.014	-10000	0	-0.12	5	5
MAPK1	0.021	0.016	-10000	0	-0.12	7	7
NUP214	0.023	0.007	-10000	0	-0.12	1	1
CTDSP1	0.022	0.011	-10000	0	-0.12	3	3
CTDSP2	0.022	0.01	-10000	0	-0.12	2	2
CTDSPL	0.023	0.006	-10000	0	-0.12	1	1
KPNB1	0.022	0.009	-10000	0	-0.12	2	2
TGFBRAP1	0.022	0.007	-10000	0	-0.12	1	1
UBE2I	0.023	0.001	-10000	0	-10000	0	0
NUP153	0.02	0.019	-10000	0	-0.12	9	9
KPNA2	0.017	0.024	-10000	0	-0.12	15	15
PIAS4	0.023	0	-10000	0	-10000	0	0

×

Glypican 2 network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MDK	0.021	0.014	-9999	-0.12	5	5
GPC2	0.023	0.009	-9999	-0.12	2	2
GPC2/Midkine	0.029	0.031	-9999	-0.14	16	16
neuron projection morphogenesis	0.029	0.031	-9999	-0.14	16	16

×

Arf1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
coatomer protein complex	0.019	0.009	-10000	0	-10000	0	0
EntrezGene:79658	0	0	-10000	0	-10000	0	0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A	0.008	0.035	-10000	0	-0.14	14	14
AP2	0.025	0.04	-10000	0	-0.13	33	33
mol:DAG	0	0	-10000	0	-10000	0	0
Arfaptin 2/Rac/GTP	0.03	0.016	-10000	0	-0.089	10	10
CLTB	0.022	0.014	-10000	0	-0.12	5	5
coatomer protein complex/ARF1/GTP/ER cargo protein	0.02	0.034	-10000	0	-0.16	16	16
CD4	0.016	0.028	-10000	0	-0.12	21	21
CLTA	0.023	0.006	-10000	0	-0.12	1	1
mol:GTP	0	0.002	-10000	0	-10000	0	0
ARFGAP1	0.012	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.009	0.009	-10000	0	-0.047	5	5
ARF1/GTP	0.011	0.015	-10000	0	-0.12	2	2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein	0.02	0.026	-10000	0	-0.15	11	11
mol:Choline	0.009	0.008	-10000	0	-0.046	5	5
mol:GDP	0	0	-10000	0	-10000	0	0
ARF1	0.017	0.028	-10000	0	-0.12	21	21
DDEF1	0.008	0.012	-10000	0	-0.2	1	1
ARF1/GDP	0.009	0.005	0.047	1	-0.063	1	2
AP2M1	0.022	0.005	-10000	0	-10000	0	0
EntrezGene:1313	0	0	-10000	0	-10000	0	0
actin filament polymerization	0.013	0.019	-10000	0	-0.11	7	7
Rac/GTP	0.016	0.016	-10000	0	-0.15	5	5
ARF1/GTP/GGA3/ARF-GAP1	0.032	0.019	-10000	0	-0.091	3	3
ARFIP2	0.021	0.014	-10000	0	-0.12	5	5
COPA	0.023	0.007	-10000	0	-0.12	1	1
RAC1	0.023	0.002	-10000	0	-10000	0	0
ARF1/GTP/coatomer protein complex	0.018	0.035	-10000	0	-0.21	11	11
ARF1/GTP/ARHGAP10	0.011	0.016	-10000	0	-0.066	23	23
GGA3	0.022	0.015	-10000	0	-0.12	6	6
ARF1/GTP/Membrin	0.019	0.018	-10000	0	-0.18	2	2
AP2A1	0.021	0.017	-10000	0	-0.12	8	8
coatomer protein complex/ARF1/GTP/ARF-GAP1	0.021	0.033	-10000	0	-0.17	13	13
ARF1/GDP/Membrin	0.021	0.019	-10000	0	-0.29	1	1
Arfaptin 2/Rac/GDP	0.029	0.016	-10000	0	-0.087	10	10
CYTH2	0	0.002	-10000	0	-10000	0	0
ARF1/GTP/GGA3	0.026	0.021	-10000	0	-0.062	30	30
mol:ATP	0	0	-10000	0	-10000	0	0
Rac/GDP	0.016	0.015	-10000	0	-0.15	5	5
mol:Brefeldin A	0	0	-10000	0	-10000	0	0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP	0.006	0.077	-10000	0	-0.26	22	22
PLD2	0.009	0.008	-10000	0	-0.046	5	5
ARF-GAP1/v-SNARE	0.012	0	-10000	0	-10000	0	0
PIP5K1A	0.009	0.009	-10000	0	-0.047	5	5
ARF1/GTP/Membrin/GBF1/p115	0.011	0.028	-10000	0	-0.1	14	14
mol:Phosphatic acid	0	0	-10000	0	-10000	0	0
mol:Phosphatidic acid	0.009	0.008	-10000	0	-0.046	5	5
KDEL Receptor/Ligand/ARF-GAP1	0.012	0	-10000	0	-10000	0	0
GOSR2	0.015	0.016	-10000	0	-0.36	1	1
USO1	-0.01	0.093	-10000	0	-0.36	37	37
GBF1	0.001	0.07	-10000	0	-0.36	21	21
ARF1/GTP/Arfaptin 2	0.027	0.021	-10000	0	-0.062	27	27
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex	0.02	0.062	-10000	0	-0.13	74	74

