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

Pathway.Name	Avg.Num.Perturbations
Syndecan-1-mediated signaling events	157
TCGA08_retinoblastoma	136
Reelin signaling pathway	107
Lissencephaly gene (LIS1) in neuronal migration and development	71
Osteopontin-mediated events	61
FOXA2 and FOXA3 transcription factor networks	57
IL4-mediated signaling events	53
Glypican 1 network	50
Signaling events mediated by Stem cell factor receptor (c-Kit)	48
IL23-mediated signaling events	47

Pathway.Name	Significance.Ratio	Avg.Num.Perturbations	Total.Perturbations	Num.Entities	Min.Mean.Truth	Max.Mean.Truth	Min.Mean.Within	Max.Mean.Within	Min.Mean.Any	Max.Mean.Within.1
Syndecan-1-mediated signaling events	0.3756	157	5352	34	-0.68	0.012	1000	-1000	-0.049	-1000
TCGA08_retinoblastoma	0.3254	136	1091	8	-0.18	0.075	1000	-1000	-0.014	-1000
Reelin signaling pathway	0.2560	107	6014	56	-0.51	0.034	1000	-1000	-0.079	-1000
Lissencephaly gene (LIS1) in neuronal migration and development	0.1699	71	3875	54	-0.51	0.022	1000	-1000	-0.08	-1000
Osteopontin-mediated events	0.1459	61	2324	38	-0.28	0.017	1000	-1000	-0.075	-1000
FOXA2 and FOXA3 transcription factor networks	0.1364	57	2647	46	-0.62	0.02	1000	-1000	-0.15	-1000
IL4-mediated signaling events	0.1268	53	4825	91	-0.71	0.53	1000	-1000	-0.19	-1000
Glypican 1 network	0.1196	50	2430	48	-0.3	0.023	1000	-1000	-0.038	-1000
Signaling events mediated by Stem cell factor receptor (c-Kit)	0.1148	48	3754	78	-0.19	0.064	1000	-1000	-0.091	-1000
IL23-mediated signaling events	0.1124	47	2830	60	-0.49	0.013	1000	-1000	-0.18	-1000
Syndecan-4-mediated signaling events	0.1100	46	3119	67	-0.41	0.044	1000	-1000	-0.062	-1000
Caspase cascade in apoptosis	0.0957	40	3028	74	-0.14	0.076	1000	-1000	-0.04	-1000
BCR signaling pathway	0.0813	34	3397	99	-0.15	0.016	1000	-1000	-0.082	-1000
Signaling events mediated by the Hedgehog family	0.0789	33	1749	52	-0.13	0.12	1000	-1000	-0.055	-1000
IL1-mediated signaling events	0.0766	32	2029	62	-0.25	0.018	1000	-1000	-0.087	-1000
Endothelins	0.0742	31	3059	96	-0.36	0.12	1000	-1000	-0.083	-1000
Ephrin B reverse signaling	0.0718	30	1484	48	-0.16	0.073	1000	-1000	-0.056	-1000
TCGA08_p53	0.0694	29	209	7	-0.13	0.064	1000	-1000	-0.013	-1000
Angiopoietin receptor Tie2-mediated signaling	0.0694	29	2560	88	-0.21	0.039	1000	-1000	-0.092	-1000
BMP receptor signaling	0.0670	28	2304	81	-0.24	0.045	1000	-1000	-0.087	-1000
Fc-epsilon receptor I signaling in mast cells	0.0670	28	2739	97	-0.12	0.029	1000	-1000	-0.073	-1000
Glucocorticoid receptor regulatory network	0.0670	28	3212	114	-0.54	0.26	1000	-1000	-0.081	-1000
Calcium signaling in the CD4+ TCR pathway	0.0670	28	889	31	-0.32	0.012	1000	-1000	-0.064	-1000
Presenilin action in Notch and Wnt signaling	0.0646	27	1674	61	-0.38	0.17	1000	-1000	-0.06	-1000
Effects of Botulinum toxin	0.0646	27	714	26	-0.11	0.016	1000	-1000	-0.05	-1000
Syndecan-2-mediated signaling events	0.0622	26	1840	69	-0.39	0.033	1000	-1000	-0.032	-1000
HIF-1-alpha transcription factor network	0.0598	25	1956	76	-0.7	0.019	1000	-1000	-0.2	-1000
Canonical Wnt signaling pathway	0.0598	25	1311	51	-0.38	0.18	1000	-1000	-0.062	-1000
Syndecan-3-mediated signaling events	0.0574	24	851	35	-0.39	0.035	1000	-1000	-0.039	-1000
Visual signal transduction: Rods	0.0574	24	1258	52	-0.17	0.012	1000	-1000	-0.079	-1000
Wnt signaling	0.0550	23	167	7	-0.14	0.012	1000	-1000	-0.024	-1000
p75(NTR)-mediated signaling	0.0526	22	2781	125	-0.81	0.035	1000	-1000	-0.095	-1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	0.0526	22	1529	68	-0.47	0.048	1000	-1000	-0.12	-1000
amb2 Integrin signaling	0.0502	21	1801	82	-0.15	0.024	1000	-1000	-0.055	-1000
EPHB forward signaling	0.0502	21	1796	85	-0.16	0.08	1000	-1000	-0.075	-1000
Ras signaling in the CD4+ TCR pathway	0.0502	21	368	17	-0.053	0.023	1000	-1000	-0.038	-1000
Ephrin A reverse signaling	0.0478	20	146	7	-0.049	0	1000	-1000	-0.017	-1000
JNK signaling in the CD4+ TCR pathway	0.0478	20	340	17	-0.088	0.019	1000	-1000	-0.036	-1000
Retinoic acid receptors-mediated signaling	0.0455	19	1117	58	-0.3	0.024	1000	-1000	-0.065	-1000
Plasma membrane estrogen receptor signaling	0.0431	18	1578	86	-0.24	0.064	1000	-1000	-0.072	-1000
S1P5 pathway	0.0407	17	303	17	-0.12	0.052	1000	-1000	-0.031	-1000
Nephrin/Neph1 signaling in the kidney podocyte	0.0383	16	559	34	-0.034	0.012	1000	-1000	-0.035	-1000
Visual signal transduction: Cones	0.0383	16	623	38	-0.12	0.012	1000	-1000	-0.036	-1000
LPA receptor mediated events	0.0383	16	1690	102	-0.19	0.023	1000	-1000	-0.084	-1000
Noncanonical Wnt signaling pathway	0.0359	15	414	26	-0.14	0.012	1000	-1000	-0.051	-1000
Nectin adhesion pathway	0.0359	15	947	63	-0.65	0.039	1000	-1000	-0.066	-1000
TCR signaling in naïve CD8+ T cells	0.0359	15	1472	93	-0.086	0.047	1000	-1000	-0.077	-1000
S1P4 pathway	0.0359	15	380	25	-0.12	0.019	1000	-1000	-0.04	-1000
IL12-mediated signaling events	0.0335	14	1245	87	-0.17	0.034	1000	-1000	-0.14	-1000
Sphingosine 1-phosphate (S1P) pathway	0.0335	14	392	28	-0.12	0.019	1000	-1000	-0.033	-1000
Signaling events regulated by Ret tyrosine kinase	0.0335	14	1157	82	-0.12	0.012	1000	-1000	-0.076	-1000
RXR and RAR heterodimerization with other nuclear receptor	0.0335	14	728	52	-0.14	0.025	1000	-1000	-0.056	-1000
Glypican 2 network	0.0335	14	57	4	-0.007	-0.007	1000	-1000	-0.021	-1000
EGFR-dependent Endothelin signaling events	0.0335	14	313	21	-0.073	0.018	1000	-1000	-0.055	-1000
Thromboxane A2 receptor signaling	0.0311	13	1381	105	-0.16	0.07	1000	-1000	-0.063	-1000
S1P1 pathway	0.0311	13	489	36	-0.12	0.012	1000	-1000	-0.057	-1000
Nongenotropic Androgen signaling	0.0311	13	715	52	-0.12	0.023	1000	-1000	-0.051	-1000
ErbB4 signaling events	0.0287	12	834	69	-0.28	0.064	1000	-1000	-0.084	-1000
Signaling mediated by p38-alpha and p38-beta	0.0287	12	545	44	-0.032	0.012	1000	-1000	-0.045	-1000
S1P3 pathway	0.0287	12	520	42	-0.12	0.024	1000	-1000	-0.041	-1000
Neurotrophic factor-mediated Trk receptor signaling	0.0287	12	1477	120	-0.13	0.12	1000	-1000	-0.081	-1000
IFN-gamma pathway	0.0263	11	772	68	-0.072	0.027	1000	-1000	-0.092	-1000
HIF-2-alpha transcription factor network	0.0263	11	497	43	-0.24	0.11	1000	-1000	-0.084	-1000
IL27-mediated signaling events	0.0263	11	593	51	-0.15	0.024	1000	-1000	-0.071	-1000
Arf6 signaling events	0.0239	10	680	62	-0.15	0.029	1000	-1000	-0.052	-1000
Signaling events mediated by PTP1B	0.0239	10	789	76	-0.33	0.049	1000	-1000	-0.079	-1000
Integrins in angiogenesis	0.0239	10	911	84	-0.28	0.03	1000	-1000	-0.084	-1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha	0.0239	10	343	33	-0.17	0.031	1000	-1000	-0.036	-1000
Aurora A signaling	0.0215	9	546	60	-0.18	0.033	1000	-1000	-0.036	-1000
Signaling mediated by p38-gamma and p38-delta	0.0215	9	136	15	-0.046	0.021	1000	-1000	-0.03	-1000
Regulation of nuclear SMAD2/3 signaling	0.0191	8	1176	136	-0.24	0.058	1000	-1000	-0.06	-1000
Signaling events mediated by PRL	0.0191	8	291	34	-0.083	0.033	1000	-1000	-0.038	-1000
Coregulation of Androgen receptor activity	0.0167	7	544	76	-0.17	0.044	1000	-1000	-0.03	-1000
Paxillin-independent events mediated by a4b1 and a4b7	0.0167	7	282	37	-0.14	0.033	1000	-1000	-0.036	-1000
Regulation of Telomerase	0.0167	7	781	102	-0.32	0.038	1000	-1000	-0.1	-1000
Regulation of Androgen receptor activity	0.0167	7	541	70	-0.18	0.023	1000	-1000	-0.074	-1000
Aurora B signaling	0.0167	7	478	67	-0.38	0.077	1000	-1000	-0.052	-1000
Cellular roles of Anthrax toxin	0.0144	6	238	39	-0.042	0.012	1000	-1000	-0.02	-1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes	0.0144	6	515	83	-0.3	0.061	1000	-1000	-0.057	-1000
Rapid glucocorticoid signaling	0.0144	6	127	20	-0.014	0.012	1000	-1000	-0.017	-1000
FAS signaling pathway (CD95)	0.0120	5	277	47	-0.02	0.025	1000	-1000	-0.047	-1000
Class I PI3K signaling events	0.0120	5	405	73	-0.11	0.028	1000	-1000	-0.057	-1000
ErbB2/ErbB3 signaling events	0.0096	4	310	65	-0.043	0.035	1000	-1000	-0.068	-1000
PLK2 and PLK4 events	0.0096	4	12	3	0.002	0.012	1000	-1000	-0.026	-1000
a4b1 and a4b7 Integrin signaling	0.0096	4	24	5	0.003	0.012	1000	-1000	-0.019	-1000
Hedgehog signaling events mediated by Gli proteins	0.0096	4	310	65	-0.12	0.047	1000	-1000	-0.061	-1000
Ceramide signaling pathway	0.0096	4	315	76	-0.073	0.04	1000	-1000	-0.045	-1000
Signaling events mediated by HDAC Class III	0.0096	4	176	40	-0.049	0.022	1000	-1000	-0.021	-1000
FoxO family signaling	0.0096	4	256	64	-0.075	0.086	1000	-1000	-0.08	-1000
Regulation of p38-alpha and p38-beta	0.0096	4	243	54	-0.11	0.031	1000	-1000	-0.06	-1000
IL6-mediated signaling events	0.0096	4	360	75	-0.039	0.05	1000	-1000	-0.067	-1000
VEGFR1 specific signals	0.0096	4	228	56	-0.005	0.041	1000	-1000	-0.048	-1000
PDGFR-beta signaling pathway	0.0096	4	466	97	-0.17	0.041	1000	-1000	-0.07	-1000
EPO signaling pathway	0.0072	3	171	55	-0.012	0.045	1000	-1000	-0.083	-1000
PLK1 signaling events	0.0072	3	269	85	-0.038	0.029	1000	-1000	-0.033	-1000
TCGA08_rtk_signaling	0.0072	3	102	26	-0.031	0.037	1000	-1000	-0.016	-1000
Stabilization and expansion of the E-cadherin adherens junction	0.0072	3	254	74	-0.073	0.057	1000	-1000	-0.082	-1000
IGF1 pathway	0.0072	3	207	57	-0.069	0.024	1000	-1000	-0.08	-1000
FOXM1 transcription factor network	0.0072	3	203	51	-0.17	0.11	1000	-1000	-0.24	-1000
Signaling events mediated by HDAC Class II	0.0048	2	198	75	-0.024	0.031	1000	-1000	-0.041	-1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)	0.0048	2	228	85	-0.014	0.041	1000	-1000	-0.061	-1000
PDGFR-alpha signaling pathway	0.0048	2	98	44	-0.006	0.026	1000	-1000	-0.039	-1000
IL2 signaling events mediated by PI3K	0.0048	2	129	58	-0.062	0.056	1000	-1000	-0.073	-1000
Arf6 trafficking events	0.0048	2	168	71	-0.033	0.031	1000	-1000	-0.061	-1000
E-cadherin signaling in keratinocytes	0.0048	2	115	43	-0.072	0.042	1000	-1000	-0.047	-1000
Class IB PI3K non-lipid kinase events	0.0048	2	6	3	-0.01	0.01	1000	-1000	-0.008	-1000
p38 MAPK signaling pathway	0.0048	2	96	44	-0.052	0.027	1000	-1000	-0.068	-1000
LPA4-mediated signaling events	0.0024	1	17	12	-0.078	0.014	1000	-1000	-0.033	-1000
Canonical NF-kappaB pathway	0.0024	1	40	39	-0.018	0.058	1000	-1000	-0.077	-1000
Arf6 downstream pathway	0.0024	1	59	43	-0.022	0.027	1000	-1000	-0.036	-1000
TRAIL signaling pathway	0.0024	1	79	48	-0.028	0.038	1000	-1000	-0.052	-1000
ceramide signaling pathway	0.0024	1	57	49	0	0.041	1000	-1000	-0.047	-1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha	0.0024	1	77	45	-0.011	0.051	1000	-1000	-0.09	-1000
Signaling events mediated by VEGFR1 and VEGFR2	0.0024	1	225	125	-0.004	0.064	1000	-1000	-0.085	-1000
E-cadherin signaling in the nascent adherens junction	0.0024	1	84	76	-0.016	0.046	1000	-1000	-0.076	-1000
IL2 signaling events mediated by STAT5	0.0024	1	42	22	-0.002	0.053	1000	-1000	-0.061	-1000
Insulin Pathway	0.0024	1	146	74	-0.021	0.031	1000	-1000	-0.076	-1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling	0.0000	0	5	23	0.008	0.036	1000	-1000	-0.05	-1000
BARD1 signaling events	0.0000	0	13	57	-0.03	0.054	1000	-1000	-0.063	-1000
Circadian rhythm pathway	0.0000	0	19	22	-0.01	0.039	1000	-1000	-0.048	-1000
Aurora C signaling	0.0000	0	0	7	0	0.023	1000	-1000	-0.022	-1000
Insulin-mediated glucose transport	0.0000	0	23	32	-0.005	0.035	1000	-1000	-0.047	-1000
mTOR signaling pathway	0.0000	0	19	53	-0.001	0.031	1000	-1000	-0.058	-1000
Class I PI3K signaling events mediated by Akt	0.0000	0	14	68	-0.034	0.045	1000	-1000	-0.05	-1000
Signaling events mediated by HDAC Class I	0.0000	0	58	104	-0.024	0.043	1000	-1000	-0.048	-1000
Paxillin-dependent events mediated by a4b1	0.0000	0	33	36	-0.029	0.037	1000	-1000	-0.051	-1000
Atypical NF-kappaB pathway	0.0000	0	9	31	-0.003	0.037	1000	-1000	-0.05	-1000
Sumoylation by RanBP2 regulates transcriptional repression	0.0000	0	15	27	-0.001	0.029	1000	-1000	-0.048	-1000
E-cadherin signaling events	0.0000	0	1	5	0.011	0.024	1000	-1000	-0.022	-1000
Arf1 pathway	0.0000	0	44	54	-0.004	0.025	1000	-1000	-0.028	-1000
Alternative NF-kappaB pathway	0.0000	0	0	13	0	0.035	1000	-1000	-0.032	-1000
Total	NA	2142	119333	7203	-21	5.8	131000	-131000	-8.1	-131000

Syndecan-1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.01	0.035	-9999	-0.71	1	1
CCL5	0.002	0.058	-9999	-0.32	13	13
SDCBP	0.01	0.023	-9999	-0.32	2	2
FGFR/FGF2/Syndecan-1	-0.32	0.13	-9999	-0.41	282	282
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
Syndecan-1/Laminin-5	-0.3	0.13	-9999	-0.39	284	284
Syndecan-1/Syntenin	-0.3	0.13	-9999	-0.38	283	283
MAPK3	-0.27	0.12	-9999	-0.35	281	281
HGF/MET	-0.001	0.09	-9999	-0.55	9	9
TGFB1/TGF beta receptor Type II	0.01	0.035	-9999	-0.7	1	1
BSG	0.011	0.016	-9999	-0.32	1	1
keratinocyte migration	-0.3	0.13	-9999	-0.38	284	284
Syndecan-1/RANTES	-0.31	0.13	-9999	-0.38	289	289
Syndecan-1/CD147	-0.29	0.13	-9999	-0.37	282	282
Syndecan-1/Syntenin/PIP2	-0.29	0.13	-9999	-0.37	283	283
LAMA5	0.008	0.052	-9999	-0.58	3	3
positive regulation of cell-cell adhesion	-0.29	0.12	-9999	-0.36	283	283
MMP7	-0.68	0.14	-9999	-0.71	401	401
HGF	0	0.065	-9999	-0.35	13	13
Syndecan-1/CASK	-0.31	0.13	-9999	-0.39	282	282
Syndecan-1/HGF/MET	-0.3	0.13	-9999	-0.38	287	287
regulation of cell adhesion	-0.26	0.12	-9999	-0.46	41	41
HPSE	0.009	0.032	-9999	-0.32	4	4
positive regulation of cell migration	-0.32	0.13	-9999	-0.41	282	282
SDC1	-0.33	0.14	-9999	-0.41	282	282
Syndecan-1/Collagen	-0.32	0.13	-9999	-0.41	282	282
PPIB	0.012	0	-9999	-10000	0	0
MET	-0.002	0.098	-9999	-0.71	8	8
PRKACA	0.012	0	-9999	-10000	0	0
MMP9	-0.075	0.23	-9999	-0.7	51	51
MAPK1	-0.27	0.12	-9999	-0.35	281	281
homophilic cell adhesion	-0.32	0.13	-9999	-0.4	282	282
MMP1	-0.46	0.34	-9999	-0.71	275	275

×

TCGA08_retinoblastoma

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2B	-0.052	0.12	-10000	0	-0.29	91	91
CDKN2C	0.025	0.03	-10000	0	-10000	0	0
CDKN2A	-0.18	0.32	-10000	0	-0.72	105	105
CCND2	0.067	0.093	0.17	179	-10000	0	179
RB1	-0.071	0.1	-10000	0	-0.18	179	179
CDK4	0.075	0.1	0.19	179	-10000	0	179
CDK6	0.075	0.1	0.19	179	-10000	0	179
G1/S progression	0.071	0.1	0.18	179	-10000	0	179

×

Reelin signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDK5R1/CDK5	0.016	0.027	-9999	-0.53	1	1
VLDLR	-0.011	0.084	-9999	-0.32	29	29
CRKL	0.012	0	-9999	-10000	0	0
LRPAP1	0.012	0	-9999	-10000	0	0
FYN	0.012	0	-9999	-10000	0	0
ITGA3	0.009	0.039	-9999	-0.51	2	2
RELN/VLDLR/Fyn	-0.08	0.11	-9999	-0.34	22	22
MAPK8IP1/MKK7/MAP3K11/JNK1	0.034	0.023	-9999	-0.43	1	1
AKT1	-0.085	0.12	-9999	-0.35	37	37
MAP2K7	0.011	0.016	-9999	-0.32	1	1
RAPGEF1	0.011	0.016	-9999	-0.32	1	1
DAB1	-0.035	0.17	-9999	-0.71	26	26
RELN/LRP8/DAB1	-0.4	0.23	-9999	-0.51	315	315
LRPAP1/LRP8	-0.38	0.24	-9999	-0.53	306	306
RELN/LRP8/DAB1/Fyn	-0.37	0.22	-9999	-0.48	315	315
DAB1/alpha3/beta1 Integrin	-0.35	0.2	-9999	-0.54	170	170
long-term memory	-0.45	0.26	-9999	-0.55	326	326
DAB1/LIS1	-0.36	0.22	-9999	-0.46	315	315
DAB1/CRLK/C3G	-0.35	0.2	-9999	-0.54	170	170
PIK3CA	0.012	0.001	-9999	-10000	0	0
DAB1/NCK2	-0.36	0.22	-9999	-0.47	315	315
ARHGEF2	0.012	0	-9999	-10000	0	0
mol:Src family inhibitors PP1 and PP2	0	0	-9999	-10000	0	0
GRIN2A	-0.091	0.15	-9999	-0.32	124	124
CDK5R1	0.01	0.035	-9999	-0.71	1	1
RELN	-0.15	0.16	-9999	-0.32	198	198
PIK3R1	0.012	0	-9999	-10000	0	0
RELN/LRP8/Fyn	-0.4	0.22	-9999	-0.53	306	306
GRIN2A/RELN/LRP8/DAB1/Fyn	-0.41	0.23	-9999	-0.52	315	315
MAPK8	0.012	0	-9999	-10000	0	0
RELN/VLDLR/DAB1	-0.099	0.14	-9999	-0.42	48	48
ITGB1	0.012	0	-9999	-10000	0	0
MAP1B	-0.36	0.22	-9999	-0.46	315	315
RELN/LRP8	-0.4	0.22	-9999	-0.53	306	306
GRIN2B/RELN/LRP8/DAB1/Fyn	-0.42	0.26	-9999	-0.53	326	326
PI3K	0.018	0	-9999	-10000	0	0
mol:PP2	0	0	-9999	-10000	0	0
alpha3/beta1 Integrin	0.016	0.029	-9999	-0.53	1	1
RAP1A	-0.32	0.2	-9999	-0.5	170	170
PAFAH1B1	0.012	0	-9999	-10000	0	0
MAPK8IP1	0.011	0.016	-9999	-0.32	1	1
CRLK/C3G	0.017	0.011	-9999	-10000	0	0
GRIN2B	-0.088	0.25	-9999	-0.71	58	58
NCK2	0.012	0	-9999	-10000	0	0
neuron differentiation	-0.19	0.13	-9999	-0.32	165	165
neuron adhesion	-0.3	0.19	-9999	-0.47	170	170
LRP8	-0.51	0.32	-9999	-0.71	306	306
GSK3B	-0.076	0.12	-9999	-0.33	37	37
RELN/VLDLR/DAB1/Fyn	-0.087	0.14	-9999	-0.43	35	35
MAP3K11	0.011	0.016	-9999	-0.32	1	1
RELN/VLDLR/DAB1/P13K	-0.095	0.13	-9999	-0.37	37	37
CDK5	0.012	0	-9999	-10000	0	0
MAPT	-0.061	0.13	-9999	-0.28	98	98
neuron migration	-0.29	0.18	-9999	-0.47	173	173
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1	-0.19	0.13	-9999	-0.32	165	165
RELN/VLDLR	-0.38	0.22	-9999	-0.5	306	306

×

Lissencephaly gene (LIS1) in neuronal migration and development

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
DYNC1H1	0.012	0	-9999	-10000	0	0
VLDLR	-0.011	0.084	-9999	-0.32	29	29
LRPAP1	0.012	0	-9999	-10000	0	0
NUDC	0.012	0	-9999	-10000	0	0
RELN/LRP8	-0.4	0.22	-9999	-0.53	306	306
CaM/Ca2+	0.009	0	-9999	-10000	0	0
KATNA1	0.012	0	-9999	-10000	0	0
GO:0030286	0	0	-9999	-10000	0	0
ABL1	-0.37	0.21	-9999	-0.48	306	306
IQGAP1/CaM	0.018	0	-9999	-10000	0	0
DAB1	-0.035	0.17	-9999	-0.71	26	26
IQGAP1	0.012	0	-9999	-10000	0	0
PLA2G7	0.01	0.023	-9999	-0.32	2	2
CALM1	0.012	0	-9999	-10000	0	0
DYNLT1	0.012	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
LRPAP1/LRP8	-0.38	0.24	-9999	-0.53	306	306
UniProt:Q4QZ09	0	0	-9999	-10000	0	0
CLIP1	0.011	0.016	-9999	-0.32	1	1
CDK5R1	0.01	0.035	-9999	-0.71	1	1
LIS1/Poliovirus Protein 3A	0.013	0	-9999	-10000	0	0
CDK5R2	-0.034	0.12	-9999	-0.35	51	51
mol:PP1	0	0	-9999	-10000	0	0
RELN/VLDLR/DAB1	-0.11	0.16	-9999	-0.45	48	48
YWHAE	0.012	0	-9999	-10000	0	0
NDEL1/14-3-3 E	-0.3	0.17	-9999	-0.45	167	167
MAP1B	-0.001	0.04	-9999	-0.22	13	13
RAC1	0.017	0	-9999	-10000	0	0
p35/CDK5	-0.32	0.19	-9999	-0.42	306	306
RELN	-0.15	0.16	-9999	-0.32	198	198
PAFAH/LIS1	0.021	0.013	-9999	-10000	0	0
LIS1/CLIP170	0.021	0.009	-9999	-10000	0	0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain	-0.24	0.13	-9999	-0.36	167	167
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3	-0.093	0.14	-9999	-0.4	42	42
GO:0005869	0	0	-9999	-10000	0	0
NDEL1	-0.32	0.18	-9999	-0.42	306	306
LIS1/IQGAP1	0.022	0	-9999	-10000	0	0
RHOA	0.017	0	-9999	-10000	0	0
PAFAH1B1	0.017	0	-9999	-10000	0	0
PAFAH1B3	-0.002	0.098	-9999	-0.71	8	8
PAFAH1B2	0.012	0.001	-9999	-10000	0	0
MAP1B/LIS1/Dynein heavy chain	0.016	0.026	-9999	-10000	0	0
NDEL1/Katanin 60/Dynein heavy chain	-0.28	0.17	-9999	-0.43	167	167
LRP8	-0.51	0.32	-9999	-0.71	306	306
NDEL1/Katanin 60	-0.3	0.17	-9999	-0.45	173	173
P39/CDK5	-0.34	0.19	-9999	-0.44	307	307
LIS1/NudC/Dynein intermediate chain/microtubule organizing center	0.022	0	-9999	-10000	0	0
CDK5	-0.34	0.2	-9999	-0.45	306	306
PPP2R5D	0.012	0	-9999	-10000	0	0
LIS1/CLIP170/Dynein Complex/Dynactin Complex	0.018	0.008	-9999	-10000	0	0
CSNK2A1	0.012	0	-9999	-10000	0	0
RELN/VLDLR/DAB1/LIS1	-0.081	0.14	-9999	-0.47	26	26
RELN/VLDLR	-0.38	0.22	-9999	-0.5	306	306
CDC42	0.016	0.017	-9999	-0.32	1	1

×

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	-0.14	0.21	-9999	-0.39	171	171
NF kappa B1 p50/RelA/I kappa B alpha	-0.11	0.2	-9999	-0.47	37	37
alphaV/beta3 Integrin/Osteopontin/Src	-0.2	0.27	-9999	-0.53	171	171
AP1	-0.11	0.2	-9999	-0.77	1	1
ILK	-0.15	0.22	-9999	-0.4	171	171
bone resorption	-0.11	0.19	-9999	-0.42	2	2
PTK2B	0.012	0	-9999	-10000	0	0
PYK2/p130Cas	-0.13	0.2	-9999	-0.42	38	38
ITGAV	0.013	0.004	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CD44/Rho Family GTPase/ROCK2	0.017	0.011	-9999	-10000	0	0
alphaV/beta3 Integrin/Osteopontin	-0.17	0.24	-9999	-0.45	172	172
MAP3K1	-0.15	0.22	-9999	-0.41	171	171
JUN	0.012	0.001	-9999	-10000	0	0
MAPK3	-0.14	0.22	-9999	-0.4	171	171
MAPK1	-0.14	0.22	-9999	-0.4	171	171
Rac1/GDP	0.009	0	-9999	-10000	0	0
NFKB1	0.012	0	-9999	-10000	0	0
MAPK8	-0.14	0.21	-9999	-0.38	171	171
ITGB3	0.006	0.048	-9999	-0.32	9	9
NFKBIA	-0.13	0.21	-9999	-0.52	37	37
FOS	0.006	0.043	-9999	-0.32	7	7
CD44	0.012	0	-9999	-10000	0	0
CHUK	0.012	0	-9999	-10000	0	0
PLAU	-0.14	0.26	-9999	-0.76	38	38
NF kappa B1 p50/RelA	-0.12	0.2	-9999	-0.51	37	37
BCAR1	0.011	0.016	-9999	-0.32	1	1
RELA	0.012	0	-9999	-10000	0	0
alphaV beta3 Integrin	0.016	0.034	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
SYK	-0.15	0.22	-9999	-0.41	171	171
VAV3	-0.15	0.22	-9999	-0.4	171	171
MAP3K14	-0.15	0.22	-9999	-0.42	171	171
ROCK2	0.011	0.016	-9999	-0.32	1	1
SPP1	-0.28	0.35	-9999	-0.7	174	174
RAC1	0.012	0	-9999	-10000	0	0
Rac1/GTP	-0.14	0.2	-9999	-0.43	58	58
MMP2	-0.089	0.17	-9999	-0.67	2	2

