Ovarian Serous Cystadenocarcinoma: PARADIGM pathway analysis of mRNA expression data

Pathway.Name	Avg.Num.Perturbations
FOXM1 transcription factor network	154
HIF-1-alpha transcription factor network	121
LPA receptor mediated events	102
TCGA08_retinoblastoma	97
Osteopontin-mediated events	93
Syndecan-1-mediated signaling events	92
Endothelins	90
PDGFR-alpha signaling pathway	82
TRAIL signaling pathway	75
TCGA08_p53	75

Pathway.Name	Avg.Num.Perturbations	Total.Perturbations	Num.Entities	Min.Mean.Truth	Max.Mean.Truth	Min.Mean.Within	Max.Mean.Within	Min.Mean.Any	Max.Mean.Within.1
FOXM1 transcription factor network	154	7884	51	-0.66	0.022	1000	-1000	-0.017	-1000
HIF-1-alpha transcription factor network	121	9201	76	-0.15	0.035	1000	-1000	-0.013	-1000
LPA receptor mediated events	102	10483	102	-0.085	0.023	1000	-1000	-0.027	-1000
TCGA08_retinoblastoma	97	780	8	-0.022	0.022	1000	-1000	-0.003	-1000
Osteopontin-mediated events	93	3537	38	-0.22	0.023	1000	-1000	0	-1000
Syndecan-1-mediated signaling events	92	3159	34	-0.086	0.023	1000	-1000	0	-1000
Endothelins	90	8681	96	-0.2	0.023	1000	-1000	-0.004	-1000
PDGFR-alpha signaling pathway	82	3638	44	-0.15	0.031	1000	-1000	0.001	-1000
TRAIL signaling pathway	75	3633	48	-0.038	0.023	1000	-1000	-0.006	-1000
TCGA08_p53	75	525	7	-0.069	0.018	1000	-1000	-0.002	-1000
Fc-epsilon receptor I signaling in mast cells	74	7224	97	-0.087	0.027	1000	-1000	-0.014	-1000
amb2 Integrin signaling	74	6090	82	-0.13	0.034	1000	-1000	0	-1000
Nectin adhesion pathway	73	4648	63	-0.083	0.031	1000	-1000	-0.025	-1000
Ephrin B reverse signaling	73	3538	48	-0.2	0.051	1000	-1000	-0.032	-1000
Thromboxane A2 receptor signaling	70	7354	105	-0.21	0.052	1000	-1000	-0.029	-1000
Cellular roles of Anthrax toxin	70	2741	39	-0.099	0.022	1000	-1000	-0.003	-1000
PLK2 and PLK4 events	68	206	3	-0.002	0.017	1000	-1000	0.017	-1000
Syndecan-4-mediated signaling events	64	4337	67	-0.11	0.027	1000	-1000	-0.008	-1000
IL23-mediated signaling events	62	3775	60	-0.26	0.025	1000	-1000	-0.002	-1000
IL1-mediated signaling events	61	3828	62	-0.075	0.046	1000	-1000	0	-1000
Nongenotropic Androgen signaling	60	3163	52	-0.13	0.066	1000	-1000	-0.014	-1000
IL6-mediated signaling events	59	4437	75	-0.13	0.025	1000	-1000	-0.013	-1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)	56	4830	85	-0.17	0.023	1000	-1000	-0.014	-1000
Integrins in angiogenesis	56	4762	84	-0.056	0.033	1000	-1000	0	-1000
IGF1 pathway	56	3212	57	-0.022	0.035	1000	-1000	-0.015	-1000
IL4-mediated signaling events	55	5016	91	-0.33	0.18	1000	-1000	-0.13	-1000
IFN-gamma pathway	55	3778	68	-0.053	0.034	1000	-1000	-0.016	-1000
BARD1 signaling events	52	3013	57	-0.036	0.027	1000	-1000	-0.032	-1000
EPHB forward signaling	51	4352	85	-0.028	0.036	1000	-1000	-0.018	-1000
PLK1 signaling events	49	4177	85	-0.066	0.025	1000	-1000	-0.001	-1000
Caspase cascade in apoptosis	48	3555	74	-0.064	0.044	1000	-1000	-0.016	-1000
Signaling events mediated by the Hedgehog family	48	2512	52	-0.084	0.034	1000	-1000	-0.016	-1000
Signaling events mediated by PTP1B	47	3572	76	-0.092	0.074	1000	-1000	-0.021	-1000
TCR signaling in naïve CD8+ T cells	47	4404	93	-0.051	0.032	1000	-1000	-0.019	-1000
Paxillin-independent events mediated by a4b1 and a4b7	46	1711	37	-0.04	0.033	1000	-1000	0	-1000
Ras signaling in the CD4+ TCR pathway	46	782	17	-0.024	0.025	1000	-1000	-0.001	-1000
IL12-mediated signaling events	45	3960	87	-0.26	0.026	1000	-1000	-0.051	-1000
a4b1 and a4b7 Integrin signaling	45	226	5	0.005	0.019	1000	-1000	0.019	-1000
Canonical Wnt signaling pathway	45	2302	51	-0.19	0.084	1000	-1000	-0.024	-1000
Circadian rhythm pathway	44	979	22	-0.079	0.024	1000	-1000	-0.006	-1000
Noncanonical Wnt signaling pathway	44	1169	26	-0.032	0.026	1000	-1000	-0.013	-1000
BMP receptor signaling	43	3560	81	-0.073	0.05	1000	-1000	-0.019	-1000
IL2 signaling events mediated by PI3K	43	2545	58	-0.11	0.023	1000	-1000	-0.014	-1000
E-cadherin signaling in keratinocytes	42	1819	43	-0.012	0.027	1000	-1000	-0.006	-1000
Aurora A signaling	41	2478	60	-0.064	0.037	1000	-1000	0	-1000
Ephrin A reverse signaling	40	284	7	0	0.023	1000	-1000	0	-1000
Arf6 downstream pathway	40	1743	43	-0.029	0.031	1000	-1000	-0.028	-1000
ceramide signaling pathway	40	1972	49	-0.014	0.038	1000	-1000	-0.005	-1000
Stabilization and expansion of the E-cadherin adherens junction	40	2986	74	-0.059	0.034	1000	-1000	-0.026	-1000
Reelin signaling pathway	39	2226	56	-0.018	0.056	1000	-1000	0	-1000
HIF-2-alpha transcription factor network	39	1685	43	-0.098	0.041	1000	-1000	-0.092	-1000
FoxO family signaling	39	2519	64	-0.27	0.041	1000	-1000	-0.008	-1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha	39	1766	45	-0.06	0.038	1000	-1000	-0.001	-1000
ErbB2/ErbB3 signaling events	38	2527	65	-0.071	0.023	1000	-1000	-0.025	-1000
Syndecan-2-mediated signaling events	38	2659	69	-0.018	0.028	1000	-1000	-0.001	-1000
Retinoic acid receptors-mediated signaling	38	2205	58	-0.092	0.029	1000	-1000	-0.005	-1000
FOXA2 and FOXA3 transcription factor networks	37	1705	46	-0.16	0.042	1000	-1000	-0.006	-1000
Aurora B signaling	37	2480	67	-0.066	0.033	1000	-1000	-0.007	-1000
ErbB4 signaling events	36	2517	69	-0.069	0.047	1000	-1000	-0.02	-1000
E-cadherin signaling in the nascent adherens junction	36	2789	76	-0.06	0.04	1000	-1000	-0.027	-1000
BCR signaling pathway	36	3637	99	-0.057	0.032	1000	-1000	-0.021	-1000
FAS signaling pathway (CD95)	35	1674	47	-0.053	0.041	1000	-1000	-0.006	-1000
Signaling mediated by p38-gamma and p38-delta	35	531	15	-0.049	0.023	1000	-1000	0	-1000
Plasma membrane estrogen receptor signaling	34	2940	86	-0.057	0.053	1000	-1000	-0.024	-1000
Signaling events mediated by PRL	33	1144	34	-0.014	0.023	1000	-1000	-0.005	-1000
p75(NTR)-mediated signaling	32	4070	125	-0.039	0.055	1000	-1000	-0.019	-1000
TCGA08_rtk_signaling	32	844	26	-0.014	0.029	1000	-1000	-0.016	-1000
RXR and RAR heterodimerization with other nuclear receptor	31	1629	52	-0.029	0.059	1000	-1000	0	-1000
Wnt signaling	31	222	7	-0.032	0.023	1000	-1000	0.008	-1000
EGFR-dependent Endothelin signaling events	31	658	21	0	0.041	1000	-1000	0	-1000
Class I PI3K signaling events	30	2199	73	-0.008	0.042	1000	-1000	-0.005	-1000
S1P4 pathway	30	770	25	-0.003	0.03	1000	-1000	0	-1000
EPO signaling pathway	28	1544	55	-0.005	0.059	1000	-1000	0	-1000
Paxillin-dependent events mediated by a4b1	28	1021	36	-0.032	0.034	1000	-1000	-0.028	-1000
S1P5 pathway	27	462	17	-0.006	0.023	1000	-1000	-0.012	-1000
Lissencephaly gene (LIS1) in neuronal migration and development	26	1437	54	-0.014	0.029	1000	-1000	0	-1000
S1P3 pathway	26	1092	42	-0.055	0.03	1000	-1000	-0.001	-1000
E-cadherin signaling events	26	131	5	0.018	0.025	1000	-1000	0.017	-1000
Regulation of Androgen receptor activity	26	1845	70	-0.092	0.034	1000	-1000	-0.015	-1000
IL2 signaling events mediated by STAT5	25	556	22	-0.075	0.032	1000	-1000	0.003	-1000
Neurotrophic factor-mediated Trk receptor signaling	24	2915	120	-0.057	0.055	1000	-1000	-0.018	-1000
Canonical NF-kappaB pathway	23	920	39	0	0.037	1000	-1000	0	-1000
Presenilin action in Notch and Wnt signaling	23	1420	61	-0.18	0.042	1000	-1000	-0.015	-1000
Atypical NF-kappaB pathway	23	721	31	0	0.023	1000	-1000	0	-1000
Regulation of Telomerase	23	2353	102	-0.13	0.045	1000	-1000	-0.009	-1000
Nephrin/Neph1 signaling in the kidney podocyte	22	751	34	-0.023	0.049	1000	-1000	-0.02	-1000
Arf6 signaling events	22	1371	62	-0.017	0.036	1000	-1000	0	-1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	22	1554	68	-0.081	0.094	1000	-1000	-0.047	-1000
PDGFR-beta signaling pathway	22	2205	97	-0.06	0.046	1000	-1000	-0.015	-1000
LPA4-mediated signaling events	21	262	12	0	0.014	1000	-1000	0	-1000
Coregulation of Androgen receptor activity	21	1662	76	-0.01	0.033	1000	-1000	-0.02	-1000
Glypican 1 network	21	1010	48	-0.021	0.039	1000	-1000	-0.019	-1000
Glucocorticoid receptor regulatory network	21	2466	114	-0.13	0.046	1000	-1000	-0.035	-1000
Regulation of nuclear SMAD2/3 signaling	19	2696	136	-0.13	0.071	1000	-1000	-0.033	-1000
Signaling events mediated by VEGFR1 and VEGFR2	19	2433	125	-0.019	0.055	1000	-1000	-0.025	-1000
p38 MAPK signaling pathway	19	876	44	-0.013	0.044	1000	-1000	0	-1000
Signaling events mediated by HDAC Class I	18	1882	104	-0.036	0.053	1000	-1000	-0.028	-1000
Arf6 trafficking events	18	1297	71	-0.025	0.033	1000	-1000	-0.019	-1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha	18	596	33	-0.003	0.053	1000	-1000	0	-1000
Class IB PI3K non-lipid kinase events	18	54	3	-0.019	0.019	1000	-1000	-0.02	-1000
Ceramide signaling pathway	17	1351	76	-0.013	0.043	1000	-1000	-0.004	-1000
Signaling events mediated by HDAC Class III	17	700	40	-0.036	0.042	1000	-1000	-0.028	-1000
Regulation of p38-alpha and p38-beta	17	962	54	-0.006	0.057	1000	-1000	0	-1000
Signaling events regulated by Ret tyrosine kinase	16	1343	82	-0.008	0.057	1000	-1000	-0.021	-1000
JNK signaling in the CD4+ TCR pathway	15	266	17	-0.003	0.044	1000	-1000	0	-1000
mTOR signaling pathway	15	847	53	-0.015	0.032	1000	-1000	-0.022	-1000
Class I PI3K signaling events mediated by Akt	15	1029	68	-0.026	0.047	1000	-1000	-0.009	-1000
Signaling mediated by p38-alpha and p38-beta	15	690	44	-0.007	0.033	1000	-1000	0	-1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes	14	1211	83	-0.006	0.048	1000	-1000	-0.01	-1000
Syndecan-3-mediated signaling events	14	518	35	-0.01	0.035	1000	-1000	-0.004	-1000
Hedgehog signaling events mediated by Gli proteins	13	895	65	-0.006	0.054	1000	-1000	-0.005	-1000
Calcium signaling in the CD4+ TCR pathway	13	407	31	-0.002	0.09	1000	-1000	-0.018	-1000
Insulin Pathway	13	977	74	-0.01	0.063	1000	-1000	-0.015	-1000
VEGFR1 specific signals	13	753	56	0	0.039	1000	-1000	-0.001	-1000
Sphingosine 1-phosphate (S1P) pathway	12	352	28	0	0.036	1000	-1000	0	-1000
Insulin-mediated glucose transport	12	415	32	0	0.033	1000	-1000	0	-1000
S1P1 pathway	12	467	36	-0.001	0.028	1000	-1000	-0.009	-1000
Effects of Botulinum toxin	12	316	26	0	0.041	1000	-1000	0	-1000
Glypican 2 network	12	49	4	0.021	0.029	1000	-1000	0.018	-1000
Alternative NF-kappaB pathway	12	160	13	0	0.056	1000	-1000	0	-1000
Signaling events mediated by HDAC Class II	11	889	75	-0.033	0.058	1000	-1000	-0.014	-1000
IL27-mediated signaling events	11	604	51	-0.006	0.033	1000	-1000	-0.017	-1000
Sumoylation by RanBP2 regulates transcriptional repression	11	315	27	-0.013	0.047	1000	-1000	-0.014	-1000
Angiopoietin receptor Tie2-mediated signaling	11	996	88	-0.028	0.058	1000	-1000	-0.044	-1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling	10	232	23	-0.012	0.043	1000	-1000	0.002	-1000
Aurora C signaling	10	71	7	0	0.033	1000	-1000	-0.002	-1000
Signaling events mediated by Stem cell factor receptor (c-Kit)	9	742	78	-0.012	0.036	1000	-1000	-0.01	-1000
Arf1 pathway	8	465	54	-0.011	0.032	1000	-1000	0	-1000
Rapid glucocorticoid signaling	7	150	20	0	0.025	1000	-1000	0	-1000
Visual signal transduction: Rods	7	405	52	0	0.066	1000	-1000	0	-1000
Visual signal transduction: Cones	2	83	38	0	0.064	1000	-1000	0	-1000
Total	4864	280149	7203	-8	5.2	131000	-131000	-1.5	-131000

FOXM1 transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC3	-0.43	0.59	-10000	0	-1.1	200	200
PLK1	-0.061	0.29	-10000	0	-1.3	30	30
BIRC5	-0.065	0.3	-10000	0	-1.3	31	31
HSPA1B	-0.44	0.59	-10000	0	-1.1	220	220
MAP2K1	0.001	0.044	-10000	0	-0.16	3	3
BRCA2	-0.45	0.6	-10000	0	-1.1	208	208
FOXM1	-0.66	0.96	-10000	0	-1.7	221	221
XRCC1	-0.44	0.59	-10000	0	-1.1	207	207
FOXM1B/p19	-0.54	0.66	-10000	0	-1.2	233	233
Cyclin D1/CDK4	-0.44	0.55	-10000	0	-1	234	234
CDC2	-0.5	0.67	-10000	0	-1.3	214	214
TGFA	-0.39	0.52	-10000	0	-0.96	218	218
SKP2	-0.44	0.6	-10000	0	-1.1	202	202
CCNE1	0	0.048	-10000	0	-0.13	70	70
CKS1B	-0.44	0.6	-10000	0	-1.1	206	206
RB1	-0.36	0.45	-10000	0	-0.9	195	195
FOXM1C/SP1	-0.54	0.72	-10000	0	-1.3	225	225
AURKB	-0.07	0.3	-10000	0	-1.3	33	33
CENPF	-0.48	0.62	-10000	0	-1.2	226	226
CDK4	0.008	0.026	-10000	0	-0.13	9	9
MYC	-0.4	0.52	-10000	0	-0.96	227	227
CHEK2	-0.003	0.05	-10000	0	-0.14	25	25
ONECUT1	-0.44	0.57	-10000	0	-1.1	223	223
CDKN2A	0.013	0.021	0.084	2	-0.12	10	12
LAMA4	-0.48	0.62	-10000	0	-1.2	221	221
FOXM1B/HNF6	-0.55	0.72	-10000	0	-1.3	224	224
FOS	-0.52	0.64	-10000	0	-1.2	241	241
SP1	0.021	0.011	-10000	0	-0.036	13	13
CDC25B	-0.44	0.59	-10000	0	-1.1	208	208
response to radiation	-0.012	0.032	-10000	0	-10000	0	0
CENPB	-0.43	0.59	-10000	0	-1.1	210	210
CENPA	-0.44	0.59	-10000	0	-1.1	197	197
NEK2	-0.45	0.61	-10000	0	-1.1	213	213
HIST1H2BA	-0.43	0.59	-10000	0	-1.1	208	208
CCNA2	0.01	0.033	-10000	0	-0.12	29	29
EP300	0.022	0.009	-10000	0	-0.12	2	2
CCNB1/CDK1	-0.58	0.79	-10000	0	-1.5	207	207
CCNB2	-0.47	0.62	-10000	0	-1.2	212	212
CCNB1	-0.48	0.65	-10000	0	-1.2	211	211
ETV5	-0.5	0.63	-10000	0	-1.2	229	229
ESR1	-0.47	0.61	-10000	0	-1.2	223	223
CCND1	-0.44	0.56	-10000	0	-1	238	238
GSK3A	0.002	0.042	-10000	0	-0.16	10	10
Cyclin A-E1/CDK1-2	-0.038	0.099	-10000	0	-0.16	180	180
CDK2	0.015	0.024	-10000	0	-0.13	14	14
G2/M transition of mitotic cell cycle	-0.015	0.038	-10000	0	-10000	0	0
FOXM1B/Cbp/p300	-0.49	0.66	-10000	0	-1.2	222	222
GAS1	-0.45	0.6	-10000	0	-1.1	207	207
MMP2	-0.53	0.64	-10000	0	-1.2	249	249
RB1/FOXM1C	-0.5	0.58	-10000	0	-1.1	238	238
CREBBP	0.021	0.015	-10000	0	-0.12	6	6

×

HIF-1-alpha transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PKM2	-0.12	0.34	-9999	-0.55	164	164
HDAC7	-0.001	0.006	-9999	-0.06	1	1
HIF1A/ARNT/Cbp/p300/Src-1	-0.062	0.33	-9999	-0.57	110	110
SMAD4	0.023	0.007	-9999	-0.12	1	1
ID2	-0.12	0.34	-9999	-0.55	164	164
AP1	-0.03	0.087	-9999	-0.15	162	162
ABCG2	-0.12	0.34	-9999	-0.55	164	164
HIF1A	-0.016	0.09	-9999	-0.12	156	156
TFF3	-0.13	0.34	-9999	-0.54	174	174
GATA2	0.02	0.023	-9999	-0.094	19	19
AKT1	-0.004	0.072	-9999	-0.1	119	119
response to hypoxia	-0.02	0.064	-9999	-0.1	134	134
MCL1	-0.12	0.34	-9999	-0.55	166	166
NDRG1	-0.13	0.35	-9999	-0.57	171	171
SERPINE1	-0.13	0.33	-9999	-0.55	169	169
FECH	-0.12	0.34	-9999	-0.55	163	163
FURIN	-0.12	0.34	-9999	-0.55	164	164
NCOA2	0.023	0.013	-9999	-0.1	5	5
EP300	0.001	0.089	-9999	-0.22	26	26
HMOX1	-0.13	0.34	-9999	-0.56	166	166
BHLHE40	-0.13	0.33	-9999	-0.55	168	168
BHLHE41	-0.13	0.33	-9999	-0.55	168	168
HIF1A/ARNT/SMAD3/SMAD4/SP1	0.035	0.12	-9999	-0.18	63	63
ENG	0.006	0.089	-9999	-0.17	54	54
JUN	0.014	0.033	-9999	-0.12	30	30
RORA	-0.12	0.34	-9999	-0.55	163	163
ABCB1	-0.024	0.1	-9999	-0.74	4	4
TFRC	-0.14	0.35	-9999	-0.56	176	176
CXCR4	-0.14	0.35	-9999	-0.56	179	179
TF	-0.12	0.34	-9999	-0.55	166	166
CITED2	-0.12	0.34	-9999	-0.55	164	164
HIF1A/ARNT	-0.077	0.44	-9999	-0.7	124	124
LDHA	-0.088	0.3	-9999	-0.99	54	54
ETS1	-0.13	0.35	-9999	-0.57	166	166
PGK1	-0.13	0.34	-9999	-0.55	170	170
NOS2	-0.13	0.33	-9999	-0.55	168	168
ITGB2	-0.14	0.35	-9999	-0.57	172	172
ALDOA	-0.12	0.34	-9999	-0.55	164	164
Cbp/p300/CITED2	-0.11	0.36	-9999	-0.62	135	135
FOS	-0.005	0.053	-9999	-0.12	95	95
HK2	-0.12	0.34	-9999	-0.54	173	173
SP1	0.031	0.009	-9999	-0.11	1	1
GCK	0.003	0.12	-9999	-0.41	1	1
HK1	-0.12	0.34	-9999	-0.55	163	163
NPM1	-0.12	0.34	-9999	-0.55	164	164
EGLN1	-0.12	0.34	-9999	-0.55	164	164
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	-0.035	0.19	-9999	-1	14	14
IGFBP1	-0.12	0.34	-9999	-0.55	163	163
VEGFA	-0.089	0.29	-9999	-0.51	136	136
HIF1A/JAB1	-0.005	0.085	-9999	-0.15	100	100
CP	-0.14	0.35	-9999	-0.57	177	177
CXCL12	-0.14	0.35	-9999	-0.56	178	178
COPS5	0.019	0.023	-9999	-0.11	15	15
SMAD3/SMAD4	0.029	0.033	-9999	-0.14	18	18
BNIP3	-0.13	0.34	-9999	-0.55	174	174
EGLN3	-0.15	0.35	-9999	-0.56	180	180
CA9	-0.14	0.34	-9999	-0.55	182	182
TERT	-0.12	0.34	-9999	-0.55	163	163
ENO1	-0.12	0.34	-9999	-0.56	163	163
PFKL	-0.12	0.34	-9999	-0.55	163	163
NCOA1	0.023	0.009	-9999	-0.12	2	2
ADM	-0.13	0.34	-9999	-0.55	172	172
ARNT	-0.008	0.069	-9999	-0.097	154	154
HNF4A	0.027	0.009	-9999	-0.12	2	2
ADFP	-0.14	0.35	-9999	-0.56	179	179
SLC2A1	-0.094	0.29	-9999	-0.52	135	135
LEP	-0.12	0.34	-9999	-0.55	163	163
HIF1A/ARNT/Cbp/p300	-0.072	0.34	-9999	-0.58	118	118
EPO	-0.073	0.28	-9999	-0.6	82	82
CREBBP	-0.001	0.09	-9999	-0.21	34	34
HIF1A/ARNT/Cbp/p300/HDAC7	-0.075	0.35	-9999	-0.6	116	116
PFKFB3	-0.13	0.34	-9999	-0.56	166	166
NT5E	-0.15	0.35	-9999	-0.57	187	187

×

LPA receptor mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.021	0.073	-10000	0	-0.13	137	137
NF kappa B1 p50/RelA/I kappa B alpha	-0.015	0.092	-10000	0	-0.19	91	91
AP1	-0.058	0.073	-10000	0	-0.13	252	252
mol:PIP3	-0.051	0.063	-10000	0	-0.13	162	162
AKT1	-0.014	0.07	0.15	1	-0.16	53	54
PTK2B	-0.028	0.066	-10000	0	-0.14	122	122
RHOA	-0.008	0.053	-10000	0	-0.35	6	6
PIK3CB	0.015	0.029	-10000	0	-0.12	24	24
mol:Ca2+	-0.004	0.039	-10000	0	-0.11	41	41
MAGI3	0.019	0.025	-10000	0	-0.12	18	18
RELA	0.023	0.009	-10000	0	-0.12	2	2
apoptosis	-0.034	0.069	-10000	0	-0.15	123	123
HRAS/GDP	0.017	0.008	-10000	0	-0.11	2	2
positive regulation of microtubule depolymerization	-0.018	0.06	-10000	0	-0.12	126	126
NF kappa B1 p50/RelA	-0.04	0.062	-10000	0	-0.13	140	140
endothelial cell migration	-0.085	0.14	-10000	0	-0.22	249	249
ADCY4	-0.042	0.098	-10000	0	-0.2	134	134
ADCY5	-0.045	0.098	-10000	0	-0.2	141	141
ADCY6	-0.042	0.098	-10000	0	-0.2	133	133
ADCY7	-0.042	0.097	-10000	0	-0.2	133	133
ADCY1	-0.042	0.097	-10000	0	-0.2	133	133
ADCY2	-0.042	0.097	-10000	0	-0.2	134	134
ADCY3	-0.043	0.098	-10000	0	-0.2	134	134
ADCY8	-0.048	0.099	-10000	0	-0.2	137	137
ADCY9	-0.045	0.1	-10000	0	-0.2	140	140
GSK3B	-0.024	0.063	-10000	0	-0.13	125	125
arachidonic acid secretion	-0.04	0.092	-10000	0	-0.19	128	128
GNG2	0.021	0.018	-10000	0	-0.12	9	9
TRIP6	0.001	0.051	-10000	0	-0.25	20	20
GNAO1	-0.04	0.073	-10000	0	-0.11	249	249
HRAS	0.023	0.006	-10000	0	-0.12	1	1
NFKBIA	-0.03	0.084	-10000	0	-0.2	74	74
GAB1	0.02	0.022	-10000	0	-0.12	13	13
mol:GTP	0	0	-10000	0	-10000	0	0
lamellipodium assembly	-0.023	0.22	-10000	0	-0.87	37	37
JUN	0.014	0.032	-10000	0	-0.12	30	30
LPA/LPA2/NHERF2	-0.009	0.035	-10000	0	-0.062	140	140
TIAM1	-0.04	0.26	-10000	0	-1	37	37
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
mol:IP3	-0.004	0.039	-10000	0	-0.11	41	41
PLCB3	-0.003	0.032	-10000	0	-0.05	140	140
FOS	-0.005	0.052	-10000	0	-0.12	95	95
positive regulation of mitosis	-0.04	0.092	-10000	0	-0.19	128	128
LPA/LPA1-2-3	-0.037	0.06	-10000	0	-0.097	249	249
mol:Ca ++	0	0	-10000	0	-10000	0	0
JNK cascade	0	0	-10000	0	-10000	0	0
BCAR1	0.023	0.01	-10000	0	-0.12	3	3
stress fiber formation	-0.025	0.073	-10000	0	-0.18	48	48
GNAZ	-0.034	0.071	-10000	0	-0.11	241	241
EGFR/PI3K-beta/Gab1	-0.053	0.065	-10000	0	-0.14	162	162
positive regulation of dendritic cell cytokine production	-0.037	0.06	-10000	0	-0.097	249	249
LPA/LPA2/MAGI-3	-0.008	0.035	-10000	0	-0.061	134	134
ARHGEF1	-0.019	0.062	-10000	0	-0.12	127	127
GNAI2	-0.034	0.07	-10000	0	-0.1	249	249
GNAI3	-0.039	0.077	-10000	0	-0.11	248	248
GNAI1	-0.044	0.081	-10000	0	-0.12	249	249
LPA/LPA3	-0.021	0.031	-10000	0	-0.052	249	249
LPA/LPA2	-0.02	0.031	-10000	0	-0.052	249	249
LPA/LPA1	-0.051	0.082	-10000	0	-0.13	249	249
HB-EGF/EGFR	-0.003	0.059	-10000	0	-0.13	77	77
HBEGF	0.004	0.039	-10000	0	-0.077	96	96
mol:DAG	-0.004	0.039	-10000	0	-0.11	41	41
cAMP biosynthetic process	-0.045	0.096	-10000	0	-0.2	134	134
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
SRC	0.023	0.008	-10000	0	-0.12	2	2
GNB1	0.023	0.006	-10000	0	-0.12	1	1
LYN	-0.03	0.089	-10000	0	-0.22	75	75
GNAQ	-0.012	0.038	-10000	0	-0.069	124	124
LPAR2	0	0	-10000	0	-10000	0	0
LPAR3	0	0	-10000	0	-10000	0	0
LPAR1	-0.033	0.049	-10000	0	-0.083	249	249
IL8	-0.084	0.15	-10000	0	-0.33	121	121
PTK2	-0.028	0.062	-10000	0	-0.09	246	246
Rac1/GDP	0.016	0.015	-10000	0	-0.15	5	5
CASP3	-0.034	0.07	-10000	0	-0.15	123	123
EGFR	0.015	0.03	-10000	0	-0.12	25	25
PLCG1	-0.007	0.041	-10000	0	-0.067	135	135
PLD2	-0.026	0.059	-10000	0	-0.087	248	248
G12/G13	-0.019	0.072	-10000	0	-0.14	127	127
PI3K-beta	-0.039	0.059	-10000	0	-0.19	48	48
cell migration	-0.011	0.078	-10000	0	-0.23	46	46
SLC9A3R2	0.017	0.029	-10000	0	-0.12	24	24
PXN	-0.026	0.075	-10000	0	-0.18	48	48
HRAS/GTP	-0.041	0.093	-10000	0	-0.19	128	128
RAC1	0.023	0.002	-10000	0	-10000	0	0
MMP9	0	0.05	-10000	0	-0.12	81	81
PRKCE	0.021	0.017	-10000	0	-0.12	8	8
PRKCD	-0.004	0.044	-10000	0	-0.11	51	51
Gi(beta/gamma)	-0.042	0.096	-10000	0	-0.19	139	139
mol:LPA	-0.033	0.049	-10000	0	-0.083	249	249
TRIP6/p130 Cas/FAK1/Paxillin	-0.021	0.091	-10000	0	-0.16	134	134
MAPKKK cascade	-0.04	0.092	-10000	0	-0.19	128	128
contractile ring contraction involved in cytokinesis	-0.008	0.053	-10000	0	-0.35	6	6
mol:GDP	0	0	-10000	0	-10000	0	0
GNA14	-0.009	0.029	-10000	0	-0.057	127	127
GNA15	-0.01	0.034	-10000	0	-0.063	127	127
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	126	126
GNA11	-0.009	0.028	-10000	0	-0.056	123	123
Rac1/GTP	-0.025	0.24	-10000	0	-0.92	37	37
MMP2	-0.085	0.14	-10000	0	-0.22	249	249

×

TCGA08_retinoblastoma

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2B	0.017	0.017	-10000	0	-0.13	4	4
CDKN2C	0.008	0.044	-10000	0	-0.12	58	58
CDKN2A	0.015	0.021	-10000	0	-0.12	10	10
CCND2	0.015	0.052	0.12	107	-10000	0	107
RB1	-0.022	0.061	0.09	1	-0.12	137	138
CDK4	0.022	0.068	0.13	138	-0.12	17	155
CDK6	0.014	0.073	0.13	131	-0.13	39	170
G1/S progression	0.019	0.065	0.12	138	-10000	0	138

×

Osteopontin-mediated 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
IKK alpha homodimer	-0.046	0.11	-9999	-0.22	124	124
NF kappa B1 p50/RelA/I kappa B alpha	-0.067	0.17	-9999	-0.31	143	143
alphaV/beta3 Integrin/Osteopontin/Src	-0.038	0.11	-9999	-0.18	169	169
AP1	-0.12	0.16	-9999	-0.3	185	185
ILK	-0.046	0.099	-9999	-0.22	106	106
bone resorption	-0.041	0.11	-9999	-0.19	153	153
PTK2B	0.023	0.009	-9999	-0.12	2	2
PYK2/p130Cas	-0.022	0.11	-9999	-0.19	118	118
ITGAV	0.008	0.036	-9999	-0.12	33	33
mol:GTP	0	0	-9999	-10000	0	0
CD44/Rho Family GTPase/ROCK2	0	0.069	-9999	-0.12	127	127
alphaV/beta3 Integrin/Osteopontin	-0.041	0.12	-9999	-0.19	173	173
MAP3K1	-0.05	0.1	-9999	-0.2	132	132
JUN	0.013	0.032	-9999	-0.12	30	30
MAPK3	-0.063	0.12	-9999	-0.25	140	140
MAPK1	-0.064	0.13	-9999	-0.25	141	141
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
NFKB1	0.021	0.013	-9999	-0.12	4	4
MAPK8	-0.053	0.1	-9999	-0.2	144	144
ITGB3	0	0.047	-9999	-0.12	70	70
NFKBIA	-0.08	0.16	-9999	-0.32	146	146
FOS	-0.006	0.053	-9999	-0.12	95	95
CD44	0.011	0.038	-9999	-0.12	42	42
CHUK	0.021	0.013	-9999	-0.12	4	4
PLAU	-0.22	0.4	-9999	-1	107	107
NF kappa B1 p50/RelA	-0.067	0.17	-9999	-0.36	123	123
BCAR1	0.023	0.01	-9999	-0.12	3	3
RELA	0.023	0.009	-9999	-0.12	2	2
alphaV beta3 Integrin	-0.027	0.087	-9999	-0.16	143	143
mol:GDP	0	0	-9999	-10000	0	0
SYK	-0.047	0.1	-9999	-0.2	136	136
VAV3	-0.054	0.11	-9999	-0.21	151	151
MAP3K14	-0.053	0.11	-9999	-0.2	153	153
ROCK2	0.019	0.021	-9999	-0.12	12	12
SPP1	0.009	0.034	-9999	-0.12	31	31
RAC1	0.023	0.002	-9999	-10000	0	0
Rac1/GTP	-0.05	0.1	-9999	-0.2	146	146
MMP2	-0.13	0.16	-9999	-0.28	244	244

×

Syndecan-1-mediated signaling 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
TGFB1	0.019	0.023	-9999	-0.12	14	14
CCL5	0.006	0.042	-9999	-0.12	55	55
SDCBP	0.021	0.01	-9999	-0.12	2	2
FGFR/FGF2/Syndecan-1	-0.083	0.12	-9999	-0.25	135	135
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
Syndecan-1/Laminin-5	-0.072	0.12	-9999	-0.24	141	141
Syndecan-1/Syntenin	-0.076	0.13	-9999	-0.24	154	154
MAPK3	-0.06	0.12	-9999	-0.21	144	144
HGF/MET	-0.017	0.074	-9999	-0.14	119	119
TGFB1/TGF beta receptor Type II	0.019	0.023	-9999	-0.12	14	14
BSG	0.022	0.012	-9999	-0.12	4	4
keratinocyte migration	-0.071	0.12	-9999	-0.23	141	141
Syndecan-1/RANTES	-0.086	0.14	-9999	-0.25	169	169
Syndecan-1/CD147	-0.062	0.12	-9999	-0.22	141	141
Syndecan-1/Syntenin/PIP2	-0.074	0.12	-9999	-0.23	156	156
LAMA5	0.019	0.025	-9999	-0.12	17	17
positive regulation of cell-cell adhesion	-0.073	0.12	-9999	-0.22	156	156
MMP7	-0.021	0.059	-9999	-0.12	144	144
HGF	0.02	0.022	-9999	-0.12	14	14
Syndecan-1/CASK	-0.079	0.12	-9999	-0.24	135	135
Syndecan-1/HGF/MET	-0.086	0.13	-9999	-0.22	199	199
regulation of cell adhesion	-0.058	0.11	-9999	-0.23	113	113
HPSE	0.013	0.034	-9999	-0.12	34	34
positive regulation of cell migration	-0.083	0.12	-9999	-0.25	135	135
SDC1	-0.084	0.12	-9999	-0.25	135	135
Syndecan-1/Collagen	-0.083	0.12	-9999	-0.25	135	135
PPIB	0.023	0.003	-9999	-10000	0	0
MET	0.001	0.047	-9999	-0.12	71	71
PRKACA	0.021	0.017	-9999	-0.12	8	8
MMP9	0	0.05	-9999	-0.12	81	81
MAPK1	-0.061	0.12	-9999	-0.21	142	142
homophilic cell adhesion	-0.082	0.12	-9999	-0.25	135	135
MMP1	-0.007	0.058	-9999	-0.12	116	116

×

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	-0.074	0.13	0.27	6	-0.25	162	168
PTK2B	0.022	0.009	-10000	0	-0.12	2	2
mol:Ca2+	-0.04	0.16	-10000	0	-0.46	51	51
EDN1	-0.056	0.11	0.2	6	-0.19	168	174
EDN3	0.019	0.024	-10000	0	-0.12	16	16
EDN2	0.018	0.027	-10000	0	-0.12	21	21
HRAS/GDP	-0.067	0.14	0.21	2	-0.3	107	109
ETA receptor/Endothelin-1/Gq/GTP/PLC beta	-0.049	0.11	0.2	3	-0.23	110	113
ADCY4	-0.058	0.11	0.2	6	-0.2	161	167
ADCY5	-0.06	0.11	0.2	5	-0.2	166	171
ADCY6	-0.057	0.11	0.2	6	-0.2	158	164
ADCY7	-0.056	0.11	0.2	6	-0.2	158	164
ADCY1	-0.057	0.11	0.2	6	-0.2	158	164
ADCY2	-0.057	0.11	0.2	6	-0.2	158	164
ADCY3	-0.058	0.11	0.2	6	-0.2	160	166
ADCY8	-0.066	0.11	0.2	4	-0.2	171	175
ADCY9	-0.059	0.11	0.2	6	-0.2	159	165
arachidonic acid secretion	-0.13	0.23	-10000	0	-0.43	160	160
ETB receptor/Endothelin-1/Gq/GTP	-0.021	0.081	-10000	0	-0.2	59	59
GNAO1	0.011	0.041	-10000	0	-0.12	50	50
HRAS	0.022	0.006	-10000	0	-0.12	1	1
ETA receptor/Endothelin-1/G12/GTP	-0.052	0.14	0.32	6	-0.23	148	154
ETA receptor/Endothelin-1/Gs/GTP	-0.049	0.13	0.3	6	-0.22	148	154
mol:GTP	-0.001	0.006	-10000	0	-10000	0	0
COL3A1	-0.13	0.19	0.28	6	-0.35	202	208
EDNRB	-0.012	0.053	-10000	0	-0.089	148	148
response to oxidative stress	0	0	-10000	0	-10000	0	0
CYSLTR2	-0.073	0.14	0.28	6	-0.27	138	144
CYSLTR1	-0.082	0.14	0.28	5	-0.28	148	153
SLC9A1	-0.042	0.088	0.19	6	-0.17	132	138
mol:GDP	-0.078	0.15	0.21	2	-0.32	112	114
SLC9A3	-0.057	0.16	-10000	0	-0.44	46	46
RAF1	-0.09	0.18	-10000	0	-0.37	127	127
JUN	-0.08	0.27	-10000	0	-0.83	55	55
JAK2	-0.08	0.14	0.27	6	-0.26	169	175
mol:IP3	-0.051	0.12	-10000	0	-0.26	90	90
ETA receptor/Endothelin-1	-0.084	0.17	0.36	6	-0.3	160	166
PLCB1	0.011	0.034	-10000	0	-0.12	33	33
PLCB2	0.019	0.019	-10000	0	-0.12	9	9
ETA receptor/Endothelin-3	-0.02	0.077	0.16	6	-0.13	142	148
FOS	-0.17	0.34	-10000	0	-0.84	109	109
Gai/GDP	0.012	0.071	-10000	0	-0.56	4	4
CRK	0.021	0.016	-10000	0	-0.12	7	7
mol:Ca ++	-0.098	0.16	0.27	3	-0.32	157	160
BCAR1	0.023	0.01	-10000	0	-0.12	3	3
PRKCB1	-0.051	0.11	-10000	0	-0.25	92	92
GNAQ	0.019	0.017	-10000	0	-0.12	6	6
GNAZ	0.022	0.012	-10000	0	-0.12	4	4
GNAL	0.021	0.019	-10000	0	-0.12	10	10
Gs family/GDP	-0.066	0.14	0.2	2	-0.29	111	113
ETA receptor/Endothelin-1/Gq/GTP	-0.042	0.12	0.21	4	-0.24	95	99
MAPK14	-0.027	0.086	-10000	0	-0.19	79	79
TRPC6	-0.042	0.17	-10000	0	-0.48	48	48
GNAI2	0.022	0.01	-10000	0	-0.12	3	3
GNAI3	0.021	0.008	-10000	0	-0.12	1	1
GNAI1	0.012	0.035	-10000	0	-0.12	36	36
ETB receptor/Endothelin-1/Gq/GTP/PLC beta	-0.031	0.089	-10000	0	-0.21	74	74
ETB receptor/Endothelin-2	0.004	0.048	-10000	0	-0.11	46	46
ETB receptor/Endothelin-3	0.007	0.043	-10000	0	-0.1	33	33
ETB receptor/Endothelin-1	-0.048	0.1	0.17	4	-0.19	160	164
MAPK3	-0.16	0.3	-10000	0	-0.73	113	113
MAPK1	-0.16	0.31	-10000	0	-0.74	114	114
Rac1/GDP	-0.067	0.14	0.21	2	-0.3	110	112
cAMP biosynthetic process	-0.039	0.1	0.21	5	-0.21	101	106
MAPK8	-0.057	0.19	-10000	0	-0.5	70	70
SRC	0.023	0.009	-10000	0	-0.12	2	2
ETB receptor/Endothelin-1/Gi/GTP	-0.034	0.096	-10000	0	-0.24	71	71
p130Cas/CRK/Src/PYK2	-0.053	0.15	-10000	0	-0.37	69	69
mol:K +	0	0	-10000	0	-10000	0	0
G12/GDP	-0.066	0.14	0.21	2	-0.3	109	111
COL1A2	-0.14	0.23	0.28	5	-0.48	148	153
EntrezGene:2778	0	0	-10000	0	-10000	0	0
ETA receptor/Endothelin-2	-0.022	0.079	0.16	6	-0.13	151	157
mol:DAG	-0.051	0.12	-10000	0	-0.26	90	90
MAP2K2	-0.12	0.23	-10000	0	-0.54	118	118
MAP2K1	-0.12	0.23	-10000	0	-0.53	117	117
EDNRA	-0.049	0.1	0.2	6	-0.17	189	195
positive regulation of muscle contraction	-0.059	0.12	0.24	6	-0.21	155	161
Gq family/GDP	-0.044	0.14	-10000	0	-0.29	98	98
HRAS/GTP	-0.068	0.14	-10000	0	-0.3	106	106
PRKCH	-0.051	0.12	-10000	0	-0.25	95	95
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCA	-0.056	0.12	-10000	0	-0.26	98	98
PRKCB	-0.053	0.11	-10000	0	-0.25	94	94
PRKCE	-0.05	0.11	-10000	0	-0.25	96	96
PRKCD	-0.054	0.12	-10000	0	-0.26	97	97
PRKCG	-0.049	0.12	-10000	0	-0.25	93	93
regulation of vascular smooth muscle contraction	-0.2	0.4	-10000	0	-1	109	109
PRKCQ	-0.058	0.12	-10000	0	-0.26	101	101
PLA2G4A	-0.14	0.25	-10000	0	-0.47	159	159
GNA14	0.018	0.022	-10000	0	-0.12	11	11
GNA15	0.02	0.018	-10000	0	-0.12	8	8
GNA12	0.023	0.001	-10000	0	-10000	0	0
GNA11	0.021	0.015	-10000	0	-0.12	5	5
Rac1/GTP	-0.052	0.14	0.32	6	-0.24	149	155
MMP1	0.016	0.14	0.23	5	-0.6	15	20

×

PDGFR-alpha signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.004	0.045	-10000	0	-0.13	59	59
PDGF/PDGFRA/CRKL	-0.008	0.067	-10000	0	-0.13	119	119
positive regulation of JUN kinase activity	0.01	0.066	-10000	0	-0.1	117	117
CRKL	0.023	0.009	-10000	0	-0.12	2	2
PDGF/PDGFRA/Caveolin-3	-0.008	0.067	-10000	0	-0.13	120	120
AP1	-0.15	0.26	-10000	0	-0.67	107	107
mol:IP3	-0.007	0.046	-10000	0	-0.073	142	142
PLCG1	-0.007	0.046	-10000	0	-0.073	142	142
PDGF/PDGFRA/alphaV Integrin	-0.036	0.092	-10000	0	-0.14	224	224
RAPGEF1	0.023	0	-10000	0	-10000	0	0
CRK	0.022	0.016	-10000	0	-0.12	7	7
mol:Ca2+	-0.007	0.046	-10000	0	-0.073	142	142
CAV3	0.022	0.01	-10000	0	-0.12	3	3
CAV1	0.012	0.038	-10000	0	-0.12	42	42
SHC/Grb2/SOS1	0.011	0.067	-10000	0	-0.1	117	117
PDGF/PDGFRA/Shf	-0.008	0.067	-10000	0	-0.13	119	119
FOS	-0.14	0.26	-10000	0	-0.64	113	113
JUN	-0.019	0.044	0.26	4	-0.12	34	38
oligodendrocyte development	-0.036	0.092	-10000	0	-0.14	224	224
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
mol:DAG	-0.007	0.046	-10000	0	-0.073	142	142
PDGF/PDGFRA	-0.004	0.045	-10000	0	-0.13	59	59
actin cytoskeleton reorganization	-0.008	0.067	-10000	0	-0.13	115	115
SRF	0.024	0.022	-10000	0	-0.068	24	24
SHC1	0.023	0.001	-10000	0	-10000	0	0
PI3K	-0.013	0.084	-10000	0	-0.14	139	139
PDGF/PDGFRA/Crk/C3G	0.009	0.06	-10000	0	-0.11	91	91
JAK1	0.004	0.031	-10000	0	-0.074	61	61
ELK1/SRF	-0.011	0.065	-10000	0	-0.13	107	107
SHB	0.023	0.008	-10000	0	-0.12	2	2
SHF	0.023	0.008	-10000	0	-0.12	2	2
CSNK2A1	0.031	0.021	-10000	0	-0.1	6	6
GO:0007205	-0.022	0.07	-10000	0	-0.14	109	109
SOS1	0.017	0.027	-10000	0	-0.12	20	20
Ras protein signal transduction	0.01	0.066	-10000	0	-0.1	117	117
PDGF/PDGFRA/SHB	-0.008	0.067	-10000	0	-0.13	115	115
PDGF/PDGFRA/Caveolin-1	-0.018	0.079	-10000	0	-0.12	178	178
ITGAV	0.012	0.033	-10000	0	-0.12	31	31
ELK1	-0.023	0.068	-10000	0	-0.12	144	144
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PDGF/PDGFRA/Crk	-0.009	0.067	-10000	0	-0.13	123	123
JAK-STAT cascade	0.004	0.031	-10000	0	-0.074	61	61
cell proliferation	-0.008	0.066	-10000	0	-0.13	119	119

×

TRAIL signaling 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
TNFSF10	0.001	0.046	-9999	-0.12	69	69
positive regulation of NF-kappaB transcription factor activity	-0.021	0.079	-9999	-0.12	206	206
MAP2K4	-0.008	0.086	-9999	-0.15	129	129
IKBKB	0.022	0.015	-9999	-0.12	6	6
TNFRSF10B	0.022	0.014	-9999	-0.12	5	5
TNFRSF10A	0.019	0.021	-9999	-0.12	12	12
SMPD1	-0.013	0.053	-9999	-0.1	131	131
IKBKG	0.023	0.008	-9999	-0.12	2	2
mol:GTP	0	0	-9999	-10000	0	0
TNFRSF10D	0.019	0.023	-9999	-0.12	15	15
TRAIL/TRAILR2	-0.02	0.078	-9999	-0.12	201	201
TRAIL/TRAILR3	-0.02	0.075	-9999	-0.12	208	208
TRAIL/TRAILR1	-0.025	0.082	-9999	-0.12	217	217
TRAIL/TRAILR4	-0.021	0.079	-9999	-0.12	206	206
TRAIL/TRAILR1/DAP3/GTP	-0.006	0.069	-9999	-0.11	144	144
IKK complex	0.006	0.079	-9999	-0.28	33	33
RIPK1	0.022	0.011	-9999	-0.12	3	3
response to oxidative stress	0	0	-9999	-10000	0	0
DAP3/GTP	0.015	0.021	-9999	-0.14	10	10
MAPK3	0.006	0.032	-9999	-0.073	73	73
MAP3K1	-0.008	0.086	-9999	-0.16	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	0.082	-9999	-0.14	140	140
CFLAR	0.022	0.011	-9999	-0.12	3	3
MAPK1	0.005	0.034	-9999	-0.074	75	75
TRAIL/TRAILR1/FADD/TRADD/RIP	0.015	0.073	-9999	-0.094	142	142
mol:ceramide	-0.013	0.053	-9999	-0.1	131	131
FADD	0.023	0.009	-9999	-0.12	2	2
MAPK8	-0.007	0.085	-9999	-0.22	43	43
TRAF2	0.023	0	-9999	-10000	0	0
TRAILR3 (trimer)	0.019	0.025	-9999	-0.12	18	18
CHUK	0.021	0.013	-9999	-0.12	4	4
TRAIL/TRAILR1/FADD	-0.007	0.074	-9999	-0.12	139	139
DAP3	0.023	0.007	-9999	-0.12	1	1
CASP10	-0.038	0.098	-9999	-0.2	130	130
JNK cascade	-0.021	0.079	-9999	-0.12	206	206
TRAIL (trimer)	0.001	0.046	-9999	-0.12	69	69
TNFRSF10C	0.019	0.025	-9999	-0.12	18	18
TRAIL/TRAILR1/DAP3/GTP/FADD	0.004	0.069	-9999	-0.098	144	144
TRAIL/TRAILR2/FADD	-0.002	0.071	-9999	-0.12	131	131
cell death	-0.013	0.052	-9999	-0.1	131	131
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2	-0.007	0.079	-9999	-0.14	133	133
TRAILR2 (trimer)	0.022	0.014	-9999	-0.12	5	5
CASP8	-0.001	0.11	-9999	-0.66	15	15
negative regulation of caspase activity	0	0	-9999	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP	0.019	0.071	-9999	-0.091	134	134

×

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	0.012	-10000	0	-0.076	10	10
TP53	-0.05	0.11	0.18	15	-0.24	126	141
Senescence	-0.069	0.13	0.18	15	-0.26	158	173
Apoptosis	-0.069	0.13	0.18	15	-0.26	158	173
Activated_Oncogenes	0	0	-10000	0	-10000	0	0
MDM2	0.002	0.01	0.056	9	-0.083	4	13
MDM4	0.018	0.023	-10000	0	-0.12	15	15

×

Fc-epsilon receptor I signaling in mast cells

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PPAP2A	0.021	0.019	-9999	-0.12	10	10
LAT2	-0.033	0.11	-9999	-0.2	140	140
AP1	-0.069	0.18	-9999	-0.36	121	121
mol:PIP3	-0.037	0.14	-9999	-0.26	133	133
IKBKB	-0.014	0.083	-9999	-0.15	129	129
AKT1	-0.025	0.07	-9999	-0.13	118	118
IKBKG	-0.014	0.082	-9999	-0.15	128	128
MS4A2	0.027	0.014	-9999	-0.13	3	3
mol:Sphingosine-1-phosphate	0	0	-9999	-10000	0	0
PIK3CA	0.02	0.017	-9999	-0.12	7	7
MAP3K1	-0.038	0.13	-9999	-0.24	134	134
mol:Ca2+	-0.027	0.11	-9999	-0.2	134	134
LYN	0.02	0.014	-9999	-0.12	4	4
CBLB	-0.032	0.1	-9999	-0.2	132	132
SHC1	0.023	0.001	-9999	-10000	0	0
RasGAP/p62DOK	-0.005	0.066	-9999	-0.11	134	134
positive regulation of cell migration	0.011	0.009	-9999	-0.076	6	6
INPP5D	0	0	-9999	-10000	0	0
PLD2	-0.008	0.05	-9999	-0.09	101	101
PTPN13	-0.087	0.19	-9999	-0.44	96	96
PTPN11	0.021	0.013	-9999	-0.12	3	3
GO:0007205	0	0	-9999	-10000	0	0
regulation of mast cell degranulation	-0.034	0.11	-9999	-0.23	88	88
SYK	0.016	0.028	-9999	-0.12	21	21
GRB2	0.023	0.006	-9999	-0.12	1	1
LAT/PLCgamma1/GRB2/SLP76/GADs	-0.062	0.13	-9999	-0.26	133	133
LAT	-0.032	0.1	-9999	-0.19	138	138
PAK2	-0.044	0.14	-9999	-0.26	135	135
NFATC2	-0.003	0.062	-9999	-0.39	12	12
HRAS	-0.048	0.15	-9999	-0.28	136	136
GAB2	0.007	0.041	-9999	-0.12	52	52
PLA2G1B	0.017	0.11	-9999	-0.91	8	8
Fc epsilon R1	0.003	0.062	-9999	-0.092	138	138
Antigen/IgE/Fc epsilon R1	0.006	0.055	-9999	-0.076	142	142
mol:GDP	-0.058	0.17	-9999	-0.32	133	133
JUN	0.014	0.032	-9999	-0.12	30	30
mol:Ca++	0	0	-9999	-10000	0	0
PIK3R1	0.015	0.031	-9999	-0.12	28	28
FOS	-0.005	0.052	-9999	-0.12	95	95
Antigen/IgE/Fc epsilon R1/LYN/SYK	-0.037	0.11	-9999	-0.21	140	140
CHUK	-0.017	0.085	-9999	-0.16	130	130
KLRG1	-0.015	0.088	-9999	-0.18	106	106
VAV1	-0.034	0.11	-9999	-0.2	133	133
calcium-dependent protein kinase C activity	0	0	-9999	-10000	0	0
CBL	-0.032	0.1	-9999	-0.19	138	138
negative regulation of mast cell degranulation	-0.027	0.086	-9999	-0.17	113	113
BTK	-0.065	0.19	-9999	-0.4	101	101
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK	-0.035	0.1	-9999	-0.19	153	153
GAB2/PI3K/SHP2	-0.045	0.059	-9999	-0.14	123	123
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP	0.003	0.072	-9999	-0.23	40	40
RAF1	0.011	0.12	-9999	-0.98	8	8
Fc epsilon R1/FcgammaRIIB/SHIP	-0.008	0.083	-9999	-0.12	184	184
FCER1G	0.002	0.044	-9999	-0.12	63	63
FCER1A	0.018	0.027	-9999	-0.12	20	20
Antigen/IgE/Fc epsilon R1/Fyn	0.002	0.065	-9999	-0.084	161	161
MAPK3	0.015	0.11	-9999	-0.92	8	8
MAPK1	0.014	0.11	-9999	-0.92	8	8
NFKB1	0.021	0.013	-9999	-0.12	4	4
MAPK8	-0.008	0.13	-9999	-0.53	27	27
DUSP1	-0.004	0.051	-9999	-0.12	90	90
NF-kappa-B/RelA	-0.005	0.062	-9999	-0.12	100	100
actin cytoskeleton reorganization	-0.065	0.19	-9999	-0.49	68	68
mol:Glucocorticoid Dexamethasone	0	0	-9999	-10000	0	0
PI3K	-0.037	0.14	-9999	-0.25	140	140
FER	-0.032	0.1	-9999	-0.2	135	135
RELA	0.023	0.009	-9999	-0.12	2	2
ITK	-0.004	0.049	-9999	-0.25	12	12
SOS1	0.017	0.027	-9999	-0.12	20	20
PLCG1	-0.055	0.17	-9999	-0.31	134	134
cytokine secretion	-0.005	0.044	-9999	-0.086	103	103
SPHK1	-0.033	0.1	-9999	-0.19	139	139
PTK2	-0.069	0.21	-9999	-0.53	67	67
NTAL/PLCgamma1/GRB2/SLP76/GADs	-0.062	0.13	-9999	-0.27	134	134
EDG1	0.011	0.009	-9999	-0.076	6	6
mol:DAG	-0.035	0.14	-9999	-0.26	128	128
MAP2K2	0.011	0.11	-9999	-0.93	8	8
MAP2K1	0.013	0.11	-9999	-0.92	8	8
MAP2K7	0.022	0.012	-9999	-0.12	4	4
KLRG1/SHP2	-0.014	0.084	-9999	-0.17	99	99
MAP2K4	0.012	0.12	-9999	-0.84	11	11
Fc epsilon R1/FcgammaRIIB	-0.009	0.09	-9999	-0.13	184	184
mol:Choline	-0.008	0.05	-9999	-0.089	101	101
SHC/Grb2/SOS1	-0.012	0.12	-9999	-0.19	142	142
FYN	0.012	0.037	-9999	-0.12	40	40
DOK1	0.022	0.015	-9999	-0.12	6	6
PXN	-0.059	0.19	-9999	-0.48	67	67
HCLS1	-0.035	0.12	-9999	-0.23	118	118
PRKCB	-0.026	0.11	-9999	-0.2	132	132
FCGR2B	0.004	0.044	-9999	-0.12	61	61
IGHE	-0.001	0.003	-9999	-10000	0	0
KLRG1/SHIP	-0.027	0.087	-9999	-0.18	103	103
LCP2	0.013	0.033	-9999	-0.12	31	31
PLA2G4A	-0.045	0.11	-9999	-0.22	135	135
RASA1	0.021	0.011	-9999	-0.12	3	3
mol:Phosphatidic acid	-0.008	0.05	-9999	-0.089	101	101
IKK complex	-0.006	0.068	-9999	-0.13	98	98
WIPF1	0.02	0.02	-9999	-0.12	11	11

×

amb2 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2	-0.029	0.082	-9999	-0.13	181	181
alphaM/beta2 Integrin/GPIbA	0.022	0.058	-9999	-0.11	77	77
alphaM/beta2 Integrin/proMMP-9	-0.005	0.08	-9999	-0.13	130	130
PLAUR	0.018	0.023	-9999	-0.12	14	14
HMGB1	0.023	0.008	-9999	-0.032	9	9
alphaM/beta2 Integrin/Talin	0.015	0.069	-9999	-0.12	94	94
AGER	0.022	0.017	-9999	-0.11	7	7
RAP1A	0.021	0.011	-9999	-0.12	3	3
SELPLG	0.02	0.021	-9999	-0.12	12	12
mol:LDL	0	0	-9999	-10000	0	0
alphaM/beta2 Integrin/RAGE/HMGB1	0.034	0.069	-9999	-0.15	22	22
mol:GTP	0	0	-9999	-10000	0	0
MMP9	0	0.05	-9999	-0.12	81	81
CYR61	0.002	0.047	-9999	-0.12	70	70
TLN1	0.021	0.013	-9999	-0.12	4	4
Rap1/GTP	-0.099	0.15	-9999	-0.28	177	177
RHOA	0.023	0.006	-9999	-0.12	1	1
P-selectin oligomer	0.018	0.026	-9999	-0.12	20	20
MYH2	-0.12	0.15	-9999	-0.28	219	219
MST1R	0.017	0.028	-9999	-0.12	23	23
leukocyte activation during inflammatory response	0.027	0.052	-9999	-0.09	78	78
APOB	0.023	0.01	-9999	-0.12	3	3
mol:GDP	0	0	-9999	-10000	0	0
complement component iC3b receptor activity	0	0	-9999	-10000	0	0
MMP2	-0.015	0.059	-9999	-0.12	131	131
JAM3	0.02	0.02	-9999	-0.12	11	11
GP1BA	0.023	0.009	-9999	-0.12	2	2
alphaM/beta2 Integrin/CTGF	0.004	0.073	-9999	-0.12	119	119
alphaM/beta2 Integrin	-0.12	0.16	-9999	-0.31	176	176
JAM3 homodimer	0.02	0.02	-9999	-0.12	11	11
ICAM2	0.017	0.028	-9999	-0.12	23	23
ICAM1	0	0.048	-9999	-0.12	75	75
phagocytosis triggered by activation of immune response cell surface activating receptor	-0.12	0.16	-9999	-0.31	176	176
cell adhesion	0.022	0.058	-9999	-0.11	77	77
NFKB1	0.022	0.07	-9999	-0.22	23	23
THY1	-0.002	0.048	-9999	-0.12	77	77
RhoA/GDP	0.016	0.016	-9999	-0.14	6	6
Lipoprotein(a)	0.03	0.013	-9999	-0.062	11	11
alphaM/beta2 Integrin/LRP/tPA	-0.017	0.087	-9999	-0.12	208	208
IL6	0.007	0.094	-9999	-0.34	17	17
ITGB2	0.013	0.032	-9999	-0.097	37	37
elevation of cytosolic calcium ion concentration	-0.015	0.1	-9999	-0.15	154	154
alphaM/beta2 Integrin/JAM2/JAM3	0.028	0.062	-9999	-0.1	84	84
JAM2	0.015	0.034	-9999	-0.12	34	34
alphaM/beta2 Integrin/ICAM1	0.005	0.087	-9999	-0.15	89	89
alphaM/beta2 Integrin/uPA/Plg	-0.005	0.087	-9999	-0.13	142	142
RhoA/GTP	-0.13	0.16	-9999	-0.29	222	222
positive regulation of phagocytosis	-0.078	0.14	-9999	-0.25	175	175
Ron/MSP	0.027	0.031	-9999	-0.087	36	36
alphaM/beta2 Integrin/uPAR/uPA	-0.014	0.1	-9999	-0.15	154	154
alphaM/beta2 Integrin/uPAR	0.012	0.077	-9999	-0.15	90	90
PLAU	-0.006	0.054	-9999	-0.12	101	101
PLAT	-0.002	0.049	-9999	-0.12	80	80
actin filament polymerization	-0.12	0.14	-9999	-0.27	219	219
MST1	0.022	0.012	-9999	-0.12	4	4
alphaM/beta2 Integrin/lipoprotein(a)	0.031	0.054	-9999	-0.091	78	78
TNF	0.015	0.076	-9999	-0.26	16	16
RAP1B	0.019	0.019	-9999	-0.12	10	10
alphaM/beta2 Integrin/uPA	-0.019	0.091	-9999	-0.15	143	143
fibrinolysis	-0.006	0.086	-9999	-0.13	142	142
HCK	0.019	0.023	-9999	-0.12	15	15
dendritic cell antigen processing and presentation	-0.12	0.16	-9999	-0.31	176	176
VTN	0.023	0.008	-9999	-0.12	2	2
alphaM/beta2 Integrin/CYR61	-0.01	0.08	-9999	-0.13	146	146
LPA	0.021	0.018	-9999	-0.12	9	9
LRP1	0.015	0.032	-9999	-0.12	29	29
cell migration	-0.043	0.086	-9999	-0.13	235	235
FN1	-0.012	0.055	-9999	-0.12	115	115
alphaM/beta2 Integrin/Thy1	-0.026	0.085	-9999	-0.12	214	214
MPO	0.023	0.006	-9999	-0.12	1	1
KNG1	0.023	0.01	-9999	-0.12	3	3
RAP1/GDP	0.015	0.05	-9999	-0.13	51	51
ROCK1	-0.12	0.15	-9999	-0.28	219	219
ELA2	0.022	0.01	-9999	-0.12	3	3
PLG	0.023	0.008	-9999	-0.12	2	2
CTGF	0.012	0.035	-9999	-0.12	37	37
alphaM/beta2 Integrin/Hck	0.018	0.07	-9999	-0.13	84	84
ITGAM	0.021	0.019	-9999	-0.11	9	9
alphaM/beta2 Integrin/P-Selectin/PSGL1	0.03	0.066	-9999	-0.11	82	82
HP	-0.034	0.062	-9999	-0.12	194	194
leukocyte adhesion	-0.009	0.088	-9999	-0.17	66	66
SELP	0.018	0.026	-9999	-0.12	20	20