×

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

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
MAP4K1	0.016	0.057	-10000	0	-0.24	7	7
CRKL	0.014	0.059	-10000	0	-0.27	6	6
HRAS	0.032	0.067	-10000	0	-0.26	7	7
mol:PIP3	0.004	0.067	0.22	5	-0.26	7	12
SPRED1	0.019	0.016	-10000	0	-0.12	6	6
SPRED2	0.022	0.014	-10000	0	-0.12	5	5
GAB1	0.011	0.061	-10000	0	-0.29	6	6
FOXO3	0.019	0.063	-10000	0	-0.28	8	8
AKT1	0.017	0.064	-10000	0	-0.3	7	7
BAD	0.021	0.061	-10000	0	-0.3	6	6
megakaryocyte differentiation	0.013	0.059	-10000	0	-0.3	5	5
GSK3B	0.02	0.062	-10000	0	-0.33	5	5
RAF1	0.031	0.06	-10000	0	-0.24	7	7
SHC1	0.023	0.001	-10000	0	-10000	0	0
STAT3	0.011	0.062	-10000	0	-0.26	9	9
STAT1	0.013	0.12	-10000	0	-0.59	9	9
HRAS/SPRED1	0.031	0.067	-10000	0	-0.24	8	8
cell proliferation	0.012	0.06	-10000	0	-0.3	6	6
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
TEC	0.01	0.038	-10000	0	-0.12	43	43
RPS6KB1	0.01	0.077	-10000	0	-0.27	18	18
HRAS/SPRED2	0.037	0.063	-10000	0	-0.22	8	8
LYN/TEC/p62DOK	0.013	0.085	-10000	0	-0.26	17	17
MAPK3	0.03	0.052	-10000	0	-0.26	4	4
STAP1	0.012	0.06	-10000	0	-0.3	5	5
GRAP2	0.022	0.012	-10000	0	-0.12	4	4
JAK2	0.005	0.12	-10000	0	-0.51	12	12
STAT1 (dimer)	0.008	0.13	-10000	0	-0.58	9	9
mol:Gleevec	-0.001	0.003	-10000	0	-10000	0	0
GRB2/SOCS1/VAV1	0.031	0.074	-10000	0	-0.28	7	7
actin filament polymerization	0.009	0.059	-10000	0	-0.3	5	5
LYN	0.021	0.013	-10000	0	-0.12	4	4
STAP1/STAT5A (dimer)	0.013	0.09	-10000	0	-0.38	9	9
PIK3R1	0.015	0.031	-10000	0	-0.12	27	27
CBL/CRKL/GRB2	0.034	0.063	-10000	0	-0.34	3	3
PI3K	0.017	0.089	-10000	0	-0.27	21	21
PTEN	0.022	0.008	-10000	0	-0.12	1	1
SCF/KIT/EPO/EPOR	0.032	0.13	-10000	0	-1.3	2	2
MAPK8	0.012	0.061	-10000	0	-0.31	6	6
STAT3 (dimer)	0.012	0.061	-10000	0	-0.26	9	9
positive regulation of transcription	0.028	0.045	0.14	1	-0.21	4	5
mol:GDP	0.031	0.072	-10000	0	-0.25	9	9
PIK3C2B	0.011	0.061	-10000	0	-0.28	6	6
CBL/CRKL	0.025	0.061	-10000	0	-0.28	5	5
FER	0.012	0.06	-10000	0	-0.3	5	5
SH2B3	0.013	0.06	-10000	0	-0.3	5	5
PDPK1	0.007	0.066	0.21	4	-0.23	11	15
SNAI2	0.002	0.065	-10000	0	-0.3	8	8
positive regulation of cell proliferation	0.008	0.11	-10000	0	-0.43	12	12
KITLG	0.02	0.029	-10000	0	-0.12	21	21
cell motility	0.008	0.11	-10000	0	-0.43	12	12
PTPN6	0.021	0.01	-10000	0	-0.12	2	2
EPOR	0.015	0.13	-10000	0	-0.55	22	22
STAT5A (dimer)	0.011	0.094	-10000	0	-0.36	13	13
SOCS1	0.016	0.031	-10000	0	-0.12	27	27
cell migration	-0.013	0.059	0.3	5	-10000	0	5
SOS1	0.017	0.027	-10000	0	-0.12	20	20
EPO	0.024	0.008	-10000	0	-0.13	1	1
VAV1	0.02	0.02	-10000	0	-0.12	10	10
GRB10	0.012	0.062	-10000	0	-0.28	8	8
PTPN11	0.021	0.012	-10000	0	-0.12	3	3
SCF/KIT	0.009	0.062	-10000	0	-0.32	5	5
GO:0007205	-0.001	0.004	-10000	0	-10000	0	0
MAP2K1	0.03	0.051	-10000	0	-0.2	6	6
CBL	0.023	0.006	-10000	0	-0.12	1	1
KIT	0.007	0.12	-10000	0	-0.63	6	6
MAP2K2	0.028	0.053	-10000	0	-0.18	8	8
SHC/Grb2/SOS1	0.033	0.071	-10000	0	-0.27	7	7
STAT5A	0.01	0.096	-10000	0	-0.37	13	13
GRB2	0.023	0.006	-10000	0	-0.12	1	1
response to radiation	0.002	0.064	-10000	0	-0.3	8	8
SHC/GRAP2	0.034	0.011	-10000	0	-0.14	1	1
PTPRO	0.013	0.06	-10000	0	-0.3	5	5
SH2B2	0.008	0.059	-10000	0	-0.31	5	5
DOK1	0.021	0.016	-10000	0	-0.12	7	7
MATK	0.013	0.06	-10000	0	-0.3	5	5
CREBBP	0.036	0.031	-10000	0	-0.12	9	9
BCL2	0.009	0.15	-10000	0	-0.62	23	23