×

FOXA2 and FOXA3 transcription factor networks

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
ACADVL	-0.4	0.31	-9999	-0.92	71	71
PCK1	-0.62	0.56	-9999	-1.3	176	176
HNF4A	-0.45	0.37	-9999	-1	85	85
KCNJ11	-0.4	0.31	-9999	-0.92	72	72
AKT1	-0.21	0.13	-9999	-0.45	4	4
response to starvation	-0.013	0.023	-9999	-10000	0	0
DLK1	-0.42	0.34	-9999	-1	72	72
NKX2-1	-0.24	0.22	-9999	-0.7	51	51
ACADM	-0.4	0.31	-9999	-0.92	73	73
TAT	-0.43	0.45	-9999	-1.1	107	107
CEBPB	0.005	0.022	-9999	-10000	0	0
CEBPA	0.005	0.031	-9999	-0.32	2	2
TTR	-0.34	0.39	-9999	-0.98	94	94
PKLR	-0.46	0.37	-9999	-1	102	102
APOA1	-0.48	0.38	-9999	-1.1	78	78
CPT1C	-0.4	0.31	-9999	-0.89	80	80
ALAS1	-0.19	0.13	-9999	-10000	0	0
TFRC	-0.32	0.22	-9999	-0.71	41	41
FOXF1	0.02	0.067	-9999	-0.32	10	10
NF1	0.017	0	-9999	-10000	0	0
HNF1A (dimer)	-0.085	0.049	-9999	-0.38	1	1
CPT1A	-0.4	0.31	-9999	-0.89	80	80
HMGCS1	-0.4	0.31	-9999	-0.9	76	76
NR3C1	-0.043	0.1	-9999	-0.34	31	31
CPT1B	-0.4	0.31	-9999	-0.89	81	81
chromatin remodeling	0	0	-9999	-10000	0	0
SP1	-0.079	0.039	-9999	-10000	0	0
GCK	-0.4	0.32	-9999	-0.91	82	82
CREB1	-0.048	0.076	-9999	-10000	0	0
IGFBP1	-0.28	0.26	-9999	-0.75	74	74
PDX1	-0.58	0.22	-9999	-0.71	265	265
UCP2	-0.4	0.31	-9999	-0.89	80	80
ALDOB	-0.47	0.37	-9999	-0.96	111	111
AFP	-0.094	0.19	-9999	-0.68	31	31
BDH1	-0.4	0.31	-9999	-0.91	74	74
HADH	-0.4	0.31	-9999	-0.91	70	70
F2	-0.52	0.41	-9999	-1.1	99	99
HNF1A	-0.085	0.049	-9999	-0.38	1	1
G6PC	-0.17	0.29	-9999	-1.2	29	29
SLC2A2	-0.32	0.19	-9999	-0.84	17	17
INS	0.007	0.036	-9999	-10000	0	0
FOXA1	-0.026	0.12	-9999	-0.34	35	35
FOXA3	-0.1	0.13	-9999	-0.35	47	47
FOXA2	-0.46	0.34	-9999	-1	80	80
ABCC8	-0.46	0.36	-9999	-0.97	108	108
ALB	-0.11	0.21	-9999	-0.6	57	57

×

IL4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.48	0.49	-10000	0	-1.2	94	94
STAT6 (cleaved dimer)	-0.54	0.49	-10000	0	-1.1	135	135
IGHG1	-0.16	0.16	-10000	0	-10000	0	0
IGHG3	-0.47	0.47	-10000	0	-1.1	112	112
AKT1	-0.24	0.26	-10000	0	-0.66	51	51
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1	-0.18	0.21	-10000	0	-0.53	38	38
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1	-0.23	0.24	-10000	0	-0.6	35	35
THY1	-0.48	0.49	-10000	0	-1.2	94	94
MYB	0.012	0	-10000	0	-10000	0	0
HMGA1	0.01	0.035	-10000	0	-0.71	1	1
IL4/IL4R/JAK1/IL2R gamma/JAK3	-0.33	0.33	-10000	0	-0.81	87	87
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP	-0.23	0.24	-10000	0	-0.6	35	35
SP1	0.017	0.008	-10000	0	-10000	0	0
INPP5D	0.012	0	-10000	0	-10000	0	0
SOCS5	0.03	0.018	-10000	0	-10000	0	0
STAT6 (dimer)/ETS1	-0.5	0.51	-10000	0	-1.2	115	115
SOCS1	-0.34	0.32	-10000	0	-0.75	92	92
SOCS3	-0.27	0.28	-10000	0	-0.76	41	41
FCER2	-0.71	0.65	-10000	0	-1.3	203	203
PARP14	0.005	0.015	-10000	0	-10000	0	0
CCL17	-0.49	0.49	-10000	0	-1.2	97	97
GRB2	0.012	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP	-0.18	0.19	-10000	0	-0.63	2	2
T cell proliferation	-0.49	0.5	-10000	0	-1.2	105	105
IL4R/JAK1	-0.48	0.49	-10000	0	-1.2	109	109
EGR2	-0.55	0.53	-10000	0	-1.3	108	108
JAK2	-0.019	0.041	-10000	0	-0.35	3	3
JAK3	0.006	0.051	-10000	0	-0.71	2	2
PIK3R1	0.012	0	-10000	0	-10000	0	0
JAK1	0.005	0.011	-10000	0	-10000	0	0
COL1A2	-0.16	0.2	-10000	0	-0.73	23	23
CCL26	-0.52	0.51	-10000	0	-1.2	109	109
IL4R	-0.51	0.52	-10000	0	-1.2	106	106
PTPN6	0.023	0.011	-10000	0	-10000	0	0
IL13RA2	-0.5	0.5	-10000	0	-1.2	106	106
IL13RA1	-0.016	0.03	-10000	0	-10000	0	0
IRF4	-0.39	0.59	-10000	0	-1.4	100	100
ARG1	-0.12	0.14	-10000	0	-0.59	4	4
CBL	-0.31	0.31	-10000	0	-0.79	78	78
GTF3A	-0.014	0.13	-10000	0	-0.72	13	13
PIK3CA	0.012	0.001	-10000	0	-10000	0	0
IL13RA1/JAK2	-0.021	0.047	-10000	0	-10000	0	0
IRF4/BCL6	-0.34	0.55	-10000	0	-1.3	100	100
CD40LG	-0.022	0.091	-10000	0	-0.34	30	30
MAPK14	-0.3	0.31	-10000	0	-0.79	75	75
mitosis	-0.23	0.25	-10000	0	-0.63	51	51
STAT6	-0.55	0.58	-10000	0	-1.3	110	110
SPI1	0.011	0.034	-10000	0	-0.32	4	4
RPS6KB1	-0.22	0.24	-10000	0	-0.6	49	49
STAT6 (dimer)	-0.55	0.57	-10000	0	-1.3	110	110
STAT6 (dimer)/PARP14	-0.55	0.55	-10000	0	-1.3	118	118
mast cell activation	0.012	0.012	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2	-0.24	0.24	-10000	0	-0.62	49	49
FRAP1	-0.24	0.26	-10000	0	-0.66	51	51
LTA	-0.48	0.5	-10000	0	-1.2	97	97
FES	0.01	0.023	-10000	0	-0.32	2	2
T-helper 1 cell differentiation	0.53	0.55	1.3	110	-10000	0	110
CCL11	-0.51	0.54	-10000	0	-1.3	106	106
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES	-0.24	0.24	-10000	0	-0.62	51	51
IL2RG	0.008	0.025	-10000	0	-0.32	2	2
IL10	-0.5	0.53	-10000	0	-1.3	101	101
IRS1	0.012	0	-10000	0	-10000	0	0
IRS2	0.01	0.035	-10000	0	-0.71	1	1
IL4	-0.12	0.12	-10000	0	-10000	0	0
IL5	-0.48	0.49	-10000	0	-1.2	95	95
IL4/IL4R/JAK1/IL13RA1/JAK2	-0.39	0.38	-10000	0	-0.89	95	95
COL1A1	-0.25	0.28	-10000	0	-0.75	65	65
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1	-0.49	0.5	-10000	0	-1.2	95	95
IL2R gamma/JAK3	0.008	0.044	-10000	0	-0.54	2	2
TFF3	-0.49	0.51	-10000	0	-1.2	94	94
ALOX15	-0.51	0.51	-10000	0	-1.2	99	99
MYBL1	0.008	0.05	-10000	0	-0.71	2	2
T-helper 2 cell differentiation	-0.41	0.39	-10000	0	-0.92	107	107
SHC1	0.012	0	-10000	0	-10000	0	0
CEBPB	0.014	0.009	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2	-0.22	0.23	-10000	0	-0.58	35	35
mol:PI-3-4-5-P3	-0.24	0.26	-10000	0	-0.66	51	51
PI3K	-0.25	0.27	-10000	0	-0.7	51	51
DOK2	0.009	0.032	-10000	0	-0.32	4	4
ETS1	0.024	0.014	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2	-0.17	0.18	-10000	0	-0.62	2	2
ITGB3	-0.48	0.5	-10000	0	-1.2	95	95
PIGR	-0.61	0.63	-10000	0	-1.4	134	134
IGHE	0.042	0.037	0.24	1	-10000	0	1
MAPKKK cascade	-0.17	0.18	-10000	0	-0.6	2	2
BCL6	0.017	0.01	-10000	0	-10000	0	0
OPRM1	-0.48	0.49	-10000	0	-1.2	95	95
RETNLB	-0.71	0.67	-10000	0	-1.4	182	182
SELP	-0.55	0.58	-10000	0	-1.4	108	108
AICDA	-0.47	0.47	-10000	0	-1.1	96	96

×

Glypican 1 network

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
GPC1/FGF2 dimer/FGFR1 dimer	-0.001	0.069	-10000	0	-0.38	3	3
fibroblast growth factor receptor signaling pathway	-0.001	0.069	-10000	0	-0.38	3	3
LAMA1	-0.059	0.14	-10000	0	-0.32	89	89
PRNP	0.011	0.016	-10000	0	-0.32	1	1
GPC1/SLIT2	-0.051	0.11	-10000	0	-0.53	1	1
SMAD2	0.023	0.024	-10000	0	-0.41	1	1
GPC1/PrPc/Cu2+	0.014	0.027	-10000	0	-0.46	1	1
GPC1/Laminin alpha1	-0.033	0.097	-10000	0	-0.53	1	1
TDGF1	-0.3	0.35	-10000	0	-0.69	182	182
CRIPTO/GPC1	-0.22	0.27	-10000	0	-0.53	176	176
APP/GPC1	0.016	0.029	-10000	0	-0.53	1	1
mol:NO	0	0	-10000	0	-10000	0	0
YES1	-0.18	0.23	-10000	0	-0.46	176	176
FLT1	0.012	0	-10000	0	-10000	0	0
GPC1/TGFB/TGFBR1/TGFBR2	0.022	0.027	-10000	0	-0.46	1	1
SERPINC1	-0.001	0.078	-10000	0	-0.71	5	5
FYN	-0.18	0.23	-10000	0	-0.46	176	176
FGR	-0.18	0.23	-10000	0	-0.46	177	177
positive regulation of MAPKKK cascade	-0.16	0.18	-10000	0	-0.35	183	183
SLIT2	-0.085	0.15	-10000	0	-0.32	122	122
GPC1/NRG	-0.011	0.078	-10000	0	-0.53	1	1
NRG1	-0.027	0.11	-10000	0	-0.32	49	49
GPC1/VEGF165 homodimer/VEGFR1 homodimer	0.018	0.053	-10000	0	-0.46	5	5
LYN	-0.18	0.23	-10000	0	-0.46	176	176
mol:Spermine	0.007	0.029	-10000	0	-0.38	2	2
cell growth	-0.001	0.069	-10000	0	-0.38	3	3
BMP signaling pathway	-0.009	0.039	0.51	2	-10000	0	2
SRC	-0.18	0.23	-10000	0	-0.46	176	176
TGFBR1	0.011	0.016	-10000	0	-0.32	1	1
mol:Cu2+	0	0	-10000	0	-10000	0	0
PLA2G2A	-0.077	0.16	-10000	0	-0.34	107	107
GPC1	0.009	0.039	-10000	0	-0.51	2	2
TGFBR1 (dimer)	0.011	0.016	-10000	0	-0.32	1	1
VEGFA	0.005	0.07	-10000	0	-0.71	4	4
BLK	-0.22	0.26	-10000	0	-0.52	177	177
HCK	-0.18	0.24	-10000	0	-0.46	176	176
FGF2	-0.025	0.1	-10000	0	-0.32	46	46
FGFR1	0.008	0.036	-10000	0	-0.32	5	5
VEGFR1 homodimer	0.012	0	-10000	0	-10000	0	0
TGFBR2	0.012	0	-10000	0	-10000	0	0
cell death	0.016	0.029	-10000	0	-0.53	1	1
ATIII/GPC1	0.006	0.066	-10000	0	-0.53	6	6
PLA2G2A/GPC1	-0.046	0.11	-10000	0	-0.53	5	5
LCK	-0.19	0.24	-10000	0	-0.46	184	184
neuron differentiation	-0.011	0.078	-10000	0	-0.53	1	1
PrPc/Cu2+	0.008	0.011	-10000	0	-0.22	1	1
APP	0.012	0	-10000	0	-10000	0	0
TGFBR2 (dimer)	0.012	0	-10000	0	-10000	0	0

×

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K1	-0.055	0.17	-10000	0	-0.4	79	79
CRKL	-0.051	0.17	-10000	0	-0.41	79	79
HRAS	-0.036	0.16	-10000	0	-0.43	26	26
mol:PIP3	-0.057	0.16	-10000	0	-0.39	79	79
SPRED1	0.012	0	-10000	0	-10000	0	0
SPRED2	0.012	0	-10000	0	-10000	0	0
GAB1	-0.059	0.18	-10000	0	-0.43	79	79
FOXO3	-0.041	0.16	-10000	0	-0.37	79	79
AKT1	-0.05	0.17	-10000	0	-0.4	79	79
BAD	-0.042	0.16	-10000	0	-0.37	79	79
megakaryocyte differentiation	-0.08	0.2	-10000	0	-0.44	96	96
GSK3B	-0.041	0.16	-10000	0	-0.37	79	79
RAF1	-0.023	0.14	-10000	0	-0.36	20	20
SHC1	0.012	0	-10000	0	-10000	0	0
STAT3	-0.059	0.18	-10000	0	-0.43	79	79
STAT1	-0.15	0.42	-10000	0	-0.99	79	79
HRAS/SPRED1	-0.023	0.14	-10000	0	-0.36	20	20
cell proliferation	-0.058	0.18	-10000	0	-0.42	79	79
PIK3CA	0.012	0.001	-10000	0	-10000	0	0
TEC	0.012	0.001	-10000	0	-10000	0	0
RPS6KB1	-0.058	0.18	-10000	0	-0.43	79	79
HRAS/SPRED2	-0.023	0.14	-10000	0	-0.36	20	20
LYN/TEC/p62DOK	-0.043	0.18	-10000	0	-0.4	79	79
MAPK3	-0.006	0.1	-10000	0	-0.27	12	12
STAP1	-0.074	0.2	-10000	0	-0.48	79	79
GRAP2	0.005	0.048	-10000	0	-0.32	9	9
JAK2	-0.13	0.36	-10000	0	-0.84	79	79
STAT1 (dimer)	-0.15	0.4	-10000	0	-0.96	79	79
mol:Gleevec	0.001	0.007	-10000	0	-10000	0	0
GRB2/SOCS1/VAV1	-0.062	0.2	-10000	0	-0.43	89	89
actin filament polymerization	-0.063	0.19	-10000	0	-0.43	83	83
LYN	0.012	0	-10000	0	-10000	0	0
STAP1/STAT5A (dimer)	-0.095	0.27	-10000	0	-0.64	79	79
PIK3R1	0.012	0	-10000	0	-10000	0	0
CBL/CRKL/GRB2	-0.035	0.16	-10000	0	-0.36	79	79
PI3K	-0.045	0.18	-10000	0	-0.41	79	79
PTEN	0.011	0.016	-10000	0	-0.32	1	1
SCF/KIT/EPO/EPOR	-0.18	0.48	-10000	0	-1.1	79	79
MAPK8	-0.059	0.18	-10000	0	-0.43	79	79
STAT3 (dimer)	-0.058	0.18	-10000	0	-0.42	79	79
positive regulation of transcription	-0.002	0.086	-10000	0	-0.24	4	4
mol:GDP	-0.043	0.17	-10000	0	-0.47	26	26
PIK3C2B	-0.059	0.18	-10000	0	-0.43	79	79
CBL/CRKL	-0.042	0.17	-10000	0	-0.38	79	79
FER	-0.059	0.18	-10000	0	-0.43	79	79
SH2B3	-0.059	0.18	-10000	0	-0.43	79	79
PDPK1	-0.048	0.15	-10000	0	-0.36	79	79
SNAI2	-0.059	0.18	-10000	0	-0.43	79	79
positive regulation of cell proliferation	-0.1	0.31	-10000	0	-0.73	79	79
KITLG	0.001	0.058	-10000	0	-0.35	11	11
cell motility	-0.1	0.31	-10000	0	-0.73	79	79
PTPN6	0.014	0.01	-10000	0	-10000	0	0
EPOR	-0.02	0.13	-10000	0	-0.77	1	1
STAT5A (dimer)	-0.083	0.26	-10000	0	-0.6	79	79
SOCS1	-0.017	0.14	-10000	0	-0.71	17	17
cell migration	0.064	0.19	0.45	79	-10000	0	79
SOS1	0.012	0	-10000	0	-10000	0	0
EPO	-0.003	0.079	-10000	0	-0.72	5	5
VAV1	0.002	0.058	-10000	0	-0.32	13	13
GRB10	-0.059	0.18	-10000	0	-0.43	79	79
PTPN11	0.013	0.007	-10000	0	-10000	0	0
SCF/KIT	-0.067	0.19	-10000	0	-0.46	79	79
GO:0007205	0.002	0.01	-10000	0	-10000	0	0
MAP2K1	-0.011	0.11	-10000	0	-0.3	13	13
CBL	0.012	0	-10000	0	-10000	0	0
KIT	-0.19	0.48	-10000	0	-1.2	79	79
MAP2K2	-0.011	0.11	-10000	0	-0.29	14	14
SHC/Grb2/SOS1	-0.043	0.18	-10000	0	-0.4	79	79
STAT5A	-0.086	0.26	-10000	0	-0.62	79	79
GRB2	0.012	0	-10000	0	-10000	0	0
response to radiation	-0.058	0.18	-10000	0	-0.42	79	79
SHC/GRAP2	0.013	0.033	-10000	0	-10000	0	0
PTPRO	-0.082	0.21	-10000	0	-0.45	96	96
SH2B2	-0.065	0.19	-10000	0	-0.44	83	83
DOK1	0.012	0	-10000	0	-10000	0	0
MATK	-0.065	0.19	-10000	0	-0.46	79	79
CREBBP	0.008	0.048	-10000	0	-10000	0	0
BCL2	-0.05	0.26	-10000	0	-1.3	14	14

×

IL23-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCL2	-0.38	0.39	-10000	0	-1.1	66	66
IL23A	-0.48	0.45	-10000	0	-1.1	90	90
NF kappa B1 p50/RelA/I kappa B alpha	-0.44	0.38	-10000	0	-1	84	84
positive regulation of T cell mediated cytotoxicity	-0.42	0.43	-10000	0	-1.1	74	74
ITGA3	-0.4	0.39	-10000	0	-1.1	63	63
IL17F	-0.32	0.31	-10000	0	-0.76	92	92
IL12B	-0.017	0.067	-10000	0	-0.74	3	3
STAT1 (dimer)	-0.4	0.42	-10000	0	-1.1	74	74
CD4	-0.38	0.39	-10000	0	-1	65	65
IL23	-0.46	0.43	-10000	0	-1.1	91	91
IL23R	-0.068	0.14	-10000	0	-1.3	4	4
IL1B	-0.45	0.45	-10000	0	-1.2	79	79
T-helper cell lineage commitment	0	0	-10000	0	-10000	0	0
IL24	-0.49	0.43	-10000	0	-1	118	118
TYK2	-0.006	0.018	-10000	0	-10000	0	0
STAT4	0.002	0.055	-10000	0	-0.32	12	12
STAT3	0.011	0.002	-10000	0	-10000	0	0
IL18RAP	-0.003	0.067	-10000	0	-0.32	18	18
IL12RB1	-0.02	0.088	-10000	0	-0.48	12	12
PIK3CA	0.011	0.002	-10000	0	-10000	0	0
IL12Rbeta1/TYK2	-0.017	0.069	-10000	0	-0.39	10	10
IL23R/JAK2	-0.078	0.15	-10000	0	-1.3	4	4
positive regulation of chronic inflammatory response	-0.42	0.43	-10000	0	-1.1	74	74
natural killer cell activation	0.006	0.009	0.075	4	-10000	0	4
JAK2	-0.009	0.038	-10000	0	-0.34	3	3
PIK3R1	0.011	0.002	-10000	0	-10000	0	0
NFKB1	0.008	0.003	-10000	0	-10000	0	0
RELA	0.008	0.003	-10000	0	-10000	0	0
positive regulation of dendritic cell antigen processing and presentation	-0.44	0.41	-10000	0	-1	91	91
ALOX12B	-0.38	0.39	-10000	0	-1	68	68
CXCL1	-0.48	0.44	-10000	0	-1	114	114
T cell proliferation	-0.42	0.43	-10000	0	-1.1	74	74
NFKBIA	0.008	0.003	-10000	0	-10000	0	0
IL17A	-0.31	0.28	-10000	0	-0.64	120	120
PI3K	-0.41	0.4	-10000	0	-1	81	81
IFNG	-0.02	0.031	0.14	1	-0.094	43	44
STAT3 (dimer)	-0.44	0.39	-10000	0	-1	90	90
IL18R1	0.006	0.04	-10000	0	-0.32	6	6
IL23/IL23R/JAK2/TYK2/SOCS3	-0.22	0.23	-10000	0	-0.67	24	24
IL18/IL18R	0.013	0.05	-10000	0	-10000	0	0
macrophage activation	-0.027	0.016	-10000	0	-0.044	99	99
TNF	-0.43	0.42	-10000	0	-1.1	69	69
STAT3/STAT4	-0.42	0.38	-10000	0	-1	78	78
STAT4 (dimer)	-0.4	0.42	-10000	0	-1.1	76	76
IL18	0.01	0.024	-10000	0	-0.32	2	2
IL19	-0.38	0.38	-10000	0	-1	64	64
STAT5A (dimer)	-0.4	0.42	-10000	0	-1.1	74	74
STAT1	0.008	0.05	-10000	0	-0.71	2	2
SOCS3	0.012	0	-10000	0	-10000	0	0
CXCL9	-0.42	0.42	-10000	0	-1.1	85	85
MPO	-0.38	0.39	-10000	0	-1	70	70
positive regulation of humoral immune response	-0.42	0.43	-10000	0	-1.1	74	74
IL23/IL23R/JAK2/TYK2	-0.43	0.46	-10000	0	-1.2	74	74
IL6	-0.42	0.42	-10000	0	-1.1	79	79
STAT5A	0.012	0	-10000	0	-10000	0	0
IL2	0.007	0.009	-10000	0	-10000	0	0
positive regulation of tyrosine phosphorylation of STAT protein	0.006	0.009	0.075	4	-10000	0	4
CD3E	-0.39	0.4	-10000	0	-1.1	73	73
keratinocyte proliferation	-0.42	0.43	-10000	0	-1.1	74	74
NOS2	-0.4	0.42	-10000	0	-1.1	81	81

×

Syndecan-4-mediated signaling events

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
PTK2	-0.019	0.082	-9999	-0.36	20	20
Syndecan-4/Syndesmos	-0.14	0.2	-9999	-0.48	73	73
positive regulation of JNK cascade	-0.15	0.19	-9999	-0.46	73	73
Syndecan-4/ADAM12	-0.36	0.25	-9999	-0.63	151	151
CCL5	0.002	0.058	-9999	-0.32	13	13
Rac1/GDP	0.009	0	-9999	-10000	0	0
DNM2	0.012	0	-9999	-10000	0	0
ITGA5	0.012	0	-9999	-10000	0	0
SDCBP	0.01	0.023	-9999	-0.32	2	2
PLG	-0.15	0.3	-9999	-0.71	89	89
ADAM12	-0.41	0.35	-9999	-0.71	246	246
mol:GTP	0	0	-9999	-10000	0	0
NUDT16L1	0.012	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
Syndecan-4/PKC alpha	-0.068	0.069	-9999	-0.18	3	3
Syndecan-4/Laminin alpha1	-0.16	0.21	-9999	-0.47	95	95
Syndecan-4/CXCL12/CXCR4	-0.16	0.2	-9999	-0.48	73	73
Syndecan-4/Laminin alpha3	-0.15	0.2	-9999	-0.48	78	78
MDK	-0.004	0.1	-9999	-0.71	9	9
Syndecan-4/FZD7	-0.14	0.2	-9999	-0.48	73	73
Syndecan-4/Midkine	-0.15	0.21	-9999	-0.5	76	76
FZD7	0.012	0	-9999	-10000	0	0
Syndecan-4/FGFR1/FGF	-0.15	0.19	-9999	-0.47	75	75
THBS1	0.01	0.035	-9999	-0.71	1	1
integrin-mediated signaling pathway	-0.14	0.19	-9999	-0.47	74	74
positive regulation of MAPKKK cascade	-0.15	0.19	-9999	-0.46	73	73
Syndecan-4/TACI	-0.18	0.22	-9999	-0.47	112	112
CXCR4	0.01	0.035	-9999	-0.71	1	1
cell adhesion	0.016	0.056	-9999	-0.24	17	17
Syndecan-4/Dynamin	-0.14	0.2	-9999	-0.48	73	73
Syndecan-4/TSP1	-0.14	0.2	-9999	-0.49	73	73
Syndecan-4/GIPC	-0.14	0.2	-9999	-0.48	73	73
Syndecan-4/RANTES	-0.15	0.2	-9999	-0.48	77	77
ITGB1	0.012	0	-9999	-10000	0	0
LAMA1	-0.059	0.14	-9999	-0.32	89	89
LAMA3	0.005	0.065	-9999	-0.55	5	5
RAC1	0.012	0	-9999	-10000	0	0
PRKCA	0.044	0.045	-9999	-10000	0	0
Syndecan-4/alpha-Actinin	-0.14	0.2	-9999	-0.48	73	73
TFPI	0.009	0.028	-9999	-0.32	3	3
F2	-0.22	0.33	-9999	-0.7	131	131
alpha5/beta1 Integrin	0.018	0	-9999	-10000	0	0
positive regulation of cell adhesion	-0.16	0.2	-9999	-0.46	99	99
ACTN1	0.012	0	-9999	-10000	0	0
TNC	0.005	0.053	-9999	-0.38	7	7
Syndecan-4/CXCL12	-0.16	0.21	-9999	-0.47	93	93
FGF6	-0.001	0.035	-9999	-0.71	1	1
RHOA	0.012	0	-9999	-10000	0	0
CXCL12	-0.051	0.13	-9999	-0.32	79	79
TNFRSF13B	-0.12	0.16	-9999	-0.32	164	164
FGF2	-0.025	0.1	-9999	-0.32	46	46
FGFR1	0.008	0.036	-9999	-0.32	5	5
Syndecan-4/PI-4-5-P2	-0.15	0.2	-9999	-0.48	73	73
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.014	0.14	-9999	-0.6	20	20
cell migration	-0.025	0.025	-9999	-10000	0	0
PRKCD	0.016	0.01	-9999	-10000	0	0
vasculogenesis	-0.14	0.19	-9999	-0.47	73	73
SDC4	-0.16	0.21	-9999	-0.51	73	73
Syndecan-4/Tenascin C	-0.15	0.2	-9999	-0.48	74	74
Syndecan-4/PI-4-5-P2/PKC alpha	-0.054	0.054	-9999	-10000	0	0
Syndecan-4/Syntenin	-0.14	0.2	-9999	-0.48	74	74
MMP9	-0.077	0.23	-9999	-0.7	51	51
Rac1/GTP	0.016	0.057	-9999	-0.25	16	16
cytoskeleton organization	-0.14	0.19	-9999	-0.46	73	73
GIPC1	0.011	0.016	-9999	-0.32	1	1
Syndecan-4/TFPI	-0.14	0.2	-9999	-0.48	73	73

×

Caspase cascade in apoptosis

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TOP1	-0.054	0.13	-10000	0	-0.26	112	112
ACTA1	-0.08	0.16	-10000	0	-0.33	113	113
NUMA1	-0.055	0.13	-10000	0	-0.26	113	113
SPTAN1	-0.077	0.16	-10000	0	-0.32	112	112
LIMK1	-0.077	0.16	-10000	0	-0.32	112	112
BIRC3	0.005	0.055	-10000	0	-0.37	8	8
BIRC2	0.012	0.001	-10000	0	-10000	0	0
BAX	0.012	0	-10000	0	-10000	0	0
CASP10	-0.12	0.22	-10000	0	-0.46	116	116
CRMA	0	0	-10000	0	-10000	0	0
XIAP	0.012	0	-10000	0	-10000	0	0
PTK2	-0.054	0.13	-10000	0	-0.26	112	112
DIABLO	0.012	0.001	-10000	0	-10000	0	0
apoptotic nuclear changes	-0.075	0.15	-10000	0	-0.32	112	112
response to UV	0	0	-10000	0	-10000	0	0
CRADD	0.012	0	-10000	0	-10000	0	0
GSN	-0.079	0.16	-10000	0	-0.33	112	112
MADD	0.012	0	-10000	0	-10000	0	0
TFAP2A	-0.055	0.091	-10000	0	-0.49	2	2
BID	-0.045	0.1	-10000	0	-0.2	116	116
MAP3K1	-0.025	0.062	-10000	0	-0.25	2	2
TRADD	0.012	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0.018	0.001	-10000	0	-10000	0	0
mol:Activated DNA	0	0	-10000	0	-10000	0	0
ARHGDIB	-0.077	0.16	-10000	0	-0.32	112	112
CASP9	0.012	0.001	-10000	0	-10000	0	0
DNA repair	0.018	0.047	-10000	0	-0.14	4	4
neuron apoptosis	0.01	0.02	-10000	0	-10000	0	0
mol:NAD	0	0	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	-0.067	0.15	-10000	0	-0.3	112	112
APAF1	0.012	0.001	-10000	0	-10000	0	0
CASP6	-0.017	0.078	-10000	0	-10000	0	0
TRAF2	0.011	0.016	-10000	0	-0.32	1	1
ICAD/CAD	-0.069	0.15	-10000	0	-0.31	112	112
CASP7	0.005	0.035	0.23	8	-10000	0	8
KRT18	0.003	0.024	-10000	0	-10000	0	0
apoptosis	-0.061	0.14	-10000	0	-0.5	2	2
DFFA	-0.077	0.16	-10000	0	-0.32	112	112
DFFB	-0.077	0.16	-10000	0	-0.32	112	112
PARP1	-0.018	0.047	0.14	4	-10000	0	4
actin filament polymerization	0.076	0.15	0.31	114	-10000	0	114
TNF	0.011	0.016	-10000	0	-0.32	1	1
CYCS	-0.034	0.082	-10000	0	-0.16	115	115
SATB1	-0.015	0.076	-10000	0	-10000	0	0
SLK	-0.077	0.15	-10000	0	-0.32	112	112
p15 BID/BAX	-0.035	0.091	-10000	0	-0.31	3	3
CASP2	0.034	0.027	-10000	0	-0.3	1	1
JNK cascade	0.025	0.061	0.24	2	-10000	0	2
CASP3	-0.086	0.16	-10000	0	-0.34	117	117
LMNB2	0.02	0.034	-10000	0	-10000	0	0
RIPK1	0.012	0	-10000	0	-10000	0	0
CASP4	0.012	0	-10000	0	-10000	0	0
Mammalian IAPs/DIABLO	0.027	0.031	-10000	0	-0.41	1	1
negative regulation of DNA binding	-0.055	0.091	-10000	0	-0.49	2	2
stress fiber formation	-0.076	0.15	-10000	0	-0.32	112	112
GZMB	-0.14	0.25	-10000	0	-0.54	116	116
CASP1	0.013	0.012	-10000	0	-0.24	1	1
LMNB1	0.02	0.034	-10000	0	-10000	0	0
APP	0.01	0.02	-10000	0	-10000	0	0
TNFRSF1A	0.012	0	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
CASP8	0.009	0	-10000	0	-10000	0	0
VIM	-0.062	0.14	-10000	0	-0.28	112	112
LMNA	0.02	0.034	-10000	0	-10000	0	0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD	0.031	0.029	-10000	0	-0.32	1	1
LRDD	0.011	0.016	-10000	0	-0.32	1	1
SREBF1	-0.077	0.16	-10000	0	-0.32	112	112
APAF-1/Caspase 9	-0.015	0.03	-10000	0	-10000	0	0
nuclear fragmentation during apoptosis	-0.054	0.13	-10000	0	-0.26	113	113
CFL2	-0.077	0.15	-10000	0	-0.32	114	114
GAS2	-0.14	0.22	-10000	0	-0.41	151	151
positive regulation of apoptosis	0.024	0.033	-10000	0	-10000	0	0
PRF1	0.006	0.05	-10000	0	-0.38	6	6