×

Nectin adhesion pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.01	0.041	-9999	-0.12	51	51
alphaV beta3 Integrin	-0.018	0.081	-9999	-0.12	193	193
PTK2	-0.074	0.15	-9999	-0.31	143	143
positive regulation of JNK cascade	-0.053	0.11	-9999	-0.27	120	120
CDC42/GDP	-0.046	0.17	-9999	-0.36	119	119
Rac1/GDP	-0.045	0.17	-9999	-0.35	120	120
RAP1B	0.019	0.019	-9999	-0.12	10	10
RAP1A	0.021	0.011	-9999	-0.12	3	3
CTNNB1	0.022	0.007	-9999	-0.12	1	1
CDC42/GTP	-0.046	0.15	-9999	-0.32	120	120
nectin-3/I-afadin	-0.021	0.08	-9999	-0.16	123	123
RAPGEF1	-0.062	0.17	-9999	-0.38	119	119
mol:GTP	0	0	-9999	-10000	0	0
CRK	-0.075	0.19	-9999	-0.43	119	119
PDGFB-D/PDGFRB	0.01	0.041	-9999	-0.12	51	51
TLN1	-0.038	0.097	-9999	-0.23	90	90
Rap1/GTP	-0.064	0.12	-9999	-0.28	120	120
IQGAP1	0.02	0.017	-9999	-0.12	7	7
Rap1/GTP/I-afadin	0.015	0.06	-9999	-0.11	88	88
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin	-0.021	0.08	-9999	-0.16	123	123
PVR	0.022	0.012	-9999	-0.12	4	4
Necl-5(dimer)	0.022	0.012	-9999	-0.12	4	4
mol:GDP	-0.068	0.2	-9999	-0.43	120	120
MLLT4	0.014	0.032	-9999	-0.12	30	30
PIK3CA	0.02	0.017	-9999	-0.12	7	7
PI3K	-0.009	0.085	-9999	-0.16	70	70
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin	0.017	0.049	-9999	-0.11	71	71
positive regulation of lamellipodium assembly	-0.06	0.12	-9999	-0.28	127	127
PVRL1	0.023	0.01	-9999	-0.12	3	3
PVRL3	0.003	0.046	-9999	-0.12	67	67
PVRL2	0.019	0.023	-9999	-0.12	15	15
PIK3R1	0.015	0.031	-9999	-0.12	28	28
CDH1	0.021	0.015	-9999	-0.12	6	6
CLDN1	-0.003	0.051	-9999	-0.12	88	88
JAM-A/CLDN1	-0.03	0.087	-9999	-0.12	221	221
SRC	-0.083	0.21	-9999	-0.48	119	119
ITGB3	0.005	0.046	-9999	-0.12	67	67
nectin-1(dimer)/I-afadin/I-afadin	0.017	0.049	-9999	-0.11	71	71
FARP2	-0.065	0.19	-9999	-0.42	120	120
RAC1	0.023	0.002	-9999	-10000	0	0
CTNNA1	0.022	0.01	-9999	-0.12	2	2
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer)	-0.004	0.073	-9999	-0.12	124	124
nectin-1/I-afadin	0.017	0.049	-9999	-0.11	71	71
nectin-2/I-afadin	0.012	0.054	-9999	-0.15	45	45
RAC1/GTP/IQGAP1/filamentous actin	0.017	0.045	-9999	-0.12	50	50
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin	-0.004	0.072	-9999	-0.12	123	123
CDC42/GTP/IQGAP1/filamentous actin	0.017	0.044	-9999	-0.12	49	49
F11R	0.023	0.007	-9999	-0.12	1	1
positive regulation of filopodium formation	-0.053	0.11	-9999	-0.27	120	120
alphaV/beta3 Integrin/Talin	-0.052	0.11	-9999	-0.22	135	135
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.012	0.054	-9999	-0.15	45	45
nectin-2(dimer)/I-afadin/I-afadin	0.012	0.054	-9999	-0.15	45	45
PIP5K1C	-0.046	0.1	-9999	-0.25	95	95
VAV2	-0.078	0.21	-9999	-0.44	130	130
RAP1/GDP	-0.046	0.16	-9999	-0.33	120	120
ITGAV	0.012	0.033	-9999	-0.12	31	31
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin	-0.008	0.074	-9999	-0.12	132	132
nectin-3(dimer)/I-afadin/I-afadin	-0.021	0.08	-9999	-0.16	123	123
Rac1/GTP	-0.052	0.16	-9999	-0.34	127	127
PTPRM	-0.056	0.11	-9999	-0.28	95	95
E-cadherin/beta catenin/alpha catenin	0.031	0.071	-9999	-0.18	27	27
adherens junction assembly	0	0	-9999	-10000	0	0
CDC42	0.023	0.002	-9999	-10000	0	0

×

Ephrin B reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EFNB2	0.007	0.041	-10000	0	-0.12	51	51
EPHB2	0.022	0.021	-10000	0	-0.12	11	11
EFNB1	0.023	0.019	-10000	0	-0.067	21	21
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.046	0.055	-10000	0	-0.15	11	11
Ephrin B2/EPHB1-2	0.011	0.061	-10000	0	-0.1	102	102
neuron projection morphogenesis	0.029	0.046	-10000	0	-0.14	12	12
Ephrin B1/EPHB1-2/Tiam1	0.04	0.056	-10000	0	-0.1	49	49
DNM1	0.022	0.02	-10000	0	-0.12	11	11
cell-cell signaling	0.002	0.004	-10000	0	-10000	0	0
MAP2K4	-0.12	0.21	-10000	0	-0.47	151	151
YES1	-0.19	0.31	-10000	0	-0.71	151	151
Ephrin B1/EPHB1-2/NCK2	0.051	0.043	-10000	0	-0.093	26	26
PI3K	-0.13	0.22	-10000	0	-0.47	156	156
mol:GDP	0.039	0.055	-10000	0	-0.1	49	49
ITGA2B	0.023	0.006	-10000	0	-0.12	1	1
endothelial cell proliferation	0.001	0.057	-10000	0	-0.12	92	92
FYN	-0.2	0.31	-10000	0	-0.71	151	151
MAP3K7	-0.13	0.22	-10000	0	-0.5	151	151
FGR	-0.18	0.31	-10000	0	-0.69	151	151
TIAM1	0.015	0.032	-10000	0	-0.12	29	29
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
RGS3	0.023	0.006	-10000	0	-0.12	1	1
cell adhesion	-0.12	0.2	-10000	0	-0.44	157	157
LYN	-0.2	0.31	-10000	0	-0.71	151	151
Ephrin B1/EPHB1-2/Src Family Kinases	-0.18	0.28	-10000	0	-0.64	151	151
Ephrin B1/EPHB1-2	-0.15	0.24	-10000	0	-0.54	151	151
SRC	-0.18	0.31	-10000	0	-0.69	151	151
ITGB3	0.005	0.046	-10000	0	-0.12	67	67
EPHB1	0.018	0.032	-10000	0	-0.12	29	29
EPHB4	0.022	0.009	-10000	0	-0.12	2	2
RAC1	0.023	0.002	-10000	0	-10000	0	0
Ephrin B2/EPHB4	0.001	0.058	-10000	0	-0.12	92	92
alphaIIb/beta3 Integrin	0.011	0.053	-10000	0	-0.14	38	38
BLK	-0.18	0.31	-10000	0	-0.69	151	151
HCK	-0.19	0.31	-10000	0	-0.7	151	151
regulation of stress fiber formation	-0.049	0.043	0.092	26	-10000	0	26
MAPK8	-0.12	0.2	-10000	0	-0.44	153	153
Ephrin B1/EPHB1-2/RGS3	0.051	0.043	-10000	0	-0.095	26	26
endothelial cell migration	-0.12	0.18	-10000	0	-0.41	154	154
NCK2	0.023	0.006	-10000	0	-0.12	1	1
PTPN13	-0.012	0.057	-10000	0	-0.13	110	110
regulation of focal adhesion formation	-0.049	0.043	0.092	26	-10000	0	26
chemotaxis	-0.049	0.042	0.094	26	-10000	0	26
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
Rac1/GTP	0.038	0.05	-10000	0	-0.15	11	11
angiogenesis	-0.15	0.23	-10000	0	-0.53	151	151
LCK	-0.18	0.31	-10000	0	-0.69	151	151

×

Thromboxane A2 receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGM2	0.005	0.046	-10000	0	-0.12	67	67
GNB1/GNG2	-0.069	0.081	-10000	0	-0.18	196	196
AKT1	-0.055	0.11	-10000	0	-0.19	197	197
EGF	0.02	0.021	-10000	0	-0.12	13	13
mol:TXA2	0	0.001	-10000	0	-10000	0	0
FGR	0.026	0.029	-10000	0	-0.11	7	7
mol:Ca2+	-0.095	0.15	-10000	0	-0.29	198	198
LYN	0.024	0.032	-10000	0	-0.14	8	8
RhoA/GTP	-0.036	0.069	-10000	0	-0.12	199	199
mol:PGI2	0	0	-10000	0	-10000	0	0
SYK	-0.12	0.17	-10000	0	-0.34	197	197
GNG2	0.02	0.018	-10000	0	-0.12	9	9
ARRB2	0.022	0.013	-10000	0	-0.12	5	5
TP alpha/Gq family/GDP/G beta5/gamma2	0.027	0.048	-10000	0	-0.24	13	13
G beta5/gamma2	-0.09	0.11	-10000	0	-0.23	196	196
PRKCH	-0.12	0.18	-10000	0	-0.35	198	198
DNM1	0.02	0.02	-10000	0	-0.12	11	11
TXA2/TP beta/beta Arrestin3	0.017	0.014	-10000	0	-10000	0	0
mol:GTP	-0.001	0.001	-10000	0	-10000	0	0
PTGDR	0.023	0.006	-10000	0	-0.12	1	1
G12 family/GTP	-0.12	0.13	-10000	0	-0.29	199	199
ADRBK1	0.023	0.001	-10000	0	-10000	0	0
ADRBK2	0.015	0.031	-10000	0	-0.12	28	28
RhoA/GTP/ROCK1	0.028	0.021	-10000	0	-0.12	11	11
mol:GDP	0.05	0.12	0.3	48	-10000	0	48
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	198	198
cell morphogenesis	0.027	0.021	-10000	0	-0.12	11	11
PLCB2	-0.17	0.25	-10000	0	-0.49	198	198
mol:cGMP	0	0.001	-10000	0	-10000	0	0
BLK	0.026	0.029	-10000	0	-0.12	6	6
mol:PDG2	0	0	-10000	0	-10000	0	0
HCK	0.024	0.032	-10000	0	-0.14	7	7
RHOA	0.023	0.006	-10000	0	-0.12	1	1
PTGIR	0.023	0.002	-10000	0	-10000	0	0
PRKCB1	-0.12	0.19	-10000	0	-0.37	198	198
GNAQ	0.021	0.015	-10000	0	-0.12	6	6
mol:L-citrulline	0.023	0	-10000	0	-10000	0	0
TXA2/TXA2-R family	-0.18	0.26	-10000	0	-0.51	196	196
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	8	8
TXA2-R family/G12 family/GDP/G beta/gamma	0.028	0.061	-10000	0	-0.43	8	8
TXA2/TP beta/beta Arrestin2/RAB11/GDP	0.041	0.028	-10000	0	-0.11	8	8
MAPK14	-0.073	0.12	-10000	0	-0.22	198	198
TGM2/GTP	-0.14	0.21	-10000	0	-0.4	205	205
MAPK11	-0.072	0.12	-10000	0	-0.22	197	197
ARHGEF1	-0.053	0.094	-10000	0	-0.17	199	199
GNAI2	0.022	0.01	-10000	0	-0.12	3	3
JNK cascade	-0.13	0.19	-10000	0	-0.38	197	197
RAB11/GDP	0.023	0.007	-10000	0	-0.12	1	1
ICAM1	-0.11	0.16	-10000	0	-0.32	197	197
cAMP biosynthetic process	-0.11	0.17	-10000	0	-0.33	202	202
Gq family/GTP/EBP50	0.018	0.042	-10000	0	-0.14	28	28
actin cytoskeleton reorganization	0.027	0.021	-10000	0	-0.12	11	11
SRC	0.026	0.029	-10000	0	-0.11	6	6
GNB5	0.022	0.01	-10000	0	-0.12	3	3
GNB1	0.023	0.006	-10000	0	-0.12	1	1
EGF/EGFR	0.018	0.057	-10000	0	-0.13	40	40
VCAM1	-0.12	0.17	-10000	0	-0.34	197	197
TP beta/Gq family/GDP/G beta5/gamma2	0.027	0.048	-10000	0	-0.24	13	13
platelet activation	-0.093	0.16	-10000	0	-0.29	198	198
PGI2/IP	0.015	0.017	-10000	0	-0.15	6	6
PRKACA	0.021	0.022	-10000	0	-0.15	8	8
Gq family/GDP/G beta5/gamma2	0.027	0.046	-10000	0	-0.22	13	13
TXA2/TP beta/beta Arrestin2	0.016	0.032	-10000	0	-0.26	5	5
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TBXA2R	0.021	0.021	-10000	0	-0.14	8	8
mol:DAG	-0.14	0.21	-10000	0	-0.41	198	198
EGFR	0.015	0.03	-10000	0	-0.12	25	25
TXA2/TP alpha	-0.15	0.23	-10000	0	-0.45	201	201
Gq family/GTP	0.014	0.036	-10000	0	-0.14	25	25
YES1	0.024	0.032	-10000	0	-0.14	8	8
GNAI2/GTP	0.02	0.03	-10000	0	-0.12	6	6
PGD2/DP	0.017	0.004	-10000	0	-0.076	1	1
SLC9A3R1	0.016	0.03	-10000	0	-0.12	26	26
FYN	0.02	0.035	-10000	0	-0.13	13	13
mol:NO	0.023	0	-10000	0	-10000	0	0
GNA15	0.021	0.017	-10000	0	-0.12	8	8
PGK/cGMP	0.028	0.016	-10000	0	-0.057	19	19
RhoA/GDP	0.023	0.006	-10000	0	-0.12	1	1
TP alpha/TGM2/GDP/G beta/gamma	0.041	0.045	-10000	0	-0.15	7	7
NOS3	0.023	0	-10000	0	-10000	0	0
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCA	-0.12	0.18	-10000	0	-0.35	199	199
PRKCB	-0.12	0.18	-10000	0	-0.34	198	198
PRKCE	-0.12	0.18	-10000	0	-0.35	198	198
PRKCD	-0.12	0.19	-10000	0	-0.37	197	197
PRKCG	-0.12	0.19	-10000	0	-0.37	198	198
muscle contraction	-0.16	0.24	-10000	0	-0.47	197	197
PRKCZ	-0.11	0.17	-10000	0	-0.33	197	197
ARR3	0.023	0.006	-10000	0	-0.12	1	1
TXA2/TP beta	0.033	0.035	-10000	0	-0.13	7	7
PRKCQ	-0.12	0.18	-10000	0	-0.35	199	199
MAPKKK cascade	-0.15	0.22	-10000	0	-0.43	198	198
SELE	-0.094	0.15	-10000	0	-0.28	196	196
TP beta/GNAI2/GDP/G beta/gamma	0.052	0.035	-10000	0	-0.2	2	2
ROCK1	0.023	0.009	-10000	0	-0.12	2	2
GNA14	0.02	0.02	-10000	0	-0.12	11	11
chemotaxis	-0.21	0.3	-10000	0	-0.6	196	196
GNA12	0.023	0.001	-10000	0	-10000	0	0
GNA13	0.022	0.009	-10000	0	-0.12	2	2
GNA11	0.022	0.013	-10000	0	-0.12	5	5
Rac1/GTP	0.015	0.015	-10000	0	-0.15	5	5

×

Cellular roles of Anthrax toxin

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ANTXR1	0.007	0.042	-10000	0	-0.12	55	55
ANTXR2	0.013	0.035	-10000	0	-0.12	36	36
negative regulation of myeloid dendritic cell antigen processing and presentation	-0.007	0.013	-10000	0	-0.033	102	102
monocyte activation	-0.099	0.16	-10000	0	-0.35	157	157
MAP2K2	0.006	0.052	-10000	0	-0.66	3	3
MAP2K1	0	0.015	-10000	0	-0.03	80	80
MAP2K7	0	0.014	-10000	0	-0.029	81	81
MAP2K6	-0.005	0.024	-10000	0	-0.044	111	111
CYAA	-0.015	0.047	-10000	0	-0.11	102	102
MAP2K4	0	0.016	-10000	0	-0.029	105	105
IL1B	-0.009	0.036	-10000	0	-0.077	88	88
Channel	-0.002	0.058	-10000	0	-0.12	102	102
NLRP1	0	0.015	-10000	0	-0.031	81	81
CALM1	0.022	0.014	-10000	0	-0.12	5	5
negative regulation of phagocytosis	0.001	0.054	-10000	0	-0.46	7	7
mol:Ca2+	0	0	-10000	0	-10000	0	0
regulation of endothelial cell proliferation	0.007	0.013	0.033	102	-10000	0	102
MAPK3	0	0.015	-10000	0	-0.03	83	83
MAPK1	-0.001	0.018	-10000	0	-0.036	85	85
PGR	-0.011	0.026	-10000	0	-0.046	173	173
PA/Cellular Receptors	-0.004	0.064	-10000	0	-0.13	102	102
apoptosis	-0.007	0.013	-10000	0	-0.033	102	102
LOC728358	0	0	-10000	0	-10000	0	0
Lethal toxin (unfolded)	-0.002	0.057	-10000	0	-0.11	102	102
macrophage activation	0.003	0.017	-10000	0	-0.053	27	27
TNF	0.02	0.02	-10000	0	-0.12	11	11
VCAM1	-0.099	0.16	-10000	0	-0.36	157	157
platelet activation	0.001	0.054	-10000	0	-0.46	7	7
MAPKKK cascade	0.003	0.02	0.048	50	-10000	0	50
IL18	-0.011	0.039	-10000	0	-0.079	104	104
negative regulation of macrophage activation	-0.007	0.013	-10000	0	-0.033	102	102
LEF	-0.007	0.013	-10000	0	-0.033	102	102
CASP1	-0.005	0.024	-10000	0	-0.043	106	106
mol:cAMP	0.001	0.055	-10000	0	-0.46	7	7
necrosis	-0.007	0.013	-10000	0	-0.033	102	102
intracellular pH reduction	0	0	-10000	0	-10000	0	0
PAGA	0	0	-10000	0	-10000	0	0
Edema toxin (unfolded)	-0.001	0.055	-10000	0	-0.11	102	102
mol:Epigallocatechin-3-gallate (EGCG)	0	0	-10000	0	-10000	0	0

×

PLK2 and PLK4 events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLK2	-0.002	0.049	-9999	-0.12	82	82
PLK4	0.017	0.028	-9999	-0.12	22	22
regulation of centriole replication	-0.002	0.047	-9999	-0.09	102	102

×

Syndecan-4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.11	0.2	-10000	0	-0.37	178	178
Syndecan-4/Syndesmos	-0.079	0.18	-10000	0	-0.4	102	102
positive regulation of JNK cascade	-0.1	0.18	-10000	0	-0.4	114	114
Syndecan-4/ADAM12	-0.093	0.18	-10000	0	-0.41	102	102
CCL5	0.006	0.042	-10000	0	-0.12	55	55
Rac1/GDP	0.016	0.015	-10000	0	-0.15	5	5
DNM2	0.02	0.022	-10000	0	-0.12	13	13
ITGA5	0.013	0.036	-10000	0	-0.12	38	38
SDCBP	0.021	0.01	-10000	0	-0.12	2	2
PLG	0.027	0.011	0.063	6	-0.1	2	8
ADAM12	-0.01	0.06	-10000	0	-0.12	129	129
mol:GTP	0	0	-10000	0	-10000	0	0
NUDT16L1	0.021	0.019	-10000	0	-0.12	10	10
mol:PI-4-5-P2	0	0	-10000	0	-10000	0	0
Syndecan-4/PKC alpha	-0.008	0.009	-10000	0	-10000	0	0
Syndecan-4/Laminin alpha1	-0.087	0.18	-10000	0	-0.41	102	102
Syndecan-4/CXCL12/CXCR4	-0.1	0.19	-10000	0	-0.42	112	112
Syndecan-4/Laminin alpha3	-0.092	0.18	-10000	0	-0.42	103	103
MDK	0.021	0.014	-10000	0	-0.12	5	5
Syndecan-4/FZD7	-0.085	0.18	-10000	0	-0.41	100	100
Syndecan-4/Midkine	-0.08	0.18	-10000	0	-0.4	102	102
FZD7	0.015	0.031	-10000	0	-0.12	27	27
Syndecan-4/FGFR1/FGF	-0.067	0.17	-10000	0	-0.38	101	101
THBS1	-0.003	0.052	-10000	0	-0.12	91	91
integrin-mediated signaling pathway	-0.096	0.18	-10000	0	-0.41	105	105
positive regulation of MAPKKK cascade	-0.1	0.18	-10000	0	-0.4	114	114
Syndecan-4/TACI	-0.078	0.18	-10000	0	-0.4	102	102
CXCR4	0.012	0.032	-10000	0	-0.12	30	30
cell adhesion	-0.053	0.095	-10000	0	-0.19	165	165
Syndecan-4/Dynamin	-0.08	0.18	-10000	0	-0.4	102	102
Syndecan-4/TSP1	-0.1	0.18	-10000	0	-0.41	109	109
Syndecan-4/GIPC	-0.08	0.18	-10000	0	-0.4	102	102
Syndecan-4/RANTES	-0.094	0.19	-10000	0	-0.43	102	102
ITGB1	0.021	0.015	-10000	0	-0.12	6	6
LAMA1	0	0.052	-10000	0	-0.12	90	90
LAMA3	0.006	0.043	-10000	0	-0.12	57	57
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCA	0.002	0.051	-10000	0	-0.16	35	35
Syndecan-4/alpha-Actinin	-0.081	0.18	-10000	0	-0.41	103	103
TFPI	0.018	0.026	-10000	0	-0.12	19	19
F2	0.02	0.016	-10000	0	-0.12	4	4
alpha5/beta1 Integrin	0.017	0.048	-10000	0	-0.14	33	33
positive regulation of cell adhesion	-0.095	0.18	-10000	0	-0.41	106	106
ACTN1	0.022	0.011	-10000	0	-0.12	3	3
TNC	-0.004	0.053	-10000	0	-0.12	95	95
Syndecan-4/CXCL12	-0.099	0.18	-10000	0	-0.43	102	102
FGF6	0.022	0.012	-10000	0	-0.12	4	4
RHOA	0.023	0.006	-10000	0	-0.12	1	1
CXCL12	-0.002	0.05	-10000	0	-0.12	85	85
TNFRSF13B	0.023	0	-10000	0	-10000	0	0
FGF2	0.023	0.008	-10000	0	-0.12	2	2
FGFR1	0.008	0.043	-10000	0	-0.12	56	56
Syndecan-4/PI-4-5-P2	-0.088	0.17	-10000	0	-0.4	102	102
mol:GDP	0	0	-10000	0	-10000	0	0
FN1	-0.012	0.055	-10000	0	-0.12	115	115
cell migration	-0.005	0.004	-10000	0	-10000	0	0
PRKCD	0.023	0.019	-10000	0	-0.12	8	8
vasculogenesis	-0.097	0.18	-10000	0	-0.4	109	109
SDC4	-0.089	0.18	-10000	0	-0.43	102	102
Syndecan-4/Tenascin C	-0.1	0.18	-10000	0	-0.42	105	105
Syndecan-4/PI-4-5-P2/PKC alpha	-0.006	0.007	-10000	0	-10000	0	0
Syndecan-4/Syntenin	-0.084	0.18	-10000	0	-0.41	102	102
MMP9	0.002	0.05	-10000	0	-0.12	81	81
Rac1/GTP	-0.053	0.097	-10000	0	-0.19	163	163
cytoskeleton organization	-0.076	0.17	-10000	0	-0.39	102	102
GIPC1	0.019	0.023	-10000	0	-0.12	15	15
Syndecan-4/TFPI	-0.08	0.18	-10000	0	-0.4	102	102

×

IL23-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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCL2	-0.26	0.57	-9999	-1.2	132	132
IL23A	-0.2	0.5	-9999	-1.2	86	86
NF kappa B1 p50/RelA/I kappa B alpha	-0.19	0.5	-9999	-1.2	94	94
positive regulation of T cell mediated cytotoxicity	-0.22	0.56	-9999	-1.2	112	112
ITGA3	-0.24	0.54	-9999	-1.2	124	124
IL17F	-0.11	0.32	-9999	-0.68	100	100
IL12B	0.016	0.04	-9999	-10000	0	0
STAT1 (dimer)	-0.22	0.54	-9999	-1.2	102	102
CD4	-0.21	0.52	-9999	-1.2	102	102
IL23	-0.18	0.48	-9999	-1.2	87	87
IL23R	0.002	0.089	-9999	-10000	0	0
IL1B	-0.22	0.54	-9999	-1.3	98	98
T-helper cell lineage commitment	0	0	-9999	-10000	0	0
IL24	-0.18	0.47	-9999	-1.1	93	93
TYK2	0.013	0.034	-9999	-0.14	7	7
STAT4	0.02	0.02	-9999	-0.12	11	11
STAT3	0.022	0.011	-9999	-0.12	3	3
IL18RAP	0.022	0.018	-9999	-0.12	8	8
IL12RB1	0.015	0.03	-9999	-0.15	1	1
PIK3CA	0.02	0.017	-9999	-0.12	7	7
IL12Rbeta1/TYK2	0.021	0.04	-9999	-0.11	8	8
IL23R/JAK2	-0.001	0.12	-9999	-10000	0	0
positive regulation of chronic inflammatory response	-0.22	0.56	-9999	-1.2	112	112
natural killer cell activation	0	0.008	-9999	-10000	0	0
JAK2	0.011	0.046	-9999	-0.12	17	17
PIK3R1	0.015	0.031	-9999	-0.12	28	28
NFKB1	0.021	0.013	-9999	-0.12	4	4
RELA	0.022	0.009	-9999	-0.12	2	2
positive regulation of dendritic cell antigen processing and presentation	-0.17	0.46	-9999	-1.1	87	87
ALOX12B	-0.18	0.47	-9999	-1.1	93	93
CXCL1	-0.23	0.52	-9999	-1.1	119	119
T cell proliferation	-0.22	0.56	-9999	-1.2	112	112
NFKBIA	0.016	0.028	-9999	-0.12	21	21
IL17A	-0.072	0.26	-9999	-0.53	100	100
PI3K	-0.2	0.51	-9999	-1.2	98	98
IFNG	-0.004	0.026	-9999	-10000	0	0
STAT3 (dimer)	-0.18	0.48	-9999	-1.1	100	100
IL18R1	0.02	0.022	-9999	-0.12	14	14
IL23/IL23R/JAK2/TYK2/SOCS3	-0.084	0.28	-9999	-0.59	91	91
IL18/IL18R	0.015	0.061	-9999	-0.11	78	78
macrophage activation	-0.009	0.021	-9999	-0.044	81	81
TNF	-0.19	0.5	-9999	-1.2	88	88
STAT3/STAT4	-0.2	0.51	-9999	-1.2	98	98
STAT4 (dimer)	-0.21	0.53	-9999	-1.2	95	95
IL18	0.004	0.046	-9999	-0.12	66	66
IL19	-0.18	0.47	-9999	-1.1	94	94
STAT5A (dimer)	-0.21	0.53	-9999	-1.2	97	97
STAT1	0.014	0.03	-9999	-0.12	25	25
SOCS3	0.015	0.031	-9999	-0.12	28	28
CXCL9	-0.26	0.56	-9999	-1.2	131	131
MPO	-0.18	0.47	-9999	-1.1	88	88
positive regulation of humoral immune response	-0.22	0.56	-9999	-1.2	112	112
IL23/IL23R/JAK2/TYK2	-0.24	0.61	-9999	-1.4	95	95
IL6	-0.2	0.48	-9999	-1.1	92	92
STAT5A	0.022	0.012	-9999	-0.12	4	4
IL2	0.025	0.014	-9999	-0.13	3	3
positive regulation of tyrosine phosphorylation of STAT protein	0	0.008	-9999	-10000	0	0
CD3E	-0.2	0.5	-9999	-1.1	97	97
keratinocyte proliferation	-0.22	0.56	-9999	-1.2	112	112
NOS2	-0.18	0.47	-9999	-0.97	118	118

×

IL1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
UBC13/UEV1A	0.014	0.022	-10000	0	-0.14	11	11
PRKCZ	0.023	0	-10000	0	-10000	0	0
MAP3K7IP2	0.02	0.016	-10000	0	-0.12	7	7
ERC1	0.016	0.029	-10000	0	-0.12	24	24
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4	-0.063	0.15	-10000	0	-0.3	127	127
IRAK/TOLLIP	0.028	0.026	-10000	0	-0.11	16	16
IKBKB	0.022	0.015	-10000	0	-0.12	6	6
IKBKG	0.023	0.008	-10000	0	-0.12	2	2
IL1 alpha/IL1R2	0.014	0.048	-10000	0	-0.15	23	23
IL1A	0.017	0.029	-10000	0	-0.12	24	24
IL1B	0.002	0.039	-10000	0	-0.083	84	84
IRAK/TRAF6/p62/Atypical PKCs	0.037	0.059	-10000	0	-0.089	84	84
IL1R2	0.006	0.045	-10000	0	-0.12	64	64
IL1R1	0.003	0.046	-10000	0	-0.12	68	68
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.065	0.15	0.16	1	-0.28	141	142
TOLLIP	0.023	0.01	-10000	0	-0.12	3	3
TICAM2	0.021	0.014	-10000	0	-0.12	5	5
MAP3K3	0.023	0	-10000	0	-10000	0	0
TAK1/TAB1/TAB2	0.034	0.05	-10000	0	-0.15	34	34
IKK complex/ELKS	0.024	0.093	-10000	0	-0.24	52	52
JUN	0.011	0.047	-10000	0	-0.17	26	26
MAP3K7	0.021	0.014	-10000	0	-0.12	5	5
IL1 beta fragment/IL1R1/IL1RAP/PI3K	-0.052	0.12	-10000	0	-0.21	143	143
IL1 alpha/IL1R1/IL1RAP/MYD88	-0.002	0.077	-10000	0	-0.11	137	137
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4	-0.004	0.087	-10000	0	-0.12	165	165
IL1 beta fragment/IL1R1/IL1RAP	-0.057	0.1	-10000	0	-0.15	246	246
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
MAPK8	0.014	0.049	-10000	0	-0.16	30	30
IRAK1	0.016	0.022	-10000	0	-0.088	22	22
IL1RN/IL1R1	-0.008	0.07	-10000	0	-0.11	167	167
IRAK4	0.019	0.02	-10000	0	-0.12	10	10
PRKCI	0.016	0.028	-10000	0	-0.12	22	22
TRAF6	0.022	0.009	-10000	0	-0.12	2	2
PI3K	0.007	0.065	-10000	0	-0.16	63	63
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.075	0.15	-10000	0	-0.3	139	139
CHUK	0.021	0.013	-10000	0	-0.12	4	4
IL1 beta fragment/IL1R1/IL1RAP/MYD88s	-0.057	0.1	-10000	0	-0.15	246	246
IL1 beta/IL1R2	-0.036	0.089	-10000	0	-0.15	182	182
IRAK/TRAF6/TAK1/TAB1/TAB2	0.046	0.055	-10000	0	-0.19	18	18
NF kappa B1 p50/RelA	-0.051	0.12	-10000	0	-0.21	150	150
IRAK3	0.009	0.041	-10000	0	-0.12	52	52
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4	-0.05	0.12	-10000	0	-0.22	132	132
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.031	0.11	-10000	0	-0.18	157	157
IL1 alpha/IL1R1/IL1RAP	-0.014	0.078	-10000	0	-0.13	134	134
RELA	0.023	0.009	-10000	0	-0.12	2	2
MAP3K7IP1	0.023	0	-10000	0	-10000	0	0
SQSTM1	0.021	0.015	-10000	0	-0.12	6	6
MYD88	0.023	0.006	-10000	0	-0.12	1	1
IRAK/TRAF6/MEKK3	0.04	0.031	-10000	0	-0.097	23	23
IL1RAP	0.009	0.038	-10000	0	-0.12	44	44
UBE2N	0.023	0.007	-10000	0	-0.12	1	1
IRAK/TRAF6	-0.047	0.099	-10000	0	-0.19	141	141
CASP1	0.006	0.04	-10000	0	-0.12	50	50
IL1RN/IL1R2	0.01	0.053	-10000	0	-0.14	34	34
IL1 beta fragment/IL1R1/IL1RAP/MYD88	-0.045	0.1	-10000	0	-0.14	246	246
TMEM189-UBE2V1	0	0	-10000	0	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.038	0.13	-10000	0	-0.27	107	107
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
IL1RN	0.018	0.025	-10000	0	-0.12	17	17
TRAF6/TAK1/TAB1/TAB2	0.042	0.052	-10000	0	-0.12	43	43
MAP2K6	0.015	0.05	-10000	0	-0.13	46	46

×

Nongenotropic Androgen signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.01	0.009	-10000	0	-0.077	6	6
GNB1/GNG2	0.011	0.059	-10000	0	-0.1	97	97
regulation of S phase of mitotic cell cycle	-0.018	0.085	-10000	0	-0.16	134	134
GNAO1	0.011	0.041	-10000	0	-0.12	50	50
HRAS	0.022	0.006	-10000	0	-0.12	1	1
SHBG/T-DHT	0.015	0.005	-10000	0	-0.061	2	2
PELP1	0.022	0.009	-10000	0	-0.12	2	2
AKT1	0.01	0.012	-10000	0	-0.076	10	10
MAP2K1	-0.013	0.061	-10000	0	-0.11	114	114
T-DHT/AR	-0.014	0.06	-10000	0	-0.12	123	123
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
mol:GTP	-0.002	0.003	-10000	0	-0.007	104	104
GNAI2	0.022	0.01	-10000	0	-0.12	3	3
GNAI3	0.021	0.008	-10000	0	-0.12	1	1
GNAI1	0.012	0.035	-10000	0	-0.12	36	36
mol:GDP	-0.048	0.097	-10000	0	-0.25	95	95
cell proliferation	-0.063	0.16	-10000	0	-0.37	109	109
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
FOS	-0.13	0.29	-10000	0	-0.7	108	108
mol:Ca2+	-0.008	0.022	-10000	0	-0.043	127	127
MAPK3	-0.042	0.11	-10000	0	-0.25	111	111
MAPK1	-0.032	0.1	-10000	0	-0.21	109	109
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
mol:IP3	-0.001	0.002	-10000	0	-0.004	104	104
cAMP biosynthetic process	0.01	0.016	0.058	18	-10000	0	18
GNG2	0.02	0.018	-10000	0	-0.12	9	9
potassium channel inhibitor activity	-0.001	0.002	-10000	0	-0.004	104	104
HRAS/GTP	0.006	0.054	-10000	0	-0.092	89	89
actin cytoskeleton reorganization	0.016	0.048	-10000	0	-0.1	67	67
SRC	0.022	0.009	-10000	0	-0.13	2	2
voltage-gated calcium channel activity	-0.001	0.002	-10000	0	-0.004	104	104
PI3K	0.008	0.055	-10000	0	-0.12	75	75
apoptosis	0.066	0.17	0.38	114	-10000	0	114
T-DHT/AR/PELP1	0.002	0.054	-10000	0	-0.11	90	90
HRAS/GDP	-0.027	0.1	-10000	0	-0.23	97	97
CREB1	-0.071	0.18	-10000	0	-0.41	114	114
RAC1-CDC42/GTP	0.023	0.052	-10000	0	-0.1	67	67
AR	0.008	0.038	-10000	0	-0.12	43	43
GNB1	0.023	0.006	-10000	0	-0.12	1	1
RAF1	-0.008	0.053	-10000	0	-0.13	33	33
RAC1-CDC42/GDP	-0.015	0.1	-10000	0	-0.22	98	98
T-DHT/AR/PELP1/Src	0.014	0.053	-10000	0	-0.098	88	88
MAP2K2	-0.015	0.062	-10000	0	-0.12	116	116
T-DHT/AR/PELP1/Src/PI3K	-0.018	0.086	-10000	0	-0.16	134	134
GNAZ	0.022	0.012	-10000	0	-0.12	4	4
SHBG	0.023	0.008	-10000	0	-0.12	2	2
Gi family/GNB1/GNG2/GDP	0.001	0.077	-10000	0	-0.26	27	27
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	-0.076	6	6
Gi family/GTP	-0.018	0.07	-10000	0	-0.15	99	99
CDC42	0.023	0.002	-10000	0	-10000	0	0

×

IL6-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.074	0.32	-10000	0	-0.76	75	75
CRP	-0.064	0.3	-10000	0	-0.74	67	67
cell cycle arrest	-0.092	0.36	-10000	0	-0.82	81	81
TIMP1	-0.11	0.35	-10000	0	-0.75	107	107
IL6ST	0.016	0.03	-10000	0	-0.085	33	33
Rac1/GDP	-0.019	0.17	-10000	0	-0.36	77	77
AP1	-0.059	0.21	-10000	0	-0.46	96	96
GAB2	0.01	0.042	-10000	0	-0.12	52	52
TNFSF11	-0.064	0.3	-10000	0	-0.74	67	67
HSP90B1	0.005	0.18	-10000	0	-1.2	12	12
GAB1	0.021	0.022	-10000	0	-0.12	13	13
MAPK14	-0.028	0.16	-10000	0	-0.46	52	52
AKT1	-0.017	0.15	-10000	0	-0.33	72	72
FOXO1	-0.015	0.14	-10000	0	-0.34	61	61
MAP2K6	-0.029	0.15	-10000	0	-0.35	77	77
mol:GTP	0	0.003	-10000	0	-10000	0	0
MAP2K4	-0.027	0.2	-10000	0	-0.4	90	90
MITF	-0.02	0.14	-10000	0	-0.33	75	75
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TYK2	0.021	0.016	-10000	0	-0.12	7	7
A2M	-0.12	0.38	-10000	0	-1.2	62	62
CEBPB	0.023	0.036	-10000	0	-0.11	37	37
GRB2/SOS1/GAB family/SHP2	-0.03	0.17	0.24	5	-0.37	94	99
STAT3	-0.1	0.38	-10000	0	-0.89	81	81
STAT1	-0.087	0.28	-10000	0	-0.84	68	68
CEBPD	-0.072	0.32	-10000	0	-0.75	73	73
PIK3CA	0.021	0.017	-10000	0	-0.12	7	7
PI3K	0.009	0.066	-10000	0	-0.16	63	63
JUN	0.014	0.032	-10000	0	-0.12	30	30
PIAS3/MITF	-0.013	0.14	-10000	0	-0.31	75	75
MAPK11	-0.028	0.16	-10000	0	-0.46	51	51
STAT3 (dimer)/FOXO1	-0.087	0.34	-10000	0	-0.69	102	102
GRB2/SOS1/GAB family	0.004	0.12	0.22	5	-0.23	79	84
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK	-0.01	0.12	-10000	0	-0.25	85	85
GRB2	0.025	0.008	-10000	0	-0.12	1	1
JAK2	0.017	0.025	-10000	0	-0.12	17	17
LBP	-0.04	0.25	-10000	0	-0.6	56	56
PIK3R1	0.016	0.031	-10000	0	-0.12	28	28
JAK1	0.022	0.015	-10000	0	-0.043	17	17
MYC	-0.13	0.4	-10000	0	-0.88	109	109
FGG	-0.064	0.3	-10000	0	-0.73	69	69
macrophage differentiation	-0.092	0.36	-10000	0	-0.82	81	81
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4	0.013	0.093	-10000	0	-0.15	104	104
JUNB	-0.11	0.37	-10000	0	-0.86	89	89
FOS	-0.005	0.052	-10000	0	-0.12	95	95
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4	-0.022	0.15	-10000	0	-0.35	74	74
STAT1/PIAS1	-0.031	0.18	-10000	0	-0.34	96	96
GRB2/SOS1/GAB family/SHP2/PI3K	-0.023	0.15	-10000	0	-0.28	115	115
STAT3 (dimer)	-0.1	0.38	-10000	0	-0.88	81	81
PRKCD	-0.044	0.25	-10000	0	-0.52	90	90
IL6R	0.019	0.024	-10000	0	-0.076	26	26
SOCS3	-0.044	0.21	-10000	0	-0.93	25	25
gp130 (dimer)/JAK1/JAK1/LMO4	0.02	0.079	-10000	0	-0.14	83	83
Rac1/GTP	-0.023	0.18	-10000	0	-0.38	80	80
HCK	0.019	0.023	-10000	0	-0.12	15	15
MAPKKK cascade	-0.048	0.22	-10000	0	-0.5	94	94
bone resorption	-0.058	0.29	-10000	0	-0.69	67	67
IRF1	-0.13	0.41	-10000	0	-0.95	95	95
mol:GDP	-0.024	0.16	-10000	0	-0.35	78	78
SOS1	0.02	0.027	-10000	0	-0.12	20	20
VAV1	-0.025	0.16	-10000	0	-0.35	79	79
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3	-0.027	0.17	-10000	0	-0.43	68	68
PTPN11	-0.006	0.16	-10000	0	-0.83	19	19
IL6/IL6RA	0.007	0.062	-10000	0	-0.13	65	65
gp130 (dimer)/TYK2/TYK2/LMO4	0.025	0.061	-10000	0	-0.12	69	69
gp130 (dimer)/JAK2/JAK2/LMO4	0.013	0.077	-10000	0	-0.14	96	96
IL6	0.005	0.049	-10000	0	-0.11	79	79
PIAS3	0.02	0.022	-10000	0	-0.12	14	14
PTPRE	0.022	0.018	0.084	12	-10000	0	12
PIAS1	0.022	0.009	-10000	0	-0.12	2	2
RAC1	0.023	0.003	-10000	0	-10000	0	0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4	-0.014	0.097	-10000	0	-0.21	76	76
LMO4	0.021	0.023	-10000	0	-0.083	14	14
STAT3 (dimer)/PIAS3	-0.088	0.35	-10000	0	-0.81	81	81
MCL1	-0.014	0.16	-10000	0	-0.54	27	27

×

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

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
MET/RANBP9	-0.018	0.078	-10000	0	-0.12	194	194
CRKL	-0.027	0.11	-10000	0	-0.33	39	39
mol:PIP3	-0.002	0.049	0.22	24	-10000	0	24
AKT1	0.005	0.038	0.17	23	-0.1	7	30
PTK2B	0.023	0.009	-10000	0	-0.12	2	2
RAPGEF1	-0.022	0.11	-10000	0	-0.31	39	39
RANBP10	0.023	0.009	-10000	0	-0.12	2	2
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
HGF/MET/SHIP2	-0.002	0.068	-10000	0	-0.11	123	123
MAP3K5	-0.015	0.11	-10000	0	-0.28	49	49
HGF/MET/CIN85/CBL/ENDOPHILINS	0.011	0.067	-10000	0	-0.096	127	127
AP1	-0.04	0.075	-10000	0	-0.14	167	167
mol:SU11274	0	0	-10000	0	-10000	0	0
SHC1	0.023	0.001	-10000	0	-10000	0	0
apoptosis	-0.17	0.32	-10000	0	-0.76	125	125
STAT3 (dimer)	-0.021	0.098	-10000	0	-0.27	38	38
GAB1/CRKL/SHP2/PI3K	-0.016	0.13	-10000	0	-0.29	61	61
INPP5D	0	0	-10000	0	-10000	0	0
CBL/CRK	-0.015	0.11	-10000	0	-0.31	39	39
PTPN11	0.022	0.011	-10000	0	-0.12	3	3
GO:0007205	0	0	-10000	0	-10000	0	0
PLCG1	0.018	0.025	-10000	0	-0.12	18	18
PTEN	0.022	0.008	-10000	0	-0.12	1	1
ELK1	-0.021	0.057	0.25	12	-10000	0	12
mol:SU5416	0	0	-10000	0	-10000	0	0
SHP2/GRB2/SOS1GAB1	-0.016	0.08	-10000	0	-0.18	68	68
PAK1	0.003	0.041	0.16	22	-0.1	23	45
HGF/MET/RANBP10	0	0.067	-10000	0	-0.11	119	119
HRAS	-0.084	0.21	-10000	0	-0.48	123	123
DOCK1	-0.027	0.11	-10000	0	-0.31	46	46
GAB1	-0.033	0.12	-10000	0	-0.22	125	125
CRK	-0.028	0.11	-10000	0	-0.33	39	39
mol:PHA665752	0	0	-10000	0	-10000	0	0
mol:GDP	-0.073	0.19	-10000	0	-0.42	123	123
JUN	0.014	0.032	-10000	0	-0.12	30	30
EntrezGene:200958	0	0	-10000	0	-10000	0	0
HGF/MET	-0.028	0.077	-10000	0	-0.16	123	123
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
cell morphogenesis	-0.029	0.12	-10000	0	-0.26	76	76
GRB2/SHC	-0.006	0.078	-10000	0	-0.14	125	125
FOS	-0.005	0.052	-10000	0	-0.12	95	95
GLMN	0.004	0.015	0.076	8	-0.055	18	26
cell motility	-0.021	0.057	0.25	12	-10000	0	12
HGF/MET/MUC20	-0.011	0.061	-10000	0	-0.12	119	119
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	-0.14	117	117
HGF/MET/Paxillin/FAK1/FAK12/RasGAP	-0.019	0.092	-10000	0	-0.27	30	30
MET/MUC20	-0.028	0.068	-10000	0	-0.12	188	188
RAP1B	-0.021	0.1	-10000	0	-0.28	44	44
RAP1A	-0.02	0.1	-10000	0	-0.28	46	46
HGF/MET/RANBP9	-0.002	0.07	-10000	0	-0.12	127	127
RAF1	-0.077	0.2	-10000	0	-0.46	124	124
STAT3	-0.019	0.097	-10000	0	-0.29	31	31
cell proliferation	-0.036	0.13	-10000	0	-0.26	124	124
RPS6KB1	-0.018	0.076	-10000	0	-0.26	37	37
MAPK3	-0.025	0.074	0.68	5	-10000	0	5
MAPK1	-0.021	0.091	0.7	8	-10000	0	8
RANBP9	0.022	0.014	-10000	0	-0.12	5	5
MAPK8	-0.017	0.12	-10000	0	-0.33	54	54
SRC	-0.016	0.086	-10000	0	-0.25	30	30
PI3K	-0.022	0.091	-10000	0	-0.16	128	128
MET/Glomulin	-0.003	0.049	-10000	0	-0.096	94	94
SOS1	0.017	0.027	-10000	0	-0.12	20	20
MAP2K1	-0.068	0.19	-10000	0	-0.42	123	123
MET	0.001	0.047	-10000	0	-0.12	71	71
MAP4K1	-0.016	0.11	-10000	0	-0.3	42	42
PTK2	0.021	0.015	-10000	0	-0.12	6	6
MAP2K2	-0.07	0.19	-10000	0	-0.43	123	123
BAD	0.008	0.036	0.16	23	-0.091	7	30
MAP2K4	-0.012	0.1	-10000	0	-0.25	52	52
SHP2/GRB2/SOS1/GAB1	-0.03	0.12	-10000	0	-0.23	132	132
INPPL1	0.021	0.018	-10000	0	-0.12	9	9
PXN	0.022	0.013	-10000	0	-0.12	5	5
SH3KBP1	0.021	0.019	-10000	0	-0.12	10	10
HGS	-0.022	0.071	-10000	0	-0.15	119	119
PLCgamma1/PKC	0.011	0.028	-10000	0	-0.1	29	29
HGF	0.02	0.022	-10000	0	-0.12	14	14
RASA1	0.021	0.011	-10000	0	-0.12	3	3
NCK1	0.02	0.019	-10000	0	-0.12	9	9
PTPRJ	0.02	0.019	-10000	0	-0.12	10	10
NCK/PLCgamma1	-0.014	0.085	-10000	0	-0.15	133	133
PDPK1	0.002	0.042	0.19	24	-0.11	6	30
HGF/MET/SHIP	-0.011	0.061	-10000	0	-0.12	119	119

×

Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer	0.019	0.049	-9999	-0.15	39	39
alphaV beta3 Integrin	0	0.073	-9999	-0.13	107	107
PTK2	-0.029	0.13	-9999	-0.27	93	93
IGF1R	0.013	0.031	-9999	-0.12	28	28
PI4KB	0.022	0.014	-9999	-0.12	5	5
MFGE8	0.006	0.043	-9999	-0.12	57	57
SRC	0.023	0.008	-9999	-0.12	2	2
CDKN1B	-0.006	0.087	-9999	-0.34	30	30
VEGFA	0.019	0.02	-9999	-0.12	11	11
ILK	0.013	0.04	-9999	-0.31	3	3
ROCK1	0.023	0.009	-9999	-0.12	2	2
AKT1	0.014	0.037	-9999	-0.28	3	3
PTK2B	-0.011	0.063	-9999	-0.11	140	140
alphaV/beta3 Integrin/JAM-A	0.014	0.068	-9999	-0.1	114	114
CBL	0.023	0.006	-9999	-0.12	1	1
mol:GTP	0	0	-9999	-10000	0	0
alphaV beta3 Integrin/ANGPTL3	0	0.073	-9999	-0.13	107	107
IGF-1R heterotetramer/IGF1/IRS1/Shp2	0.013	0.071	-9999	-0.11	111	111
VEGF/Rho/ROCK/alphaV/beta3 Integrin	-0.011	0.095	-9999	-0.25	51	51
alphaV/beta3 Integrin/Syndecan-1	-0.003	0.074	-9999	-0.13	113	113
PI4KA	0.021	0.016	-9999	-0.12	7	7
IGF-1R heterotetramer/IGF1/IRS1	-0.055	0.086	-9999	-0.16	153	153
PI4 Kinase	0.028	0.032	-9999	-0.12	24	24
PIK3CA	0.02	0.017	-9999	-0.12	7	7
alphaV/beta3 Integrin/Osteopontin	-0.029	0.098	-9999	-0.16	166	166
RPS6KB1	-0.056	0.081	-9999	-0.16	164	164
TLN1	0.021	0.013	-9999	-0.12	4	4
MAPK3	-0.054	0.14	-9999	-0.34	102	102
GPR124	0.023	0.01	-9999	-0.12	3	3
MAPK1	-0.055	0.14	-9999	-0.34	102	102
PXN	0.022	0.013	-9999	-0.12	5	5
PIK3R1	0.015	0.031	-9999	-0.12	28	28
alphaV/beta3 Integrin/Tumstatin	0	0.073	-9999	-0.13	107	107
cell adhesion	-0.03	0.097	-9999	-0.18	118	118
ANGPTL3	0.023	0.01	-9999	-0.12	3	3
VEGFR2 homodimer/VEGFA homodimer/Src	0.033	0.044	-9999	-0.11	39	39
IGF-1R heterotetramer	0.013	0.031	-9999	-0.12	28	28
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
TGFBR2	0.02	0.02	-9999	-0.12	11	11
ITGB3	0.005	0.046	-9999	-0.12	67	67
IGF1	0.007	0.045	-9999	-0.12	62	62
RAC1	0.023	0.002	-9999	-10000	0	0
regulation of cell-matrix adhesion	-0.001	0.072	-9999	-0.13	107	107
apoptosis	0.012	0.033	-9999	-0.12	31	31
CD47	0.021	0.012	-9999	-0.12	3	3
alphaV/beta3 Integrin/CD47	-0.01	0.083	-9999	-0.14	126	126
VCL	0.021	0.014	-9999	-0.12	5	5
alphaV/beta3 Integrin/Del1	-0.029	0.083	-9999	-0.14	161	161
CSF1	0.013	0.033	-9999	-0.12	31	31
PIK3C2A	-0.013	0.1	-9999	-0.35	44	44
PI4 Kinase/Pyk2	0.001	0.059	-9999	-0.14	49	49
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.001	0.079	-9999	-0.12	140	140
FAK1/Vinculin	-0.016	0.11	-9999	-0.23	93	93
alphaV beta3/Integrin/ppsTEM5	0	0.073	-9999	-0.13	107	107
RHOA	0.023	0.006	-9999	-0.12	1	1
VTN	0.023	0.008	-9999	-0.12	2	2
BCAR1	0.023	0.01	-9999	-0.12	3	3
FGF2	0.023	0.008	-9999	-0.12	2	2
F11R	0.022	0.012	-9999	-0.12	3	3
alphaV/beta3 Integrin/Lactadherin	-0.028	0.088	-9999	-0.14	173	173
alphaV/beta3 Integrin/TGFBR2	-0.005	0.079	-9999	-0.14	113	113
alphaV/beta3 Integrin/c-FMS/Cbl/Cas	0.015	0.075	-9999	-0.12	112	112
HSP90AA1	0.023	0.004	-9999	-10000	0	0
alphaV/beta3 Integrin/Talin	-0.004	0.074	-9999	-0.12	123	123
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.012	0.055	-9999	-0.12	115	115
alphaV/beta3 Integrin/Pyk2	0	0.072	-9999	-0.11	143	143
SDC1	0.021	0.019	-9999	-0.12	10	10
VAV3	-0.012	0.074	-9999	-0.14	118	118
PTPN11	0.022	0.011	-9999	-0.12	3	3
IRS1	0.02	0.022	-9999	-0.12	14	14
FAK1/Paxillin	-0.013	0.11	-9999	-0.23	88	88
cell migration	-0.011	0.11	-9999	-0.22	78	78
ITGAV	0.012	0.033	-9999	-0.12	31	31
PI3K	0.006	0.083	-9999	-0.17	61	61
SPP1	0.012	0.031	-9999	-0.12	28	28
KDR	0.021	0.019	-9999	-0.12	10	10
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Caspase 8	0.012	0.033	-9999	-0.12	31	31
COL4A3	0.023	0.008	-9999	-0.12	2	2
angiogenesis	-0.055	0.16	-9999	-0.37	102	102
Rac1/GTP	-0.007	0.074	-9999	-0.18	54	54
EDIL3	-0.006	0.056	-9999	-0.12	110	110
cell proliferation	-0.005	0.078	-9999	-0.14	113	113

×

IGF1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NCK2	0.023	0.006	-10000	0	-0.12	1	1
PTK2	0.021	0.015	-10000	0	-0.12	6	6
CRKL	-0.005	0.055	-10000	0	-0.12	96	96
GRB2/SOS1/SHC	0.035	0.042	-10000	0	-0.12	32	32
HRAS	0.023	0.006	-10000	0	-0.12	1	1
IRS1/Crk	-0.001	0.057	-10000	0	-0.12	96	96
IGF-1R heterotetramer/IGF1/PTP1B	0.007	0.062	-10000	0	-0.12	94	94
AKT1	-0.01	0.059	-10000	0	-0.11	112	112
BAD	-0.008	0.056	-10000	0	-0.1	112	112
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	-0.006	0.055	-10000	0	-0.12	96	96
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.003	0.063	-10000	0	-0.12	109	109
RAF1	-0.004	0.09	-10000	0	-0.52	10	10
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos	0.009	0.071	-10000	0	-0.11	115	115
YWHAZ	0.023	0.003	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.005	0.063	-10000	0	-0.13	96	96
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
RPS6KB1	-0.012	0.063	-10000	0	-0.12	116	116
GNB2L1	0.023	0.003	-10000	0	-10000	0	0
positive regulation of MAPKKK cascade	-0.006	0.077	0.2	6	-0.39	11	17
PXN	0.022	0.013	-10000	0	-0.12	5	5
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
cell adhesion	0	0	-10000	0	-10000	0	0
GRB2/SOS1	0.021	0.046	-10000	0	-0.15	31	31
HRAS/GTP	-0.003	0.053	-10000	0	-0.1	94	94
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc	0.021	0.069	-10000	0	-0.12	46	46
IGF-1R heterotetramer	0.012	0.033	-10000	0	-0.091	42	42
IGF-1R heterotetramer/IGF1/IRS/Nck	0.008	0.063	-10000	0	-0.12	96	96
Crk/p130 Cas/Paxillin	0.02	0.061	-10000	0	-0.099	90	90
IGF1R	0.012	0.033	-10000	0	-0.091	42	42
IGF1	0.001	0.047	-10000	0	-0.12	64	64
IRS2/Crk	0.003	0.055	-10000	0	-0.11	91	91
PI3K	-0.001	0.077	-10000	0	-0.11	152	152
apoptosis	-0.003	0.056	0.12	57	-10000	0	57
HRAS/GDP	0.017	0.008	-10000	0	-0.11	2	2
PRKCD	-0.016	0.095	-10000	0	-0.2	97	97
RAF1/14-3-3 E	0.007	0.082	-10000	0	-0.42	11	11
BAD/14-3-3	0.003	0.059	-10000	0	-0.12	57	57
PRKCZ	-0.009	0.059	-10000	0	-0.11	111	111
Crk/p130 Cas/Paxillin/FAK1	0.004	0.068	-10000	0	-0.15	56	56
PTPN1	0.023	0.006	-10000	0	-0.12	1	1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1	-0.018	0.097	-10000	0	-0.21	94	94
BCAR1	0.023	0.01	-10000	0	-0.12	3	3
IGF-1R heterotetramer/IGF1/SHC/GRB10	0.019	0.061	-10000	0	-0.094	100	100
mol:GDP	0	0	-10000	0	-10000	0	0
SOS1	0.017	0.027	-10000	0	-0.12	20	20
IRS1/NCK2	0.001	0.058	-10000	0	-0.12	96	96
GRB10	0.022	0.014	-10000	0	-0.12	5	5
PTPN11	-0.007	0.058	-10000	0	-0.12	97	97
IRS1	-0.012	0.059	-10000	0	-0.13	96	96
IRS2	-0.006	0.054	-10000	0	-0.12	97	97
IGF-1R heterotetramer/IGF1	-0.013	0.077	-10000	0	-0.16	96	96
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PDPK1	-0.012	0.063	-10000	0	-0.12	111	111
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
PRKD1	-0.022	0.099	-10000	0	-0.21	102	102
SHC1	0.023	0.001	-10000	0	-10000	0	0

×

IL4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.17	0.46	-10000	0	-1.1	76	76
STAT6 (cleaved dimer)	-0.26	0.38	-10000	0	-0.98	96	96
IGHG1	-0.032	0.2	-10000	0	-0.55	13	13
IGHG3	-0.16	0.42	-10000	0	-0.96	85	85
AKT1	-0.12	0.34	-10000	0	-0.82	72	72
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1	-0.11	0.34	-10000	0	-0.88	67	67
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1	-0.13	0.37	-10000	0	-0.91	71	71
THY1	-0.33	0.62	-10000	0	-1.2	162	162
MYB	0.01	0.04	-10000	0	-0.12	48	48
HMGA1	0.012	0.038	-10000	0	-0.12	42	42
IL4/IL4R/JAK1/IL2R gamma/JAK3	-0.11	0.33	-10000	0	-0.72	78	78
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP	-0.13	0.37	-10000	0	-0.89	74	74
SP1	-0.001	0.049	-10000	0	-0.09	109	109
INPP5D	0	0	-10000	0	-10000	0	0
SOCS5	0.017	0.023	-10000	0	-0.086	3	3
STAT6 (dimer)/ETS1	-0.17	0.45	-10000	0	-1	90	90
SOCS1	-0.097	0.32	-10000	0	-0.68	76	76
SOCS3	-0.11	0.34	-10000	0	-0.94	46	46
FCER2	-0.099	0.33	-10000	0	-0.83	25	25
PARP14	0.014	0.033	-10000	0	-0.12	30	30
CCL17	-0.15	0.44	-10000	0	-1.1	63	63
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	-0.64	60	60
T cell proliferation	-0.18	0.47	-10000	0	-1.1	87	87
IL4R/JAK1	-0.17	0.46	-10000	0	-1	86	86
EGR2	-0.15	0.45	-10000	0	-1.1	65	65
JAK2	0.013	0.051	-10000	0	-0.16	14	14
JAK3	0.023	0.016	-10000	0	-0.12	5	5
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
JAK1	0.024	0.021	-10000	0	-0.12	2	2
COL1A2	-0.24	0.54	-10000	0	-1.3	112	112
CCL26	-0.16	0.46	-10000	0	-1.1	73	73
IL4R	-0.17	0.49	-10000	0	-1.1	79	79
PTPN6	0.023	0.018	-10000	0	-0.12	2	2
IL13RA2	-0.16	0.45	-10000	0	-1.1	69	69
IL13RA1	0.015	0.048	-10000	0	-0.13	12	12
IRF4	0	0.13	-10000	0	-0.85	2	2
ARG1	-0.001	0.16	-10000	0	-0.79	4	4
CBL	-0.1	0.31	-10000	0	-0.68	78	78
GTF3A	-0.013	0.055	-10000	0	-0.097	148	148
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
IL13RA1/JAK2	0.004	0.092	-10000	0	-0.17	74	74
IRF4/BCL6	-0.004	0.12	-10000	0	-0.84	2	2
CD40LG	0.031	0.012	-10000	0	-0.12	2	2
MAPK14	-0.11	0.32	-10000	0	-0.73	75	75
mitosis	-0.11	0.32	-10000	0	-0.76	72	72
STAT6	-0.18	0.51	-10000	0	-1.2	82	82
SPI1	0.027	0.021	-10000	0	-0.12	12	12
RPS6KB1	-0.1	0.31	-10000	0	-0.74	71	71
STAT6 (dimer)	-0.18	0.51	-10000	0	-1.2	82	82
STAT6 (dimer)/PARP14	-0.19	0.47	-10000	0	-1.1	87	87
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	-0.85	74	74
FRAP1	-0.12	0.34	-10000	0	-0.82	72	72
LTA	-0.15	0.44	-10000	0	-1.1	64	64
FES	0.023	0.01	-10000	0	-0.12	3	3
T-helper 1 cell differentiation	0.18	0.5	1.1	82	-10000	0	82
CCL11	-0.19	0.47	-10000	0	-1.1	85	85
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES	-0.12	0.35	-10000	0	-0.84	73	73
IL2RG	0.001	0.05	-10000	0	-0.12	82	82
IL10	-0.15	0.44	-10000	0	-1.1	63	63
IRS1	0.02	0.022	-10000	0	-0.12	14	14
IRS2	0.022	0.016	-10000	0	-0.12	7	7
IL4	0.002	0.14	-10000	0	-10000	0	0
IL5	-0.15	0.44	-10000	0	-1.1	63	63
IL4/IL4R/JAK1/IL13RA1/JAK2	-0.14	0.43	-10000	0	-0.92	84	84
COL1A1	-0.31	0.6	-10000	0	-1.3	143	143
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1	-0.17	0.47	-10000	0	-1.1	69	69
IL2R gamma/JAK3	-0.007	0.072	-10000	0	-0.13	109	109
TFF3	-0.17	0.47	-10000	0	-1.1	74	74
ALOX15	-0.15	0.44	-10000	0	-1.1	63	63
MYBL1	0.017	0.028	-10000	0	-0.12	22	22
T-helper 2 cell differentiation	-0.15	0.42	-10000	0	-0.92	86	86
SHC1	0.023	0.001	-10000	0	-10000	0	0
CEBPB	0.023	0.032	-10000	0	-0.12	29	29
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2	-0.12	0.36	-10000	0	-0.89	72	72
mol:PI-3-4-5-P3	-0.12	0.34	-10000	0	-0.82	72	72
PI3K	-0.13	0.37	-10000	0	-0.89	72	72
DOK2	0.02	0.021	-10000	0	-0.12	12	12
ETS1	0.013	0.035	-10000	0	-0.12	27	27
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2	-0.074	0.26	-10000	0	-0.61	68	68
ITGB3	-0.2	0.51	-10000	0	-1.2	85	85
PIGR	-0.18	0.46	-10000	0	-1.1	71	71
IGHE	0.001	0.059	0.17	15	-0.17	7	22
MAPKKK cascade	-0.072	0.26	-10000	0	-0.6	67	67
BCL6	0.018	0.02	-10000	0	-0.12	10	10
OPRM1	-0.15	0.44	-10000	0	-1.1	63	63
RETNLB	-0.15	0.44	-10000	0	-1	68	68
SELP	-0.16	0.44	-10000	0	-1.1	64	64
AICDA	-0.15	0.42	-10000	0	-1	63	63