×

Visual signal transduction: Rods

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:K +	0.023	0.009	-9999	-0.12	2	2
GNAT1/GTP	0.017	0.006	-9999	-0.077	2	2
Metarhodopsin II/Arrestin	0.031	0.007	-9999	-10000	0	0
PDE6G/GNAT1/GTP	0.025	0.024	-9999	-0.061	38	38
mol:GTP	0	0	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
GNAT1	0.023	0.009	-9999	-0.12	2	2
GRK1	0	0	-9999	-10000	0	0
CNG Channel	0.039	0.024	-9999	-0.11	3	3
mol:Na +	0.052	0.02	-9999	-0.31	1	1
mol:ADP	0	0	-9999	-10000	0	0
RGS9-1/Gbeta5/R9AP	0.042	0.023	-9999	-0.11	2	2
mol:GDP	0	0	-9999	-10000	0	0
cGMP/CNG Channel	0.065	0.021	-9999	-0.32	1	1
CNGB1	0.023	0.006	-9999	-0.12	1	1
RDH5	0.011	0.041	-9999	-0.12	48	48
SAG	0.022	0.011	-9999	-0.12	3	3
mol:Ca2+	0.04	0.018	-9999	-0.3	1	1
Na + (4 Units)	0.042	0.018	-9999	-0.29	1	1
RGS9	0.017	0.029	-9999	-0.12	23	23
GNB1/GNGT1	0.03	0.027	-9999	-0.1	20	20
GNAT1/GDP	0.05	0.022	-9999	-0.089	2	2
GUCY2D	0.022	0.011	-9999	-0.12	3	3
GNGT1	0.02	0.023	-9999	-0.12	14	14
GUCY2F	0.023	0.006	-9999	-0.12	1	1
GNB5	0.023	0.009	-9999	-0.12	2	2
mol:GMP (4 units)	0.031	0.023	-9999	-0.1	4	4
mol:11-cis-retinal	0.011	0.04	-9999	-0.12	48	48
mol:cGMP	0.057	0.019	-9999	-0.12	4	4
GNB1	0.023	0.007	-9999	-0.12	1	1
Rhodopsin	0.023	0.035	-9999	-0.08	57	57
SLC24A1	0.023	0.009	-9999	-0.12	2	2
CNGA1	0.022	0.014	-9999	-0.12	5	5
Metarhodopsin II	0.015	0.003	-9999	-0.055	1	1
mol:Ca ++	0	0	-9999	-10000	0	0
GC1/GCAP Family	0.058	0.019	-9999	-0.12	4	4
RGS9BP	0.022	0.011	-9999	-0.12	3	3
Metarhodopsin II/Transducin	0.025	0.022	-9999	-0.15	7	7
GCAP Family/Ca ++	0.043	0.015	-9999	-0.12	4	4
PDE6A/B	0.033	0.014	-9999	-0.071	10	10
mol:Pi	0.042	0.022	-9999	-0.11	2	2
mol:all-trans-retinal	0	0	-9999	-10000	0	0
Transducin	0.041	0.023	-9999	-0.11	8	8
PDE6B	0.022	0.015	-9999	-0.12	6	6
PDE6A	0.022	0.012	-9999	-0.12	4	4
PDE6G	0.014	0.035	-9999	-0.12	35	35
RHO	0.023	0.006	-9999	-0.12	1	1
PDE6	0.056	0.035	-9999	-0.15	2	2
GUCA1A	0.022	0.011	-9999	-0.12	3	3
GC2/GCAP Family	0.058	0.018	-9999	-0.12	4	4
GUCA1C	0.022	0.012	-9999	-0.12	4	4
GUCA1B	0.023	0.006	-9999	-0.12	1	1