×

BCR signaling 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
JUN	-0.068	0.16	-9999	-0.44	54	54
IKBKB	-0.03	0.085	-9999	-0.24	31	31
AKT1	-0.052	0.11	-9999	-0.26	51	51
IKBKG	-0.032	0.092	-9999	-0.26	35	35
CALM1	-0.086	0.19	-9999	-0.49	61	61
PIK3CA	0.012	0.001	-9999	-10000	0	0
MAP3K1	-0.11	0.24	-9999	-0.62	61	61
MAP3K7	0.012	0	-9999	-10000	0	0
mol:Ca2+	-0.096	0.2	-9999	-0.52	62	62
DOK1	0.012	0	-9999	-10000	0	0
AP-1	-0.034	0.1	-9999	-0.25	50	50
LYN	0.012	0	-9999	-10000	0	0
BLNK	0.008	0.036	-9999	-0.32	5	5
SHC1	0.012	0	-9999	-10000	0	0
BCR complex	-0.082	0.15	-9999	-0.4	46	46
CD22	-0.14	0.27	-9999	-0.56	99	99
CAMK2G	-0.075	0.17	-9999	-0.47	56	56
CSNK2A1	0.012	0	-9999	-10000	0	0
INPP5D	0.012	0	-9999	-10000	0	0
SHC/GRB2/SOS1	-0.051	0.082	-9999	-0.37	3	3
GO:0007205	-0.098	0.2	-9999	-0.53	62	62
SYK	0.012	0	-9999	-10000	0	0
ELK1	-0.087	0.19	-9999	-0.5	61	61
NFATC1	-0.1	0.2	-9999	-0.54	58	58
B-cell antigen/BCR complex	-0.082	0.15	-9999	-0.4	46	46
PAG1/CSK	0.016	0.019	-9999	-10000	0	0
NFKBIB	-0.002	0.029	-9999	-10000	0	0
HRAS	-0.07	0.16	-9999	-0.44	53	53
NFKBIA	-0.001	0.029	-9999	-10000	0	0
NF-kappa-B/RelA/I kappa B beta	0.004	0.024	-9999	-10000	0	0
RasGAP/Csk	-0.055	0.14	-9999	-0.42	24	24
mol:GDP	-0.093	0.19	-9999	-0.51	61	61
PTEN	0.011	0.016	-9999	-0.32	1	1
CD79B	-0.025	0.1	-9999	-0.32	47	47
NF-kappa-B/RelA/I kappa B alpha	0.004	0.024	-9999	-10000	0	0
GRB2	0.012	0	-9999	-10000	0	0
PI3K/BCAP/CD19	-0.14	0.24	-9999	-0.51	102	102
PIK3R1	0.012	0	-9999	-10000	0	0
mol:IP3	-0.099	0.21	-9999	-0.54	62	62
CSK	0.012	0	-9999	-10000	0	0
FOS	-0.079	0.18	-9999	-0.48	55	55
CHUK	-0.031	0.09	-9999	-0.26	32	32
IBTK	0.011	0.016	-9999	-0.32	1	1
CARD11/BCL10/MALT1/TAK1	-0.079	0.18	-9999	-0.45	66	66
PTPN6	-0.13	0.26	-9999	-0.6	75	75
RELA	0.012	0	-9999	-10000	0	0
BCL2A1	0.004	0.026	-9999	-0.11	11	11
VAV2	-0.14	0.27	-9999	-0.56	100	100
ubiquitin-dependent protein catabolic process	0.002	0.029	-9999	-10000	0	0
BTK	-0.1	0.31	-9999	-1.1	40	40
CD19	-0.14	0.27	-9999	-0.55	99	99
MAP4K1	-0.017	0.093	-9999	-0.32	36	36
CD72	0.011	0.016	-9999	-0.32	1	1
PAG1	0.009	0.028	-9999	-0.32	3	3
MAPK14	-0.088	0.2	-9999	-0.52	58	58
SH3BP5	0.009	0.028	-9999	-0.32	3	3
PIK3AP1	-0.087	0.2	-9999	-0.54	55	55
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72	-0.12	0.24	-9999	-0.6	61	61
RAF1	-0.062	0.15	-9999	-0.42	50	50
RasGAP/p62DOK/SHIP	-0.05	0.13	-9999	-0.4	24	24
CD79A	-0.1	0.16	-9999	-0.32	142	142
re-entry into mitotic cell cycle	-0.035	0.1	-9999	-0.26	50	50
RASA1	0.012	0.001	-9999	-10000	0	0
MAPK3	-0.043	0.13	-9999	-0.39	34	34
MAPK1	-0.043	0.13	-9999	-0.39	34	34
CD72/SHP1	-0.12	0.24	-9999	-0.62	60	60
NFKB1	0.012	0	-9999	-10000	0	0
MAPK8	-0.088	0.2	-9999	-0.52	58	58
actin cytoskeleton organization	-0.12	0.22	-9999	-0.58	60	60
NF-kappa-B/RelA	0.013	0.046	-9999	-10000	0	0
Calcineurin	-0.06	0.16	-9999	-0.51	36	36
PI3K	-0.13	0.19	-9999	-0.52	58	58
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2	-0.097	0.21	-9999	-0.54	62	62
SOS1	0.012	0	-9999	-10000	0	0
Bam32/HPK1	-0.13	0.3	-9999	-0.82	57	57
DAPP1	-0.15	0.33	-9999	-0.9	57	57
cytokine secretion	-0.096	0.19	-9999	-0.5	58	58
mol:DAG	-0.099	0.21	-9999	-0.54	62	62
PLCG2	-0.012	0.086	-9999	-0.32	30	30
MAP2K1	-0.052	0.14	-9999	-0.43	36	36
B-cell antigen/BCR complex/FcgammaRIIB	-0.08	0.16	-9999	-0.4	59	59
mol:PI-3-4-5-P3	-0.095	0.13	-9999	-0.36	56	56
ETS1	-0.064	0.16	-9999	-0.44	50	50
B-cell antigen/BCR complex/LYN/SYK/BLNK	-0.04	0.11	-9999	-0.43	3	3
B-cell antigen/BCR complex/LYN	-0.13	0.24	-9999	-0.69	55	55
MALT1	0.011	0.016	-9999	-0.32	1	1
TRAF6	0.012	0	-9999	-10000	0	0
RAC1	-0.13	0.24	-9999	-0.63	60	60
B-cell antigen/BCR complex/LYN/SYK	-0.14	0.22	-9999	-0.65	54	54
CARD11	-0.11	0.21	-9999	-0.5	77	77
FCGR2B	-0.026	0.1	-9999	-0.32	47	47
PPP3CA	0.012	0	-9999	-10000	0	0
BCL10	0.012	0	-9999	-10000	0	0
IKK complex	-0.006	0.037	-9999	-0.1	3	3
PTPRC	-0.01	0.083	-9999	-0.32	28	28
PDPK1	-0.049	0.099	-9999	-0.25	49	49
PPP3CB	0.012	0	-9999	-10000	0	0
PPP3CC	0.012	0	-9999	-10000	0	0
POU2F2	0.005	0.021	-9999	-10000	0	0

×

Signaling events mediated by the Hedgehog family

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
TGFB2	0.021	0.12	-10000	0	-0.54	16	16
IHH	0.014	0.049	-10000	0	-0.44	4	4
SHH Np/Cholesterol/GAS1	-0.12	0.2	-10000	0	-0.44	107	107
LRPAP1	0.012	0	-10000	0	-10000	0	0
dorsoventral neural tube patterning	0.12	0.2	0.44	107	-10000	0	107
SMO/beta Arrestin2	0.005	0.089	-10000	0	-0.48	4	4
SMO	0	0.093	-10000	0	-0.46	7	7
AKT1	0.018	0.046	-10000	0	-10000	0	0
ARRB2	0.012	0	-10000	0	-10000	0	0
BOC	-0.013	0.087	-10000	0	-0.32	31	31
ADRBK1	0.012	0	-10000	0	-10000	0	0
heart looping	0	0.092	-10000	0	-0.45	7	7
STIL	-0.068	0.18	-10000	0	-0.52	7	7
DHH N/PTCH2	0.008	0.044	-10000	0	-10000	0	0
DHH N/PTCH1	0.018	0.078	-10000	0	-0.58	2	2
PIK3CA	0.012	0.001	-10000	0	-10000	0	0
DHH	-0.002	0.064	-10000	0	-0.32	16	16
PTHLH	0.015	0.15	-10000	0	-0.82	10	10
determination of left/right symmetry	0	0.092	-10000	0	-0.45	7	7
PIK3R1	0.012	0	-10000	0	-10000	0	0
skeletal system development	0.015	0.15	-10000	0	-0.81	10	10
IHH N/Hhip	-0.029	0.11	-10000	0	-0.42	5	5
DHH N/Hhip	-0.031	0.099	-10000	0	-0.4	6	6
mol:Cholesterol	0	0	-10000	0	-10000	0	0
heart development	0	0.092	-10000	0	-0.45	7	7
pancreas development	-0.046	0.12	-10000	0	-0.32	72	72
HHAT	0.009	0.028	-10000	0	-0.32	3	3
PI3K	0.018	0	-10000	0	-10000	0	0
EntrezGene:84976	0	0	-10000	0	-10000	0	0
GAS1	-0.038	0.12	-10000	0	-0.33	60	60
somite specification	0	0.092	-10000	0	-0.45	7	7
SHH Np/Cholesterol/PTCH1	-0.075	0.18	-10000	0	-0.38	107	107
SHH Np/Cholesterol/PTCH2	-0.091	0.19	-10000	0	-0.42	105	105
SHH Np/Cholesterol/Megalin	-0.13	0.22	-10000	0	-0.45	127	127
SHH	-0.12	0.24	-10000	0	-0.53	105	105
catabolic process	0.021	0.077	-10000	0	-0.47	4	4
SMO/Vitamin D3	-0.064	0.18	-10000	0	-0.55	7	7
SHH Np/Cholesterol/Hhip	-0.12	0.19	-10000	0	-0.43	107	107
LRP2	-0.047	0.19	-10000	0	-0.71	31	31
receptor-mediated endocytosis	-0.073	0.18	-10000	0	-0.53	18	18
SHH Np/Cholesterol/BOC	-0.1	0.19	-10000	0	-0.43	106	106
SHH Np/Cholesterol/CDO	-0.091	0.19	-10000	0	-0.42	105	105
mesenchymal cell differentiation	0.12	0.19	0.43	107	-10000	0	107
mol:Vitamin D3	-0.073	0.18	-10000	0	-0.38	107	107
IHH N/PTCH2	0.015	0.039	-10000	0	-0.26	2	2
CDON	0.012	0	-10000	0	-10000	0	0
IHH N/PTCH1	0.023	0.079	-10000	0	-0.48	4	4
Megalin/LRPAP1	-0.027	0.14	-10000	0	-0.53	31	31
PTCH2	0.012	0.001	-10000	0	-10000	0	0
SHH Np/Cholesterol	-0.098	0.19	-10000	0	-0.42	105	105
PTCH1	0.021	0.078	-10000	0	-0.47	4	4
HHIP	-0.046	0.12	-10000	0	-0.32	72	72

×

IL1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
UBC13/UEV1A	-0.056	0.18	-9999	-0.53	52	52
PRKCZ	0.012	0	-9999	-10000	0	0
MAP3K7IP2	0	0	-9999	-10000	0	0
ERC1	0.012	0	-9999	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4	-0.003	0.069	-9999	-10000	0	0
IRAK/TOLLIP	-0.031	0.14	-9999	-0.41	52	52
IKBKB	0.012	0	-9999	-10000	0	0
IKBKG	0.011	0.016	-9999	-0.32	1	1
IL1 alpha/IL1R2	-0.22	0.26	-9999	-0.54	152	152
IL1A	-0.25	0.35	-9999	-0.71	152	152
IL1B	-0.055	0.18	-9999	-0.53	53	53
IRAK/TRAF6/p62/Atypical PKCs	-0.011	0.13	-9999	-0.35	52	52
IL1R2	-0.048	0.13	-9999	-0.32	75	75
IL1R1	0.007	0.04	-9999	-0.32	6	6
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.01	0.081	-9999	-0.29	11	11
TOLLIP	0.012	0	-9999	-10000	0	0
TICAM2	0.005	0.043	-9999	-0.32	7	7
MAP3K3	0.012	0	-9999	-10000	0	0
TAK1/TAB1/TAB2	0.008	0	-9999	-10000	0	0
IKK complex/ELKS	0.009	0.1	-9999	-10000	0	0
JUN	-0.012	0.11	-9999	-0.42	1	1
MAP3K7	0.012	0	-9999	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/PI3K	-0.016	0.14	-9999	-0.37	53	53
IL1 alpha/IL1R1/IL1RAP/MYD88	-0.13	0.21	-9999	-0.42	152	152
PIK3R1	0.012	0	-9999	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4	-0.12	0.2	-9999	-0.39	152	152
IL1 beta fragment/IL1R1/IL1RAP	-0.032	0.15	-9999	-0.41	54	54
NFKB1	0.012	0	-9999	-10000	0	0
MAPK8	-0.018	0.12	-9999	-0.33	52	52
IRAK1	-0.042	0.16	-9999	-0.45	52	52
IL1RN/IL1R1	-0.081	0.21	-9999	-0.53	73	73
IRAK4	0.012	0	-9999	-10000	0	0
PRKCI	0.01	0.023	-9999	-0.32	2	2
TRAF6	0.012	0	-9999	-10000	0	0
PI3K	0.018	0	-9999	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.001	0.078	-9999	-0.28	1	1
CHUK	0.012	0	-9999	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s	-0.032	0.15	-9999	-0.41	54	54
IL1 beta/IL1R2	-0.074	0.16	-9999	-0.45	56	56
IRAK/TRAF6/TAK1/TAB1/TAB2	-0.023	0.13	-9999	-0.36	52	52
NF kappa B1 p50/RelA	-0.045	0.11	-9999	-10000	0	0
IRAK3	0.005	0.048	-9999	-0.32	9	9
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4	-0.02	0.14	-9999	-0.37	53	53
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.06	0.12	-9999	-0.39	2	2
IL1 alpha/IL1R1/IL1RAP	-0.15	0.23	-9999	-0.46	152	152
RELA	0.012	0	-9999	-10000	0	0
MAP3K7IP1	0	0	-9999	-10000	0	0
SQSTM1	0.012	0	-9999	-10000	0	0
MYD88	0.012	0	-9999	-10000	0	0
IRAK/TRAF6/MEKK3	-0.022	0.14	-9999	-0.38	52	52
IL1RAP	0.012	0	-9999	-10000	0	0
UBE2N	0.012	0	-9999	-10000	0	0
IRAK/TRAF6	-0.082	0.15	-9999	-0.55	15	15
CASP1	0.011	0.016	-9999	-0.32	1	1
IL1RN/IL1R2	-0.12	0.21	-9999	-0.53	73	73
IL1 beta fragment/IL1R1/IL1RAP/MYD88	-0.023	0.14	-9999	-0.39	53	53
TMEM189-UBE2V1	-0.085	0.24	-9999	-0.7	53	53
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.058	0.11	-9999	-0.34	22	22
PIK3CA	0.012	0.001	-9999	-10000	0	0
IL1RN	-0.11	0.27	-9999	-0.71	73	73
TRAF6/TAK1/TAB1/TAB2	-0.03	0.13	-9999	-0.38	52	52
MAP2K6	-0.024	0.13	-9999	-0.36	52	52

×

Endothelins

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
AKT1	0.026	0.18	-10000	0	-0.44	31	31
PTK2B	0.012	0.001	-10000	0	-10000	0	0
mol:Ca2+	0.017	0.21	-10000	0	-0.92	18	18
EDN1	0.051	0.13	-10000	0	-0.46	4	4
EDN3	-0.13	0.16	-10000	0	-0.32	178	178
EDN2	-0.044	0.12	-10000	0	-0.32	70	70
HRAS/GDP	0.01	0.13	-10000	0	-0.45	7	7
ETA receptor/Endothelin-1/Gq/GTP/PLC beta	0.045	0.095	-10000	0	-0.44	3	3
ADCY4	-0.009	0.14	-10000	0	-0.45	16	16
ADCY5	-0.055	0.16	-10000	0	-0.45	34	34
ADCY6	-0.009	0.14	-10000	0	-0.45	16	16
ADCY7	-0.009	0.14	-10000	0	-0.46	14	14
ADCY1	-0.018	0.15	-10000	0	-0.44	24	24
ADCY2	-0.026	0.16	-10000	0	-0.45	29	29
ADCY3	-0.009	0.14	-10000	0	-0.45	16	16
ADCY8	-0.022	0.14	-10000	0	-0.42	23	23
ADCY9	-0.01	0.14	-10000	0	-0.45	16	16
arachidonic acid secretion	-0.01	0.15	-10000	0	-0.47	18	18
ETB receptor/Endothelin-1/Gq/GTP	0.026	0.077	-10000	0	-0.4	4	4
GNAO1	-0.12	0.16	-10000	0	-0.32	170	170
HRAS	0.011	0.016	-10000	0	-0.32	1	1
ETA receptor/Endothelin-1/G12/GTP	0.11	0.22	0.3	211	-0.42	25	236
ETA receptor/Endothelin-1/Gs/GTP	0.086	0.22	0.28	199	-0.4	29	228
mol:GTP	0.001	0.004	-10000	0	-10000	0	0
COL3A1	0.019	0.21	-10000	0	-0.66	19	19
EDNRB	-0.002	0.065	-10000	0	-0.32	15	15
response to oxidative stress	0	0	-10000	0	-10000	0	0
CYSLTR2	0.01	0.21	-10000	0	-0.5	41	41
CYSLTR1	-0.007	0.24	-10000	0	-0.48	71	71
SLC9A1	0.032	0.1	-10000	0	-0.27	9	9
mol:GDP	0.004	0.13	-10000	0	-0.44	10	10
SLC9A3	-0.14	0.3	-10000	0	-0.58	99	99
RAF1	-0.006	0.12	-10000	0	-0.48	7	7
JUN	0.041	0.13	-10000	0	-0.93	1	1
JAK2	0.025	0.18	-10000	0	-0.45	28	28
mol:IP3	0.036	0.093	-10000	0	-0.54	3	3
ETA receptor/Endothelin-1	0.12	0.28	0.35	214	-0.49	38	252
PLCB1	0.01	0.035	-10000	0	-0.71	1	1
PLCB2	0.012	0.002	-10000	0	-10000	0	0
ETA receptor/Endothelin-3	-0.077	0.19	-10000	0	-0.53	25	25
FOS	0.004	0.14	-10000	0	-0.84	8	8
Gai/GDP	-0.23	0.33	-10000	0	-0.62	170	170
CRK	0.012	0.001	-10000	0	-10000	0	0
mol:Ca ++	0.026	0.16	-10000	0	-0.52	15	15
BCAR1	0.011	0.016	-10000	0	-0.32	1	1
PRKCB1	0.033	0.09	-10000	0	-0.52	3	3
GNAQ	0.011	0.024	-10000	0	-0.32	2	2
GNAZ	0.005	0.048	-10000	0	-0.32	9	9
GNAL	-0.014	0.088	-10000	0	-0.32	32	32
Gs family/GDP	-0.033	0.11	-10000	0	-0.41	14	14
ETA receptor/Endothelin-1/Gq/GTP	0.044	0.12	-10000	0	-0.38	8	8
MAPK14	0.033	0.067	-10000	0	-0.54	2	2
TRPC6	0.015	0.23	-10000	0	-0.99	18	18
GNAI2	0.012	0	-10000	0	-10000	0	0
GNAI3	0.012	0	-10000	0	-10000	0	0
GNAI1	0.001	0.06	-10000	0	-0.32	14	14
ETB receptor/Endothelin-1/Gq/GTP/PLC beta	0.03	0.071	-10000	0	-0.57	2	2
ETB receptor/Endothelin-2	-0.03	0.096	-10000	0	-0.35	5	5
ETB receptor/Endothelin-3	-0.088	0.12	-10000	0	-0.4	8	8
ETB receptor/Endothelin-1	0.039	0.12	-10000	0	-0.33	13	13
MAPK3	0.002	0.14	-10000	0	-0.74	8	8
MAPK1	0.002	0.14	-10000	0	-0.74	8	8
Rac1/GDP	0.01	0.13	-10000	0	-0.44	8	8
cAMP biosynthetic process	-0.059	0.15	-10000	0	-0.43	32	32
MAPK8	0.035	0.15	-10000	0	-0.55	13	13
SRC	0.012	0	-10000	0	-10000	0	0
ETB receptor/Endothelin-1/Gi/GTP	-0.049	0.13	-10000	0	-0.37	30	30
p130Cas/CRK/Src/PYK2	-0.029	0.16	-10000	0	-0.56	15	15
mol:K +	0	0	-10000	0	-10000	0	0
G12/GDP	0.01	0.13	-10000	0	-0.45	7	7
COL1A2	0.023	0.22	-10000	0	-0.58	31	31
EntrezGene:2778	0	0	-10000	0	-10000	0	0
ETA receptor/Endothelin-2	-0.014	0.17	-10000	0	-0.57	17	17
mol:DAG	0.036	0.094	-10000	0	-0.54	3	3
MAP2K2	0.001	0.12	-10000	0	-0.55	9	9
MAP2K1	0.001	0.12	-10000	0	-0.55	9	9
EDNRA	0.026	0.19	-10000	0	-0.72	16	16
positive regulation of muscle contraction	0.029	0.16	-10000	0	-0.47	13	13
Gq family/GDP	-0.044	0.096	-10000	0	-0.47	7	7
HRAS/GTP	-0.011	0.12	-10000	0	-0.39	10	10
PRKCH	0.038	0.089	-10000	0	-0.52	3	3
RAC1	0.012	0	-10000	0	-10000	0	0
PRKCA	0.038	0.089	-10000	0	-0.52	3	3
PRKCB	0.014	0.12	-10000	0	-0.4	8	8
PRKCE	0.039	0.089	-10000	0	-0.51	3	3
PRKCD	0.038	0.09	-10000	0	-0.51	3	3
PRKCG	-0.13	0.21	-10000	0	-0.35	184	184
regulation of vascular smooth muscle contraction	0.001	0.16	-10000	0	-0.99	8	8
PRKCQ	0.038	0.093	-10000	0	-0.48	4	4
PLA2G4A	-0.012	0.16	-10000	0	-0.51	18	18
GNA14	0.011	0.024	-10000	0	-0.32	2	2
GNA15	0.001	0.092	-10000	0	-0.7	7	7
GNA12	0.012	0	-10000	0	-10000	0	0
GNA11	0.012	0.017	-10000	0	-0.32	1	1
Rac1/GTP	0.11	0.22	0.3	212	-0.4	31	243
MMP1	-0.36	0.3	-10000	0	-0.57	275	275

×

Ephrin B reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EFNB2	0.012	0	-10000	0	-10000	0	0
EPHB2	0.008	0.05	-10000	0	-0.71	2	2
EFNB1	0.012	0.046	-10000	0	-0.53	3	3
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	-0.077	0.18	-10000	0	-0.38	104	104
Ephrin B2/EPHB1-2	-0.086	0.19	-10000	0	-0.42	102	102
neuron projection morphogenesis	-0.097	0.16	-10000	0	-0.36	104	104
Ephrin B1/EPHB1-2/Tiam1	-0.086	0.19	-10000	0	-0.41	104	104
DNM1	0.006	0.06	-10000	0	-0.7	3	3
cell-cell signaling	-0.001	0.002	-10000	0	-10000	0	0
MAP2K4	0	0.079	-10000	0	-0.58	7	7
YES1	-0.013	0.11	-10000	0	-0.8	7	7
Ephrin B1/EPHB1-2/NCK2	-0.073	0.19	-10000	0	-0.39	104	104
PI3K	0.005	0.08	-10000	0	-0.58	7	7
mol:GDP	-0.086	0.19	-10000	0	-0.4	104	104
ITGA2B	-0.015	0.13	-10000	0	-0.71	15	15
endothelial cell proliferation	0.016	0.001	-10000	0	-10000	0	0
FYN	-0.013	0.1	-10000	0	-0.8	7	7
MAP3K7	-0.007	0.083	-10000	0	-0.61	7	7
FGR	-0.013	0.11	-10000	0	-0.81	7	7
TIAM1	-0.016	0.092	-10000	0	-0.32	35	35
PIK3R1	0.012	0	-10000	0	-10000	0	0
RGS3	0.012	0	-10000	0	-10000	0	0
cell adhesion	-0.003	0.11	-10000	0	-0.46	21	21
LYN	-0.013	0.1	-10000	0	-0.8	7	7
Ephrin B1/EPHB1-2/Src Family Kinases	-0.013	0.096	-10000	0	-0.73	7	7
Ephrin B1/EPHB1-2	-0.017	0.089	-10000	0	-0.48	12	12
SRC	-0.013	0.1	-10000	0	-0.79	7	7
ITGB3	0.005	0.048	-10000	0	-0.32	9	9
EPHB1	-0.16	0.31	-10000	0	-0.71	102	102
EPHB4	0.012	0	-10000	0	-10000	0	0
RAC1	0.012	0	-10000	0	-10000	0	0
Ephrin B2/EPHB4	0.016	0.001	-10000	0	-10000	0	0
alphaIIb/beta3 Integrin	-0.008	0.11	-10000	0	-0.53	15	15
BLK	-0.073	0.13	-10000	0	-0.71	10	10
HCK	-0.017	0.11	-10000	0	-0.81	7	7
regulation of stress fiber formation	0.073	0.18	0.39	104	-10000	0	104
MAPK8	0.005	0.076	-10000	0	-0.55	7	7
Ephrin B1/EPHB1-2/RGS3	-0.073	0.19	-10000	0	-0.39	104	104
endothelial cell migration	-0.003	0.071	-10000	0	-0.51	7	7
NCK2	0.012	0	-10000	0	-10000	0	0
PTPN13	-0.001	0.093	-10000	0	-0.53	12	12
regulation of focal adhesion formation	0.073	0.18	0.39	104	-10000	0	104
chemotaxis	0.073	0.18	0.39	104	-10000	0	104
PIK3CA	0.012	0.001	-10000	0	-10000	0	0
Rac1/GTP	-0.078	0.18	-10000	0	-0.37	104	104
angiogenesis	-0.017	0.088	-10000	0	-0.48	12	12
LCK	-0.015	0.11	-10000	0	-0.81	7	7

×

TCGA08_p53

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
CDKN2A	-0.13	0.24	-10000	0	-0.54	105	105
TP53	-0.034	0.059	-10000	0	-10000	0	0
Senescence	-0.034	0.059	-10000	0	-10000	0	0
Apoptosis	-0.034	0.059	-10000	0	-10000	0	0
Activated_Oncogenes	0	0	-10000	0	-10000	0	0
MDM2	0.064	0.11	0.26	104	-10000	0	104
MDM4	0.012	0	-10000	0	-10000	0	0

×

Angiopoietin receptor Tie2-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	0.023	0.28	-10000	0	-0.8	37	37
NCK1/PAK1/Dok-R	-0.037	0.11	-10000	0	-0.39	34	34
NCK1/Dok-R	-0.007	0.32	-10000	0	-0.93	40	40
PIK3CA	0.011	0.001	-10000	0	-10000	0	0
mol:beta2-estradiol	0.011	0.068	0.25	30	-10000	0	30
RELA	0.012	0	-10000	0	-10000	0	0
SHC1	0.013	0.001	-10000	0	-10000	0	0
Rac/GDP	0.009	0	-10000	0	-10000	0	0
F2	-0.21	0.33	0.24	16	-0.69	131	147
TNIP2	0.012	0	-10000	0	-10000	0	0
NF kappa B/RelA	-0.042	0.28	-10000	0	-0.87	40	40
FN1	-0.018	0.14	-10000	0	-0.61	20	20
PLD2	-0.012	0.33	-10000	0	-0.97	40	40
PTPN11	0.012	0	-10000	0	-10000	0	0
GRB14	-0.021	0.12	-10000	0	-0.44	29	29
ELK1	0	0.3	-10000	0	-0.87	40	40
GRB7	-0.007	0.12	-10000	0	-0.71	11	11
PAK1	0.012	0	-10000	0	-10000	0	0
Tie2/Ang1/alpha5/beta1 Integrin	-0.059	0.3	-10000	0	-0.91	40	40
CDKN1A	0.036	0.21	-10000	0	-0.6	25	25
ITGA5	0.012	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
RasGAP/Dok-R	-0.007	0.32	-10000	0	-0.93	40	40
CRK	0.012	0	-10000	0	-10000	0	0
mol:NO	0.035	0.22	-10000	0	-0.59	38	38
PLG	-0.099	0.36	-10000	0	-1	40	40
mol:GDP	0	0	-10000	0	-10000	0	0
chemokinesis	0.021	0.27	-10000	0	-0.75	40	40
GRB2	0.012	0	-10000	0	-10000	0	0
PIK3R1	0.013	0.002	-10000	0	-10000	0	0
ANGPT2	0.006	0.19	0.36	7	-0.58	11	18
BMX	-0.05	0.34	-10000	0	-1	40	40
ANGPT1	-0.005	0.3	-10000	0	-1.1	30	30
tube development	0.028	0.23	-10000	0	-0.66	28	28
ANGPT4	0.002	0.049	-10000	0	-0.7	2	2
response to hypoxia	-0.003	0.02	-10000	0	-10000	0	0
Tie2/Ang1/GRB14	-0.028	0.34	-10000	0	-1	40	40
alpha5/beta1 Integrin	0.018	0	-10000	0	-10000	0	0
FGF2	-0.026	0.1	-10000	0	-0.32	46	46
STAT5A (dimer)	0.027	0.25	-10000	0	-0.75	28	28
mol:L-citrulline	0.035	0.22	-10000	0	-0.59	38	38
AGTR1	-0.15	0.16	-10000	0	-0.32	202	202
MAPK14	-0.009	0.34	-10000	0	-0.98	40	40
Tie2/SHP2	-0.03	0.23	-10000	0	-1	19	19
TEK	-0.033	0.25	-10000	0	-1.1	19	19
RPS6KB1	0.022	0.27	-10000	0	-0.75	40	40
Angiotensin II/AT1	-0.1	0.11	-10000	0	-0.22	202	202
Tie2/Ang1/GRB2	-0.015	0.34	-10000	0	-0.99	40	40
MAPK3	-0.003	0.3	-10000	0	-0.89	40	40
MAPK1	-0.003	0.3	-10000	0	-0.89	40	40
Tie2/Ang1/GRB7	-0.024	0.34	-10000	0	-1	40	40
NFKB1	0.012	0	-10000	0	-10000	0	0
MAPK8	-0.012	0.33	-10000	0	-0.97	40	40
PI3K	0.008	0.32	-10000	0	-0.89	40	40
FES	-0.01	0.34	-10000	0	-0.97	40	40
Crk/Dok-R	-0.007	0.32	-10000	0	-0.93	40	40
Tie2/Ang1/ABIN2	-0.015	0.34	-10000	0	-0.99	40	40
blood circulation	0	0	-10000	0	-10000	0	0
negative regulation of caspase activity	0.03	0.25	-10000	0	-0.71	37	37
STAT5A	0.012	0	-10000	0	-10000	0	0
mol:ROS	0	0	-10000	0	-10000	0	0
PTK2	0.022	0.27	-10000	0	-0.77	37	37
Tie2/Ang2	0.011	0.29	-10000	0	-0.9	28	28
Tie2/Ang1	-0.019	0.36	-10000	0	-1	40	40
FOXO1	0.034	0.26	-10000	0	-0.76	30	30
ELF1	0.015	0.023	-10000	0	-10000	0	0
ELF2	-0.012	0.33	-10000	0	-0.97	40	40
mol:Choline	-0.008	0.31	-10000	0	-0.92	40	40
cell migration	-0.025	0.065	-10000	0	-0.23	30	30
FYN	0.023	0.25	-10000	0	-0.75	28	28
DOK2	0.009	0.032	-10000	0	-0.32	4	4
negative regulation of cell cycle	0.039	0.2	-10000	0	-0.55	25	25
ETS1	0	0.067	-10000	0	-0.27	14	14
PXN	0.034	0.23	-10000	0	-0.64	37	37
ITGB1	0.012	0	-10000	0	-10000	0	0
NOS3	0.03	0.24	-10000	0	-0.68	36	36
RAC1	0.012	0	-10000	0	-10000	0	0
TNF	0	0.069	-10000	0	-0.27	15	15
MAPKKK cascade	-0.008	0.31	-10000	0	-0.92	40	40
RASA1	0.012	0.001	-10000	0	-10000	0	0
Tie2/Ang1/Shc	-0.014	0.34	-10000	0	-0.99	40	40
NCK1	0.012	0	-10000	0	-10000	0	0
vasculogenesis	0.039	0.2	-10000	0	-0.53	38	38
mol:Phosphatidic acid	-0.008	0.31	-10000	0	-0.92	40	40
mol:Angiotensin II	0.001	0.003	-10000	0	-10000	0	0
mol:NADP	0.035	0.22	-10000	0	-0.59	38	38
Rac1/GTP	-0.058	0.22	-10000	0	-0.7	40	40
MMP2	-0.013	0.33	-10000	0	-0.97	40	40