×

IFN-gamma pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	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	112	112
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	128	128
IFN-gammaR/JAK1/JAK1/JAK2/JAK2	0.007	0.08	-10000	0	-0.15	103	103
antigen processing and presentation of peptide antigen via MHC class I	-0.053	0.093	-10000	0	-0.19	156	156
CaM/Ca2+	0.01	0.077	-10000	0	-0.14	85	85
RAP1A	0.021	0.011	-10000	0	-0.12	3	3
STAT1 (dimer)/SHP2	-0.017	0.092	-10000	0	-0.18	98	98
AKT1	-0.014	0.081	-10000	0	-0.18	86	86
MAP2K1	-0.007	0.068	-10000	0	-0.14	87	87
MAP3K11	-0.006	0.066	-10000	0	-0.12	104	104
IFNGR1	0.016	0.026	-10000	0	-0.12	17	17
mol:GTP	0	0	-10000	0	-10000	0	0
CaM/Ca2+/CAMKII	0.015	0.082	-10000	0	-0.29	27	27
Rap1/GTP	-0.023	0.056	-10000	0	-0.16	62	62
CRKL/C3G	0.034	0.01	-10000	0	-0.14	1	1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP	0.024	0.079	-10000	0	-0.12	106	106
CEBPB	-0.014	0.15	-10000	0	-0.39	59	59
STAT3	0.022	0.011	-10000	0	-0.12	3	3
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1	0.019	0.11	-10000	0	-0.99	3	3
STAT1	-0.018	0.086	-10000	0	-0.18	89	89
CALM1	0.022	0.014	-10000	0	-0.12	5	5
IFN-gamma (dimer)	0.01	0.038	-10000	0	-0.12	43	43
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
STAT1 (dimer)/PIAS1	-0.015	0.091	-10000	0	-0.18	96	96
CEBPB/PTGES2/Cbp/p300	-0.036	0.11	-10000	0	-0.29	67	67
mol:Ca2+	0.005	0.078	-10000	0	-0.13	112	112
MAPK3	-0.009	0.12	-10000	0	-0.53	13	13
STAT1 (dimer)	-0.041	0.15	-10000	0	-0.27	135	135
MAPK1	-0.013	0.13	-10000	0	-0.51	21	21
JAK2	0.016	0.026	-10000	0	-0.11	19	19
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
JAK1	0.02	0.012	-10000	0	-0.12	2	2
CAMK2D	0.018	0.024	-10000	0	-0.12	16	16
DAPK1	-0.014	0.16	-10000	0	-0.48	48	48
SMAD7	-0.009	0.064	-10000	0	-0.11	117	117
CBL/CRKL/C3G	0.018	0.068	-10000	0	-0.14	64	64
PI3K	-0.004	0.092	-10000	0	-0.18	92	92
IFNG	0.01	0.038	-10000	0	-0.12	43	43
apoptosis	-0.017	0.13	0.22	1	-0.39	48	49
CAMK2G	0.023	0.006	-10000	0	-0.12	1	1
STAT3 (dimer)	0.022	0.011	-10000	0	-0.12	3	3
CAMK2A	0.023	0.006	-10000	0	-0.12	1	1
CAMK2B	0.023	0.008	-10000	0	-0.12	2	2
FRAP1	-0.012	0.077	-10000	0	-0.17	81	81
PRKCD	-0.016	0.086	-10000	0	-0.19	88	88
RAP1B	0.019	0.019	-10000	0	-0.12	10	10
negative regulation of cell growth	-0.053	0.093	-10000	0	-0.19	156	156
PTPN2	0.023	0.006	-10000	0	-0.12	1	1
EP300	0.022	0.01	-10000	0	-0.12	2	2
IRF1	-0.038	0.13	-10000	0	-0.27	106	106
STAT1 (dimer)/PIASy	-0.015	0.089	0.19	3	-0.19	83	86
SOCS1	0.008	0.095	-10000	0	-1.2	3	3
mol:GDP	0.015	0.065	-10000	0	-0.13	64	64
CASP1	-0.031	0.095	-10000	0	-0.17	158	158
PTGES2	0.022	0.01	-10000	0	-0.12	3	3
IRF9	0.004	0.071	-10000	0	-0.15	74	74
mol:PI-3-4-5-P3	-0.013	0.084	-10000	0	-0.18	91	91
RAP1/GDP	0.006	0.073	-10000	0	-0.17	59	59
CBL	-0.005	0.066	-10000	0	-0.12	105	105
MAP3K1	-0.008	0.071	-10000	0	-0.13	105	105
PIAS1	0.022	0.009	-10000	0	-0.12	2	2
PIAS4	0.023	0.001	-10000	0	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class II	-0.053	0.093	-10000	0	-0.19	156	156
PTPN11	-0.009	0.067	-10000	0	-0.13	107	107
CREBBP	0.02	0.016	-10000	0	-0.12	6	6
RAPGEF1	0.023	0	-10000	0	-10000	0	0

×

BARD1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BARD1/CSTF1	0.016	0.052	-10000	0	-0.12	70	70
ATM	0.018	0.022	-10000	0	-0.12	13	13
UBE2D3	0.023	0.001	-10000	0	-10000	0	0
PRKDC	0.021	0.016	-10000	0	-0.12	7	7
ATR	0.02	0.014	-10000	0	-0.12	5	5
UBE2L3	0.022	0.011	-10000	0	-0.12	3	3
FANCD2	-0.009	0.096	-10000	0	-0.24	72	72
protein ubiquitination	-0.016	0.087	-10000	0	-0.16	78	78
XRCC5	0.021	0.01	-10000	0	-0.12	2	2
XRCC6	0.022	0.004	-10000	0	-10000	0	0
M/R/N Complex	0.022	0.066	-10000	0	-0.14	67	67
MRE11A	0.02	0.017	-10000	0	-0.12	8	8
DNA-PK	0.026	0.06	-10000	0	-0.14	61	61
FA complex/FANCD2/Ubiquitin	0.01	0.093	-10000	0	-0.33	26	26
FANCF	0.022	0.011	-10000	0	-0.12	3	3
BRCA1	0.015	0.029	-10000	0	-0.12	24	24
CCNE1	0.002	0.047	-10000	0	-0.12	70	70
CDK2/Cyclin E1	-0.016	0.076	-10000	0	-0.12	192	192
FANCG	0.021	0.016	-10000	0	-0.12	7	7
BRCA1/BACH1/BARD1	-0.001	0.07	-10000	0	-0.15	88	88
FANCE	0.023	0	-10000	0	-10000	0	0
FANCC	0.022	0.013	-10000	0	-0.12	5	5
NBN	0.021	0.013	-10000	0	-0.12	4	4
FANCA	0.021	0.019	-10000	0	-0.12	10	10
DNA repair	-0.015	0.11	-10000	0	-0.32	41	41
BRCA1/BARD1/ubiquitin	-0.001	0.07	-10000	0	-0.15	88	88
BARD1/DNA-PK	0.027	0.076	-10000	0	-0.14	81	81
FANCL	0.019	0.023	-10000	0	-0.12	14	14
mRNA polyadenylation	-0.016	0.052	0.12	70	-10000	0	70
BRCA1/BARD1/CTIP/M/R/N Complex	-0.036	0.14	-10000	0	-0.33	75	75
BRCA1/BACH1/BARD1/TopBP1	0.009	0.072	-10000	0	-0.13	105	105
BRCA1/BARD1/P53	-0.027	0.092	-10000	0	-0.12	257	257
BARD1/CSTF1/BRCA1	0.013	0.065	-10000	0	-0.12	95	95
BRCA1/BACH1	0.015	0.029	-10000	0	-0.12	24	24
BARD1	0.016	0.029	-10000	0	-0.12	23	23
PCNA	0.019	0.017	-10000	0	-0.12	7	7
BRCA1/BARD1/UbcH5C	0.015	0.063	-10000	0	-0.12	89	89
BRCA1/BARD1/UbcH7	0.013	0.064	-10000	0	-0.12	94	94
BRCA1/BARD1/RAD51/PCNA	0	0.085	-10000	0	-0.12	157	157
BARD1/DNA-PK/P53	-0.009	0.096	-10000	0	-0.19	62	62
BRCA1/BARD1/Ubiquitin	-0.001	0.07	-10000	0	-0.15	88	88
BRCA1/BARD1/CTIP	-0.011	0.083	-10000	0	-0.13	160	160
FA complex	0.018	0.074	-10000	0	-0.31	17	17
BARD1/EWS	0.018	0.049	-10000	0	-0.14	41	41
RBBP8	0.011	0.029	-10000	0	-0.076	48	48
TP53	0.01	0.029	-10000	0	-0.12	24	24
TOPBP1	0.021	0.015	-10000	0	-0.12	6	6
G1/S transition of mitotic cell cycle	0.027	0.091	0.12	257	-10000	0	257
BRCA1/BARD1	-0.013	0.09	-10000	0	-0.16	78	78
CSTF1	0.023	0.007	-10000	0	-0.12	1	1
BARD1/EWS-Fli1	0.002	0.044	-10000	0	-0.12	62	62
CDK2	0.018	0.023	-10000	0	-0.12	14	14
UniProt:Q9BZD1	0	0	-10000	0	-10000	0	0
RAD51	0.015	0.03	-10000	0	-0.12	26	26
RAD50	0.021	0.015	-10000	0	-0.12	6	6
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme	-0.001	0.07	-10000	0	-0.15	88	88
EWSR1	0.023	0.001	-10000	0	-10000	0	0

×

EPHB forward signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Ephrin A5/EPHB2	0.011	0.049	-10000	0	-0.097	90	90
cell-cell adhesion	0.023	0.04	0.14	40	-10000	0	40
Ephrin B/EPHB2/RasGAP	0.016	0.076	-10000	0	-0.099	144	144
ITSN1	0.022	0.011	-10000	0	-0.12	3	3
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
SHC1	0.023	0.001	-10000	0	-10000	0	0
Ephrin B1/EPHB3	0.022	0.033	-10000	0	-0.086	47	47
Ephrin B1/EPHB1	0.024	0.028	-10000	0	-0.068	44	44
HRAS/GDP	-0.002	0.07	-10000	0	-0.14	88	88
Ephrin B/EPHB1/GRB7	0.018	0.071	-10000	0	-0.096	120	120
Endophilin/SYNJ1	-0.001	0.052	-10000	0	-0.087	125	125
KRAS	0.014	0.034	-10000	0	-0.12	33	33
Ephrin B/EPHB1/Src	0.023	0.067	-10000	0	-0.092	110	110
endothelial cell migration	0.001	0.071	-10000	0	-0.11	146	146
GRB2	0.023	0.006	-10000	0	-0.12	1	1
GRB7	0.018	0.025	-10000	0	-0.12	18	18
PAK1	-0.003	0.057	-10000	0	-0.12	51	51
HRAS	0.023	0.006	-10000	0	-0.12	1	1
RRAS	-0.006	0.056	-10000	0	-0.096	128	128
DNM1	0.02	0.02	-10000	0	-0.12	11	11
cell-cell signaling	0	0	-10000	0	-10000	0	0
CRK	0	0.049	-10000	0	-0.087	111	111
lamellipodium assembly	-0.023	0.04	-10000	0	-0.14	40	40
Ephrin B/EPHB1/Src/p52 SHC/GRB2	0.019	0.051	-10000	0	-0.16	31	31
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
EPHB2	0.02	0.02	-10000	0	-0.12	11	11
EPHB3	0.019	0.023	-10000	0	-0.12	15	15
EPHB1	0.016	0.032	-10000	0	-0.12	29	29
EPHB4	0.022	0.009	-10000	0	-0.12	2	2
mol:GDP	-0.01	0.079	-10000	0	-0.17	98	98
Ephrin B/EPHB2	0.012	0.066	-10000	0	-0.097	124	124
Ephrin B/EPHB3	0.011	0.065	-10000	0	-0.095	124	124
JNK cascade	0.014	0.045	-10000	0	-0.1	57	57
Ephrin B/EPHB1	0.013	0.063	-10000	0	-0.095	110	110
RAP1/GDP	0	0.084	-10000	0	-0.16	100	100
EFNB2	0.007	0.041	-10000	0	-0.12	51	51
EFNB3	0.018	0.027	-10000	0	-0.12	20	20
EFNB1	0.021	0.019	-10000	0	-0.12	10	10
Ephrin B2/EPHB1-2	0.006	0.061	-10000	0	-0.1	102	102
RAP1B	0.019	0.019	-10000	0	-0.12	10	10
RAP1A	0.021	0.011	-10000	0	-0.12	3	3
CDC42/GTP	0.008	0.078	-10000	0	-0.18	32	32
Rap1/GTP	-0.028	0.045	-10000	0	-0.14	60	60
axon guidance	0.011	0.049	-10000	0	-0.096	90	90
MAPK3	0.008	0.063	-10000	0	-0.19	18	18
MAPK1	0.008	0.063	-10000	0	-0.18	19	19
Rac1/GDP	0.001	0.079	-10000	0	-0.16	87	87
actin cytoskeleton reorganization	-0.025	0.045	-10000	0	-0.14	45	45
CDC42/GDP	0.001	0.079	-10000	0	-0.16	86	86
PI3K	0.004	0.074	-10000	0	-0.11	146	146
EFNA5	0.014	0.033	-10000	0	-0.12	31	31
Ephrin B2/EPHB4	0	0.058	-10000	0	-0.12	90	90
Ephrin B/EPHB2/Intersectin/N-WASP	-0.005	0.08	-10000	0	-0.26	18	18
CDC42	0.023	0.002	-10000	0	-10000	0	0
RAS family/GTP	-0.025	0.042	-10000	0	-0.13	55	55
PTK2	-0.001	0.05	-10000	0	-0.2	32	32
MAP4K4	0.015	0.045	-10000	0	-0.1	57	57
SRC	0.023	0.008	-10000	0	-0.12	2	2
KALRN	0.015	0.033	-10000	0	-0.12	31	31
Intersectin/N-WASP	0.031	0.023	-10000	0	-0.14	8	8
neuron projection morphogenesis	0.005	0.07	-10000	0	-0.16	45	45
MAP2K1	0.005	0.066	-10000	0	-0.2	16	16
WASL	0.023	0.008	-10000	0	-0.12	2	2
Ephrin B1/EPHB1-2/NCK1	0.036	0.055	-10000	0	-0.11	56	56
cell migration	0.002	0.077	-10000	0	-0.2	29	29
NRAS	0.022	0.011	-10000	0	-0.12	3	3
SYNJ1	-0.001	0.052	-10000	0	-0.088	125	125
PXN	0.022	0.013	-10000	0	-0.12	5	5
TF	-0.001	0.049	-10000	0	-0.081	128	128
HRAS/GTP	0.01	0.063	-10000	0	-0.15	31	31
Ephrin B1/EPHB1-2	0.032	0.039	-10000	0	-0.11	27	27
cell adhesion mediated by integrin	0.014	0.047	0.1	103	-10000	0	103
RAC1	0.023	0.002	-10000	0	-10000	0	0
mol:GTP	0.011	0.069	-10000	0	-0.16	31	31
RAC1-CDC42/GTP	-0.024	0.039	-10000	0	-0.13	41	41
RASA1	0.021	0.011	-10000	0	-0.12	3	3
RAC1-CDC42/GDP	0.009	0.081	-10000	0	-0.16	87	87
ruffle organization	0.004	0.057	-10000	0	-0.13	42	42
NCK1	0.02	0.019	-10000	0	-0.12	9	9
receptor internalization	0	0.049	-10000	0	-0.082	126	126
Ephrin B/EPHB2/KALRN	0.019	0.073	-10000	0	-0.097	132	132
ROCK1	0.017	0.028	-10000	0	-0.097	24	24
RAS family/GDP	-0.028	0.049	-10000	0	-0.16	45	45
Rac1/GTP	-0.024	0.041	-10000	0	-0.14	40	40
Ephrin B/EPHB1/Src/Paxillin	0	0.071	-10000	0	-0.23	12	12

×

PLK1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
regulation of centriole-centriole cohesion	0.011	0.057	0.19	48	-10000	0	48
BUB1B	-0.029	0.1	-10000	0	-0.24	84	84
PLK1	-0.01	0.049	-10000	0	-0.1	94	94
PLK1S1	-0.003	0.022	-10000	0	-0.05	79	79
KIF2A	-0.007	0.047	-10000	0	-0.11	79	79
regulation of mitotic centrosome separation	-0.01	0.049	-10000	0	-0.1	94	94
GOLGA2	0.023	0.006	-10000	0	-0.12	1	1
Hec1/SPC24	-0.015	0.088	-10000	0	-0.15	137	137
WEE1	-0.015	0.077	-10000	0	-0.2	55	55
cytokinesis	-0.052	0.14	-10000	0	-0.29	124	124
PP2A-alpha B56	-0.039	0.24	-10000	0	-0.7	64	64
AURKA	-0.026	0.092	-10000	0	-0.26	74	74
PICH/PLK1	-0.025	0.1	-10000	0	-0.17	147	147
CENPE	-0.005	0.046	-10000	0	-0.12	62	62
RhoA/GTP	0.016	0.016	-10000	0	-0.14	6	6
positive regulation of microtubule depolymerization	-0.007	0.047	-10000	0	-0.11	79	79
PPP2CA	0.023	0.003	-10000	0	-10000	0	0
FZR1	0.023	0	-10000	0	-10000	0	0
TPX2	-0.034	0.1	-10000	0	-0.26	92	92
PAK1	0.016	0.029	-10000	0	-0.12	24	24
SPC24	0.016	0.03	-10000	0	-0.12	25	25
FBXW11	0.023	0.003	-10000	0	-10000	0	0
CLSPN	0	0.035	-10000	0	-0.17	8	8
GORASP1	0.023	0.006	-10000	0	-0.12	1	1
metaphase	-0.001	0.004	-10000	0	-0.014	32	32
mol:GTP	0	0	-10000	0	-10000	0	0
NLP	-0.003	0.022	-10000	0	-0.05	79	79
G2 phase of mitotic cell cycle	-0.001	0.003	-10000	0	-0.009	60	60
STAG2	0.02	0.02	-10000	0	-0.12	11	11
GRASP65/GM130/RAB1/GTP	0.017	0.031	-10000	0	-0.16	8	8
spindle elongation	-0.01	0.049	-10000	0	-0.1	94	94
ODF2	0.021	0.014	-10000	0	-0.12	5	5
BUB1	-0.066	0.25	-10000	0	-0.76	64	64
TPT1	0.001	0.035	-10000	0	-0.16	17	17
CDC25C	-0.016	0.095	-10000	0	-0.39	32	32
CDC25B	0.015	0.024	-10000	0	-0.13	14	14
SGOL1	-0.011	0.057	-10000	0	-0.19	48	48
RHOA	0.023	0.006	-10000	0	-0.12	1	1
CCNB1/CDK1	-0.029	0.13	-10000	0	-0.24	142	142
CDC14B	0.011	0.004	-10000	0	-0.084	1	1
CDC20	0.016	0.026	-10000	0	-0.12	19	19
PLK1/PBIP1	-0.004	0.042	-10000	0	-0.099	70	70
mitosis	0.003	0.009	0.026	69	-0.011	1	70
FBXO5	-0.02	0.07	-10000	0	-0.17	79	79
CDC2	0.007	0.04	-10000	0	-0.12	48	48
NDC80	0.008	0.038	-10000	0	-0.12	43	43
metaphase plate congression	0	0.042	-10000	0	-0.17	19	19
ERCC6L	-0.034	0.12	-10000	0	-0.23	138	138
NLP/gamma Tubulin	-0.002	0.029	-10000	0	-0.084	43	43
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	0.023	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	88	88
mitotic prometaphase	-0.001	0.003	0.02	6	-0.01	24	30
proteasomal ubiquitin-dependent protein catabolic process	0.013	0.057	-10000	0	-0.25	14	14
microtubule-based process	-0.01	0.072	-10000	0	-0.14	101	101
Golgi organization	-0.01	0.049	-10000	0	-0.1	94	94
Cohesin/SA2	-0.003	0.054	-10000	0	-0.12	84	84
PPP1CB/MYPT1	0.024	0.039	-10000	0	-0.15	28	28
KIF20A	0.009	0.037	-10000	0	-0.12	42	42
APC/C/CDC20	-0.005	0.069	-10000	0	-0.13	96	96
PPP2R1A	0.022	0.009	-10000	0	-0.12	2	2
chromosome segregation	-0.004	0.042	-10000	0	-0.097	70	70
PRC1	0.015	0.03	-10000	0	-0.12	25	25
ECT2	-0.021	0.072	-10000	0	-0.16	102	102
C13orf34	-0.01	0.05	-10000	0	-0.12	79	79
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	84	84
spindle assembly	-0.005	0.037	-10000	0	-0.084	79	79
spindle stabilization	-0.003	0.022	-10000	0	-0.05	79	79
APC/C/HCDH1	0.025	0.007	-10000	0	-0.089	2	2
MKLP2/PLK1	-0.01	0.073	-10000	0	-0.14	101	101
CCNB1	0.014	0.027	-10000	0	-0.12	20	20
PPP1CB	0.022	0.003	-10000	0	-10000	0	0
BTRC	0.023	0.002	-10000	0	-10000	0	0
ROCK2	-0.015	0.094	-10000	0	-0.32	42	42
TUBG1	0	0.039	-10000	0	-0.21	13	13
G2/M transition of mitotic cell cycle	-0.044	0.12	-10000	0	-0.24	138	138
MLF1IP	0.01	0.011	-10000	0	-0.078	8	8
INCENP	0.022	0.009	-10000	0	-0.12	2	2

×

Caspase cascade in apoptosis

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TOP1	0.005	0.11	0.16	16	-0.24	60	76
ACTA1	0.023	0.073	0.15	60	-0.21	16	76
NUMA1	0.001	0.11	0.17	9	-0.25	64	73
SPTAN1	0.019	0.077	0.15	61	-0.2	22	83
LIMK1	0.025	0.072	0.15	63	-0.22	14	77
BIRC3	-0.005	0.052	-10000	0	-0.12	93	93
BIRC2	0.021	0.013	-10000	0	-0.12	4	4
BAX	0.023	0	-10000	0	-10000	0	0
CASP10	0.005	0.036	-10000	0	-0.072	88	88
CRMA	0	0	-10000	0	-10000	0	0
XIAP	0	0	-10000	0	-10000	0	0
PTK2	-0.008	0.14	0.16	15	-0.3	71	86
DIABLO	0.02	0.016	-10000	0	-0.12	6	6
apoptotic nuclear changes	0.019	0.076	0.15	61	-0.2	22	83
response to UV	0	0	-10000	0	-10000	0	0
CRADD	0.023	0.009	-10000	0	-0.12	2	2
GSN	0.021	0.074	0.15	58	-0.21	18	76
MADD	0.023	0.006	-10000	0	-0.12	1	1
TFAP2A	-0.031	0.15	-10000	0	-0.47	50	50
BID	0.01	0.037	-10000	0	-0.22	5	5
MAP3K1	0.008	0.082	-10000	0	-0.36	22	22
TRADD	0.023	0.006	-10000	0	-0.12	1	1
mol:Ca2+	0	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0.025	0.04	-10000	0	-0.16	22	22
mol:Activated DNA	0	0	-10000	0	-10000	0	0
ARHGDIB	0.006	0.076	0.14	37	-0.22	23	60
CASP9	0.022	0.014	-10000	0	-0.12	5	5
DNA repair	-0.024	0.074	0.26	22	-0.14	67	89
neuron apoptosis	-0.026	0.16	-10000	0	-0.58	40	40
mol:NAD	0	0	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	0.009	0.1	0.17	34	-0.26	31	65
APAF1	0.021	0.014	-10000	0	-0.12	5	5
CASP6	-0.055	0.25	-10000	0	-0.78	60	60
TRAF2	0.023	0	-10000	0	-10000	0	0
ICAD/CAD	0.028	0.069	0.15	61	-0.2	14	75
CASP7	0.044	0.077	0.19	106	-0.19	6	112
KRT18	-0.014	0.12	-10000	0	-0.56	22	22
apoptosis	-0.006	0.13	0.18	32	-0.31	61	93
DFFA	0.025	0.072	0.15	61	-0.22	14	75
DFFB	0.025	0.072	0.15	63	-0.22	14	77
PARP1	0.024	0.074	0.14	67	-0.26	22	89
actin filament polymerization	-0.025	0.069	0.2	15	-0.15	60	75
TNF	0.02	0.02	-10000	0	-0.12	11	11
CYCS	-0.005	0.05	-10000	0	-0.21	22	22
SATB1	-0.063	0.24	-10000	0	-0.75	60	60
SLK	0.018	0.077	0.15	61	-0.21	18	79
p15 BID/BAX	0.016	0.044	-10000	0	-0.2	7	7
CASP2	0.008	0.066	-10000	0	-0.21	22	22
JNK cascade	-0.008	0.082	0.36	22	-10000	0	22
CASP3	0.023	0.077	0.16	63	-0.2	19	82
LMNB2	-0.002	0.099	-10000	0	-0.26	63	63
RIPK1	0.022	0.011	-10000	0	-0.12	3	3
CASP4	0.015	0.029	-10000	0	-0.12	23	23
Mammalian IAPs/DIABLO	-0.019	0.083	-10000	0	-0.13	159	159
negative regulation of DNA binding	-0.03	0.15	-10000	0	-0.47	50	50
stress fiber formation	0.018	0.076	0.15	61	-0.21	18	79
GZMB	0.006	0.044	-10000	0	-0.098	78	78
CASP1	-0.064	0.14	-10000	0	-0.28	149	149
LMNB1	-0.028	0.14	-10000	0	-0.28	103	103
APP	-0.027	0.17	-10000	0	-0.59	40	40
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	33	-0.31	61	94
LMNA	-0.008	0.11	-10000	0	-0.27	74	74
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD	0.006	0.07	-10000	0	-0.23	21	21
LRDD	0.022	0.015	-10000	0	-0.12	6	6
SREBF1	0.024	0.074	0.15	63	-0.22	15	78
APAF-1/Caspase 9	0.028	0.11	0.26	15	-0.75	8	23
nuclear fragmentation during apoptosis	0.001	0.11	0.16	13	-0.25	64	77
CFL2	0.025	0.07	0.15	60	-0.2	15	75
GAS2	0.023	0.072	0.15	60	-0.21	16	76
positive regulation of apoptosis	-0.014	0.12	-10000	0	-0.29	69	69
PRF1	0.014	0.035	-10000	0	-0.12	37	37

×

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	-0.084	0.19	-10000	0	-0.4	137	137
IHH	-0.001	0.048	-10000	0	-0.075	143	143
SHH Np/Cholesterol/GAS1	0.022	0.029	-10000	0	-0.098	19	19
LRPAP1	0.018	0.023	-10000	0	-0.12	15	15
dorsoventral neural tube patterning	-0.022	0.029	0.097	19	-10000	0	19
SMO/beta Arrestin2	-0.01	0.11	-10000	0	-0.28	11	11
SMO	-0.019	0.11	-10000	0	-0.31	8	8
AKT1	-0.018	0.11	-10000	0	-0.33	40	40
ARRB2	0.022	0.013	-10000	0	-0.12	5	5
BOC	0.011	0.038	-10000	0	-0.12	44	44
ADRBK1	0.023	0.001	-10000	0	-10000	0	0
heart looping	-0.018	0.1	-10000	0	-0.3	8	8
STIL	-0.017	0.082	-10000	0	-0.15	137	137
DHH N/PTCH2	0.034	0.011	-10000	0	-0.089	4	4
DHH N/PTCH1	-0.019	0.099	-10000	0	-0.18	137	137
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
DHH	0.023	0.01	-10000	0	-0.12	3	3
PTHLH	-0.072	0.18	-10000	0	-0.38	137	137
determination of left/right symmetry	-0.018	0.1	-10000	0	-0.3	8	8
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
skeletal system development	-0.072	0.18	-10000	0	-0.37	137	137
IHH N/Hhip	0.016	0.039	-10000	0	-0.11	17	17
DHH N/Hhip	0.029	0.024	-10000	0	-0.072	29	29
mol:Cholesterol	0	0	-10000	0	-10000	0	0
heart development	-0.018	0.1	-10000	0	-0.3	8	8
pancreas development	0.017	0.029	-10000	0	-0.12	25	25
HHAT	0.022	0.011	-10000	0	-0.12	3	3
PI3K	0.007	0.065	-10000	0	-0.16	63	63
EntrezGene:84976	0	0	-10000	0	-10000	0	0
GAS1	0.014	0.035	-10000	0	-0.12	35	35
somite specification	-0.018	0.1	-10000	0	-0.3	8	8
SHH Np/Cholesterol/PTCH1	-0.013	0.086	-10000	0	-0.15	137	137
SHH Np/Cholesterol/PTCH2	0.03	0.014	-10000	0	-0.099	5	5
SHH Np/Cholesterol/Megalin	0.007	0.039	-10000	0	-0.1	20	20
SHH	0.022	0.011	-10000	0	-0.085	5	5
catabolic process	-0.033	0.11	-10000	0	-0.21	137	137
SMO/Vitamin D3	-0.01	0.097	-10000	0	-0.24	8	8
SHH Np/Cholesterol/Hhip	0.027	0.02	-10000	0	-0.098	5	5
LRP2	-0.015	0.063	-10000	0	-0.12	150	150
receptor-mediated endocytosis	-0.02	0.098	-10000	0	-0.21	58	58
SHH Np/Cholesterol/BOC	0.02	0.034	-10000	0	-0.11	23	23
SHH Np/Cholesterol/CDO	0.018	0.037	-10000	0	-0.098	40	40
mesenchymal cell differentiation	-0.026	0.02	0.098	5	-10000	0	5
mol:Vitamin D3	-0.012	0.088	-10000	0	-0.15	137	137
IHH N/PTCH2	0.021	0.031	-10000	0	-0.14	3	3
CDON	0.013	0.035	-10000	0	-0.12	35	35
IHH N/PTCH1	-0.028	0.11	-10000	0	-0.21	137	137
Megalin/LRPAP1	-0.01	0.065	-10000	0	-0.092	200	200
PTCH2	0.023	0.008	-10000	0	-0.12	2	2
SHH Np/Cholesterol	0.018	0.012	-10000	0	-0.076	8	8
PTCH1	-0.033	0.11	-10000	0	-0.21	137	137
HHIP	0.017	0.029	-10000	0	-0.12	25	25

×

Signaling events mediated by PTP1B

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
PDGFRB	0.01	0.041	-10000	0	-0.12	51	51
Jak2/Leptin Receptor	-0.042	0.13	0.18	1	-0.34	67	68
PTP1B/AKT1	-0.059	0.1	-10000	0	-0.23	97	97
FYN	0.012	0.037	-10000	0	-0.12	40	40
p210 bcr-abl/PTP1B	-0.074	0.1	-10000	0	-0.26	96	96
EGFR	0.015	0.03	-10000	0	-0.12	25	25
EGF/EGFR	-0.057	0.1	-10000	0	-0.23	109	109
CSF1	0.013	0.033	-10000	0	-0.12	31	31
AKT1	0.021	0.019	-10000	0	-0.12	10	10
INSR	0.021	0.017	-10000	0	-0.12	8	8
PTP1B/N-cadherin	-0.092	0.12	-10000	0	-0.24	188	188
Insulin Receptor/Insulin	-0.03	0.091	-10000	0	-0.21	75	75
HCK	0.019	0.023	-10000	0	-0.12	15	15
CRK	0.022	0.016	-10000	0	-0.12	7	7
TYK2	-0.067	0.1	-10000	0	-0.25	95	95
EGF	0.018	0.022	-10000	0	-0.12	13	13
YES1	0.02	0.018	-10000	0	-0.12	8	8
CAV1	-0.055	0.096	-10000	0	-0.23	93	93
TXN	0.019	0.014	-10000	0	-0.12	5	5
PTP1B/IRS1/GRB2	-0.053	0.11	-10000	0	-0.23	104	104
cell migration	0.074	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	55	55
ITGA2B	0.022	0.006	-10000	0	-0.12	1	1
CSF1R	0.014	0.031	-10000	0	-0.12	28	28
Prolactin Receptor/Prolactin	0.035	0.035	-10000	0	-0.17	2	2
FGR	0.023	0.006	-10000	0	-0.12	1	1
PTP1B/p130 Cas	-0.062	0.1	-10000	0	-0.25	94	94
Crk/p130 Cas	-0.051	0.1	-10000	0	-0.24	95	95
DOK1	-0.055	0.094	-10000	0	-0.24	79	79
JAK2	-0.05	0.13	-10000	0	-0.37	62	62
Jak2/Leptin Receptor/Leptin	-0.054	0.12	-10000	0	-0.24	128	128
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
PTPN1	-0.074	0.1	-10000	0	-0.26	96	96
LYN	0.021	0.013	-10000	0	-0.12	4	4
CDH2	-0.014	0.056	-10000	0	-0.12	121	121
SRC	-0.007	0.053	-10000	0	-0.61	2	2
ITGB3	0.004	0.046	-10000	0	-0.12	67	67
CAT1/PTP1B	-0.056	0.12	-10000	0	-0.26	105	105
CAPN1	0.02	0.013	-10000	0	-0.12	4	4
CSK	0.023	0.009	-10000	0	-0.12	2	2
PI3K	-0.032	0.1	-10000	0	-0.21	96	96
mol:H2O2	0.002	0.004	-10000	0	-10000	0	0
STAT3 (dimer)	-0.048	0.12	-10000	0	-0.23	128	128
negative regulation of transcription	-0.049	0.13	-10000	0	-0.36	62	62
FCGR2A	0.013	0.03	-10000	0	-0.12	26	26
FER	0.019	0.017	-10000	0	-0.12	8	8
alphaIIb/beta3 Integrin	0.008	0.053	-10000	0	-0.14	38	38
BLK	0.022	0.013	-10000	0	-0.12	5	5
Insulin Receptor/Insulin/Shc	0.043	0.022	-10000	0	-0.11	8	8
RHOA	0.021	0.007	-10000	0	-0.12	1	1
LEPR	0.018	0.028	-10000	0	-0.12	22	22
BCAR1	0.023	0.01	-10000	0	-0.12	3	3
p210 bcr-abl/Grb2	0.023	0.006	-10000	0	-0.12	1	1
mol:NADPH	-0.001	0.002	-10000	0	-10000	0	0
TRPV6	0.001	0.085	-10000	0	-0.19	64	64
PRL	0.027	0.012	-10000	0	-0.13	3	3
SOCS3	-0.027	0.22	-10000	0	-1.2	20	20
SPRY2	-0.008	0.054	-10000	0	-0.12	103	103
Insulin Receptor/Insulin/IRS1	0.039	0.03	-10000	0	-0.11	13	13
CSF1/CSF1R	-0.076	0.13	-10000	0	-0.26	130	130
Ras protein signal transduction	0.028	0.034	0.098	31	-0.14	6	37
IRS1	0.02	0.022	-10000	0	-0.12	14	14
INS	0.022	0.011	-10000	0	-0.12	3	3
LEP	0.023	0.006	-10000	0	-0.12	1	1
STAT5B	-0.059	0.1	-10000	0	-0.24	101	101
STAT5A	-0.061	0.1	-10000	0	-0.24	107	107
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PDGFB-D/PDGFRB	-0.067	0.1	-10000	0	-0.24	106	106
CSN2	0.04	0.027	-10000	0	-10000	0	0
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
LAT	-0.082	0.19	-10000	0	-0.5	88	88
YBX1	0.033	0.015	-10000	0	-0.15	3	3
LCK	0.022	0.015	-10000	0	-0.12	6	6
SHC1	0.023	0.001	-10000	0	-10000	0	0
NOX4	-0.021	0.062	-10000	0	-0.12	156	156

×

TCR signaling in naïve CD8+ T cells

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GRB2/SOS1/SHC	-0.004	0.14	-10000	0	-0.32	68	68
FYN	-0.047	0.18	-10000	0	-0.38	96	96
LAT/GRAP2/SLP76	-0.01	0.15	-10000	0	-0.32	85	85
IKBKB	0.022	0.015	-10000	0	-0.12	6	6
AKT1	-0.009	0.13	-10000	0	-0.29	81	81
B2M	0.022	0.007	-10000	0	-10000	0	0
IKBKG	0.008	0.044	-10000	0	-0.084	80	80
MAP3K8	0.023	0.009	-10000	0	-0.12	2	2
mol:Ca2+	-0.004	0.011	-10000	0	-0.034	46	46
integrin-mediated signaling pathway	0.021	0.035	-10000	0	-0.12	29	29
LAT/GRAP2/SLP76/VAV1/PI3K Class IA	-0.024	0.18	-10000	0	-0.4	84	84
TRPV6	0.003	0.017	-10000	0	-0.13	7	7
CD28	0.022	0.01	-10000	0	-0.12	3	3
SHC1	-0.019	0.16	-10000	0	-0.37	72	72
receptor internalization	-0.015	0.14	-10000	0	-0.34	68	68
PRF1	-0.019	0.18	-10000	0	-0.65	30	30
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	79	79
LAT	-0.019	0.16	-10000	0	-0.37	72	72
EntrezGene:6955	0	0.003	-10000	0	-0.022	3	3
CD3D	0.008	0.044	-10000	0	-0.12	58	58
CD3E	0.015	0.033	-10000	0	-0.12	29	29
CD3G	0.002	0.05	-10000	0	-0.12	78	78
RASGRP2	0.007	0.015	-10000	0	-0.049	1	1
RASGRP1	-0.017	0.14	-10000	0	-0.29	89	89
HLA-A	0.02	0.019	-10000	0	-0.12	8	8
RASSF5	0.02	0.022	-10000	0	-0.12	13	13
RAP1A/GTP/RAPL	0.022	0.035	-10000	0	-0.12	29	29
mol:GTP	0	0	-10000	0	-10000	0	0
mol:GDP	0.008	0.05	-10000	0	-0.09	78	78
PDK1/CARD11/BCL10/MALT1/TRAF6	-0.026	0.054	-10000	0	-0.14	88	88
PRKCA	-0.005	0.08	-10000	0	-0.18	80	80
GRAP2	0.022	0.012	-10000	0	-0.12	4	4
mol:IP3	-0.045	0.099	0.096	4	-0.26	82	86
EntrezGene:6957	0	0.004	-10000	0	-0.023	2	2
TCR/CD3/MHC I/CD8	-0.015	0.13	-10000	0	-0.35	55	55
ORAI1	0	0.023	0.09	7	-0.15	7	14
CSK	-0.019	0.16	-10000	0	-0.39	68	68
B7 family/CD28	-0.008	0.16	-10000	0	-0.35	75	75
CHUK	0.021	0.013	-10000	0	-0.12	4	4
TCR/CD3/MHC I/CD8/LCK/ZAP-70	-0.027	0.18	-10000	0	-0.41	75	75
PTPN6	-0.024	0.16	-10000	0	-0.36	78	78
VAV1	-0.023	0.16	-10000	0	-0.38	76	76
Monovalent TCR/CD3	-0.016	0.096	-10000	0	-0.2	101	101
CBL	0.023	0.006	-10000	0	-0.12	1	1
LCK	-0.037	0.18	-10000	0	-0.39	85	85
PAG1	-0.02	0.16	-10000	0	-0.39	69	69
RAP1A	0.021	0.011	-10000	0	-0.12	3	3
TCR/CD3/MHC I/CD8/LCK	-0.029	0.17	-10000	0	-0.4	78	78
CD80	0.019	0.024	-10000	0	-0.12	16	16
CD86	0.013	0.033	-10000	0	-0.12	32	32
PDK1/CARD11/BCL10/MALT1	-0.027	0.066	-10000	0	-0.17	83	83
HRAS	0.023	0.006	-10000	0	-0.12	1	1
GO:0035030	-0.017	0.13	-10000	0	-0.31	75	75
CD8A	0.023	0.012	-10000	0	-0.13	3	3
CD8B	0.021	0.017	-10000	0	-0.13	7	7
PTPRC	-0.004	0.05	-10000	0	-0.12	86	86
PDK1/PKC theta	-0.016	0.15	-10000	0	-0.34	83	83
CSK/PAG1	-0.015	0.16	-10000	0	-0.37	68	68
SOS1	0.017	0.027	-10000	0	-0.12	20	20
peptide-MHC class I	0.012	0.073	-10000	0	-0.19	57	57
GRAP2/SLP76	-0.015	0.17	-10000	0	-0.36	86	86
STIM1	-0.002	0.032	-10000	0	-0.17	18	18
RAS family/GTP	0.007	0.07	-10000	0	-0.14	72	72
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin	-0.015	0.15	-10000	0	-0.32	81	81
mol:DAG	-0.042	0.089	-10000	0	-0.22	90	90
RAP1A/GDP	0.005	0.026	-10000	0	-0.05	62	62
PLCG1	0.018	0.025	-10000	0	-0.12	18	18
CD247	0.024	0.004	-10000	0	-0.011	1	1
cytotoxic T cell degranulation	-0.017	0.18	-10000	0	-0.62	30	30
RAP1A/GTP	-0.002	0.009	-10000	0	-0.037	25	25
mol:PI-3-4-5-P3	-0.016	0.15	-10000	0	-0.34	83	83
LAT/GRAP2/SLP76/VAV1/PLCgamma1	-0.051	0.13	0.12	4	-0.32	82	86
NRAS	0.022	0.011	-10000	0	-0.12	3	3
ZAP70	0.023	0.006	-10000	0	-0.12	1	1
GRB2/SOS1	0.021	0.046	-10000	0	-0.15	31	31
LAT/GRAP2/SLP76/VAV1	-0.013	0.15	-10000	0	-0.31	85	85
MALT1	0.018	0.026	-10000	0	-0.12	19	19
TRAF6	0.022	0.009	-10000	0	-0.12	2	2
CD8 heterodimer	0.032	0.017	-10000	0	-0.081	7	7
CARD11	0.018	0.028	-10000	0	-0.12	22	22
PRKCB	-0.03	0.064	-10000	0	-0.16	90	90
PRKCE	0	0.08	-10000	0	-0.17	80	80
PRKCQ	-0.024	0.17	-10000	0	-0.38	84	84
LCP2	0.013	0.033	-10000	0	-0.12	31	31
BCL10	0.023	0.001	-10000	0	-10000	0	0
regulation of survival gene product expression	-0.005	0.12	-10000	0	-0.25	81	81
IKK complex	0.007	0.044	-10000	0	-0.084	53	53
RAS family/GDP	-0.006	0.01	-10000	0	-0.035	37	37
MAP3K14	0.008	0.088	-10000	0	-0.18	78	78
PDPK1	-0.007	0.13	-10000	0	-0.28	80	80
TCR/CD3/MHC I/CD8/Fyn	-0.031	0.19	-10000	0	-0.49	67	67

×

Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.003	0.075	-9999	-0.16	90	90
CRKL	0.023	0.009	-9999	-0.12	2	2
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
DOCK1	0.019	0.02	-9999	-0.12	11	11
ITGA4	0.015	0.029	-9999	-0.12	24	24
alpha4/beta7 Integrin/MAdCAM1	0.032	0.059	-9999	-0.1	79	79
EPO	0.023	0.006	-9999	-0.12	1	1
alpha4/beta7 Integrin	0.005	0.065	-9999	-0.13	107	107
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.022	0.016	-9999	-0.12	7	7
alpha4/beta1 Integrin	0.006	0.063	-9999	-0.14	74	74
EPO/EPOR (dimer)	0.032	0.019	-9999	-0.079	15	15
lamellipodium assembly	0.004	0.086	-9999	-0.19	69	69
PIK3CA	0.02	0.017	-9999	-0.12	7	7
PI3K	0.007	0.065	-9999	-0.16	63	63
ARF6	0.023	0.003	-9999	-10000	0	0
JAK2	0.003	0.081	-9999	-0.18	74	74
PXN	0.022	0.013	-9999	-0.12	5	5
PIK3R1	0.015	0.031	-9999	-0.12	28	28
MADCAM1	0.023	0.006	-9999	-0.12	1	1
cell adhesion	0.03	0.058	-9999	-0.1	79	79
CRKL/CBL	0.033	0.013	-9999	-0.098	5	5
ITGB1	0.021	0.015	-9999	-0.12	6	6
SRC	-0.037	0.074	-9999	-0.13	188	188
ITGB7	0.019	0.023	-9999	-0.12	15	15
RAC1	0.023	0.002	-9999	-10000	0	0
alpha4/beta1 Integrin/VCAM1	-0.04	0.09	-9999	-0.15	188	188
p130Cas/Crk/Dock1	-0.021	0.075	-9999	-0.16	78	78
VCAM1	-0.018	0.059	-9999	-0.12	139	139
RHOA	0.023	0.006	-9999	-0.12	1	1
alpha4/beta1 Integrin/Paxillin/GIT1	0.033	0.057	-9999	-0.099	75	75
BCAR1	-0.032	0.067	-9999	-0.11	188	188
EPOR	0.02	0.021	-9999	-0.12	12	12
mol:GDP	0	0	-9999	-10000	0	0
CBL	0.023	0.006	-9999	-0.12	1	1
GIT1	0.022	0.013	-9999	-0.12	5	5
Rac1/GTP	0.004	0.089	-9999	-0.2	69	69

×

Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1	-0.024	0.13	-9999	-0.26	111	111
MAP3K8	0.021	0.009	-9999	-0.12	2	2
FOS	-0.013	0.092	-9999	-0.28	27	27
PRKCA	0.008	0.038	-9999	-0.12	42	42
PTPN7	0.017	0.013	-9999	-10000	0	0
HRAS	0.022	0.006	-9999	-0.12	1	1
PRKCB	-0.003	0.006	-9999	-0.01	194	194
NRAS	0.021	0.011	-9999	-0.12	3	3
RAS family/GTP	0.025	0.043	-9999	-0.11	38	38
MAPK3	0.003	0.067	-9999	-0.49	5	5
MAP2K1	-0.015	0.09	-9999	-0.3	41	41
ELK1	0.016	0.02	-9999	-0.13	6	6
BRAF	-0.015	0.084	-9999	-0.3	40	40
mol:GTP	-0.001	0.002	-9999	-0.003	185	185
MAPK1	0	0.075	-9999	-0.44	9	9
RAF1	-0.016	0.083	-9999	-0.29	45	45
KRAS	0.014	0.034	-9999	-0.12	33	33

×

IL12-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1	-0.002	0.095	-10000	0	-0.22	55	55
TBX21	-0.085	0.28	-10000	0	-0.71	63	63
B2M	0.024	0.006	-10000	0	-10000	0	0
TYK2	0.015	0.029	-10000	0	-0.13	7	7
IL12RB1	0.016	0.025	-10000	0	-0.12	1	1
GADD45B	-0.096	0.33	-10000	0	-0.88	62	62
IL12RB2	0.014	0.033	-10000	0	-0.12	16	16
GADD45G	-0.083	0.28	-10000	0	-0.78	54	54
natural killer cell activation	-0.003	0.019	-10000	0	-0.04	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	0.005	0.046	-10000	0	-0.12	66	66
IL2RA	0.021	0.018	-10000	0	-0.12	9	9
IFNG	0.013	0.037	-10000	0	-0.12	41	41
STAT3 (dimer)	-0.077	0.27	-10000	0	-0.6	90	90
HLA-DRB5	-0.014	0.057	-10000	0	-0.12	119	119
FASLG	-0.087	0.28	-10000	0	-0.72	64	64
NF kappa B2 p52/RelB	-0.081	0.28	-10000	0	-0.61	93	93
CD4	0.012	0.029	-10000	0	-0.12	21	21
SOCS1	0.017	0.03	-10000	0	-0.12	26	26
EntrezGene:6955	-0.002	0.008	-10000	0	-10000	0	0
CD3D	0.004	0.045	-10000	0	-0.12	58	58
CD3E	0.012	0.033	-10000	0	-0.12	29	29
CD3G	-0.001	0.051	-10000	0	-0.12	78	78
IL12Rbeta2/JAK2	0.009	0.063	-10000	0	-0.14	61	61
CCL3	-0.11	0.33	-10000	0	-0.85	65	65
CCL4	-0.094	0.28	-10000	0	-0.62	93	93
HLA-A	0.021	0.018	-10000	0	-0.12	8	8
IL18/IL18R	0.025	0.076	-10000	0	-0.12	82	82
NOS2	-0.086	0.26	-10000	0	-0.56	98	98
IL12/IL12R/TYK2/JAK2/SPHK2	0.001	0.092	-10000	0	-0.21	51	51
IL1R1	-0.18	0.43	-10000	0	-1	103	103
IL4	0.026	0.021	0.069	13	-0.11	3	16
JAK2	0.012	0.034	-10000	0	-0.099	25	25
EntrezGene:6957	-0.001	0.007	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.01	0.12	-10000	0	-0.41	32	32
RAB7A	-0.067	0.27	-10000	0	-0.72	55	55
lysosomal transport	-0.062	0.26	-10000	0	-0.66	60	60
FOS	-0.26	0.49	-10000	0	-1.1	131	131
STAT4 (dimer)	-0.077	0.28	-10000	0	-0.62	90	90
STAT5A (dimer)	-0.086	0.28	-10000	0	-0.61	94	94
GZMA	-0.12	0.35	-10000	0	-0.88	73	73
GZMB	-0.11	0.32	-10000	0	-0.81	66	66
HLX	0.023	0.006	-10000	0	-0.12	1	1
LCK	-0.096	0.29	-10000	0	-0.65	92	92
TCR/CD3/MHC II/CD4	-0.11	0.21	-10000	0	-0.34	198	198
IL2/IL2R	0.013	0.068	-10000	0	-0.1	116	116
MAPK14	-0.089	0.31	-10000	0	-0.74	76	76
CCR5	-0.067	0.25	-10000	0	-0.67	52	52
IL1B	0.005	0.044	-10000	0	-0.12	45	45
STAT6	-0.024	0.13	-10000	0	-0.4	27	27
STAT4	0.02	0.02	-10000	0	-0.12	11	11
STAT3	0.022	0.011	-10000	0	-0.12	3	3
STAT1	0.014	0.03	-10000	0	-0.12	25	25
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
NFKB2	0.023	0.009	-10000	0	-0.12	2	2
IL12B	0.017	0.023	-10000	0	-10000	0	0
CD8A	0.024	0.01	-10000	0	-0.12	3	3
CD8B	0.023	0.016	-10000	0	-0.12	7	7
T-helper 1 cell differentiation	0	0	-10000	0	-10000	0	0
natural killer cell mediated cytotoxicity	0.001	0.094	0.22	55	-10000	0	55
IL2RB	0.019	0.023	-10000	0	-0.12	15	15
proteasomal ubiquitin-dependent protein catabolic process	-0.069	0.26	-10000	0	-0.57	90	90
IL2RG	-0.002	0.049	-10000	0	-0.12	82	82
IL12	0.004	0.063	-10000	0	-0.14	51	51
STAT5A	0.022	0.012	-10000	0	-0.12	4	4
CD247	0.021	0.01	-10000	0	-10000	0	0
IL2	0.023	0.01	-10000	0	-0.12	3	3
SPHK2	0.023	0.01	-10000	0	-0.12	3	3
FRAP1	0.022	0.012	-10000	0	-0.12	4	4
IL12A	-0.001	0.05	-10000	0	-0.12	70	70
IL12/IL12R/TYK2/JAK2	-0.1	0.31	-10000	0	-0.69	92	92
MAP2K3	-0.083	0.3	-10000	0	-0.69	83	83
RIPK2	0.013	0.034	-10000	0	-0.12	34	34
MAP2K6	-0.1	0.31	-10000	0	-0.68	92	92
regulation of dendritic cell antigen processing and presentation	0	0	-10000	0	-10000	0	0
HLA-DRA	0.009	0.031	-10000	0	-0.13	23	23
IL18RAP	0.022	0.02	-10000	0	-0.12	8	8
IL12Rbeta1/TYK2	0.024	0.037	-10000	0	-0.11	6	6
EOMES	0.018	0.031	-10000	0	-10000	0	0
STAT1 (dimer)	-0.1	0.28	-10000	0	-0.6	101	101
T cell proliferation	-0.064	0.22	-10000	0	-0.48	93	93
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
IL18R1	0.02	0.025	-10000	0	-0.12	14	14
CD8-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.11	0.21	-10000	0	-0.53	90	90
ATF2	-0.081	0.29	-10000	0	-0.67	79	79

×

a4b1 and a4b7 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ITGB1	0.021	0.015	-9999	-0.12	6	6
ITGB7	0.019	0.023	-9999	-0.12	15	15
ITGA4	0.015	0.029	-9999	-0.12	24	24
alpha4/beta7 Integrin	0.005	0.065	-9999	-0.13	107	107
alpha4/beta1 Integrin	0.006	0.063	-9999	-0.14	74	74

×

Canonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.037	0.047	0.11	118	-0.087	10	128
AES	0.036	0.043	0.099	128	-0.11	10	138
FBXW11	0.023	0.003	-10000	0	-10000	0	0
mol:GTP	0.001	0.002	-10000	0	-10000	0	0
LRP6/FZD1	0.018	0.047	-10000	0	-0.11	67	67
SMAD4	0.022	0.007	-10000	0	-0.12	1	1
DKK2	0.023	0.01	-10000	0	-0.12	3	3
TLE1	0.033	0.038	0.1	89	-0.11	8	97
MACF1	0.016	0.026	-10000	0	-0.12	18	18
CTNNB1	0.021	0.097	0.18	8	-0.31	27	35
WIF1	0.02	0.021	-10000	0	-0.12	13	13
beta catenin/RanBP3	0.084	0.19	0.38	136	-0.35	13	149
KREMEN2	0.022	0.012	-10000	0	-0.12	4	4
DKK1	0.015	0.034	-10000	0	-0.12	34	34
beta catenin/beta TrCP1	0.034	0.095	0.19	8	-0.29	28	36
FZD1	0.023	0.006	-10000	0	-0.12	1	1
AXIN2	-0.037	0.16	-10000	0	-0.75	14	14
AXIN1	0.023	0.011	-10000	0	-0.12	3	3
RAN	0.024	0.002	-10000	0	-10000	0	0
Axin1/APC/GSK3/beta catenin	0.036	0.083	-10000	0	-0.48	10	10
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4	0.023	0.11	0.24	8	-0.28	41	49
Axin1/APC/GSK3	0.027	0.06	-10000	0	-0.25	16	16
Axin1/APC/GSK3/beta catenin/Macf1	0.03	0.068	-10000	0	-0.25	18	18
HNF1A	0.037	0.038	0.1	108	-0.12	3	111
CTBP1	0.037	0.04	0.1	109	-0.11	7	116
MYC	-0.17	0.44	-10000	0	-1.3	76	76
RANBP3	0.023	0.009	-10000	0	-0.12	2	2
DKK2/LRP6/Kremen 2	0.032	0.043	-10000	0	-0.11	33	33
NKD1	0.022	0.012	-10000	0	-0.12	4	4
TCF4	0.036	0.042	0.1	120	-0.091	8	128
TCF3	0.037	0.039	0.1	110	-0.12	5	115
WNT1/LRP6/FZD1/Axin1	0.044	0.044	-10000	0	-0.097	37	37
Ran/GTP	0.018	0.012	-10000	0	-0.14	3	3
CtBP/CBP/TCF/TLE1/AES	0.08	0.23	0.45	130	-0.34	12	142
LEF1	0.012	0.056	0.13	20	-0.11	73	93
DVL1	0.027	0.076	-10000	0	-0.32	19	19
CSNK2A1	0.022	0.015	-10000	0	-0.12	6	6
beta catenin/TCF/CtBP/CBP/TLE1/AES	-0.025	0.14	-10000	0	-0.3	71	71
DKK1/LRP6/Kremen 2	0.027	0.047	-10000	0	-0.11	35	35
LRP6	0.014	0.033	-10000	0	-0.12	32	32
CSNK1A1	0.04	0.044	0.11	132	-0.13	1	133
NLK	0.017	0.021	-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	-0.19	17	17
APC	0.022	0.033	-10000	0	-0.084	39	39
WNT1/LRP6/FZD1	0.018	0.056	-10000	0	-0.15	36	36
CREBBP	0.035	0.038	0.1	105	-0.1	5	110

×

Circadian rhythm pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
chromatin modification	-0.067	0.31	-10000	0	-1	51	51
CLOCK	0.017	0.024	-10000	0	-0.052	49	49
TIMELESS/CRY2	-0.063	0.31	-10000	0	-1	50	50
DEC1/BMAL1	0.024	0.038	-10000	0	-0.12	30	30
ATR	0.02	0.014	-10000	0	-0.12	5	5
NR1D1	-0.01	0.11	-10000	0	-0.36	50	50
ARNTL	0.018	0.023	-10000	0	-0.05	47	47
TIMELESS	-0.079	0.32	-10000	0	-1.1	50	50
NPAS2	0.003	0.048	-10000	0	-0.096	93	93
CRY2	0.023	0	-10000	0	-10000	0	0
mol:CO	0.001	0.042	0.13	50	-10000	0	50
CHEK1	0.012	0.034	-10000	0	-0.12	34	34
mol:HEME	-0.001	0.042	-10000	0	-0.13	50	50
PER1	0.022	0.013	-10000	0	-0.12	5	5
BMAL/CLOCK/NPAS2	0.001	0.086	-10000	0	-0.12	154	154
BMAL1/CLOCK	-0.033	0.19	-10000	0	-0.55	56	56
S phase of mitotic cell cycle	-0.067	0.31	-10000	0	-1	51	51
TIMELESS/CHEK1/ATR	-0.07	0.32	-10000	0	-1.1	51	51
mol:NADPH	-0.001	0.042	-10000	0	-0.13	50	50
PER1/TIMELESS	-0.063	0.31	-10000	0	-1.1	50	50
PER1-2 / CRY1-2	0	0	-10000	0	-10000	0	0
DEC1	0.023	0.01	-10000	0	-0.12	3	3

×

Noncanonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC2	0.02	0.019	-9999	-0.12	10	10
GNB1/GNG2	-0.011	0.1	-9999	-0.23	68	68
mol:DAG	-0.018	0.095	-9999	-0.21	76	76
PLCG1	-0.018	0.097	-9999	-0.21	76	76
YES1	-0.029	0.1	-9999	-0.26	63	63
FZD3	0.013	0.032	-9999	-0.12	30	30
FZD6	0.017	0.024	-9999	-0.12	15	15
G protein	-0.008	0.1	-9999	-0.22	68	68
MAP3K7	-0.014	0.084	-9999	-0.18	76	76
mol:Ca2+	-0.017	0.093	-9999	-0.2	76	76
mol:IP3	-0.018	0.095	-9999	-0.21	76	76
NLK	0.026	0.045	-9999	-0.98	1	1
GNB1	0.023	0.006	-9999	-0.12	1	1
CAMK2A	-0.015	0.087	-9999	-0.19	76	76
MAP3K7IP1	0.023	0	-9999	-10000	0	0
Noncanonical Wnts/FZD	-0.032	0.1	-9999	-0.26	61	61
CSNK1A1	0.022	0.007	-9999	-0.12	1	1
GNAS	-0.028	0.097	-9999	-0.25	61	61
GO:0007205	-0.021	0.092	-9999	-0.22	68	68
WNT6	0.022	0.011	-9999	-0.12	3	3
WNT4	0.023	0.01	-9999	-0.12	3	3
NFAT1/CK1 alpha	-0.01	0.11	-9999	-0.23	78	78
GNG2	0.02	0.018	-9999	-0.12	9	9
WNT5A	0.014	0.031	-9999	-0.12	27	27
WNT11	0.002	0.051	-9999	-0.12	83	83
CDC42	-0.024	0.095	-9999	-0.24	63	63