×

Rapid glucocorticoid signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma	0.034	0.029	-10000	0	-0.093	20	20
MAPK9	0	0.045	-10000	0	-0.21	25	25
adrenocorticotropin secretion	0.011	0.006	-10000	0	-0.077	3	3
GNB1/GNG2	0.025	0.029	-10000	0	-0.12	20	20
GNB1	0.023	0.007	-10000	0	-0.12	1	1
regulation of calcium ion transport via voltage-gated calcium channel activity	0	0	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
MAPK14	0.006	0.03	-10000	0	-0.21	11	11
Gs family/GTP	0.014	0.009	-10000	0	-0.055	9	9
EntrezGene:2778	0	0	-10000	0	-10000	0	0
vasopressin secretion	0	0	-10000	0	-10000	0	0
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
ChemicalAbstracts:86-01-1	0	0	-10000	0	-10000	0	0
glutamate secretion	0	0.002	0.017	9	-10000	0	9
GNAL	0.021	0.018	-10000	0	-0.12	9	9
GNG2	0.02	0.018	-10000	0	-0.12	9	9
CRH	0.022	0.011	-10000	0	-0.12	3	3
mol:cortisol	0	0	-10000	0	-10000	0	0
MAPK8	0.003	0.038	-10000	0	-0.21	17	17
MAPK11	0.01	0	-10000	0	-10000	0	0

×

Visual signal transduction: Cones

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin	0.04	0.013	-9999	-0.09	2	2
RGS9BP	0.022	0.011	-9999	-0.12	3	3
mol:GTP	0	0	-9999	-10000	0	0
GRK1	0	0	-9999	-10000	0	0
mol:Na +	0.031	0.004	-9999	-10000	0	0
mol:ADP	0.011	0.004	-9999	-0.077	1	1
GNAT2	0.023	0	-9999	-10000	0	0
RGS9-1/Gbeta5/R9AP	0.042	0.023	-9999	-0.11	2	2
mol:GDP	0	0	-9999	-10000	0	0
PDE6H/GNAT2/GTP	0.031	0.004	-9999	-0.057	1	1
GRK7	0.023	0.006	-9999	-0.12	1	1
CNGB3	0.023	0.006	-9999	-0.12	1	1
Cone Metarhodopsin II/X-Arrestin	0.017	0.004	-9999	-0.077	1	1
mol:Ca2+	0.025	0.008	-9999	-0.1	1	1
Cone PDE6	0.064	0.024	-9999	-0.11	2	2
Cone Metarhodopsin II	0.015	0.003	-9999	-0.055	1	1
Na + (4 Units)	0.043	0.01	-9999	-0.1	1	1
GNAT2/GDP	0.05	0.021	-9999	-0.089	2	2
GNB5	0.023	0.009	-9999	-0.12	2	2
mol:GMP (4 units)	0.026	0.005	-9999	-0.1	1	1
Cone Transducin	0.043	0.014	-9999	-0.097	2	2
SLC24A2	0.022	0.014	-9999	-0.12	5	5
GNB3/GNGT2	0.032	0.016	-9999	-0.14	2	2
GNB3	0.022	0.011	-9999	-0.12	3	3
GNAT2/GTP	0.017	0	-9999	-10000	0	0
CNGA3	0.023	0	-9999	-10000	0	0
ARR3	0.023	0.006	-9999	-0.12	1	1
absorption of light	0	0	-9999	-10000	0	0
cGMP/Cone CNG Channel	0.031	0.004	-9999	-10000	0	0
mol:Pi	0.042	0.022	-9999	-0.11	2	2
Cone CNG Channel	0.057	0.008	-9999	-0.14	1	1
mol:all-trans-retinal	0	0	-9999	-10000	0	0
mol:K +	0.022	0.014	-9999	-0.12	5	5
RGS9	0.017	0.029	-9999	-0.12	23	23
PDE6C	0.023	0.006	-9999	-0.12	1	1
GNGT2	0.022	0.014	-9999	-0.12	5	5
mol:cGMP (4 units)	0	0	-9999	-10000	0	0
PDE6H	0.023	0.006	-9999	-0.12	1	1