×

BMP receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS	-0.14	0.21	-9999	-0.41	151	151
SMAD6-7/SMURF1	0.024	0	-9999	-10000	0	0
NOG	0.007	0.035	-9999	-0.71	1	1
SMAD9	-0.059	0.17	-9999	-0.52	45	45
SMAD4	0.012	0	-9999	-10000	0	0
SMAD5	-0.022	0.088	-9999	-0.32	10	10
BMP7/USAG1	-0.21	0.26	-9999	-0.55	144	144
SMAD5/SKI	-0.015	0.084	-9999	-0.32	7	7
SMAD1	0.031	0.015	-9999	-10000	0	0
BMP2	-0.006	0.076	-9999	-0.32	23	23
SMAD1/SMAD1/SMAD4	0	0.002	-9999	-10000	0	0
BMPR1A	0.012	0	-9999	-10000	0	0
BMPR1B	-0.016	0.12	-9999	-0.52	21	21
BMPR1A-1B/BAMBI	-0.034	0.15	-9999	-0.46	46	46
AHSG	-0.11	0.27	-9999	-0.71	70	70
CER1	-0.017	0.12	-9999	-0.71	12	12
BMP2-4/CER1	-0.026	0.13	-9999	-0.48	30	30
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA	-0.04	0.11	-9999	-0.3	30	30
BMP2-4 (homodimer)	-0.019	0.13	-9999	-0.56	18	18
RGMB	0.012	0	-9999	-10000	0	0
BMP6/BMPR2/BMPR1A-1B	0.008	0.081	-9999	-0.41	11	11
RGMA	-0.091	0.15	-9999	-0.32	130	130
SMURF1	0.012	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP	-0.044	0.1	-9999	-0.32	28	28
BMP2-4/USAG1	-0.042	0.13	-9999	-0.46	26	26
SMAD6/SMURF1/SMAD5	-0.015	0.084	-9999	-0.31	8	8
SOSTDC1	-0.049	0.13	-9999	-0.32	76	76
BMP7/BMPR2/BMPR1A-1B	-0.14	0.22	-9999	-0.42	150	150
SKI	0.012	0	-9999	-10000	0	0
BMP6 (homodimer)	0.002	0.058	-9999	-0.32	13	13
HFE2	0.002	0.005	-9999	-10000	0	0
ZFYVE16	0.01	0.023	-9999	-0.32	2	2
MAP3K7	0.012	0	-9999	-10000	0	0
BMP2-4/CHRD	-0.011	0.11	-9999	-0.47	20	20
SMAD5/SMAD5/SMAD4	-0.015	0.084	-9999	-0.32	7	7
MAPK1	0.012	0	-9999	-10000	0	0
TAK1/TAB family	-0.051	0.075	-9999	-0.3	10	10
BMP7 (homodimer)	-0.24	0.34	-9999	-0.68	150	150
NUP214	0.012	0	-9999	-10000	0	0
BMP6/FETUA	-0.084	0.21	-9999	-0.54	70	70
SMAD1/SKI	0.037	0.015	-9999	-10000	0	0
SMAD6	0.012	0	-9999	-10000	0	0
CTDSP2	0.012	0	-9999	-10000	0	0
BMP2-4/FETUA	-0.089	0.21	-9999	-0.5	81	81
MAP3K7IP1	0	0	-9999	-10000	0	0
GREM1	-0.015	0.11	-9999	-0.41	27	27
BMPR2 (homodimer)	0.011	0.016	-9999	-0.32	1	1
GADD34/PP1CA	0.023	0.013	-9999	-10000	0	0
BMPR1A-1B (homodimer)	-0.003	0.094	-9999	-0.53	11	11
CHRDL1	-0.19	0.16	-9999	-0.32	251	251
ENDOFIN/SMAD1	0.036	0.017	-9999	-10000	0	0
SMAD6-7/SMURF1/SMAD1	0.045	0.014	-9999	-10000	0	0
SMAD6/SMURF1	0.012	0	-9999	-10000	0	0
BAMBI	-0.048	0.2	-9999	-0.71	35	35
SMURF2	0.011	0.016	-9999	-0.32	1	1
BMP2-4/CHRDL1	-0.12	0.14	-9999	-0.47	33	33
BMP2-4/GREM1	-0.024	0.13	-9999	-0.48	25	25
SMAD7	0.012	0	-9999	-10000	0	0
SMAD8A/SMAD8A/SMAD4	-0.05	0.16	-9999	-0.48	45	45
SMAD1/SMAD6	0.037	0.015	-9999	-10000	0	0
TAK1/SMAD6	0.018	0	-9999	-10000	0	0
BMP7	-0.24	0.34	-9999	-0.68	150	150
BMP6	0.002	0.058	-9999	-0.32	13	13
MAP3K7IP2	0	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1	-0.039	0.1	-9999	-0.3	28	28
PPM1A	0.012	0	-9999	-10000	0	0
SMAD1/SMURF2	0.036	0.017	-9999	-10000	0	0
SMAD7/SMURF1	0.018	0	-9999	-10000	0	0
CTDSPL	0.012	0	-9999	-10000	0	0
PPP1CA	0.012	0	-9999	-10000	0	0
XIAP	0.012	0	-9999	-10000	0	0
CTDSP1	0.012	0	-9999	-10000	0	0
PPP1R15A	0.012	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS	-0.066	0.14	-9999	-0.42	41	41
CHRD	0.006	0.043	-9999	-0.32	7	7
BMPR2	0.011	0.016	-9999	-0.32	1	1
BMP2-4/BMPR2/BMPR1A-1B/RGM	-0.052	0.11	-9999	-0.35	28	28
BMP4	-0.021	0.15	-9999	-0.67	20	20
FST	-0.012	0.094	-9999	-0.35	28	28
BMP2-4/NOG	-0.011	0.11	-9999	-0.48	19	19
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1	-0.12	0.2	-9999	-0.4	150	150

×

Fc-epsilon receptor I signaling in mast cells

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PPAP2A	0.011	0.016	-9999	-0.32	1	1
LAT2	-0.072	0.14	-9999	-0.34	61	61
AP1	-0.087	0.19	-9999	-0.54	41	41
mol:PIP3	-0.085	0.17	-9999	-0.4	66	66
IKBKB	-0.055	0.12	-9999	-0.28	50	50
AKT1	-0.029	0.092	-9999	-10000	0	0
IKBKG	-0.055	0.12	-9999	-0.28	50	50
MS4A2	-0.08	0.15	-9999	-0.32	114	114
mol:Sphingosine-1-phosphate	0	0	-9999	-10000	0	0
PIK3CA	0.011	0.001	-9999	-10000	0	0
MAP3K1	-0.066	0.15	-9999	-0.45	26	26
mol:Ca2+	-0.064	0.13	-9999	-0.3	66	66
LYN	0.012	0.002	-9999	-10000	0	0
CBLB	-0.071	0.13	-9999	-0.33	61	61
SHC1	0.012	0	-9999	-10000	0	0
RasGAP/p62DOK	0.022	0.012	-9999	-10000	0	0
positive regulation of cell migration	0	0	-9999	-10000	0	0
INPP5D	0.012	0	-9999	-10000	0	0
PLD2	-0.054	0.11	-9999	-0.38	3	3
PTPN13	-0.082	0.16	-9999	-0.52	15	15
PTPN11	0.009	0.007	-9999	-10000	0	0
GO:0007205	0	0	-9999	-10000	0	0
regulation of mast cell degranulation	-0.034	0.11	-9999	-0.3	8	8
SYK	0.012	0.002	-9999	-10000	0	0
GRB2	0.012	0.001	-9999	-10000	0	0
LAT/PLCgamma1/GRB2/SLP76/GADs	-0.11	0.16	-9999	-0.41	66	66
LAT	-0.072	0.14	-9999	-0.34	61	61
PAK2	-0.078	0.17	-9999	-0.47	33	33
NFATC2	-0.043	0.094	-9999	-0.53	12	12
HRAS	-0.089	0.18	-9999	-0.4	79	79
GAB2	0.012	0	-9999	-10000	0	0
PLA2G1B	0.029	0.018	-9999	-10000	0	0
Fc epsilon R1	-0.084	0.14	-9999	-0.34	61	61
Antigen/IgE/Fc epsilon R1	-0.073	0.12	-9999	-0.3	61	61
mol:GDP	-0.1	0.2	-9999	-0.46	79	79
JUN	0.012	0	-9999	-10000	0	0
mol:Ca++	0	0	-9999	-10000	0	0
PIK3R1	0.011	0.001	-9999	-10000	0	0
FOS	0.006	0.043	-9999	-0.32	7	7
Antigen/IgE/Fc epsilon R1/LYN/SYK	-0.08	0.14	-9999	-0.35	61	61
CHUK	-0.055	0.12	-9999	-0.28	50	50
KLRG1	-0.054	0.12	-9999	-0.3	61	61
VAV1	-0.074	0.14	-9999	-0.34	65	65
calcium-dependent protein kinase C activity	0	0	-9999	-10000	0	0
CBL	-0.071	0.13	-9999	-0.33	61	61
negative regulation of mast cell degranulation	-0.054	0.11	-9999	-0.36	11	11
BTK	-0.12	0.23	-9999	-0.51	83	83
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK	-0.1	0.18	-9999	-0.44	80	80
GAB2/PI3K/SHP2	-0.058	0.08	-9999	-0.35	1	1
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP	-0.076	0.14	-9999	-0.36	61	61
RAF1	0.023	0.021	-9999	-10000	0	0
Fc epsilon R1/FcgammaRIIB/SHIP	-0.073	0.14	-9999	-0.43	23	23
FCER1G	0.013	0.03	-9999	-0.33	3	3
FCER1A	-0.093	0.16	-9999	-0.33	127	127
Antigen/IgE/Fc epsilon R1/Fyn	-0.061	0.11	-9999	-0.28	61	61
MAPK3	0.029	0.018	-9999	-10000	0	0
MAPK1	0.029	0.018	-9999	-10000	0	0
NFKB1	0.012	0	-9999	-10000	0	0
MAPK8	-0.013	0.064	-9999	-0.46	2	2
DUSP1	0.01	0.023	-9999	-0.32	2	2
NF-kappa-B/RelA	-0.046	0.059	-9999	-0.21	5	5
actin cytoskeleton reorganization	-0.083	0.16	-9999	-0.38	61	61
mol:Glucocorticoid Dexamethasone	0	0	-9999	-10000	0	0
PI3K	-0.069	0.15	-9999	-0.45	25	25
FER	-0.071	0.13	-9999	-0.33	62	62
RELA	0.012	0	-9999	-10000	0	0
ITK	-0.02	0.072	-9999	-0.36	13	13
SOS1	0.012	0	-9999	-10000	0	0
PLCG1	-0.099	0.2	-9999	-0.44	79	79
cytokine secretion	-0.034	0.043	-9999	-10000	0	0
SPHK1	-0.1	0.16	-9999	-0.37	88	88
PTK2	-0.086	0.16	-9999	-0.4	61	61
NTAL/PLCgamma1/GRB2/SLP76/GADs	-0.12	0.16	-9999	-0.42	66	66
EDG1	0	0	-9999	-10000	0	0
mol:DAG	-0.081	0.17	-9999	-0.39	66	66
MAP2K2	0.026	0.018	-9999	-10000	0	0
MAP2K1	0.026	0.018	-9999	-10000	0	0
MAP2K7	0.011	0.016	-9999	-0.32	1	1
KLRG1/SHP2	-0.053	0.11	-9999	-0.38	8	8
MAP2K4	0.009	0.064	-9999	-0.91	2	2
Fc epsilon R1/FcgammaRIIB	-0.085	0.15	-9999	-0.34	80	80
mol:Choline	-0.053	0.1	-9999	-0.38	3	3
SHC/Grb2/SOS1	-0.056	0.13	-9999	-0.39	11	11
FYN	0.012	0	-9999	-10000	0	0
DOK1	0.012	0	-9999	-10000	0	0
PXN	-0.076	0.15	-9999	-0.47	12	12
HCLS1	-0.071	0.14	-9999	-0.34	61	61
PRKCB	-0.084	0.16	-9999	-0.35	84	84
FCGR2B	-0.026	0.1	-9999	-0.32	47	47
IGHE	-0.001	0.004	-9999	-10000	0	0
KLRG1/SHIP	-0.055	0.12	-9999	-0.37	11	11
LCP2	0.009	0.028	-9999	-0.32	3	3
PLA2G4A	-0.087	0.15	-9999	-0.34	89	89
RASA1	0.012	0.001	-9999	-10000	0	0
mol:Phosphatidic acid	-0.053	0.1	-9999	-0.38	3	3
IKK complex	-0.032	0.091	-9999	-0.23	24	24
WIPF1	0.011	0.016	-9999	-0.32	1	1

×

Glucocorticoid receptor regulatory network

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
PCK2	0.014	0.061	0.29	2	-10000	0	2
SMARCC2	0.012	0.007	-10000	0	-10000	0	0
SMARCC1	0.012	0.008	-10000	0	-10000	0	0
TBX21	-0.094	0.15	-10000	0	-0.64	18	18
SUMO2	0.012	0.005	-10000	0	-10000	0	0
STAT1 (dimer)	0.015	0.049	-10000	0	-0.7	2	2
FKBP4	0.01	0.035	-10000	0	-0.71	1	1
FKBP5	0.011	0.016	-10000	0	-0.32	1	1
GR alpha/HSP90/FKBP51/HSP90	0.097	0.094	0.28	14	-0.29	3	17
PRL	-0.074	0.13	-10000	0	-0.63	12	12
cortisol/GR alpha (dimer)/TIF2	0.23	0.2	0.52	65	-0.49	2	67
RELA	-0.052	0.075	-10000	0	-10000	0	0
FGG	0.12	0.24	0.45	34	-0.51	32	66
GR beta/TIF2	0.098	0.11	0.31	14	-0.35	3	17
IFNG	-0.32	0.26	-10000	0	-0.76	77	77
apoptosis	0.004	0.14	0.49	7	-0.57	3	10
CREB1	0.007	0.039	-10000	0	-10000	0	0
histone acetylation	-0.049	0.096	0.31	1	-0.32	9	10
BGLAP	-0.068	0.11	-10000	0	-0.51	4	4
GR/PKAc	0.071	0.11	0.31	4	-0.33	6	10
NF kappa B1 p50/RelA	-0.093	0.13	-10000	0	-0.36	21	21
SMARCD1	0.012	0.008	-10000	0	-10000	0	0
MDM2	0.083	0.068	0.24	21	-10000	0	21
GATA3	0.01	0.049	-10000	0	-0.42	4	4
AKT1	0.006	0.001	-10000	0	-10000	0	0
CSF2	-0.2	0.21	-10000	0	-0.46	125	125
GSK3B	0.012	0.005	-10000	0	-10000	0	0
NR1I3	0.011	0.14	0.47	7	-0.74	4	11
CSN2	0.13	0.13	0.39	21	-0.45	2	23
BRG1/BAF155/BAF170/BAF60A	0.033	0.025	-10000	0	-10000	0	0
NFATC1	0.01	0.033	-10000	0	-0.32	4	4
POU2F1	0.011	0.022	-10000	0	-10000	0	0
CDKN1A	0.029	0.011	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
response to UV	0	0.006	-10000	0	-10000	0	0
SFN	0.011	0.016	-10000	0	-0.32	1	1
GR alpha/HSP90/FKBP51/HSP90/14-3-3	0.1	0.088	0.3	6	-0.28	1	7
prolactin receptor activity	0	0	-10000	0	-10000	0	0
EGR1	0.013	0.13	0.45	7	-0.66	2	9
JUN	-0.25	0.16	-10000	0	-0.52	57	57
IL4	-0.081	0.1	-10000	0	-0.43	3	3
CDK5R1	0.01	0.035	-10000	0	-0.7	1	1
PRKACA	0.012	0	-10000	0	-10000	0	0
cortisol/GR alpha (monomer)/AP-1	-0.28	0.25	-10000	0	-0.57	120	120
GR alpha/HSP90/FKBP51/HSP90/PP5C	0.1	0.088	0.3	6	-0.28	1	7
cortisol/GR alpha (monomer)	0.26	0.23	0.59	77	-0.57	2	79
NCOA2	0.011	0.016	-10000	0	-0.32	1	1
response to hypoxia	0	0	-10000	0	-10000	0	0
FOS	-0.091	0.061	-10000	0	-0.39	7	7
AP-1/NFAT1-c-4	-0.43	0.27	-10000	0	-0.75	123	123
AFP	-0.19	0.17	-10000	0	-0.7	23	23
SUV420H1	0.012	0	-10000	0	-10000	0	0
IRF1	0.13	0.12	0.39	17	-10000	0	17
TP53	0.029	0	-10000	0	-10000	0	0
PPP5C	0.012	0	-10000	0	-10000	0	0
KRT17	-0.54	0.31	-10000	0	-0.73	271	271
KRT14	-0.12	0.18	-10000	0	-0.71	22	22
TBP	0.019	0.009	-10000	0	-10000	0	0
CREBBP	0.036	0.058	-10000	0	-10000	0	0
HDAC1	0.011	0.009	-10000	0	-10000	0	0
HDAC2	0.03	0.023	-10000	0	-10000	0	0
AP-1	-0.44	0.28	-10000	0	-0.75	125	125
MAPK14	0.012	0.005	-10000	0	-10000	0	0
MAPK10	-0.041	0.12	-10000	0	-0.32	66	66
MAPK11	0.008	0.05	-10000	0	-0.71	2	2
KRT5	-0.34	0.3	-10000	0	-0.8	100	100
interleukin-1 receptor activity	0.018	0.023	-10000	0	-10000	0	0
NCOA1	0.014	0.001	-10000	0	-10000	0	0
STAT1	0.015	0.049	-10000	0	-0.7	2	2
CGA	-0.091	0.14	-10000	0	-0.59	14	14
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2	0.16	0.18	0.37	127	-0.4	4	131
MAPK3	0.012	0.006	-10000	0	-10000	0	0
MAPK1	0.012	0.005	-10000	0	-10000	0	0
ICAM1	-0.16	0.18	-10000	0	-0.55	34	34
NFKB1	-0.052	0.075	-10000	0	-10000	0	0
MAPK8	-0.18	0.14	-10000	0	-0.43	42	42
MAPK9	0.012	0.005	-10000	0	-10000	0	0
cortisol/GR alpha (dimer)	0.001	0.14	0.5	7	-0.6	3	10
BAX	0.029	0.011	-10000	0	-10000	0	0
POMC	-0.12	0.24	-10000	0	-1.3	13	13
EP300	0.038	0.06	-10000	0	-10000	0	0
cortisol/GR alpha (dimer)/p53	0.24	0.2	0.55	55	-0.48	2	57
proteasomal ubiquitin-dependent protein catabolic process	0.06	0.053	0.23	3	-10000	0	3
SGK1	0.062	0.19	-10000	0	-1.2	8	8
IL13	-0.21	0.18	-10000	0	-0.72	22	22
IL6	-0.18	0.23	-10000	0	-0.64	57	57
PRKACG	0.002	0.035	-10000	0	-0.71	1	1
IL5	-0.18	0.15	-10000	0	-0.74	9	9
IL2	-0.28	0.19	-10000	0	-0.64	46	46
CDK5	0.012	0.003	-10000	0	-10000	0	0
PRKACB	-0.026	0.11	-10000	0	-0.32	48	48
HSP90AA1	0.012	0	-10000	0	-10000	0	0
IL8	-0.36	0.32	-10000	0	-0.62	235	235
CDK5R1/CDK5	0.016	0.027	-10000	0	-0.52	1	1
NF kappa B1 p50/RelA/PKAc	-0.067	0.11	-10000	0	-0.48	2	2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90	0.23	0.18	0.5	59	-0.45	2	61
SMARCA4	0.012	0.007	-10000	0	-10000	0	0
chromatin remodeling	0.14	0.14	0.35	39	-0.43	8	47
NF kappa B1 p50/RelA/Cbp	-0.027	0.12	0.35	3	-0.46	2	5
JUN (dimer)	-0.25	0.16	-10000	0	-0.52	57	57
YWHAH	0.012	0	-10000	0	-10000	0	0
VIPR1	-0.088	0.14	-10000	0	-0.6	17	17
NR3C1	0.13	0.15	0.39	45	-0.36	12	57
NR4A1	-0.005	0.12	-10000	0	-0.56	16	16
TIF2/SUV420H1	0.017	0.011	-10000	0	-10000	0	0
MAPKKK cascade	0.004	0.14	0.49	7	-0.57	3	10
cortisol/GR alpha (dimer)/Src-1	0.24	0.2	0.52	71	-0.49	2	73
PBX1	0	0.063	-10000	0	-0.32	14	14
POU1F1	-0.001	0.047	-10000	0	-0.85	1	1
SELE	-0.22	0.29	-10000	0	-0.74	84	84
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A	0.14	0.14	0.35	39	-0.44	8	47
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90	0.23	0.18	0.5	59	-0.45	2	61
mol:cortisol	0.14	0.13	0.33	87	-0.2	1	88
MMP1	-0.42	0.27	-10000	0	-0.61	275	275

×

Calcium signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC1	-0.01	0.036	-9999	-10000	0	0
NFATC2	-0.013	0.043	-9999	-0.21	9	9
NFATC3	-0.008	0.032	-9999	-10000	0	0
CD40LG	-0.13	0.22	-9999	-0.55	47	47
PTGS2	-0.13	0.22	-9999	-0.58	39	39
JUNB	0.01	0.023	-9999	-0.32	2	2
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.007	0.02	-9999	-10000	0	0
CaM/Ca2+	-0.007	0.02	-9999	-10000	0	0
CALM1	0.003	0.012	-9999	-10000	0	0
JUN	0.003	0.012	-9999	-10000	0	0
mol:Ca2+	-0.011	0.013	-9999	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0.003	0.007	-9999	-10000	0	0
FOSL1	-0.32	0.36	-9999	-0.71	190	190
CREM	0.012	0	-9999	-10000	0	0
Jun/NFAT1-c-4/p21SNFT	-0.063	0.14	-9999	-0.56	7	7
FOS	-0.003	0.043	-9999	-0.32	7	7
IFNG	-0.16	0.27	-9999	-0.68	58	58
AP-1/NFAT1-c-4	-0.14	0.24	-9999	-0.62	39	39
FASLG	-0.12	0.22	-9999	-0.56	41	41
NFAT1-c-4/ICER1	-0.031	0.08	-9999	-0.37	1	1
IL2RA	-0.12	0.2	-9999	-0.54	38	38
FKBP12/FK506	0.009	0	-9999	-10000	0	0
CSF2	-0.25	0.34	-9999	-0.62	177	177
JunB/Fra1/NFAT1-c-4	-0.2	0.21	-9999	-0.42	191	191
IL4	-0.12	0.2	-9999	-0.53	37	37
IL2	-0.007	0.011	-9999	-10000	0	0
IL3	-0.017	0.017	-9999	-10000	0	0
FKBP1A	0.012	0	-9999	-10000	0	0
BATF3	0.002	0.08	-9999	-0.64	6	6
mol:FK506	0	0	-9999	-10000	0	0
POU2F1	0.012	0.001	-9999	-10000	0	0

×

Presenilin action in Notch and Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved)	0.024	0.018	-10000	0	-10000	0	0
HDAC1	0.009	0.004	-10000	0	-10000	0	0
AES	0.011	0.001	-10000	0	-10000	0	0
FBXW11	0.012	0	-10000	0	-10000	0	0
DTX1	0.009	0.028	-10000	0	-0.32	3	3
LRP6/FZD1	0.017	0.011	-10000	0	-10000	0	0
TLE1	0.011	0.016	-10000	0	-0.32	1	1
AP1	-0.12	0.14	-10000	0	-0.24	227	227
NCSTN	0.012	0	-10000	0	-10000	0	0
ADAM10	0.012	0	-10000	0	-10000	0	0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4	0.05	0.032	-10000	0	-10000	0	0
NICD/RBPSUH	0.027	0.013	-10000	0	-10000	0	0
WIF1	-0.14	0.29	-10000	0	-0.71	86	86
NOTCH1	0	0.013	-10000	0	-10000	0	0
PSENEN	0.011	0.016	-10000	0	-0.32	1	1
KREMEN2	-0.093	0.25	-10000	0	-0.71	61	61
DKK1	-0.13	0.29	-10000	0	-0.71	83	83
beta catenin/beta TrCP1	0.1	0.08	0.22	1	-10000	0	1
APH1B	0.012	0.001	-10000	0	-10000	0	0
APH1A	0.012	0	-10000	0	-10000	0	0
AXIN1	-0.033	0.039	-10000	0	-0.39	1	1
CtBP/CBP/TCF1/TLE1/AES	0.018	0.019	-10000	0	-10000	0	0
PSEN1	0.012	0	-10000	0	-10000	0	0
FOS	0.006	0.043	-10000	0	-0.32	7	7
JUN	0.012	0	-10000	0	-10000	0	0
MAP3K7	0.011	0.002	-10000	0	-10000	0	0
CTNNB1	0.1	0.086	0.19	154	-10000	0	154
MAPK3	0.012	0	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	-0.078	0.2	-10000	0	-0.46	86	86
HNF1A	0.01	0.016	-10000	0	-0.32	1	1
CTBP1	0.011	0.001	-10000	0	-10000	0	0
MYC	0.018	0.052	-10000	0	-0.5	4	4
NKD1	-0.38	0.36	-10000	0	-0.71	229	229
FZD1	0.011	0.016	-10000	0	-0.32	1	1
NOTCH1 precursor/Deltex homolog 1	0.027	0.013	-10000	0	-10000	0	0
apoptosis	-0.12	0.14	-10000	0	-0.24	227	227
Delta 1/NOTCHprecursor	0.027	0.013	-10000	0	-10000	0	0
DLL1	0.009	0.028	-10000	0	-0.32	3	3
PPARD	0.022	0.01	-10000	0	-10000	0	0
Gamma Secretase	0.036	0.008	-10000	0	-10000	0	0
APC	-0.038	0.059	-10000	0	-0.4	7	7
DVL1	0.006	0.04	-10000	0	-0.3	1	1
CSNK2A1	0.012	0.001	-10000	0	-10000	0	0
MAP3K7IP1	-0.001	0.002	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	-0.14	0.25	-10000	0	-0.5	131	131
LRP6	0.012	0	-10000	0	-10000	0	0
CSNK1A1	0.012	0.001	-10000	0	-10000	0	0
NLK	0.011	0.004	-10000	0	-10000	0	0
CCND1	0.015	0.063	-10000	0	-0.5	6	6
WNT1	0.001	0.07	-10000	0	-0.71	4	4
Axin1/APC/beta catenin	0.056	0.049	-10000	0	-0.35	1	1
DKK2	-0.037	0.18	-10000	0	-0.67	30	30
NOTCH1 precursor/DVL1	0.015	0.033	-10000	0	-10000	0	0
GSK3B	0.012	0.001	-10000	0	-10000	0	0
FRAT1	0.011	0.001	-10000	0	-10000	0	0
NOTCH/Deltex homolog 1	0.024	0.018	-10000	0	-10000	0	0
PPP2R5D	0.17	0.15	0.3	229	-10000	0	229
MAPK1	0.012	0	-10000	0	-10000	0	0
WNT1/LRP6/FZD1	-0.069	0.18	-10000	0	-0.42	89	89
RBPJ	0.012	0	-10000	0	-10000	0	0
CREBBP	0.014	0.002	-10000	0	-10000	0	0

×

Effects of Botulinum toxin

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
STX1A	-0.015	0.11	-9999	-0.54	18	18
UniProt:P19321	0	0	-9999	-10000	0	0
RIMS1/UNC13B	0.009	0.053	-9999	-0.53	4	4
STXBP1	0.012	0	-9999	-10000	0	0
ACh/CHRNA1	-0.04	0.064	-9999	-0.24	23	23
RAB3GAP2/RIMS1/UNC13B	0.016	0.047	-9999	-0.46	4	4
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	0.001	0.07	-9999	-0.71	4	4
mol:ACh	-0.048	0.053	-9999	-0.096	220	220
RAB3GAP2	0.011	0.016	-9999	-0.32	1	1
STX1A/SNAP25/VAMP2	-0.063	0.087	-9999	-0.36	22	22
UniProt:P10844	0	0	-9999	-10000	0	0
muscle contraction	-0.04	0.064	-9999	-0.24	23	23
UNC13B	0.012	0	-9999	-10000	0	0
CHRNA1	-0.008	0.082	-9999	-0.34	23	23
UniProt:P10845	0	0	-9999	-10000	0	0
ACh/Synaptotagmin 1	-0.057	0.083	-9999	-0.23	62	62
SNAP25	-0.11	0.11	-9999	-0.22	208	208
VAMP2	0.005	0	-9999	-10000	0	0
SYT1	-0.037	0.12	-9999	-0.32	62	62
UniProt:Q00496	0	0	-9999	-10000	0	0
STXIA/STXBP1	-0.005	0.097	-9999	-0.46	18	18
STX1A/SNAP25 fragment 1/VAMP2	-0.063	0.087	-9999	-0.36	22	22