×

BMP receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS	-0.035	0.09	-9999	-0.12	247	247
SMAD6-7/SMURF1	0.042	0.03	-9999	-0.14	11	11
NOG	0.017	0.028	-9999	-0.12	23	23
SMAD9	0.02	0.049	-9999	-0.54	2	2
SMAD4	0.022	0.007	-9999	-0.12	1	1
SMAD5	0	0.092	-9999	-0.27	36	36
BMP7/USAG1	-0.073	0.092	-9999	-0.13	373	373
SMAD5/SKI	0.012	0.091	-9999	-0.26	35	35
SMAD1	0.021	0.073	-9999	-0.28	26	26
BMP2	0.022	0.013	-9999	-0.12	5	5
SMAD1/SMAD1/SMAD4	-0.003	0.065	-9999	-0.25	26	26
BMPR1A	0.02	0.014	-9999	-0.12	4	4
BMPR1B	0.008	0.041	-9999	-0.12	52	52
BMPR1A-1B/BAMBI	-0.025	0.086	-9999	-0.14	159	159
AHSG	0.023	0.008	-9999	-0.12	2	2
CER1	0.022	0.012	-9999	-0.12	4	4
BMP2-4/CER1	0.033	0.039	-9999	-0.12	16	16
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA	0.004	0.098	-9999	-0.27	43	43
BMP2-4 (homodimer)	0.02	0.041	-9999	-0.15	15	15
RGMB	0.023	0.008	-9999	-0.12	2	2
BMP6/BMPR2/BMPR1A-1B	0.013	0.076	-9999	-0.12	114	114
RGMA	0.021	0.017	-9999	-0.12	8	8
SMURF1	0.023	0.009	-9999	-0.12	2	2
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP	0.005	0.076	-9999	-0.22	42	42
BMP2-4/USAG1	-0.012	0.069	-9999	-0.12	116	116
SMAD6/SMURF1/SMAD5	0.012	0.092	-9999	-0.26	35	35
SOSTDC1	-0.017	0.062	-9999	-0.12	148	148
BMP7/BMPR2/BMPR1A-1B	-0.033	0.092	-9999	-0.13	221	221
SKI	0.023	0.01	-9999	-0.12	3	3
BMP6 (homodimer)	0.02	0.022	-9999	-0.12	14	14
HFE2	0.023	0.008	-9999	-0.12	2	2
ZFYVE16	0.02	0.018	-9999	-0.12	8	8
MAP3K7	0.021	0.014	-9999	-0.12	5	5
BMP2-4/CHRD	0.033	0.038	-9999	-0.11	16	16
SMAD5/SMAD5/SMAD4	0.01	0.094	-9999	-0.26	38	38
MAPK1	0.021	0.016	-9999	-0.12	7	7
TAK1/TAB family	0.023	0.095	-9999	-0.22	50	50
BMP7 (homodimer)	-0.01	0.055	-9999	-0.12	109	109
NUP214	0.023	0.007	-9999	-0.12	1	1
BMP6/FETUA	0.032	0.017	-9999	-0.07	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	0.009	-9999	-0.12	2	2
BMP2-4/FETUA	0.033	0.039	-9999	-0.12	15	15
MAP3K7IP1	0.023	0	-9999	-10000	0	0
GREM1	0.008	0.044	-9999	-0.12	59	59
BMPR2 (homodimer)	0.021	0.014	-9999	-0.12	5	5
GADD34/PP1CA	0.031	0.047	-9999	-0.12	45	45
BMPR1A-1B (homodimer)	-0.011	0.08	-9999	-0.13	157	157
CHRDL1	-0.008	0.054	-9999	-0.12	104	104
ENDOFIN/SMAD1	0.03	0.075	-9999	-0.27	27	27
SMAD6-7/SMURF1/SMAD1	0.05	0.075	-9999	-0.25	27	27
SMAD6/SMURF1	0.023	0.009	-9999	-0.12	2	2
BAMBI	-0.004	0.054	-9999	-0.12	98	98
SMURF2	0.022	0.013	-9999	-0.12	4	4
BMP2-4/CHRDL1	-0.014	0.072	-9999	-0.12	138	138
BMP2-4/GREM1	0.023	0.049	-9999	-0.12	31	31
SMAD7	0.023	0.003	-9999	-10000	0	0
SMAD8A/SMAD8A/SMAD4	0.028	0.052	-9999	-0.36	4	4
SMAD1/SMAD6	0.033	0.072	-9999	-0.26	26	26
TAK1/SMAD6	0.027	0.035	-9999	-0.12	28	28
BMP7	-0.01	0.055	-9999	-0.12	109	109
BMP6	0.02	0.022	-9999	-0.12	14	14
MAP3K7IP2	0.02	0.016	-9999	-0.12	7	7
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1	0.003	0.082	-9999	-0.22	43	43
PPM1A	0.023	0.001	-9999	-10000	0	0
SMAD1/SMURF2	0.031	0.074	-9999	-0.27	26	26
SMAD7/SMURF1	0.031	0.024	-9999	-0.13	12	12
CTDSPL	0.023	0.006	-9999	-0.12	1	1
PPP1CA	0.023	0.002	-9999	-10000	0	0
XIAP	0	0	-9999	-10000	0	0
CTDSP1	0.022	0.011	-9999	-0.12	3	3
PPP1R15A	0.019	0.025	-9999	-0.12	18	18
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS	0.002	0.079	-9999	-0.21	50	50
CHRD	0.023	0.006	-9999	-0.12	1	1
BMPR2	0.021	0.014	-9999	-0.12	5	5
BMP2-4/BMPR2/BMPR1A-1B/RGM	-0.004	0.086	-9999	-0.24	42	42
BMP4	0.009	0.042	-9999	-0.12	54	54
FST	0.004	0.048	-9999	-0.12	74	74
BMP2-4/NOG	0.027	0.047	-9999	-0.12	33	33
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1	-0.023	0.09	-9999	-0.12	222	222

×

IL2 signaling events mediated by PI3K

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.019	0.16	-10000	0	-0.69	21	21
UGCG	-0.001	0.079	-10000	0	-0.73	5	5
AKT1/mTOR/p70S6K/Hsp90/TERT	-0.031	0.16	-10000	0	-0.31	107	107
mol:GTP	0	0.001	-10000	0	-10000	0	0
mol:glucosylceramide	0	0.078	-10000	0	-0.71	5	5
mol:DAG	-0.042	0.2	-10000	0	-0.9	29	29
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.04	0.18	-10000	0	-0.37	104	104
FRAP1	-0.053	0.2	-10000	0	-0.42	106	106
FOXO3	-0.053	0.2	-10000	0	-0.4	111	111
AKT1	-0.059	0.21	-10000	0	-0.44	109	109
GAB2	0.007	0.041	-10000	0	-0.12	52	52
SMPD1	0.006	0.042	-10000	0	-0.52	1	1
SGMS1	-0.029	0.16	-10000	0	-0.68	29	29
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
mol:GDP	-0.005	0.05	-10000	0	-0.13	68	68
CALM1	0.022	0.014	-10000	0	-0.12	5	5
cell proliferation	-0.039	0.16	-10000	0	-0.31	98	98
EIF3A	0.022	0.004	-10000	0	-10000	0	0
PI3K	0.008	0.067	-10000	0	-0.15	68	68
RPS6KB1	-0.03	0.18	-10000	0	-0.8	24	24
mol:sphingomyelin	-0.042	0.2	-10000	0	-0.9	29	29
natural killer cell activation	-0.001	0.003	-10000	0	-0.011	29	29
JAK3	0.022	0.016	-10000	0	-0.065	13	13
PIK3R1	0.015	0.033	-10000	0	-0.1	36	36
JAK1	0.022	0.013	-10000	0	-0.045	12	12
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
MYC	-0.11	0.32	-10000	0	-0.85	83	83
MYB	-0.061	0.28	-10000	0	-1.1	39	39
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	-0.039	0.16	-10000	0	-0.29	132	132
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	-0.007	0.17	-10000	0	-0.76	23	23
mol:PI-3-4-5-P3	-0.037	0.16	-10000	0	-0.28	132	132
Rac1/GDP	0.007	0.051	-10000	0	-0.12	67	67
T cell proliferation	-0.032	0.14	-10000	0	-0.27	123	123
SHC1	0.023	0.004	-10000	0	-10000	0	0
RAC1	0.023	0.002	-10000	0	-10000	0	0
positive regulation of cyclin-dependent protein kinase activity	-0.001	0.018	-10000	0	-0.064	39	39
PRKCZ	-0.033	0.15	-10000	0	-0.27	129	129
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	-0.31	55	55
HSP90AA1	0.023	0.004	-10000	0	-10000	0	0
RELA	0.023	0.009	-10000	0	-0.12	2	2
IL2RA	0.02	0.018	-10000	0	-0.12	9	9
IL2RB	0.019	0.024	-10000	0	-0.086	24	24
TERT	0.023	0	-10000	0	-10000	0	0
E2F1	-0.016	0.12	-10000	0	-0.42	42	42
SOS1	0.017	0.027	-10000	0	-0.12	20	20
RPS6	0.023	0.002	-10000	0	-10000	0	0
mol:cAMP	0	0.009	0.021	65	-10000	0	65
PTPN11	0.021	0.012	-10000	0	-0.12	3	3
IL2RG	-0.001	0.05	-10000	0	-0.11	90	90
actin cytoskeleton organization	-0.032	0.14	-10000	0	-0.27	123	123
GRB2	0.022	0.007	-10000	0	-0.12	1	1
IL2	0.023	0.014	-10000	0	-0.058	11	11
PIK3CA	0.02	0.019	-10000	0	-0.073	15	15
Rac1/GTP	0.02	0.056	-10000	0	-0.11	67	67
LCK	0.022	0.017	-10000	0	-0.067	15	15
BCL2	-0.034	0.17	-10000	0	-0.41	62	62

×

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	-0.006	0.11	-10000	0	-0.28	52	52
adherens junction organization	-0.008	0.12	-10000	0	-0.26	70	70
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.002	0.098	-10000	0	-0.25	51	51
FMN1	-0.003	0.11	-10000	0	-0.25	69	69
mol:IP3	-0.003	0.093	-10000	0	-0.25	48	48
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin	-0.005	0.11	-10000	0	-0.27	67	67
CTNNB1	0.022	0.008	-10000	0	-0.12	1	1
AKT1	0	0.098	-10000	0	-0.26	46	46
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.006	0.13	-10000	0	-0.36	49	49
CTNND1	0.023	0.004	-10000	0	-10000	0	0
mol:PI-4-5-P2	-0.001	0.1	-10000	0	-0.24	68	68
VASP	-0.002	0.11	-10000	0	-0.25	68	68
ZYX	-0.004	0.11	-10000	0	-0.26	67	67
JUB	-0.006	0.11	-10000	0	-0.26	69	69
EGFR(dimer)	-0.001	0.11	-10000	0	-0.26	70	70
E-cadherin/beta catenin-gamma catenin	0.027	0.052	-10000	0	-0.11	63	63
mol:PI-3-4-5-P3	0.003	0.1	-10000	0	-0.28	47	47
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PI3K	0.003	0.11	-10000	0	-0.28	47	47
FYN	-0.012	0.11	-10000	0	-0.27	68	68
mol:Ca2+	-0.003	0.091	-10000	0	-0.25	48	48
JUP	0.019	0.021	-10000	0	-0.12	12	12
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
mol:DAG	-0.003	0.093	-10000	0	-0.25	48	48
CDH1	0.02	0.015	-10000	0	-0.12	6	6
RhoA/GDP	0.002	0.098	-10000	0	-0.24	50	50
establishment of polarity of embryonic epithelium	-0.001	0.1	-10000	0	-0.25	68	68
SRC	0.023	0.008	-10000	0	-0.12	2	2
RAC1	0.023	0.002	-10000	0	-10000	0	0
RHOA	0.023	0.006	-10000	0	-0.12	1	1
EGFR	0.015	0.03	-10000	0	-0.12	25	25
CASR	0	0.087	-10000	0	-0.24	44	44
RhoA/GTP	0.005	0.089	-10000	0	-0.24	43	43
AKT2	-0.001	0.098	-10000	0	-0.25	52	52
actin cable formation	0	0.1	-10000	0	-0.24	68	68
apoptosis	0.005	0.099	0.25	54	-10000	0	54
CTNNA1	0.022	0.01	-10000	0	-0.12	2	2
mol:GDP	-0.006	0.098	-10000	0	-0.25	54	54
PIP5K1A	-0.002	0.11	-10000	0	-0.25	68	68
PLCG1	-0.004	0.095	-10000	0	-0.26	48	48
Rac1/GTP	0.004	0.11	-10000	0	-0.24	71	71
homophilic cell adhesion	0	0.003	-10000	0	-10000	0	0

×

Aurora A signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Aurora A/GADD45A	0	0.075	-10000	0	-0.18	71	71
BIRC5	0.018	0.023	-10000	0	-0.12	15	15
NFKBIA	0.013	0.038	0.11	7	-0.18	15	22
CPEB1	0.02	0.022	-10000	0	-0.12	14	14
AKT1	0.017	0.026	0.11	7	-0.15	6	13
NDEL1	0.023	0.006	-10000	0	-0.12	1	1
Aurora A/BRCA1	-0.007	0.069	-10000	0	-0.16	69	69
NDEL1/TACC3	0.005	0.075	-10000	0	-0.16	77	77
GADD45A	0.014	0.032	-10000	0	-0.12	30	30
GSK3B	0.022	0.013	0.069	15	-0.12	3	18
PAK1/Aurora A	0.003	0.071	-10000	0	-0.17	69	69
MDM2	0.02	0.02	-10000	0	-0.12	11	11
JUB	0.018	0.024	-10000	0	-0.12	16	16
TPX2	0.017	0.017	-10000	0	-0.07	15	15
TP53	-0.064	0.13	-10000	0	-0.25	182	182
DLG7	0.012	0.025	0.11	2	-0.11	8	10
AURKAIP1	0.02	0.021	-10000	0	-0.12	12	12
ARHGEF7	0.023	0.006	-10000	0	-0.12	1	1
G2 phase of mitotic cell cycle	0	0	-10000	0	-10000	0	0
Aurora A/NDEL1/TACC3	0.005	0.08	-10000	0	-0.17	77	77
G2/M transition of mitotic cell cycle	-0.007	0.069	-10000	0	-0.16	69	69
AURKA	-0.005	0.078	0.14	3	-0.2	69	72
AURKB	0.008	0.044	-10000	0	-0.2	19	19
CDC25B	0.006	0.066	-10000	0	-0.25	29	29
G2/M transition checkpoint	-0.002	0.067	-10000	0	-0.15	76	76
mRNA polyadenylation	0.005	0.061	-10000	0	-0.15	69	69
Aurora A/CPEB	0.005	0.061	-10000	0	-0.15	69	69
Aurora A/TACC1/TRAP/chTOG	0.005	0.09	-10000	0	-0.18	79	79
BRCA1	0.015	0.029	-10000	0	-0.12	24	24
centrosome duplication	0.002	0.071	-10000	0	-0.17	69	69
regulation of centrosome cycle	0.005	0.074	-10000	0	-0.16	77	77
spindle assembly	0.004	0.089	-10000	0	-0.18	79	79
TDRD7	0.014	0.031	-10000	0	-0.12	28	28
Aurora A/RasGAP/Survivin	0.003	0.082	-10000	0	-0.16	84	84
CENPA	0.012	0.046	-10000	0	-0.33	9	9
Aurora A/PP2A	0.007	0.068	-10000	0	-0.16	69	69
meiosis	0	0	-10000	0	-10000	0	0
protein catabolic process	-0.026	0.095	-10000	0	-0.25	69	69
negative regulation of DNA binding	-0.064	0.13	-10000	0	-0.25	182	182
prophase	0	0	-10000	0	-10000	0	0
GIT1/beta-PIX	0.034	0.011	-10000	0	-0.07	6	6
RASA1	0.021	0.011	-10000	0	-0.12	3	3
Ajuba/Aurora A	-0.002	0.068	-10000	0	-0.15	76	76
mitotic prometaphase	0.002	0.018	0.072	33	-10000	0	33
proteasomal ubiquitin-dependent protein catabolic process	-0.005	0.077	0.14	3	-0.2	69	72
TACC1	0.014	0.035	-10000	0	-0.12	35	35
TACC3	0.014	0.032	-10000	0	-0.12	29	29
Aurora A/Antizyme1	0.004	0.076	-10000	0	-0.16	77	77
Aurora A/RasGAP	0.004	0.073	-10000	0	-0.18	70	70
OAZ1	0.017	0.025	-10000	0	-0.12	17	17
RAN	0.023	0.002	-10000	0	-10000	0	0
mitosis	0	0	-10000	0	-10000	0	0
PRKACA	0.02	0.019	0.073	5	-0.12	8	13
GIT1	0.022	0.013	-10000	0	-0.12	5	5
GIT1/beta-PIX/PAK1	0.037	0.036	-10000	0	-0.11	21	21
Importin alpha/Importin beta/TPX2	0.017	0.017	-10000	0	-0.07	15	15
PPP2R5D	0.022	0.013	-10000	0	-0.12	5	5
Aurora A/TPX2	-0.004	0.083	-10000	0	-0.2	78	78
PAK1	0.016	0.029	-10000	0	-0.12	24	24
CKAP5	0.021	0.013	-10000	0	-0.12	4	4

×

Ephrin A reverse signaling

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

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

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

×

Arf6 downstream 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
PLAUR	-0.029	0.22	-10000	0	-0.83	39	39
regulation of axonogenesis	-0.005	0.06	0.18	45	-10000	0	45
myoblast fusion	0.001	0.1	0.38	39	-10000	0	39
mol:GTP	-0.001	0.066	-10000	0	-0.22	46	46
regulation of calcium-dependent cell-cell adhesion	-0.006	0.088	0.16	105	-10000	0	105
ARF1/GTP	0.013	0.055	-10000	0	-0.16	47	47
mol:GM1	-0.002	0.049	-10000	0	-0.16	46	46
mol:Choline	0.004	0.052	-10000	0	-0.15	48	48
lamellipodium assembly	-0.007	0.12	-10000	0	-0.41	46	46
MAPK3	0.005	0.087	-10000	0	-0.28	46	46
ARF6/GTP/NME1/Tiam1	0.007	0.089	-10000	0	-0.16	105	105
ARF1	0.018	0.027	-10000	0	-0.12	21	21
ARF6/GDP	-0.001	0.11	-10000	0	-0.38	39	39
ARF1/GDP	0.004	0.1	-10000	0	-0.33	46	46
ARF6	0.016	0.035	-10000	0	-0.12	37	37
RAB11A	0.023	0.007	-10000	0	-0.12	1	1
TIAM1	0.014	0.034	-10000	0	-0.12	29	29
fibronectin binding	0	0	-10000	0	-10000	0	0
MAPK1	0.004	0.088	-10000	0	-0.28	46	46
actin filament bundle formation	-0.006	0.1	0.34	46	-10000	0	46
KALRN	0.002	0.082	-10000	0	-0.29	39	39
RAB11FIP3/RAB11A	0.031	0.023	-10000	0	-0.13	11	11
RhoA/GDP	0.007	0.11	-10000	0	-0.34	46	46
NME1	0.014	0.03	-10000	0	-0.12	23	23
Rac1/GDP	0.007	0.1	-10000	0	-0.34	46	46
substrate adhesion-dependent cell spreading	-0.001	0.065	-10000	0	-0.22	46	46
cortical actin cytoskeleton organization	-0.007	0.12	-10000	0	-0.41	46	46
RAC1	0.023	0.002	-10000	0	-10000	0	0
liver development	-0.001	0.065	-10000	0	-0.22	46	46
ARF6/GTP	-0.001	0.066	-10000	0	-0.22	46	46
RhoA/GTP	0.015	0.057	-10000	0	-0.17	46	46
mol:GDP	-0.005	0.11	-10000	0	-0.36	46	46
ARF6/GTP/RAB11FIP3/RAB11A	0.028	0.052	-10000	0	-0.13	52	52
RHOA	0.023	0.006	-10000	0	-0.12	1	1
PLD1	0	0.06	-10000	0	-0.18	46	46
RAB11FIP3	0.023	0.01	-10000	0	-0.12	3	3
tube morphogenesis	-0.007	0.12	-10000	0	-0.41	46	46
ruffle organization	0.005	0.06	-10000	0	-0.18	45	45
regulation of epithelial cell migration	-0.001	0.065	-10000	0	-0.22	46	46
PLD2	0.01	0.051	-10000	0	-0.16	47	47
PIP5K1A	0.005	0.06	-10000	0	-0.18	45	45
mol:Phosphatidic acid	0.004	0.052	-10000	0	-0.15	48	48
Rac1/GTP	-0.008	0.12	-10000	0	-0.41	46	46

×

ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K4	-0.012	0.11	-10000	0	-0.21	120	120
BAG4	0.022	0.012	-10000	0	-0.12	4	4
BAD	0.007	0.036	-10000	0	-0.11	20	20
NFKBIA	0.016	0.027	-10000	0	-0.12	21	21
BIRC3	-0.005	0.052	-10000	0	-0.12	93	93
BAX	0.007	0.036	-10000	0	-0.11	19	19
EnzymeConsortium:3.1.4.12	0	0.027	-10000	0	-0.047	121	121
IKBKB	-0.009	0.11	-10000	0	-0.2	121	121
MAP2K2	0.013	0.036	-10000	0	-0.097	28	28
MAP2K1	0.015	0.033	-10000	0	-0.098	21	21
SMPD1	0.005	0.028	-10000	0	-0.092	17	17
GO:0005551	0	0	-10000	0	-10000	0	0
FADD/Caspase 8	-0.005	0.12	-10000	0	-0.2	121	121
MAP2K4	0.007	0.039	-10000	0	-0.1	34	34
protein ubiquitination	-0.012	0.11	-10000	0	-0.2	121	121
EnzymeConsortium:2.7.1.37	0.016	0.034	-10000	0	-0.095	22	22
response to UV	0	0	-10000	0	-0.001	12	12
RAF1	0.011	0.034	-10000	0	-0.1	24	24
CRADD	0.023	0.009	-10000	0	-0.12	2	2
mol:ceramide	0.003	0.038	-10000	0	-0.099	31	31
I-kappa-B-alpha/RELA/p50/ubiquitin	0.018	0.041	-10000	0	-0.12	41	41
MADD	0.023	0.006	-10000	0	-0.12	1	1
MAP3K1	0.004	0.041	-10000	0	-0.12	31	31
TRADD	0.023	0.006	-10000	0	-0.12	1	1
RELA/p50	0.023	0.009	-10000	0	-0.12	2	2
MAPK3	0.017	0.035	-10000	0	-0.099	22	22
MAPK1	0.016	0.037	-10000	0	-0.1	26	26
p50/RELA/I-kappa-B-alpha	0.018	0.05	-10000	0	-0.14	41	41
FADD	-0.01	0.11	-10000	0	-0.2	120	120
KSR1	0.008	0.035	-10000	0	-0.11	21	21
MAPK8	0.008	0.042	-10000	0	-0.11	40	40
TRAF2	0.024	0.001	-10000	0	-10000	0	0
response to radiation	0	0	-10000	0	-10000	0	0
CHUK	-0.012	0.11	-10000	0	-0.2	121	121
TNF R/SODD	0.027	0.033	-10000	0	-0.11	29	29
TNF	0.021	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	121	121
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD	-0.014	0.12	-10000	0	-0.22	120	120
RELA	0.023	0.009	-10000	0	-0.12	2	2
RIPK1	0.023	0.011	-10000	0	-0.12	3	3
AIFM1	0.001	0.044	0.097	1	-0.12	39	40
TNF/TNF R/SODD	0.038	0.034	-10000	0	-0.11	20	20
TNFRSF1A	0.021	0.016	-10000	0	-0.12	7	7
response to heat	0	0	-10000	0	-10000	0	0
CASP8	0.005	0.12	-10000	0	-0.67	17	17
NSMAF	-0.011	0.11	-10000	0	-0.2	120	120
response to hydrogen peroxide	0	0	-10000	0	-0.001	12	12
BCL2	0.016	0.031	-10000	0	-0.12	28	28

×

Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
adherens junction organization	-0.001	0.089	-10000	0	-0.24	42	42
epithelial cell differentiation	0.028	0.06	-10000	0	-0.12	71	71
CYFIP2	0.02	0.017	-10000	0	-0.12	8	8
ENAH	0.008	0.057	-10000	0	-0.14	50	50
EGFR	0.015	0.03	-10000	0	-0.12	25	25
EPHA2	0.02	0.021	-10000	0	-0.12	13	13
MYO6	0.009	0.058	-10000	0	-0.12	71	71
CTNNB1	0.022	0.007	-10000	0	-0.12	1	1
ABI1/Sra1/Nap1	0.03	0.05	-10000	0	-0.12	54	54
AQP5	-0.059	0.15	-10000	0	-0.31	127	127
CTNND1	0.023	0.004	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.014	0.05	-10000	0	-0.11	71	71
regulation of calcium-dependent cell-cell adhesion	0.013	0.051	-10000	0	-0.11	71	71
EGF	0.02	0.021	-10000	0	-0.12	13	13
NCKAP1	0.023	0.004	-10000	0	-10000	0	0
AQP3	0.011	0.077	-10000	0	-0.28	25	25
cortical microtubule organization	0.028	0.06	-10000	0	-0.12	71	71
GO:0000145	0.007	0.046	-10000	0	-0.1	71	71
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.033	0.062	-10000	0	-0.12	71	71
MLLT4	0.014	0.032	-10000	0	-0.12	30	30
ARF6/GDP	-0.023	0.051	-10000	0	-0.17	46	46
ARF6	0.023	0.003	-10000	0	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	0.029	0.063	-10000	0	-0.11	77	77
mol:Ca2+	0	0	-10000	0	-10000	0	0
VASP	0.014	0.06	-10000	0	-0.19	32	32
PVRL2	0.019	0.023	-10000	0	-0.12	15	15
ZYX	0.01	0.055	-10000	0	-0.12	71	71
ARF6/GTP	0.034	0.064	-10000	0	-0.15	23	23
CDH1	0.021	0.015	-10000	0	-0.12	6	6
EGFR/EGFR/EGF/EGF	0.015	0.063	-10000	0	-0.19	25	25
RhoA/GDP	0.03	0.059	-10000	0	-0.21	17	17
actin cytoskeleton organization	0.007	0.06	-10000	0	-0.13	70	70
IGF-1R heterotetramer	0.013	0.031	-10000	0	-0.12	28	28
GIT1	0.022	0.013	-10000	0	-0.12	5	5
IGF1R	0.013	0.031	-10000	0	-0.12	28	28
IGF1	0.007	0.045	-10000	0	-0.12	62	62
DIAPH1	-0.022	0.2	-10000	0	-0.56	71	71
Wnt receptor signaling pathway	-0.028	0.06	0.12	71	-10000	0	71
RHOA	0.023	0.006	-10000	0	-0.12	1	1
RhoA/GTP	-0.022	0.05	-10000	0	-0.17	45	45
CTNNA1	0.022	0.01	-10000	0	-0.12	2	2
VCL	0.007	0.062	-10000	0	-0.13	70	70
EFNA1	0.014	0.031	-10000	0	-0.12	28	28
LPP	0.011	0.055	-10000	0	-0.19	24	24
Ephrin A1/EPHA2	0.011	0.064	-10000	0	-0.18	31	31
SEC6/SEC8	-0.021	0.05	-10000	0	-0.19	35	35
MGAT3	0.013	0.052	-10000	0	-0.11	71	71
HGF/MET	-0.006	0.072	-10000	0	-0.18	47	47
HGF	0.02	0.022	-10000	0	-0.12	14	14
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN	-0.001	0.089	-10000	0	-0.24	42	42
actin cable formation	0.011	0.08	-10000	0	-0.2	45	45
KIAA1543	0.012	0.05	-10000	0	-0.18	24	24
KIFC3	0.014	0.051	-10000	0	-0.11	71	71
NCK1	0.02	0.019	-10000	0	-0.12	9	9
EXOC3	0.023	0.009	-10000	0	-0.12	2	2
ACTN1	0.012	0.058	-10000	0	-0.12	71	71
NCK1/GIT1	0.022	0.043	-10000	0	-0.14	32	32
mol:GDP	0.028	0.06	-10000	0	-0.12	71	71
EXOC4	0.023	0.007	-10000	0	-0.12	1	1
STX4	0.013	0.052	-10000	0	-0.11	71	71
PIP5K1C	0.014	0.051	-10000	0	-0.11	71	71
LIMA1	0.019	0.023	-10000	0	-0.12	14	14
ABI1	0.022	0.009	-10000	0	-0.12	2	2
ROCK1	0.01	0.061	-10000	0	-0.16	41	41
adherens junction assembly	0.021	0.059	-10000	0	-0.23	14	14
IGF-1R heterotetramer/IGF1	-0.002	0.071	-10000	0	-0.17	50	50
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.012	0.054	-10000	0	-0.15	45	45
MET	0.001	0.047	-10000	0	-0.12	71	71
PLEKHA7	0.013	0.053	-10000	0	-0.11	71	71
mol:GTP	0.027	0.062	-10000	0	-0.11	77	77
establishment of epithelial cell apical/basal polarity	0.012	0.063	-10000	0	-0.18	37	37
cortical actin cytoskeleton stabilization	-0.001	0.089	-10000	0	-0.24	42	42
regulation of cell-cell adhesion	0.007	0.06	-10000	0	-0.13	70	70
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton	-0.001	0.089	-10000	0	-0.24	42	42

×

Reelin signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDK5R1/CDK5	0.021	0.042	-9999	-0.14	25	25
VLDLR	0.01	0.038	-9999	-0.12	42	42
CRKL	0.023	0.009	-9999	-0.12	2	2
LRPAP1	0.018	0.023	-9999	-0.12	15	15
FYN	0.012	0.037	-9999	-0.12	40	40
ITGA3	0.013	0.034	-9999	-0.12	33	33
RELN/VLDLR/Fyn	-0.005	0.073	-9999	-0.13	102	102
MAPK8IP1/MKK7/MAP3K11/JNK1	0.056	0.042	-9999	-0.093	30	30
AKT1	-0.015	0.078	-9999	-0.15	113	113
MAP2K7	0.022	0.012	-9999	-0.12	4	4
RAPGEF1	0.023	0	-9999	-10000	0	0
DAB1	0.023	0.01	-9999	-0.12	3	3
RELN/LRP8/DAB1	0.025	0.042	-9999	-0.11	21	21
LRPAP1/LRP8	0.015	0.054	-9999	-0.15	45	45
RELN/LRP8/DAB1/Fyn	0.02	0.055	-9999	-0.097	62	62
DAB1/alpha3/beta1 Integrin	-0.006	0.069	-9999	-0.14	61	61
long-term memory	0.016	0.062	-9999	-0.13	21	21
DAB1/LIS1	0.016	0.067	-9999	-0.14	25	25
DAB1/CRLK/C3G	0.012	0.057	-9999	-0.13	21	21
PIK3CA	0.02	0.017	-9999	-0.12	7	7
DAB1/NCK2	0.019	0.067	-9999	-0.14	22	22
ARHGEF2	0.023	0.009	-9999	-0.12	2	2
mol:Src family inhibitors PP1 and PP2	0	0	-9999	-10000	0	0
GRIN2A	0.001	0.051	-9999	-0.12	86	86
CDK5R1	0.023	0.006	-9999	-0.12	1	1
RELN	0	0.053	-9999	-0.12	91	91
PIK3R1	0.015	0.031	-9999	-0.12	28	28
RELN/LRP8/Fyn	0.01	0.06	-9999	-0.12	61	61
GRIN2A/RELN/LRP8/DAB1/Fyn	0.015	0.066	-9999	-0.096	88	88
MAPK8	0.021	0.015	-9999	-0.12	6	6
RELN/VLDLR/DAB1	0.011	0.055	-9999	-0.1	71	71
ITGB1	0.021	0.015	-9999	-0.12	6	6
MAP1B	-0.006	0.056	-9999	-0.11	97	97
RELN/LRP8	0.015	0.058	-9999	-0.12	53	53
GRIN2B/RELN/LRP8/DAB1/Fyn	0.029	0.06	-9999	-0.093	64	64
PI3K	0.007	0.065	-9999	-0.16	63	63
mol:PP2	0	0	-9999	-10000	0	0
alpha3/beta1 Integrin	0.004	0.064	-9999	-0.14	74	74
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	0.02	0.02	-9999	-0.12	11	11
NCK2	0.023	0.006	-9999	-0.12	1	1
neuron differentiation	0.018	0.056	-9999	-0.18	23	23
neuron adhesion	-0.004	0.061	-9999	-0.13	68	68
LRP8	0.02	0.021	-9999	-0.12	12	12
GSK3B	-0.011	0.074	-9999	-0.14	114	114
RELN/VLDLR/DAB1/Fyn	0.007	0.066	-9999	-0.11	103	103
MAP3K11	0.022	0.013	-9999	-0.12	5	5
RELN/VLDLR/DAB1/P13K	-0.018	0.083	-9999	-0.16	112	112
CDK5	0.015	0.032	-9999	-0.12	30	30
MAPT	0.01	0.016	-9999	-0.093	5	5
neuron migration	-0.013	0.079	-9999	-0.19	53	53
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1	0.018	0.056	-9999	-0.18	23	23
RELN/VLDLR	0.008	0.07	-9999	-0.11	121	121

×

HIF-2-alpha transcription factor network

Figure 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
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	-0.19	81	81
EPO	0.004	0.18	-10000	0	-0.39	44	44
FIH (dimer)	0.023	0.013	-10000	0	-0.12	1	1
APEX1	0.02	0.026	-10000	0	-0.12	11	11
SERPINE1	-0.014	0.19	-10000	0	-0.38	60	60
FLT1	-0.022	0.22	-10000	0	-0.75	43	43
ADORA2A	-0.01	0.17	-10000	0	-0.37	55	55
germ cell development	-0.018	0.19	-10000	0	-0.37	78	78
SLC11A2	-0.011	0.19	-10000	0	-0.39	64	64
BHLHE40	-0.013	0.18	-10000	0	-0.36	68	68
HIF1AN	0.023	0.013	-10000	0	-0.12	1	1
HIF2A/ARNT/SIRT1	0.012	0.14	-10000	0	-0.27	55	55
ETS1	0.027	0.036	-10000	0	-0.11	34	34
CITED2	0.025	0.079	-10000	0	-0.86	3	3
KDR	-0.022	0.22	-10000	0	-0.74	43	43
PGK1	-0.014	0.2	-10000	0	-0.4	71	71
SIRT1	0.023	0.003	-10000	0	-10000	0	0
response to hypoxia	0	0	-10000	0	-10000	0	0
HIF2A/ARNT	0.022	0.23	-10000	0	-0.43	55	55
EPAS1	-0.009	0.11	-10000	0	-0.21	90	90
SP1	0.016	0.035	-10000	0	-0.077	60	60
ABCG2	-0.007	0.19	-10000	0	-0.39	57	57
EFNA1	-0.02	0.2	-10000	0	-0.4	79	79
FXN	-0.011	0.17	-10000	0	-0.38	52	52
POU5F1	-0.02	0.2	-10000	0	-0.38	78	78
neuron apoptosis	-0.021	0.23	0.42	55	-10000	0	55
EP300	0.022	0.009	-10000	0	-0.12	2	2
EGLN3	-0.001	0.051	-10000	0	-0.12	87	87
EGLN2	0.023	0.014	-10000	0	-0.12	2	2
EGLN1	0.023	0.014	-10000	0	-0.12	2	2
VHL/Elongin B/Elongin C	0.041	0.031	-10000	0	-0.12	17	17
VHL	0.021	0.016	-10000	0	-0.12	7	7
ARNT	0.023	0.021	-10000	0	-0.12	4	4
SLC2A1	-0.024	0.19	-10000	0	-0.4	70	70
TWIST1	-0.01	0.17	-10000	0	-0.38	53	53
ELK1	0.028	0.018	-10000	0	-0.1	9	9
HIF2A/ARNT/Cbp/p300	0.008	0.15	-10000	0	-0.28	58	58
VEGFA	-0.013	0.2	-10000	0	-0.41	63	63
CREBBP	0.021	0.015	-10000	0	-0.12	6	6

×

FoxO family signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G6PC	0.022	0.061	-10000	0	-0.41	1	1
PLK1	-0.15	0.36	-10000	0	-0.91	74	74
CDKN1B	-0.052	0.19	-10000	0	-0.36	113	113
FOXO3	-0.13	0.32	-10000	0	-0.6	133	133
KAT2B	-0.011	0.027	-10000	0	-0.045	197	197
FOXO1/SIRT1	0.024	0.066	-10000	0	-0.24	15	15
CAT	-0.16	0.38	-10000	0	-0.92	83	83
CTNNB1	0.022	0.007	-10000	0	-0.12	1	1
AKT1	0.009	0.038	-10000	0	-0.062	58	58
FOXO1	0.015	0.066	-10000	0	-0.27	11	11
MAPK10	0.013	0.042	-10000	0	-0.1	39	39
mol:GTP	0	0.003	-10000	0	-10000	0	0
FOXO4	0.011	0.13	-10000	0	-0.36	36	36
response to oxidative stress	-0.008	0.029	-10000	0	-0.052	105	105
FOXO3A/SIRT1	-0.14	0.3	-10000	0	-0.56	145	145
XPO1	0.022	0.01	-10000	0	-0.12	2	2
EP300	0.024	0.01	-10000	0	-0.12	2	2
BCL2L11	0.005	0.086	-10000	0	-1.3	2	2
FOXO1/SKP2	0.021	0.07	-10000	0	-0.24	20	20
mol:GDP	-0.008	0.029	-10000	0	-0.052	105	105
RAN	0.024	0.003	-10000	0	-10000	0	0
GADD45A	-0.083	0.27	-10000	0	-0.83	49	49
YWHAQ	0.023	0.003	-10000	0	-10000	0	0
FOXO1/14-3-3 family	0.041	0.085	-10000	0	-0.27	20	20
MST1	0.007	0.034	-10000	0	-0.053	57	57
CSNK1D	0.023	0.001	-10000	0	-10000	0	0
CSNK1E	0.022	0.015	-10000	0	-0.12	6	6
FOXO4/14-3-3 family	0.013	0.12	-10000	0	-0.26	59	59
YWHAB	0.023	0.007	-10000	0	-0.12	1	1
MAPK8	0.016	0.041	-10000	0	-0.11	31	31
MAPK9	0.016	0.041	-10000	0	-0.12	27	27
YWHAG	0.02	0.021	-10000	0	-0.12	13	13
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
YWHAZ	0.023	0.003	-10000	0	-10000	0	0
SIRT1	0.02	0.008	0.066	2	-10000	0	2
SOD2	-0.092	0.3	-10000	0	-0.72	77	77
RBL2	-0.079	0.26	-10000	0	-0.74	39	39
RAL/GDP	0.019	0.043	-10000	0	-0.13	26	26
CHUK	0.007	0.034	-10000	0	-0.058	45	45
Ran/GTP	0.017	0.014	-10000	0	-0.14	3	3
CSNK1G2	0.023	0.01	-10000	0	-0.12	3	3
RAL/GTP	0.022	0.044	-10000	0	-0.12	26	26
CSNK1G1	0.023	0.008	-10000	0	-0.12	2	2
FASLG	0.007	0.067	-10000	0	-1.2	1	1
SKP2	0.018	0.024	-10000	0	-0.12	16	16
USP7	0.02	0.02	-10000	0	-0.12	10	10
IKBKB	0.007	0.036	-10000	0	-0.052	75	75
CCNB1	-0.18	0.42	-10000	0	-0.96	103	103
FOXO1-3a-4/beta catenin	-0.037	0.21	-10000	0	-0.39	91	91
proteasomal ubiquitin-dependent protein catabolic process	0.021	0.069	-10000	0	-0.24	20	20
CSNK1A1	0.022	0.007	-10000	0	-0.12	1	1
SGK1	-0.011	0.027	-10000	0	-0.045	197	197
CSNK1G3	0.022	0.007	-10000	0	-0.12	1	1
Ran/GTP/Exportin 1	0.027	0.032	-10000	0	-0.12	24	24
ZFAND5	0.019	0.12	-10000	0	-0.53	9	9
SFN	0.014	0.031	-10000	0	-0.12	28	28
CDK2	0.022	0.023	-10000	0	-0.12	14	14
FOXO3A/14-3-3	-0.006	0.13	-10000	0	-0.32	51	51
CREBBP	0.025	0.016	-10000	0	-0.12	6	6
FBXO32	-0.27	0.51	-10000	0	-1.1	152	152
BCL6	-0.12	0.34	-10000	0	-0.82	78	78
RALB	0.023	0.008	-10000	0	-0.12	1	1
RALA	0.023	0.009	-10000	0	-0.12	2	2
YWHAH	0.021	0.015	-10000	0	-0.12	6	6

×

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

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
BAG4	0.022	0.012	-9999	-0.12	4	4
Caspase 8 (4 units)	0.023	0.085	-9999	-0.24	35	35
NEF	0.005	0.007	-9999	-0.066	5	5
NFKBIA	-0.001	0.039	-9999	-0.073	88	88
BIRC3	-0.058	0.13	-9999	-0.21	207	207
CYCS	0.013	0.071	-9999	-0.22	32	32
RIPK1	0.022	0.011	-9999	-0.12	3	3
CD247	0.028	0.008	-9999	-0.054	5	5
MAP2K7	0.018	0.092	-9999	-0.36	20	20
protein ubiquitination	0.021	0.067	-9999	-0.17	35	35
CRADD	0.023	0.009	-9999	-0.12	2	2
DAXX	0.022	0.012	-9999	-0.12	4	4
FAS	0.016	0.025	-9999	-0.12	17	17
BID	0.02	0.065	-9999	-0.24	30	30
NF-kappa-B/RelA/I kappa B alpha	-0.021	0.11	-9999	-0.18	148	148
TRADD	0.023	0.006	-9999	-0.12	1	1
MAP3K5	0.018	0.025	-9999	-0.12	17	17
CFLAR	0.022	0.011	-9999	-0.12	3	3
FADD	0.023	0.009	-9999	-0.12	2	2
NF-kappa-B/RelA/I kappa B alpha/ubiquitin	-0.021	0.11	-9999	-0.18	148	148
MAPK8	0.019	0.09	-9999	-0.34	20	20
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	-0.23	35	35
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD	0.02	0.075	-9999	-0.2	36	36
CHUK	0.021	0.07	-9999	-0.19	35	35
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8	0.038	0.069	-9999	-0.11	85	85
TCRz/NEF	0.029	0.014	-9999	-0.1	6	6
TNF	0.02	0.02	-9999	-0.12	11	11
FASLG	0.029	0.02	-9999	-0.15	6	6
NFKB1	0.004	0.031	-9999	-0.055	87	87
TNFR1A/BAG4/TNF-alpha	0.038	0.034	-9999	-0.11	20	20
CASP6	-0.041	0.21	-9999	-0.53	80	80
CASP7	-0.059	0.19	-9999	-0.41	119	119
RELA	0.004	0.032	-9999	-0.058	68	68
CASP2	0.023	0.009	-9999	-0.12	2	2
CASP3	-0.06	0.2	-9999	-0.41	120	120
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	-0.19	36	36
APAF-1/Caspase 9	-0.028	0.12	-9999	-0.22	125	125
BCL2	0.019	0.087	-9999	-0.31	23	23

×

ErbB2/ErbB3 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
USP8	0.012	0.012	-10000	0	-0.057	15	15
RAS family/GTP	0.005	0.084	-10000	0	-0.18	52	52
NFATC4	0.001	0.053	0.18	6	-0.098	87	93
ERBB2IP	0.02	0.019	-10000	0	-0.12	10	10
HSP90 (dimer)	0.023	0.004	-10000	0	-10000	0	0
mammary gland morphogenesis	0	0.066	0.19	7	-0.12	86	93
JUN	0.004	0.071	0.18	1	-10000	0	1
HRAS	0.023	0.006	-10000	0	-0.12	1	1
DOCK7	-0.005	0.066	0.19	6	-0.13	90	96
ErbB2/ErbB3/neuregulin 1 beta/SHC	0.018	0.06	0.21	7	-0.1	87	94
AKT1	0.01	0.012	-10000	0	-0.077	10	10
BAD	0.013	0.011	-10000	0	-0.056	13	13
MAPK10	0.002	0.045	0.14	6	-0.1	41	47
mol:GTP	-0.001	0.001	-10000	0	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta	0.001	0.07	0.2	7	-0.13	84	91
RAF1	-0.004	0.084	-10000	0	-0.18	59	59
ErbB2/ErbB3/neuregulin 2	0.005	0.054	-10000	0	-0.11	87	87
STAT3	-0.005	0.18	-10000	0	-0.93	21	21
cell migration	0.001	0.052	0.16	5	-0.12	40	45
mol:PI-3-4-5-P3	0	0.001	-10000	0	-10000	0	0
cell proliferation	-0.062	0.21	-10000	0	-0.52	67	67
FOS	-0.071	0.2	-10000	0	-0.41	128	128
NRAS	0.021	0.011	-10000	0	-0.12	3	3
mol:Ca2+	0	0.066	0.19	7	-0.12	86	93
MAPK3	-0.039	0.17	-10000	0	-0.47	47	47
MAPK1	-0.041	0.17	-10000	0	-0.47	51	51
JAK2	-0.005	0.065	0.19	6	-0.13	90	96
NF2	0.013	0.046	-10000	0	-0.73	2	2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1	0.012	0.053	0.13	8	-0.17	30	38
NRG1	0.021	0.017	-10000	0	-0.12	8	8
GRB2/SOS1	0.02	0.046	-10000	0	-0.15	31	31
MAPK8	-0.011	0.092	0.18	6	-0.19	98	104
MAPK9	0.003	0.044	0.14	5	-0.11	35	40
ERBB2	0	0.048	0.27	15	-0.092	8	23
ERBB3	0.013	0.031	-10000	0	-0.12	27	27
SHC1	0.023	0.001	-10000	0	-10000	0	0
RAC1	0.023	0.002	-10000	0	-10000	0	0
apoptosis	-0.009	0.017	0.13	4	-10000	0	4
STAT3 (dimer)	-0.005	0.18	-10000	0	-0.9	21	21
RNF41	0.013	0.012	-10000	0	-0.046	17	17
FRAP1	0.013	0.011	-10000	0	-0.056	14	14
RAC1-CDC42/GTP	-0.005	0.05	-10000	0	-0.12	47	47
ErbB2/ErbB2/HSP90 (dimer)	0.012	0.028	-10000	0	-0.13	15	15
CHRNA1	-0.025	0.14	-10000	0	-0.35	44	44
myelination	0	0.053	0.18	6	-0.12	35	41
PPP3CB	-0.001	0.058	0.18	6	-0.11	85	91
KRAS	0.014	0.034	-10000	0	-0.12	33	33
RAC1-CDC42/GDP	0.017	0.074	-10000	0	-0.14	82	82
NRG2	0.023	0.006	-10000	0	-0.12	1	1
mol:GDP	0.012	0.052	0.13	8	-0.17	30	38
SOS1	0.017	0.027	-10000	0	-0.12	20	20
MAP2K2	-0.01	0.09	-10000	0	-0.18	74	74
SRC	0.023	0.008	-10000	0	-0.12	2	2
mol:cAMP	0	0.001	-10000	0	-10000	0	0
PTPN11	-0.001	0.062	0.19	5	-0.12	86	91
MAP2K1	-0.041	0.16	-10000	0	-0.39	58	58
heart morphogenesis	0	0.066	0.19	7	-0.12	86	93
RAS family/GDP	0.012	0.084	-10000	0	-0.18	49	49
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PRKACA	0.01	0.048	-10000	0	-0.77	2	2
CHRNE	0.01	0.019	-10000	0	-10000	0	0
HSP90AA1	0.023	0.004	-10000	0	-10000	0	0
activation of caspase activity	-0.01	0.012	0.077	10	-10000	0	10
nervous system development	0	0.066	0.19	7	-0.12	86	93
CDC42	0.023	0.002	-10000	0	-10000	0	0

×

Syndecan-2-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Syndecan-2/Fibronectin	-0.018	0.069	-9999	-0.16	81	81
EPHB2	0.02	0.02	-9999	-0.12	11	11
Syndecan-2/TACI	0.014	0.042	-9999	-0.11	46	46
LAMA1	0	0.052	-9999	-0.12	90	90
Syndecan-2/alpha2 ITGB1	-0.005	0.079	-9999	-0.16	62	62
HRAS	0.023	0.006	-9999	-0.12	1	1
Syndecan-2/CASK	-0.001	0.038	-9999	-0.11	46	46
ITGA5	0.013	0.036	-9999	-0.12	38	38
BAX	0.025	0.02	-9999	-10000	0	0
EPB41	0.02	0.018	-9999	-0.12	9	9
positive regulation of cell-cell adhesion	0.004	0.049	-9999	-0.1	83	83
LAMA3	0.006	0.043	-9999	-0.12	57	57
EZR	0	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
CAV2	0.01	0.038	-9999	-0.12	44	44
Syndecan-2/MMP2	-0.015	0.066	-9999	-0.16	69	69
RP11-540L11.1	0	0	-9999	-10000	0	0
alpha2 ITGB1	0.008	0.06	-9999	-0.11	104	104
dendrite morphogenesis	0.011	0.048	-9999	-0.12	48	48
Syndecan-2/GM-CSF	0.014	0.043	-9999	-0.11	47	47
determination of left/right symmetry	0.012	0.025	-9999	-10000	0	0
Syndecan-2/PKC delta	0.01	0.048	-9999	-0.12	53	53
GNB2L1	0.023	0.003	-9999	-10000	0	0
MAPK3	0.014	0.038	-9999	-0.094	47	47
MAPK1	0.013	0.039	-9999	-0.096	47	47
Syndecan-2/RACK1	0.025	0.042	-9999	-0.087	53	53
NF1	0.018	0.02	-9999	-0.12	10	10
FGFR/FGF/Syndecan-2	0.012	0.025	-9999	-10000	0	0
ITGA2	0.011	0.037	-9999	-0.12	41	41
MAPK8	0.02	0.023	-9999	-10000	0	0
Syndecan-2/alpha2/beta1 Integrin	0.006	0.07	-9999	-0.16	35	35
Syndecan-2/Kininogen	0.014	0.043	-9999	-0.11	46	46
ITGB1	0.021	0.015	-9999	-0.12	6	6
SRC	0.018	0.036	-9999	-0.1	5	5
Syndecan-2/CASK/Protein 4.1	0.009	0.045	-9999	-0.1	61	61
extracellular matrix organization	0.01	0.048	-9999	-0.12	52	52
actin cytoskeleton reorganization	-0.018	0.068	-9999	-0.16	81	81
Syndecan-2/Caveolin-2/Ras	0.01	0.061	-9999	-0.11	97	97
Syndecan-2/Laminin alpha3	0	0.058	-9999	-0.14	60	60
Syndecan-2/RasGAP	0.028	0.05	-9999	-0.15	7	7
alpha5/beta1 Integrin	0.017	0.048	-9999	-0.14	33	33
PRKCD	0.02	0.018	-9999	-0.12	8	8
Syndecan-2 dimer	0.011	0.048	-9999	-0.12	48	48
GO:0007205	0.004	0	-9999	-10000	0	0
DNA mediated transformation	0	0	-9999	-10000	0	0
Syndecan-2/RasGAP/Src	0.027	0.047	-9999	-0.14	7	7
RHOA	0.023	0.006	-9999	-0.12	1	1
SDCBP	0.021	0.01	-9999	-0.12	2	2
TNFRSF13B	0.023	0	-9999	-10000	0	0
RASA1	0.021	0.011	-9999	-0.12	3	3
alpha2/beta1 Integrin	0.008	0.06	-9999	-0.11	104	104
Syndecan-2/Synbindin	0.007	0.051	-9999	-0.12	55	55
TGFB1	0.019	0.023	-9999	-0.12	14	14
CASP3	0.01	0.043	-9999	-0.1	53	53
FN1	-0.012	0.055	-9999	-0.12	115	115
Syndecan-2/IL8	0.001	0.055	-9999	-0.13	61	61
SDC2	0.012	0.025	-9999	-10000	0	0
KNG1	0.023	0.01	-9999	-0.12	3	3
Syndecan-2/Neurofibromin	0.008	0.05	-9999	-0.13	51	51
TRAPPC4	0.016	0.025	-9999	-0.12	17	17
CSF2	0.023	0.008	-9999	-0.12	2	2
Syndecan-2/TGFB1	0.01	0.048	-9999	-0.12	52	52
Syndecan-2/Syntenin/PI-4-5-P2	0.005	0.05	-9999	-0.1	83	83
Syndecan-2/Ezrin	0.012	0.04	-9999	-0.097	50	50
PRKACA	0.008	0.045	-9999	-0.11	52	52
angiogenesis	0.001	0.055	-9999	-0.13	61	61
MMP2	-0.015	0.059	-9999	-0.12	131	131
IL8	0.004	0.047	-9999	-0.12	70	70
calcineurin-NFAT signaling pathway	0.014	0.042	-9999	-0.11	46	46

×

Retinoic acid receptors-mediated signaling

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
HDAC1	0.019	0.019	-10000	0	-0.12	10	10
HDAC3	0.023	0.002	-10000	0	-10000	0	0
VDR	0.019	0.022	-10000	0	-0.12	13	13
Cbp/p300/PCAF	0.02	0.044	-10000	0	-0.13	43	43
EP300	0.022	0.009	-10000	0	-0.12	2	2
RARs/AIB1/Cbp/p300/PCAF/9cRA	0	0.093	-10000	0	-0.25	47	47
KAT2B	0	0	-10000	0	-10000	0	0
MAPK14	0.023	0.007	-10000	0	-0.12	1	1
AKT1	0.019	0.089	0.17	80	-0.21	28	108
RAR alpha/9cRA/Cyclin H	-0.015	0.12	-10000	0	-0.22	98	98
mol:9cRA	0	0	-10000	0	-10000	0	0
RARs/Src-1/Cbp/p300/PCAF/9cRA	0.001	0.081	-10000	0	-0.2	58	58
CDC2	0.006	0.04	-10000	0	-0.12	48	48
response to UV	-0.001	0.007	-10000	0	-10000	0	0
RAR alpha/Jnk1	0.007	0.061	-10000	0	-0.16	42	42
NCOR2	0.019	0.023	-10000	0	-0.12	15	15
VDR/VDR/Vit D3	0.009	0.035	-10000	0	-0.12	36	36
RXRs/RARs/NRIP1/9cRA	-0.041	0.19	-10000	0	-0.49	69	69
NCOA2	0.021	0.013	-10000	0	-0.12	4	4
NCOA3	0.021	0.011	-10000	0	-0.12	3	3
NCOA1	0.022	0.009	-10000	0	-0.12	2	2
VDR/VDR/DNA	0.019	0.022	-10000	0	-0.12	13	13
RARG	0.02	0.016	-10000	0	-0.12	6	6
RAR gamma1/9cRA	0.024	0.028	-10000	0	-0.12	17	17
MAPK3	0.021	0.015	-10000	0	-0.12	5	5
MAPK1	0.021	0.016	-10000	0	-0.12	7	7
MAPK8	0.019	0.018	-10000	0	-0.12	6	6
mol:Vit D3	0	0	-10000	0	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.034	0.14	-10000	0	-0.32	86	86
RARA	0.01	0.055	-10000	0	-0.19	26	26
negative regulation of phosphoinositide 3-kinase cascade	0	0	-10000	0	-10000	0	0
RARs/TIF2/Cbp/p300/PCAF/9cRA	0	0.086	-10000	0	-0.21	60	60
PRKCA	0.008	0.043	-10000	0	-0.09	77	77
RXRs/RARs/NRIP1/9cRA/HDAC1	-0.06	0.2	-10000	0	-0.55	70	70
RXRG	-0.005	0.069	-10000	0	-0.2	45	45
RXRA	-0.034	0.11	-10000	0	-0.22	92	92
RXRB	0.005	0.062	-10000	0	-0.19	37	37
VDR/Vit D3/DNA	0.009	0.035	-10000	0	-0.12	36	36
RBP1	0.01	0.035	-10000	0	-0.12	36	36
CRBP1/9-cic-RA	-0.018	0.064	-10000	0	-0.13	138	138
RARB	0.012	0.036	-10000	0	-0.076	59	59
PRKCG	0.018	0.024	-10000	0	-0.052	50	50
MNAT1	0.023	0.007	-10000	0	-0.12	1	1
RAR alpha/RXRs	-0.019	0.16	-10000	0	-0.36	80	80
RXRs/RARs/SMRT(N-CoR2)/9cRA	-0.014	0.13	-10000	0	-0.28	77	77
proteasomal ubiquitin-dependent protein catabolic process	-0.009	0.098	-10000	0	-0.25	50	50
RXRs/RARs/NRIP1/9cRA/HDAC3	-0.057	0.2	-10000	0	-0.55	70	70
positive regulation of DNA binding	-0.019	0.11	-10000	0	-0.21	98	98
NRIP1	-0.092	0.31	-10000	0	-0.96	58	58
RXRs/RARs	-0.046	0.17	-10000	0	-0.4	87	87
RXRs/RXRs/DNA/9cRA	-0.04	0.14	-10000	0	-0.32	91	91
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
CDK7	0.018	0.023	-10000	0	-0.12	15	15
TFIIH	0.029	0.053	-10000	0	-0.13	46	46
RAR alpha/9cRA	0.024	0.07	-10000	0	-0.2	24	24
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	-0.17	16	16

×

FOXA2 and FOXA3 transcription factor networks

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ACADVL	-0.052	0.28	-10000	0	-0.62	62	62
PCK1	-0.15	0.4	-10000	0	-1.1	81	81
HNF4A	-0.1	0.36	-10000	0	-0.74	108	108
KCNJ11	-0.008	0.27	-10000	0	-0.64	37	37
AKT1	-0.002	0.16	-10000	0	-0.32	44	44
response to starvation	-0.018	0.045	-10000	0	-0.13	71	71
DLK1	-0.023	0.28	-10000	0	-0.65	46	46
NKX2-1	-0.007	0.15	-10000	0	-10000	0	0
ACADM	-0.064	0.3	-10000	0	-0.64	77	77
TAT	-0.022	0.2	-10000	0	-0.58	16	16
CEBPB	0.021	0.032	-10000	0	-0.12	29	29
CEBPA	0.029	0.015	-10000	0	-0.12	5	5
TTR	0.013	0.16	-10000	0	-0.75	5	5
PKLR	-0.041	0.26	-10000	0	-0.61	49	49
APOA1	-0.16	0.48	-10000	0	-1	110	110
CPT1C	-0.048	0.27	-10000	0	-0.61	56	56
ALAS1	-0.01	0.19	-10000	0	-0.67	11	11
TFRC	-0.099	0.4	-10000	0	-0.96	82	82
FOXF1	0.015	0.012	-10000	0	-0.11	5	5
NF1	0.024	0.026	-10000	0	-0.13	12	12
HNF1A (dimer)	0.042	0.018	-10000	0	-0.13	5	5
CPT1A	-0.058	0.29	-10000	0	-0.63	72	72
HMGCS1	-0.055	0.28	-10000	0	-0.64	63	63
NR3C1	0.035	0.017	-10000	0	-0.11	5	5
CPT1B	-0.042	0.26	-10000	0	-0.61	53	53
chromatin remodeling	0	0	-10000	0	-10000	0	0
SP1	0.029	0.013	-10000	0	-0.14	2	2
GCK	-0.041	0.26	-10000	0	-0.6	51	51
CREB1	-0.008	0.069	-10000	0	-0.17	74	74
IGFBP1	-0.012	0.16	-10000	0	-0.52	8	8
PDX1	0.03	0.17	-10000	0	-0.71	5	5
UCP2	-0.089	0.33	-10000	0	-0.69	91	91
ALDOB	-0.008	0.26	-10000	0	-0.64	37	37
AFP	0.018	0.05	-10000	0	-0.34	1	1
BDH1	-0.066	0.3	-10000	0	-0.64	74	74
HADH	-0.017	0.28	-10000	0	-0.65	45	45
F2	-0.06	0.33	-10000	0	-0.81	43	43
HNF1A	0.042	0.018	-10000	0	-0.13	5	5
G6PC	0.026	0.075	-10000	0	-0.42	1	1
SLC2A2	0.024	0.18	-10000	0	-0.66	2	2
INS	0.009	0.012	0.16	1	-0.13	2	3
FOXA1	0.035	0.03	-10000	0	-0.21	2	2
FOXA3	0.004	0.096	-10000	0	-0.2	67	67
FOXA2	-0.003	0.32	-10000	0	-0.69	47	47
ABCC8	-0.007	0.26	-10000	0	-0.62	40	40
ALB	0.018	0.051	-10000	0	-0.3	3	3

×

Aurora B 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
Condensin I complex	-0.049	0.17	-9999	-0.3	125	125
STMN1	0.019	0.019	-9999	-0.068	23	23
Aurora B/RasGAP/Survivin	0.017	0.073	-9999	-0.16	72	72
Chromosomal passenger complex/Cul3 protein complex	-0.002	0.089	-9999	-0.25	48	48
BIRC5	0.018	0.024	-9999	-0.12	15	15
DES	-0.03	0.23	-9999	-0.94	33	33
Aurora C/Aurora B/INCENP	0.033	0.039	-9999	-0.11	33	33
Aurora B/TACC1	0.014	0.048	-9999	-0.1	67	67
Aurora B/PP2A	0.02	0.048	-9999	-0.12	59	59
mol:GTP	0	0	-9999	-10000	0	0
CBX5	-0.006	0.062	-9999	-0.19	53	53
mitotic metaphase/anaphase transition	0.002	0.005	-9999	-10000	0	0
NDC80	0.009	0.032	-9999	-0.08	55	55
Cul3 protein complex	0.016	0.056	-9999	-0.11	57	57
KIF2C	-0.066	0.21	-9999	-0.46	99	99
PEBP1	0.022	0.008	-9999	-0.12	1	1
KIF20A	0.009	0.038	-9999	-0.12	42	42
mol:GDP	0	0	-9999	-10000	0	0
Aurora B/RasGAP	0.012	0.058	-9999	-0.14	65	65
SEPT1	0.022	0.013	-9999	-0.12	5	5
SMC2	0.015	0.03	-9999	-0.12	25	25
SMC4	0.018	0.025	-9999	-0.12	17	17
NSUN2/NPM1/Nucleolin	-0.025	0.17	-9999	-0.64	36	36
PSMA3	0.019	0.02	-9999	-0.12	11	11
G2/M transition of mitotic cell cycle	0	0.003	-9999	-10000	0	0
H3F3B	-0.002	0.065	-9999	-0.21	48	48
AURKB	0.019	0.027	-9999	-0.12	19	19
AURKC	0.023	0.006	-9999	-0.12	1	1
CDCA8	0.019	0.021	-9999	-0.12	11	11
cytokinesis	-0.04	0.2	-9999	-0.46	76	76
Aurora B/Septin1	-0.022	0.19	-9999	-0.43	74	74
AURKA	0.015	0.027	-9999	-0.12	20	20
INCENP	0.021	0.011	-9999	-0.12	2	2
KLHL13	-0.001	0.052	-9999	-0.12	91	91
BUB1	0.017	0.025	-9999	-0.12	17	17
hSgo1/Aurora B/Survivin	0.011	0.078	-9999	-0.16	78	78
EVI5	0.021	0.015	-9999	-0.12	6	6
RhoA/GTP	-0.023	0.18	-9999	-0.39	81	81
SGOL1	0.016	0.028	-9999	-0.12	22	22
CENPA	-0.037	0.18	-9999	-0.36	90	90
NCAPG	0.01	0.036	-9999	-0.12	39	39
Aurora B/HC8 Proteasome	0.007	0.064	-9999	-0.13	99	99
NCAPD2	0.015	0.029	-9999	-0.12	24	24
Aurora B/PP1-gamma	0.012	0.059	-9999	-0.14	66	66
RHOA	0.023	0.006	-9999	-0.12	1	1
NCAPH	0.019	0.02	-9999	-0.12	10	10
NPM1	-0.011	0.12	-9999	-0.41	40	40
RASA1	0.021	0.011	-9999	-0.12	3	3
KLHL9	0.023	0.007	-9999	-0.12	1	1
mitotic prometaphase	-0.001	0.004	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.007	0.064	-9999	-0.13	99	99
PPP1CC	0.022	0.005	-9999	-10000	0	0
Centraspindlin	-0.032	0.19	-9999	-0.4	87	87
RhoA/GDP	0.016	0.016	-9999	-0.14	6	6
NSUN2	-0.01	0.11	-9999	-0.39	41	41
MYLK	-0.005	0.067	-9999	-0.21	52	52
KIF23	0.013	0.033	-9999	-0.12	31	31
VIM	0.016	0.026	-9999	-0.084	28	28
RACGAP1	0.018	0.024	-9999	-0.12	16	16
mitosis	0	0	-9999	-10000	0	0
NCL	-0.02	0.12	-9999	-0.37	58	58
Chromosomal passenger complex	-0.037	0.17	-9999	-0.34	94	94
Chromosomal passenger complex/EVI5	0.032	0.085	-9999	-0.16	68	68
TACC1	0.014	0.035	-9999	-0.12	35	35
PPP2R5D	0.022	0.013	-9999	-0.12	5	5
CUL3	0.023	0.004	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0