×

Syndecan-2-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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Syndecan-2/Fibronectin	-0.001	0.093	-9999	-0.45	16	16
EPHB2	0.008	0.05	-9999	-0.71	2	2
Syndecan-2/TACI	-0.057	0.094	-9999	-0.34	3	3
LAMA1	-0.059	0.14	-9999	-0.32	89	89
Syndecan-2/alpha2 ITGB1	0.028	0.04	-9999	-0.39	3	3
HRAS	0.011	0.016	-9999	-0.32	1	1
Syndecan-2/CASK	0.01	0.018	-9999	-10000	0	0
ITGA5	0.012	0	-9999	-10000	0	0
BAX	0.029	0.003	-9999	-10000	0	0
EPB41	0.012	0	-9999	-10000	0	0
positive regulation of cell-cell adhesion	0.016	0.02	-9999	-10000	0	0
LAMA3	0.005	0.065	-9999	-0.55	5	5
EZR	0.012	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
CAV2	0.007	0.055	-9999	-0.51	4	4
Syndecan-2/MMP2	0.017	0.033	-9999	-0.4	2	2
RP11-540L11.1	0	0	-9999	-10000	0	0
alpha2 ITGB1	0.018	0	-9999	-10000	0	0
dendrite morphogenesis	0.016	0.037	-9999	-0.45	2	2
Syndecan-2/GM-CSF	-0.18	0.23	-9999	-0.46	174	174
determination of left/right symmetry	0.013	0.022	-9999	-0.21	4	4
Syndecan-2/PKC delta	0.018	0.018	-9999	-10000	0	0
GNB2L1	0.012	0	-9999	-10000	0	0
MAPK3	-0.16	0.21	-9999	-0.41	174	174
MAPK1	-0.16	0.21	-9999	-0.41	174	174
Syndecan-2/RACK1	0.023	0.017	-9999	-10000	0	0
NF1	0.012	0	-9999	-10000	0	0
FGFR/FGF/Syndecan-2	0.013	0.022	-9999	-0.21	4	4
ITGA2	0.012	0	-9999	-10000	0	0
MAPK8	0.023	0.018	-9999	-10000	0	0
Syndecan-2/alpha2/beta1 Integrin	-0.003	0.07	-9999	-0.28	2	2
Syndecan-2/Kininogen	-0.021	0.078	-9999	-0.34	2	2
ITGB1	0.012	0	-9999	-10000	0	0
SRC	0.025	0.016	-9999	-10000	0	0
Syndecan-2/CASK/Protein 4.1	0.017	0.016	-9999	-10000	0	0
extracellular matrix organization	0.017	0.029	-9999	-0.45	1	1
actin cytoskeleton reorganization	-0.001	0.092	-9999	-0.45	16	16
Syndecan-2/Caveolin-2/Ras	0.022	0.039	-9999	-0.38	3	3
Syndecan-2/Laminin alpha3	0.014	0.046	-9999	-0.46	3	3
Syndecan-2/RasGAP	0.028	0.017	-9999	-10000	0	0
alpha5/beta1 Integrin	0.018	0	-9999	-10000	0	0
PRKCD	0.012	0	-9999	-10000	0	0
Syndecan-2 dimer	0.016	0.037	-9999	-0.46	2	2
GO:0007205	0.003	0	-9999	-10000	0	0
DNA mediated transformation	0	0	-9999	-10000	0	0
Syndecan-2/RasGAP/Src	0.033	0.016	-9999	-10000	0	0
RHOA	0.012	0	-9999	-10000	0	0
SDCBP	0.01	0.023	-9999	-0.32	2	2
TNFRSF13B	-0.12	0.16	-9999	-0.32	164	164
RASA1	0.012	0.001	-9999	-10000	0	0
alpha2/beta1 Integrin	0.018	0	-9999	-10000	0	0
Syndecan-2/Synbindin	0.018	0.018	-9999	-10000	0	0
TGFB1	0.01	0.035	-9999	-0.71	1	1
CASP3	0.023	0.016	-9999	-10000	0	0
FN1	-0.018	0.14	-9999	-0.61	20	20
Syndecan-2/IL8	-0.25	0.24	-9999	-0.46	233	233
SDC2	0.013	0.022	-9999	-0.21	4	4
KNG1	-0.058	0.13	-9999	-0.32	84	84
Syndecan-2/Neurofibromin	0.018	0.018	-9999	-10000	0	0
TRAPPC4	0.012	0	-9999	-10000	0	0
CSF2	-0.29	0.35	-9999	-0.71	174	174
Syndecan-2/TGFB1	0.017	0.03	-9999	-0.46	1	1
Syndecan-2/Syntenin/PI-4-5-P2	0.016	0.02	-9999	-10000	0	0
Syndecan-2/Ezrin	0.025	0.017	-9999	-10000	0	0
PRKACA	0.023	0.016	-9999	-10000	0	0
angiogenesis	-0.25	0.23	-9999	-0.45	233	233
MMP2	0.009	0.039	-9999	-0.51	2	2
IL8	-0.39	0.36	-9999	-0.71	233	233
calcineurin-NFAT signaling pathway	-0.057	0.094	-9999	-0.34	3	3

×

HIF-1-alpha transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PKM2	-0.4	0.31	-9999	-1	35	35
HDAC7	0.012	0.004	-9999	-10000	0	0
HIF1A/ARNT/Cbp/p300/Src-1	-0.3	0.25	-9999	-0.88	20	20
SMAD4	0.013	0	-9999	-10000	0	0
ID2	-0.4	0.31	-9999	-1	34	34
AP1	0.015	0.03	-9999	-10000	0	0
ABCG2	-0.5	0.34	-9999	-1	66	66
HIF1A	-0.066	0.047	-9999	-10000	0	0
TFF3	-0.4	0.32	-9999	-1	32	32
GATA2	0.006	0.048	-9999	-0.32	9	9
AKT1	-0.065	0.053	-9999	-10000	0	0
response to hypoxia	-0.079	0.054	-9999	-0.24	1	1
MCL1	-0.4	0.31	-9999	-1	34	34
NDRG1	-0.4	0.31	-9999	-1	36	36
SERPINE1	-0.45	0.37	-9999	-1.1	69	69
FECH	-0.4	0.31	-9999	-1	32	32
FURIN	-0.4	0.31	-9999	-1	34	34
NCOA2	0.012	0.016	-9999	-0.32	1	1
EP300	-0.063	0.069	-9999	-0.35	8	8
HMOX1	-0.4	0.31	-9999	-1	32	32
BHLHE40	-0.4	0.32	-9999	-1	35	35
BHLHE41	-0.4	0.32	-9999	-1	34	34
HIF1A/ARNT/SMAD3/SMAD4/SP1	-0.057	0.061	-9999	-10000	0	0
ENG	-0.045	0.06	-9999	-10000	0	0
JUN	0.013	0.001	-9999	-10000	0	0
RORA	-0.4	0.32	-9999	-1	32	32
ABCB1	-0.26	0.39	-9999	-1.1	72	72
TFRC	-0.4	0.31	-9999	-1	35	35
CXCR4	-0.4	0.31	-9999	-1	35	35
TF	-0.42	0.34	-9999	-1.1	41	41
CITED2	-0.4	0.31	-9999	-1	32	32
HIF1A/ARNT	-0.43	0.37	-9999	-1.1	38	38
LDHA	-0.052	0.04	-9999	-10000	0	0
ETS1	-0.4	0.31	-9999	-1	34	34
PGK1	-0.4	0.31	-9999	-1	35	35
NOS2	-0.41	0.33	-9999	-1.1	40	40
ITGB2	-0.4	0.31	-9999	-1	34	34
ALDOA	-0.4	0.31	-9999	-1	32	32
Cbp/p300/CITED2	-0.38	0.32	-9999	-1.1	25	25
FOS	0.007	0.043	-9999	-0.32	7	7
HK2	-0.4	0.31	-9999	-1	32	32
SP1	0.011	0.023	-9999	-10000	0	0
GCK	-0.11	0.2	-9999	-1.2	10	10
HK1	-0.4	0.31	-9999	-1	34	34
NPM1	-0.4	0.31	-9999	-1	36	36
EGLN1	-0.4	0.31	-9999	-1	33	33
CREB1	0.018	0	-9999	-10000	0	0
PGM1	-0.4	0.31	-9999	-1	34	34
SMAD3	0.013	0	-9999	-10000	0	0
EDN1	-0.046	0.097	-9999	-0.63	2	2
IGFBP1	-0.46	0.38	-9999	-1.1	66	66
VEGFA	-0.27	0.24	-9999	-0.82	20	20
HIF1A/JAB1	-0.033	0.03	-9999	-10000	0	0
CP	-0.46	0.34	-9999	-1.1	46	46
CXCL12	-0.42	0.34	-9999	-1	43	43
COPS5	0.012	0.001	-9999	-10000	0	0
SMAD3/SMAD4	0.019	0	-9999	-10000	0	0
BNIP3	-0.4	0.32	-9999	-1	34	34
EGLN3	-0.4	0.31	-9999	-1	33	33
CA9	-0.7	0.36	-9999	-1.1	141	141
TERT	-0.43	0.36	-9999	-1.1	49	49
ENO1	-0.4	0.31	-9999	-1	34	34
PFKL	-0.4	0.31	-9999	-1	32	32
NCOA1	0.012	0	-9999	-10000	0	0
ADM	-0.4	0.31	-9999	-1	32	32
ARNT	-0.067	0.049	-9999	-0.36	1	1
HNF4A	0.013	0.012	-9999	-10000	0	0
ADFP	-0.4	0.31	-9999	-1	39	39
SLC2A1	-0.29	0.27	-9999	-0.91	32	32
LEP	-0.42	0.33	-9999	-1	46	46
HIF1A/ARNT/Cbp/p300	-0.32	0.26	-9999	-0.9	21	21
EPO	-0.22	0.18	-9999	-0.81	5	5
CREBBP	-0.063	0.069	-9999	-0.35	8	8
HIF1A/ARNT/Cbp/p300/HDAC7	-0.3	0.27	-9999	-0.94	21	21
PFKFB3	-0.4	0.31	-9999	-1	32	32
NT5E	-0.4	0.31	-9999	-1	36	36

×

Canonical Wnt signaling pathway

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
HDAC1	0.018	0.019	-10000	0	-10000	0	0
AES	0.017	0.016	-10000	0	-10000	0	0
FBXW11	0.012	0	-10000	0	-10000	0	0
mol:GTP	0	0.001	-10000	0	-10000	0	0
LRP6/FZD1	0.018	0.011	-10000	0	-10000	0	0
SMAD4	0.012	0	-10000	0	-10000	0	0
DKK2	-0.037	0.18	-10000	0	-0.67	30	30
TLE1	0.016	0.022	-10000	0	-0.3	1	1
MACF1	0.012	0	-10000	0	-10000	0	0
CTNNB1	0.063	0.091	0.23	21	-0.32	1	22
WIF1	-0.14	0.29	-10000	0	-0.71	86	86
beta catenin/RanBP3	0.052	0.13	0.3	68	-10000	0	68
KREMEN2	-0.093	0.25	-10000	0	-0.71	61	61
DKK1	-0.13	0.29	-10000	0	-0.71	83	83
beta catenin/beta TrCP1	0.066	0.086	0.23	16	-10000	0	16
FZD1	0.012	0.016	-10000	0	-0.32	1	1
AXIN2	-0.097	0.22	-10000	0	-0.51	91	91
AXIN1	0.012	0.016	-10000	0	-0.32	1	1
RAN	0.012	0.001	-10000	0	-10000	0	0
Axin1/APC/GSK3/beta catenin	0.029	0.042	-10000	0	-0.5	1	1
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4	0.043	0.08	-10000	0	-0.38	2	2
Axin1/APC/GSK3	0.088	0.062	0.2	1	-0.29	1	2
Axin1/APC/GSK3/beta catenin/Macf1	0.05	0.057	-10000	0	-0.33	1	1
HNF1A	0.016	0.023	-10000	0	-0.32	1	1
CTBP1	0.017	0.017	-10000	0	-10000	0	0
MYC	-0.012	0.076	-10000	0	-0.57	4	4
RANBP3	0.012	0.001	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	-0.078	0.2	-10000	0	-0.46	86	86
NKD1	-0.38	0.36	-10000	0	-0.71	229	229
TCF4	0.015	0.033	-10000	0	-0.32	3	3
TCF3	0.017	0.017	-10000	0	-10000	0	0
WNT1/LRP6/FZD1/Axin1	0.025	0.045	-10000	0	-0.41	4	4
Ran/GTP	0.009	0.002	-10000	0	-10000	0	0
CtBP/CBP/TCF/TLE1/AES	0.043	0.13	0.53	3	-10000	0	3
LEF1	-0.074	0.24	-10000	0	-0.7	53	53
DVL1	0.042	0.034	-10000	0	-0.23	1	1
CSNK2A1	0.012	0	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES	0.023	0.089	-10000	0	-0.44	2	2
DKK1/LRP6/Kremen 2	-0.14	0.25	-10000	0	-0.5	131	131
LRP6	0.012	0.001	-10000	0	-10000	0	0
CSNK1A1	0.018	0.019	-10000	0	-10000	0	0
NLK	0.011	0.003	-10000	0	-10000	0	0
CCND1	-0.014	0.082	-10000	0	-0.53	6	6
WNT1	0.002	0.07	-10000	0	-0.71	4	4
GSK3A	0.012	0.001	-10000	0	-10000	0	0
GSK3B	0.012	0.001	-10000	0	-10000	0	0
FRAT1	0.011	0	-10000	0	-10000	0	0
PPP2R5D	0.18	0.15	0.31	229	-10000	0	229
APC	0.024	0.042	-10000	0	-0.38	4	4
WNT1/LRP6/FZD1	0.06	0.077	0.21	85	-10000	0	85
CREBBP	0.017	0.017	-10000	0	-10000	0	0

×

Syndecan-3-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	0.012	0	-9999	-10000	0	0
Syndecan-3/Src/Cortactin	-0.003	0.063	-9999	-10000	0	0
Syndecan-3/Neurocan	0.008	0.029	-9999	-0.38	2	2
POMC	0	0.065	-9999	-0.35	13	13
EGFR	0.012	0	-9999	-10000	0	0
Syndecan-3/EGFR	0.021	0.002	-9999	-10000	0	0
AGRP	-0.001	0.06	-9999	-0.71	3	3
NCSTN	0.012	0	-9999	-10000	0	0
PSENEN	0.011	0.016	-9999	-0.32	1	1
RP11-540L11.1	0	0	-9999	-10000	0	0
APH1B	0.012	0.001	-9999	-10000	0	0
APH1A	0.012	0	-9999	-10000	0	0
NCAN	0.002	0.05	-9999	-0.71	2	2
long-term memory	0.027	0.002	-9999	-10000	0	0
Syndecan-3/IL8	-0.2	0.2	-9999	-0.38	233	233
PSEN1	0.012	0	-9999	-10000	0	0
Src/Cortactin	0.018	0	-9999	-10000	0	0
FYN	0.012	0	-9999	-10000	0	0
limb bud formation	0	0.001	-9999	-10000	0	0
MC4R	-0.009	0.091	-9999	-0.71	7	7
SRC	0.012	0	-9999	-10000	0	0
PTN	-0.07	0.14	-9999	-0.32	103	103
FGFR/FGF/Syndecan-3	0	0.001	-9999	-10000	0	0
neuron projection morphogenesis	-0.006	0.064	-9999	-0.34	2	2
Syndecan-3/AgRP	0.005	0.035	-9999	-0.38	3	3
Syndecan-3/AgRP/MC4R	0.002	0.065	-9999	-0.41	9	9
Fyn/Cortactin	0.018	0	-9999	-10000	0	0
SDC3	0	0.001	-9999	-10000	0	0
GO:0007205	0	0	-9999	-10000	0	0
positive regulation of leukocyte migration	-0.2	0.2	-9999	-0.38	233	233
IL8	-0.39	0.36	-9999	-0.71	233	233
Syndecan-3/Fyn/Cortactin	0.028	0.002	-9999	-10000	0	0
Syndecan-3/CASK	0	0.001	-9999	-10000	0	0
alpha-MSH/MC4R	-0.006	0.088	-9999	-0.59	7	7
Gamma Secretase	0.035	0.008	-9999	-10000	0	0

×

Visual signal transduction: Rods

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:K +	0.012	0	-9999	-10000	0	0
GNAT1/GTP	0	0	-9999	-10000	0	0
Metarhodopsin II/Arrestin	-0.001	0.039	-9999	-0.46	3	3
PDE6G/GNAT1/GTP	0	0.038	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
GNAT1	0	0	-9999	-10000	0	0
GRK1	-0.003	0.06	-9999	-0.71	3	3
CNG Channel	-0.1	0.11	-9999	-0.42	15	15
mol:Na +	-0.065	0.13	-9999	-0.42	42	42
mol:ADP	-0.003	0.06	-9999	-0.7	3	3
RGS9-1/Gbeta5/R9AP	-0.024	0.087	-9999	-0.46	2	2
mol:GDP	0	0	-9999	-10000	0	0
cGMP/CNG Channel	-0.051	0.15	-9999	-0.43	42	42
CNGB1	-0.045	0.12	-9999	-0.32	64	64
RDH5	-0.006	0.076	-9999	-0.32	23	23
SAG	0.002	0.005	-9999	-10000	0	0
mol:Ca2+	-0.043	0.14	-9999	-0.55	12	12
Na + (4 Units)	-0.06	0.12	-9999	-0.54	12	12
RGS9	-0.065	0.14	-9999	-0.32	97	97
GNB1/GNGT1	-0.12	0.23	-9999	-0.53	102	102
GNAT1/GDP	-0.019	0.073	-9999	-0.39	2	2
GUCY2D	-0.031	0.16	-9999	-0.71	23	23
GNGT1	-0.17	0.31	-9999	-0.71	102	102
GUCY2F	-0.001	0.035	-9999	-0.71	1	1
GNB5	0.012	0	-9999	-10000	0	0
mol:GMP (4 units)	-0.079	0.096	-9999	-0.39	4	4
mol:11-cis-retinal	-0.006	0.076	-9999	-0.32	23	23
mol:cGMP	-0.029	0.14	-9999	-0.43	43	43
GNB1	0.012	0	-9999	-10000	0	0
Rhodopsin	-0.007	0.068	-9999	-0.53	3	3
SLC24A1	0.012	0	-9999	-10000	0	0
CNGA1	-0.007	0.076	-9999	-0.32	23	23
Metarhodopsin II	-0.004	0.058	-9999	-0.5	5	5
mol:Ca ++	0	0	-9999	-10000	0	0
GC1/GCAP Family	-0.029	0.14	-9999	-0.45	43	43
RGS9BP	0.007	0.05	-9999	-0.71	2	2
Metarhodopsin II/Transducin	-0.051	0.1	-9999	-0.23	103	103
GCAP Family/Ca ++	-0.011	0.1	-9999	-0.42	23	23
PDE6A/B	-0.11	0.12	-9999	-0.42	13	13
mol:Pi	-0.024	0.086	-9999	-0.45	2	2
mol:all-trans-retinal	0	0	-9999	-10000	0	0
Transducin	-0.094	0.19	-9999	-0.42	102	102
PDE6B	-0.003	0.072	-9999	-0.34	17	17
PDE6A	-0.16	0.16	-9999	-0.32	222	222
PDE6G	-0.003	0.067	-9999	-0.32	18	18
RHO	-0.004	0.06	-9999	-0.71	3	3
PDE6	-0.097	0.12	-9999	-0.42	15	15
GUCA1A	-0.026	0.15	-9999	-0.71	20	20
GC2/GCAP Family	-0.011	0.1	-9999	-0.44	23	23
GUCA1C	0	0	-9999	-10000	0	0
GUCA1B	0.007	0.061	-9999	-0.71	3	3

×

Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Noncanonical Wnts/FZD	-0.051	0.13	-9999	-0.42	18	18
FZD6	0.012	0	-9999	-10000	0	0
WNT6	-0.027	0.14	-9999	-0.44	34	34
WNT4	-0.004	0.084	-9999	-0.39	17	17
FZD3	0.007	0.061	-9999	-0.71	3	3
WNT5A	0.006	0.063	-9999	-0.61	4	4
WNT11	-0.14	0.29	-9999	-0.67	91	91

×

p75(NTR)-mediated signaling

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Sortilin/TRAF6	0.018	0	-9999	-10000	0	0
Necdin/E2F1	-0.007	0.099	-9999	-0.55	10	10
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E	-0.031	0.09	-9999	-0.43	1	1
NGF (dimer)/p75(NTR)/BEX1	-0.1	0.14	-9999	-0.36	60	60
NT-4/5 (dimer)/p75(NTR)	-0.09	0.15	-9999	-0.57	18	18
IKBKB	0.012	0	-9999	-10000	0	0
AKT1	-0.034	0.085	-9999	-10000	0	0
IKBKG	0.011	0.016	-9999	-0.32	1	1
BDNF	0	0.092	-9999	-0.71	7	7
MGDIs/NGR/p75(NTR)/LINGO1	-0.082	0.16	-9999	-0.52	34	34
FURIN	0.011	0.016	-9999	-0.32	1	1
proBDNF (dimer)/p75(NTR)/Sortilin	-0.051	0.11	-9999	-0.48	7	7
LINGO1	-0.021	0.15	-9999	-0.71	19	19
Sortilin/TRAF6/NRIF	-0.001	0.011	-9999	-10000	0	0
proBDNF (dimer)	0	0.092	-9999	-0.7	7	7
NTRK1	0.003	0.072	-9999	-0.63	5	5
RTN4R	-0.016	0.14	-9999	-0.68	17	17
neuron apoptosis	-0.047	0.12	-9999	-0.4	9	9
IRAK1	0.012	0	-9999	-10000	0	0
SHC1	-0.054	0.1	-9999	-0.34	11	11
ARHGDIA	0.011	0.016	-9999	-0.32	1	1
RhoA/GTP	0.009	0	-9999	-10000	0	0
Gamma Secretase	0.035	0.008	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1	-0.042	0.095	-9999	-0.32	11	11
MAGEH1	0.007	0.04	-9999	-0.32	6	6
proNGF (dimer)/p75(NTR)/Sortilin/Necdin	-0.048	0.11	-9999	-0.31	26	26
Mammalian IAPs/DIABLO	0.027	0.031	-9999	-0.41	1	1
proNGF (dimer)	-0.006	0.072	-9999	-0.32	21	21
MAGED1	0.012	0	-9999	-10000	0	0
APP	0.012	0	-9999	-10000	0	0
NT-4/5 (dimer)	-0.026	0.14	-9999	-0.7	18	18
ZNF274	0.009	0.032	-9999	-0.32	4	4
RhoA/GDP/RHOGDI	-0.038	0.086	-9999	-10000	0	0
NGF	-0.006	0.072	-9999	-0.32	21	21
cell cycle arrest	-0.016	0.085	-9999	-10000	0	0
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK	-0.047	0.1	-9999	-0.34	11	11
NT-4/5 (dimer)/p75(NTR)/TRAF6	-0.067	0.13	-9999	-0.49	18	18
NCSTN	0.012	0	-9999	-10000	0	0
mol:GTP	-0.073	0.12	-9999	-0.35	29	29
PSENEN	0.011	0.016	-9999	-0.32	1	1
mol:ceramide	-0.042	0.09	-9999	-0.3	11	11
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs	-0.035	0.092	-9999	-0.3	11	11
p75(NTR)/beta APP	-0.062	0.11	-9999	-10000	0	0
BEX1	-0.081	0.15	-9999	-0.32	113	113
mol:GDP	-0.061	0.1	-9999	-0.34	11	11
NGF (dimer)	-0.49	0.18	-9999	-0.51	404	404
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI	-0.067	0.15	-9999	-0.48	33	33
PIK3R1	0.012	0	-9999	-10000	0	0
RAC1/GTP	-0.043	0.086	-9999	-0.29	11	11
MYD88	0.012	0	-9999	-10000	0	0
CHUK	0.012	0	-9999	-10000	0	0
NGF (dimer)/p75(NTR)/PKA	-0.073	0.12	-9999	-0.35	29	29
RHOB	0.012	0	-9999	-10000	0	0
RHOA	0.012	0	-9999	-10000	0	0
MAGE-G1/E2F1	0.005	0.084	-9999	-0.53	10	10
NT3 (dimer)	0.004	0.051	-9999	-0.32	10	10
TP53	-0.028	0.087	-9999	-0.38	7	7
PRDM4	-0.043	0.091	-9999	-0.3	11	11
BDNF (dimer)	-0.81	0.24	-9999	-0.82	414	414
PIK3CA	0.012	0.001	-9999	-10000	0	0
SORT1	0.012	0	-9999	-10000	0	0
activation of caspase activity	-0.032	0.088	-9999	-0.42	1	1
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.039	0.094	-9999	-0.3	11	11
RHOC	0.012	0	-9999	-10000	0	0
XIAP	0.012	0	-9999	-10000	0	0
MAPK10	-0.07	0.14	-9999	-0.37	41	41
DIABLO	0.012	0.001	-9999	-10000	0	0
SMPD2	-0.043	0.091	-9999	-0.3	11	11
APH1B	0.012	0.001	-9999	-10000	0	0
APH1A	0.012	0	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin	-0.052	0.1	-9999	-0.34	11	11
PSEN1	0.012	0	-9999	-10000	0	0
APAF-1/Pro-Caspase 9	0.018	0	-9999	-10000	0	0
NT3 (dimer)/p75(NTR)	-0.067	0.11	-9999	-0.4	4	4
MAPK8	-0.043	0.12	-9999	-0.46	1	1
MAPK9	-0.043	0.12	-9999	-0.46	1	1
APAF1	0.012	0.001	-9999	-10000	0	0
NTF3	0.004	0.051	-9999	-0.32	10	10
NTF4	-0.026	0.14	-9999	-0.71	18	18
NDN	-0.006	0.074	-9999	-0.32	22	22
RAC1/GDP	0.009	0	-9999	-10000	0	0
RhoA-B-C/GDP	-0.044	0.093	-9999	-0.4	2	2
p75 CTF/Sortilin/TRAF6/NRIF	0.029	0.017	-9999	-10000	0	0
RhoA-B-C/GTP	-0.073	0.12	-9999	-0.35	29	29
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.031	0.094	-9999	-0.41	7	7
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.038	0.098	-9999	-0.43	7	7
PRKACB	-0.026	0.11	-9999	-0.32	48	48
proBDNF (dimer)/p75 ECD	0.008	0.07	-9999	-0.53	7	7
ChemicalAbstracts:86-01-1	0	0	-9999	-10000	0	0
BIRC3	0.005	0.055	-9999	-0.37	8	8
BIRC2	0.012	0.001	-9999	-10000	0	0
neuron projection morphogenesis	-0.056	0.12	-9999	-0.34	12	12
BAD	-0.055	0.13	-9999	-0.39	7	7
RIPK2	0.012	0	-9999	-10000	0	0
NGFR	-0.1	0.16	-9999	-0.32	145	145
CYCS	-0.034	0.085	-9999	-10000	0	0
ADAM17	0.012	0	-9999	-10000	0	0
NGF (dimer)/p75(NTR)/TRAF6/RIP2	-0.039	0.094	-9999	-0.3	11	11
BCL2L11	-0.055	0.13	-9999	-0.39	7	7
BDNF (dimer)/p75(NTR)	-0.071	0.13	-9999	-0.56	7	7
PI3K	-0.039	0.094	-9999	-0.3	11	11
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1	-0.039	0.094	-9999	-10000	0	0
NDNL2	0.012	0.001	-9999	-10000	0	0
YWHAE	0.012	0	-9999	-10000	0	0
PRKCI	0.01	0.023	-9999	-0.32	2	2
NGF (dimer)/p75(NTR)	-0.073	0.12	-9999	-0.4	11	11
ChemicalAbstracts:146-91-8	0	0	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE	-0.039	0.094	-9999	-10000	0	0
TRAF6	0.012	0	-9999	-10000	0	0
RAC1	0.012	0	-9999	-10000	0	0
PRKCZ	0.012	0	-9999	-10000	0	0
PLG	-0.15	0.29	-9999	-0.71	89	89
oligodendrocyte cell fate commitment	0	0	-9999	-10000	0	0
CASP6	-0.054	0.11	-9999	-0.34	18	18
SQSTM1	0.012	0	-9999	-10000	0	0
NGFRAP1	0.011	0.016	-9999	-0.32	1	1
CASP3	-0.052	0.13	-9999	-0.37	7	7
E2F1	-0.005	0.11	-9999	-0.71	10	10
CASP9	0.012	0	-9999	-10000	0	0
IKK complex	-0.049	0.075	-9999	-0.44	2	2
NGF (dimer)/TRKA	-0.001	0.074	-9999	-0.51	5	5
MMP7	-0.68	0.14	-9999	-0.71	401	401
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.032	0.09	-9999	-10000	0	0
MMP3	-0.58	0.27	-9999	-0.71	346	346
APAF-1/Caspase 9	-0.036	0.052	-9999	-10000	0	0