×

ErbB4 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF	-0.048	0.2	-10000	0	-0.65	45	45
epithelial cell differentiation	-0.039	0.19	-10000	0	-0.6	46	46
ITCH	0.027	0.027	0.085	4	-0.072	29	33
WWP1	-0.053	0.29	-10000	0	-1.2	34	34
FYN	0.012	0.037	-10000	0	-0.12	40	40
EGFR	0.015	0.03	-10000	0	-0.12	25	25
PRL	0.023	0.01	-10000	0	-0.12	3	3
neuron projection morphogenesis	-0.016	0.16	-10000	0	-0.52	41	41
PTPRZ1	0.021	0.017	-10000	0	-0.12	8	8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC	-0.008	0.18	-10000	0	-0.58	41	41
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta	-0.037	0.19	-10000	0	-0.62	44	44
ADAM17	0.023	0.031	0.085	2	-0.085	34	36
ErbB4/ErbB4	-0.036	0.22	-10000	0	-0.77	40	40
ErbB4/ErbB4/neuregulin 3/neuregulin 3	-0.054	0.2	-10000	0	-0.65	46	46
NCOR1	0.022	0.009	-10000	0	-0.12	2	2
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn	-0.038	0.18	-10000	0	-0.58	47	47
GRIN2B	-0.036	0.18	-10000	0	-0.55	47	47
ErbB4/ErbB2/betacellulin	-0.041	0.18	-10000	0	-0.59	46	46
STAT1	0.014	0.03	-10000	0	-0.12	25	25
HBEGF	0.018	0.026	-10000	0	-0.12	20	20
PRLR	0.009	0.042	-10000	0	-0.12	55	55
E4ICDs/ETO2	-0.046	0.2	-10000	0	-0.65	45	45
axon guidance	-0.062	0.23	-10000	0	-0.72	49	49
NEDD4	0.024	0.034	0.085	7	-0.081	42	49
Prolactin receptor/Prolactin receptor/Prolactin	0.024	0.032	-10000	0	-0.072	56	56
CBFA2T3	0.023	0.006	-10000	0	-0.12	1	1
ErbB4/ErbB2/HBEGF	-0.033	0.18	-10000	0	-0.6	43	43
MAPK3	-0.017	0.16	-10000	0	-0.54	41	41
STAT1 (dimer)	-0.058	0.21	-10000	0	-0.5	72	72
MAPK1	-0.018	0.16	-10000	0	-0.55	41	41
JAK2	0.017	0.025	-10000	0	-0.12	17	17
ErbB4/ErbB2/neuregulin 1 beta	-0.031	0.18	-10000	0	-0.59	44	44
NRG1	0.021	0.027	-10000	0	-0.07	30	30
NRG3	0.005	0.048	-10000	0	-0.12	73	73
NRG2	0.023	0.006	-10000	0	-0.12	1	1
NRG4	0.002	0.047	-10000	0	-0.12	70	70
heart development	-0.062	0.23	-10000	0	-0.72	49	49
neural crest cell migration	-0.031	0.18	-10000	0	-0.58	44	44
ERBB2	0.021	0.027	-10000	0	-0.067	32	32
WWOX/E4ICDs	-0.046	0.2	-10000	0	-0.65	45	45
SHC1	0.023	0.001	-10000	0	-10000	0	0
ErbB4/EGFR/neuregulin 4	-0.069	0.2	-10000	0	-0.55	58	58
apoptosis	0.047	0.2	0.66	43	-10000	0	43
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta	-0.046	0.2	-10000	0	-0.65	45	45
ErbB4/ErbB2/epiregulin	-0.031	0.18	-10000	0	-0.6	44	44
ErbB4/ErbB4/betacellulin/betacellulin	-0.056	0.2	-10000	0	-0.56	57	57
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2	-0.029	0.19	-10000	0	-0.59	46	46
MDM2	-0.033	0.2	-10000	0	-0.74	38	38
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta	-0.025	0.17	-10000	0	-0.57	42	42
STAT5A	-0.057	0.22	-10000	0	-0.67	51	51
ErbB4/EGFR/neuregulin 1 beta	-0.036	0.18	-10000	0	-0.56	48	48
DLG4	0.023	0.008	-10000	0	-0.12	2	2
GRB2/SHC	0.032	0.02	-10000	0	-0.13	8	8
E4ICDs/TAB2/NCoR1	-0.041	0.2	-10000	0	-0.63	46	46
STAT5A (dimer)	-0.039	0.21	-10000	0	-0.69	45	45
MAP3K7IP2	0.02	0.016	-10000	0	-0.12	7	7
STAT5B (dimer)	-0.052	0.22	-10000	0	-0.69	49	49
LRIG1	0.01	0.036	-10000	0	-0.12	39	39
EREG	0.021	0.017	-10000	0	-0.12	8	8
BTC	0.011	0.038	-10000	0	-0.12	43	43
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta	-0.062	0.23	-10000	0	-0.73	49	49
ERBB4	-0.034	0.22	-10000	0	-0.77	40	40
STAT5B	0.023	0.006	-10000	0	-0.12	1	1
YAP1	0.002	0.076	-10000	0	-0.5	11	11
GRB2	0.023	0.006	-10000	0	-0.12	1	1
ErbB4/ErbB2/neuregulin 4	-0.05	0.18	-10000	0	-0.52	56	56
glial cell differentiation	0.04	0.2	0.62	46	-10000	0	46
WWOX	0.023	0.006	-10000	0	-0.12	1	1
cell proliferation	-0.069	0.21	-10000	0	-0.56	67	67

×

E-cadherin signaling in the nascent adherens junction

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
CTTN	-0.011	0.14	-9999	-0.41	51	51
KLHL20	-0.013	0.085	-9999	-0.2	68	68
CYFIP2	0.02	0.017	-9999	-0.12	8	8
Rac1/GDP	0.011	0.093	-9999	-0.23	53	53
ENAH	-0.012	0.13	-9999	-0.4	52	52
AP1M1	0.021	0.017	-9999	-0.12	8	8
RAP1B	0.019	0.019	-9999	-0.12	10	10
RAP1A	0.021	0.011	-9999	-0.12	3	3
CTNNB1	0.022	0.007	-9999	-0.12	1	1
CDC42/GTP	0.009	0.071	-9999	-0.2	37	37
ABI1/Sra1/Nap1	-0.028	0.049	-9999	-0.14	73	73
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin	0.038	0.055	-9999	-0.1	65	65
RAPGEF1	-0.002	0.12	-9999	-0.34	51	51
CTNND1	0.023	0.004	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.012	0.14	-9999	-0.42	51	51
CRK	-0.007	0.12	-9999	-0.37	51	51
E-cadherin/gamma catenin/alpha catenin	0.024	0.061	-9999	-0.13	63	63
alphaE/beta7 Integrin	0.026	0.034	-9999	-0.11	33	33
IQGAP1	0.02	0.017	-9999	-0.12	7	7
NCKAP1	0.023	0.004	-9999	-10000	0	0
Rap1/GTP/I-afadin	0.015	0.06	-9999	-0.11	88	88
DLG1	-0.012	0.14	-9999	-0.42	51	51
ChemicalAbstracts:7440-70-2	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.023	0.05	-9999	-0.16	55	55
MLLT4	0.014	0.032	-9999	-0.12	30	30
ARF6/GTP/NME1/Tiam1	0.018	0.057	-9999	-0.11	74	74
PI3K	-0.029	0.065	-9999	-0.2	54	54
ARF6	0.023	0.003	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
E-cadherin/gamma catenin	0.017	0.054	-9999	-0.16	44	44
TIAM1	0.015	0.032	-9999	-0.12	29	29
E-cadherin(dimer)/Ca2+	0.032	0.061	-9999	-0.12	71	71
AKT1	0.004	0.049	-9999	-0.13	46	46
PIK3R1	0.015	0.031	-9999	-0.12	28	28
CDH1	0.02	0.015	-9999	-0.12	6	6
RhoA/GDP	0.012	0.092	-9999	-0.23	52	52
actin cytoskeleton organization	-0.008	0.064	-9999	-0.14	68	68
CDC42/GDP	0.012	0.092	-9999	-0.23	53	53
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin	0.001	0.08	-9999	-0.19	68	68
ITGB7	0.019	0.023	-9999	-0.12	15	15
RAC1	0.023	0.002	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/p120 catenin	0.035	0.066	-9999	-0.13	71	71
E-cadherin/Ca2+/beta catenin/alpha catenin	0.022	0.051	-9999	-0.11	68	68
mol:GDP	0	0.1	-9999	-0.27	54	54
CDC42/GTP/IQGAP1	0.017	0.044	-9999	-0.12	49	49
JUP	0.02	0.021	-9999	-0.12	12	12
p120 catenin/RhoA/GDP	0.016	0.095	-9999	-0.24	51	51
RAC1/GTP/IQGAP1	0.017	0.045	-9999	-0.12	50	50
PIP5K1C/AP1M1	0.033	0.014	-9999	-0.078	9	9
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	117	117
NME1	0.016	0.029	-9999	-0.12	23	23
clathrin coat assembly	0	0	-9999	-10000	0	0
TJP1	-0.013	0.14	-9999	-0.42	53	53
regulation of cell-cell adhesion	-0.019	0.051	-9999	-0.18	37	37
WASF2	-0.002	0.036	-9999	-0.08	66	66
Rap1/GTP	0.012	0.081	-9999	-0.23	35	35
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin	0.04	0.064	-9999	-0.16	22	22
CCND1	-0.018	0.076	-9999	-0.15	114	114
VAV2	-0.021	0.18	-9999	-0.52	49	49
RAP1/GDP	0.015	0.088	-9999	-0.25	36	36
adherens junction assembly	-0.012	0.14	-9999	-0.4	53	53
homophilic cell adhesion	0	0	-9999	-10000	0	0
ABI1	0.022	0.009	-9999	-0.12	2	2
PIP5K1C	0.023	0	-9999	-10000	0	0
regulation of heterotypic cell-cell adhesion	0.033	0.065	-9999	-0.17	24	24
E-cadherin/beta catenin	0.007	0.057	-9999	-0.23	30	30
mol:GTP	0	0	-9999	-10000	0	0
SRC	-0.01	0.13	-9999	-0.4	51	51
PIK3CA	0.02	0.017	-9999	-0.12	7	7
Rac1/GTP	-0.06	0.11	-9999	-0.32	67	67
E-cadherin/beta catenin/alpha catenin	0.025	0.06	-9999	-0.13	68	68
ITGAE	0.023	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.012	0.14	-9999	-0.43	51	51

×

BCR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
JUN	-0.025	0.11	-10000	0	-0.25	77	77
IKBKB	0.013	0.078	0.19	15	-0.23	27	42
AKT1	-0.008	0.06	0.14	12	-0.15	44	56
IKBKG	0.012	0.067	-10000	0	-0.21	25	25
CALM1	-0.009	0.11	0.16	4	-0.3	46	50
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
MAP3K1	-0.029	0.13	-10000	0	-0.34	59	59
MAP3K7	0.021	0.014	-10000	0	-0.12	5	5
mol:Ca2+	-0.013	0.11	0.16	4	-0.32	45	49
DOK1	0.022	0.015	-10000	0	-0.12	6	6
AP-1	-0.015	0.077	0.14	1	-0.18	71	72
LYN	0.02	0.013	-10000	0	-0.12	4	4
BLNK	0.014	0.033	-10000	0	-0.12	32	32
SHC1	0.023	0.001	-10000	0	-10000	0	0
BCR complex	0.028	0.026	-10000	0	-0.14	3	3
CD22	-0.04	0.1	-10000	0	-0.28	57	57
CAMK2G	-0.004	0.1	0.15	4	-0.28	46	50
CSNK2A1	0.022	0.015	-10000	0	-0.12	6	6
INPP5D	0	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1	0	0.052	-10000	0	-0.14	38	38
GO:0007205	-0.013	0.11	0.16	4	-0.33	45	49
SYK	0.016	0.027	-10000	0	-0.12	21	21
ELK1	-0.009	0.11	0.16	4	-0.31	45	49
NFATC1	-0.014	0.084	-10000	0	-0.23	55	55
B-cell antigen/BCR complex	0.028	0.026	-10000	0	-0.14	3	3
PAG1/CSK	0.032	0.02	-10000	0	-0.097	13	13
NFKBIB	0.008	0.045	-10000	0	-0.13	46	46
HRAS	-0.002	0.088	-10000	0	-0.26	41	41
NFKBIA	0.011	0.041	-10000	0	-0.12	36	36
NF-kappa-B/RelA/I kappa B beta	0.014	0.043	-10000	0	-0.12	42	42
RasGAP/Csk	0.023	0.068	-10000	0	-0.088	128	128
mol:GDP	-0.012	0.11	0.15	4	-0.31	48	52
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	39	39
GRB2	0.023	0.006	-10000	0	-0.12	1	1
PI3K/BCAP/CD19	-0.029	0.13	-10000	0	-0.38	54	54
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
mol:IP3	-0.013	0.11	0.16	4	-0.33	45	49
CSK	0.023	0.009	-10000	0	-0.12	2	2
FOS	-0.023	0.11	0.15	2	-0.3	57	59
CHUK	-0.003	0.095	-10000	0	-0.26	53	53
IBTK	0.019	0.017	-10000	0	-0.12	7	7
CARD11/BCL10/MALT1/TAK1	0.006	0.1	0.19	1	-0.26	51	52
PTPN6	-0.036	0.095	-10000	0	-0.26	57	57
RELA	0.023	0.009	-10000	0	-0.12	2	2
BCL2A1	0.009	0.034	-10000	0	-0.081	50	50
VAV2	-0.031	0.11	-10000	0	-0.31	56	56
ubiquitin-dependent protein catabolic process	0.012	0.045	-10000	0	-0.12	44	44
BTK	-0.051	0.25	-10000	0	-1.1	33	33
CD19	-0.032	0.096	-10000	0	-0.3	41	41
MAP4K1	0.019	0.023	-10000	0	-0.12	15	15
CD72	0.023	0.006	-10000	0	-0.12	1	1
PAG1	0.022	0.015	-10000	0	-0.12	6	6
MAPK14	-0.022	0.11	-10000	0	-0.29	60	60
SH3BP5	0.021	0.015	-10000	0	-0.12	6	6
PIK3AP1	-0.01	0.11	0.17	4	-0.34	45	49
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72	-0.013	0.14	-10000	0	-0.3	83	83
RAF1	0.001	0.084	0.13	1	-0.26	37	38
RasGAP/p62DOK/SHIP	0.015	0.062	-10000	0	-0.12	24	24
CD79A	0.016	0.032	-10000	0	-0.12	29	29
re-entry into mitotic cell cycle	-0.014	0.077	0.14	1	-0.18	71	72
RASA1	0.021	0.011	-10000	0	-0.12	3	3
MAPK3	0.008	0.074	-10000	0	-0.22	35	35
MAPK1	0.008	0.074	0.13	1	-0.22	35	36
CD72/SHP1	-0.026	0.095	-10000	0	-0.25	56	56
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
MAPK8	-0.023	0.11	-10000	0	-0.3	61	61
actin cytoskeleton organization	-0.024	0.098	-10000	0	-0.28	56	56
NF-kappa-B/RelA	0.022	0.096	-10000	0	-0.24	50	50
Calcineurin	0.013	0.1	-10000	0	-0.29	38	38
PI3K	-0.038	0.075	-10000	0	-0.24	49	49
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2	-0.013	0.11	0.17	4	-0.35	42	46
SOS1	0.017	0.027	-10000	0	-0.12	20	20
Bam32/HPK1	-0.042	0.18	-10000	0	-0.54	47	47
DAPP1	-0.057	0.19	-10000	0	-0.61	46	46
cytokine secretion	-0.013	0.08	0.16	1	-0.22	55	56
mol:DAG	-0.013	0.11	0.16	4	-0.33	45	49
PLCG2	0.02	0.02	-10000	0	-0.12	11	11
MAP2K1	0.005	0.079	-10000	0	-0.24	35	35
B-cell antigen/BCR complex/FcgammaRIIB	0.009	0.063	-10000	0	-0.11	101	101
mol:PI-3-4-5-P3	-0.034	0.057	0.094	1	-0.18	49	50
ETS1	-0.007	0.098	0.15	2	-0.28	48	50
B-cell antigen/BCR complex/LYN/SYK/BLNK	0.029	0.069	-10000	0	-0.15	26	26
B-cell antigen/BCR complex/LYN	-0.037	0.1	-10000	0	-0.32	41	41
MALT1	0.018	0.026	-10000	0	-0.12	19	19
TRAF6	0.022	0.009	-10000	0	-0.12	2	2
RAC1	-0.026	0.1	-10000	0	-0.29	56	56
B-cell antigen/BCR complex/LYN/SYK	-0.004	0.091	-10000	0	-0.22	49	49
CARD11	-0.01	0.11	0.16	4	-0.31	46	50
FCGR2B	0.004	0.044	-10000	0	-0.12	61	61
PPP3CA	0.021	0.014	-10000	0	-0.12	5	5
BCL10	0.023	0.001	-10000	0	-10000	0	0
IKK complex	0.012	0.038	0.1	17	-0.095	25	42
PTPRC	-0.004	0.05	-10000	0	-0.12	86	86
PDPK1	-0.01	0.054	0.13	13	-0.13	48	61
PPP3CB	0.023	0.007	-10000	0	-0.12	1	1
PPP3CC	0.023	0.01	-10000	0	-0.12	3	3
POU2F2	0.011	0.033	-10000	0	-0.076	51	51

×

FAS signaling pathway (CD95)

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPTAN1	0.003	0.039	0.15	3	-0.26	10	13
RFC1	0.003	0.04	0.16	4	-0.26	10	14
PRKDC	0.003	0.039	0.16	4	-0.25	10	14
RIPK1	0.022	0.011	-10000	0	-0.12	3	3
CASP7	0.002	0.091	-10000	0	-0.45	16	16
FASLG/FAS/FADD/FAF1	0.036	0.085	0.16	118	-0.17	43	161
MAP2K4	-0.001	0.11	-10000	0	-0.3	44	44
mol:ceramide	0.004	0.096	-10000	0	-0.25	42	42
GSN	0.002	0.038	0.16	1	-0.26	10	11
FASLG/FAS/FADD/FAF1/Caspase 8	0.041	0.09	0.16	111	-0.18	45	156
FAS	0.016	0.026	-10000	0	-0.12	17	17
BID	0.005	0.017	0.25	2	-10000	0	2
MAP3K1	0	0.093	0.17	2	-0.31	31	33
MAP3K7	0.021	0.014	-10000	0	-0.12	5	5
RB1	0.001	0.041	0.16	4	-0.25	11	15
CFLAR	0.022	0.011	-10000	0	-0.12	3	3
HGF/MET	-0.053	0.089	-10000	0	-0.14	248	248
ARHGDIB	-0.002	0.043	0.16	3	-0.28	10	13
FADD	0.022	0.01	-10000	0	-0.12	2	2
actin filament polymerization	-0.002	0.038	0.25	10	-0.16	1	11
NFKB1	-0.039	0.2	-10000	0	-0.73	40	40
MAPK8	-0.002	0.12	-10000	0	-0.34	40	40
DFFA	0.003	0.04	0.16	4	-0.25	11	15
DNA fragmentation during apoptosis	0.004	0.04	0.16	4	-0.25	11	15
FAS/FADD/MET	-0.015	0.082	-10000	0	-0.13	168	168
CFLAR/RIP1	0.03	0.027	-10000	0	-0.12	16	16
FAIM3	0.022	0.013	-10000	0	-0.12	5	5
FAF1	0.021	0.015	-10000	0	-0.12	5	5
PARP1	0.004	0.037	0.16	4	-0.24	10	14
DFFB	0.004	0.04	0.16	4	-0.25	11	15
CHUK	-0.035	0.19	-10000	0	-0.7	40	40
FASLG	0.022	0.013	-10000	0	-0.12	4	4
FAS/FADD	0.012	0.058	-10000	0	-0.13	81	81
HGF	0.02	0.022	-10000	0	-0.12	14	14
LMNA	0	0.046	0.14	4	-0.26	13	17
CASP6	-0.002	0.05	0.16	4	-0.29	12	16
CASP10	0.019	0.02	-10000	0	-0.12	10	10
CASP3	-0.002	0.045	0.18	4	-0.28	11	15
PTPN13	-0.011	0.055	-10000	0	-0.12	110	110
CASP8	-0.005	0.019	0.28	2	-10000	0	2
IL6	-0.039	0.21	-10000	0	-0.74	37	37
MET	0.001	0.047	-10000	0	-0.12	71	71
ICAD/CAD	0.007	0.038	0.15	2	-0.22	12	14
FASLG/FAS/FADD/FAF1/Caspase 10	0.004	0.097	-10000	0	-0.26	42	42
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	28	28

×

Signaling mediated by p38-gamma and p38-delta

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
EEF2K	0.019	0.015	-9999	-0.057	18	18
SNTA1	0.023	0.009	-9999	-0.12	2	2
response to hypoxia	0	0	-9999	-10000	0	0
STMN1	0.017	0.021	-9999	-0.074	21	21
MAPK12	0.01	0.028	-9999	-0.044	83	83
CCND1	-0.049	0.14	-9999	-0.36	90	90
p38 gamma/SNTA1	0.005	0.058	-9999	-0.12	84	84
MAP2K3	0.023	0.006	-9999	-0.12	1	1
PKN1	0.016	0.031	-9999	-0.12	27	27
G2/M transition checkpoint	0.002	0.045	-9999	-0.15	39	39
MAP2K6	0.007	0.03	-9999	-0.052	82	82
MAPT	0.007	0.04	-9999	-0.13	28	28
MAPK13	0.019	0.019	-9999	-0.078	17	17
hyperosmotic response	0	0	-9999	-10000	0	0
ZAK	-0.002	0.059	-9999	-0.21	39	39

×

Plasma membrane estrogen receptor signaling

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
GNB1/GNG2	0.036	0.049	-10000	0	-0.093	64	64
ER alpha/Gai/GDP/Gbeta gamma	0.005	0.095	-10000	0	-0.26	56	56
AKT1	-0.056	0.23	-10000	0	-0.6	80	80
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
E2/ER alpha (dimer)/PELP1/Src/PI3K	-0.057	0.23	-10000	0	-0.61	80	80
mol:Ca2+	0.011	0.068	-10000	0	-0.24	30	30
IGF1R	0.013	0.031	-10000	0	-0.12	28	28
E2/ER alpha (dimer)/Striatin	0.014	0.047	-10000	0	-0.1	74	74
SHC1	0.023	0.001	-10000	0	-10000	0	0
apoptosis	0.053	0.22	0.58	80	-10000	0	80
RhoA/GTP	-0.016	0.034	-10000	0	-0.14	17	17
E2/ER alpha (dimer)/PELP1/Src/p130 Cas	0.006	0.1	-10000	0	-0.26	60	60
regulation of stress fiber formation	-0.007	0.049	0.14	39	-10000	0	39
E2/ERA-ERB (dimer)	0.018	0.041	-10000	0	-0.099	61	61
KRAS	0.014	0.034	-10000	0	-0.12	33	33
G13/GTP	0.014	0.042	-10000	0	-0.091	74	74
pseudopodium formation	0.007	0.049	-10000	0	-0.14	39	39
E2/ER alpha (dimer)/PELP1	0.017	0.041	-10000	0	-0.12	45	45
GRB2	0.023	0.006	-10000	0	-0.12	1	1
GNG2	0.02	0.018	-10000	0	-0.12	9	9
GNAO1	0.011	0.041	-10000	0	-0.12	50	50
HRAS	0.023	0.006	-10000	0	-0.12	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
mol:NO	-0.013	0.13	-10000	0	-0.32	71	71
E2/ER beta (dimer)	0.017	0.004	-10000	0	-0.076	1	1
mol:GDP	0.002	0.076	-10000	0	-0.24	46	46
mol:NADP	-0.013	0.13	-10000	0	-0.32	71	71
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
mol:IP3	0.011	0.07	-10000	0	-0.25	30	30
IGF-1R heterotetramer	0.013	0.031	-10000	0	-0.12	28	28
PLCB1	0.01	0.072	-10000	0	-0.26	30	30
PLCB2	0.016	0.068	-10000	0	-0.26	27	27
IGF1	0.007	0.045	-10000	0	-0.12	62	62
mol:L-citrulline	-0.013	0.13	-10000	0	-0.32	71	71
RHOA	0.023	0.006	-10000	0	-0.12	1	1
Gai/GDP	0.022	0.062	-10000	0	-0.54	3	3
JNK cascade	0.017	0.004	-10000	0	-0.076	1	1
BCAR1	0.023	0.01	-10000	0	-0.12	3	3
ESR2	0.023	0.006	-10000	0	-0.12	1	1
GNAQ	0.021	0.015	-10000	0	-0.12	6	6
ESR1	0.018	0.024	-10000	0	-0.12	15	15
Gq family/GDP/Gbeta gamma	0.03	0.063	-10000	0	-0.3	17	17
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1	0.015	0.092	-10000	0	-0.49	11	11
E2/ER alpha (dimer)/PELP1/Src/p52 SHC	0.006	0.1	-10000	0	-0.25	60	60
GNAZ	0.022	0.012	-10000	0	-0.12	4	4
E2/ER alpha (dimer)	0.002	0.046	-10000	0	-0.13	60	60
STRN	0.022	0.012	-10000	0	-0.12	4	4
GNAL	0.021	0.019	-10000	0	-0.12	10	10
PELP1	0.023	0.008	-10000	0	-0.12	2	2
MAPK11	0.021	0.003	-10000	0	-0.056	1	1
GNAI2	0.022	0.01	-10000	0	-0.12	3	3
GNAI3	0.021	0.008	-10000	0	-0.12	1	1
GNAI1	0.012	0.035	-10000	0	-0.12	36	36
HBEGF	-0.025	0.1	-10000	0	-0.25	68	68
cAMP biosynthetic process	0.015	0.033	-10000	0	-0.086	46	46
SRC	0.004	0.097	-10000	0	-0.25	61	61
PI3K	0.007	0.065	-10000	0	-0.16	63	63
GNB1	0.023	0.006	-10000	0	-0.12	1	1
G13/GDP/Gbeta gamma	0.022	0.076	-10000	0	-0.2	48	48
SOS1	0.017	0.027	-10000	0	-0.12	20	20
IGF-1R heterotetramer/IGF1	-0.039	0.073	-10000	0	-0.22	64	64
Gs family/GTP	0.021	0.035	-10000	0	-0.087	46	46
EntrezGene:2778	0	0	-10000	0	-10000	0	0
RAS family/GTP	0.03	0.043	-10000	0	-0.11	38	38
vasodilation	-0.012	0.12	-10000	0	-0.31	71	71
mol:DAG	0.011	0.07	-10000	0	-0.25	30	30
Gs family/GDP/Gbeta gamma	0.005	0.068	-10000	0	-0.2	48	48
MSN	0.007	0.051	-10000	0	-0.14	39	39
Gq family/GTP	0.015	0.072	-10000	0	-0.27	27	27
mol:PI-3-4-5-P3	-0.054	0.22	-10000	0	-0.59	80	80
NRAS	0.022	0.011	-10000	0	-0.12	3	3
mol:E2	0	0	-10000	0	-10000	0	0
cell adhesion	0.012	0.12	0.31	71	-10000	0	71
GRB2/SOS1	0.021	0.046	-10000	0	-0.15	31	31
RhoA/GDP	0.013	0.077	-10000	0	-0.22	48	48
NOS3	-0.015	0.13	-10000	0	-0.34	71	71
GNA11	0.022	0.013	-10000	0	-0.12	5	5
MAPKKK cascade	-0.006	0.15	-10000	0	-0.44	55	55
E2/ER alpha (dimer)/PELP1/Src	0.002	0.11	-10000	0	-0.26	61	61
ruffle organization	0.007	0.049	-10000	0	-0.14	39	39
ROCK2	0.01	0.049	-10000	0	-0.15	24	24
GNA14	0.02	0.02	-10000	0	-0.12	11	11
GNA15	0.021	0.017	-10000	0	-0.12	8	8
GNA13	0.022	0.009	-10000	0	-0.12	2	2
MMP9	-0.012	0.1	-10000	0	-0.25	62	62
MMP2	-0.019	0.1	-10000	0	-0.26	67	67

×

Signaling events mediated by PRL

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
CCNE1	0.002	0.047	-10000	0	-0.12	70	70
mol:Halofuginone	0.003	0.025	-10000	0	-0.18	10	10
ITGA1	0.014	0.029	-10000	0	-0.12	24	24
CDKN1A	0.014	0.061	-10000	0	-0.29	19	19
PRL-3/alpha Tubulin	0.014	0.051	-10000	0	-0.14	42	42
mol:Ca2+	0.018	0.077	0.28	42	-10000	0	42
AGT	0.02	0.02	-10000	0	-0.12	11	11
CCNA2	0	0.093	-10000	0	-0.67	10	10
TUBA1B	0.023	0	-10000	0	-10000	0	0
EGR1	-0.001	0.06	-10000	0	-0.34	12	12
CDK2/Cyclin E1	0.005	0.075	-10000	0	-0.31	15	15
MAPK3	0.014	0.026	-10000	0	-0.071	44	44
PRL-2 /Rab GGTase beta	0.008	0.063	-10000	0	-0.15	75	75
MAPK1	0.013	0.031	-10000	0	-0.083	45	45
PTP4A1	0.002	0.091	-10000	0	-0.64	10	10
PTP4A3	0.011	0.037	-10000	0	-0.12	40	40
PTP4A2	0.022	0.009	-10000	0	-0.12	2	2
ITGB1	0.013	0.027	-10000	0	-0.073	46	46
SRC	0.023	0.008	-10000	0	-0.12	2	2
RAC1	-0.014	0.11	-10000	0	-0.34	55	55
Rab GGTase beta/Rab GGTase alpha	0.012	0.058	-10000	0	-0.13	80	80
PRL-1/ATF-5	-0.003	0.095	-10000	0	-0.6	10	10
RABGGTA	0.023	0.006	-10000	0	-0.12	1	1
BCAR1	0.019	0.076	0.28	42	-10000	0	42
RHOC	-0.013	0.11	-10000	0	-0.35	52	52
RHOA	-0.014	0.11	-10000	0	-0.34	55	55
cell motility	-0.011	0.11	-10000	0	-0.33	54	54
PRL-1/alpha Tubulin	0	0.094	-10000	0	-0.6	10	10
PRL-3/alpha1 Integrin	-0.01	0.079	-10000	0	-0.13	157	157
ROCK1	-0.012	0.11	-10000	0	-0.33	54	54
RABGGTB	0.018	0.022	-10000	0	-0.12	12	12
CDK2	0.018	0.023	-10000	0	-0.12	14	14
mitosis	0.002	0.09	-10000	0	-0.64	10	10
ATF5	0.018	0.026	-10000	0	-0.12	19	19

×

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	-0.15	39	39
Necdin/E2F1	0.017	0.046	-10000	0	-0.088	84	84
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E	0.038	0.049	-10000	0	-0.1	53	53
NGF (dimer)/p75(NTR)/BEX1	-0.008	0.054	-10000	0	-0.075	214	214
NT-4/5 (dimer)/p75(NTR)	0.016	0.013	-10000	0	-0.083	10	10
IKBKB	0.022	0.015	-10000	0	-0.12	6	6
AKT1	0.009	0.045	-10000	0	-0.1	64	64
IKBKG	0.023	0.008	-10000	0	-0.12	2	2
BDNF	0.023	0.01	-10000	0	-0.12	3	3
MGDIs/NGR/p75(NTR)/LINGO1	0.04	0.031	-10000	0	-0.12	13	13
FURIN	0.02	0.02	-10000	0	-0.12	11	11
proBDNF (dimer)/p75(NTR)/Sortilin	0.035	0.042	-10000	0	-0.12	34	34
LINGO1	0.018	0.026	-10000	0	-0.12	19	19
Sortilin/TRAF6/NRIF	0.004	0.054	-10000	0	-0.17	23	23
proBDNF (dimer)	0.022	0.01	-10000	0	-0.12	3	3
NTRK1	0.023	0.006	-10000	0	-0.12	1	1
RTN4R	0.021	0.018	-10000	0	-0.12	9	9
neuron apoptosis	-0.039	0.12	-10000	0	-0.31	47	47
IRAK1	0.02	0.022	-10000	0	-0.12	13	13
SHC1	0.019	0.011	-10000	0	-0.062	10	10
ARHGDIA	0.016	0.032	-10000	0	-0.12	29	29
RhoA/GTP	0.016	0.016	-10000	0	-0.14	6	6
Gamma Secretase	0.035	0.067	-10000	0	-0.22	10	10
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1	0.025	0.051	-10000	0	-0.11	62	62
MAGEH1	0.018	0.023	-10000	0	-0.12	15	15
proNGF (dimer)/p75(NTR)/Sortilin/Necdin	0.021	0.051	-10000	0	-0.11	54	54
Mammalian IAPs/DIABLO	-0.018	0.083	-10000	0	-0.13	159	159
proNGF (dimer)	0	0	-10000	0	-10000	0	0
MAGED1	0.02	0.019	-10000	0	-0.12	10	10
APP	0.022	0.008	-10000	0	-0.12	1	1
NT-4/5 (dimer)	0	0	-10000	0	-10000	0	0
ZNF274	0.023	0	-10000	0	-10000	0	0
RhoA/GDP/RHOGDI	0.029	0.027	-10000	0	-0.1	12	12
NGF	0	0	-10000	0	-10000	0	0
cell cycle arrest	0.023	0.042	0.098	62	-0.099	34	96
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK	0.01	0.062	-10000	0	-0.15	62	62
NT-4/5 (dimer)/p75(NTR)/TRAF6	0.028	0.022	-10000	0	-0.087	19	19
NCSTN	0.022	0.012	-10000	0	-0.12	4	4
mol:GTP	0.022	0.034	-10000	0	-0.093	43	43
PSENEN	0.016	0.03	-10000	0	-0.12	25	25
mol:ceramide	0.016	0.034	-10000	0	-0.11	34	34
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs	-0.004	0.09	-10000	0	-0.3	30	30
p75(NTR)/beta APP	0.022	0.044	-10000	0	-0.13	43	43
BEX1	-0.016	0.062	-10000	0	-0.12	146	146
mol:GDP	0.006	0.01	-10000	0	-0.067	10	10
NGF (dimer)	-0.028	0.064	-10000	0	-0.1	198	198
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI	0.046	0.041	-10000	0	-0.11	21	21
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
RAC1/GTP	0.025	0.016	-10000	0	-0.07	14	14
MYD88	0.023	0.006	-10000	0	-0.12	1	1
CHUK	0.021	0.013	-10000	0	-0.12	4	4
NGF (dimer)/p75(NTR)/PKA	0.022	0.034	-10000	0	-0.093	43	43
RHOB	0.022	0.013	-10000	0	-0.12	5	5
RHOA	0.023	0.006	-10000	0	-0.12	1	1
MAGE-G1/E2F1	0.032	0.018	-10000	0	-0.087	12	12
NT3 (dimer)	-0.003	0.055	-10000	0	-0.12	101	101
TP53	0.011	0.047	-10000	0	-0.13	40	40
PRDM4	0.017	0.032	-10000	0	-0.1	34	34
BDNF (dimer)	-0.02	0.069	-10000	0	-0.096	204	204
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
SORT1	0.02	0.018	-10000	0	-0.12	8	8
activation of caspase activity	0.034	0.047	-10000	0	-0.1	53	53
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6	0.032	0.042	-10000	0	-0.11	40	40
RHOC	0.023	0.002	-10000	0	-10000	0	0
XIAP	0	0	-10000	0	-10000	0	0
MAPK10	0.022	0.055	-10000	0	-0.18	21	21
DIABLO	0.02	0.016	-10000	0	-0.12	6	6
SMPD2	0.016	0.034	-10000	0	-0.11	34	34
APH1B	0.014	0.031	-10000	0	-0.12	28	28
APH1A	0.023	0.009	-10000	0	-0.12	2	2
proNGF (dimer)/p75(NTR)/Sortilin	0.02	0.038	-10000	0	-0.1	47	47
PSEN1	0.022	0.008	-10000	0	-0.12	1	1
APAF-1/Pro-Caspase 9	0.025	0.04	-10000	0	-0.16	22	22
NT3 (dimer)/p75(NTR)	0.012	0.046	-10000	0	-0.076	119	119
MAPK8	0.022	0.058	-10000	0	-0.2	22	22
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	0.055	-10000	0	-0.12	101	101
NTF4	0	0	-10000	0	-10000	0	0
NDN	0.008	0.044	-10000	0	-0.12	59	59
RAC1/GDP	0.016	0.015	-10000	0	-0.15	5	5
RhoA-B-C/GDP	0.04	0.035	-10000	0	-0.13	5	5
p75 CTF/Sortilin/TRAF6/NRIF	0.038	0.058	-10000	0	-0.12	62	62
RhoA-B-C/GTP	0.022	0.034	-10000	0	-0.092	43	43
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	0.055	0.045	-10000	0	-0.093	40	40
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6	0.046	0.046	-10000	0	-0.1	40	40
PRKACB	0.02	0.02	-10000	0	-0.12	11	11
proBDNF (dimer)/p75 ECD	0.022	0.044	-10000	0	-0.12	45	45
ChemicalAbstracts:86-01-1	0	0	-10000	0	-10000	0	0
BIRC3	-0.005	0.052	-10000	0	-0.12	93	93
BIRC2	0.021	0.013	-10000	0	-0.12	4	4
neuron projection morphogenesis	0.003	0.056	0.1	48	-0.14	36	84
BAD	0.02	0.06	-10000	0	-0.19	21	21
RIPK2	0.013	0.034	-10000	0	-0.12	34	34
NGFR	0.021	0.018	-10000	0	-0.12	9	9
CYCS	0.014	0.042	-10000	0	-0.11	49	49
ADAM17	0.019	0.02	-10000	0	-0.12	11	11
NGF (dimer)/p75(NTR)/TRAF6/RIP2	0.024	0.049	-10000	0	-0.11	55	55
BCL2L11	0.02	0.06	-10000	0	-0.19	22	22
BDNF (dimer)/p75(NTR)	0.032	0.017	-10000	0	-0.082	12	12
PI3K	0.021	0.054	-10000	0	-0.11	64	64
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1	0.033	0.039	-10000	0	-0.1	36	36
NDNL2	0.023	0.009	-10000	0	-0.12	2	2
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
PRKCI	0.016	0.028	-10000	0	-0.12	22	22
NGF (dimer)/p75(NTR)	0.016	0.013	-10000	0	-0.083	10	10
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE	0.029	0.046	-10000	0	-0.11	49	49
TRAF6	0.022	0.009	-10000	0	-0.12	2	2
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCZ	0.023	0	-10000	0	-10000	0	0
PLG	0.023	0.008	-10000	0	-0.12	2	2
oligodendrocyte cell fate commitment	0	0	-10000	0	-10000	0	0
CASP6	0.013	0.05	-10000	0	-0.16	34	34
SQSTM1	0.021	0.015	-10000	0	-0.12	6	6
NGFRAP1	0.022	0.009	-10000	0	-0.12	2	2
CASP3	0.021	0.058	-10000	0	-0.19	21	21
E2F1	0.021	0.016	-10000	0	-0.12	7	7
CASP9	0.022	0.014	-10000	0	-0.12	5	5
IKK complex	0.021	0.08	-10000	0	-0.22	33	33
NGF (dimer)/TRKA	0.017	0.004	-10000	0	-0.076	1	1
MMP7	-0.021	0.059	-10000	0	-0.12	144	144
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	0.042	0.042	-10000	0	-0.096	40	40
MMP3	0.017	0.029	-10000	0	-0.12	24	24
APAF-1/Caspase 9	-0.037	0.06	-10000	0	-0.16	87	87

×

TCGA08_rtk_signaling

Figure 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	0.005	0.043	-10000	0	-0.12	59	59
HRAS	0.023	0.006	-10000	0	-0.12	1	1
EGFR	0.015	0.03	-10000	0	-0.12	25	25
AKT	0.001	0.064	0.13	8	-0.12	81	89
FOXO3	0.021	0.017	-10000	0	-0.12	8	8
AKT1	0.021	0.019	-10000	0	-0.12	10	10
FOXO1	0.023	0.008	-10000	0	-0.12	2	2
AKT3	-0.003	0.055	-10000	0	-0.12	101	101
FOXO4	0.023	0	-10000	0	-10000	0	0
MET	0.001	0.047	-10000	0	-0.12	71	71
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PIK3CB	0.015	0.029	-10000	0	-0.12	24	24
NRAS	0.022	0.011	-10000	0	-0.12	3	3
PIK3CG	0.011	0.036	-10000	0	-0.12	39	39
PIK3R3	0.012	0.035	-10000	0	-0.12	36	36
PIK3R2	0.017	0.029	-10000	0	-0.12	25	25
NF1	0.018	0.02	-10000	0	-0.12	10	10
RAS	0.006	0.06	0.15	34	-0.15	43	77
ERBB2	0.02	0.021	-10000	0	-0.12	12	12
proliferation/survival/translation	0.002	0.074	0.22	37	-10000	0	37
PI3K	-0.014	0.077	0.13	9	-0.14	106	115
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
KRAS	0.014	0.034	-10000	0	-0.12	33	33
FOXO	0.029	0.037	0.14	9	-0.044	4	13
AKT2	0.019	0.025	-10000	0	-0.12	18	18
PTEN	0.022	0.008	-10000	0	-0.12	1	1

×

RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1	-0.021	0.2	-10000	0	-0.97	24	24
VDR	0.019	0.022	-10000	0	-0.12	13	13
FAM120B	0.022	0.011	-10000	0	-0.12	3	3
RXRs/LXRs/DNA/9cRA	0.025	0.095	-10000	0	-0.24	55	55
RXRs/LXRs/DNA/Oxysterols	0.019	0.13	-10000	0	-0.35	60	60
MED1	0.022	0.014	-10000	0	-0.12	5	5
mol:9cRA	0.002	0.017	-10000	0	-0.047	51	51
RARs/THRs/DNA/Src-1	-0.003	0.087	-10000	0	-0.29	24	24
RXRs/NUR77	0.033	0.067	0.18	8	-0.12	30	38
RXRs/PPAR	0.032	0.039	-10000	0	-0.16	5	5
NCOR2	0.019	0.023	-10000	0	-0.12	15	15
VDR/VDR/Vit D3	0.009	0.035	-10000	0	-0.12	36	36
RARs/VDR/DNA/Vit D3	0.03	0.056	-10000	0	-0.1	67	67
RARA	0.023	0	-10000	0	-10000	0	0
NCOA1	0.022	0.009	-10000	0	-0.12	2	2
VDR/VDR/DNA	0.019	0.022	-10000	0	-0.12	13	13
RARs/RARs/DNA/9cRA	0.025	0.045	-10000	0	-0.094	58	58
RARG	0.021	0.015	-10000	0	-0.12	6	6
RPS6KB1	-0.004	0.09	-10000	0	-0.32	39	39
RARs/THRs/DNA/SMRT	-0.002	0.083	-10000	0	-0.16	103	103
THRA	0.022	0.015	-10000	0	-0.12	6	6
mol:Bile acids	0	0	-10000	0	-10000	0	0
VDR/Vit D3/DNA	0.009	0.035	-10000	0	-0.12	36	36
RXRs/PPAR/9cRA/PGJ2/DNA	0.041	0.073	0.27	14	-0.13	48	62
NR1H4	0.022	0.016	-10000	0	-0.12	7	7
RXRs/LXRs/DNA	0.059	0.086	-10000	0	-0.16	55	55
NR1H2	0.021	0.027	-10000	0	-0.12	12	12
NR1H3	0.02	0.029	-10000	0	-0.095	18	18
RXRs/VDR/DNA/Vit D3	0.039	0.059	0.17	6	-0.12	23	29
NR4A1	0.003	0.049	-10000	0	-0.12	76	76
mol:ATRA	0	0	-10000	0	-10000	0	0
RXRs/FXR/9cRA/MED1	0.023	0.048	-10000	0	-0.14	23	23
RXRG	0.007	0.05	-10000	0	-0.12	70	70
RXR alpha/CCPG	0.031	0.026	-10000	0	-0.12	9	9
RXRA	0.021	0.025	-10000	0	-0.11	10	10
RXRB	0.024	0.02	-10000	0	-0.035	50	50
THRB	0.012	0.035	-10000	0	-0.12	36	36
PPARG	0.017	0.029	-10000	0	-0.12	24	24
PPARD	0.023	0.008	-10000	0	-0.12	2	2
TNF	0.021	0.13	-10000	0	-0.4	22	22
mol:Oxysterols	0.001	0.015	-10000	0	-0.041	59	59
cholesterol transport	0.019	0.13	-10000	0	-0.34	60	60
PPARA	0.022	0.012	-10000	0	-0.12	4	4
mol:Vit D3	0	0	-10000	0	-10000	0	0
RARB	0.013	0.034	-10000	0	-0.12	33	33
RXRs/NUR77/BCL2	0.013	0.046	-10000	0	-0.15	23	23
SREBF1	0.022	0.13	-10000	0	-0.48	10	10
RXRs/RXRs/DNA/9cRA	0.041	0.073	0.26	14	-0.13	48	62
ABCA1	-0.029	0.27	-10000	0	-0.82	58	58
RARs/THRs	0.027	0.072	-10000	0	-0.1	105	105
RXRs/FXR	0.049	0.056	0.18	8	-0.12	15	23
BCL2	0.016	0.031	-10000	0	-0.12	28	28

×

Wnt signaling

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Noncanonical Wnts/FZD	-0.032	0.1	-9999	-0.26	61	61
FZD6	0.017	0.024	-9999	-0.12	15	15
WNT6	0.022	0.011	-9999	-0.12	3	3
WNT4	0.023	0.01	-9999	-0.12	3	3
FZD3	0.013	0.032	-9999	-0.12	30	30
WNT5A	0.014	0.031	-9999	-0.12	27	27
WNT11	0.002	0.051	-9999	-0.12	83	83

×

EGFR-dependent Endothelin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HRAS	0.023	0.006	-9999	-0.12	1	1
EGFR	0.015	0.03	-9999	-0.12	25	25
EGF/EGFR	0.013	0.053	-9999	-0.092	80	80
EGF/EGFR dimer/SHC/GRB2/SOS1	0.041	0.059	-9999	-0.095	69	69
mol:GTP	0	0	-9999	-10000	0	0
EDNRA	0.014	0.034	-9999	-0.12	34	34
response to oxidative stress	0	0	-9999	-10000	0	0
EGF	0.02	0.021	-9999	-0.12	13	13
EGF/EGFR dimer/SHC	0.03	0.046	-9999	-0.11	40	40
mol:GDP	0.036	0.056	-9999	-0.094	69	69
mol:Ca2+	0	0	-9999	-10000	0	0
EDN1	0.009	0.042	-9999	-0.12	54	54
GRB2/SOS1	0.021	0.046	-9999	-0.15	31	31
HRAS/GTP	0.023	0.045	-9999	-0.15	10	10
SHC1	0.023	0.001	-9999	-10000	0	0
HRAS/GDP	0.036	0.052	-9999	-0.16	10	10
FRAP1	0.016	0.044	-9999	-0.15	12	12
EGF/EGFR dimer	0.016	0.05	-9999	-0.11	74	74
SOS1	0.017	0.027	-9999	-0.12	20	20
GRB2	0.023	0.006	-9999	-0.12	1	1
ETA receptor/Endothelin-1	0.008	0.056	-9999	-0.095	115	115

×

Class I PI3K signaling events

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
ARF5/GTP	0.005	0.042	-10000	0	-0.11	49	49
DAPP1	0.006	0.078	-10000	0	-0.2	39	39
Src family/SYK family/BLNK-LAT/BTK-ITK	0.001	0.12	-10000	0	-0.29	54	54
mol:DAG	0.015	0.065	0.16	14	-0.14	43	57
HRAS	0.023	0.007	-10000	0	-0.13	1	1
RAP1A	0.022	0.012	-10000	0	-0.12	3	3
ARF5/GDP	0.003	0.086	-10000	0	-0.2	60	60
PLCG2	0.02	0.02	-10000	0	-0.12	11	11
PLCG1	0.018	0.025	-10000	0	-0.12	18	18
ARF5	0.02	0.019	-10000	0	-0.12	10	10
mol:GTP	-0.006	0.038	-10000	0	-0.11	54	54
ARF1/GTP	0.003	0.05	0.16	21	-0.12	41	62
RHOA	0.023	0.006	-10000	0	-0.12	1	1
YES1	0.02	0.018	-10000	0	-0.12	8	8
RAP1A/GTP	0.012	0.05	0.17	22	-0.12	38	60
ADAP1	-0.005	0.036	-10000	0	-0.1	54	54
ARAP3	-0.006	0.037	-10000	0	-0.11	54	54
INPPL1	0.021	0.018	-10000	0	-0.12	9	9
PREX1	0.021	0.017	-10000	0	-0.12	8	8
ARHGEF6	0.014	0.032	-10000	0	-0.12	29	29
ARHGEF7	0.023	0.006	-10000	0	-0.12	1	1
ARF1	0.018	0.027	-10000	0	-0.12	21	21
NRAS	0.022	0.012	-10000	0	-0.12	3	3
FYN	0.012	0.037	-10000	0	-0.12	40	40
ARF6	0.023	0.003	-10000	0	-10000	0	0
FGR	0.023	0.006	-10000	0	-0.12	1	1
mol:Ca2+	0.012	0.037	0.092	14	-0.077	37	51
mol:IP4	0	0	-10000	0	-10000	0	0
TIAM1	0.015	0.032	-10000	0	-0.12	29	29
ZAP70	0.023	0.006	-10000	0	-0.12	1	1
mol:IP3	0.013	0.049	0.11	14	-0.1	45	59
LYN	0.021	0.013	-10000	0	-0.12	4	4
ARF1/GDP	0.003	0.087	-10000	0	-0.21	57	57
RhoA/GDP	0.015	0.066	0.17	19	-0.15	44	63
PDK1/Src/Hsp90	0.042	0.03	-10000	0	-0.12	18	18
BLNK	0.014	0.033	-10000	0	-0.12	32	32
actin cytoskeleton reorganization	0.006	0.086	0.19	17	-0.22	43	60
SRC	0.023	0.008	-10000	0	-0.12	2	2
PLEKHA2	0.013	0.011	-10000	0	-0.056	13	13
RAC1	0.023	0.002	-10000	0	-10000	0	0
PTEN	0.022	0.008	-10000	0	-0.12	1	1
HSP90AA1	0.023	0.004	-10000	0	-10000	0	0
ARF6/GTP	0.006	0.042	-10000	0	-0.11	47	47
RhoA/GTP	0.013	0.051	0.17	22	-0.11	40	62
Src family/SYK family/BLNK-LAT	0.007	0.096	-10000	0	-0.26	37	37
BLK	0.022	0.013	-10000	0	-0.12	5	5
PDPK1	0.023	0.006	-10000	0	-0.12	1	1
CYTH1	-0.005	0.036	-10000	0	-0.1	54	54
HCK	0.019	0.023	-10000	0	-0.12	15	15
CYTH3	-0.005	0.036	-10000	0	-0.1	54	54
CYTH2	-0.005	0.036	-10000	0	-0.1	54	54
KRAS	0.015	0.034	-10000	0	-0.12	33	33
GO:0030676	0	0	-10000	0	-10000	0	0
FOXO3	0.016	0.053	0.13	22	-0.21	19	41
SGK1	0.009	0.049	-10000	0	-0.21	19	19
INPP5D	0	0	-10000	0	-10000	0	0
mol:GDP	-0.008	0.085	-10000	0	-0.22	56	56
SOS1	0.017	0.027	-10000	0	-0.12	20	20
SYK	0.016	0.027	-10000	0	-0.12	21	21
ARF6/GDP	0.008	0.063	0.17	19	-0.15	45	64
mol:PI-3-4-5-P3	-0.004	0.038	0.084	1	-0.11	54	55
ARAP3/RAP1A/GTP	0.012	0.05	0.17	22	-0.12	38	60
VAV1	0.02	0.019	-10000	0	-0.12	10	10
mol:PI-3-4-P2	0.01	0.011	-10000	0	-0.076	9	9
RAS family/GTP/PI3K Class I	0.026	0.058	0.19	22	-0.11	54	76
PLEKHA1	0.013	0.012	-10000	0	-0.056	17	17
Rac1/GDP	0.004	0.087	-10000	0	-0.2	58	58
LAT	0.022	0.01	-10000	0	-0.12	3	3
Rac1/GTP	-0.001	0.1	-10000	0	-0.24	69	69
ITK	-0.001	0.039	-10000	0	-0.11	43	43
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma	0.014	0.083	0.19	14	-0.19	43	57
LCK	0.022	0.015	-10000	0	-0.12	6	6
BTK	-0.003	0.043	-10000	0	-0.11	56	56

×

S1P4 pathway

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

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

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

×

EPO signaling pathway

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
BCL2L1	0.015	0.15	-9999	-0.43	40	40
CRKL	0.029	0.037	-9999	-0.084	26	26
mol:DAG	0.025	0.075	-9999	-0.19	48	48
HRAS	0.031	0.045	-9999	-0.12	17	17
MAPK8	0.021	0.042	-9999	-0.11	45	45
RAP1A	0.026	0.044	-9999	-0.12	26	26
GAB1	0.027	0.038	-9999	-0.084	31	31
MAPK14	0.021	0.041	-9999	-0.11	46	46
EPO	0.025	0.008	-9999	-0.12	1	1
PLCG1	0.026	0.077	-9999	-0.2	48	48
EPOR/TRPC2/IP3 Receptors	0.022	0.021	-9999	-0.12	12	12
RAPGEF1	0.023	0	-9999	-10000	0	0
EPO/EPOR (dimer)/SOCS3	0.036	0.042	-9999	-0.11	25	25
GAB1/SHC/GRB2/SOS1	0.041	0.053	-9999	-0.12	20	20
EPO/EPOR (dimer)	0.034	0.022	-9999	-0.087	11	11
IRS2	0.029	0.038	-9999	-0.078	46	46
STAT1	0.021	0.099	-9999	-0.26	54	54
STAT5B	0.031	0.076	-9999	-0.2	41	41
cell proliferation	0.019	0.039	-9999	-0.1	46	46
GAB1/SHIP/PIK3R1/SHP2/SHC	0.022	0.046	-9999	-0.11	27	27
TEC	0.02	0.044	-9999	-0.11	36	36
SOCS3	0.015	0.031	-9999	-0.12	28	28
STAT1 (dimer)	0.021	0.098	-9999	-0.25	54	54
JAK2	0.019	0.025	-9999	-0.12	17	17
PIK3R1	0.015	0.031	-9999	-0.12	28	28
EPO/EPOR (dimer)/JAK2	0.059	0.054	-9999	-0.085	45	45
EPO/EPOR	0.034	0.022	-9999	-0.087	11	11
LYN	0.022	0.014	-9999	-0.12	4	4
TEC/VAV2	0.021	0.059	-9999	-0.12	38	38
elevation of cytosolic calcium ion concentration	0.022	0.021	-9999	-0.12	12	12
SHC1	0.023	0.001	-9999	-10000	0	0
EPO/EPOR (dimer)/LYN	0.039	0.053	-9999	-0.13	45	45
mol:IP3	0.025	0.075	-9999	-0.19	48	48
PI3K regualtory subunit polypeptide 1/IRS2/SHIP	0.029	0.047	-9999	-0.12	20	20
SH2B3	0.024	0.004	-9999	-10000	0	0
NFKB1	0.017	0.054	-9999	-0.15	45	45
EPO/EPOR (dimer)/JAK2/SOCS3	-0.005	0.059	-9999	-0.17	61	61
PTPN6	0.025	0.038	-9999	-0.084	49	49
TEC/VAV2/GRB2	0.029	0.062	-9999	-0.12	34	34
EPOR	0.022	0.021	-9999	-0.12	12	12
INPP5D	0	0	-9999	-10000	0	0
mol:GDP	0.041	0.053	-9999	-0.12	20	20
SOS1	0.017	0.027	-9999	-0.12	20	20
PLCG2	0.02	0.02	-9999	-0.12	11	11
CRKL/CBL/C3G	0.053	0.041	-9999	-0.12	5	5
VAV2	0.028	0.037	-9999	-0.091	17	17
CBL	0.029	0.038	-9999	-0.079	45	45
SHC/Grb2/SOS1	0.03	0.044	-9999	-0.14	15	15
STAT5A	0.029	0.08	-9999	-0.19	55	55
GRB2	0.023	0.006	-9999	-0.12	1	1
STAT5 (dimer)	0.049	0.089	-9999	-0.23	34	34
LYN/PLCgamma2	0.019	0.05	-9999	-0.13	56	56
PTPN11	0.022	0.011	-9999	-0.12	3	3
BTK	0.022	0.046	-9999	-0.12	31	31
BCL2	0.019	0.12	-9999	-0.37	34	34

×

Paxillin-dependent events mediated by a4b1

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
CRKL	0.023	0.009	-10000	0	-0.12	2	2
Rac1/GDP	0.021	0.007	-10000	0	-10000	0	0
DOCK1	0.019	0.02	-10000	0	-0.12	11	11
ITGA4	0.015	0.029	-10000	0	-0.12	24	24
RAC1	0.023	0.002	-10000	0	-10000	0	0
alpha4/beta7 Integrin	0.005	0.065	-10000	0	-0.13	107	107
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.022	0.016	-10000	0	-0.12	7	7
alpha4/beta1 Integrin	0.02	0.059	-10000	0	-0.12	76	76
alpha4/beta7 Integrin/Paxillin	0.021	0.055	-10000	0	-0.1	80	80
lamellipodium assembly	0	0.12	-10000	0	-0.3	64	64
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
PI3K	0.007	0.065	-10000	0	-0.16	63	63
ARF6	0.023	0.003	-10000	0	-10000	0	0
TLN1	0.021	0.013	-10000	0	-0.12	4	4
PXN	0.021	0.014	-10000	0	-0.07	13	13
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
ARF6/GTP	0.031	0.051	-10000	0	-0.14	11	11
cell adhesion	0.026	0.061	-10000	0	-0.15	22	22
CRKL/CBL	0.033	0.013	-10000	0	-0.098	5	5
alpha4/beta1 Integrin/Paxillin	0.022	0.053	-10000	0	-0.1	77	77
ITGB1	0.021	0.015	-10000	0	-0.12	6	6
ITGB7	0.019	0.023	-10000	0	-0.12	15	15
ARF6/GDP	0.02	0.008	-10000	0	-10000	0	0
alpha4/beta1 Integrin/Paxillin/VCAM1	-0.021	0.082	-10000	0	-0.17	77	77
p130Cas/Crk/Dock1	0.034	0.041	-10000	0	-0.11	36	36
VCAM1	-0.018	0.059	-10000	0	-0.12	139	139
alpha4/beta1 Integrin/Paxillin/Talin	0.028	0.062	-10000	0	-0.15	22	22
alpha4/beta1 Integrin/Paxillin/GIT1	0.034	0.055	-10000	0	-0.14	11	11
BCAR1	0.023	0.01	-10000	0	-0.12	3	3
mol:GDP	-0.032	0.054	0.14	11	-10000	0	11
CBL	0.023	0.006	-10000	0	-0.12	1	1
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
GIT1	0.022	0.013	-10000	0	-0.12	5	5
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton	0.028	0.062	-10000	0	-0.15	22	22
Rac1/GTP	-0.002	0.13	-10000	0	-0.32	64	64

×

S1P5 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-10000	0	-10000	0	0
telencephalon oligodendrocyte cell migration	-0.006	0.066	0.13	91	-10000	0	91
GNAI2	0.022	0.01	-10000	0	-0.12	3	3
S1P/S1P5/G12	0.016	0.006	-10000	0	-0.12	1	1
mol:GDP	0	0	-10000	0	-10000	0	0
GNAO1	0.011	0.041	-10000	0	-0.12	50	50
RhoA/GTP	0.007	0.067	-10000	0	-0.13	91	91
negative regulation of cAMP metabolic process	-0.003	0.069	-10000	0	-0.15	89	89
GNAZ	0.022	0.012	-10000	0	-0.12	4	4
GNAI3	0.021	0.008	-10000	0	-0.12	1	1
GNA12	0.023	0.001	-10000	0	-10000	0	0
S1PR5	0	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
S1P/S1P5/Gi	-0.003	0.069	-10000	0	-0.15	89	89
RhoA/GDP	0.016	0.016	-10000	0	-0.14	6	6
RHOA	0.023	0.006	-10000	0	-0.12	1	1
GNAI1	0.012	0.035	-10000	0	-0.12	36	36

×

Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
DYNC1H1	0.021	0.014	-10000	0	-0.12	5	5
VLDLR	0.01	0.038	-10000	0	-0.12	42	42
LRPAP1	0.018	0.023	-10000	0	-0.12	15	15
NUDC	0.022	0.011	-10000	0	-0.12	3	3
RELN/LRP8	0.015	0.058	-10000	0	-0.12	53	53
CaM/Ca2+	0.014	0.02	-10000	0	-0.12	12	12
KATNA1	0.02	0.019	-10000	0	-0.12	10	10
GO:0030286	0	0	-10000	0	-10000	0	0
ABL1	0.006	0.047	-10000	0	-0.11	53	53
IQGAP1/CaM	0.016	0.054	-10000	0	-0.15	53	53
DAB1	0.023	0.01	-10000	0	-0.12	3	3
IQGAP1	0.02	0.017	-10000	0	-0.12	7	7
PLA2G7	0.005	0.044	-10000	0	-0.12	62	62
CALM1	0.022	0.014	-10000	0	-0.12	5	5
DYNLT1	0.019	0.022	-10000	0	-0.12	13	13
mol:Ca2+	0	0	-10000	0	-10000	0	0
LRPAP1/LRP8	0.015	0.054	-10000	0	-0.15	45	45
UniProt:Q4QZ09	0	0	-10000	0	-10000	0	0
CLIP1	0.023	0.009	-10000	0	-0.12	2	2
CDK5R1	0.023	0.006	-10000	0	-0.12	1	1
LIS1/Poliovirus Protein 3A	0.013	0.023	-10000	0	-0.12	11	11
CDK5R2	0.023	0.01	-10000	0	-0.12	3	3
mol:PP1	0	0	-10000	0	-10000	0	0
RELN/VLDLR/DAB1	0.01	0.06	-10000	0	-0.12	71	71
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
NDEL1/14-3-3 E	0.022	0.055	-10000	0	-0.16	19	19
MAP1B	-0.014	0.059	0.2	3	-0.19	47	50
RAC1	0.014	0.048	-10000	0	-0.36	7	7
p35/CDK5	0.008	0.053	-10000	0	-0.09	96	96
RELN	0	0.053	-10000	0	-0.12	91	91
PAFAH/LIS1	0.015	0.038	-10000	0	-0.13	14	14
LIS1/CLIP170	0.029	0.027	-10000	0	-0.13	11	11
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain	0.016	0.063	-10000	0	-0.15	38	38
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3	-0.014	0.098	-10000	0	-0.21	94	94
GO:0005869	0	0	-10000	0	-10000	0	0
NDEL1	0.011	0.052	-10000	0	-0.15	21	21
LIS1/IQGAP1	0.025	0.034	-10000	0	-0.16	13	13
RHOA	0.014	0.047	-10000	0	-0.32	8	8
PAFAH1B1	0.02	0.015	-10000	0	-0.07	15	15
PAFAH1B3	0.014	0.033	-10000	0	-0.12	31	31
PAFAH1B2	0.022	0.012	-10000	0	-0.12	4	4
MAP1B/LIS1/Dynein heavy chain	0.009	0.053	0.13	3	-0.13	54	57
NDEL1/Katanin 60/Dynein heavy chain	0.025	0.064	-10000	0	-0.17	24	24
LRP8	0.02	0.021	-10000	0	-0.12	12	12
NDEL1/Katanin 60	0.02	0.056	-10000	0	-0.16	22	22
P39/CDK5	0.008	0.053	-10000	0	-0.12	35	35
LIS1/NudC/Dynein intermediate chain/microtubule organizing center	0.028	0.028	-10000	0	-0.13	11	11
CDK5	0.004	0.043	-10000	0	-0.098	58	58
PPP2R5D	0.022	0.013	-10000	0	-0.12	5	5
LIS1/CLIP170/Dynein Complex/Dynactin Complex	0.025	0.023	-10000	0	-0.11	11	11
CSNK2A1	0.022	0.015	-10000	0	-0.12	6	6
RELN/VLDLR/DAB1/LIS1	0.021	0.059	-10000	0	-0.091	83	83
RELN/VLDLR	0.008	0.07	-10000	0	-0.11	121	121
CDC42	0.015	0.044	-10000	0	-0.35	6	6