×

Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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
FOXP3	-0.031	0.18	-10000	0	-0.76	24	24
NFATC2	-0.003	0.14	-10000	0	-0.59	7	7
NFATC3	-0.021	0.053	-10000	0	-10000	0	0
CD40LG	-0.29	0.33	-10000	0	-0.94	39	39
ITCH	0.035	0.014	-10000	0	-10000	0	0
CBLB	0.035	0.024	-10000	0	-0.41	1	1
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment	-0.15	0.25	-10000	0	-0.83	27	27
JUNB	0.01	0.023	-10000	0	-0.32	2	2
CaM/Ca2+/Calcineurin A alpha-beta B1	0.031	0.017	-10000	0	-10000	0	0
T cell anergy	0.034	0.041	-10000	0	-10000	0	0
TLE4	0.009	0.1	-10000	0	-0.53	5	5
Jun/NFAT1-c-4/p21SNFT	-0.14	0.24	-10000	0	-0.86	20	20
AP-1/NFAT1-c-4	-0.31	0.37	-10000	0	-0.92	58	58
IKZF1	-0.01	0.16	-10000	0	-0.58	26	26
T-helper 2 cell differentiation	-0.073	0.16	-10000	0	-0.62	17	17
AP-1/NFAT1	-0.066	0.11	-10000	0	-0.5	3	3
CALM1	0.023	0.01	-10000	0	-10000	0	0
EGR2	-0.049	0.22	-10000	0	-1.1	11	11
EGR3	-0.055	0.25	-10000	0	-1.1	16	16
NFAT1/FOXP3	-0.026	0.18	-10000	0	-0.61	27	27
EGR1	0.012	0.016	-10000	0	-0.32	1	1
JUN	-0.028	0.035	-10000	0	-10000	0	0
EGR4	-0.11	0.26	-10000	0	-0.7	68	68
mol:Ca2+	0.011	0.01	-10000	0	-10000	0	0
GBP3	-0.02	0.17	-10000	0	-0.55	34	34
FOSL1	-0.32	0.36	-10000	0	-0.71	190	190
NFAT1-c-4/MAF/IRF4	-0.093	0.23	-10000	0	-0.93	19	19
DGKA	0.01	0.096	-10000	0	-0.51	4	4
CREM	0.012	0	-10000	0	-10000	0	0
NFAT1-c-4/PPARG	-0.064	0.21	-10000	0	-0.87	16	16
CTLA4	-0.032	0.2	-10000	0	-0.6	35	35
NFAT1-c-4 (dimer)/EGR1	-0.061	0.21	-10000	0	-0.87	16	16
NFAT1-c-4 (dimer)/EGR4	-0.13	0.26	-10000	0	-0.88	21	21
FOS	-0.034	0.052	-10000	0	-0.33	7	7
IFNG	-0.1	0.22	-10000	0	-0.6	37	37
T cell activation	-0.09	0.14	-10000	0	-0.7	3	3
MAF	0.005	0.048	-10000	0	-0.32	9	9
T-helper 2 cell lineage commitment	0	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	0.048	0.18	0.78	15	-10000	0	15
TNF	-0.1	0.22	-10000	0	-0.82	17	17
FASLG	-0.1	0.33	-10000	0	-1.2	30	30
TBX21	-0.008	0.076	-10000	0	-0.35	15	15
BATF3	0.002	0.08	-10000	0	-0.64	6	6
PRKCQ	0.008	0.048	-10000	0	-0.42	4	4
PTPN1	0.011	0.094	-10000	0	-0.49	3	3
NFAT1-c-4/ICER1	-0.065	0.2	-10000	0	-0.87	16	16
GATA3	0.008	0.045	-10000	0	-0.42	4	4
T-helper 1 cell differentiation	-0.1	0.22	-10000	0	-0.6	37	37
IL2RA	-0.16	0.22	-10000	0	-0.75	29	29
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
CASP3	0.011	0.094	-10000	0	-0.49	3	3
E2F1	-0.001	0.11	-10000	0	-0.7	10	10
PPARG	0.011	0.016	-10000	0	-0.32	1	1
SLC3A2	0.011	0.094	-10000	0	-0.49	3	3
IRF4	-0.064	0.14	-10000	0	-0.32	96	96
PTGS2	-0.29	0.33	-10000	0	-0.92	39	39
CSF2	-0.42	0.44	-10000	0	-0.91	166	166
JunB/Fra1/NFAT1-c-4	-0.24	0.29	-10000	0	-0.86	31	31
IL4	-0.076	0.17	-10000	0	-0.67	15	15
IL5	-0.29	0.32	-10000	0	-0.91	39	39
IL2	-0.091	0.14	-10000	0	-0.71	3	3
IL3	-0.061	0.048	-10000	0	-10000	0	0
RNF128	0.034	0.024	-10000	0	-0.41	1	1
NFATC1	-0.048	0.18	-10000	0	-0.79	15	15
CDK4	0.029	0.12	0.58	5	-10000	0	5
PTPRK	0.011	0.094	-10000	0	-0.49	3	3
IL8	-0.47	0.44	-10000	0	-0.9	180	180
POU2F1	0.012	0.001	-10000	0	-10000	0	0

×

amb2 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2	0.011	0.059	-9999	-0.38	4	4
alphaM/beta2 Integrin/GPIbA	0.009	0.062	-9999	-0.37	5	5
alphaM/beta2 Integrin/proMMP-9	-0.045	0.16	-9999	-0.45	54	54
PLAUR	0.012	0	-9999	-10000	0	0
HMGB1	0.011	0.011	-9999	-10000	0	0
alphaM/beta2 Integrin/Talin	0.013	0.053	-9999	-0.36	3	3
AGER	0.009	0.039	-9999	-0.75	1	1
RAP1A	0.012	0	-9999	-10000	0	0
SELPLG	0.01	0.023	-9999	-0.32	2	2
mol:LDL	0	0	-9999	-10000	0	0
alphaM/beta2 Integrin/RAGE/HMGB1	0.02	0.074	-9999	-0.42	4	4
mol:GTP	0	0	-9999	-10000	0	0
MMP9	-0.075	0.23	-9999	-0.7	51	51
CYR61	0.012	0	-9999	-10000	0	0
TLN1	0.012	0	-9999	-10000	0	0
Rap1/GTP	-0.044	0.075	-9999	-0.31	14	14
RHOA	0.012	0	-9999	-10000	0	0
P-selectin oligomer	-0.034	0.11	-9999	-0.32	57	57
MYH2	-0.036	0.11	-9999	-0.39	20	20
MST1R	0.012	0	-9999	-10000	0	0
leukocyte activation during inflammatory response	-0.045	0.14	-9999	-0.4	44	44
APOB	-0.062	0.18	-9999	-0.44	66	66
mol:GDP	0	0	-9999	-10000	0	0
complement component iC3b receptor activity	0	0	-9999	-10000	0	0
MMP2	0.009	0.039	-9999	-0.51	2	2
JAM3	0.012	0	-9999	-10000	0	0
GP1BA	0.005	0.048	-9999	-0.4	5	5
alphaM/beta2 Integrin/CTGF	0.012	0.059	-9999	-0.39	4	4
alphaM/beta2 Integrin	-0.035	0.1	-9999	-0.32	27	27
JAM3 homodimer	0.012	0	-9999	-10000	0	0
ICAM2	0.012	0	-9999	-10000	0	0
ICAM1	0.008	0.05	-9999	-0.71	2	2
phagocytosis triggered by activation of immune response cell surface activating receptor	-0.034	0.1	-9999	-0.32	27	27
cell adhesion	0.008	0.061	-9999	-0.37	5	5
NFKB1	0.02	0.095	-9999	-0.52	4	4
THY1	0.012	0	-9999	-10000	0	0
RhoA/GDP	0.009	0	-9999	-10000	0	0
Lipoprotein(a)	-0.056	0.15	-9999	-0.48	38	38
alphaM/beta2 Integrin/LRP/tPA	0.018	0.052	-9999	-0.32	3	3
IL6	0.006	0.15	-9999	-0.56	26	26
ITGB2	0.008	0.035	-9999	-0.33	4	4
elevation of cytosolic calcium ion concentration	-0.029	0.14	-9999	-0.41	49	49
alphaM/beta2 Integrin/JAM2/JAM3	-0.023	0.1	-9999	-0.33	19	19
JAM2	-0.072	0.14	-9999	-0.32	106	106
alphaM/beta2 Integrin/ICAM1	-0.033	0.15	-9999	-0.4	58	58
alphaM/beta2 Integrin/uPA/Plg	-0.13	0.22	-9999	-0.43	134	134
RhoA/GTP	-0.039	0.12	-9999	-0.39	21	21
positive regulation of phagocytosis	-0.012	0.094	-9999	-0.4	9	9
Ron/MSP	-0.056	0.19	-9999	-0.53	56	56
alphaM/beta2 Integrin/uPAR/uPA	-0.028	0.15	-9999	-0.41	49	49
alphaM/beta2 Integrin/uPAR	0.013	0.053	-9999	-0.36	3	3
PLAU	-0.067	0.22	-9999	-0.71	46	46
PLAT	0.009	0.028	-9999	-0.32	3	3
actin filament polymerization	-0.035	0.11	-9999	-0.37	20	20
MST1	-0.084	0.24	-9999	-0.71	56	56
alphaM/beta2 Integrin/lipoprotein(a)	-0.044	0.14	-9999	-0.41	44	44
TNF	0.024	0.092	-9999	-0.6	3	3
RAP1B	0.012	0	-9999	-10000	0	0
alphaM/beta2 Integrin/uPA	-0.04	0.16	-9999	-0.46	49	49
fibrinolysis	-0.12	0.21	-9999	-0.43	134	134
HCK	0.009	0.032	-9999	-0.32	4	4
dendritic cell antigen processing and presentation	-0.034	0.1	-9999	-0.32	27	27
VTN	-0.005	0.1	-9999	-0.71	9	9
alphaM/beta2 Integrin/CYR61	0.013	0.053	-9999	-0.36	3	3
LPA	-0.028	0.15	-9999	-0.71	20	20
LRP1	0.01	0.023	-9999	-0.32	2	2
cell migration	-0.036	0.15	-9999	-0.42	51	51
FN1	-0.018	0.14	-9999	-0.61	20	20
alphaM/beta2 Integrin/Thy1	0.013	0.053	-9999	-0.36	3	3
MPO	-0.015	0.13	-9999	-0.71	15	15
KNG1	-0.058	0.13	-9999	-0.32	84	84
RAP1/GDP	0.016	0	-9999	-10000	0	0
ROCK1	-0.032	0.11	-9999	-0.38	19	19
ELA2	0	0	-9999	-10000	0	0
PLG	-0.15	0.29	-9999	-0.71	89	89
CTGF	0.01	0.035	-9999	-0.71	1	1
alphaM/beta2 Integrin/Hck	0.011	0.063	-9999	-0.41	5	5
ITGAM	-0.005	0.074	-9999	-0.32	21	21
alphaM/beta2 Integrin/P-Selectin/PSGL1	-0.004	0.089	-9999	-0.36	13	13
HP	-0.026	0.16	-9999	-0.71	21	21
leukocyte adhesion	-0.012	0.1	-9999	-0.45	6	6
SELP	-0.034	0.11	-9999	-0.32	57	57

×

EPHB forward signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Ephrin A5/EPHB2	-0.021	0.08	-10000	0	-0.46	2	2
cell-cell adhesion	0.08	0.14	0.52	5	-10000	0	5
Ephrin B/EPHB2/RasGAP	0.03	0.044	-10000	0	-0.39	4	4
ITSN1	0.011	0.016	-10000	0	-0.32	1	1
PIK3CA	0.012	0.001	-10000	0	-10000	0	0
SHC1	0.012	0	-10000	0	-10000	0	0
Ephrin B1/EPHB3	-0.016	0.12	-10000	0	-0.46	28	28
Ephrin B1/EPHB1	-0.1	0.2	-10000	0	-0.46	102	102
HRAS/GDP	-0.08	0.14	-10000	0	-0.33	93	93
Ephrin B/EPHB1/GRB7	-0.082	0.2	-10000	0	-0.4	110	110
Endophilin/SYNJ1	0.022	0.04	-10000	0	-0.36	4	4
KRAS	0.012	0	-10000	0	-10000	0	0
Ephrin B/EPHB1/Src	-0.071	0.18	-10000	0	-0.39	103	103
endothelial cell migration	0.025	0	-10000	0	-10000	0	0
GRB2	0.012	0	-10000	0	-10000	0	0
GRB7	-0.007	0.12	-10000	0	-0.71	11	11
PAK1	0.027	0.042	-10000	0	-0.36	4	4
HRAS	0.011	0.016	-10000	0	-0.32	1	1
RRAS	0.022	0.041	-10000	0	-0.37	4	4
DNM1	0.007	0.061	-10000	0	-0.71	3	3
cell-cell signaling	0	0	-10000	0	-10000	0	0
CRK	-0.072	0.17	-10000	0	-0.37	103	103
lamellipodium assembly	-0.08	0.14	-10000	0	-0.52	5	5
Ephrin B/EPHB1/Src/p52 SHC/GRB2	-0.029	0.1	-10000	0	-0.38	2	2
PIK3R1	0.012	0	-10000	0	-10000	0	0
EPHB2	0.008	0.05	-10000	0	-0.71	2	2
EPHB3	-0.036	0.18	-10000	0	-0.71	28	28
EPHB1	-0.16	0.31	-10000	0	-0.71	102	102
EPHB4	0.012	0	-10000	0	-10000	0	0
mol:GDP	-0.039	0.14	-10000	0	-0.43	4	4
Ephrin B/EPHB2	0.023	0.044	-10000	0	-0.39	4	4
Ephrin B/EPHB3	-0.003	0.11	-10000	0	-0.4	30	30
JNK cascade	-0.073	0.18	-10000	0	-0.39	102	102
Ephrin B/EPHB1	-0.077	0.18	-10000	0	-0.4	103	103
RAP1/GDP	-0.024	0.13	-10000	0	-0.41	3	3
EFNB2	0.012	0	-10000	0	-10000	0	0
EFNB3	0.005	0.059	-10000	0	-0.45	6	6
EFNB1	0.012	0	-10000	0	-10000	0	0
Ephrin B2/EPHB1-2	-0.087	0.2	-10000	0	-0.43	102	102
RAP1B	0.012	0	-10000	0	-10000	0	0
RAP1A	0.012	0	-10000	0	-10000	0	0
CDC42/GTP	-0.082	0.14	-10000	0	-0.58	5	5
Rap1/GTP	-0.08	0.14	-10000	0	-0.58	4	4
axon guidance	-0.021	0.08	-10000	0	-0.46	2	2
MAPK3	-0.016	0.094	-10000	0	-0.33	2	2
MAPK1	-0.016	0.094	-10000	0	-0.33	2	2
Rac1/GDP	-0.029	0.13	-10000	0	-0.43	3	3
actin cytoskeleton reorganization	-0.066	0.12	-10000	0	-0.43	5	5
CDC42/GDP	-0.03	0.14	-10000	0	-0.47	3	3
PI3K	0.028	0	-10000	0	-10000	0	0
EFNA5	-0.049	0.13	-10000	0	-0.32	77	77
Ephrin B2/EPHB4	0.016	0	-10000	0	-10000	0	0
Ephrin B/EPHB2/Intersectin/N-WASP	0.025	0.031	-10000	0	-10000	0	0
CDC42	0.011	0.016	-10000	0	-0.32	1	1
RAS family/GTP	-0.079	0.14	-10000	0	-0.54	5	5
PTK2	0.021	0.036	-10000	0	-10000	0	0
MAP4K4	-0.074	0.18	-10000	0	-0.39	102	102
SRC	0.012	0	-10000	0	-10000	0	0
KALRN	0.011	0.016	-10000	0	-0.32	1	1
Intersectin/N-WASP	0.017	0.011	-10000	0	-10000	0	0
neuron projection morphogenesis	-0.022	0.13	-10000	0	-0.42	5	5
MAP2K1	-0.022	0.099	-10000	0	-0.35	2	2
WASL	0.012	0	-10000	0	-10000	0	0
Ephrin B1/EPHB1-2/NCK1	-0.08	0.2	-10000	0	-0.42	102	102
cell migration	-0.017	0.1	-10000	0	-0.39	2	2
NRAS	0.011	0.016	-10000	0	-0.32	1	1
SYNJ1	0.022	0.041	-10000	0	-0.37	4	4
PXN	0.012	0	-10000	0	-10000	0	0
TF	0.012	0.082	-10000	0	-0.41	13	13
HRAS/GTP	-0.086	0.15	-10000	0	-0.34	103	103
Ephrin B1/EPHB1-2	-0.087	0.2	-10000	0	-0.43	102	102
cell adhesion mediated by integrin	-0.002	0.059	0.31	5	-10000	0	5
RAC1	0.012	0	-10000	0	-10000	0	0
mol:GTP	-0.064	0.18	-10000	0	-0.37	103	103
RAC1-CDC42/GTP	-0.1	0.17	-10000	0	-0.62	13	13
RASA1	0.012	0.001	-10000	0	-10000	0	0
RAC1-CDC42/GDP	-0.024	0.13	-10000	0	-0.45	3	3
ruffle organization	-0.048	0.16	-10000	0	-0.58	4	4
NCK1	0.012	0	-10000	0	-10000	0	0
receptor internalization	0.023	0.053	-10000	0	-0.37	7	7
Ephrin B/EPHB2/KALRN	0.029	0.045	-10000	0	-0.39	4	4
ROCK1	-0.01	0.11	-10000	0	-0.42	28	28
RAS family/GDP	-0.057	0.1	-10000	0	-0.39	5	5
Rac1/GTP	-0.084	0.15	-10000	0	-0.56	5	5
Ephrin B/EPHB1/Src/Paxillin	-0.032	0.11	-10000	0	-0.41	2	2

×

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	0.002	0.1	-9999	-0.44	8	8
MAP3K8	0.012	0.001	-9999	-10000	0	0
FOS	-0.006	0.095	-9999	-0.38	8	8
PRKCA	0.012	0.002	-9999	-10000	0	0
PTPN7	-0.001	0.095	-9999	-0.62	9	9
HRAS	0.011	0.016	-9999	-0.32	1	1
PRKCB	-0.053	0.13	-9999	-0.32	82	82
NRAS	0.011	0.016	-9999	-0.32	1	1
RAS family/GTP	0.023	0.012	-9999	-10000	0	0
MAPK3	-0.002	0.071	-9999	-0.44	3	3
MAP2K1	-0.033	0.14	-9999	-0.31	82	82
ELK1	0.012	0.002	-9999	-10000	0	0
BRAF	-0.039	0.13	-9999	-0.3	82	82
mol:GTP	0	0.001	-9999	-0.004	7	7
MAPK1	-0.002	0.071	-9999	-0.44	3	3
RAF1	-0.039	0.13	-9999	-0.3	82	82
KRAS	0.012	0	-9999	-10000	0	0

×

Ephrin A reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAPKKK cascade	-0.039	0.09	-9999	-0.34	8	8
EFNA5	-0.049	0.13	-9999	-0.32	77	77
FYN	-0.029	0.081	-9999	-0.31	8	8
neuron projection morphogenesis	-0.039	0.09	-9999	-0.34	8	8
cell-cell signaling	0	0	-9999	-10000	0	0
Ephrin A5/EPHA5	-0.039	0.091	-9999	-0.34	8	8
EPHA5	-0.023	0.093	-9999	-0.32	37	37

×

JNK signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1	0.009	0.07	-9999	-0.33	9	9
MAP4K1	-0.017	0.093	-9999	-0.32	36	36
MAP3K8	0.012	0	-9999	-10000	0	0
PRKCB	-0.053	0.13	-9999	-0.32	82	82
DBNL	0.012	0	-9999	-10000	0	0
CRKL	0.012	0	-9999	-10000	0	0
MAP3K1	0.014	0.067	-9999	-0.34	8	8
JUN	-0.079	0.22	-9999	-0.52	82	82
MAP3K7	0.014	0.067	-9999	-0.34	8	8
GRAP2	0.005	0.048	-9999	-0.32	9	9
CRK	0.012	0	-9999	-10000	0	0
MAP2K4	0.019	0.068	-9999	-0.34	8	8
LAT	0.009	0.042	-9999	-0.45	3	3
LCP2	0.009	0.028	-9999	-0.32	3	3
MAPK8	-0.088	0.24	-9999	-0.56	82	82
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family	0.01	0.071	-9999	-0.36	8	8
LAT/GRAP2/SLP76/HPK1/HIP-55	0.015	0.066	-9999	-0.41	2	2

×

Retinoic acid receptors-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.012	0	-9999	-10000	0	0
HDAC3	0.012	0	-9999	-10000	0	0
VDR	0.012	0	-9999	-10000	0	0
Cbp/p300/PCAF	0.016	0.038	-9999	-10000	0	0
EP300	0.012	0	-9999	-10000	0	0
RARs/AIB1/Cbp/p300/PCAF/9cRA	-0.007	0.053	-9999	-0.31	1	1
KAT2B	-0.002	0.066	-9999	-0.32	17	17
MAPK14	0.012	0	-9999	-10000	0	0
AKT1	-0.013	0.065	-9999	-0.26	1	1
RAR alpha/9cRA/Cyclin H	-0.062	0.071	-9999	-0.33	1	1
mol:9cRA	0	0	-9999	-10000	0	0
RARs/Src-1/Cbp/p300/PCAF/9cRA	-0.01	0.058	-9999	-0.25	9	9
CDC2	0	0.001	-9999	-10000	0	0
response to UV	0.001	0.002	-9999	-10000	0	0
RAR alpha/Jnk1	-0.057	0.088	-9999	-0.34	2	2
NCOR2	0.011	0.016	-9999	-0.32	1	1
VDR/VDR/Vit D3	0.009	0	-9999	-10000	0	0
RXRs/RARs/NRIP1/9cRA	-0.086	0.12	-9999	-0.45	3	3
NCOA2	0.011	0.016	-9999	-0.32	1	1
NCOA3	0.012	0	-9999	-10000	0	0
NCOA1	0.012	0	-9999	-10000	0	0
VDR/VDR/DNA	0.012	0	-9999	-10000	0	0
RARG	0.012	0.001	-9999	-10000	0	0
RAR gamma1/9cRA	0.016	0.001	-9999	-10000	0	0
MAPK3	0.012	0.001	-9999	-10000	0	0
MAPK1	0.012	0	-9999	-10000	0	0
MAPK8	0.012	0.002	-9999	-10000	0	0
mol:Vit D3	0	0	-9999	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.1	0.13	-9999	-0.34	1	1
RARA	-0.069	0.1	-9999	-0.19	183	183
negative regulation of phosphoinositide 3-kinase cascade	0	0	-9999	-10000	0	0
RARs/TIF2/Cbp/p300/PCAF/9cRA	-0.011	0.059	-9999	-0.25	9	9
PRKCA	0.014	0.004	-9999	-10000	0	0
RXRs/RARs/NRIP1/9cRA/HDAC1	-0.1	0.13	-9999	-0.52	3	3
RXRG	-0.23	0.2	-9999	-0.34	296	296
RXRA	-0.058	0.096	-9999	-0.34	1	1
RXRB	-0.11	0.15	-9999	-0.29	183	183
VDR/Vit D3/DNA	0.009	0	-9999	-10000	0	0
RBP1	-0.041	0.19	-9999	-0.71	31	31
CRBP1/9-cic-RA	-0.032	0.14	-9999	-0.54	31	31
RARB	0.01	0.033	-9999	-0.32	4	4
PRKCG	-0.3	0.36	-9999	-0.7	183	183
MNAT1	0.012	0.001	-9999	-10000	0	0
RAR alpha/RXRs	-0.081	0.12	-9999	-0.34	3	3
RXRs/RARs/SMRT(N-CoR2)/9cRA	-0.077	0.12	-9999	-0.39	2	2
proteasomal ubiquitin-dependent protein catabolic process	-0.032	0.08	-9999	-0.26	12	12
RXRs/RARs/NRIP1/9cRA/HDAC3	-0.1	0.13	-9999	-0.52	3	3
positive regulation of DNA binding	-0.06	0.068	-9999	-0.31	1	1
NRIP1	-0.1	0.14	-9999	-1.1	2	2
RXRs/RARs	-0.11	0.13	-9999	-0.31	67	67
RXRs/RXRs/DNA/9cRA	-0.11	0.13	-9999	-0.3	66	66
PRKACA	0.012	0	-9999	-10000	0	0
CDK7	0.012	0	-9999	-10000	0	0
TFIIH	0.024	0	-9999	-10000	0	0
RAR alpha/9cRA	-0.027	0.071	-9999	-10000	0	0
CCNH	0.012	0	-9999	-10000	0	0
CREBBP	0.012	0	-9999	-10000	0	0
RAR gamma2/9cRA	0	0	-9999	-10000	0	0

×

Plasma membrane estrogen receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	0.005	0.061	-10000	0	-0.29	5	5
ER alpha/Gai/GDP/Gbeta gamma	-0.12	0.21	-10000	0	-0.59	49	49
AKT1	-0.056	0.23	-10000	0	-0.81	36	36
PIK3CA	0.012	0.001	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/PI3K	-0.061	0.24	-10000	0	-0.83	36	36
mol:Ca2+	0.02	0.05	-10000	0	-0.38	3	3
IGF1R	0.012	0	-10000	0	-10000	0	0
E2/ER alpha (dimer)/Striatin	-0.001	0.053	-10000	0	-10000	0	0
SHC1	0.012	0	-10000	0	-10000	0	0
apoptosis	0.053	0.22	0.77	36	-10000	0	36
RhoA/GTP	-0.01	0.032	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas	-0.099	0.16	-10000	0	-0.55	34	34
regulation of stress fiber formation	-0.024	0.036	-10000	0	-10000	0	0
E2/ERA-ERB (dimer)	-0.002	0.057	-10000	0	-0.34	1	1
KRAS	0.012	0	-10000	0	-10000	0	0
G13/GTP	0	0.048	-10000	0	-10000	0	0
pseudopodium formation	0.024	0.036	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1	-0.001	0.053	-10000	0	-10000	0	0
GRB2	0.012	0	-10000	0	-10000	0	0
GNG2	-0.003	0.069	-10000	0	-0.32	19	19
GNAO1	-0.12	0.16	-10000	0	-0.32	170	170
HRAS	0.011	0.016	-10000	0	-0.32	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
mol:NO	-0.067	0.19	-10000	0	-0.59	40	40
E2/ER beta (dimer)	0.007	0.019	-10000	0	-0.22	3	3
mol:GDP	-0.024	0.076	-10000	0	-0.27	36	36
mol:NADP	-0.067	0.19	-10000	0	-0.59	40	40
PIK3R1	0.012	0	-10000	0	-10000	0	0
mol:IP3	0.02	0.051	-10000	0	-0.39	3	3
IGF-1R heterotetramer	0.012	0	-10000	0	-10000	0	0
PLCB1	0.016	0.053	-10000	0	-0.37	4	4
PLCB2	0.017	0.049	-10000	0	-0.43	2	2
IGF1	-0.067	0.14	-10000	0	-0.32	99	99
mol:L-citrulline	-0.067	0.19	-10000	0	-0.59	40	40
RHOA	0.012	0	-10000	0	-10000	0	0
Gai/GDP	-0.24	0.33	-10000	0	-0.62	170	170
JNK cascade	0.007	0.019	-10000	0	-0.22	3	3
BCAR1	0.011	0.016	-10000	0	-0.32	1	1
ESR2	0.009	0.028	-10000	0	-0.32	3	3
GNAQ	0.01	0.023	-10000	0	-0.32	2	2
ESR1	-0.017	0.093	-10000	0	-0.32	36	36
Gq family/GDP/Gbeta gamma	0.016	0.059	-10000	0	-0.42	2	2
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1	-0.007	0.072	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC	-0.099	0.16	-10000	0	-0.55	34	34
GNAZ	0.005	0.048	-10000	0	-0.32	9	9
E2/ER alpha (dimer)	-0.011	0.064	-10000	0	-0.22	36	36
STRN	0.012	0.001	-10000	0	-10000	0	0
GNAL	-0.014	0.088	-10000	0	-0.32	32	32
PELP1	0.012	0	-10000	0	-10000	0	0
MAPK11	0.011	0.036	-10000	0	-0.46	2	2
GNAI2	0.012	0	-10000	0	-10000	0	0
GNAI3	0.012	0	-10000	0	-10000	0	0
GNAI1	0.001	0.06	-10000	0	-0.32	14	14
HBEGF	-0.11	0.19	-10000	0	-0.5	53	53
cAMP biosynthetic process	-0.023	0.059	-10000	0	-0.28	11	11
SRC	-0.1	0.2	-10000	0	-0.55	49	49
PI3K	0.018	0	-10000	0	-10000	0	0
GNB1	0.012	0	-10000	0	-10000	0	0
G13/GDP/Gbeta gamma	-0.025	0.07	-10000	0	-0.35	5	5
SOS1	0.012	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1	-0.1	0.15	-10000	0	-0.45	45	45
Gs family/GTP	-0.009	0.066	-10000	0	-0.28	11	11
EntrezGene:2778	0	0	-10000	0	-10000	0	0
RAS family/GTP	0.022	0.012	-10000	0	-10000	0	0
vasodilation	-0.064	0.18	-10000	0	-0.56	40	40
mol:DAG	0.02	0.051	-10000	0	-0.39	3	3
Gs family/GDP/Gbeta gamma	-0.032	0.081	-10000	0	-0.35	13	13
MSN	0.025	0.038	-10000	0	-10000	0	0
Gq family/GTP	0.012	0.052	-10000	0	-0.4	3	3
mol:PI-3-4-5-P3	-0.058	0.23	-10000	0	-0.8	36	36
NRAS	0.011	0.016	-10000	0	-0.32	1	1
mol:E2	0	0	-10000	0	-10000	0	0
cell adhesion	0.064	0.18	0.56	40	-10000	0	40
GRB2/SOS1	0.018	0	-10000	0	-10000	0	0
RhoA/GDP	-0.023	0.071	-10000	0	-0.38	1	1
NOS3	-0.071	0.2	-10000	0	-0.62	40	40
GNA11	0.011	0.016	-10000	0	-0.32	1	1
MAPKKK cascade	-0.051	0.19	-10000	0	-0.62	36	36
E2/ER alpha (dimer)/PELP1/Src	-0.1	0.16	-10000	0	-0.58	34	34
ruffle organization	0.024	0.036	-10000	0	-10000	0	0
ROCK2	0.021	0.04	-10000	0	-10000	0	0
GNA14	0.01	0.023	-10000	0	-0.32	2	2
GNA15	0	0.092	-10000	0	-0.71	7	7
GNA13	0.012	0	-10000	0	-10000	0	0
MMP9	-0.14	0.2	-10000	0	-0.44	97	97
MMP2	-0.095	0.19	-10000	0	-0.52	49	49

×

S1P5 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	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	0.052	0.099	0.3	20	-10000	0	20
GNAI2	0.012	0	-10000	0	-10000	0	0
S1P/S1P5/G12	0.007	0.065	-10000	0	-0.46	8	8
mol:GDP	0	0	-10000	0	-10000	0	0
GNAO1	-0.12	0.16	-10000	0	-0.32	170	170
RhoA/GTP	-0.052	0.1	-10000	0	-0.3	20	20
negative regulation of cAMP metabolic process	-0.063	0.11	-10000	0	-0.3	27	27
GNAZ	0.005	0.048	-10000	0	-0.32	9	9
GNAI3	0.012	0	-10000	0	-10000	0	0
GNA12	0.012	0	-10000	0	-10000	0	0
S1PR5	-0.002	0.098	-10000	0	-0.71	8	8
mol:GTP	0	0	-10000	0	-10000	0	0
S1P/S1P5/Gi	-0.064	0.11	-10000	0	-0.3	27	27
RhoA/GDP	0.009	0	-10000	0	-10000	0	0
RHOA	0.012	0	-10000	0	-10000	0	0
GNAI1	0.001	0.06	-10000	0	-0.32	14	14