×

S1P3 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.01	0.041	-9999	-0.12	51	51
mol:S1P	-0.002	0.007	-9999	-0.029	25	25
S1P1/S1P/Gi	0.008	0.066	-9999	-0.22	33	33
GNAO1	0.008	0.042	-9999	-0.12	50	50
S1P/S1P3/G12/G13	0.024	0.024	-9999	-0.097	16	16
AKT1	0.006	0.059	-9999	-0.42	5	5
AKT3	-0.055	0.23	-9999	-1	25	25
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.01	0.041	-9999	-0.12	51	51
GNAI2	0.02	0.014	-9999	-0.041	17	17
GNAI3	0.02	0.012	-9999	-0.12	1	1
GNAI1	0.01	0.036	-9999	-0.12	36	36
mol:GDP	0	0	-9999	-10000	0	0
S1PR3	-0.002	0.008	-9999	-0.031	25	25
S1PR2	0	0	-9999	-10000	0	0
EDG1	0.022	0.015	-9999	-0.12	6	6
mol:Ca2+	-0.016	0.089	-9999	-0.24	50	50
MAPK3	-0.013	0.085	-9999	-0.22	53	53
MAPK1	-0.013	0.085	-9999	-0.22	52	52
JAK2	-0.023	0.1	-9999	-0.25	72	72
CXCR4	-0.021	0.093	-9999	-0.24	63	63
FLT1	0.019	0.019	-9999	-0.13	5	5
RhoA/GDP	0.016	0.016	-9999	-0.14	6	6
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
SRC	-0.012	0.084	-9999	-0.22	50	50
S1P/S1P3/Gi	-0.016	0.089	-9999	-0.24	50	50
RAC1	0.023	0.002	-9999	-10000	0	0
RhoA/GTP	-0.006	0.085	-9999	-0.22	47	47
VEGFA	0.017	0.023	-9999	-0.12	11	11
S1P/S1P2/Gi	-0.011	0.077	-9999	-0.15	108	108
VEGFR1 homodimer/VEGFA homodimer	0.016	0.056	-9999	-0.15	45	45
RHOA	0.023	0.006	-9999	-0.12	1	1
S1P/S1P3/Gq	0.014	0.044	-9999	-0.15	34	34
GNAQ	0.021	0.015	-9999	-0.12	6	6
GNAZ	0.02	0.015	-9999	-0.12	4	4
G12/G13	0.03	0.028	-9999	-0.13	16	16
GNA14	0.02	0.02	-9999	-0.12	11	11
GNA15	0.021	0.017	-9999	-0.12	8	8
GNA12	0.023	0.001	-9999	-10000	0	0
GNA13	0.022	0.009	-9999	-0.12	2	2
GNA11	0.022	0.013	-9999	-0.12	5	5
Rac1/GTP	-0.006	0.086	-9999	-0.23	47	47

×

E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin	0.025	0.057	-9999	-0.12	63	63
E-cadherin/beta catenin	0.018	0.053	-9999	-0.15	49	49
CTNNB1	0.022	0.007	-9999	-0.12	1	1
JUP	0.02	0.021	-9999	-0.12	12	12
CDH1	0.021	0.015	-9999	-0.12	6	6

×

Regulation of Androgen receptor activity

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
HDAC1	0.02	0.015	-9999	-0.069	13	13
SMARCC1	-0.002	0.18	-9999	-1.1	14	14
REL	0.02	0.016	-9999	-0.12	7	7
HDAC7	-0.018	0.096	-9999	-0.2	78	78
JUN	0.015	0.032	-9999	-0.12	30	30
EP300	0.022	0.009	-9999	-0.12	2	2
KAT2B	0	0	-9999	-10000	0	0
KAT5	0	0	-9999	-10000	0	0
MAPK14	0.013	0.026	-9999	-0.071	36	36
FOXO1	0.023	0.008	-9999	-0.12	2	2
T-DHT/AR	-0.001	0.11	-9999	-0.21	78	78
MAP2K6	0.012	0.035	-9999	-0.12	35	35
BRM/BAF57	0.007	0.061	-9999	-0.11	110	110
MAP2K4	0.022	0.011	-9999	-0.12	3	3
SMARCA2	0.012	0.035	-9999	-0.12	36	36
PDE9A	-0.092	0.31	-9999	-0.86	78	78
NCOA2	0.022	0.013	-9999	-0.12	4	4
CEBPA	0.022	0.013	-9999	-0.12	5	5
EHMT2	0.023	0.009	-9999	-0.12	2	2
cell proliferation	-0.011	0.11	-9999	-0.26	54	54
NR0B1	0.013	0.037	-9999	-0.12	41	41
EGR1	-0.005	0.053	-9999	-0.12	98	98
RXRs/9cRA	0.034	0.032	-9999	-0.096	4	4
AR/RACK1/Src	0.01	0.073	-9999	-0.18	42	42
AR/GR	-0.013	0.085	-9999	-0.17	104	104
GNB2L1	0.023	0.003	-9999	-10000	0	0
PKN1	0.016	0.031	-9999	-0.12	27	27
RCHY1	0.018	0.022	-9999	-0.12	13	13
epidermal growth factor receptor activity	0	0	-9999	-10000	0	0
MAPK8	0.019	0.017	-9999	-0.073	9	9
T-DHT/AR/TIF2/CARM1	0.01	0.084	-9999	-0.16	67	67
SRC	0.015	0.027	-9999	-0.066	17	17
NR3C1	0.021	0.014	-9999	-0.12	5	5
KLK3	0.004	0.047	-9999	-10000	0	0
APPBP2	0.019	0.016	-9999	-0.12	6	6
TRIM24	0.023	0.014	-9999	-0.12	5	5
T-DHT/AR/TIP60	-0.014	0.071	-9999	-0.15	82	82
TMPRSS2	0.002	0.091	-9999	-0.68	4	4
RXRG	0.006	0.047	-9999	-0.12	68	68
mol:9cRA	0	0	-9999	-10000	0	0
RXRA	0.021	0.017	-9999	-0.12	8	8
RXRB	0.023	0	-9999	-10000	0	0
CARM1	0.019	0.026	-9999	-0.12	19	19
NR2C2	0.023	0.006	-9999	-0.12	1	1
KLK2	0.019	0.073	-9999	-0.25	13	13
AR	-0.01	0.075	-9999	-0.16	97	97
SENP1	0.022	0.011	-9999	-0.12	3	3
HSP90AA1	0.023	0.004	-9999	-10000	0	0
MDM2	0.018	0.02	-9999	-0.12	11	11
SRY	0.021	0.008	-9999	-0.11	2	2
GATA2	0.02	0.021	-9999	-0.12	13	13
MYST2	0.022	0.011	-9999	-0.12	3	3
HOXB13	0.02	0.027	-9999	-0.12	20	20
T-DHT/AR/RACK1/Src	0.006	0.074	-9999	-0.17	48	48
positive regulation of transcription	0.02	0.021	-9999	-0.12	13	13
DNAJA1	0.02	0.012	-9999	-0.13	2	2
proteasomal ubiquitin-dependent protein catabolic process	-0.001	0.09	-9999	-0.28	48	48
NCOA1	0.025	0.033	-9999	-0.16	16	16
SPDEF	0.012	0.041	-9999	-0.12	49	49
T-DHT/AR/TIF2	-0.007	0.088	-9999	-0.21	63	63
T-DHT/AR/Hsp90	-0.004	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	-0.073	16	16
SIRT1	0.023	0.003	-9999	-10000	0	0
ZMIZ2	0.02	0.013	-9999	-0.12	5	5
POU2F1	0.018	0.041	-9999	-0.077	77	77
T-DHT/AR/DAX-1	-0.007	0.077	-9999	-0.17	65	65
CREBBP	0.021	0.015	-9999	-0.12	6	6
SMARCE1	0.023	0.011	-9999	-0.12	3	3

×

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	52	52
ELF1	0.032	0.023	-9999	-0.2	3	3
CCNA2	0.013	0.032	-9999	-0.12	29	29
PIK3CA	0.02	0.017	-9999	-0.12	7	7
JAK3	0.023	0.013	-9999	-0.12	5	5
PIK3R1	0.015	0.031	-9999	-0.12	28	28
JAK1	0.022	0.01	-9999	-0.12	2	2
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	-0.005	0.13	-9999	-0.3	57	57
SHC1	0.024	0.002	-9999	-10000	0	0
SP1	0.012	0.054	-9999	-0.25	11	11
IL2RA	0.03	0.037	-9999	-0.49	2	2
IL2RB	0.02	0.023	-9999	-0.12	15	15
SOS1	0.018	0.027	-9999	-0.12	20	20
IL2RG	-0.001	0.049	-9999	-0.12	82	82
G1/S transition of mitotic cell cycle	-0.075	0.17	-9999	-0.31	155	155
PTPN11	0.022	0.011	-9999	-0.12	3	3
CCND2	0	0.087	-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	0.039	-9999	-0.12	47	47
CCND3	-0.003	0.14	-9999	-0.5	18	18

×

Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.023	0.009	-10000	0	-0.12	2	2
RAS family/GTP/Tiam1	0.002	0.065	-10000	0	-0.16	63	63
NT3 (dimer)/TRKC	0.008	0.05	-10000	0	-0.08	131	131
NT3 (dimer)/TRKB	0.023	0.046	-10000	0	-0.12	19	19
SHC/Grb2/SOS1/GAB1/PI3K	0.002	0.087	-10000	0	-0.17	94	94
RAPGEF1	0.023	0	-10000	0	-10000	0	0
BDNF	0.023	0.01	-10000	0	-0.12	3	3
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
DYNLT1	0.019	0.022	-10000	0	-0.12	13	13
NTRK1	0.023	0.006	-10000	0	-0.12	1	1
NTRK2	0.019	0.025	-10000	0	-0.12	18	18
NTRK3	0.015	0.033	-10000	0	-0.12	31	31
NT-4/5 (dimer)/TRKB	0.027	0.02	-10000	0	-0.063	26	26
neuron apoptosis	-0.043	0.037	-10000	0	-10000	0	0
SHC 2-3/Grb2	0.045	0.039	-10000	0	-10000	0	0
SHC1	0.023	0.001	-10000	0	-10000	0	0
SHC2	0.027	0.034	-10000	0	-10000	0	0
SHC3	0.027	0.034	-10000	0	-10000	0	0
STAT3 (dimer)	-0.019	0.1	-10000	0	-0.25	86	86
NT3 (dimer)/TRKA	0.026	0.043	-10000	0	-0.12	11	11
RIN/GDP	0.03	0.062	-10000	0	-0.18	29	29
GIPC1	0.019	0.023	-10000	0	-0.12	15	15
KRAS	0.014	0.034	-10000	0	-0.12	33	33
DNAJA3	0.009	0.042	0.16	14	-0.14	8	22
RIN/GTP	0.017	0.007	-10000	0	-0.076	3	3
CCND1	-0.057	0.18	-10000	0	-0.48	85	85
MAGED1	0.02	0.019	-10000	0	-0.12	10	10
PTPN11	0.022	0.011	-10000	0	-0.12	3	3
RICS	0.017	0.027	-10000	0	-0.12	20	20
NT-4/5 (dimer)	0	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1	0.035	0.042	-10000	0	-0.12	32	32
GRB2	0.023	0.006	-10000	0	-0.12	1	1
NGF (dimer)/TRKA/MATK	0.031	0.01	-10000	0	-0.12	1	1
TRKA/NEDD4-2	0.022	0.042	-10000	0	-0.11	50	50
ELMO1	0.01	0.04	-10000	0	-0.12	48	48
RhoG/GTP/ELMO1/DOCK1	0.009	0.049	-10000	0	-0.088	109	109
NGF	0	0	-10000	0	-10000	0	0
HRAS	0.023	0.006	-10000	0	-0.12	1	1
DOCK1	0.019	0.02	-10000	0	-0.12	11	11
GAB2	0.007	0.041	-10000	0	-0.12	52	52
RIT2	0.023	0.01	-10000	0	-0.12	3	3
RIT1	0.021	0.014	-10000	0	-0.12	5	5
FRS2	0.019	0.023	-10000	0	-0.12	15	15
DNM1	0.02	0.02	-10000	0	-0.12	11	11
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.022	0.016	-10000	0	-0.12	7	7
SH2B1 (homopentamer)	0	0	-10000	0	-10000	0	0
RhoG/GTP	0.006	0.044	0.13	3	-0.14	12	15
mol:GDP	0.026	0.083	-10000	0	-0.27	29	29
NGF (dimer)	0	0	-10000	0	-10000	0	0
RhoG/GDP	0.004	0.039	-10000	0	-0.097	68	68
RIT1/GDP	0.029	0.064	-10000	0	-0.19	29	29
TIAM1	0.015	0.032	-10000	0	-0.12	29	29
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
BDNF (dimer)/TRKB	0.043	0.021	-10000	0	-0.11	3	3
KIDINS220/CRKL/C3G	0.034	0.01	-10000	0	-0.14	1	1
SHC/RasGAP	0.025	0.039	-10000	0	-0.13	32	32
FRS2 family/SHP2	0.035	0.041	-10000	0	-0.12	33	33
SHC/GRB2/SOS1/GAB1	0.042	0.048	-10000	0	-0.1	44	44
RIT1/GTP	0.012	0.028	-10000	0	-0.13	20	20
NT3 (dimer)	-0.003	0.055	-10000	0	-0.12	101	101
RAP1/GDP	0.017	0.056	-10000	0	-0.17	31	31
KIDINS220/CRKL	0.023	0.009	-10000	0	-0.12	2	2
BDNF (dimer)	0.022	0.01	-10000	0	-0.12	3	3
ubiquitin-dependent protein catabolic process	0.021	0.035	-10000	0	-0.088	50	50
Schwann cell development	-0.004	0.009	-10000	0	-0.052	2	2
EHD4	0.023	0.001	-10000	0	-10000	0	0
FRS2 family/GRB2/SOS1	0.041	0.051	-10000	0	-0.11	41	41
FRS2 family/SHP2/CRK family/C3G/GAB2	0.013	0.064	-10000	0	-0.13	83	83
RAP1B	0.019	0.019	-10000	0	-0.12	10	10
RAP1A	0.021	0.011	-10000	0	-0.12	3	3
CDC42/GTP	0.031	0.04	-10000	0	-0.15	4	4
ABL1	0.022	0.007	-10000	0	-0.12	1	1
SH2B family/GRB2/SOS1	0.021	0.046	-10000	0	-0.15	31	31
Rap1/GTP	0.023	0.081	-10000	0	-0.25	35	35
STAT3	-0.019	0.1	-10000	0	-0.25	86	86
axon guidance	0.021	0.034	-10000	0	-0.14	4	4
MAPK3	0.024	0.013	-10000	0	-0.21	1	1
MAPK1	0.024	0.014	-10000	0	-0.21	1	1
CDC42/GDP	0.03	0.062	-10000	0	-0.18	29	29
NTF3	-0.003	0.055	-10000	0	-0.12	101	101
NTF4	0	0	-10000	0	-10000	0	0
NGF (dimer)/TRKA/FAIM	0.03	0.012	-10000	0	-0.12	2	2
PI3K	0.007	0.065	-10000	0	-0.16	63	63
FRS3	0.023	0.008	-10000	0	-0.12	2	2
FAIM	0.022	0.012	-10000	0	-0.12	4	4
GAB1	0.02	0.022	-10000	0	-0.12	13	13
RASGRF1	0.01	0.042	0.16	14	-0.14	8	22
SOS1	0.017	0.027	-10000	0	-0.12	20	20
MCF2L	0.008	0.038	-10000	0	-0.12	18	18
RGS19	0.023	0	-10000	0	-10000	0	0
CDC42	0.023	0.002	-10000	0	-10000	0	0
RAS family/GTP	0.017	0.11	-10000	0	-0.32	48	48
Rac1/GDP	0.03	0.062	-10000	0	-0.18	29	29
NGF (dimer)/TRKA/GRIT	0.021	0.035	-10000	0	-0.12	28	28
neuron projection morphogenesis	-0.042	0.18	-10000	0	-0.82	22	22
NGF (dimer)/TRKA/NEDD4-2	0.021	0.035	-10000	0	-0.089	50	50
MAP2K1	0.021	0.037	-10000	0	-0.091	44	44
NGFR	0.021	0.018	-10000	0	-0.12	9	9
NGF (dimer)/TRKA/GIPC/GAIP	0.019	0.047	-10000	0	-0.14	42	42
RAS family/GTP/PI3K	-0.003	0.084	-10000	0	-0.18	88	88
FRS2 family/SHP2/GRB2/SOS1	0.046	0.059	-10000	0	-0.11	54	54
NRAS	0.022	0.011	-10000	0	-0.12	3	3
GRB2/SOS1	0.021	0.046	-10000	0	-0.15	31	31
PRKCI	0.016	0.028	-10000	0	-0.12	22	22
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
RAC1	0.023	0.002	-10000	0	-10000	0	0
PRKCZ	0.023	0	-10000	0	-10000	0	0
MAPKKK cascade	0.027	0.033	-10000	0	-0.4	2	2
RASA1	0.021	0.011	-10000	0	-0.12	3	3
TRKA/c-Abl	0.029	0.031	-10000	0	-0.14	18	18
SQSTM1	0.021	0.015	-10000	0	-0.12	6	6
BDNF (dimer)/TRKB/GIPC	0.041	0.048	-10000	0	-0.1	42	42
NGF (dimer)/TRKA/p62/Atypical PKCs	0.033	0.052	-10000	0	-0.097	66	66
MATK	0.022	0.013	-10000	0	-0.12	5	5
NEDD4L	0.017	0.027	-10000	0	-0.12	21	21
RAS family/GDP	-0.013	0.034	-10000	0	-0.13	34	34
NGF (dimer)/TRKA	0.003	0.036	-10000	0	-0.15	8	8
Rac1/GTP	-0.016	0.041	-10000	0	-0.13	38	38
FRS2 family/SHP2/CRK family	0.055	0.042	-10000	0	-0.086	37	37

×

Canonical NF-kappaB 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
FBXW11	0.019	0.02	-9999	-0.055	28	28
mol:GTP	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.012	0.11	-9999	-0.26	54	54
ERC1	0.016	0.029	-9999	-0.12	24	24
RIP2/NOD2	0.013	0.053	-9999	-0.11	84	84
NFKBIA	0.001	0.087	-9999	-0.27	43	43
BIRC2	0.021	0.013	-9999	-0.12	4	4
IKBKB	0.022	0.015	-9999	-0.12	6	6
RIPK2	0.013	0.034	-9999	-0.12	34	34
IKBKG	0.012	0.09	-9999	-0.35	23	23
IKK complex/A20	0.037	0.095	-9999	-0.31	26	26
NEMO/A20/RIP2	0.013	0.034	-9999	-0.12	34	34
XPO1	0.022	0.01	-9999	-0.12	2	2
NEMO/ATM	0.017	0.099	-9999	-0.31	35	35
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
RAN	0.023	0.002	-9999	-10000	0	0
Exportin 1/RanGTP	0.025	0.03	-9999	-0.12	24	24
IKK complex/ELKS	0.02	0.093	-9999	-0.33	25	25
BCL10/MALT1/TRAF6	0.035	0.041	-9999	-0.12	31	31
NOD2	0.023	0.006	-9999	-0.12	1	1
NFKB1	0.017	0.023	-9999	-0.063	32	32
RELA	0.019	0.022	-9999	-0.061	30	30
MALT1	0.018	0.026	-9999	-0.12	19	19
cIAP1/UbcH5C	0.021	0.047	-9999	-0.14	41	41
ATM	0.018	0.022	-9999	-0.12	13	13
TNF/TNFR1A	0.025	0.036	-9999	-0.11	37	37
TRAF6	0.022	0.009	-9999	-0.12	2	2
PRKCA	0.011	0.038	-9999	-0.12	42	42
CHUK	0.021	0.013	-9999	-0.12	4	4
UBE2D3	0.023	0.001	-9999	-10000	0	0
TNF	0.02	0.02	-9999	-0.12	11	11
NF kappa B1 p50/RelA	0.029	0.075	-9999	-0.15	76	76
BCL10	0.023	0.001	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.001	0.086	-9999	-0.27	43	43
beta TrCP1/SCF ubiquitin ligase complex	0.019	0.02	-9999	-0.056	28	28
TNFRSF1A	0.021	0.016	-9999	-0.12	7	7
IKK complex	0.029	0.097	-9999	-0.31	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

×

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)	0.016	0.12	-10000	0	-0.48	29	29
HDAC1	0.027	0.027	0.092	19	-0.1	10	29
AES	0.023	0.02	0.063	2	-0.12	10	12
FBXW11	0.023	0.003	-10000	0	-10000	0	0
DTX1	0.023	0.008	-10000	0	-0.12	2	2
LRP6/FZD1	0.018	0.047	-10000	0	-0.11	67	67
TLE1	0.022	0.02	0.075	1	-0.11	10	11
AP1	-0.003	0.071	-10000	0	-0.2	46	46
NCSTN	0.022	0.012	-10000	0	-0.12	4	4
ADAM10	0.021	0.014	-10000	0	-0.12	5	5
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4	-0.059	0.19	-10000	0	-0.44	68	68
NICD/RBPSUH	0.014	0.12	-10000	0	-0.48	29	29
WIF1	0.02	0.021	-10000	0	-0.12	13	13
NOTCH1	0.001	0.12	-10000	0	-0.51	29	29
PSENEN	0.016	0.03	-10000	0	-0.12	25	25
KREMEN2	0.022	0.012	-10000	0	-0.12	4	4
DKK1	0.015	0.034	-10000	0	-0.12	34	34
beta catenin/beta TrCP1	-0.005	0.081	-10000	0	-0.27	30	30
APH1B	0.014	0.031	-10000	0	-0.12	28	28
APH1A	0.023	0.009	-10000	0	-0.12	2	2
AXIN1	-0.001	0.046	0.19	4	-0.19	16	20
CtBP/CBP/TCF1/TLE1/AES	0.037	0.096	0.18	107	-0.19	31	138
PSEN1	0.022	0.008	-10000	0	-0.12	1	1
FOS	-0.005	0.052	-10000	0	-0.12	95	95
JUN	0.014	0.032	-10000	0	-0.12	30	30
MAP3K7	0.024	0.017	-10000	0	-0.12	5	5
CTNNB1	-0.016	0.078	-10000	0	-0.28	29	29
MAPK3	0.022	0.014	-10000	0	-0.12	5	5
DKK2/LRP6/Kremen 2	0.032	0.043	-10000	0	-0.11	33	33
HNF1A	0.024	0.014	-10000	0	-0.12	4	4
CTBP1	0.024	0.017	0.065	1	-0.12	7	8
MYC	-0.16	0.42	-10000	0	-1.2	75	75
NKD1	0.023	0.012	-10000	0	-0.12	4	4
FZD1	0.023	0.006	-10000	0	-0.12	1	1
NOTCH1 precursor/Deltex homolog 1	0.014	0.12	-10000	0	-0.48	29	29
apoptosis	-0.003	0.07	-10000	0	-0.2	46	46
Delta 1/NOTCHprecursor	0.014	0.12	-10000	0	-0.48	29	29
DLL1	0.022	0.012	-10000	0	-0.12	4	4
PPARD	0.001	0.045	-10000	0	-10000	0	0
Gamma Secretase	0.033	0.067	-10000	0	-0.15	22	22
APC	-0.004	0.057	0.19	4	-0.25	16	20
DVL1	0.017	0.066	-10000	0	-0.3	20	20
CSNK2A1	0.021	0.015	-10000	0	-0.12	6	6
MAP3K7IP1	0.026	0.008	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	0.026	0.047	-10000	0	-0.11	35	35
LRP6	0.014	0.033	-10000	0	-0.12	32	32
CSNK1A1	0.022	0.007	-10000	0	-0.12	1	1
NLK	0.029	0.042	-10000	0	-0.22	11	11
CCND1	-0.18	0.43	-10000	0	-1.2	82	82
WNT1	0.023	0.008	-10000	0	-0.12	2	2
Axin1/APC/beta catenin	-0.001	0.085	0.2	3	-0.28	27	30
DKK2	0.023	0.01	-10000	0	-0.12	3	3
NOTCH1 precursor/DVL1	0.015	0.13	-10000	0	-0.44	34	34
GSK3B	0.023	0.011	-10000	0	-0.12	3	3
FRAT1	0.024	0.007	-10000	0	-0.12	1	1
NOTCH/Deltex homolog 1	0.016	0.12	-10000	0	-0.48	29	29
PPP2R5D	0.009	0.04	-10000	0	-0.2	13	13
MAPK1	0.021	0.016	-10000	0	-0.12	7	7
WNT1/LRP6/FZD1	0.042	0.045	-10000	0	-0.096	38	38
RBPJ	0.023	0.009	-10000	0	-0.12	2	2
CREBBP	0.017	0.018	-10000	0	-0.11	6	6

×

Atypical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL3/RelA	0.03	0.026	-9999	-0.17	5	5
FBXW11	0.023	0.003	-9999	-10000	0	0
NF kappa B1 p50/c-Rel	0.021	0.041	-9999	-0.11	43	43
NF kappa B1 p50/RelA/I kappa B alpha	0.018	0.073	-9999	-0.21	28	28
NFKBIA	0	0.066	-9999	-0.15	79	79
MAPK14	0.023	0.007	-9999	-0.12	1	1
NF kappa B1 p105/p50	0.021	0.043	-9999	-0.12	42	42
ARRB2	0.014	0.035	-9999	-0.2	14	14
REL	0.021	0.016	-9999	-0.12	7	7
response to oxidative stress	0	0	-9999	-10000	0	0
BCL3/NF kappa B1 p50	0.02	0.042	-9999	-0.12	42	42
response to UV	0	0	-9999	-10000	0	0
NF kappa B1 p105/RelA	0.022	0.04	-9999	-0.11	42	42
PIK3CA	0.02	0.017	-9999	-0.12	7	7
NF kappa B1 p50 dimer	0.012	0.044	-9999	-0.13	49	49
PIK3R1	0.015	0.031	-9999	-0.12	28	28
NFKB1	0.02	0.013	-9999	-0.07	10	10
RELA	0.023	0.009	-9999	-0.12	2	2
positive regulation of anti-apoptosis	0.013	0.051	-9999	-0.2	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	0.008	-9999	-0.12	2	2
PI3K	0.007	0.065	-9999	-0.16	63	63
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	21	21
I kappa B alpha/PIK3R1	0.008	0.069	-9999	-0.14	79	79
cell death	0.019	0.072	-9999	-0.19	35	35
NF kappa B1 p105/c-Rel	0.021	0.041	-9999	-0.11	43	43
LCK	0.022	0.015	-9999	-0.12	6	6
BCL3	0.02	0.022	-9999	-0.12	14	14

×

Regulation of Telomerase

Figure S85. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S85. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Telomerase catalytic core complex	-0.045	0.18	-10000	0	-0.49	32	32
RAD9A	0.023	0	-10000	0	-10000	0	0
AP1	-0.03	0.086	-10000	0	-0.15	160	160
IFNAR2	0.018	0.02	-10000	0	-0.12	8	8
AKT1	0.012	0.041	-10000	0	-0.17	7	7
ER alpha/Oestrogen	0.001	0.046	-10000	0	-0.13	60	60
NFX1/SIN3/HDAC complex	0.01	0.089	-10000	0	-0.24	42	42
EGF	0.02	0.022	-10000	0	-0.12	13	13
SMG5	0.022	0.011	-10000	0	-0.12	3	3
SMG6	0.023	0.01	-10000	0	-0.12	3	3
SP3/HDAC2	0.027	0.031	-10000	0	-0.1	22	22
TERT/c-Abl	-0.041	0.17	-10000	0	-0.46	34	34
SAP18	0.023	0.003	-10000	0	-10000	0	0
MRN complex	0.022	0.066	-10000	0	-0.14	67	67
WT1	0.019	0.016	-10000	0	-0.12	5	5
WRN	0.019	0.02	-10000	0	-0.12	10	10
SP1	0.02	0.015	-10000	0	-0.14	1	1
SP3	0.023	0.003	-10000	0	-10000	0	0
TERF2IP	0.023	0.009	-10000	0	-0.12	2	2
Telomerase/Nucleolin	-0.032	0.17	-10000	0	-0.43	38	38
Mad/Max	0.032	0.015	-10000	0	-0.078	4	4
TERT	-0.047	0.18	-10000	0	-0.51	28	28
CCND1	-0.13	0.36	-10000	0	-0.98	83	83
MAX	0.023	0.004	-10000	0	-10000	0	0
RBBP7	0.021	0.011	-10000	0	-0.12	3	3
RBBP4	0.021	0.014	-10000	0	-0.12	5	5
TERF2	0.025	0.017	0.082	40	-0.11	1	41
PTGES3	0.014	0.035	-10000	0	-0.12	36	36
SIN3A	0.021	0.014	-10000	0	-0.12	5	5
Telomerase/911	0.017	0.095	-10000	0	-0.34	27	27
CDKN1B	-0.015	0.096	-10000	0	-0.24	57	57
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	-0.12	14	14
UBE3A	0.023	0.004	-10000	0	-10000	0	0
JUN	0.014	0.032	-10000	0	-0.12	30	30
E6	-0.001	0.003	-10000	0	-10000	0	0
HPV-16 E6/E6AP	0.014	0.02	-10000	0	-0.15	7	7
FOS	-0.005	0.052	-10000	0	-0.12	95	95
IFN-gamma/IRF1	-0.007	0.086	-10000	0	-0.16	114	114
PARP2	0.018	0.025	-10000	0	-0.12	18	18
BLM	0.015	0.031	-10000	0	-0.12	28	28
Telomerase	0.013	0.1	-10000	0	-0.39	24	24
IRF1	0.003	0.059	-10000	0	-0.13	71	71
ESR1	0.017	0.024	-10000	0	-0.12	15	15
KU/TER	0.018	0.058	-10000	0	-0.17	44	44
ATM/TRF2	0.02	0.05	-10000	0	-0.13	53	53
ubiquitin-dependent protein catabolic process	0.014	0.086	-10000	0	-0.25	34	34
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex	0.014	0.088	-10000	0	-0.25	36	36
HDAC1	0.019	0.019	-10000	0	-0.12	10	10
HDAC2	0.017	0.024	-10000	0	-0.12	12	12
ATM	-0.012	0.068	0.14	1	-0.26	40	41
SMAD3	0.019	0.019	-10000	0	-0.07	21	21
ABL1	0.022	0.007	-10000	0	-0.12	1	1
MXD1	0.021	0.017	-10000	0	-0.12	8	8
MRE11A	0.02	0.017	-10000	0	-0.12	8	8
HUS1	0.023	0	-10000	0	-10000	0	0
RPS6KB1	0.021	0.014	-10000	0	-0.12	5	5
TERT/NF kappa B1/14-3-3	-0.023	0.17	-10000	0	-0.46	23	23
NR2F2	0.022	0.015	-10000	0	-0.12	5	5
MAPK3	0.021	0.016	-10000	0	-0.09	8	8
MAPK1	0.02	0.017	-10000	0	-0.086	10	10
TGFB1/TGF beta receptor Type II	0.019	0.023	-10000	0	-0.12	14	14
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
HNRNPC	0.022	0.012	-10000	0	-0.12	4	4
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis	-0.012	0.068	0.14	1	-0.26	40	41
NBN	0.021	0.013	-10000	0	-0.12	4	4
EGFR	0.015	0.03	-10000	0	-0.12	25	25
mol:Oestrogen	0	0.002	-10000	0	-10000	0	0
EGF/EGFR	0.015	0.051	-10000	0	-0.11	74	74
MYC	0.015	0.027	-10000	0	-0.12	20	20
IL2	0.02	0.016	-10000	0	-0.12	3	3
KU	0.018	0.058	-10000	0	-0.17	44	44
RAD50	0.021	0.015	-10000	0	-0.12	6	6
HSP90AA1	0.023	0.004	-10000	0	-10000	0	0
TGFB1	0.019	0.023	-10000	0	-0.12	14	14
TRF2/BLM	0.024	0.043	-10000	0	-0.12	29	29
FRAP1	0.022	0.012	-10000	0	-0.12	4	4
KU/TERT	-0.033	0.18	-10000	0	-0.46	35	35
SP1/HDAC2	0.025	0.037	-10000	0	-0.13	20	20
PINX1	0.021	0.017	-10000	0	-0.12	8	8
Telomerase/EST1A	-0.028	0.16	-10000	0	-0.42	36	36
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	78	78
Telomerase/PinX1	-0.031	0.17	-10000	0	-0.43	35	35
Telomerase/AKT1/mTOR/p70S6K	0.004	0.11	-10000	0	-0.4	21	21
SIN3B	0.022	0.015	-10000	0	-0.12	6	6
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
Telomerase/EST1B	-0.029	0.16	-10000	0	-0.42	36	36
response to DNA damage stimulus	-0.004	0.031	0.052	1	-0.12	40	41
MRN complex/TRF2/Rap1	0.045	0.061	-10000	0	-0.11	57	57
TRF2/WRN	0.024	0.041	-10000	0	-0.11	47	47
Telomerase/hnRNP C1/C2	-0.028	0.16	-10000	0	-0.42	35	35
E2F1	0.02	0.018	-10000	0	-0.12	7	7
ZNFX1	0.019	0.021	-10000	0	-0.12	12	12
PIF1	0.023	0.006	-10000	0	-0.12	1	1
NCL	0.022	0.008	-10000	0	-0.12	1	1
DKC1	0.022	0.011	-10000	0	-0.12	3	3
telomeric DNA binding	0	0	-10000	0	-10000	0	0

×

Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity	-0.023	0.043	0.14	29	-10000	0	29
KIRREL	0.018	0.027	-10000	0	-0.12	20	20
Nephrin/NEPH1Par3/Par6/Atypical PKCs	0.023	0.043	-10000	0	-0.14	29	29
PLCG1	0.018	0.025	-10000	0	-0.12	18	18
ARRB2	0.022	0.013	-10000	0	-0.12	5	5
WASL	0.023	0.008	-10000	0	-0.12	2	2
Nephrin/NEPH1/podocin/CD2AP	0.036	0.056	-10000	0	-0.11	66	66
ChemicalAbstracts:57-88-5	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP	0.021	0.053	-10000	0	-0.16	12	12
FYN	0.014	0.034	-10000	0	-0.11	27	27
mol:Ca2+	0.04	0.048	-10000	0	-0.11	40	40
mol:DAG	0.041	0.048	-10000	0	-0.11	40	40
NPHS2	0.022	0.014	-10000	0	-0.12	4	4
mol:IP3	0.041	0.048	-10000	0	-0.11	40	40
regulation of endocytosis	0.032	0.045	-10000	0	-0.097	33	33
Nephrin/NEPH1/podocin/Cholesterol	0.034	0.035	-10000	0	-0.099	28	28
establishment of cell polarity	0.023	0.043	-10000	0	-0.14	29	29
Nephrin/NEPH1/podocin/NCK1-2	0.049	0.054	-10000	0	-0.1	39	39
Nephrin/NEPH1/beta Arrestin2	0.033	0.046	-10000	0	-0.098	33	33
NPHS1	0.021	0.02	-10000	0	-0.13	9	9
Nephrin/NEPH1/podocin	0.026	0.045	-10000	0	-0.11	29	29
TJP1	0.021	0.01	-10000	0	-0.12	2	2
NCK1	0.02	0.019	-10000	0	-0.12	9	9
NCK2	0.023	0.006	-10000	0	-0.12	1	1
heterophilic cell adhesion	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/PLCgamma1	0.042	0.049	-10000	0	-0.11	40	40
CD2AP	0.02	0.017	-10000	0	-0.12	7	7
Nephrin/NEPH1/podocin/GRB2	0.046	0.042	-10000	0	-0.11	30	30
GRB2	0.023	0.006	-10000	0	-0.12	1	1
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
TRPC6	0.019	0.029	-10000	0	-0.086	28	28
cytoskeleton organization	0.022	0.047	-10000	0	-0.15	15	15
Nephrin/NEPH1	0.021	0.029	-10000	0	-0.091	29	29
Nephrin/NEPH1/ZO-1	0.027	0.055	-10000	0	-0.13	57	57

×

Arf6 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CENTA1/KIF3B	0.013	0.017	-9999	-0.077	18	18
ARNO/beta Arrestin1-2	0.029	0.019	-9999	-0.076	11	11
EGFR	0.015	0.03	-9999	-0.12	25	25
EPHA2	0.02	0.021	-9999	-0.12	13	13
USP6	0.023	0.006	-9999	-0.12	1	1
IQSEC1	0.023	0.006	-9999	-0.12	1	1
EGFR/EGFR/EGF/EGF	0.016	0.05	-9999	-0.11	74	74
ARRB2	0.017	0.018	-9999	-0.2	3	3
mol:GTP	0.003	0.006	-9999	-10000	0	0
ARRB1	0.02	0.022	-9999	-0.12	13	13
FBXO8	0.022	0.011	-9999	-0.12	3	3
TSHR	0.013	0.037	-9999	-0.12	41	41
EGF	0.02	0.021	-9999	-0.12	13	13
somatostatin receptor activity	0	0	-9999	0	26	26
ARAP2	0	0	-9999	0	25	25
mol:GDP	0.015	0.045	-9999	-0.16	25	25
mol:PI-3-4-5-P3	0	0	-9999	0	26	26
ITGA2B	0.023	0.006	-9999	-0.12	1	1
ARF6	0.023	0.003	-9999	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	0.029	0.063	-9999	-0.11	77	77
ADAP1	0	0	-9999	0	25	25
KIF13B	0.02	0.022	-9999	-0.12	13	13
HGF/MET	-0.017	0.074	-9999	-0.14	119	119
PXN	0.022	0.013	-9999	-0.12	5	5
ARF6/GTP	0.023	0.057	-9999	-0.2	26	26
EGFR/EGFR/EGF/EGF/ARFGEP100	0.031	0.045	-9999	-0.11	40	40
ADRB2	0.023	0.006	-9999	-0.12	1	1
receptor agonist activity	0	0	-9999	0	26	26
actin filament binding	0	0	-9999	0	26	26
SRC	0.023	0.008	-9999	-0.12	2	2
ITGB3	0.005	0.046	-9999	-0.12	67	67
GNAQ	0.021	0.015	-9999	-0.12	6	6
EFA6/PI-4-5-P2	0	0	-9999	-0.001	25	25
ARF6/GDP	0.021	0.05	-9999	-0.23	12	12
ARF6/GDP/GULP/ACAP1	0.018	0.06	-9999	-0.16	28	28
alphaIIb/beta3 Integrin/paxillin/GIT1	0.036	0.049	-9999	-0.096	39	39
ACAP1	0	0	-9999	0	9	9
ACAP2	0	0	-9999	0	25	25
LHCGR/beta Arrestin2	0.023	0.016	-9999	-0.14	3	3
EFNA1	0.014	0.031	-9999	-0.12	28	28
HGF	0.02	0.022	-9999	-0.12	14	14
CYTH3	0	0	-9999	-0.001	26	26
CYTH2	0	0.001	-9999	-0.004	26	26
NCK1	0.02	0.019	-9999	-0.12	9	9
fibronectin binding	0	0	-9999	0	27	27
endosomal lumen acidification	0	0	-9999	0	16	16
microtubule-based process	0	0	-9999	-10000	0	0
GULP1	0.005	0.045	-9999	-0.12	63	63
GNAQ/ARNO	0.015	0.007	-9999	-0.046	6	6
mol:Phosphatidic acid	0	0	-9999	0	25	25
PIP3-E	0.018	0.028	-9999	-0.12	22	22
MET	0.001	0.047	-9999	-0.12	71	71
GNA14	0.021	0.02	-9999	-0.12	11	11
GNA15	0.021	0.017	-9999	-0.12	8	8
GIT1	0.022	0.013	-9999	-0.12	5	5
mol:PI-4-5-P2	0	0	-9999	-0.001	25	25
GNA11	0.022	0.013	-9999	-0.12	5	5
LHCGR	0.022	0.013	-9999	-0.12	5	5
AGTR1	0.022	0.012	-9999	-0.12	4	4
desensitization of G-protein coupled receptor protein signaling pathway	0.023	0.016	-9999	-0.14	3	3
IPCEF1/ARNO	0.026	0.038	-9999	-0.083	41	41
alphaIIb/beta3 Integrin	0.011	0.053	-9999	-0.14	38	38

×

Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FOXP3	0.028	0.018	-10000	0	-0.097	7	7
NFATC2	0.019	0.19	-10000	0	-0.4	53	53
NFATC3	0.059	0.058	0.26	28	-0.24	2	30
CD40LG	0.043	0.14	-10000	0	-0.56	4	4
ITCH	0.025	0.067	-10000	0	-0.23	31	31
CBLB	0.023	0.073	-10000	0	-0.24	31	31
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment	0.039	0.15	-10000	0	-0.48	15	15
JUNB	0.008	0.042	-10000	0	-0.12	53	53
CaM/Ca2+/Calcineurin A alpha-beta B1	0.033	0.06	-10000	0	-0.18	35	35
T cell anergy	0.012	0.088	-10000	0	-0.3	31	31
TLE4	-0.013	0.18	-10000	0	-0.44	62	62
Jun/NFAT1-c-4/p21SNFT	0.081	0.15	-10000	0	-0.56	4	4
AP-1/NFAT1-c-4	0.081	0.19	-10000	0	-0.62	4	4
IKZF1	0.021	0.12	-10000	0	-0.31	27	27
T-helper 2 cell differentiation	0.024	0.14	-10000	0	-0.52	2	2
AP-1/NFAT1	0.008	0.15	-10000	0	-0.26	75	75
CALM1	0.026	0.038	-10000	0	-0.11	34	34
EGR2	0.068	0.15	-10000	0	-0.86	3	3
EGR3	0.07	0.14	-10000	0	-0.52	1	1
NFAT1/FOXP3	0.039	0.14	-10000	0	-0.27	48	48
EGR1	-0.004	0.053	-10000	0	-0.12	98	98
JUN	0.02	0.034	-10000	0	-0.12	31	31
EGR4	0.023	0.014	-10000	0	-0.12	5	5
mol:Ca2+	0.006	0.031	-10000	0	-0.12	29	29
GBP3	-0.058	0.23	-10000	0	-0.44	133	133
FOSL1	0.021	0.018	-10000	0	-0.12	9	9
NFAT1-c-4/MAF/IRF4	0.094	0.14	-10000	0	-0.57	3	3
DGKA	0.014	0.14	-10000	0	-0.31	53	53
CREM	0.021	0.012	-10000	0	-0.12	4	4
NFAT1-c-4/PPARG	0.082	0.14	-10000	0	-0.62	3	3
CTLA4	0.02	0.1	-10000	0	-0.25	32	32
NFAT1-c-4 (dimer)/EGR1	0.054	0.15	-10000	0	-0.56	5	5
NFAT1-c-4 (dimer)/EGR4	0.09	0.14	-10000	0	-0.56	4	4
FOS	0	0.052	-10000	0	-0.11	96	96
IFNG	0.019	0.14	-10000	0	-0.43	8	8
T cell activation	0.028	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	-0.071	0.13	0.61	3	-0.5	22	25
TNF	0.038	0.14	-10000	0	-0.53	5	5
FASLG	0.056	0.15	-10000	0	-0.98	3	3
TBX21	0.026	0.018	-10000	0	-0.13	3	3
BATF3	0	0	-10000	0	-10000	0	0
PRKCQ	0.019	0.03	-10000	0	-0.12	26	26
PTPN1	0.021	0.13	-10000	0	-0.28	46	46
NFAT1-c-4/ICER1	0.082	0.14	-10000	0	-0.56	4	4
GATA3	0.024	0.02	-10000	0	-0.12	11	11
T-helper 1 cell differentiation	0.018	0.13	-10000	0	-0.43	8	8
IL2RA	0.041	0.15	-10000	0	-0.43	18	18
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
CASP3	0.017	0.14	-10000	0	-0.36	33	33
E2F1	0.017	0.044	-10000	0	-0.15	36	36
PPARG	0.017	0.029	-10000	0	-0.12	24	24
SLC3A2	0.015	0.14	-10000	0	-0.34	37	37
IRF4	0.019	0.025	-10000	0	-0.12	18	18
PTGS2	0.035	0.15	-10000	0	-0.57	5	5
CSF2	0.043	0.14	-10000	0	-0.56	4	4
JunB/Fra1/NFAT1-c-4	0.072	0.15	-10000	0	-0.54	4	4
IL4	0.023	0.14	-10000	0	-0.54	2	2
IL5	0.043	0.14	-10000	0	-0.56	4	4
IL2	0.028	0.11	-10000	0	-0.47	1	1
IL3	0.012	0.041	-10000	0	-0.38	3	3
RNF128	0.025	0.052	-10000	0	-0.16	30	30
NFATC1	0.071	0.13	0.5	22	-0.62	3	25
CDK4	-0.081	0.28	-10000	0	-1.2	29	29
PTPRK	-0.005	0.17	-10000	0	-0.38	75	75
IL8	0.029	0.15	-10000	0	-0.55	6	6
POU2F1	0.031	0.007	-10000	0	-0.12	1	1

×

PDGFR-beta signaling pathway

Figure 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
S1P1/Sphingosine-1-phosphate	0.025	0.071	-9999	-0.22	19	19
PDGFB-D/PDGFRB/SLAP	0.02	0.039	-9999	-0.092	36	36
PDGFB-D/PDGFRB/APS/CBL	0.022	0.028	-9999	-0.059	56	56
AKT1	0.009	0.053	-9999	-0.12	44	44
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
mol:Sphingosine-1-phosphate	0.019	0.069	-9999	-0.23	18	18
PIK3CA	0.02	0.017	-9999	-0.12	7	7
FGR	0.014	0.04	-9999	-0.18	6	6
mol:Ca2+	0.011	0.066	-9999	-0.28	14	14
MYC	-0.06	0.26	-9999	-0.7	78	78
SHC1	0.023	0.001	-9999	-10000	0	0
HRAS/GDP	0.026	0.038	-9999	-0.087	38	38
LRP1/PDGFRB/PDGFB	0.024	0.052	-9999	-0.11	58	58
GRB10	0.022	0.014	-9999	-0.12	5	5
PTPN11	0.022	0.011	-9999	-0.12	3	3
GO:0007205	0.011	0.067	-9999	-0.28	14	14
PTEN	0.022	0.008	-9999	-0.12	1	1
GRB2	0.023	0.006	-9999	-0.12	1	1
GRB7	0.018	0.025	-9999	-0.12	18	18
PDGFB-D/PDGFRB/SHP2	0.018	0.044	-9999	-0.091	76	76
PDGFB-D/PDGFRB/GRB10	0.021	0.039	-9999	-0.1	27	27
cell cycle arrest	0.02	0.039	-9999	-0.092	36	36
HRAS	0.023	0.006	-9999	-0.12	1	1
HIF1A	0.007	0.054	-9999	-0.13	51	51
GAB1	0.005	0.08	-9999	-0.24	24	24
mol:GTP	0	0	-9999	-10000	0	0
DNM2	0.006	0.078	-9999	-0.21	37	37
PDGFB-D/PDGFRB	0.032	0.039	-9999	-0.095	23	23
mol:GDP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/LMW-PTP	0.017	0.046	-9999	-0.11	49	49
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB	0.018	0.086	-9999	-0.2	45	45
positive regulation of MAPKKK cascade	0.018	0.044	-9999	-0.09	76	76
PIK3R1	0.015	0.031	-9999	-0.12	28	28
mol:IP3	0.011	0.067	-9999	-0.28	14	14
E5	0	0.001	-9999	-10000	0	0
CSK	0.023	0.009	-9999	-0.12	2	2
PDGFB-D/PDGFRB/GRB7	0.017	0.045	-9999	-0.087	80	80
SHB	0.023	0.008	-9999	-0.12	2	2
BLK	0.014	0.038	-9999	-0.19	4	4
PTPN2	0.022	0.008	-9999	-0.13	1	1
PDGFB-D/PDGFRB/SNX15	0.024	0.032	-9999	-0.073	54	54
BCAR1	0.023	0.01	-9999	-0.12	3	3
VAV2	-0.005	0.11	-9999	-0.24	83	83
CBL	0.023	0.006	-9999	-0.12	1	1
PDGFB-D/PDGFRB/DEP1	0.017	0.045	-9999	-0.12	38	38
LCK	0.014	0.039	-9999	-0.16	9	9
PDGFRB	0.01	0.042	-9999	-0.12	51	51
ACP1	0.021	0.014	-9999	-0.12	5	5
HCK	-0.001	0.089	-9999	-0.41	19	19
ABL1	0.007	0.068	-9999	-0.21	23	23
PDGFB-D/PDGFRB/CBL	0.007	0.082	-9999	-0.27	19	19
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	0.03	-9999	-0.12	25	25
cell proliferation	-0.05	0.23	-9999	-0.62	78	78
SLA	0.02	0.02	-9999	-0.12	11	11
actin cytoskeleton reorganization	0.032	0.041	-9999	-0.15	7	7
SRC	0.015	0.038	-9999	-0.2	3	3
PI3K	-0.021	0.04	-9999	-0.14	43	43
PDGFB-D/PDGFRB/GRB7/SHC	0.031	0.041	-9999	-0.13	16	16
SH2B2	0	0	-9999	-10000	0	0
PLCgamma1/SPHK1	0.019	0.07	-9999	-0.24	18	18
LYN	-0.022	0.13	-9999	-0.43	48	48
LRP1	0.015	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	0.012	-9999	-0.12	4	4
NCK1-2/p130 Cas	0.046	0.051	-9999	-0.12	16	16
SPHK1	0.021	0.017	-9999	-0.12	8	8
EDG1	0.022	0.015	-9999	-0.12	6	6
mol:DAG	0.011	0.067	-9999	-0.28	14	14
PLCG1	0.011	0.068	-9999	-0.29	14	14
NHERF/PDGFRB	0.025	0.049	-9999	-0.12	30	30
YES1	-0.01	0.12	-9999	-0.44	32	32
cell migration	0.024	0.048	-9999	-0.12	30	30
SHC/Grb2/SOS1	0.044	0.051	-9999	-0.12	13	13
SLC9A3R2	0.017	0.029	-9999	-0.12	24	24
SLC9A3R1	0.016	0.03	-9999	-0.12	26	26
NHERF1-2/PDGFRB/PTEN	0.031	0.056	-9999	-0.11	51	51
FYN	-0.02	0.12	-9999	-0.38	45	45
DOK1	0.021	0.028	-9999	-0.11	10	10
HRAS/GTP	0.017	0.008	-9999	-0.11	2	2
PDGFB	0.023	0.01	-9999	-0.12	3	3
RAC1	-0.023	0.16	-9999	-0.4	83	83
PRKCD	0.02	0.03	-9999	-0.12	10	10
FER	0.02	0.029	-9999	-0.11	11	11
MAPKKK cascade	-0.008	0.027	-9999	-0.14	9	9
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	0.033	0.032	-9999	-0.091	18	18
PDGFB-D/PDGFRB/SHB	0.024	0.033	-9999	-0.086	17	17
chemotaxis	0.007	0.067	-9999	-0.2	23	23
STAT1-3-5/STAT1-3-5	0.021	0.058	-9999	-0.14	22	22
Bovine Papilomavirus E5/PDGFRB	0.008	0.029	-9999	-0.08	54	54
PTPRJ	0.02	0.019	-9999	-0.12	10	10

×

LPA4-mediated signaling events

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

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

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

×

Coregulation of Androgen receptor activity

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NRIP1	0.014	0.035	-9999	-0.12	35	35
SVIL	0.016	0.031	-9999	-0.12	27	27
ZNF318	0.019	0.013	-9999	-0.12	5	5
JMJD2C	0.029	0.016	-9999	-0.12	6	6
T-DHT/AR/Ubc9	0.017	0.058	-9999	-0.11	87	87
CARM1	0.019	0.026	-9999	-0.12	19	19
PRDX1	0.022	0.004	-9999	-10000	0	0
PELP1	0.022	0.008	-9999	-0.12	2	2
CTNNB1	0.023	0.008	-9999	-0.12	1	1
AKT1	0.02	0.019	-9999	-0.12	10	10
PTK2B	0.024	0.009	-9999	-0.12	2	2
MED1	0.02	0.014	-9999	-0.12	5	5
MAK	0.008	0.04	-9999	-0.12	48	48
response to oxidative stress	0	0	-9999	-10000	0	0
HIP1	0.022	0.018	-9999	-0.12	9	9
GSN	0.023	0.011	-9999	-0.12	3	3
NCOA2	0.022	0.013	-9999	-0.12	4	4
NCOA6	0.024	0.014	-9999	-0.12	5	5
DNA-PK	0.023	0.06	-9999	-0.14	61	61
NCOA4	0.023	0.004	-9999	-10000	0	0
PIAS3	0.021	0.022	-9999	-0.12	14	14
cell proliferation	0.004	0.045	-9999	-0.49	2	2
XRCC5	0.021	0.01	-9999	-0.12	2	2
UBE3A	0.025	0.004	-9999	-10000	0	0
T-DHT/AR/SNURF	0.015	0.059	-9999	-0.11	81	81
FHL2	0.017	0.078	-9999	-0.67	5	5
RANBP9	0.023	0.014	-9999	-0.12	5	5
JMJD1A	0.033	0.024	-9999	-0.11	6	6
CDK6	0.008	0.039	-9999	-0.12	47	47
TGFB1I1	0.024	0.012	-9999	-0.12	4	4
T-DHT/AR/CyclinD1	-0.01	0.078	-9999	-0.13	142	142
XRCC6	0.022	0.004	-9999	-10000	0	0
T-DHT/AR	0.026	0.077	-9999	-0.18	21	21
CTDSP1	0.023	0.011	-9999	-0.12	3	3
CTDSP2	0.02	0.009	-9999	-0.12	2	2
BRCA1	0.017	0.029	-9999	-0.12	24	24
TCF4	0.019	0.017	-9999	-0.12	8	8
CDKN2A	0.014	0.021	-9999	-0.12	10	10
SRF	0.024	0.03	-9999	-0.12	24	24
NKX3-1	0.013	0.086	-9999	-0.29	34	34
KLK3	0.014	0.038	-9999	-10000	0	0
TMF1	0.022	0.012	-9999	-0.12	3	3
HNRNPA1	0.022	0.002	-9999	-10000	0	0
AOF2	0.024	0.009	-9999	-0.12	2	2
APPL1	0.019	0.014	-9999	-0.072	12	12
T-DHT/AR/Caspase 8	0.012	0.061	-9999	-0.11	93	93
AR	0.015	0.038	-9999	-0.11	44	44
UBA3	0.001	0	-9999	-10000	0	0
PATZ1	0.021	0.012	-9999	-0.12	4	4
PAWR	0.023	0.009	-9999	-0.12	2	2
PRKDC	0.02	0.016	-9999	-0.12	7	7
PA2G4	0.021	0.009	-9999	-0.12	2	2
UBE2I	0.023	0.001	-9999	-10000	0	0
T-DHT/AR/Cyclin D3/CDK11 p58	0.014	0.055	-9999	-0.1	84	84
RPS6KA3	0.019	0.024	-9999	-0.12	15	15
T-DHT/AR/ARA70	0.014	0.062	-9999	-0.11	95	95
LATS2	0.022	0.006	-9999	-0.12	1	1
T-DHT/AR/PRX1	0.011	0.056	-9999	-0.099	97	97
Cyclin D3/CDK11 p58	0.014	0.019	-9999	-0.1	14	14
VAV3	0.011	0.037	-9999	-0.12	41	41
KLK2	0.016	0.072	-9999	-0.29	23	23
CASP8	0.022	0.004	-9999	-10000	0	0
T-DHT/AR/TIF2/CARM1	0.022	0.065	-9999	-0.099	105	105
TMPRSS2	0.005	0.098	-9999	-0.49	5	5
CCND1	0.007	0.042	-9999	-0.12	54	54
PIAS1	0.025	0.009	-9999	-0.12	2	2
mol:T-DHT	0.005	0.007	-9999	-0.055	2	2
CDC2L1	0	0	-9999	-10000	0	0
PIAS4	0.027	0.002	-9999	-10000	0	0
T-DHT/AR/CDK6	-0.008	0.078	-9999	-0.13	137	137
CMTM2	0.023	0.006	-9999	-0.12	1	1
SNURF	0.021	0.017	-9999	-0.12	8	8
ZMIZ1	0.022	0.031	-9999	-0.11	27	27
CCND3	0.021	0.018	-9999	-0.12	9	9
TGIF1	0.022	0.001	-9999	-10000	0	0
FKBP4	0.022	0.019	-9999	-0.12	10	10

×

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	0.044	-10000	0	-0.11	29	29
fibroblast growth factor receptor signaling pathway	0.029	0.044	-10000	0	-0.11	29	29
LAMA1	0	0.052	-10000	0	-0.12	90	90
PRNP	0.021	0.014	-10000	0	-0.12	5	5
GPC1/SLIT2	-0.01	0.07	-10000	0	-0.14	102	102
SMAD2	0.024	0.028	-10000	0	-0.1	18	18
GPC1/PrPc/Cu2+	0.021	0.037	-10000	0	-0.12	36	36
GPC1/Laminin alpha1	0.015	0.043	-10000	0	-0.075	102	102
TDGF1	0.022	0.015	-10000	0	-0.12	6	6
CRIPTO/GPC1	0.032	0.017	-10000	0	-0.075	14	14
APP/GPC1	0.023	0.043	-10000	0	-0.14	34	34
mol:NO	0	0	-10000	0	-10000	0	0
YES1	0.024	0.016	-10000	0	-0.11	1	1
FLT1	0.022	0.014	-10000	0	-0.12	5	5
GPC1/TGFB/TGFBR1/TGFBR2	0.039	0.032	-10000	0	-0.11	18	18
SERPINC1	0.023	0.008	-10000	0	-0.12	2	2
FYN	0.019	0.024	-10000	0	-0.11	1	1
FGR	0.026	0.013	-10000	0	-0.11	1	1
positive regulation of MAPKKK cascade	0.017	0.051	-10000	0	-0.18	16	16
SLIT2	0.001	0.047	-10000	0	-0.12	72	72
GPC1/NRG	0.032	0.019	-10000	0	-0.08	15	15
NRG1	0.021	0.017	-10000	0	-0.12	8	8
GPC1/VEGF165 homodimer/VEGFR1 homodimer	0.032	0.046	-10000	0	-0.12	42	42
LYN	0.024	0.015	-10000	0	-0.11	1	1
mol:Spermine	0.011	0.01	-10000	0	-0.076	7	7
cell growth	0.029	0.044	-10000	0	-0.11	29	29
BMP signaling pathway	-0.021	0.016	0.12	7	-10000	0	7
SRC	0.026	0.014	-10000	0	-0.11	2	2
TGFBR1	0.022	0.01	-10000	0	-0.12	3	3
mol:Cu2+	0	0	-10000	0	-10000	0	0
PLA2G2A	0.011	0.04	-10000	0	-0.12	48	48
GPC1	0.021	0.016	-10000	0	-0.12	7	7
TGFBR1 (dimer)	0.022	0.01	-10000	0	-0.12	3	3
VEGFA	0.019	0.02	-10000	0	-0.12	11	11
BLK	0.026	0.015	-10000	0	-0.11	2	2
HCK	0.024	0.019	-10000	0	-0.17	1	1
FGF2	0.023	0.008	-10000	0	-0.12	2	2
FGFR1	0.008	0.043	-10000	0	-0.12	56	56
VEGFR1 homodimer	0.022	0.014	-10000	0	-0.12	5	5
TGFBR2	0.02	0.02	-10000	0	-0.12	11	11
cell death	0.023	0.043	-10000	0	-0.14	34	34
ATIII/GPC1	0.033	0.015	-10000	0	-0.077	10	10
PLA2G2A/GPC1	0.024	0.033	-10000	0	-0.075	57	57
LCK	0.026	0.016	-10000	0	-0.17	1	1
neuron differentiation	0.031	0.019	-10000	0	-0.079	15	15
PrPc/Cu2+	0.006	0.04	-10000	0	-0.14	40	40
APP	0.022	0.008	-10000	0	-0.12	1	1
TGFBR2 (dimer)	0.02	0.02	-10000	0	-0.12	11	11

×

Glucocorticoid receptor regulatory network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PCK2	-0.011	0.059	-10000	0	-0.7	2	2
SMARCC2	0.022	0.012	-10000	0	-0.12	4	4
SMARCC1	0.023	0.004	-10000	0	-10000	0	0
TBX21	0.043	0.046	-10000	0	-0.31	1	1
SUMO2	0.021	0.005	-10000	0	-10000	0	0
STAT1 (dimer)	-0.007	0.079	-10000	0	-0.17	93	93
FKBP4	0.02	0.019	-10000	0	-0.12	10	10
FKBP5	0.006	0.042	-10000	0	-0.12	55	55
GR alpha/HSP90/FKBP51/HSP90	-0.013	0.081	0.18	1	-0.22	31	32
PRL	0.045	0.057	-10000	0	-0.5	1	1
cortisol/GR alpha (dimer)/TIF2	-0.021	0.11	0.38	3	-0.34	3	6
RELA	-0.021	0.076	-10000	0	-0.15	120	120
FGG	-0.016	0.1	0.34	1	-0.32	2	3
GR beta/TIF2	-0.006	0.07	0.2	2	-0.2	24	26
IFNG	-0.003	0.11	-10000	0	-0.45	2	2
apoptosis	-0.053	0.17	-10000	0	-0.43	48	48
CREB1	0.033	0.008	-10000	0	-10000	0	0
histone acetylation	0.025	0.083	0.28	7	-0.3	17	24
BGLAP	0.04	0.083	-10000	0	-0.87	3	3
GR/PKAc	0.028	0.062	0.22	1	-0.15	18	19
NF kappa B1 p50/RelA	-0.045	0.15	-10000	0	-0.27	142	142
SMARCD1	0.021	0.018	-10000	0	-0.12	9	9
MDM2	-0.003	0.045	-10000	0	-0.22	8	8
GATA3	0.037	0.022	-10000	0	-0.11	11	11
AKT1	0.015	0.021	0.15	2	-0.13	10	12
CSF2	0.029	0.057	-10000	0	-10000	0	0
GSK3B	0.02	0.012	-10000	0	-0.13	3	3
NR1I3	-0.039	0.15	-10000	0	-0.46	11	11
CSN2	-0.015	0.092	0.28	2	-0.29	3	5
BRG1/BAF155/BAF170/BAF60A	0.042	0.051	-10000	0	-0.11	45	45
NFATC1	0.033	0.012	-10000	0	-10000	0	0
POU2F1	0.031	0.008	-10000	0	-0.11	1	1
CDKN1A	-0.042	0.12	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
response to UV	-0.002	0.004	-10000	0	-10000	0	0
SFN	0.014	0.031	-10000	0	-0.12	28	28
GR alpha/HSP90/FKBP51/HSP90/14-3-3	-0.007	0.086	-10000	0	-0.2	44	44
prolactin receptor activity	0	0	-10000	0	-10000	0	0
EGR1	-0.12	0.28	-10000	0	-0.72	95	95
JUN	0.021	0.088	-10000	0	-0.31	4	4
IL4	0.046	0.046	-10000	0	-10000	0	0
CDK5R1	0.022	0.006	-10000	0	-0.12	1	1
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
cortisol/GR alpha (monomer)/AP-1	-0.041	0.08	0.19	15	-0.2	59	74
GR alpha/HSP90/FKBP51/HSP90/PP5C	0.006	0.079	-10000	0	-0.2	28	28
cortisol/GR alpha (monomer)	-0.04	0.12	0.42	3	-0.39	2	5
NCOA2	0.021	0.013	-10000	0	-0.12	4	4
response to hypoxia	0	0	-10000	0	-10000	0	0
FOS	-0.014	0.079	-10000	0	-0.17	76	76
AP-1/NFAT1-c-4	-0.011	0.15	-10000	0	-0.39	25	25
AFP	0.016	0.083	-10000	0	-0.56	1	1
SUV420H1	0.021	0.015	-10000	0	-0.12	6	6
IRF1	-0.094	0.23	-10000	0	-0.64	78	78
TP53	0.026	0.034	-10000	0	-10000	0	0
PPP5C	0.022	0.015	-10000	0	-0.12	6	6
KRT17	-0.011	0.15	-10000	0	-0.88	8	8
KRT14	0	0.18	0.49	7	-1.1	12	19
TBP	0.03	0.03	-10000	0	-0.22	6	6
CREBBP	0.022	0.047	0.29	12	-0.13	5	17
HDAC1	0.013	0.019	-10000	0	-0.13	10	10
HDAC2	0.018	0.021	-10000	0	-0.12	12	12
AP-1	-0.012	0.15	-10000	0	-0.4	25	25
MAPK14	0.02	0.008	-10000	0	-0.12	1	1
MAPK10	0.011	0.036	-10000	0	-0.12	38	38
MAPK11	0.021	0.004	-10000	0	-10000	0	0
KRT5	-0.069	0.26	-10000	0	-0.88	46	46
interleukin-1 receptor activity	-0.002	0.001	-10000	0	-10000	0	0
NCOA1	0.024	0.01	-10000	0	-0.095	3	3
STAT1	-0.007	0.079	-10000	0	-0.17	93	93
CGA	0.043	0.057	-10000	0	-0.51	1	1
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2	-0.048	0.11	0.28	5	-0.34	36	41
MAPK3	0.019	0.015	-10000	0	-0.12	5	5
MAPK1	0.019	0.017	-10000	0	-0.12	7	7
ICAM1	-0.13	0.32	-10000	0	-0.79	103	103
NFKB1	-0.032	0.099	-10000	0	-0.18	142	142
MAPK8	0.033	0.074	-10000	0	-0.26	5	5
MAPK9	0.019	0.012	-10000	0	-0.12	3	3
cortisol/GR alpha (dimer)	-0.056	0.17	-10000	0	-0.44	50	50
BAX	-0.04	0.12	-10000	0	-10000	0	0
POMC	0.03	0.081	-10000	0	-10000	0	0
EP300	0.022	0.045	0.29	12	-0.13	1	13
cortisol/GR alpha (dimer)/p53	-0.046	0.12	0.36	1	-0.38	2	3
proteasomal ubiquitin-dependent protein catabolic process	-0.006	0.057	0.26	15	-0.2	7	22
SGK1	-0.001	0.1	0.33	12	-0.31	34	46
IL13	0.022	0.088	-10000	0	-0.52	1	1
IL6	-0.028	0.15	-10000	0	-0.63	15	15
PRKACG	0.023	0.008	-10000	0	-0.12	2	2
IL5	0.025	0.088	-10000	0	-10000	0	0
IL2	0.005	0.11	-10000	0	-0.46	1	1
CDK5	0.013	0.032	-10000	0	-0.12	30	30
PRKACB	0.02	0.02	-10000	0	-0.12	11	11
HSP90AA1	0.023	0.004	-10000	0	-10000	0	0
IL8	-0.06	0.23	-10000	0	-0.74	46	46
CDK5R1/CDK5	0.018	0.043	-10000	0	-0.13	33	33
NF kappa B1 p50/RelA/PKAc	-0.003	0.12	-10000	0	-0.19	129	129
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90	-0.01	0.11	0.33	2	-0.36	1	3
SMARCA4	0.016	0.031	-10000	0	-0.12	27	27
chromatin remodeling	-0.009	0.091	0.26	1	-0.33	11	12
NF kappa B1 p50/RelA/Cbp	-0.022	0.14	0.34	7	-0.25	83	90
JUN (dimer)	0.021	0.088	-10000	0	-0.31	4	4
YWHAH	0.021	0.015	-10000	0	-0.12	6	6
VIPR1	0.043	0.044	-10000	0	-0.21	1	1
NR3C1	-0.015	0.08	0.26	2	-0.33	10	12
NR4A1	0.01	0.048	-10000	0	-10000	0	0
TIF2/SUV420H1	0.02	0.048	-10000	0	-0.13	50	50
MAPKKK cascade	-0.053	0.17	-10000	0	-0.43	48	48
cortisol/GR alpha (dimer)/Src-1	-0.014	0.11	0.39	3	-10000	0	3
PBX1	0.029	0.014	-10000	0	-0.11	4	4
POU1F1	0.03	0.014	-10000	0	-0.12	4	4
SELE	-0.007	0.11	-10000	0	-0.36	4	4
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A	-0.009	0.091	0.27	1	-0.34	11	12
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90	-0.01	0.11	0.33	2	-0.36	1	3
mol:cortisol	-0.028	0.064	0.24	2	-10000	0	2
MMP1	-0.042	0.17	-10000	0	-0.96	15	15

×

Regulation of nuclear SMAD2/3 signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EP300	0.02	0.011	-10000	0	-0.12	2	2
HSPA8	0.023	0.003	-10000	0	-10000	0	0
SMAD3/SMAD4/ER alpha	0.06	0.084	0.2	43	-0.15	23	66
AKT1	0.023	0.021	-10000	0	-0.1	15	15
GSC	0.022	0.094	-10000	0	-1.2	3	3
NKX2-5	0.022	0.015	-10000	0	-0.047	19	19
muscle cell differentiation	-0.039	0.081	0.28	20	-10000	0	20
SMAD2-3/SMAD4/SP1	0.049	0.094	-10000	0	-0.24	18	18
SMAD4	0.024	0.039	-10000	0	-0.14	13	13
CBFB	0.023	0.007	-10000	0	-0.12	1	1
SAP18	0.023	0.003	-10000	0	-10000	0	0
Cbp/p300/MSG1	0.026	0.052	-10000	0	-0.14	39	39
SMAD3/SMAD4/VDR	0.046	0.073	-10000	0	-0.17	30	30
MYC	0.013	0.028	0.098	5	-0.12	20	25
CDKN2B	0.031	0.12	-10000	0	-1.2	5	5
AP1	0.005	0.1	-10000	0	-0.22	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	-0.036	27	27
CREB1	0.023	0.003	-10000	0	-10000	0	0
FOXH1	0.024	0.018	-10000	0	-0.11	7	7
SMAD3/SMAD4/GR	0.035	0.07	0.18	1	-0.15	34	35
GATA3	0.027	0.021	-10000	0	-0.11	11	11
SKI/SIN3/HDAC complex/NCoR1	0.02	0.079	-10000	0	-0.26	26	26
MEF2C/TIF2	0.042	0.064	-10000	0	-0.2	25	25
endothelial cell migration	0.013	0.11	1.2	3	-10000	0	3
MAX	0.023	0.006	0.074	3	-10000	0	3
RBBP7	0.022	0.011	-10000	0	-0.12	3	3
RBBP4	0.021	0.014	-10000	0	-0.12	5	5
RUNX2	0.019	0.023	-10000	0	-0.12	15	15
RUNX3	0.018	0.028	-10000	0	-0.12	22	22
RUNX1	0.019	0.022	-10000	0	-0.12	13	13
CTBP1	0.021	0.016	-10000	0	-0.12	7	7
NR3C1	0.021	0.016	0.074	3	-0.12	5	8
VDR	0.019	0.022	-10000	0	-0.12	13	13
CDKN1A	0.017	0.065	-10000	0	-0.52	1	1
KAT2B	-0.001	0.003	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1	0.055	0.055	-10000	0	-0.19	12	12
DCP1A	0.023	0.001	-10000	0	-10000	0	0
SKI	0.023	0.01	-10000	0	-0.12	3	3
SERPINE1	-0.013	0.11	-10000	0	-1.2	3	3
SMAD3/SMAD4/ATF2	0.041	0.064	-10000	0	-0.2	16	16
SMAD3/SMAD4/ATF3	0.035	0.062	-10000	0	-0.15	18	18
SAP30	0.023	0.001	-10000	0	-10000	0	0
Cbp/p300/PIAS3	0.027	0.051	0.14	3	-0.14	40	43
JUN	-0.008	0.098	-10000	0	-0.22	65	65
SMAD3/SMAD4/IRF7	0.051	0.059	-10000	0	-0.18	11	11
TFE3	0.018	0.031	-10000	0	-0.081	44	44
COL1A2	-0.13	0.26	-10000	0	-0.64	112	112
mesenchymal cell differentiation	-0.041	0.057	0.15	14	-10000	0	14
DLX1	0.021	0.017	-10000	0	-0.12	8	8
TCF3	0.022	0.013	-10000	0	-0.12	5	5
FOS	-0.004	0.054	-10000	0	-0.11	102	102
SMAD3/SMAD4/Max	0.046	0.056	0.18	1	-0.17	8	9
Cbp/p300/SNIP1	0.033	0.047	-10000	0	-0.13	38	38
ZBTB17	0.022	0.006	0.081	5	-10000	0	5
LAMC1	0.021	0.083	-10000	0	-0.27	34	34
TGIF2/HDAC complex/SMAD3/SMAD4	0.04	0.061	-10000	0	-0.16	20	20
IRF7	0.024	0.017	-10000	0	-0.12	7	7
ESR1	0.032	0.038	0.098	99	-0.12	11	110
HNF4A	0.023	0.008	-10000	0	-0.12	2	2
MEF2C	0.034	0.061	-10000	0	-0.21	24	24
SMAD2-3/SMAD4	0.049	0.063	-10000	0	-0.19	10	10
Cbp/p300/Src-1	0.029	0.053	-10000	0	-0.13	48	48
IGHV3OR16-13	0.005	0.074	-10000	0	-0.49	12	12
TGIF2/HDAC complex	0.022	0.013	-10000	0	-0.12	4	4
CREBBP	0.02	0.016	-10000	0	-0.12	6	6
SKIL	0.011	0.035	-10000	0	-0.12	35	35
HDAC1	0.02	0.019	-10000	0	-0.12	10	10
HDAC2	0.02	0.021	-10000	0	-0.12	12	12
SNIP1	0.023	0.01	-10000	0	-0.12	3	3
GCN5L2	0.021	0.013	-10000	0	-0.12	4	4
SMAD3/SMAD4/TFE3	0.048	0.072	-10000	0	-0.18	21	21
MSG1/HSC70	0.027	0.031	-10000	0	-0.13	9	9
SMAD2	0.027	0.016	-10000	0	-0.071	8	8
SMAD3	0.022	0.036	-10000	0	-0.11	17	17
SMAD3/E2F4-5/DP1/p107/SMAD4	0.024	0.067	-10000	0	-0.21	22	22
SMAD2/SMAD2/SMAD4	-0.002	0.044	0.12	2	-0.21	17	19
NCOR1	0.022	0.009	-10000	0	-0.12	2	2
NCOA2	0.021	0.013	-10000	0	-0.12	4	4
NCOA1	0.022	0.009	-10000	0	-0.12	2	2
MYOD/E2A	0.032	0.015	-10000	0	-0.076	11	11
SMAD2-3/SMAD4/SP1/MIZ-1	0.061	0.092	-10000	0	-0.22	17	17
IFNB1	0.035	0.044	-10000	0	-0.17	9	9
SMAD3/SMAD4/MEF2C	0.058	0.076	-10000	0	-0.22	21	21
CITED1	0.015	0.035	-10000	0	-0.12	35	35
SMAD2-3/SMAD4/ARC105	0.061	0.061	-10000	0	-0.19	8	8
RBL1	0.019	0.022	-10000	0	-0.12	13	13
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB	0.042	0.067	-10000	0	-0.4	8	8
RUNX1-3/PEBPB2	0.036	0.039	-10000	0	-0.12	27	27
SMAD7	-0.004	0.14	-10000	0	-0.4	32	32
MYC/MIZ-1	0.003	0.063	0.17	5	-0.15	75	80
SMAD3/SMAD4	-0.018	0.099	0.28	3	-0.3	40	43
IL10	0.039	0.044	-10000	0	-0.18	7	7
PIASy/HDAC complex	0.024	0.005	-10000	0	-10000	0	0
PIAS3	0.019	0.022	-10000	0	-0.12	14	14
CDK2	0.017	0.023	-10000	0	-0.12	14	14
IL5	0.039	0.044	-10000	0	-0.21	5	5
CDK4	0.019	0.019	-10000	0	-0.12	9	9
PIAS4	0.024	0.005	-10000	0	-10000	0	0
ATF3	0.011	0.04	-10000	0	-0.12	47	47
SMAD3/SMAD4/SP1	0.028	0.09	-10000	0	-0.21	31	31
FOXG1	0.02	0.019	-10000	0	-0.12	10	10
FOXO3	0.024	0.02	-10000	0	-0.069	23	23
FOXO1	0.025	0.017	-10000	0	-0.071	17	17
FOXO4	0.025	0.016	-10000	0	-0.071	15	15
heart looping	0.034	0.061	-10000	0	-0.21	24	24
CEBPB	0.017	0.032	-10000	0	-0.11	34	34
SMAD3/SMAD4/DLX1	0.044	0.055	-10000	0	-0.16	12	12
MYOD1	0.022	0.013	-10000	0	-0.12	5	5
SMAD3/SMAD4/HNF4	0.045	0.054	-10000	0	-0.16	10	10
SMAD3/SMAD4/GATA3	0.059	0.059	-10000	0	-0.22	6	6
SnoN/SIN3/HDAC complex/NCoR1	0.011	0.035	-10000	0	-0.12	35	35
SMAD3/SMAD4/RUNX1-3/PEBPB2	0.058	0.062	-10000	0	-0.15	13	13
SMAD3/SMAD4/SP1-3	0.042	0.097	-10000	0	-0.22	33	33
MED15	0.022	0.012	-10000	0	-0.12	4	4
SP1	-0.004	0.053	-10000	0	-0.093	113	113
SIN3B	0.022	0.015	-10000	0	-0.12	6	6
SIN3A	0.022	0.014	-10000	0	-0.12	5	5
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5	0.071	0.062	-10000	0	-0.15	25	25
ITGB5	0.007	0.094	-10000	0	-0.27	40	40
TGIF/SIN3/HDAC complex/CtBP	0.022	0.078	-10000	0	-0.27	23	23
SMAD3/SMAD4/AR	0.015	0.078	-10000	0	-0.15	49	49
AR	0.009	0.038	-10000	0	-0.12	43	43
negative regulation of cell growth	0.026	0.073	-10000	0	-0.23	28	28
SMAD3/SMAD4/MYOD	0.044	0.055	-10000	0	-0.17	11	11
E2F5	0.02	0.02	-10000	0	-0.12	11	11
E2F4	0.022	0.012	-10000	0	-0.12	4	4
SMAD2/SMAD2/SMAD4/FOXH1/SMIF	0.068	0.058	-10000	0	-0.16	13	13
SMAD2-3/SMAD4/FOXO1-3a-4	0.041	0.061	-10000	0	-0.31	10	10
TFDP1	0.019	0.022	-10000	0	-0.12	14	14
SMAD3/SMAD4/AP1	0.013	0.11	-10000	0	-0.25	52	52
SMAD3/SMAD4/RUNX2	0.041	0.058	-10000	0	-0.15	14	14
TGIF2	0.022	0.013	-10000	0	-0.12	4	4
TGIF1	0.023	0	-10000	0	-10000	0	0
ATF2	0.022	0.004	-10000	0	-10000	0	0

×

Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaV beta3 Integrin	-0.018	0.081	-9999	-0.12	193	193
AKT1	0.019	0.12	-9999	-0.33	29	29
PTK2B	-0.004	0.08	-9999	-0.2	48	48
VEGFR2 homodimer/Frs2	0.025	0.058	-9999	-0.27	8	8
CAV1	0.012	0.038	-9999	-0.12	42	42
CALM1	0.022	0.014	-9999	-0.12	5	5
VEGFR2 homodimer/VEGFA homodimer/Frs2	0.03	0.073	-9999	-0.24	17	17
endothelial cell proliferation	0.026	0.1	-9999	-0.31	21	21
mol:Ca2+	0.027	0.067	-9999	-0.23	18	18
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac	0.036	0.083	-9999	-0.22	28	28
RP11-342D11.1	0.019	0.062	-9999	-0.23	17	17
CDH5	0.022	0.012	-9999	-0.12	4	4
VEGFA homodimer	0.038	0.058	-9999	-0.1	71	71
SHC1	0.023	0.001	-9999	-10000	0	0
SHC2	0.023	0.008	-9999	-0.12	2	2
HRAS/GDP	0.03	0.061	-9999	-0.24	12	12
SH2D2A	0.023	0.006	-9999	-0.12	1	1
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS	0.054	0.082	-9999	-0.3	11	11
VEGFR2 homodimer/VEGFA homodimer/TsAd	0.036	0.07	-9999	-0.23	16	16
VEGFR1 homodimer	0.022	0.014	-9999	-0.12	5	5
SHC/GRB2/SOS1	0.055	0.078	-9999	-0.26	12	12
GRB10	0.029	0.072	-9999	-0.34	11	11
PTPN11	0.022	0.011	-9999	-0.12	3	3
GRB2	0.023	0.006	-9999	-0.12	1	1
PAK1	0.016	0.029	-9999	-0.12	24	24
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin	0.04	0.086	-9999	-0.21	31	31
HRAS	0.023	0.006	-9999	-0.12	1	1
VEGF/Rho/ROCK1/Integrin Complex	-0.019	0.12	-9999	-0.3	63	63
HIF1A	0.022	0.01	-9999	-0.12	2	2
FRS2	0.019	0.023	-9999	-0.12	15	15
oxygen and reactive oxygen species metabolic process	0.034	0.081	-9999	-0.22	28	28
mol:GTP	0	0	-9999	-10000	0	0
FLT4	0.023	0.008	-9999	-0.12	2	2
Nck/Pak	0.013	0.056	-9999	-0.15	50	50
VEGFR2 homodimer/VEGFA homodimer/Fyn	0.021	0.079	-9999	-0.22	24	24
mol:GDP	0.041	0.071	-9999	-0.25	12	12
mol:NADP	0.037	0.07	-9999	-0.28	10	10
eNOS/Hsp90	0.045	0.071	-9999	-0.26	10	10
PIK3R1	0.015	0.031	-9999	-0.12	28	28
mol:IP3	0.027	0.068	-9999	-0.24	18	18
HIF1A/ARNT	0.024	0.042	-9999	-0.14	34	34
SHB	0.023	0.008	-9999	-0.12	2	2
VEGFA	0.022	0.021	-9999	-0.12	11	11
VEGFC	0.017	0.029	-9999	-0.12	24	24
FAK1/Vinculin	-0.007	0.13	-9999	-0.38	33	33
mol:Ca ++	0	0	-9999	-10000	0	0
RHOA	0.023	0.006	-9999	-0.12	1	1
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.008	0.094	-9999	-0.21	46	46
PTPN6	0.023	0.009	-9999	-0.12	2	2
EPAS1	0.025	0.04	-9999	-0.13	27	27
mol:L-citrulline	0.037	0.07	-9999	-0.28	10	10
ITGAV	0.012	0.033	-9999	-0.12	31	31
PIK3CA	0.02	0.017	-9999	-0.12	7	7
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2	0.042	0.074	-9999	-0.21	21	21
VEGFR2 homodimer/VEGFA homodimer	0.047	0.078	-9999	-0.25	17	17
VEGFR2/3 heterodimer	0.028	0.056	-9999	-0.28	7	7
VEGFB	0.015	0.032	-9999	-0.12	30	30
MAPK11	0.022	0.069	-9999	-0.25	17	17
VEGFR2 homodimer	0.028	0.052	-9999	-0.34	7	7
FLT1	0.022	0.014	-9999	-0.12	5	5
NEDD4	0.023	0.022	-9999	-0.1	15	15
MAPK3	0.014	0.064	-9999	-0.23	17	17
MAPK1	0.013	0.064	-9999	-0.24	17	17
VEGFA145/NRP2	0.002	0.072	-9999	-0.15	86	86
VEGFR1/2 heterodimer	0.027	0.058	-9999	-0.26	9	9
KDR	0.028	0.052	-9999	-0.34	7	7
VEGFA165/NRP1/VEGFR2 homodimer	0.033	0.083	-9999	-0.28	13	13
SRC	0.023	0.008	-9999	-0.12	2	2
platelet activating factor biosynthetic process	0.015	0.066	-9999	-0.24	16	16
PI3K	0.034	0.099	-9999	-0.3	22	22
VEGFR2 homodimer/VEGFA homodimer/NCK1	0.027	0.076	-9999	-0.22	21	21
FES	0.03	0.066	-9999	-0.23	17	17
GAB1	0.026	0.095	-9999	-0.3	26	26
VEGFR2 homodimer/VEGFA homodimer/Src	0.036	0.07	-9999	-0.23	16	16
CTNNB1	0.022	0.007	-9999	-0.12	1	1
SOS1	0.017	0.027	-9999	-0.12	20	20
ARNT	0.022	0.012	-9999	-0.12	4	4
eNOS/Caveolin-1	0.039	0.074	-9999	-0.27	12	12
VEGFR2 homodimer/VEGFA homodimer/Yes	0.028	0.076	-9999	-0.22	22	22
PI3K/GAB1	0.027	0.12	-9999	-0.34	30	30
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak	0.036	0.082	-9999	-0.19	29	29
PRKACA	0.021	0.017	-9999	-0.12	8	8
VEGFR2/3 heterodimer/VEGFC homodimer	0.036	0.06	-9999	-0.32	6	6
HSP90AA1	0.023	0.004	-9999	-10000	0	0
CDC42	0.03	0.065	-9999	-0.23	17	17
actin cytoskeleton reorganization	0.036	0.069	-9999	-0.23	16	16
PTK2	-0.015	0.13	-9999	-0.4	32	32
EDG1	0.031	0.067	-9999	-0.29	10	10
mol:DAG	0.027	0.068	-9999	-0.24	18	18
CaM/Ca2+	0.033	0.068	-9999	-0.26	12	12
MAP2K3	0.023	0.064	-9999	-0.24	14	14
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4	0.052	0.083	-9999	-0.35	11	11
PLCG1	0.027	0.068	-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	19	19
VEGFR2 homodimer/VEGFA homodimer/SHP1	0.036	0.07	-9999	-0.24	16	16
cell migration	-0.002	0.14	-9999	-0.38	42	42
mol:PI-3-4-5-P3	0.034	0.094	-9999	-0.28	22	22
FYN	0.012	0.037	-9999	-0.12	40	40
VEGFB/NRP1	0.027	0.063	-9999	-0.21	19	19
mol:NO	0.037	0.07	-9999	-0.28	10	10
PXN	0.022	0.013	-9999	-0.12	5	5
HRAS/GTP	-0.013	0.043	-9999	-0.24	12	12
VEGFR2 homodimer/VEGFA homodimer/GRB10	0.048	0.077	-9999	-0.35	11	11
VHL	0.021	0.016	-9999	-0.12	7	7
ITGB3	0.005	0.046	-9999	-0.12	67	67
NOS3	0.037	0.076	-9999	-0.31	10	10
VEGFR2 homodimer/VEGFA homodimer/Sck	0.036	0.07	-9999	-0.23	16	16
RAC1	0.023	0.002	-9999	-10000	0	0
PRKCA	0.02	0.063	-9999	-0.25	13	13
PRKCB	0.02	0.061	-9999	-0.22	18	18
VCL	0.021	0.014	-9999	-0.12	5	5
VEGFA165/NRP1	0.033	0.064	-9999	-0.23	17	17
VEGFR1/2 heterodimer/VEGFA homodimer	0.035	0.072	-9999	-0.24	18	18
VEGFA165/NRP2	0.002	0.072	-9999	-0.15	86	86
MAPKKK cascade	0.048	0.074	-9999	-0.28	13	13
NRP2	0.012	0.036	-9999	-0.12	38	38
VEGFC homodimer	0.017	0.029	-9999	-0.12	24	24
NCK1	0.02	0.019	-9999	-0.12	9	9
ROCK1	0.023	0.009	-9999	-0.12	2	2
FAK1/Paxillin	-0.004	0.12	-9999	-0.37	33	33
MAP3K13	0.024	0.068	-9999	-0.23	19	19
PDPK1	0.03	0.085	-9999	-0.26	22	22

×

p38 MAPK signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TRAF6/ASK1	0.01	0.052	-9999	-0.14	51	51
TRAF2/ASK1	0.023	0.033	-9999	-0.12	25	25
ATM	0.018	0.022	-9999	-0.12	13	13
MAP2K3	-0.003	0.12	-9999	-0.32	66	66
response to stress	0	0	-9999	-10000	0	0
MAP2K6	-0.013	0.12	-9999	-0.26	75	75
hyperosmotic response	0	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
GADD45G	0.015	0.033	-9999	-0.12	32	32
TXN	-0.003	0.051	-9999	-0.21	33	33
CALM1	0.022	0.014	-9999	-0.12	5	5
GADD45A	0.014	0.032	-9999	-0.12	30	30
GADD45B	0.016	0.029	-9999	-0.12	24	24
MAP3K1	0.021	0.015	-9999	-0.12	6	6
MAP3K6	0.022	0.012	-9999	-0.12	4	4
MAP3K7	0.021	0.014	-9999	-0.12	5	5
MAP3K4	0.023	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
ASK1/ASK2	0.023	0.041	-9999	-0.11	47	47
TAK1/TAB family	0	0.069	-9999	-0.33	22	22
RAC1/OSM/MEKK3	0.044	0.015	-9999	-0.097	6	6
TRAF2	0.023	0	-9999	-10000	0	0
RAC1/OSM/MEKK3/MKK3	0.015	0.1	-9999	-0.25	66	66
TRAF6	0.006	0.056	-9999	-0.21	32	32
RAC1	0.023	0.002	-9999	-10000	0	0
mol:LPS	0	0	-9999	-10000	0	0
CAMK2B	0.023	0.008	-9999	-0.12	2	2
CCM2	0.023	0.001	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB	0.029	0.019	-9999	-0.092	13	13
MAPK11	0.023	0	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB/ASK1	0.033	0.037	-9999	-0.1	32	32
OSM/MEKK3	0.034	0.007	-9999	-0.14	1	1
TAOK1	-0.002	0.068	-9999	-0.22	46	46
TAOK2	0.003	0.057	-9999	-0.2	40	40
TAOK3	-0.004	0.068	-9999	-0.21	53	53
MAP3K7IP1	0.023	0	-9999	-10000	0	0
MAPK14	0.023	0.007	-9999	-0.12	1	1
MAP3K7IP2	0.02	0.016	-9999	-0.12	7	7
MAP3K5	0.018	0.025	-9999	-0.12	17	17
MAP3K10	0.022	0.015	-9999	-0.12	6	6
MAP3K3	0.023	0	-9999	-10000	0	0
TRX/ASK1	0.009	0.051	-9999	-0.18	33	33
GADD45/MTK1/MTK1	0.024	0.058	-9999	-0.096	83	83

×

Signaling events mediated by HDAC Class I

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NF kappa B/RelA	0.032	0.075	-10000	0	-0.2	37	37
Ran/GTP/Exportin 1/HDAC1	-0.012	0.04	-10000	0	-0.12	55	55
NF kappa B1 p50/RelA/I kappa B alpha	0.019	0.09	-10000	0	-0.26	39	39
SUMO1	0.023	0.009	-10000	0	-0.12	2	2
ZFPM1	0.023	0.01	-10000	0	-0.12	3	3
NPC/RanGAP1/SUMO1/Ubc9	0.015	0.036	-10000	0	-0.14	30	30
FKBP3	0.021	0.013	-10000	0	-0.12	4	4
Histones	0.04	0.067	-10000	0	-0.22	19	19
YY1/LSF	0.017	0.063	-10000	0	-0.2	36	36
SMG5	0.022	0.011	-10000	0	-0.12	3	3
RAN	0.023	0.002	-10000	0	-10000	0	0
I kappa B alpha/HDAC3	0.016	0.066	-10000	0	-0.17	51	51
I kappa B alpha/HDAC1	0.012	0.083	-10000	0	-0.24	48	48
SAP18	0.023	0.003	-10000	0	-10000	0	0
RELA	0.017	0.076	-10000	0	-0.19	53	53
HDAC1/Smad7	0.034	0.042	-10000	0	-0.11	41	41
RANGAP1	0.023	0.006	-10000	0	-0.12	1	1
HDAC3/TR2	0.031	0.045	-10000	0	-0.24	11	11
NuRD/MBD3 Complex	0.013	0.098	-10000	0	-0.32	32	32
NF kappa B1 p50/RelA	0.021	0.079	-10000	0	-0.2	46	46
EntrezGene:23225	0	0	-10000	0	-10000	0	0
GATA2	0.02	0.021	-10000	0	-0.12	13	13
GATA1	0.023	0.006	-10000	0	-0.12	1	1
Mad/Max	0.033	0.012	-10000	0	-10000	0	0
NuRD/MBD3 Complex/GATA1/Fog1	0.025	0.094	-10000	0	-0.29	32	32
RBBP7	0.022	0.011	-10000	0	-0.12	3	3
NPC	0.009	0.023	-10000	0	-0.095	27	27
RBBP4	0.021	0.014	-10000	0	-0.12	5	5
MAX	0.023	0	-10000	0	-10000	0	0
EntrezGene:9972	0	0	-10000	0	-10000	0	0
FBXW11	0.023	0.003	-10000	0	-10000	0	0
NFKBIA	0.004	0.082	-10000	0	-0.26	43	43
KAT2B	0	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
SIN3/HDAC complex	0.015	0.082	-10000	0	-0.31	22	22
SIN3 complex	0.053	0.032	-10000	0	-0.098	19	19
SMURF1	0.023	0.009	-10000	0	-0.12	2	2
CHD3	0.021	0.016	-10000	0	-0.12	7	7
SAP30	0.023	0	-10000	0	-10000	0	0
EntrezGene:23636	0	0	-10000	0	-10000	0	0
NCOR1	0.022	0.009	-10000	0	-0.12	2	2
YY1/HDAC3	0.022	0.065	-10000	0	-0.25	19	19
YY1/HDAC2	0.018	0.059	-10000	0	-0.19	36	36
YY1/HDAC1	0.016	0.061	-10000	0	-0.2	36	36
NuRD/MBD2 Complex (MeCP1)	0.013	0.098	-10000	0	-0.31	32	32
PPARG	0.021	0.061	-10000	0	-0.2	35	35
HDAC8/hEST1B	0.037	0.038	-10000	0	-0.12	28	28
UBE2I	0.023	0.001	-10000	0	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.023	0.003	-10000	0	-10000	0	0
TNFRSF1A	0.021	0.016	-10000	0	-0.12	7	7
HDAC3/SMRT (N-CoR2)	0.031	0.046	-10000	0	-0.25	10	10
MBD3L2	0.023	0.01	-10000	0	-0.12	3	3
ubiquitin-dependent protein catabolic process	0.034	0.042	-10000	0	-0.11	41	41
CREBBP	0.021	0.015	-10000	0	-0.12	6	6
NuRD/MBD3/MBD3L2 Complex	0.023	0.095	-10000	0	-0.3	32	32
HDAC1	0.019	0.019	-10000	0	-0.12	10	10
HDAC3	0.023	0.044	-10000	0	-0.26	9	9
HDAC2	0.02	0.021	-10000	0	-0.12	12	12
YY1	0.008	0.065	-10000	0	-0.22	36	36
HDAC8	0.021	0.013	-10000	0	-0.12	4	4
SMAD7	0.023	0.003	-10000	0	-10000	0	0
NCOR2	0.019	0.023	-10000	0	-0.12	15	15
MXD1	0.021	0.017	-10000	0	-0.12	8	8
STAT3	0.004	0.079	-10000	0	-0.23	52	52
NFKB1	0.021	0.013	-10000	0	-0.12	4	4
EntrezGene:8021	0	0	-10000	0	-10000	0	0
RANBP2	0.022	0.01	-10000	0	-0.12	2	2
YY1/LSF/HDAC1	0.018	0.072	-10000	0	-0.19	43	43
YY1/SAP30/HDAC1	0.025	0.063	-10000	0	-0.17	37	37
EP300	0.022	0.009	-10000	0	-0.12	2	2
STAT3 (dimer non-phopshorylated)	0.004	0.079	-10000	0	-0.23	52	52
proteasomal ubiquitin-dependent protein catabolic process	0.004	0.082	-10000	0	-0.26	43	43
histone deacetylation	0.013	0.097	-10000	0	-0.31	32	32
STAT3 (dimer non-phopshorylated)/HDAC3	0.019	0.078	-10000	0	-0.26	24	24
nuclear export	-0.036	0.038	0.12	28	-10000	0	28
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
GATAD2B	0.022	0.009	-10000	0	-0.12	2	2
GATAD2A	0.02	0.021	-10000	0	-0.12	13	13
GATA2/HDAC3	0.032	0.047	-10000	0	-0.25	10	10
GATA1/HDAC1	0.023	0.042	-10000	0	-0.14	31	31
GATA1/HDAC3	0.033	0.044	-10000	0	-0.24	10	10
CHD4	0.022	0.009	-10000	0	-0.12	2	2
TNF-alpha/TNFR1A	0.025	0.036	-10000	0	-0.11	37	37
SIN3/HDAC complex/Mad/Max	0.022	0.078	-10000	0	-0.28	22	22
NuRD Complex	0.023	0.095	-10000	0	-0.3	32	32
positive regulation of chromatin silencing	0.038	0.066	-10000	0	-0.22	19	19
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	67	67
GATA1/Fog1	0.034	0.01	-10000	0	-0.15	1	1
FKBP25/HDAC1/HDAC2	0.027	0.054	-10000	0	-0.12	55	55
TNF	0.02	0.02	-10000	0	-0.12	11	11
negative regulation of cell growth	0.022	0.077	-10000	0	-0.28	22	22
NuRD/MBD2/PRMT5 Complex	0.013	0.098	-10000	0	-0.31	32	32
Ran/GTP/Exportin 1	0.034	0.049	-10000	0	-0.15	30	30
NF kappa B/RelA/I kappa B alpha	0.018	0.079	-10000	0	-0.27	31	31
SIN3/HDAC complex/NCoR1	0.019	0.079	-10000	0	-0.27	27	27
TFCP2	0.021	0.014	-10000	0	-0.12	5	5
NR2C1	0.022	0.01	-10000	0	-0.12	2	2
MBD3	0.023	0.008	-10000	0	-0.12	2	2
MBD2	0.023	0	-10000	0	-10000	0	0

×

Arf6 trafficking events

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
SLC2A4	0.023	0.006	-10000	0	-0.12	1	1
CLTC	0.005	0.082	-10000	0	-0.33	20	20
calcium ion-dependent exocytosis	0.01	0.043	-10000	0	-0.17	16	16
Dynamin 2/GTP	0.013	0.044	-10000	0	-0.1	58	58
EXOC4	0.023	0.007	-10000	0	-0.12	1	1
CD59	0.008	0.061	-10000	0	-0.35	12	12
CPE	0.009	0.027	-10000	0	-0.065	59	59
CTNNB1	0.022	0.007	-10000	0	-0.12	1	1
membrane fusion	0.015	0.036	-10000	0	-0.15	22	22
CTNND1	0.012	0.042	-10000	0	-0.098	57	57
DNM2	0.02	0.022	-10000	0	-0.12	13	13
mol:PI-4-5-P2	0.014	0.048	-10000	0	-0.25	14	14
TSHR	0.013	0.026	-10000	0	-0.068	49	49
INS	0.018	0.017	-10000	0	-0.16	1	1
BIN1	0.022	0.013	-10000	0	-0.12	5	5
mol:Choline	0.015	0.036	-10000	0	-0.15	22	22
growth hormone secretagogue receptor activity	0	0	-10000	0	-10000	0	0
mol:GDP	0.014	0.022	-10000	0	-0.072	29	29
membrane depolarization	0	0	-10000	0	-10000	0	0
ARF6	0.023	0.003	-10000	0	-10000	0	0
mol:Ca2+	0.013	0.044	-10000	0	-0.1	58	58
JUP	0.006	0.065	-10000	0	-0.35	13	13
ASAP2/amphiphysin II	0.026	0.02	-10000	0	-0.086	17	17
ARF6/GTP	0.015	0.02	-10000	0	-0.15	9	9
CDH1	0.004	0.069	-10000	0	-0.36	13	13
clathrin-independent pinocytosis	0.015	0.02	-10000	0	-0.15	9	9
MAPK8IP3	0.023	0.006	-10000	0	-0.12	1	1
positive regulation of endocytosis	0.015	0.02	-10000	0	-0.15	9	9
EXOC2	0.022	0.014	-10000	0	-0.12	5	5
substrate adhesion-dependent cell spreading	0.011	0.1	-10000	0	-0.28	51	51
insulin receptor binding	0	0	-10000	0	-10000	0	0
SPAG9	0.021	0.015	-10000	0	-0.12	6	6
regulation of calcium-dependent cell-cell adhesion	-0.013	0.08	0.27	23	-10000	0	23
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	0.04	-10000	0	-0.1	39	39
EXOC1	0.021	0.012	-10000	0	-0.12	3	3
exocyst	0.011	0.11	-10000	0	-0.28	51	51
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	0.02	-10000	0	-0.15	9	9
CTNNA1	0.011	0.041	-10000	0	-0.097	56	56
NME1	0.014	0.022	-10000	0	-0.072	29	29
clathrin coat assembly	0.005	0.081	-10000	0	-0.32	20	20
IL2RA	0.009	0.06	-10000	0	-0.36	11	11
VAMP3	0.019	0.016	-10000	0	-0.11	8	8
GLUT4/clathrin heavy chain/ACAP1	0.018	0.065	-10000	0	-0.25	20	20
EXOC6	0.021	0.012	-10000	0	-0.12	3	3
PLD1	0.001	0.057	-10000	0	-0.19	41	41
PLD2	0.018	0.028	-10000	0	-0.19	6	6
EXOC5	0.022	0.011	-10000	0	-0.12	3	3
PIP5K1C	0.014	0.048	-10000	0	-0.25	14	14
SDC1	0.008	0.061	-10000	0	-0.35	12	12
ARF6/GDP	0.011	0.042	-10000	0	-0.099	66	66
EXOC7	0.023	0.001	-10000	0	-10000	0	0
E-cadherin/beta catenin	0.015	0.083	-10000	0	-0.28	23	23
mol:Phosphatidic acid	0.015	0.036	-10000	0	-0.15	22	22
endocytosis	-0.025	0.02	0.086	17	-10000	0	17
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	0.045	-10000	0	-0.1	58	58
KLC1	0.021	0.013	-10000	0	-0.12	4	4
AVPR2	0.008	0.079	-10000	0	-0.32	20	20
RALA	0.022	0.009	-10000	0	-0.12	2	2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.013	0.087	-10000	0	-0.24	35	35

×

Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HIF3A	0.016	0.031	-9999	-0.12	28	28
oxygen homeostasis	0	0	-9999	-10000	0	0
TCEB2	0.023	0.006	-9999	-0.12	1	1
TCEB1	0.022	0.011	-9999	-0.12	3	3
HIF1A/p53	0.002	0.061	-9999	-0.21	32	32
HIF1A	0.007	0.046	-9999	-0.19	22	22
COPS5	0.018	0.023	-9999	-0.12	14	14
VHL/Elongin B/Elongin C/RBX1/CUL2	0.053	0.049	-9999	-0.097	49	49
FIH (dimer)	0.023	0.006	-9999	-0.12	1	1
CDKN2A	0.015	0.021	-9999	-0.12	10	10
ARNT/IPAS	0.028	0.028	-9999	-0.078	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	-0.19	22	22
CUL2	0.022	0.011	-9999	-0.12	3	3
OS9	0.022	0.009	-9999	-0.12	2	2
RACK1/Elongin B/Elongin C	0.043	0.025	-9999	-0.11	14	14
response to hypoxia	0	0	-9999	-10000	0	0
HIF1A/Hsp90	0.014	0.055	-9999	-0.19	23	23
PHD1-3/OS9	0.015	0.065	-9999	-0.097	110	110
HIF1A/RACK1/Elongin B/Elongin C	0.035	0.058	-9999	-0.25	9	9
VHL	0.021	0.016	-9999	-0.12	7	7
HSP90AA1	0.023	0.004	-9999	-10000	0	0
HIF1A/JAB1	0.011	0.057	-9999	-0.2	25	25
EGLN3	-0.003	0.051	-9999	-0.12	87	87
EGLN2	0.023	0.008	-9999	-0.12	2	2
EGLN1	0.023	0.009	-9999	-0.12	2	2
TP53	0.01	0.029	-9999	-0.12	24	24
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A	0.025	0.097	-9999	-0.53	16	16
ARNT	0.022	0.012	-9999	-0.12	4	4
ARD1A	0.018	0.025	-9999	-0.12	18	18
RBX1	0.022	0.011	-9999	-0.12	3	3
HIF1A/p19ARF	0.004	0.063	-9999	-0.22	28	28

×

Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process	-0.019	0.025	0.12	18	-10000	0	18
PI3K Class IB/PDE3B	0.019	0.025	-10000	0	-0.12	18	18
PDE3B	0.019	0.025	-10000	0	-0.12	18	18

×

Ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.02	0.016	-10000	0	-0.075	15	15
MAP4K4	0.003	0.069	-10000	0	-0.22	22	22
BAG4	0.022	0.012	-10000	0	-0.12	4	4
PKC zeta/ceramide	0.013	0.009	0.071	7	-10000	0	7
NFKBIA	0.016	0.027	-10000	0	-0.12	21	21
BIRC3	-0.005	0.052	-10000	0	-0.12	93	93
BAX	0.01	0.005	-10000	0	-10000	0	0
RIPK1	0.022	0.011	-10000	0	-0.12	3	3
AKT1	0.007	0.02	-10000	0	-0.13	12	12
BAD	0.001	0.01	0.063	7	-0.054	3	10
SMPD1	0.009	0.036	-10000	0	-0.12	25	25
RB1	-0.013	0.034	0.068	3	-0.1	66	69
FADD/Caspase 8	0.003	0.095	-10000	0	-0.24	49	49
MAP2K4	-0.001	0.024	0.068	5	-0.092	30	35
NSMAF	0.021	0.014	-10000	0	-0.12	5	5
response to UV	0	0	-10000	0	-10000	0	0
RAF1	0.004	0.015	0.068	5	-0.097	7	12
EGF	0.02	0.021	-10000	0	-0.12	13	13
mol:ceramide	-0.004	0.01	0.063	7	-10000	0	7
MADD	0.023	0.006	-10000	0	-0.12	1	1
response to oxidative stress	0	0	-10000	0	-10000	0	0
mol:Free Fatty acid	0.018	0.022	-10000	0	-0.084	20	20
ASAH1	0.021	0.016	-10000	0	-0.12	7	7
negative regulation of cell cycle	-0.013	0.033	0.067	3	-0.099	66	69
cell proliferation	0.017	0.041	-10000	0	-0.12	16	16
BID	0.009	0.079	-10000	0	-0.6	4	4
MAP3K1	-0.003	0.021	0.063	7	-0.091	25	32
EIF2A	-0.007	0.043	0.07	4	-0.11	60	64
TRADD	0.023	0.006	-10000	0	-0.12	1	1
CRADD	0.023	0.009	-10000	0	-0.12	2	2
MAPK3	0.009	0.021	-10000	0	-0.1	12	12
response to heat	0	0	-10000	0	-10000	0	0
MAPK1	0.008	0.023	0.074	4	-0.11	16	20
Cathepsin D/ceramide	0.011	0.012	0.07	6	-0.055	9	15
FADD	0.004	0.068	-10000	0	-0.22	20	20
KSR1	0.001	0.01	0.063	7	-0.054	3	10
MAPK8	0.004	0.039	-10000	0	-0.19	18	18
PRKRA	-0.002	0.02	0.063	7	-0.098	17	24
PDGFA	0.02	0.022	-10000	0	-0.12	13	13
TRAF2	0.023	0	-10000	0	-10000	0	0
IGF1	0.007	0.045	-10000	0	-0.12	62	62
mol:GD3	0	0	-10000	0	-10000	0	0
ganglioside biosynthetic process	-0.004	0.01	0.063	7	-10000	0	7
CTSD	0.02	0.02	-10000	0	-0.12	11	11
regulation of nitric oxide biosynthetic process	0.02	0.047	-10000	0	-0.14	42	42
response to radiation	0	0	-10000	0	-10000	0	0
ERK1/PKC delta	0.019	0.044	-10000	0	-0.13	16	16
PRKCD	0.02	0.018	-10000	0	-0.12	8	8
PRKCZ	0.023	0	-10000	0	-10000	0	0
mol:GW4869	0	0	-10000	0	-10000	0	0
mol:sphingosine	0.018	0.022	-10000	0	-0.084	20	20
RelA/NF kappa B1	0.021	0.047	-10000	0	-0.14	42	42
mol:glutathione	0	0	-10000	0	-10000	0	0
PAWR	0.023	0.009	-10000	0	-0.12	2	2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD	0.001	0.072	-10000	0	-0.24	19	19
TNFR1A/BAG4/TNF-alpha	0.038	0.034	-10000	0	-0.11	20	20
mol:Sphingosine-1-phosphate	0.02	0.016	-10000	0	-0.075	15	15
MAP2K1	0.007	0.016	0.07	5	-0.094	9	14
mol:C11AG	0	0	-10000	0	-10000	0	0
RELA	0.023	0.009	-10000	0	-0.12	2	2
CYCS	0.004	0.024	0.13	2	-0.12	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	0.068	5	-0.1	54	59
TNF-alpha/TNFR1A/FAN	0.033	0.047	-10000	0	-0.13	35	35
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
CASP8	-0.003	0.12	-10000	0	-0.39	40	40
MAP2K2	0.005	0.019	0.07	4	-0.094	11	15
SMPD3	0.011	0.041	-10000	0	-0.16	15	15
TNF	0.02	0.02	-10000	0	-0.12	11	11
PKC zeta/PAR4	0.033	0.014	-10000	0	-0.14	3	3
mol:PHOSPHOCHOLINE	-0.008	0.016	0.092	5	-10000	0	5
NF kappa B1/RelA/I kappa B alpha	0.043	0.059	-10000	0	-0.17	12	12
AIFM1	-0.005	0.036	0.13	1	-0.12	41	42
BCL2	0.016	0.031	-10000	0	-0.12	28	28

×

Signaling events mediated by HDAC Class III

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

×

Regulation of p38-alpha and p38-beta

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
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	0.012	0.035	-9999	-0.12	35	35
mol:GTP	0	0	-9999	-10000	0	0
MAP2K4	0.022	0.011	-9999	-0.12	3	3
RAC1-CDC42/GTP/PAK family	0.007	0.055	-9999	-0.17	30	30
response to UV	0	0	-9999	-10000	0	0
YES1	0.02	0.018	-9999	-0.12	8	8
interleukin-1 receptor activity	0	0	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
MAP3K3	0.023	0	-9999	-10000	0	0
FYN	0.012	0.037	-9999	-0.12	40	40
MAP3K12	0.022	0.011	-9999	-0.12	3	3
FGR	0.023	0.006	-9999	-0.12	1	1
p38 alpha/TAB1	0.02	0.083	-9999	-0.2	44	44
PRKG1	0.018	0.026	-9999	-0.12	19	19
DUSP8	0.023	0.006	-9999	-0.12	1	1
PGK/cGMP/p38 alpha	0.014	0.079	-9999	-0.2	44	44
apoptosis	0.018	0.079	-9999	-0.2	44	44
RAL/GTP	0.024	0.032	-9999	-0.11	29	29
LYN	0.021	0.013	-9999	-0.12	4	4
DUSP1	-0.004	0.051	-9999	-0.12	90	90
PAK1	0.016	0.029	-9999	-0.12	24	24
SRC	0.023	0.008	-9999	-0.12	2	2
RAC1/OSM/MEKK3/MKK3	0.057	0.021	-9999	-0.093	11	11
TRAF6	0.022	0.009	-9999	-0.12	2	2
RAC1	0.023	0.002	-9999	-10000	0	0
epidermal growth factor receptor activity	0	0	-9999	-10000	0	0
mol:LPS	0	0	-9999	-10000	0	0
mol:cGMP	0	0	-9999	-10000	0	0
CCM2	0.023	0.001	-9999	-10000	0	0
RAC1-CDC42/GTP	0.029	0.019	-9999	-0.13	8	8
MAPK11	0.005	0.099	-9999	-0.23	55	55
BLK	0.022	0.013	-9999	-0.12	5	5
HCK	0.019	0.023	-9999	-0.12	15	15
MAP2K3	0.023	0.006	-9999	-0.12	1	1
DUSP16	0.018	0.025	-9999	-0.12	18	18
DUSP10	0.012	0.035	-9999	-0.12	36	36
TRAF6/MEKK3	0.028	0.016	-9999	-0.091	10	10
MAP3K7IP1	0.023	0	-9999	-10000	0	0
MAPK14	0.011	0.086	-9999	-0.22	45	45
positive regulation of innate immune response	0.008	0.11	-9999	-0.27	51	51
LCK	0.022	0.015	-9999	-0.12	6	6
p38alpha-beta/MKP7	0.014	0.11	-9999	-0.26	53	53
p38alpha-beta/MKP5	0.006	0.12	-9999	-0.25	63	63
PGK/cGMP	0.014	0.017	-9999	-0.076	19	19
PAK2	0.022	0.011	-9999	-0.12	3	3
p38alpha-beta/MKP1	-0.006	0.12	-9999	-0.26	66	66
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 regulated by Ret tyrosine kinase

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
PTK2	0.009	0.096	-9999	-0.39	31	31
Crk/p130 Cas/Paxillin	-0.007	0.025	-9999	-0.14	8	8
JUN	0.013	0.059	-9999	-0.21	22	22
HRAS	0.023	0.006	-9999	-0.12	1	1
RET51/GFRalpha1/GDNF/GRB10	0.045	0.038	-9999	-0.099	11	11
RAP1A	0.021	0.011	-9999	-0.12	3	3
FRS2	0.019	0.023	-9999	-0.12	15	15
RAP1A/GDP	0.01	0.034	-9999	-0.14	28	28
RET51/GFRalpha1/GDNF/DOK1	0.046	0.038	-9999	-0.11	9	9
EntrezGene:5979	0	0	-9999	-10000	0	0
PTPN11	0.022	0.011	-9999	-0.12	3	3
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.022	0.016	-9999	-0.12	7	7
RET9/GFRalpha1/GDNF/Enigma	0.034	0.031	-9999	-0.11	7	7
RHOA	0.023	0.006	-9999	-0.12	1	1
RAP1A/GTP	0.04	0.041	-9999	-0.092	30	30
GRB7	0.018	0.025	-9999	-0.12	18	18
RET51/GFRalpha1/GDNF	0.046	0.036	-9999	-0.096	8	8
MAPKKK cascade	0.037	0.037	-9999	-0.16	6	6
BCAR1	0.023	0.01	-9999	-0.12	3	3
RET9/GFRalpha1/GDNF/IRS1	0.034	0.032	-9999	-0.099	10	10
lamellipodium assembly	0.025	0.043	-9999	-0.14	12	12
RET51/GFRalpha1/GDNF/SHC	0.048	0.034	-9999	-0.096	5	5
PIK3CA	0.02	0.017	-9999	-0.12	7	7
RET9/GFRalpha1/GDNF/SHC	0.037	0.027	-9999	-0.099	3	3
RET9/GFRalpha1/GDNF/Shank3	0.037	0.027	-9999	-0.1	3	3
MAPK3	0.022	0.033	-9999	-0.12	10	10
DOK1	0.022	0.015	-9999	-0.12	6	6
DOK6	0.023	0.008	-9999	-0.12	2	2
PXN	0.022	0.013	-9999	-0.12	5	5
neurite development	0.029	0.039	-9999	-0.17	10	10
DOK5	-0.008	0.054	-9999	-0.12	103	103
GFRA1	0.011	0.04	-9999	-0.12	49	49
MAPK8	0.015	0.061	-9999	-0.23	17	17
HRAS/GTP	0.042	0.04	-9999	-0.15	9	9
tube development	0.038	0.03	-9999	-0.12	7	7
MAPK1	0.022	0.033	-9999	-0.12	10	10
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2	0.017	0.053	-9999	-0.16	36	36
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
SRC	0.023	0.008	-9999	-0.12	2	2
PDLIM7	0.02	0.021	-9999	-0.12	12	12
RET51/GFRalpha1/GDNF/Dok6	0.057	0.035	-9999	-0.096	5	5
SHC1	0.023	0.001	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/Dok4	0.048	0.035	-9999	-0.097	7	7
RET51/GFRalpha1/GDNF/Dok5	-0.003	0.072	-9999	-0.1	146	146
PRKCA	0.011	0.038	-9999	-0.12	42	42
HRAS/GDP	0.017	0.008	-9999	-0.11	2	2
CREB1	0.021	0.072	-9999	-0.24	30	30
PIK3R1	0.015	0.031	-9999	-0.12	28	28
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2	0.024	0.036	-9999	-0.14	20	20
RET51/GFRalpha1/GDNF/Grb7	0.042	0.043	-9999	-0.11	17	17
mol:GDP	0	0	-9999	-10000	0	0
RET	0.019	0.024	-9999	-0.12	17	17
DOK4	0.022	0.012	-9999	-0.12	4	4
JNK cascade	0.01	0.063	-9999	-0.2	29	29
RET9/GFRalpha1/GDNF/FRS2	0.031	0.037	-9999	-0.1	19	19
SHANK3	0.023	0.006	-9999	-0.12	1	1
RASA1	0.021	0.011	-9999	-0.12	3	3
NCK1	0.02	0.019	-9999	-0.12	9	9
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1	0.019	0.048	-9999	-0.15	33	33
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2	0.022	0.054	-9999	-0.16	36	36
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK	0.015	0.065	-9999	-0.24	16	16
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1	0.024	0.049	-9999	-0.15	33	33
PI3K	0.034	0.052	-9999	-0.18	13	13
SOS1	0.017	0.027	-9999	-0.12	20	20
RET9/GFRalpha1/GDNF/Shank3/Grb2	0.046	0.032	-9999	-0.12	7	7
GRB10	0.022	0.014	-9999	-0.12	5	5
activation of MAPKK activity	0.021	0.054	-9999	-0.27	10	10
RET51/GFRalpha1/GDNF/FRS2	0.042	0.043	-9999	-0.096	21	21
GAB1	0.02	0.022	-9999	-0.12	13	13
IRS1	0.02	0.022	-9999	-0.12	14	14
IRS2	0.022	0.016	-9999	-0.12	7	7
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2	0.029	0.038	-9999	-0.14	20	20
RET51/GFRalpha1/GDNF/PKC alpha	0.031	0.052	-9999	-0.097	44	44
GRB2	0.023	0.006	-9999	-0.12	1	1
PRKACA	0.021	0.017	-9999	-0.12	8	8
GDNF	0.023	0.008	-9999	-0.12	2	2
RAC1	0.023	0.002	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/IRS1	0.045	0.039	-9999	-0.095	13	13
Rac1/GTP	0.032	0.051	-9999	-0.17	12	12
RET9/GFRalpha1/GDNF	0.024	0.026	-9999	-0.058	51	51
GFRalpha1/GDNF	0.025	0.031	-9999	-0.073	51	51

×

JNK signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1	0.036	0.054	-9999	-0.1	61	61
MAP4K1	0.019	0.023	-9999	-0.12	15	15
MAP3K8	0.023	0.009	-9999	-0.12	2	2
PRKCB	0	0	-9999	-10000	0	0
DBNL	0.023	0.002	-9999	-10000	0	0
CRKL	0.023	0.009	-9999	-0.12	2	2
MAP3K1	0.021	0.052	-9999	-0.19	9	9
JUN	-0.003	0.095	-9999	-0.49	18	18
MAP3K7	0.021	0.052	-9999	-0.18	8	8
GRAP2	0.022	0.012	-9999	-0.12	4	4
CRK	0.022	0.016	-9999	-0.12	7	7
MAP2K4	0.021	0.058	-9999	-0.2	14	14
LAT	0.022	0.01	-9999	-0.12	3	3
LCP2	0.013	0.033	-9999	-0.12	31	31
MAPK8	0.003	0.096	-9999	-0.52	18	18
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family	0.031	0.038	-9999	-0.19	10	10
LAT/GRAP2/SLP76/HPK1/HIP-55	0.044	0.056	-9999	-0.092	64	64

×

mTOR signaling pathway

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
GBL	0.023	0.008	-10000	0	-0.12	2	2
MKNK1	0.023	0.006	-10000	0	-0.12	1	1
mol:PIP3	-0.005	0.043	-10000	0	-0.16	20	20
FRAP1	0.011	0.072	-10000	0	-0.42	13	13
AKT1	0.006	0.057	0.18	19	-0.15	31	50
INSR	0.021	0.017	-10000	0	-0.12	8	8
Insulin Receptor/Insulin	0.028	0.019	-10000	0	-0.077	17	17
mol:GTP	0.023	0.056	0.18	18	-0.14	22	40
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit	-0.015	0.044	-10000	0	-0.17	31	31
TSC2	0.021	0.017	-10000	0	-0.12	8	8
RHEB/GDP	0.008	0.047	-10000	0	-0.14	25	25
TSC1	0.023	0.006	-10000	0	-0.12	1	1
Insulin Receptor/IRS1	0.02	0.029	-10000	0	-0.22	6	6
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA	0.01	0.06	-10000	0	-0.2	30	30
mol:GDP	0	0	-10000	0	-10000	0	0
EIF3A	0.022	0.004	-10000	0	-10000	0	0
RPS6KB1	0.006	0.084	0.16	14	-0.3	28	42
MAP3K5	-0.004	0.058	-10000	0	-0.27	25	25
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
apoptosis	-0.004	0.058	-10000	0	-0.27	25	25
mol:LY294002	0	0	0	6	-0.001	6	12
EIF4B	0.008	0.077	0.16	14	-0.28	25	39
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.022	0.076	0.16	12	-0.26	26	38
eIF4E/eIF4G1/eIF4A1	-0.007	0.042	-10000	0	-0.26	13	13
KIAA1303	0.023	0.008	-10000	0	-0.12	2	2
PI3K	0.016	0.052	-10000	0	-0.17	21	21
mTOR/RHEB/GTP/Raptor/GBL	0.026	0.053	0.16	16	-0.17	14	30
FKBP1A	0.022	0.012	-10000	0	-0.12	4	4
RHEB/GTP	0.02	0.052	0.14	3	-0.14	25	28
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	-0.52	34	34
mTOR/RHEB/GTP/Raptor/GBL/eIF4E	0.032	0.061	-10000	0	-0.32	1	1
TSC1/TSC2	0.025	0.061	0.19	18	-0.16	19	37
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	0.015	-10000	0	-0.12	6	6
EIF4G1	0.023	0.004	-10000	0	-10000	0	0
IRS1	0.006	0.028	-10000	0	-0.27	5	5
INS	0.023	0.01	-10000	0	-0.12	3	3
PTEN	0.022	0.007	-10000	0	-0.12	1	1
PDK2	0.004	0.054	0.18	17	-0.16	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	16	36
EEF2	0.023	0.018	-10000	0	-0.12	6	6
eIF4E/4E-BP1	0.023	0.097	-10000	0	-1	5	5