×

Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity	0.021	0.13	0.53	26	-10000	0	26
KIRREL	0.004	0.039	-10000	0	-0.32	5	5
Nephrin/NEPH1Par3/Par6/Atypical PKCs	-0.021	0.13	-10000	0	-0.53	26	26
PLCG1	0.012	0	-10000	0	-10000	0	0
ARRB2	0.012	0	-10000	0	-10000	0	0
WASL	0.012	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/CD2AP	-0.012	0.12	-10000	0	-0.41	29	29
ChemicalAbstracts:57-88-5	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP	0.007	0.066	-10000	0	-0.45	1	1
FYN	-0.011	0.097	-10000	0	-0.36	29	29
mol:Ca2+	-0.008	0.11	-10000	0	-0.4	29	29
mol:DAG	-0.007	0.11	-10000	0	-0.4	29	29
NPHS2	-0.005	0.072	-10000	0	-0.72	4	4
mol:IP3	-0.007	0.11	-10000	0	-0.4	29	29
regulation of endocytosis	-0.001	0.093	-10000	0	-0.33	29	29
Nephrin/NEPH1/podocin/Cholesterol	-0.015	0.11	-10000	0	-0.4	29	29
establishment of cell polarity	-0.021	0.13	-10000	0	-0.53	26	26
Nephrin/NEPH1/podocin/NCK1-2	0.001	0.1	-10000	0	-0.36	29	29
Nephrin/NEPH1/beta Arrestin2	0	0.094	-10000	0	-0.34	29	29
NPHS1	-0.034	0.17	-10000	0	-0.7	26	26
Nephrin/NEPH1/podocin	-0.009	0.098	-10000	0	-0.36	29	29
TJP1	0.012	0	-10000	0	-10000	0	0
NCK1	0.012	0	-10000	0	-10000	0	0
NCK2	0.012	0	-10000	0	-10000	0	0
heterophilic cell adhesion	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/PLCgamma1	-0.007	0.11	-10000	0	-0.4	29	29
CD2AP	0.002	0.055	-10000	0	-0.32	12	12
Nephrin/NEPH1/podocin/GRB2	-0.007	0.11	-10000	0	-0.4	29	29
GRB2	0.012	0	-10000	0	-10000	0	0
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
TRPC6	-0.011	0.1	-10000	0	-0.37	29	29
cytoskeleton organization	0.006	0.084	-10000	0	-0.37	4	4
Nephrin/NEPH1	-0.013	0.098	-10000	0	-0.38	26	26
Nephrin/NEPH1/ZO-1	-0.008	0.11	-10000	0	-0.43	26	26

×

Visual signal transduction: Cones

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin	0.008	0.066	-9999	-0.4	10	10
RGS9BP	0.007	0.05	-9999	-0.71	2	2
mol:GTP	0	0	-9999	-10000	0	0
GRK1	-0.003	0.06	-9999	-0.71	3	3
mol:Na +	-0.094	0.14	-9999	-0.53	27	27
mol:ADP	-0.004	0.08	-9999	-0.6	7	7
GNAT2	0	0.085	-9999	-0.71	6	6
RGS9-1/Gbeta5/R9AP	-0.024	0.087	-9999	-0.46	2	2
mol:GDP	0	0	-9999	-10000	0	0
PDE6H/GNAT2/GTP	0	0.061	-9999	-0.46	7	7
GRK7	-0.001	0.078	-9999	-0.71	5	5
CNGB3	-0.041	0.17	-9999	-0.71	26	26
Cone Metarhodopsin II/X-Arrestin	0	0.037	-9999	-0.54	2	2
mol:Ca2+	-0.11	0.17	-9999	-0.5	48	48
Cone PDE6	-0.018	0.075	-9999	-0.39	3	3
Cone Metarhodopsin II	-0.002	0.065	-9999	-0.48	7	7
Na + (4 Units)	-0.11	0.17	-9999	-0.5	48	48
GNAT2/GDP	-0.019	0.086	-9999	-0.39	8	8
GNB5	0.012	0	-9999	-10000	0	0
mol:GMP (4 units)	0	0.056	-9999	-0.42	7	7
Cone Transducin	0.009	0.07	-9999	-0.42	10	10
SLC24A2	-0.036	0.17	-9999	-0.71	25	25
GNB3/GNGT2	0.009	0.06	-9999	-0.53	4	4
GNB3	0.004	0.072	-9999	-0.63	5	5
GNAT2/GTP	0	0.065	-9999	-0.54	6	6
CNGA3	-0.12	0.16	-9999	-0.32	162	162
ARR3	0	0.049	-9999	-0.71	2	2
absorption of light	0	0	-9999	-10000	0	0
cGMP/Cone CNG Channel	-0.094	0.15	-9999	-0.53	27	27
mol:Pi	-0.024	0.086	-9999	-0.45	2	2
Cone CNG Channel	-0.077	0.13	-9999	-0.43	34	34
mol:all-trans-retinal	0	0	-9999	-10000	0	0
mol:K +	-0.036	0.17	-9999	-0.7	25	25
RGS9	-0.065	0.14	-9999	-0.32	97	97
PDE6C	0.003	0.005	-9999	-10000	0	0
GNGT2	0.008	0.036	-9999	-0.32	5	5
mol:cGMP (4 units)	0	0	-9999	-10000	0	0
PDE6H	-0.001	0.035	-9999	-0.71	1	1

×

LPA receptor mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.006	0.078	-9999	-0.32	9	9
NF kappa B1 p50/RelA/I kappa B alpha	0.007	0.065	-9999	-10000	0	0
AP1	-0.033	0.07	-9999	-0.36	6	6
mol:PIP3	-0.027	0.059	-9999	-0.33	3	3
AKT1	0.023	0.056	-9999	-10000	0	0
PTK2B	-0.006	0.064	-9999	-0.28	2	2
RHOA	0.018	0.026	-9999	-10000	0	0
PIK3CB	0.012	0.001	-9999	-10000	0	0
mol:Ca2+	0.011	0.056	-9999	-0.27	4	4
MAGI3	0.012	0	-9999	-10000	0	0
RELA	0.012	0	-9999	-10000	0	0
apoptosis	-0.024	0.09	-9999	-0.34	11	11
HRAS/GDP	0.008	0.011	-9999	-0.22	1	1
positive regulation of microtubule depolymerization	-0.033	0.087	-9999	-0.3	4	4
NF kappa B1 p50/RelA	-0.029	0.063	-9999	-10000	0	0
endothelial cell migration	-0.009	0.076	-9999	-0.57	2	2
ADCY4	-0.076	0.16	-9999	-0.46	51	51
ADCY5	-0.17	0.22	-9999	-0.42	144	144
ADCY6	-0.076	0.16	-9999	-0.46	51	51
ADCY7	-0.076	0.16	-9999	-0.46	51	51
ADCY1	-0.08	0.16	-9999	-0.45	54	54
ADCY2	-0.11	0.21	-9999	-0.46	87	87
ADCY3	-0.076	0.16	-9999	-0.46	51	51
ADCY8	-0.082	0.16	-9999	-0.44	60	60
ADCY9	-0.077	0.16	-9999	-0.45	53	53
GSK3B	0	0.061	-9999	-0.28	1	1
arachidonic acid secretion	-0.086	0.17	-9999	-0.48	51	51
GNG2	-0.003	0.069	-9999	-0.32	19	19
TRIP6	0.018	0.018	-9999	-0.27	1	1
GNAO1	-0.035	0.12	-9999	-0.34	50	50
HRAS	0.011	0.016	-9999	-0.32	1	1
NFKBIA	0.002	0.071	-9999	-10000	0	0
GAB1	0.012	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
lamellipodium assembly	-0.051	0.24	-9999	-0.85	35	35
JUN	0.012	0	-9999	-10000	0	0
LPA/LPA2/NHERF2	0.015	0.026	-9999	-0.46	1	1
TIAM1	-0.081	0.28	-9999	-1	35	35
PIK3R1	0.012	0	-9999	-10000	0	0
mol:IP3	0.011	0.057	-9999	-0.28	4	4
PLCB3	0.019	0.023	-9999	-0.41	1	1
FOS	0.006	0.043	-9999	-0.32	7	7
positive regulation of mitosis	-0.086	0.17	-9999	-0.48	51	51
LPA/LPA1-2-3	-0.019	0.089	-9999	-0.36	12	12
mol:Ca ++	0	0	-9999	-10000	0	0
JNK cascade	-0.001	0.001	-9999	-10000	0	0
BCAR1	0.011	0.016	-9999	-0.32	1	1
stress fiber formation	-0.005	0.071	-9999	-0.29	2	2
GNAZ	-0.01	0.075	-9999	-0.34	5	5
EGFR/PI3K-beta/Gab1	-0.028	0.061	-9999	-0.34	3	3
positive regulation of dendritic cell cytokine production	-0.02	0.088	-9999	-0.36	12	12
LPA/LPA2/MAGI-3	0.016	0.024	-9999	-0.46	1	1
ARHGEF1	0.004	0.058	-9999	-10000	0	0
GNAI2	-0.008	0.069	-9999	-0.3	2	2
GNAI3	-0.008	0.069	-9999	-0.34	1	1
GNAI1	-0.013	0.084	-9999	-0.35	11	11
LPA/LPA3	-0.012	0.078	-9999	-0.27	30	30
LPA/LPA2	0.009	0.027	-9999	-0.53	1	1
LPA/LPA1	-0.019	0.083	-9999	-0.36	2	2
HB-EGF/EGFR	-0.044	0.16	-9999	-0.46	54	54
HBEGF	-0.056	0.18	-9999	-0.53	54	54
mol:DAG	0.011	0.057	-9999	-0.28	4	4
cAMP biosynthetic process	-0.1	0.18	-9999	-0.49	52	52
NFKB1	0.012	0	-9999	-10000	0	0
SRC	0.012	0	-9999	-10000	0	0
GNB1	0.012	0	-9999	-10000	0	0
LYN	0.002	0.071	-9999	-10000	0	0
GNAQ	0	0.06	-9999	-0.3	7	7
LPAR2	0.01	0.035	-9999	-0.71	1	1
LPAR3	-0.02	0.11	-9999	-0.38	30	30
LPAR1	-0.035	0.12	-9999	-0.32	62	62
IL8	-0.19	0.18	-9999	-0.38	99	99
PTK2	-0.014	0.083	-9999	-0.38	6	6
Rac1/GDP	0.009	0	-9999	-10000	0	0
CASP3	-0.024	0.091	-9999	-0.34	11	11
EGFR	0.011	0.001	-9999	-10000	0	0
PLCG1	0.003	0.064	-9999	-0.28	7	7
PLD2	-0.014	0.083	-9999	-0.38	6	6
G12/G13	0.002	0.064	-9999	-0.3	1	1
PI3K-beta	-0.017	0.044	-9999	-0.36	1	1
cell migration	-0.006	0.085	-9999	-0.26	35	35
SLC9A3R2	0.011	0.016	-9999	-0.32	1	1
PXN	-0.005	0.072	-9999	-0.29	2	2
HRAS/GTP	-0.088	0.18	-9999	-0.5	51	51
RAC1	0.012	0	-9999	-10000	0	0
MMP9	-0.076	0.23	-9999	-0.7	51	51
PRKCE	0.012	0.001	-9999	-10000	0	0
PRKCD	0.015	0.054	-9999	-0.3	1	1
Gi(beta/gamma)	-0.076	0.16	-9999	-0.45	51	51
mol:LPA	0.002	0.01	-9999	-0.19	1	1
TRIP6/p130 Cas/FAK1/Paxillin	0.001	0.086	-9999	-10000	0	0
MAPKKK cascade	-0.086	0.17	-9999	-0.48	51	51
contractile ring contraction involved in cytokinesis	0.018	0.026	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
GNA14	0	0.06	-9999	-0.3	7	7
GNA15	-0.005	0.072	-9999	-0.32	13	13
GNA12	0.012	0	-9999	-10000	0	0
GNA13	0.012	0	-9999	-10000	0	0
MAPT	-0.034	0.089	-9999	-0.31	4	4
GNA11	0	0.059	-9999	-0.31	6	6
Rac1/GTP	-0.054	0.26	-9999	-0.9	35	35
MMP2	-0.009	0.077	-9999	-0.57	2	2

×

Noncanonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC2	0.002	0.055	-9999	-0.32	12	12
GNB1/GNG2	-0.041	0.12	-9999	-0.36	25	25
mol:DAG	-0.034	0.11	-9999	-0.35	17	17
PLCG1	-0.035	0.12	-9999	-0.36	17	17
YES1	-0.043	0.12	-9999	-0.4	18	18
FZD3	0.007	0.061	-9999	-0.71	3	3
FZD6	0.012	0	-9999	-10000	0	0
G protein	-0.034	0.12	-9999	-0.36	19	19
MAP3K7	-0.028	0.1	-9999	-0.37	5	5
mol:Ca2+	-0.033	0.11	-9999	-0.34	17	17
mol:IP3	-0.034	0.11	-9999	-0.35	17	17
NLK	0.006	0.01	-9999	-10000	0	0
GNB1	0.012	0	-9999	-10000	0	0
CAMK2A	-0.034	0.11	-9999	-0.36	12	12
MAP3K7IP1	0	0	-9999	-10000	0	0
Noncanonical Wnts/FZD	-0.051	0.13	-9999	-0.42	18	18
CSNK1A1	0.012	0	-9999	-10000	0	0
GNAS	-0.043	0.12	-9999	-0.4	18	18
GO:0007205	-0.035	0.11	-9999	-0.33	23	23
WNT6	-0.027	0.14	-9999	-0.44	34	34
WNT4	-0.004	0.084	-9999	-0.39	17	17
NFAT1/CK1 alpha	-0.028	0.12	-9999	-0.41	9	9
GNG2	-0.003	0.069	-9999	-0.32	19	19
WNT5A	0.006	0.063	-9999	-0.61	4	4
WNT11	-0.14	0.29	-9999	-0.67	91	91
CDC42	-0.037	0.12	-9999	-0.37	19	19

×

Nectin adhesion pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.008	0.05	-9999	-0.71	2	2
alphaV beta3 Integrin	0.013	0.033	-9999	-10000	0	0
PTK2	0.027	0.053	-9999	-0.44	1	1
positive regulation of JNK cascade	-0.006	0.039	-9999	-0.26	10	10
CDC42/GDP	0.038	0.06	-9999	-0.34	10	10
Rac1/GDP	0.039	0.06	-9999	-0.33	10	10
RAP1B	0.012	0	-9999	-10000	0	0
RAP1A	0.012	0	-9999	-10000	0	0
CTNNB1	0.012	0	-9999	-10000	0	0
CDC42/GTP	-0.008	0.047	-9999	-0.31	10	10
nectin-3/I-afadin	0.012	0.035	-9999	-10000	0	0
RAPGEF1	0.033	0.063	-9999	-0.36	10	10
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.029	0.07	-9999	-0.41	10	10
PDGFB-D/PDGFRB	0.008	0.049	-9999	-0.7	2	2
TLN1	0.02	0.022	-9999	-10000	0	0
Rap1/GTP	-0.007	0.041	-9999	-0.32	1	1
IQGAP1	0.012	0	-9999	-10000	0	0
Rap1/GTP/I-afadin	0.023	0.008	-9999	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin	0.012	0.035	-9999	-10000	0	0
PVR	0.012	0	-9999	-10000	0	0
Necl-5(dimer)	0.012	0	-9999	-10000	0	0
mol:GDP	0.036	0.071	-9999	-0.4	10	10
MLLT4	0.011	0.016	-9999	-0.32	1	1
PIK3CA	0.012	0.001	-9999	-10000	0	0
PI3K	0.029	0.038	-9999	-0.38	2	2
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin	0.017	0.011	-9999	-10000	0	0
positive regulation of lamellipodium assembly	-0.008	0.044	-9999	-0.26	11	11
PVRL1	0.012	0	-9999	-10000	0	0
PVRL3	0.005	0.048	-9999	-0.32	9	9
PVRL2	0.012	0	-9999	-10000	0	0
PIK3R1	0.012	0	-9999	-10000	0	0
CDH1	0.012	0	-9999	-10000	0	0
CLDN1	-0.65	0.19	-9999	-0.71	386	386
JAM-A/CLDN1	-0.38	0.12	-9999	-0.42	386	386
SRC	0.025	0.075	-9999	-0.45	10	10
ITGB3	0.005	0.048	-9999	-0.32	9	9
nectin-1(dimer)/I-afadin/I-afadin	0.017	0.011	-9999	-10000	0	0
FARP2	0.033	0.068	-9999	-0.4	10	10
RAC1	0.012	0	-9999	-10000	0	0
CTNNA1	0.012	0	-9999	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer)	0.02	0.029	-9999	-10000	0	0
nectin-1/I-afadin	0.017	0.011	-9999	-10000	0	0
nectin-2/I-afadin	0.017	0.011	-9999	-10000	0	0
RAC1/GTP/IQGAP1/filamentous actin	0.016	0	-9999	-10000	0	0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin	0.02	0.029	-9999	-10000	0	0
CDC42/GTP/IQGAP1/filamentous actin	0.016	0.009	-9999	-10000	0	0
F11R	0.012	0	-9999	-10000	0	0
positive regulation of filopodium formation	-0.006	0.039	-9999	-0.26	10	10
alphaV/beta3 Integrin/Talin	0.029	0.034	-9999	-0.34	1	1
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.017	0.011	-9999	-10000	0	0
nectin-2(dimer)/I-afadin/I-afadin	0.017	0.011	-9999	-10000	0	0
PIP5K1C	0.016	0.025	-9999	-0.24	1	1
VAV2	0.03	0.076	-9999	-0.41	12	12
RAP1/GDP	-0.008	0.048	-9999	-0.31	10	10
ITGAV	0.012	0	-9999	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin	0.02	0.029	-9999	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin	0.012	0.035	-9999	-10000	0	0
Rac1/GTP	-0.009	0.052	-9999	-0.32	11	11
PTPRM	0.011	0.027	-9999	-0.28	1	1
E-cadherin/beta catenin/alpha catenin	0.035	0.008	-9999	-10000	0	0
adherens junction assembly	0	0	-9999	-10000	0	0
CDC42	0.011	0.016	-9999	-0.32	1	1

×

TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC	0.017	0.12	-10000	0	-0.45	21	21
FYN	0.006	0.15	-10000	0	-0.54	24	24
LAT/GRAP2/SLP76	-0.027	0.12	-10000	0	-0.46	23	23
IKBKB	0.012	0	-10000	0	-10000	0	0
AKT1	0.018	0.11	-10000	0	-0.37	25	25
B2M	0.013	0.002	-10000	0	-10000	0	0
IKBKG	-0.012	0.035	-10000	0	-0.16	7	7
MAP3K8	0.012	0	-10000	0	-10000	0	0
mol:Ca2+	-0.019	0.047	-10000	0	-0.14	50	50
integrin-mediated signaling pathway	0.015	0.013	-10000	0	-10000	0	0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA	0.011	0.16	-10000	0	-0.52	26	26
TRPV6	-0.086	0.23	-10000	0	-0.71	51	51
CD28	0.001	0.06	-10000	0	-0.32	14	14
SHC1	0.007	0.15	-10000	0	-0.53	24	24
receptor internalization	-0.001	0.16	-10000	0	-0.54	27	27
PRF1	0.001	0.17	-10000	0	-0.86	12	12
KRAS	0.012	0	-10000	0	-10000	0	0
GRB2	0.012	0	-10000	0	-10000	0	0
COT/AKT1	0.024	0.09	-10000	0	-0.32	17	17
LAT	0.006	0.15	-10000	0	-0.52	25	25
EntrezGene:6955	0.001	0.002	-10000	0	-10000	0	0
CD3D	0.004	0.055	-10000	0	-0.33	11	11
CD3E	0.002	0.062	-10000	0	-0.33	14	14
CD3G	-0.008	0.081	-10000	0	-0.32	26	26
RASGRP2	-0.014	0.058	-10000	0	-0.16	51	51
RASGRP1	0.024	0.11	-10000	0	-0.4	18	18
HLA-A	0.013	0.003	-10000	0	-10000	0	0
RASSF5	0.01	0.023	-10000	0	-0.32	2	2
RAP1A/GTP/RAPL	0.015	0.013	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
mol:GDP	0.02	0.042	-10000	0	-0.12	17	17
PDK1/CARD11/BCL10/MALT1/TRAF6	-0.022	0.059	-10000	0	-0.24	17	17
PRKCA	-0.012	0.06	-10000	0	-0.26	13	13
GRAP2	0.005	0.048	-10000	0	-0.32	9	9
mol:IP3	0.001	0.13	0.25	48	-0.39	17	65
EntrezGene:6957	0.001	0.003	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.001	0.13	-10000	0	-0.46	26	26
ORAI1	0.047	0.11	0.35	50	-10000	0	50
CSK	0.006	0.15	-10000	0	-0.53	24	24
B7 family/CD28	0.005	0.16	-10000	0	-0.56	22	22
CHUK	0.012	0	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8/LCK/ZAP-70	0	0.17	-10000	0	-0.59	25	25
PTPN6	0.005	0.14	-10000	0	-0.52	24	24
VAV1	0.004	0.15	-10000	0	-0.56	24	24
Monovalent TCR/CD3	-0.006	0.12	-10000	0	-0.49	19	19
CBL	0.012	0	-10000	0	-10000	0	0
LCK	0.003	0.15	-10000	0	-0.55	23	23
PAG1	0.006	0.15	-10000	0	-0.53	24	24
RAP1A	0.012	0	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8/LCK	0	0.16	-10000	0	-0.56	26	26
CD80	-0.001	0.094	-10000	0	-0.66	8	8
CD86	0.006	0.043	-10000	0	-0.32	7	7
PDK1/CARD11/BCL10/MALT1	-0.027	0.072	-10000	0	-0.28	19	19
HRAS	0.011	0.016	-10000	0	-0.32	1	1
GO:0035030	0.006	0.13	-10000	0	-0.47	22	22
CD8A	-0.003	0.076	-10000	0	-0.35	18	18
CD8B	0.004	0.06	-10000	0	-0.36	10	10
PTPRC	-0.01	0.084	-10000	0	-0.32	28	28
PDK1/PKC theta	0.021	0.13	-10000	0	-0.45	24	24
CSK/PAG1	0.01	0.14	-10000	0	-0.52	22	22
SOS1	0.012	0	-10000	0	-10000	0	0
peptide-MHC class I	0.019	0.005	-10000	0	-10000	0	0
GRAP2/SLP76	-0.032	0.14	-10000	0	-0.55	22	22
STIM1	0.023	0.057	-10000	0	-10000	0	0
RAS family/GTP	0.031	0.049	-10000	0	-0.17	8	8
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin	-0.003	0.17	-10000	0	-0.57	27	27
mol:DAG	-0.013	0.091	-10000	0	-0.34	20	20
RAP1A/GDP	0.01	0.019	-10000	0	-0.063	1	1
PLCG1	0.012	0	-10000	0	-10000	0	0
CD247	0.006	0.046	-10000	0	-0.33	8	8
cytotoxic T cell degranulation	0.003	0.16	-10000	0	-0.75	14	14
RAP1A/GTP	-0.008	0.019	-10000	0	-0.066	19	19
mol:PI-3-4-5-P3	0.015	0.13	-10000	0	-0.43	26	26
LAT/GRAP2/SLP76/VAV1/PLCgamma1	-0.004	0.15	0.27	47	-0.48	19	66
NRAS	0.011	0.016	-10000	0	-0.32	1	1
ZAP70	0.002	0.062	-10000	0	-0.36	11	11
GRB2/SOS1	0.018	0	-10000	0	-10000	0	0
LAT/GRAP2/SLP76/VAV1	-0.028	0.12	-10000	0	-0.46	23	23
MALT1	0.011	0.016	-10000	0	-0.32	1	1
TRAF6	0.012	0	-10000	0	-10000	0	0
CD8 heterodimer	0.003	0.074	-10000	0	-0.46	6	6
CARD11	-0.026	0.15	-10000	0	-0.6	26	26
PRKCB	-0.021	0.08	-10000	0	-0.29	25	25
PRKCE	-0.012	0.06	-10000	0	-0.27	10	10
PRKCQ	0.015	0.15	-10000	0	-0.5	26	26
LCP2	0.009	0.028	-10000	0	-0.32	3	3
BCL10	0.012	0	-10000	0	-10000	0	0
regulation of survival gene product expression	0.02	0.096	-10000	0	-0.32	25	25
IKK complex	0.021	0.042	-10000	0	-0.11	14	14
RAS family/GDP	-0.002	0.007	-10000	0	-10000	0	0
MAP3K14	0.026	0.071	-10000	0	-0.28	9	9
PDPK1	0.021	0.11	-10000	0	-0.36	22	22
TCR/CD3/MHC I/CD8/Fyn	-0.001	0.16	-10000	0	-0.6	24	24

×

S1P4 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-9999	-10000	0	0
GNAO1	-0.12	0.16	-9999	-0.32	170	170
CDC42/GTP	-0.053	0.1	-9999	-0.32	23	23
PLCG1	-0.056	0.11	-9999	-0.33	23	23
mol:GTP	0	0	-9999	-10000	0	0
GNAI2	0.012	0	-9999	-10000	0	0
GNAI3	0.012	0	-9999	-10000	0	0
G12/G13	0.018	0	-9999	-10000	0	0
cell migration	-0.053	0.1	-9999	-0.31	23	23
S1PR5	-0.002	0.098	-9999	-0.71	8	8
S1PR4	0.003	0.059	-9999	-0.36	10	10
MAPK3	-0.056	0.11	-9999	-0.33	23	23
MAPK1	-0.056	0.11	-9999	-0.33	23	23
S1P/S1P5/Gi	-0.064	0.11	-9999	-0.34	20	20
GNAI1	0.001	0.06	-9999	-0.32	14	14
CDC42/GDP	0.008	0.011	-9999	-10000	0	0
S1P/S1P5/G12	0.007	0.065	-9999	-0.46	8	8
RHOA	0.019	0.03	-9999	-0.39	1	1
S1P/S1P4/Gi	-0.064	0.12	-9999	-0.35	23	23
mol:GDP	0	0	-9999	-10000	0	0
GNAZ	0.005	0.048	-9999	-0.32	9	9
S1P/S1P4/G12/G13	0.018	0.033	-9999	-0.42	1	1
GNA12	0.012	0	-9999	-10000	0	0
GNA13	0.012	0	-9999	-10000	0	0
CDC42	0.011	0.016	-9999	-0.32	1	1

×

IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1	0	0.11	-10000	0	-0.34	21	21
TBX21	-0.085	0.34	-10000	0	-1	32	32
B2M	0.012	0.008	-10000	0	-10000	0	0
TYK2	0.011	0.019	-10000	0	-10000	0	0
IL12RB1	-0.002	0.089	-10000	0	-0.48	12	12
GADD45B	-0.036	0.25	-10000	0	-0.86	13	13
IL12RB2	0.007	0.06	-10000	0	-0.53	4	4
GADD45G	-0.04	0.25	-10000	0	-0.84	16	16
natural killer cell activation	-0.001	0.02	-10000	0	-10000	0	0
RELB	0.012	0	-10000	0	-10000	0	0
RELA	0.012	0	-10000	0	-10000	0	0
IL18	0.013	0.024	-10000	0	-0.32	2	2
IL2RA	0.005	0.046	-10000	0	-0.32	8	8
IFNG	-0.074	0.23	-10000	0	-0.71	49	49
STAT3 (dimer)	-0.037	0.25	-10000	0	-0.66	31	31
HLA-DRB5	-0.021	0.14	-10000	0	-0.53	26	26
FASLG	-0.091	0.35	-10000	0	-0.95	41	41
NF kappa B2 p52/RelB	-0.14	0.24	-10000	0	-0.76	39	39
CD4	0.008	0.04	-10000	0	-0.32	6	6
SOCS1	-0.017	0.14	-10000	0	-0.71	17	17
EntrezGene:6955	0	0.009	-10000	0	-10000	0	0
CD3D	0.003	0.054	-10000	0	-0.32	11	11
CD3E	0.001	0.061	-10000	0	-0.32	14	14
CD3G	-0.009	0.083	-10000	0	-0.33	26	26
IL12Rbeta2/JAK2	0.014	0.058	-10000	0	-0.58	2	2
CCL3	-0.084	0.32	-10000	0	-0.84	42	42
CCL4	-0.072	0.31	-10000	0	-0.87	33	33
HLA-A	0.012	0.008	-10000	0	-10000	0	0
IL18/IL18R	0.034	0.06	-10000	0	-10000	0	0
NOS2	-0.09	0.36	-10000	0	-1	38	38
IL12/IL12R/TYK2/JAK2/SPHK2	0.01	0.086	-10000	0	-0.31	10	10
IL1R1	-0.074	0.31	-10000	0	-0.9	32	32
IL4	0.003	0.02	-10000	0	-10000	0	0
JAK2	0.009	0.036	-10000	0	-0.35	3	3
EntrezGene:6957	0	0.009	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.026	0.23	-10000	0	-0.81	27	27
RAB7A	-0.015	0.22	-10000	0	-0.76	9	9
lysosomal transport	-0.012	0.21	-10000	0	-0.72	9	9
FOS	-0.03	0.24	-10000	0	-0.93	18	18
STAT4 (dimer)	-0.034	0.26	-10000	0	-0.8	21	21
STAT5A (dimer)	-0.17	0.28	-10000	0	-0.78	56	56
GZMA	-0.096	0.36	-10000	0	-1	38	38
GZMB	-0.14	0.35	-10000	0	-0.86	48	48
HLX	0.011	0.016	-10000	0	-0.32	1	1
LCK	-0.081	0.32	-10000	0	-0.82	42	42
TCR/CD3/MHC II/CD4	-0.01	0.15	-10000	0	-0.48	26	26
IL2/IL2R	0.019	0.039	-10000	0	-0.31	3	3
MAPK14	-0.031	0.26	-10000	0	-0.83	16	16
CCR5	-0.046	0.27	-10000	0	-0.95	17	17
IL1B	-0.082	0.24	-10000	0	-0.69	56	56
STAT6	-0.005	0.097	-10000	0	-10000	0	0
STAT4	0.002	0.055	-10000	0	-0.32	12	12
STAT3	0.012	0	-10000	0	-10000	0	0
STAT1	0.008	0.05	-10000	0	-0.71	2	2
NFKB1	0.012	0	-10000	0	-10000	0	0
NFKB2	0.012	0	-10000	0	-10000	0	0
IL12B	0.002	0.064	-10000	0	-0.71	3	3
CD8A	-0.004	0.077	-10000	0	-0.35	18	18
CD8B	0.003	0.061	-10000	0	-0.37	10	10
T-helper 1 cell differentiation	0	0	-10000	0	-10000	0	0
natural killer cell mediated cytotoxicity	-0.001	0.1	0.33	21	-10000	0	21
IL2RB	0.007	0.04	-10000	0	-0.32	6	6
proteasomal ubiquitin-dependent protein catabolic process	-0.028	0.25	-10000	0	-0.73	21	21
IL2RG	0.01	0.023	-10000	0	-0.32	2	2
IL12	0.009	0.065	-10000	0	-0.54	4	4
STAT5A	0.012	0	-10000	0	-10000	0	0
CD247	0.006	0.047	-10000	0	-0.33	8	8
IL2	0.003	0.005	-10000	0	-10000	0	0
SPHK2	0.011	0.016	-10000	0	-0.32	1	1
FRAP1	0	0	-10000	0	-10000	0	0
IL12A	0.007	0.049	-10000	0	-0.42	4	4
IL12/IL12R/TYK2/JAK2	-0.082	0.33	-10000	0	-0.82	47	47
MAP2K3	-0.034	0.26	-10000	0	-0.8	19	19
RIPK2	0.012	0	-10000	0	-10000	0	0
MAP2K6	-0.036	0.26	-10000	0	-0.82	17	17
regulation of dendritic cell antigen processing and presentation	0	0	-10000	0	-10000	0	0
HLA-DRA	0.011	0.023	-10000	0	-0.32	2	2
IL18RAP	0	0.069	-10000	0	-0.32	18	18
IL12Rbeta1/TYK2	0.007	0.073	-10000	0	-0.38	10	10
EOMES	-0.029	0.22	-10000	0	-1.1	16	16
STAT1 (dimer)	-0.059	0.26	-10000	0	-0.69	35	35
T cell proliferation	-0.019	0.21	-10000	0	-0.62	18	18
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
IL18R1	0.009	0.041	-10000	0	-0.32	6	6
CD8-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.094	0.17	-10000	0	-0.68	17	17
ATF2	-0.023	0.24	-10000	0	-0.8	13	13