×

Class I PI3K signaling events mediated by Akt

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.02	0.016	-10000	0	-0.07	16	16
BAD/BCL-XL/YWHAZ	0.039	0.031	-10000	0	-0.095	22	22
CDKN1B	0.013	0.076	-10000	0	-0.33	23	23
CDKN1A	0.017	0.074	-10000	0	-0.33	23	23
FRAP1	0.022	0.012	-10000	0	-0.12	4	4
PRKDC	0.021	0.016	-10000	0	-0.12	7	7
FOXO3	0.016	0.075	-10000	0	-0.33	23	23
AKT1	0.014	0.077	-10000	0	-0.34	23	23
BAD	0.023	0.01	-10000	0	-0.12	3	3
AKT3	-0.004	0.054	-10000	0	-0.2	30	30
mol:GTP	0	0	-10000	0	-10000	0	0
FOXO4	0.017	0.073	-10000	0	-0.32	23	23
AKT1/ASK1	0.019	0.077	-10000	0	-0.32	23	23
BAD/YWHAZ	0.043	0.025	-10000	0	-0.11	11	11
RICTOR	0.02	0.016	-10000	0	-0.12	7	7
RAF1	0.023	0.003	-10000	0	-10000	0	0
JNK cascade	-0.018	0.074	0.31	23	-10000	0	23
TSC1	0.017	0.073	-10000	0	-0.32	23	23
YWHAZ	0.023	0.003	-10000	0	-10000	0	0
AKT1/RAF1	0.026	0.078	-10000	0	-0.33	24	24
EP300	0.022	0.009	-10000	0	-0.12	2	2
mol:GDP	0.014	0.076	-10000	0	-0.34	23	23
mol:PI-3-4-5-P3	0	0	-10000	0	-10000	0	0
TSC2	0.016	0.074	-10000	0	-0.32	23	23
YWHAQ	0.023	0.003	-10000	0	-10000	0	0
TBC1D4	0.018	0.013	-10000	0	-0.04	29	29
MAP3K5	0.018	0.025	-10000	0	-0.12	17	17
MAPKAP1	0.023	0.002	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.017	0.072	0.23	23	-10000	0	23
YWHAH	0.021	0.015	-10000	0	-0.12	6	6
AKT1S1	0.017	0.073	-10000	0	-0.32	23	23
CASP9	0.016	0.074	-10000	0	-0.33	23	23
YWHAB	0.023	0.007	-10000	0	-0.12	1	1
p27Kip1/KPNA1	0.021	0.081	-10000	0	-0.32	25	25
GBL	0.023	0.008	-10000	0	-0.12	2	2
PDK1/Src/Hsp90	0.042	0.03	-10000	0	-0.12	18	18
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
SRC	0.023	0.008	-10000	0	-0.12	2	2
AKT2/p21CIP1	0.022	0.067	-10000	0	-0.28	24	24
KIAA1303	0.023	0.008	-10000	0	-0.12	2	2
mTOR/RHEB/GTP/Raptor/GBL	0.026	0.071	-10000	0	-0.34	17	17
CHUK	0.014	0.077	-10000	0	-0.33	24	24
BAD/BCL-XL	0.035	0.076	-10000	0	-0.31	23	23
mTORC2	0.047	0.043	-10000	0	-0.1	39	39
AKT2	0.015	0.024	-10000	0	-0.2	5	5
FOXO1-3a-4/14-3-3 family	0.023	0.087	-10000	0	-0.25	33	33
PDPK1	0.023	0.006	-10000	0	-0.12	1	1
MDM2	0.015	0.076	-10000	0	-0.33	23	23
MAPKKK cascade	-0.026	0.076	0.32	24	-10000	0	24
MDM2/Cbp/p300	0.032	0.085	-10000	0	-0.33	23	23
TSC1/TSC2	0.018	0.072	-10000	0	-0.31	23	23
proteasomal ubiquitin-dependent protein catabolic process	0.03	0.082	-10000	0	-0.32	23	23
glucose import	0.018	0.019	-10000	0	-0.14	5	5
mTOR/RHEB/GDP/Raptor/GBL/PRAS40	0.027	0.07	-10000	0	-0.24	21	21
response to stress	0	0	-10000	0	-10000	0	0
SLC2A4	0.02	0.012	-10000	0	-0.036	11	11
GSK3A	0.016	0.075	-10000	0	-0.33	23	23
FOXO1	0.017	0.073	-10000	0	-0.32	23	23
GSK3B	0.016	0.075	-10000	0	-0.33	23	23
SFN	0.014	0.031	-10000	0	-0.12	28	28
G1/S transition of mitotic cell cycle	0.019	0.074	-10000	0	-0.32	23	23
p27Kip1/14-3-3 family	0.028	0.078	-10000	0	-0.32	18	18
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
KPNA1	0.023	0.003	-10000	0	-10000	0	0
HSP90AA1	0.023	0.004	-10000	0	-10000	0	0
YWHAG	0.02	0.021	-10000	0	-0.12	13	13
RHEB	0.019	0.022	-10000	0	-0.12	13	13
CREBBP	0.021	0.015	-10000	0	-0.12	6	6

×

Signaling mediated by p38-alpha and p38-beta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTGS2	0.006	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	0.016	0.049	-9999	-0.21	14	14
MITF	0.019	0.061	-9999	-0.24	19	19
MAPKAPK5	0.02	0.057	-9999	-0.27	14	14
KRT8	0.016	0.065	-9999	-0.28	20	20
MAPKAPK3	0.022	0.012	-9999	-0.12	4	4
MAPKAPK2	0.023	0.009	-9999	-0.12	2	2
p38alpha-beta/CK2	0.02	0.072	-9999	-0.28	15	15
CEBPB	0.016	0.063	-9999	-0.3	14	14
SLC9A1	0.02	0.059	-9999	-0.29	13	13
mol:GDP	0	0	-9999	-10000	0	0
ATF2	0.017	0.069	-9999	-0.27	18	18
p38alpha-beta/MNK1	0.033	0.063	-9999	-0.27	11	11
JUN	-0.007	0.11	-9999	-0.33	51	51
PPARGC1A	0.016	0.06	-9999	-0.29	13	13
USF1	0.019	0.059	-9999	-0.26	16	16
RAB5/GDP/GDI1	0.018	0.051	-9999	-0.17	26	26
NOS2	0.011	0.056	-9999	-0.24	18	18
DDIT3	0.015	0.06	-9999	-0.26	17	17
RAB5A	0.023	0.006	-9999	-0.12	1	1
HSPB1	0.019	0.045	-9999	-0.24	11	11
p38alpha-beta/HBP1	0.025	0.069	-9999	-0.24	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	0.021	0.057	-9999	-0.28	13	13
PLA2G4A	0	0.06	-9999	-0.23	18	18
GDI1	0.018	0.061	-9999	-0.26	18	18
TP53	0.005	0.065	-9999	-0.28	19	19
RPS6KA5	0.018	0.059	-9999	-0.25	17	17
ESR1	0.01	0.076	-9999	-0.29	27	27
HBP1	0.022	0.005	-9999	-10000	0	0
MEF2C	0.016	0.067	-9999	-0.24	24	24
MEF2A	0.019	0.061	-9999	-0.28	15	15
EIF4EBP1	0.02	0.067	-9999	-0.28	20	20
KRT19	0.009	0.075	-9999	-0.28	26	26
ELK4	0.021	0.056	-9999	-0.27	13	13
ATF6	0.019	0.063	-9999	-0.32	14	14
ATF1	0.019	0.07	-9999	-0.3	20	20
p38alpha-beta/MAPKAPK2	0.033	0.061	-9999	-0.27	10	10
p38alpha-beta/MAPKAPK3	0.033	0.061	-9999	-0.27	10	10

×

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	0.064	-10000	0	-0.25	14	14
NFATC2	0.02	0.048	-10000	0	-0.18	16	16
NFATC3	0.024	0.021	-10000	0	-0.24	2	2
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
Calcineurin A alpha-beta B1/CABIN1	-0.006	0.081	-10000	0	-0.27	24	24
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	-0.24	24	24
BCL2/BAX	0.029	0.025	-10000	0	-0.074	30	30
CaM/Ca2+/Calcineurin A alpha-beta B1	0.013	0.02	-10000	0	-0.12	12	12
CaM/Ca2+	0.013	0.02	-10000	0	-0.12	12	12
BAX	0.023	0	-10000	0	-10000	0	0
MAPK14	0.022	0.007	-10000	0	-0.12	1	1
BAD	0.023	0.01	-10000	0	-0.12	3	3
CABIN1/MEF2D	0.006	0.08	-10000	0	-0.26	24	24
Calcineurin A alpha-beta B1/BCL2	0.016	0.031	-10000	0	-0.12	28	28
FKBP8	0.016	0.031	-10000	0	-0.12	27	27
activation-induced cell death of T cells	-0.006	0.079	0.25	24	-10000	0	24
KPNB1	0.022	0.009	-10000	0	-0.12	2	2
KPNA2	0.017	0.024	-10000	0	-0.12	15	15
XPO1	0.022	0.01	-10000	0	-0.12	2	2
SFN	0.014	0.031	-10000	0	-0.12	28	28
MAP3K8	0.022	0.009	-10000	0	-0.12	2	2
NFAT4/CK1 alpha	0.029	0.038	-10000	0	-0.13	18	18
MEF2D/NFAT1/Cbp/p300	0.039	0.079	-10000	0	-0.15	44	44
CABIN1	-0.006	0.081	-10000	0	-0.28	24	24
CALM1	0.021	0.014	-10000	0	-0.12	5	5
RAN	0.023	0.002	-10000	0	-10000	0	0
MAP3K1	0.021	0.015	-10000	0	-0.12	6	6
CAMK4	0.016	0.031	-10000	0	-0.12	27	27
mol:Ca2+	0	0.003	-10000	0	-10000	0	0
MAPK3	0.022	0.014	-10000	0	-0.12	5	5
YWHAH	0.021	0.015	-10000	0	-0.12	6	6
Calcineurin A alpha-beta B1/AKAP79/PKA	0.032	0.017	-10000	0	-0.082	12	12
YWHAB	0.023	0.007	-10000	0	-0.12	1	1
MAPK8	0.021	0.015	-10000	0	-0.12	6	6
MAPK9	0.021	0.011	-10000	0	-0.12	3	3
YWHAG	0.02	0.021	-10000	0	-0.12	13	13
FKBP1A	0.022	0.012	-10000	0	-0.12	4	4
NFAT1-c-4/YWHAQ	0.048	0.071	-10000	0	-0.29	10	10
PRKCH	0.019	0.023	-10000	0	-0.12	15	15
CABIN1/Cbp/p300	0.02	0.052	-10000	0	-0.15	43	43
CASP3	0.022	0.009	-10000	0	-0.12	2	2
PIM1	0.019	0.023	-10000	0	-0.12	15	15
Calcineurin A alpha-beta B1/FKBP12/FK506	0.014	0.012	-10000	0	-0.087	7	7
apoptosis	0.019	0.036	0.14	2	-0.21	11	13
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1	0.017	0.07	-10000	0	-0.25	17	17
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	-0.1	22	22
PRKCD	0.02	0.018	-10000	0	-0.12	8	8
NUP214	0.023	0.007	-10000	0	-0.12	1	1
PRKCZ	0.023	0.001	-10000	0	-10000	0	0
PRKCA	0.011	0.038	-10000	0	-0.12	42	42
PRKCG	0.022	0.016	-10000	0	-0.12	7	7
PRKCQ	0.015	0.03	-10000	0	-0.12	25	25
FKBP38/BCL2	0.023	0.035	-10000	0	-0.079	56	56
EP300	0.022	0.01	-10000	0	-0.12	2	2
PRKCB1	0.015	0.034	-10000	0	-0.12	34	34
CSNK2A1	0.022	0.015	-10000	0	-0.12	6	6
NFATc/JNK1	0.039	0.068	-10000	0	-0.24	18	18
CaM/Ca2+/FKBP38	0.024	0.028	-10000	0	-0.073	39	39
FKBP12/FK506	0.016	0.014	-10000	0	-0.11	7	7
CSNK1A1	0.017	0.016	-10000	0	-0.085	12	12
CaM/Ca2+/CAMK IV	0.023	0.028	-10000	0	-0.072	41	41
NFATc/ERK1	0.041	0.066	-10000	0	-0.25	13	13
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV	0.014	0.08	-10000	0	-0.24	25	25
NR4A1	0.017	0.082	-10000	0	-0.19	44	44
GSK3B	0.022	0.011	-10000	0	-0.12	3	3
positive T cell selection	0.024	0.021	-10000	0	-0.24	2	2
NFAT1/CK1 alpha	0.021	0.044	-10000	0	-0.16	18	18
RCH1/ KPNB1	0.011	0.061	-10000	0	-0.13	82	82
YWHAQ	0.023	0.003	-10000	0	-10000	0	0
PRKACA	0.021	0.017	-10000	0	-0.12	8	8
AKAP5	0.023	0.008	-10000	0	-0.12	2	2
MEF2D	0.023	0.002	-10000	0	-10000	0	0
mol:FK506	0	0	-10000	0	-10000	0	0
YWHAZ	0.023	0.003	-10000	0	-10000	0	0
NFATc/p38 alpha	0.041	0.067	-10000	0	-0.24	16	16
CREBBP	0.02	0.016	-10000	0	-0.12	6	6
BCL2	0.016	0.031	-10000	0	-0.12	28	28

×

Syndecan-3-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	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	-0.37	8	8
Syndecan-3/Neurocan	0.021	0.051	-9999	-0.47	5	5
POMC	0.023	0.01	-9999	-0.12	3	3
EGFR	0.015	0.03	-9999	-0.12	25	25
Syndecan-3/EGFR	0.016	0.053	-9999	-0.47	5	5
AGRP	0.023	0.001	-9999	-10000	0	0
NCSTN	0.022	0.012	-9999	-0.12	4	4
PSENEN	0.016	0.03	-9999	-0.12	25	25
RP11-540L11.1	0	0	-9999	-10000	0	0
APH1B	0.014	0.031	-9999	-0.12	28	28
APH1A	0.023	0.009	-9999	-0.12	2	2
NCAN	0.023	0.01	-9999	-0.12	3	3
long-term memory	0.018	0.064	-9999	-0.39	7	7
Syndecan-3/IL8	0.011	0.056	-9999	-0.48	5	5
PSEN1	0.022	0.008	-9999	-0.12	1	1
Src/Cortactin	0.03	0.027	-9999	-0.12	17	17
FYN	0.012	0.037	-9999	-0.12	40	40
limb bud formation	0.006	0.051	-9999	-0.49	5	5
MC4R	0	0	-9999	-10000	0	0
SRC	0.023	0.008	-9999	-0.12	2	2
PTN	-0.01	0.055	-9999	-0.12	111	111
FGFR/FGF/Syndecan-3	0.006	0.052	-9999	-0.49	5	5
neuron projection morphogenesis	-0.006	0.068	-9999	-0.39	7	7
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	0.055	-9999	-0.11	92	92
SDC3	0.006	0.052	-9999	-0.5	5	5
GO:0007205	0	0	-9999	-10000	0	0
positive regulation of leukocyte migration	0.011	0.055	-9999	-0.48	5	5
IL8	0.004	0.047	-9999	-0.12	70	70
Syndecan-3/Fyn/Cortactin	0.019	0.065	-9999	-0.4	7	7
Syndecan-3/CASK	0.005	0.049	-9999	-0.47	5	5
alpha-MSH/MC4R	0.017	0.007	-9999	-0.076	3	3
Gamma Secretase	0.035	0.067	-9999	-0.22	10	10

×

Hedgehog signaling events mediated by Gli proteins

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
HDAC1	0.019	0.019	-9999	-0.12	10	10
HDAC2	0.02	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	-0.41	22	22
GNAO1	0.011	0.041	-9999	-0.12	50	50
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	0.052	0.031	-9999	-0.099	19	19
GNAI1	0.013	0.035	-9999	-0.12	36	36
XPO1	0.025	0.01	-9999	-0.12	2	2
GLI1/Su(fu)	0.033	0.1	-9999	-0.38	26	26
SAP30	0.023	0	-9999	-10000	0	0
mol:GDP	0.024	0.011	-9999	-0.12	3	3
MIM/GLI2A	0.023	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	0.041	-9999	-0.22	7	7
GLI3	-0.006	0.11	-9999	-0.32	35	35
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	88	88
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)	0.054	0.043	-9999	-0.21	8	8
FOXA2	0.028	0.084	-9999	-0.74	5	5
neural tube patterning	0.027	0.11	-9999	-0.41	22	22
SPOP	0.022	0.011	-9999	-0.12	3	3
Su(fu)/PIAS1	0.036	0.04	-9999	-0.2	13	13
GNB1	0.023	0.006	-9999	-0.12	1	1
CSNK1G2	0.023	0.01	-9999	-0.12	3	3
CSNK1G3	0.022	0.007	-9999	-0.12	1	1
MTSS1	0.023	0.034	-9999	-0.11	31	31
embryonic limb morphogenesis	0.027	0.11	-9999	-0.41	22	22
SUFU	0.026	0.041	-9999	-0.22	12	12
LGALS3	0.018	0.023	-9999	-0.12	14	14
catabolic process	0.031	0.1	-9999	-0.32	24	24
GLI3A/CBP	0.033	0.022	-9999	-0.13	7	7
KIF3A	0.019	0.021	-9999	-0.12	12	12
GLI1	0.026	0.11	-9999	-0.43	21	21
RAB23	0.023	0.01	-9999	-0.12	3	3
CSNK1A1	0.022	0.007	-9999	-0.12	1	1
IFT172	0.022	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	0.012	-9999	-0.12	4	4
RBBP4	0.021	0.014	-9999	-0.12	5	5
CSNK1G1	0.023	0.008	-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	0.046	0.042	-9999	-0.24	6	6
STK36	0.022	0.021	-9999	-0.12	12	12
Gi family/GNB1/GNG2/GDP	0.008	0.077	-9999	-0.22	31	31
PTCH1	0.033	0.11	-9999	-0.53	9	9
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	0.095	-9999	-0.32	27	27

×

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	-0.11	10	10
NFATC2	0.024	0.022	-9999	-0.083	15	15
NFATC3	0.026	0.02	-9999	-0.1	9	9
CD40LG	0.045	0.078	-9999	-0.25	8	8
PTGS2	0.037	0.089	-9999	-0.22	20	20
JUNB	0.007	0.042	-9999	-0.12	53	53
CaM/Ca2+/Calcineurin A alpha-beta B1	0.019	0.021	-9999	-0.12	12	12
CaM/Ca2+	0.019	0.021	-9999	-0.12	12	12
CALM1	0.024	0.014	-9999	-0.12	5	5
JUN	0.017	0.032	-9999	-0.12	30	30
mol:Ca2+	0.002	0.003	-9999	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0.016	0.012	-9999	-0.085	7	7
FOSL1	0.021	0.018	-9999	-0.12	9	9
CREM	0.021	0.012	-9999	-0.12	4	4
Jun/NFAT1-c-4/p21SNFT	0.062	0.06	-9999	-0.17	9	9
FOS	-0.002	0.052	-9999	-0.12	95	95
IFNG	0.041	0.084	-9999	-0.25	12	12
AP-1/NFAT1-c-4	0.09	0.11	-9999	-0.24	12	12
FASLG	0.044	0.079	-9999	-0.22	13	13
NFAT1-c-4/ICER1	0.052	0.038	-9999	-0.13	8	8
IL2RA	0.044	0.08	-9999	-0.22	15	15
FKBP12/FK506	0.016	0.014	-9999	-0.11	7	7
CSF2	0.045	0.079	-9999	-0.24	9	9
JunB/Fra1/NFAT1-c-4	0.046	0.06	-9999	-0.14	17	17
IL4	0.045	0.079	-9999	-0.25	8	8
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

×

Insulin Pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CBL/APS/CAP	0.034	0.028	-9999	-0.099	11	11
TC10/GTP	0.031	0.023	-9999	-0.081	15	15
Insulin Receptor/Insulin/IRS1/Shp2	0.05	0.042	-9999	-0.1	29	29
HRAS	0.023	0.006	-9999	-0.12	1	1
APS homodimer	0	0	-9999	-10000	0	0
GRB14	0.013	0.036	-9999	-0.12	39	39
FOXO3	0.009	0.065	-9999	-0.6	6	6
AKT1	0.016	0.047	-9999	-0.12	27	27
INSR	0.023	0.017	-9999	-0.11	9	9
Insulin Receptor/Insulin	0.06	0.027	-9999	-0.16	3	3
mol:GTP	0	0	-9999	-10000	0	0
GRB10	0.022	0.014	-9999	-0.12	5	5
SORBS1	0.02	0.021	-9999	-0.12	12	12
CRK	0.022	0.016	-9999	-0.12	7	7
PTPN1	0.025	0.021	-9999	-0.16	3	3
CAV1	0.02	0.027	-9999	-0.09	13	13
CBL/APS/CAP/Crk-II/C3G	0.051	0.024	-9999	-0.1	7	7
Insulin Receptor/Insulin/IRS1/NCK2	0.055	0.03	-9999	-0.09	13	13
mol:GDP	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	0.025	0.052	-9999	-0.093	70	70
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B	0.037	0.054	-9999	-0.3	13	13
RPS6KB1	0.014	0.048	-9999	-0.13	33	33
PARD6A	0.023	0.009	-9999	-0.12	2	2
CBL	0.023	0.006	-9999	-0.12	1	1
tumor necrosis factor-mediated signaling pathway	0	0	-9999	-10000	0	0
DOK1	0.009	0.073	-9999	-0.68	6	6
PIK3R1	0.015	0.031	-9999	-0.12	28	28
Insulin Receptor/Insuli/IRS1/GRB2/Shc	0.027	0.055	-9999	-0.15	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	-0.084	19	19
PRKCI	-0.01	0.13	-9999	-0.38	62	62
Insulin Receptor/Insulin/GRB14/PDK1	0.008	0.045	-9999	-0.14	24	24
SHC1	0.023	0.001	-9999	-10000	0	0
negative regulation of MAPKKK cascade	0.021	0.079	-9999	-0.6	6	6
PI3K	0.033	0.057	-9999	-0.094	70	70
NCK2	0.023	0.006	-9999	-0.12	1	1
RHOQ	0.021	0.017	-9999	-0.12	8	8
mol:H2O2	0	0.002	-9999	-10000	0	0
HRAS/GDP	0.017	0.008	-9999	-0.11	2	2
AKT2	0.015	0.048	-9999	-0.13	26	26
PRKCZ	0.028	0.063	-9999	-0.36	13	13
SH2B2	0	0	-9999	-10000	0	0
SHC/SHIP	0.025	0.02	-9999	-0.079	13	13
F2RL2	0.02	0.022	-9999	-0.12	14	14
TRIP10	0.021	0.018	-9999	-0.12	9	9
Insulin Receptor/Insulin/Shc	0.044	0.02	-9999	-0.095	7	7
TC10/GTP/CIP4/Exocyst	0.026	0.026	-9999	-0.084	29	29
Insulin Receptor/Insulin/SHC/GRB2/Sos1	0.056	0.046	-9999	-0.095	32	32
RAPGEF1	0.023	0	-9999	-10000	0	0
RASA1	0.021	0.011	-9999	-0.12	3	3
NCK1	0.02	0.019	-9999	-0.12	9	9
CBL/APS/CAP/Crk-II	0.04	0.024	-9999	-0.11	7	7
TC10/GDP	0.014	0.022	-9999	-0.11	16	16
Insulin Receptor/Insulin/SHC/GRB10	0.056	0.029	-9999	-0.092	15	15
INPP5D	0.012	0.018	-9999	-0.086	12	12
SOS1	0.017	0.027	-9999	-0.12	20	20
SGK1	-0.002	0.004	-9999	-10000	0	0
mol:cAMP	0	0	-9999	-10000	0	0
PTPN11	0.022	0.011	-9999	-0.12	3	3
IRS1	0.02	0.022	-9999	-0.12	14	14
p62DOK/RasGAP	0.022	0.08	-9999	-0.61	6	6
INS	0.024	0.011	-9999	-0.12	3	3
mol:PI-3-4-P2	0.012	0.018	-9999	-0.085	12	12
GRB2	0.023	0.006	-9999	-0.12	1	1
EIF4EBP1	0.016	0.045	-9999	-0.12	31	31
PTPRA	0.024	0.012	-9999	-0.12	4	4
PIK3CA	0.02	0.017	-9999	-0.12	7	7
TC10/GTP/CIP4	0.026	0.026	-9999	-0.084	29	29
PDPK1	0.023	0.006	-9999	-0.12	1	1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos	0.027	0.049	-9999	-0.17	11	11
Insulin Receptor/Insulin/IRS1	0.041	0.027	-9999	-0.094	12	12
Insulin Receptor/Insulin/IRS3	0.034	0.023	-9999	-0.093	17	17
Par3/Par6	0.046	0.032	-9999	-0.089	18	18

×

VEGFR1 specific signals

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

×

Sphingosine 1-phosphate (S1P) pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.023	0.01	-9999	-0.12	3	3
SPHK1	0.021	0.017	-9999	-0.12	8	8
GNAI2	0.022	0.01	-9999	-0.12	3	3
mol:S1P	0.018	0.03	-9999	-0.18	12	12
GNAO1	0.011	0.041	-9999	-0.12	50	50
mol:Sphinganine-1-P	0.021	0.013	-9999	-0.07	11	11
growth factor activity	0	0	-9999	-10000	0	0
S1P/S1P2/G12/G13	0.036	0.034	-9999	-0.11	23	23
GNAI3	0.021	0.008	-9999	-0.12	1	1
G12/G13	0.03	0.028	-9999	-0.13	16	16
S1PR3	0	0	-9999	-10000	0	0
S1PR2	0	0	-9999	-10000	0	0
EDG1	0.022	0.015	-9999	-0.12	6	6
S1P1/S1P	0.028	0.029	-9999	-0.14	13	13
S1PR5	0	0	-9999	-10000	0	0
S1PR4	0	0	-9999	-10000	0	0
GNAI1	0.012	0.035	-9999	-0.12	36	36
S1P/S1P5/G12	0.026	0.025	-9999	-0.13	13	13
S1P/S1P3/Gq	0.022	0.056	-9999	-0.22	25	25
S1P/S1P4/Gi	0.002	0.075	-9999	-0.16	88	88
GNAQ	0.021	0.015	-9999	-0.12	6	6
GNAZ	0.022	0.012	-9999	-0.12	4	4
GNA14	0.02	0.02	-9999	-0.12	11	11
GNA15	0.021	0.017	-9999	-0.12	8	8
GNA12	0.023	0.001	-9999	-10000	0	0
GNA13	0.022	0.009	-9999	-0.12	2	2
GNA11	0.022	0.013	-9999	-0.12	5	5
ABCC1	0.021	0.017	-9999	-0.12	8	8

×

Insulin-mediated glucose transport

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Insulin responsive Vesicles	0.022	0.073	-10000	0	-0.21	23	23
CaM/Ca2+	0.014	0.02	-10000	0	-0.12	12	12
AKT1	0.021	0.019	-10000	0	-0.12	10	10
AKT2	0.019	0.025	-10000	0	-0.12	18	18
STXBP4	0.018	0.026	-10000	0	-0.12	19	19
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucose	0.015	0.067	0.18	6	-0.2	20	26
YWHAZ	0.023	0.003	-10000	0	-10000	0	0
CALM1	0.022	0.014	-10000	0	-0.12	5	5
YWHAQ	0.023	0.003	-10000	0	-10000	0	0
TBC1D4	0.02	0.017	-10000	0	-0.07	20	20
mol:Ca2+	0	0	-10000	0	-10000	0	0
YWHAH	0.021	0.015	-10000	0	-0.12	6	6
YWHAB	0.023	0.007	-10000	0	-0.12	1	1
SNARE/Synip	0.033	0.041	-10000	0	-0.13	19	19
YWHAG	0.02	0.021	-10000	0	-0.12	13	13
ASIP	0.021	0.015	-10000	0	-0.12	6	6
PRKCI	0.016	0.028	-10000	0	-0.12	22	22
AS160/CaM/Ca2+	0.014	0.02	-10000	0	-0.12	12	12
RHOQ	0.021	0.017	-10000	0	-0.12	8	8
GYS1	0.025	0.017	-10000	0	-0.22	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	0.026	-10000	0	-0.084	29	29
AS160/14-3-3	0.024	0.064	-10000	0	-0.19	36	36
VAMP2	0.016	0.032	-10000	0	-0.12	30	30
SLC2A4	0.015	0.071	0.18	6	-0.22	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	0.031	-10000	0	-0.12	28	28
LNPEP	0.017	0.027	-10000	0	-0.12	20	20
YWHAE	0.022	0.014	-10000	0	-0.12	5	5

×

S1P1 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
VEGFR2 homodimer/VEGFA homodimer	0.029	0.053	-9999	-0.14	40	40
PDGFRB	0.01	0.041	-9999	-0.12	51	51
SPHK1	0.001	0.015	-9999	-10000	0	0
mol:S1P	0.015	0.028	-9999	-10000	0	0
S1P1/S1P/Gi	0.023	0.072	-9999	-0.32	13	13
GNAO1	0.01	0.041	-9999	-0.12	50	50
PDGFB-D/PDGFRB/PLCgamma1	0.009	0.087	-9999	-0.26	28	28
PLCG1	0.021	0.071	-9999	-0.28	17	17
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.01	0.041	-9999	-0.12	51	51
GNAI2	0.022	0.011	-9999	-0.12	3	3
GNAI3	0.022	0.009	-9999	-0.12	1	1
GNAI1	0.012	0.035	-9999	-0.12	36	36
mol:GDP	0	0	-9999	-10000	0	0
EDG1	0.023	0.046	-9999	-0.27	4	4
S1P1/S1P	0.025	0.053	-9999	-0.2	11	11
negative regulation of cAMP metabolic process	0.023	0.07	-9999	-0.3	14	14
MAPK3	0.022	0.09	-9999	-0.44	13	13
calcium-dependent phospholipase C activity	-0.001	0.001	-9999	-10000	0	0
Rac1/GDP	0.016	0.015	-9999	-0.15	5	5
RhoA/GDP	0.016	0.016	-9999	-0.14	6	6
KDR	0.025	0.021	-9999	-0.12	11	11
PLCB2	0.025	0.049	-9999	-0.19	9	9
RAC1	0.023	0.002	-9999	-10000	0	0
RhoA/GTP	0.021	0.046	-9999	-0.19	11	11
receptor internalization	0.023	0.05	-9999	-0.19	11	11
PTGS2	0.001	0.14	-9999	-0.92	9	9
Rac1/GTP	0.021	0.045	-9999	-0.18	10	10
RHOA	0.023	0.006	-9999	-0.12	1	1
VEGFA	0.023	0.022	-9999	-0.11	12	12
negative regulation of T cell proliferation	0.023	0.07	-9999	-0.3	14	14
GO:0007205	0	0	-9999	-10000	0	0
GNAZ	0.022	0.012	-9999	-0.12	4	4
MAPK1	0.021	0.091	-9999	-0.44	13	13
S1P1/S1P/PDGFB-D/PDGFRB	0.028	0.065	-9999	-0.24	11	11
ABCC1	0.021	0.017	-9999	-0.12	8	8

×

Effects of Botulinum toxin

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
STX1A	0.011	0.006	-9999	-0.076	3	3
UniProt:P19321	0	0	-9999	-10000	0	0
RIMS1/UNC13B	0.033	0.016	-9999	-0.084	10	10
STXBP1	0.02	0.02	-9999	-0.12	11	11
ACh/CHRNA1	0.013	0.025	-9999	-0.062	51	51
RAB3GAP2/RIMS1/UNC13B	0.041	0.029	-9999	-0.11	16	16
mol:Ca2+	0	0	-9999	-10000	0	0
UniProt:P30996	0	0	-9999	-10000	0	0
UniProt:Q60393	0	0	-9999	-10000	0	0
CST086	0	0	-9999	-10000	0	0
RIMS1	0.023	0.006	-9999	-0.12	1	1
mol:ACh	0.005	0.011	-9999	-0.076	4	4
RAB3GAP2	0.022	0.009	-9999	-0.12	2	2
STX1A/SNAP25/VAMP2	0.039	0.031	-9999	-0.1	8	8
UniProt:P10844	0	0	-9999	-10000	0	0
muscle contraction	0.013	0.025	-9999	-0.062	51	51
UNC13B	0.021	0.016	-9999	-0.12	7	7
CHRNA1	0.011	0.04	-9999	-0.12	48	48
UniProt:P10845	0	0	-9999	-10000	0	0
ACh/Synaptotagmin 1	0.015	0.023	-9999	-0.061	41	41
SNAP25	0.004	0.018	-9999	-0.19	2	2
VAMP2	0.004	0.016	-9999	-0.18	2	2
SYT1	0.014	0.035	-9999	-0.12	37	37
UniProt:Q00496	0	0	-9999	-10000	0	0
STXIA/STXBP1	0.024	0.013	-9999	-0.056	14	14
STX1A/SNAP25 fragment 1/VAMP2	0.039	0.031	-9999	-0.1	8	8

×

Glypican 2 network

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

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

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

×

Alternative NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IKK alpha homodimer	0.024	0.04	-9999	-0.14	30	30
FBXW11	0.023	0.003	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.023	0.003	-9999	-10000	0	0
CHUK	0.021	0.013	-9999	-0.12	4	4
NF kappa B2 p100/RelB	0.056	0.044	-9999	-0.091	43	43
NFKB1	0.021	0.013	-9999	-0.12	4	4
MAP3K14	0.023	0.006	-9999	-0.12	1	1
NF kappa B1 p50/RelB	0.02	0.048	-9999	-0.13	49	49
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 S121. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G beta1gamma2/HDAC5	0.053	0.032	-10000	0	-0.098	21	21
HDAC3	0.023	0.002	-10000	0	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	-0.007	0.028	-10000	0	-0.11	36	36
GATA1/HDAC4	0.034	0.004	-10000	0	-0.07	1	1
GATA1/HDAC5	0.034	0.004	-10000	0	-10000	0	0
GATA2/HDAC5	0.032	0.016	-10000	0	-10000	0	0
HDAC5/BCL6/BCoR	0.033	0.045	-10000	0	-0.12	43	43
HDAC9	0.015	0.031	-10000	0	-0.12	28	28
Glucocorticoid receptor/Hsp90/HDAC6	0.031	0.048	-10000	0	-0.12	47	47
HDAC4/ANKRA2	0.028	0.031	-10000	0	-0.14	14	14
HDAC5/YWHAB	0.032	0.02	-10000	0	-0.14	7	7
NPC/RanGAP1/SUMO1/Ubc9	0.015	0.036	-10000	0	-0.14	30	30
GATA2	0.02	0.021	-10000	0	-0.12	13	13
HDAC4/RFXANK	0.025	0.038	-10000	0	-0.11	39	39
BCOR	0.023	0.007	-10000	0	-0.12	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
HDAC10	0.023	0	-10000	0	-10000	0	0
HDAC5	0.023	0	-10000	0	-10000	0	0
GNB1/GNG2	0.027	0.035	-10000	0	-0.12	30	30
Histones	0.026	0.035	-10000	0	-0.12	26	26
ADRBK1	0.023	0.001	-10000	0	-10000	0	0
HDAC4	0.023	0	-10000	0	-10000	0	0
XPO1	0.022	0.01	-10000	0	-0.12	2	2
HDAC5/ANKRA2	0.028	0.031	-10000	0	-0.14	14	14
HDAC4/Ubc9	0.034	0.007	-10000	0	-0.14	1	1
HDAC7	0	0	-10000	0	-10000	0	0
HDAC5/14-3-3 E	0.031	0.024	-10000	0	-0.12	14	14
TUBA1B	0.023	0	-10000	0	-10000	0	0
HDAC6	0.019	0.023	-10000	0	-0.12	15	15
HDAC5/RFXANK	0.025	0.038	-10000	0	-0.11	39	39
CAMK4	0.016	0.031	-10000	0	-0.12	27	27
Tubulin/HDAC6	0.043	0.019	-10000	0	-10000	0	0
SUMO1	0.023	0.009	-10000	0	-0.12	2	2
EntrezGene:9972	0	0	-10000	0	-10000	0	0
YWHAB	0.023	0.007	-10000	0	-0.12	1	1
GATA1	0.023	0.006	-10000	0	-0.12	1	1
EntrezGene:8021	0	0	-10000	0	-10000	0	0
YWHAE	0.022	0.014	-10000	0	-0.12	5	5
NR3C1	0.021	0.014	-10000	0	-0.12	5	5
SUMO1/HDAC4	0.036	0.035	-10000	0	-0.17	6	6
SRF	0.018	0.026	-10000	0	-0.12	20	20
HDAC4/YWHAB	0.032	0.02	-10000	0	-0.14	7	7
Tubulin	0.033	0.012	-10000	0	-10000	0	0
HDAC4/14-3-3 E	0.031	0.024	-10000	0	-0.12	14	14
GNB1	0.023	0.006	-10000	0	-0.12	1	1
RANGAP1	0.023	0.006	-10000	0	-0.12	1	1
BCL6/BCoR	0.019	0.05	-10000	0	-0.13	54	54
HDAC4/HDAC3/SMRT (N-CoR2)	0.043	0.024	-10000	0	-0.11	8	8
HDAC4/SRF	0.038	0.03	-10000	0	-0.12	5	5
HDAC4/ER alpha	0.018	0.049	-10000	0	-0.12	60	60
EntrezGene:23225	0	0	-10000	0	-10000	0	0
positive regulation of chromatin silencing	0.026	0.035	-10000	0	-0.12	26	26
cell motility	0.043	0.019	-10000	0	-10000	0	0
EntrezGene:23636	0	0	-10000	0	-10000	0	0
UBE2I	0.023	0.001	-10000	0	-10000	0	0
HDAC7/HDAC3	0.016	0.014	-10000	0	-0.15	4	4
BCL6	0.019	0.02	-10000	0	-0.12	10	10
HDAC4/CaMK II delta B	0.023	0	-10000	0	-10000	0	0
Hsp90/HDAC6	0.028	0.031	-10000	0	-0.14	14	14
ESR1	0.018	0.024	-10000	0	-0.12	15	15
HDAC6/HDAC11	0.029	0.028	-10000	0	-0.15	8	8
Ran/GTP/Exportin 1	0.034	0.049	-10000	0	-0.15	30	30
NPC	0.009	0.023	-10000	0	-0.095	27	27
MEF2C	0.02	0.02	-10000	0	-0.12	11	11
RAN	0.023	0.002	-10000	0	-10000	0	0
HDAC4/MEF2C	0.058	0.038	-10000	0	-0.09	24	24
GNG2	0.02	0.018	-10000	0	-0.12	9	9
NCOR2	0.019	0.023	-10000	0	-0.12	15	15
TUBB2A	0.021	0.017	-10000	0	-0.12	8	8
HDAC11	0.022	0.012	-10000	0	-0.12	4	4
HSP90AA1	0.023	0.004	-10000	0	-10000	0	0
RANBP2	0.022	0.01	-10000	0	-0.12	2	2
ANKRA2	0.02	0.021	-10000	0	-0.12	12	12
RFXANK	0.018	0.025	-10000	0	-0.12	17	17
nuclear import	-0.033	0.034	0.16	15	-10000	0	15

×

IL27-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.025	0.034	-10000	0	-0.4	2	2
CD4-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
cytokine production during immune response	-0.001	0.096	0.38	20	-10000	0	20
IL27/IL27R/JAK1	0.027	0.098	-10000	0	-0.95	3	3
TBX21	-0.001	0.081	-10000	0	-0.55	4	4
IL12B	0.024	0.002	-10000	0	-10000	0	0
IL12A	0.001	0.029	-10000	0	-0.076	70	70
IL6ST	0.016	0.027	-10000	0	-0.12	20	20
IL27RA/JAK1	0.01	0.086	-10000	0	-1.1	3	3
IL27	0.023	0.004	-10000	0	-10000	0	0
TYK2	0.021	0.017	-10000	0	-0.12	7	7
T-helper cell lineage commitment	0.014	0.09	-10000	0	-1.2	2	2
T-helper 2 cell differentiation	-0.001	0.096	0.38	20	-10000	0	20
T cell proliferation during immune response	-0.001	0.096	0.38	20	-10000	0	20
MAPKKK cascade	0.001	0.096	-10000	0	-0.38	20	20
STAT3	0.022	0.011	-10000	0	-0.12	3	3
STAT2	0.02	0.018	-10000	0	-0.12	9	9
STAT1	0.014	0.03	-10000	0	-0.12	25	25
IL12RB1	0.023	0.006	-10000	0	-0.12	1	1
positive regulation of tyrosine phosphorylation of STAT protein	0	0	-10000	0	-10000	0	0
IL12RB2	-0.001	0.083	-10000	0	-0.5	5	5
IL27/IL27R/JAK2/TYK2	0.001	0.097	-10000	0	-0.39	20	20
positive regulation of T cell mediated cytotoxicity	0.001	0.096	-10000	0	-0.38	20	20
STAT1 (dimer)	0.013	0.11	0.4	1	-0.77	4	5
JAK2	0.016	0.025	-10000	0	-0.12	17	17
JAK1	0.022	0.01	-10000	0	-0.12	2	2
STAT2 (dimer)	0.003	0.1	-10000	0	-0.38	20	20
T cell proliferation	-0.001	0.093	-10000	0	-0.37	20	20
IL12/IL12R/TYK2/JAK2	0.026	0.066	-10000	0	-0.72	1	1
IL17A	0.014	0.09	-10000	0	-1.2	2	2
mast cell activation	-0.001	0.096	0.38	20	-10000	0	20
IFNG	0.003	0.021	-10000	0	-0.076	5	5
T cell differentiation	-0.001	0.004	-10000	0	-0.019	5	5
STAT3 (dimer)	0.003	0.1	-10000	0	-0.38	20	20
STAT5A (dimer)	0.005	0.1	-10000	0	-0.37	20	20
STAT4 (dimer)	0.005	0.1	-10000	0	-0.37	20	20
STAT4	0.02	0.02	-10000	0	-0.12	11	11
T cell activation	-0.006	0.011	0.12	2	-10000	0	2
IL27R/JAK2/TYK2	0.008	0.1	-10000	0	-0.84	4	4
GATA3	0.014	0.029	-10000	0	-10000	0	0
IL18	0	0.028	-10000	0	-0.076	66	66
positive regulation of mast cell cytokine production	0.003	0.1	-10000	0	-0.37	20	20
IL27/EBI3	0.033	0.009	-10000	0	-10000	0	0
IL27RA	-0.004	0.09	-10000	0	-1.1	3	3
IL6	0.012	0.053	-10000	0	-0.33	3	3
STAT5A	0.022	0.012	-10000	0	-0.12	4	4
monocyte differentiation	0	0.001	-10000	0	-10000	0	0
IL2	0.006	0.046	0.48	3	-10000	0	3
IL1B	0.004	0.024	-10000	0	-0.076	45	45
EBI3	0.023	0.008	-10000	0	-0.12	1	1
TNF	0.01	0.012	-10000	0	-0.076	11	11

×

Sumoylation by RanBP2 regulates transcriptional repression

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
HDAC1	0.019	0.019	-9999	-0.12	10	10
Ran/GTP/Exportin 1/HDAC4	-0.008	0.033	-9999	-0.15	26	26
MDM2/SUMO1	0.033	0.04	-9999	-0.18	7	7
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	-0.1	33	33
NPC/RanGAP1/SUMO1/RanBP2/Ubc9	0.015	0.036	-9999	-0.14	30	30
Ran/GTP	0.026	0.036	-9999	-0.12	30	30
EntrezGene:23225	0	0	-9999	-10000	0	0
MDM2	0.02	0.02	-9999	-0.12	11	11
UBE2I	0.023	0.001	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.025	0.047	-9999	-0.15	30	30
NPC	0.009	0.023	-9999	-0.095	27	27
PIAS2	0.021	0.018	-9999	-0.12	9	9
PIAS1	0.022	0.009	-9999	-0.12	2	2
EntrezGene:9972	0	0	-9999	-10000	0	0

×

Angiopoietin receptor Tie2-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	0.023	0.17	-9999	-0.68	14	14
NCK1/PAK1/Dok-R	-0.028	0.072	-9999	-0.32	15	15
NCK1/Dok-R	0.05	0.086	-9999	-0.84	2	2
PIK3CA	0.02	0.017	-9999	-0.12	7	7
mol:beta2-estradiol	-0.008	0.012	-9999	-10000	0	0
RELA	0.023	0.009	-9999	-0.12	2	2
SHC1	0.024	0.002	-9999	-10000	0	0
Rac/GDP	0.016	0.015	-9999	-0.15	5	5
F2	0.014	0.02	-9999	-0.13	4	4
TNIP2	0.021	0.018	-9999	-0.12	9	9
NF kappa B/RelA	0.058	0.086	-9999	-0.79	2	2
FN1	-0.012	0.055	-9999	-0.12	115	115
PLD2	0.042	0.076	-9999	-0.87	2	2
PTPN11	0.022	0.011	-9999	-0.12	3	3
GRB14	0.013	0.036	-9999	-0.12	39	39
ELK1	0.045	0.073	-9999	-0.82	2	2
GRB7	0.018	0.025	-9999	-0.12	18	18
PAK1	0.016	0.029	-9999	-0.12	24	24
Tie2/Ang1/alpha5/beta1 Integrin	0.012	0.1	-9999	-0.82	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	0.052	0.083	-9999	-0.84	2	2
CRK	0.022	0.016	-9999	-0.12	7	7
mol:NO	0.03	0.14	-9999	-0.5	17	17
PLG	0.042	0.076	-9999	-0.87	2	2
mol:GDP	0	0	-9999	-10000	0	0
chemokinesis	0.037	0.14	-9999	-0.74	6	6
GRB2	0.023	0.006	-9999	-0.12	1	1
PIK3R1	0.015	0.031	-9999	-0.12	28	28
ANGPT2	-0.028	0.27	-9999	-1	39	39
BMX	0.042	0.076	-9999	-0.87	2	2
ANGPT1	0.023	0.047	-9999	-10000	0	0
tube development	0.01	0.2	-9999	-0.69	41	41
ANGPT4	0.023	0.009	-9999	-0.12	2	2
response to hypoxia	0.002	0.008	-9999	-0.061	2	2
Tie2/Ang1/GRB14	0.044	0.082	-9999	-0.88	2	2
alpha5/beta1 Integrin	0.017	0.048	-9999	-0.14	33	33
FGF2	0.023	0.01	-9999	-0.12	2	2
STAT5A (dimer)	0.025	0.23	-9999	-0.78	41	41
mol:L-citrulline	0.03	0.14	-9999	-0.5	17	17
AGTR1	0.021	0.016	-9999	-0.12	4	4
MAPK14	0.038	0.12	-9999	-1	4	4
Tie2/SHP2	0.037	0.081	-9999	-0.67	4	4
TEK	0.034	0.087	-9999	-0.84	3	3
RPS6KB1	0.026	0.15	-9999	-0.71	9	9
Angiotensin II/AT1	0.016	0.018	-9999	-0.077	4	4
Tie2/Ang1/GRB2	0.049	0.081	-9999	-0.88	2	2
MAPK3	0.042	0.071	-9999	-0.81	2	2
MAPK1	0.042	0.073	-9999	-0.81	2	2
Tie2/Ang1/GRB7	0.046	0.082	-9999	-0.88	2	2
NFKB1	0.021	0.013	-9999	-0.12	4	4
MAPK8	0.04	0.076	-9999	-0.87	2	2
PI3K	0.025	0.16	-9999	-0.92	6	6
FES	0.046	0.097	-9999	-1	2	2
Crk/Dok-R	0.056	0.081	-9999	-0.84	2	2
Tie2/Ang1/ABIN2	0.048	0.08	-9999	-0.88	2	2
blood circulation	0	0	-9999	-10000	0	0
negative regulation of caspase activity	0.025	0.16	-9999	-0.62	14	14
STAT5A	0.022	0.012	-9999	-0.12	4	4
mol:ROS	0	0	-9999	-10000	0	0
PTK2	0.025	0.15	-9999	-0.74	7	7
Tie2/Ang2	0.003	0.26	-9999	-0.93	41	41
Tie2/Ang1	0.041	0.08	-9999	-0.92	2	2
FOXO1	0.02	0.18	-9999	-0.6	41	41
ELF1	0.03	0.013	-9999	-0.097	3	3
ELF2	0.042	0.077	-9999	-0.88	2	2
mol:Choline	0.042	0.074	-9999	-0.84	2	2
cell migration	-0.02	0.045	-9999	-0.18	16	16
FYN	0.004	0.23	-9999	-0.79	41	41
DOK2	0.02	0.021	-9999	-0.12	12	12
negative regulation of cell cycle	0.03	0.17	-9999	-0.55	41	41
ETS1	0.022	0.035	-9999	-0.12	27	27
PXN	0.028	0.13	-9999	-0.62	7	7
ITGB1	0.021	0.015	-9999	-0.12	6	6
NOS3	0.028	0.15	-9999	-0.56	17	17
RAC1	0.023	0.002	-9999	-10000	0	0
TNF	0.029	0.025	-9999	-0.12	11	11
MAPKKK cascade	0.042	0.074	-9999	-0.84	2	2
RASA1	0.021	0.011	-9999	-0.12	3	3
Tie2/Ang1/Shc	0.05	0.081	-9999	-0.88	2	2
NCK1	0.02	0.019	-9999	-0.12	9	9
vasculogenesis	0.031	0.13	-9999	-0.45	17	17
mol:Phosphatidic acid	0.042	0.074	-9999	-0.84	2	2
mol:Angiotensin II	-0.001	0.009	-9999	-10000	0	0
mol:NADP	0.03	0.14	-9999	-0.5	17	17
Rac1/GTP	0.03	0.14	-9999	-0.73	6	6
MMP2	0.016	0.082	-9999	-0.87	2	2

×

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	9	11
SMAD3	0.027	0.046	-10000	0	-0.29	4	4
SMAD3/SMAD4	-0.012	0.15	-10000	0	-0.36	81	81
SMAD4/Ubc9/PIASy	0.043	0.028	-10000	0	-0.12	16	16
SMAD2/SMAD2/SMAD4	0.034	0.064	0.17	2	-0.17	18	20
PPM1A	0.023	0.001	-10000	0	-10000	0	0
CALM1	0.022	0.014	-10000	0	-0.12	5	5
SMAD2/SMAD4	0.027	0.033	0.16	2	-0.14	9	11
MAP3K1	0.021	0.015	-10000	0	-0.12	6	6
TRAP-1/SMAD4	0.025	0.042	-10000	0	-0.14	31	31
MAPK3	0.022	0.014	-10000	0	-0.12	5	5
MAPK1	0.021	0.016	-10000	0	-0.12	7	7
NUP214	0.023	0.007	-10000	0	-0.12	1	1
CTDSP1	0.022	0.011	-10000	0	-0.12	3	3
CTDSP2	0.022	0.009	-10000	0	-0.12	2	2
CTDSPL	0.023	0.006	-10000	0	-0.12	1	1
KPNB1	0.022	0.009	-10000	0	-0.12	2	2
TGFBRAP1	0.022	0.007	-10000	0	-0.12	1	1
UBE2I	0.023	0.001	-10000	0	-10000	0	0
NUP153	0.02	0.018	-10000	0	-0.12	9	9
KPNA2	0.017	0.024	-10000	0	-0.12	15	15
PIAS4	0.023	0	-10000	0	-10000	0	0

×

Aurora C signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
INCENP	0.023	0.008	-9999	-0.12	2	2
Aurora C/Aurora B/INCENP	0.033	0.037	-9999	-0.097	33	33
metaphase	0	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
H3F3B	0.003	0.068	-9999	-0.39	16	16
AURKB	0.017	0.026	-9999	-0.12	19	19
AURKC	0.023	0.006	-9999	-0.12	1	1

×

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

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
MAP4K1	0.015	0.058	-10000	0	-0.24	7	7
CRKL	0.013	0.059	-10000	0	-0.27	6	6
HRAS	0.031	0.068	-10000	0	-0.27	7	7
mol:PIP3	0.004	0.068	0.22	5	-0.24	10	15
SPRED1	0.019	0.016	-10000	0	-0.12	6	6
SPRED2	0.022	0.014	-10000	0	-0.12	5	5
GAB1	0.01	0.062	-10000	0	-0.27	7	7
FOXO3	0.019	0.063	-10000	0	-0.3	7	7
AKT1	0.017	0.064	-10000	0	-0.34	5	5
BAD	0.02	0.061	-10000	0	-0.32	5	5
megakaryocyte differentiation	0.012	0.06	-10000	0	-0.3	5	5
GSK3B	0.02	0.062	-10000	0	-0.33	5	5
RAF1	0.03	0.061	-10000	0	-0.24	7	7
SHC1	0.023	0.001	-10000	0	-10000	0	0
STAT3	0.011	0.063	-10000	0	-0.26	10	10
STAT1	0.012	0.12	-10000	0	-0.54	12	12
HRAS/SPRED1	0.031	0.068	-10000	0	-0.22	12	12
cell proliferation	0.011	0.061	-10000	0	-0.28	7	7
PIK3CA	0.02	0.017	-10000	0	-0.12	7	7
TEC	0.01	0.038	-10000	0	-0.12	44	44
RPS6KB1	0.01	0.077	-10000	0	-0.28	16	16
HRAS/SPRED2	0.036	0.064	-10000	0	-0.22	10	10
LYN/TEC/p62DOK	0.013	0.086	-10000	0	-0.25	21	21
MAPK3	0.029	0.052	-10000	0	-0.23	6	6
STAP1	0.011	0.061	-10000	0	-0.3	5	5
GRAP2	0.022	0.012	-10000	0	-0.12	4	4
JAK2	0.005	0.12	-10000	0	-0.47	16	16
STAT1 (dimer)	0.008	0.13	-10000	0	-0.53	12	12
mol:Gleevec	-0.001	0.003	-10000	0	-10000	0	0
GRB2/SOCS1/VAV1	0.03	0.075	-10000	0	-0.27	9	9
actin filament polymerization	0.008	0.059	-10000	0	-0.3	5	5
LYN	0.021	0.013	-10000	0	-0.12	4	4
STAP1/STAT5A (dimer)	0.012	0.09	-10000	0	-0.34	13	13
PIK3R1	0.015	0.031	-10000	0	-0.12	28	28
CBL/CRKL/GRB2	0.033	0.064	-10000	0	-0.26	6	6
PI3K	0.017	0.089	-10000	0	-0.28	19	19
PTEN	0.022	0.008	-10000	0	-0.12	1	1
SCF/KIT/EPO/EPOR	0.03	0.13	-10000	0	-1.3	2	2
MAPK8	0.011	0.062	-10000	0	-0.29	7	7
STAT3 (dimer)	0.011	0.062	-10000	0	-0.25	10	10
positive regulation of transcription	0.028	0.045	0.14	1	-0.2	5	6
mol:GDP	0.03	0.074	-10000	0	-0.24	12	12
PIK3C2B	0.011	0.062	-10000	0	-0.26	8	8
CBL/CRKL	0.024	0.062	-10000	0	-0.27	6	6
FER	0.011	0.061	-10000	0	-0.3	5	5
SH2B3	0.013	0.06	-10000	0	-0.3	5	5
PDPK1	0.007	0.066	0.2	5	-0.22	13	18
SNAI2	0.001	0.065	-10000	0	-0.29	9	9
positive regulation of cell proliferation	0.008	0.1	-10000	0	-0.43	12	12
KITLG	0.02	0.029	-10000	0	-0.12	21	21
cell motility	0.008	0.1	-10000	0	-0.43	12	12
PTPN6	0.022	0.009	-10000	0	-0.12	2	2
EPOR	0.013	0.13	-10000	0	-0.54	25	25
STAT5A (dimer)	0.01	0.094	-10000	0	-0.35	14	14
SOCS1	0.017	0.03	-10000	0	-0.12	26	26
cell migration	-0.012	0.06	0.28	6	-10000	0	6
SOS1	0.017	0.027	-10000	0	-0.12	20	20
EPO	0.024	0.008	-10000	0	-0.13	1	1
VAV1	0.02	0.019	-10000	0	-0.12	10	10
GRB10	0.011	0.063	-10000	0	-0.28	8	8
PTPN11	0.021	0.011	-10000	0	-0.12	3	3
SCF/KIT	0.009	0.063	-10000	0	-0.3	6	6
GO:0007205	-0.001	0.004	-10000	0	-10000	0	0
MAP2K1	0.029	0.051	-10000	0	-0.19	7	7
CBL	0.023	0.006	-10000	0	-0.12	1	1
KIT	0.005	0.13	-10000	0	-0.5	20	20
MAP2K2	0.028	0.053	-10000	0	-0.18	10	10
SHC/Grb2/SOS1	0.032	0.072	-10000	0	-0.26	9	9
STAT5A	0.01	0.096	-10000	0	-0.36	14	14
GRB2	0.023	0.006	-10000	0	-0.12	1	1
response to radiation	0.001	0.065	-10000	0	-0.28	9	9
SHC/GRAP2	0.034	0.011	-10000	0	-0.084	5	5
PTPRO	0.012	0.061	-10000	0	-0.3	5	5
SH2B2	0.008	0.06	-10000	0	-0.28	6	6
DOK1	0.022	0.015	-10000	0	-0.12	6	6
MATK	0.012	0.061	-10000	0	-0.29	6	6
CREBBP	0.036	0.031	-10000	0	-0.12	9	9
BCL2	0.006	0.15	-10000	0	-0.62	26	26

×

Arf1 pathway

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
coatomer protein complex	0.018	0.009	-10000	0	-10000	0	0
EntrezGene:79658	0	0	-10000	0	-10000	0	0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A	0.008	0.035	-10000	0	-0.14	14	14
AP2	0.025	0.04	-10000	0	-0.15	26	26
mol:DAG	0	0	-10000	0	-10000	0	0
Arfaptin 2/Rac/GTP	0.03	0.016	-10000	0	-0.089	10	10
CLTB	0.022	0.014	-10000	0	-0.12	5	5
coatomer protein complex/ARF1/GTP/ER cargo protein	0.02	0.034	-10000	0	-0.16	16	16
CD4	0.016	0.027	-10000	0	-0.12	21	21
CLTA	0.023	0.006	-10000	0	-0.12	1	1
mol:GTP	0	0.002	-10000	0	-10000	0	0
ARFGAP1	0.012	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.009	0.008	0.044	4	-0.046	5	9
ARF1/GTP	0.011	0.014	-10000	0	-0.12	2	2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein	0.02	0.026	-10000	0	-0.15	11	11
mol:Choline	0.009	0.008	0.044	4	-0.045	5	9
mol:GDP	0	0	-10000	0	-10000	0	0
ARF1	0.017	0.027	-10000	0	-0.12	21	21
DDEF1	0.008	0.012	-10000	0	-0.2	1	1
ARF1/GDP	0.009	0.004	-10000	0	-0.063	1	1
AP2M1	0.022	0.005	-10000	0	-10000	0	0
EntrezGene:1313	0	0	-10000	0	-10000	0	0
actin filament polymerization	0.014	0.018	-10000	0	-0.11	7	7
Rac/GTP	0.016	0.016	-10000	0	-0.15	5	5
ARF1/GTP/GGA3/ARF-GAP1	0.032	0.018	-10000	0	-0.091	3	3
ARFIP2	0.021	0.013	-10000	0	-0.12	5	5
COPA	0.023	0.007	-10000	0	-0.12	1	1
RAC1	0.023	0.002	-10000	0	-10000	0	0
ARF1/GTP/coatomer protein complex	0.018	0.035	-10000	0	-0.21	11	11
ARF1/GTP/ARHGAP10	0.011	0.016	-10000	0	-0.065	23	23
GGA3	0.022	0.015	-10000	0	-0.12	6	6
ARF1/GTP/Membrin	0.019	0.018	-10000	0	-0.15	3	3
AP2A1	0.021	0.017	-10000	0	-0.12	8	8
coatomer protein complex/ARF1/GTP/ARF-GAP1	0.021	0.033	-10000	0	-0.16	16	16
ARF1/GDP/Membrin	0.021	0.019	-10000	0	-0.19	2	2
Arfaptin 2/Rac/GDP	0.029	0.016	-10000	0	-0.086	10	10
CYTH2	0	0.002	-10000	0	-10000	0	0
ARF1/GTP/GGA3	0.026	0.021	-10000	0	-0.08	9	9
mol:ATP	0	0	-10000	0	-10000	0	0
Rac/GDP	0.016	0.015	-10000	0	-0.15	5	5
mol:Brefeldin A	0	0	-10000	0	-10000	0	0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP	0.006	0.077	-10000	0	-0.26	22	22
PLD2	0.009	0.008	0.044	4	-0.046	5	9
ARF-GAP1/v-SNARE	0.012	0	-10000	0	-10000	0	0
PIP5K1A	0.009	0.008	0.044	4	-0.046	5	9
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	0.044	4	-0.045	5	9
KDEL Receptor/Ligand/ARF-GAP1	0.012	0	-10000	0	-10000	0	0
GOSR2	0.015	0.016	-10000	0	-0.36	1	1
USO1	-0.011	0.094	-10000	0	-0.36	38	38
GBF1	0.001	0.07	-10000	0	-0.36	21	21
ARF1/GTP/Arfaptin 2	0.028	0.021	-10000	0	-0.092	6	6
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex	0.02	0.062	-10000	0	-0.13	75	75

×

Rapid glucocorticoid signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma	0.034	0.028	-10000	0	-0.093	20	20
MAPK9	0	0.045	-10000	0	-0.21	25	25
adrenocorticotropin secretion	0.011	0.006	-10000	0	-0.076	3	3
GNB1/GNG2	0.025	0.029	-10000	0	-0.095	30	30
GNB1	0.023	0.006	-10000	0	-0.12	1	1
regulation of calcium ion transport via voltage-gated calcium channel activity	0	0	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
MAPK14	0.006	0.03	-10000	0	-0.21	11	11
Gs family/GTP	0.014	0.009	-10000	0	-0.054	10	10
EntrezGene:2778	0	0	-10000	0	-10000	0	0
vasopressin secretion	0	0	-10000	0	-10000	0	0
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
ChemicalAbstracts:86-01-1	0	0	-10000	0	-10000	0	0
glutamate secretion	0	0.002	0.017	10	-10000	0	10
GNAL	0.021	0.019	-10000	0	-0.12	10	10
GNG2	0.02	0.018	-10000	0	-0.12	9	9
CRH	0.023	0.01	-10000	0	-0.12	3	3
mol:cortisol	0	0	-10000	0	-10000	0	0
MAPK8	0.002	0.039	-10000	0	-0.21	18	18
MAPK11	0.01	0	-10000	0	-10000	0	0

×

Visual signal transduction: Rods

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

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

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

×

Visual signal transduction: Cones

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin	0.04	0.012	-9999	-0.09	2	2
RGS9BP	0.023	0.01	-9999	-0.12	3	3
mol:GTP	0	0	-9999	-10000	0	0
GRK1	0	0	-9999	-10000	0	0
mol:Na +	0.031	0.004	-9999	-0.056	1	1
mol:ADP	0.011	0.004	-9999	-0.076	1	1
GNAT2	0.023	0	-9999	-10000	0	0
RGS9-1/Gbeta5/R9AP	0.042	0.022	-9999	-0.11	2	2
mol:GDP	0	0	-9999	-10000	0	0
PDE6H/GNAT2/GTP	0.031	0.004	-9999	-10000	0	0
GRK7	0.023	0.006	-9999	-0.12	1	1
CNGB3	0.023	0.006	-9999	-0.12	1	1
Cone Metarhodopsin II/X-Arrestin	0.017	0.004	-9999	-0.076	1	1
mol:Ca2+	0.025	0.008	-9999	-0.1	1	1
Cone PDE6	0.064	0.024	-9999	-0.1	3	3
Cone Metarhodopsin II	0.015	0.003	-9999	-0.054	1	1
Na + (4 Units)	0.043	0.01	-9999	-0.1	1	1
GNAT2/GDP	0.05	0.021	-9999	-0.088	2	2
GNB5	0.023	0.01	-9999	-0.12	3	3
mol:GMP (4 units)	0.026	0.005	-9999	-0.1	1	1
Cone Transducin	0.043	0.013	-9999	-0.097	2	2
SLC24A2	0.022	0.013	-9999	-0.12	5	5
GNB3/GNGT2	0.033	0.016	-9999	-0.084	10	10
GNB3	0.022	0.01	-9999	-0.12	3	3
GNAT2/GTP	0.017	0	-9999	-10000	0	0
CNGA3	0.023	0	-9999	-10000	0	0
ARR3	0.023	0.006	-9999	-0.12	1	1
absorption of light	0	0	-9999	-10000	0	0
cGMP/Cone CNG Channel	0.031	0.004	-9999	-0.056	1	1
mol:Pi	0.042	0.022	-9999	-0.11	2	2
Cone CNG Channel	0.057	0.008	-9999	-0.13	1	1
mol:all-trans-retinal	0	0	-9999	-10000	0	0
mol:K +	0.022	0.013	-9999	-0.12	5	5
RGS9	0.018	0.028	-9999	-0.12	22	22
PDE6C	0.023	0.006	-9999	-0.12	1	1
GNGT2	0.022	0.013	-9999	-0.12	5	5
mol:cGMP (4 units)	0	0	-9999	-10000	0	0
PDE6H	0.023	0.006	-9999	-0.12	1	1