×

Sphingosine 1-phosphate (S1P) 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
SPHK2	0.011	0.016	-9999	-0.32	1	1
SPHK1	-0.041	0.19	-9999	-0.71	31	31
GNAI2	0.012	0	-9999	-10000	0	0
mol:S1P	-0.002	0.067	-9999	-0.23	32	32
GNAO1	-0.12	0.16	-9999	-0.32	170	170
mol:Sphinganine-1-P	-0.024	0.14	-9999	-0.53	31	31
growth factor activity	0	0	-9999	-10000	0	0
S1P/S1P2/G12/G13	0.019	0.05	-9999	-10000	0	0
GNAI3	0.012	0	-9999	-10000	0	0
G12/G13	0.018	0	-9999	-10000	0	0
S1PR3	0.012	0	-9999	-10000	0	0
S1PR2	0.012	0	-9999	-10000	0	0
EDG1	0	0	-9999	-10000	0	0
S1P1/S1P	-0.004	0.056	-9999	-0.2	32	32
S1PR5	-0.002	0.098	-9999	-0.71	8	8
S1PR4	0.003	0.059	-9999	-0.36	10	10
GNAI1	0.001	0.06	-9999	-0.32	14	14
S1P/S1P5/G12	0.004	0.082	-9999	-0.45	8	8
S1P/S1P3/Gq	0.016	0.056	-9999	-0.34	5	5
S1P/S1P4/Gi	-0.064	0.12	-9999	-0.34	29	29
GNAQ	0.01	0.023	-9999	-0.32	2	2
GNAZ	0.005	0.048	-9999	-0.32	9	9
GNA14	0.01	0.023	-9999	-0.32	2	2
GNA15	0	0.092	-9999	-0.71	7	7
GNA12	0.012	0	-9999	-10000	0	0
GNA13	0.012	0	-9999	-10000	0	0
GNA11	0.011	0.016	-9999	-0.32	1	1
ABCC1	0.012	0	-9999	-10000	0	0

×

Signaling events regulated by Ret tyrosine kinase

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.01	0.039	-9999	-10000	0	0
Crk/p130 Cas/Paxillin	-0.081	0.096	-9999	-0.35	3	3
JUN	-0.057	0.11	-9999	-0.31	38	38
HRAS	0.011	0.016	-9999	-0.32	1	1
RET51/GFRalpha1/GDNF/GRB10	-0.065	0.12	-9999	-0.33	24	24
RAP1A	0.012	0	-9999	-10000	0	0
FRS2	0.012	0.001	-9999	-10000	0	0
RAP1A/GDP	0.009	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/DOK1	-0.065	0.12	-9999	-0.33	24	24
EntrezGene:5979	0	0	-9999	-10000	0	0
PTPN11	0.012	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.012	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/Enigma	-0.046	0.086	-9999	-0.31	1	1
RHOA	0.012	0	-9999	-10000	0	0
RAP1A/GTP	-0.056	0.1	-9999	-0.43	3	3
GRB7	-0.007	0.12	-9999	-0.71	11	11
RET51/GFRalpha1/GDNF	-0.065	0.12	-9999	-0.32	39	39
MAPKKK cascade	-0.077	0.099	-9999	-0.42	3	3
BCAR1	0.011	0.016	-9999	-0.32	1	1
RET9/GFRalpha1/GDNF/IRS1	-0.046	0.086	-9999	-0.31	1	1
lamellipodium assembly	-0.081	0.096	-9999	-0.27	38	38
RET51/GFRalpha1/GDNF/SHC	-0.065	0.12	-9999	-0.33	24	24
PIK3CA	0.012	0.001	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/SHC	-0.046	0.086	-9999	-0.31	1	1
RET9/GFRalpha1/GDNF/Shank3	-0.046	0.087	-9999	-0.31	2	2
MAPK3	-0.049	0.098	-9999	-0.4	3	3
DOK1	0.012	0	-9999	-10000	0	0
DOK6	0.002	0.055	-9999	-0.32	12	12
PXN	0.012	0	-9999	-10000	0	0
neurite development	-0.041	0.1	-9999	-0.41	2	2
DOK5	0.004	0.051	-9999	-0.32	10	10
GFRA1	-0.12	0.16	-9999	-0.32	159	159
MAPK8	-0.065	0.12	-9999	-0.33	38	38
HRAS/GTP	-0.088	0.11	-9999	-0.35	38	38
tube development	-0.038	0.081	-9999	-0.29	2	2
MAPK1	-0.049	0.098	-9999	-0.4	3	3
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.05	0.094	-9999	-0.35	1	1
Rac1/GDP	0.009	0	-9999	-10000	0	0
SRC	0.012	0	-9999	-10000	0	0
PDLIM7	0.012	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/Dok6	-0.06	0.12	-9999	-0.44	7	7
SHC1	0.012	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/Dok4	-0.066	0.12	-9999	-0.32	40	40
RET51/GFRalpha1/GDNF/Dok5	-0.069	0.12	-9999	-0.32	44	44
PRKCA	0.012	0	-9999	-10000	0	0
HRAS/GDP	0.008	0.011	-9999	-0.22	1	1
CREB1	-0.081	0.14	-9999	-0.36	38	38
PIK3R1	0.012	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.05	0.094	-9999	-0.35	1	1
RET51/GFRalpha1/GDNF/Grb7	-0.077	0.14	-9999	-0.37	48	48
mol:GDP	0	0	-9999	-10000	0	0
RET	-0.041	0.13	-9999	-0.33	64	64
DOK4	0.011	0.016	-9999	-0.32	1	1
JNK cascade	-0.056	0.11	-9999	-0.3	38	38
RET9/GFRalpha1/GDNF/FRS2	-0.046	0.086	-9999	-0.31	1	1
SHANK3	0.011	0.016	-9999	-0.32	1	1
RASA1	0.012	0.001	-9999	-10000	0	0
NCK1	0.012	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.051	0.095	-9999	-0.35	1	1
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.074	0.13	-9999	-0.35	38	38
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK	-0.074	0.13	-9999	-0.35	38	38
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.08	0.14	-9999	-0.41	38	38
PI3K	-0.088	0.16	-9999	-0.4	38	38
SOS1	0.012	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/Shank3/Grb2	-0.037	0.082	-9999	-0.29	2	2
GRB10	0.012	0	-9999	-10000	0	0
activation of MAPKK activity	-0.062	0.11	-9999	-0.28	38	38
RET51/GFRalpha1/GDNF/FRS2	-0.065	0.12	-9999	-0.32	39	39
GAB1	0.012	0	-9999	-10000	0	0
IRS1	0.012	0	-9999	-10000	0	0
IRS2	0.01	0.035	-9999	-0.71	1	1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.08	0.14	-9999	-0.41	38	38
RET51/GFRalpha1/GDNF/PKC alpha	-0.065	0.12	-9999	-0.32	39	39
GRB2	0.012	0	-9999	-10000	0	0
PRKACA	0.012	0	-9999	-10000	0	0
GDNF	0.007	0.023	-9999	-0.32	2	2
RAC1	0.012	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/IRS1	-0.065	0.12	-9999	-0.32	39	39
Rac1/GTP	-0.093	0.11	-9999	-0.32	38	38
RET9/GFRalpha1/GDNF	-0.059	0.094	-9999	-0.34	1	1
GFRalpha1/GDNF	-0.073	0.11	-9999	-0.4	1	1

×

RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.016	0.035	-9999	-0.52	1	1
VDR	0.012	0	-9999	-10000	0	0
FAM120B	0.012	0	-9999	-10000	0	0
RXRs/LXRs/DNA/9cRA	-0.037	0.098	-9999	-0.39	2	2
RXRs/LXRs/DNA/Oxysterols	-0.024	0.094	-9999	-0.51	1	1
MED1	0.01	0.035	-9999	-0.71	1	1
mol:9cRA	0.004	0.006	-9999	-10000	0	0
RARs/THRs/DNA/Src-1	-0.03	0.09	-9999	-0.34	2	2
RXRs/NUR77	-0.041	0.098	-9999	-0.45	5	5
RXRs/PPAR	-0.048	0.094	-9999	-0.34	1	1
NCOR2	0.011	0.016	-9999	-0.32	1	1
VDR/VDR/Vit D3	0.009	0	-9999	-10000	0	0
RARs/VDR/DNA/Vit D3	0.025	0.027	-9999	-0.39	1	1
RARA	0.009	0.039	-9999	-0.51	2	2
NCOA1	0.012	0	-9999	-10000	0	0
VDR/VDR/DNA	0.012	0	-9999	-10000	0	0
RARs/RARs/DNA/9cRA	0.021	0.027	-9999	-0.39	1	1
RARG	0.012	0	-9999	-10000	0	0
RPS6KB1	0.024	0.036	-9999	-0.3	1	1
RARs/THRs/DNA/SMRT	-0.03	0.092	-9999	-0.34	3	3
THRA	0.01	0.035	-9999	-0.71	1	1
mol:Bile acids	0	0	-9999	-10000	0	0
VDR/Vit D3/DNA	0.009	0	-9999	-10000	0	0
RXRs/PPAR/9cRA/PGJ2/DNA	-0.04	0.087	-9999	-10000	0	0
NR1H4	-0.14	0.16	-9999	-0.32	184	184
RXRs/LXRs/DNA	-0.019	0.086	-9999	-10000	0	0
NR1H2	0.016	0.017	-9999	-0.32	1	1
NR1H3	0.016	0.005	-9999	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.035	0.081	-9999	-10000	0	0
NR4A1	0.004	0.072	-9999	-0.63	5	5
mol:ATRA	0	0	-9999	-10000	0	0
RXRs/FXR/9cRA/MED1	-0.13	0.13	-9999	-0.32	90	90
RXRG	-0.13	0.16	-9999	-0.32	176	176
RXR alpha/CCPG	0.02	0.012	-9999	-10000	0	0
RXRA	0.015	0.017	-9999	-0.32	1	1
RXRB	0.016	0.005	-9999	-10000	0	0
THRB	-0.085	0.15	-9999	-0.32	122	122
PPARG	0.011	0.016	-9999	-0.32	1	1
PPARD	0.012	0	-9999	-10000	0	0
TNF	-0.017	0.096	-9999	-0.88	1	1
mol:Oxysterols	0.005	0.005	-9999	-10000	0	0
cholesterol transport	-0.024	0.094	-9999	-0.51	1	1
PPARA	0.012	0	-9999	-10000	0	0
mol:Vit D3	0	0	-9999	-10000	0	0
RARB	0.009	0.032	-9999	-0.32	4	4
RXRs/NUR77/BCL2	-0.065	0.11	-9999	-0.4	11	11
SREBF1	-0.016	0.087	-9999	-10000	0	0
RXRs/RXRs/DNA/9cRA	-0.039	0.088	-9999	-10000	0	0
ABCA1	-0.021	0.12	-9999	-0.9	4	4
RARs/THRs	-0.017	0.082	-9999	-0.39	2	2
RXRs/FXR	-0.11	0.12	-9999	-0.3	88	88
BCL2	0.001	0.06	-9999	-0.32	14	14

×

Glypican 2 network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MDK	-0.004	0.1	-9999	-0.71	9	9
GPC2	-0.005	0.11	-9999	-0.71	10	10
GPC2/Midkine	-0.007	0.11	-9999	-0.53	19	19
neuron projection morphogenesis	-0.007	0.11	-9999	-0.53	19	19

×

EGFR-dependent Endothelin 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HRAS	0.011	0.016	-9999	-0.32	1	1
EGFR	0.012	0	-9999	-10000	0	0
EGF/EGFR	-0.036	0.14	-9999	-0.44	36	36
EGF/EGFR dimer/SHC/GRB2/SOS1	-0.011	0.11	-9999	-0.39	23	23
mol:GTP	0	0	-9999	-10000	0	0
EDNRA	-0.016	0.14	-9999	-0.71	16	16
response to oxidative stress	0	0	-9999	-10000	0	0
EGF	-0.073	0.19	-9999	-0.43	79	79
EGF/EGFR dimer/SHC	-0.029	0.12	-9999	-0.46	23	23
mol:GDP	-0.013	0.1	-9999	-0.38	23	23
mol:Ca2+	0	0	-9999	-10000	0	0
EDN1	0.008	0.05	-9999	-0.71	2	2
GRB2/SOS1	0.018	0	-9999	-10000	0	0
HRAS/GTP	-0.035	0.086	-9999	-0.35	23	23
SHC1	0.012	0	-9999	-10000	0	0
HRAS/GDP	-0.011	0.098	-9999	-0.36	23	23
FRAP1	-0.017	0.098	-9999	-0.37	23	23
EGF/EGFR dimer	-0.044	0.14	-9999	-0.53	23	23
SOS1	0.012	0	-9999	-10000	0	0
GRB2	0.012	0	-9999	-10000	0	0
ETA receptor/Endothelin-1	-0.006	0.11	-9999	-0.53	18	18

×

Thromboxane A2 receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGM2	0.004	0.07	-10000	0	-0.71	4	4
GNB1/GNG2	-0.068	0.057	-10000	0	-0.19	27	27
AKT1	-0.042	0.077	-10000	0	-0.21	2	2
EGF	-0.073	0.19	-10000	0	-0.43	79	79
mol:TXA2	0	0	-10000	0	-10000	0	0
FGR	-0.039	0.069	-10000	0	-0.32	1	1
mol:Ca2+	-0.072	0.11	-10000	0	-0.27	27	27
LYN	-0.038	0.067	-10000	0	-10000	0	0
RhoA/GTP	-0.035	0.042	-10000	0	-10000	0	0
mol:PGI2	0	0	-10000	0	-10000	0	0
SYK	-0.079	0.12	-10000	0	-0.34	13	13
GNG2	-0.003	0.069	-10000	0	-0.32	19	19
ARRB2	0.012	0	-10000	0	-10000	0	0
TP alpha/Gq family/GDP/G beta5/gamma2	-0.002	0.057	-10000	0	-0.32	7	7
G beta5/gamma2	-0.083	0.072	-10000	0	-0.27	13	13
PRKCH	-0.076	0.12	-10000	0	-0.34	12	12
DNM1	0.007	0.061	-10000	0	-0.71	3	3
TXA2/TP beta/beta Arrestin3	-0.018	0.025	-10000	0	-0.24	1	1
mol:GTP	-0.001	0.001	-10000	0	-10000	0	0
PTGDR	-0.16	0.17	-10000	0	-0.32	216	216
G12 family/GTP	-0.088	0.089	-10000	0	-0.3	13	13
ADRBK1	0.012	0	-10000	0	-10000	0	0
ADRBK2	0.012	0	-10000	0	-10000	0	0
RhoA/GTP/ROCK1	0.015	0.009	-10000	0	-10000	0	0
mol:GDP	0.07	0.081	0.24	21	-10000	0	21
mol:NADP	0.001	0.085	-10000	0	-0.71	6	6
RAB11A	0.012	0	-10000	0	-10000	0	0
PRKG1	-0.01	0.082	-10000	0	-0.32	27	27
mol:IP3	-0.088	0.13	-10000	0	-0.34	27	27
cell morphogenesis	0.015	0.009	-10000	0	-10000	0	0
PLCB2	-0.12	0.16	-10000	0	-0.45	27	27
mol:cGMP	0	0	-10000	0	-10000	0	0
BLK	-0.072	0.1	-10000	0	-0.28	1	1
mol:PDG2	0	0	-10000	0	-10000	0	0
HCK	-0.039	0.069	-10000	0	-10000	0	0
RHOA	0.012	0	-10000	0	-10000	0	0
PTGIR	0.012	0.001	-10000	0	-10000	0	0
PRKCB1	-0.083	0.12	-10000	0	-0.37	12	12
GNAQ	0.01	0.023	-10000	0	-0.32	2	2
mol:L-citrulline	0.001	0.085	-10000	0	-0.71	6	6
TXA2/TXA2-R family	-0.12	0.17	-10000	0	-0.47	27	27
LCK	-0.045	0.081	-10000	0	-0.37	8	8
TXA2/TP beta/beta Arrestin3/RAB11/GDP	-0.06	0.078	-10000	0	-0.34	2	2
TXA2-R family/G12 family/GDP/G beta/gamma	-0.009	0.042	-10000	0	-10000	0	0
TXA2/TP beta/beta Arrestin2/RAB11/GDP	-0.052	0.078	-10000	0	-10000	0	0
MAPK14	-0.05	0.084	-10000	0	-0.24	4	4
TGM2/GTP	-0.11	0.15	-10000	0	-0.4	27	27
MAPK11	-0.051	0.086	-10000	0	-0.25	8	8
ARHGEF1	-0.041	0.068	-10000	0	-0.2	3	3
GNAI2	0.012	0	-10000	0	-10000	0	0
JNK cascade	-0.092	0.13	-10000	0	-0.35	27	27
RAB11/GDP	0.013	0.001	-10000	0	-10000	0	0
ICAM1	-0.063	0.1	-10000	0	-0.3	11	11
cAMP biosynthetic process	-0.095	0.12	-10000	0	-0.34	27	27
Gq family/GTP/EBP50	0.017	0.039	-10000	0	-0.46	1	1
actin cytoskeleton reorganization	0.015	0.009	-10000	0	-10000	0	0
SRC	-0.038	0.067	-10000	0	-10000	0	0
GNB5	0.012	0	-10000	0	-10000	0	0
GNB1	0.012	0	-10000	0	-10000	0	0
EGF/EGFR	-0.06	0.082	-10000	0	-0.26	8	8
VCAM1	-0.069	0.11	-10000	0	-0.34	13	13
TP beta/Gq family/GDP/G beta5/gamma2	-0.002	0.057	-10000	0	-0.32	7	7
platelet activation	-0.068	0.11	-10000	0	-0.3	12	12
PGI2/IP	0.009	0.001	-10000	0	-10000	0	0
PRKACA	-0.08	0.093	-10000	0	-0.26	1	1
Gq family/GDP/G beta5/gamma2	-0.011	0.061	-10000	0	-0.32	7	7
TXA2/TP beta/beta Arrestin2	-0.011	0.022	-10000	0	-0.24	3	3
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TBXA2R	-0.07	0.087	-10000	0	-0.24	1	1
mol:DAG	-0.091	0.13	-10000	0	-0.37	27	27
EGFR	0.012	0	-10000	0	-10000	0	0
TXA2/TP alpha	-0.12	0.16	-10000	0	-0.45	27	27
Gq family/GTP	0.006	0.04	-10000	0	-0.21	10	10
YES1	-0.038	0.067	-10000	0	-10000	0	0
GNAI2/GTP	-0.061	0.059	-10000	0	-10000	0	0
PGD2/DP	-0.11	0.12	-10000	0	-0.22	216	216
SLC9A3R1	0.012	0	-10000	0	-10000	0	0
FYN	-0.038	0.067	-10000	0	-10000	0	0
mol:NO	0.001	0.085	-10000	0	-0.71	6	6
GNA15	0	0.092	-10000	0	-0.71	7	7
PGK/cGMP	-0.003	0.075	-10000	0	-0.49	6	6
RhoA/GDP	0.013	0.001	-10000	0	-10000	0	0
TP alpha/TGM2/GDP/G beta/gamma	-0.055	0.094	-10000	0	-0.41	4	4
NOS3	0.001	0.085	-10000	0	-0.71	6	6
RAC1	0.012	0	-10000	0	-10000	0	0
PRKCA	-0.076	0.12	-10000	0	-0.34	12	12
PRKCB	-0.092	0.12	-10000	0	-0.38	14	14
PRKCE	-0.073	0.12	-10000	0	-0.34	12	12
PRKCD	-0.078	0.12	-10000	0	-0.37	12	12
PRKCG	-0.15	0.18	-10000	0	-0.43	59	59
muscle contraction	-0.11	0.16	-10000	0	-0.44	27	27
PRKCZ	-0.079	0.12	-10000	0	-0.34	13	13
ARR3	0	0.049	-10000	0	-0.71	2	2
TXA2/TP beta	-0.054	0.08	-10000	0	-10000	0	0
PRKCQ	-0.075	0.12	-10000	0	-0.34	13	13
MAPKKK cascade	-0.1	0.14	-10000	0	-0.41	27	27
SELE	-0.086	0.13	-10000	0	-0.3	87	87
TP beta/GNAI2/GDP/G beta/gamma	-0.052	0.088	-10000	0	-10000	0	0
ROCK1	0.011	0.016	-10000	0	-0.32	1	1
GNA14	0.01	0.023	-10000	0	-0.32	2	2
chemotaxis	-0.13	0.18	-10000	0	-0.52	27	27
GNA12	0.012	0	-10000	0	-10000	0	0
GNA13	0.012	0	-10000	0	-10000	0	0
GNA11	0.011	0.016	-10000	0	-0.32	1	1
Rac1/GTP	0.008	0.001	-10000	0	-10000	0	0

×

S1P1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	0.013	0.054	-9999	-0.53	4	4
PDGFRB	0.008	0.05	-9999	-0.71	2	2
SPHK1	-0.024	0.054	-9999	-0.26	5	5
mol:S1P	-0.024	0.053	-9999	-0.27	4	4
S1P1/S1P/Gi	-0.078	0.15	-9999	-0.39	43	43
GNAO1	-0.12	0.16	-9999	-0.32	170	170
PDGFB-D/PDGFRB/PLCgamma1	-0.06	0.13	-9999	-0.48	14	14
PLCG1	-0.067	0.14	-9999	-0.4	30	30
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.008	0.05	-9999	-0.71	2	2
GNAI2	0.012	0.003	-9999	-10000	0	0
GNAI3	0.011	0.003	-9999	-10000	0	0
GNAI1	0	0.061	-9999	-0.32	14	14
mol:GDP	0	0	-9999	-10000	0	0
EDG1	0.01	0.047	-9999	-0.45	4	4
S1P1/S1P	0.003	0.069	-9999	-0.32	6	6
negative regulation of cAMP metabolic process	-0.076	0.15	-9999	-0.38	43	43
MAPK3	-0.074	0.16	-9999	-0.55	22	22
calcium-dependent phospholipase C activity	-0.001	0.002	-9999	-10000	0	0
Rac1/GDP	0.009	0	-9999	-10000	0	0
RhoA/GDP	0.009	0	-9999	-10000	0	0
KDR	0.012	0.016	-9999	-0.32	1	1
PLCB2	0.007	0.064	-9999	-0.29	4	4
RAC1	0.012	0	-9999	-10000	0	0
RhoA/GTP	-0.012	0.054	-9999	-0.28	5	5
receptor internalization	-0.014	0.06	-9999	-0.3	6	6
PTGS2	-0.079	0.21	-9999	-0.84	20	20
Rac1/GTP	-0.012	0.054	-9999	-0.28	5	5
RHOA	0.012	0	-9999	-10000	0	0
VEGFA	0.005	0.07	-9999	-0.7	4	4
negative regulation of T cell proliferation	-0.076	0.15	-9999	-0.38	43	43
GO:0007205	0	0	-9999	-10000	0	0
GNAZ	0.004	0.049	-9999	-0.32	9	9
MAPK1	-0.074	0.16	-9999	-0.55	22	22
S1P1/S1P/PDGFB-D/PDGFRB	0.006	0.081	-9999	-0.38	7	7
ABCC1	0.011	0.002	-9999	-10000	0	0

×

Nongenotropic Androgen signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.009	0	-10000	0	-10000	0	0
GNB1/GNG2	-0.011	0.072	-10000	0	-0.34	4	4
regulation of S phase of mitotic cell cycle	-0.003	0.066	-10000	0	-10000	0	0
GNAO1	-0.12	0.16	-10000	0	-0.32	170	170
HRAS	0.011	0.016	-10000	0	-0.32	1	1
SHBG/T-DHT	0.001	0.051	-10000	0	-0.47	5	5
PELP1	0.012	0	-10000	0	-10000	0	0
AKT1	0.009	0	-10000	0	-10000	0	0
MAP2K1	0.012	0.054	-10000	0	-0.32	1	1
T-DHT/AR	-0.025	0.081	-10000	0	-0.22	58	58
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
mol:GTP	0	0.001	-10000	0	-0.007	7	7
GNAI2	0.012	0	-10000	0	-10000	0	0
GNAI3	0.012	0	-10000	0	-10000	0	0
GNAI1	0.001	0.06	-10000	0	-0.32	14	14
mol:GDP	-0.041	0.1	-10000	0	-0.29	58	58
cell proliferation	0.013	0.076	-10000	0	-0.39	7	7
PIK3CA	0.012	0.001	-10000	0	-10000	0	0
FOS	0.015	0.1	-10000	0	-0.74	7	7
mol:Ca2+	-0.012	0.027	-10000	0	-0.077	60	60
MAPK3	0.012	0.066	-10000	0	-0.36	2	2
MAPK1	0.012	0.038	-10000	0	-0.23	2	2
PIK3R1	0.012	0	-10000	0	-10000	0	0
mol:IP3	0	0.001	-10000	0	-0.004	7	7
cAMP biosynthetic process	0.005	0.053	-10000	0	-0.43	5	5
GNG2	-0.003	0.069	-10000	0	-0.32	19	19
potassium channel inhibitor activity	0	0.001	-10000	0	-0.004	7	7
HRAS/GTP	0.002	0.056	-10000	0	-0.37	1	1
actin cytoskeleton reorganization	0	0.006	-10000	0	-10000	0	0
SRC	0.012	0	-10000	0	-10000	0	0
voltage-gated calcium channel activity	0	0.001	-10000	0	-0.004	7	7
PI3K	0.016	0	-10000	0	-10000	0	0
apoptosis	-0.016	0.067	0.4	7	-10000	0	7
T-DHT/AR/PELP1	-0.012	0.069	-10000	0	-0.46	1	1
HRAS/GDP	-0.021	0.1	-10000	0	-0.27	58	58
CREB1	0.016	0.07	-10000	0	-0.43	7	7
RAC1-CDC42/GTP	0.023	0.007	-10000	0	-10000	0	0
AR	-0.037	0.12	-10000	0	-0.33	58	58
GNB1	0.012	0	-10000	0	-10000	0	0
RAF1	0.007	0.055	-10000	0	-0.35	1	1
RAC1-CDC42/GDP	-0.011	0.1	-10000	0	-10000	0	0
T-DHT/AR/PELP1/Src	-0.003	0.063	-10000	0	-0.42	1	1
MAP2K2	0.012	0.054	-10000	0	-0.32	1	1
T-DHT/AR/PELP1/Src/PI3K	-0.003	0.066	-10000	0	-10000	0	0
GNAZ	0.005	0.048	-10000	0	-0.32	9	9
SHBG	0.001	0.078	-10000	0	-0.71	5	5
Gi family/GNB1/GNG2/GDP	-0.1	0.17	-10000	0	-0.41	62	62
mol:T-DHT	0	0	-10000	0	-0.002	5	5
RAC1	0.012	0	-10000	0	-10000	0	0
GNRH1	0.008	0.001	-10000	0	-10000	0	0
Gi family/GTP	-0.065	0.11	-10000	0	-0.3	57	57
CDC42	0.011	0.016	-10000	0	-0.32	1	1

×

ErbB4 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF	0.022	0.056	-10000	0	-0.47	5	5
epithelial cell differentiation	-0.015	0.063	-10000	0	-0.61	1	1
ITCH	0.012	0.005	-10000	0	-10000	0	0
WWP1	0.024	0.059	-10000	0	-1.2	1	1
FYN	0.012	0	-10000	0	-10000	0	0
EGFR	0.012	0	-10000	0	-10000	0	0
PRL	-0.013	0.11	-10000	0	-0.71	11	11
neuron projection morphogenesis	0.03	0.051	-10000	0	-0.46	1	1
PTPRZ1	-0.13	0.16	-10000	0	-0.32	175	175
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC	0.025	0.056	-10000	0	-0.51	1	1
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta	0.024	0.032	-10000	0	-0.59	1	1
ADAM17	0.012	0.005	-10000	0	-10000	0	0
ErbB4/ErbB4	0.026	0.037	-10000	0	-0.72	1	1
ErbB4/ErbB4/neuregulin 3/neuregulin 3	0.022	0.041	-10000	0	-0.54	2	2
NCOR1	0.012	0	-10000	0	-10000	0	0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn	0.014	0.058	-10000	0	-0.55	1	1
GRIN2B	-0.038	0.14	-10000	0	-0.37	59	59
ErbB4/ErbB2/betacellulin	0.025	0.057	-10000	0	-0.41	6	6
STAT1	0.008	0.05	-10000	0	-0.71	2	2
HBEGF	0.005	0.07	-10000	0	-0.71	4	4
PRLR	0.005	0.048	-10000	0	-0.32	9	9
E4ICDs/ETO2	0.023	0.041	-10000	0	-0.54	2	2
axon guidance	0.063	0.077	-10000	0	-0.73	1	1
NEDD4	0.012	0.006	-10000	0	-10000	0	0
Prolactin receptor/Prolactin receptor/Prolactin	-0.006	0.093	-10000	0	-0.53	11	11
CBFA2T3	-0.028	0.11	-10000	0	-0.33	49	49
ErbB4/ErbB2/HBEGF	0.023	0.067	-10000	0	-0.4	10	10
MAPK3	0.027	0.052	-10000	0	-0.48	1	1
STAT1 (dimer)	0.025	0.046	-10000	0	-0.5	3	3
MAPK1	0.027	0.052	-10000	0	-0.48	1	1
JAK2	0.009	0.028	-10000	0	-0.32	3	3
ErbB4/ErbB2/neuregulin 1 beta	0.007	0.074	-10000	0	-0.44	6	6
NRG1	-0.01	0.075	-10000	0	-10000	0	0
NRG3	0.005	0.035	-10000	0	-0.71	1	1
NRG2	-0.043	0.12	-10000	0	-0.32	65	65
NRG4	0	0.059	-10000	0	-0.36	10	10
heart development	0.063	0.077	-10000	0	-0.73	1	1
neural crest cell migration	0.007	0.073	-10000	0	-0.43	6	6
ERBB2	0.011	0.061	-10000	0	-0.54	5	5
WWOX/E4ICDs	0.027	0.034	-10000	0	-0.65	1	1
SHC1	0.012	0	-10000	0	-10000	0	0
ErbB4/EGFR/neuregulin 4	0.026	0.045	-10000	0	-0.5	2	2
apoptosis	0.023	0.054	0.61	1	-10000	0	1
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta	0.02	0.035	-10000	0	-0.66	1	1
ErbB4/ErbB2/epiregulin	-0.14	0.21	-10000	0	-0.39	168	168
ErbB4/ErbB4/betacellulin/betacellulin	0.026	0.034	-10000	0	-0.65	1	1
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2	0.02	0.083	-10000	0	-0.51	2	2
MDM2	0.027	0.035	-10000	0	-0.65	1	1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta	0.009	0.058	-10000	0	-0.52	1	1
STAT5A	0.063	0.072	-10000	0	-0.69	1	1
ErbB4/EGFR/neuregulin 1 beta	0.014	0.058	-10000	0	-0.55	1	1
DLG4	0.011	0.016	-10000	0	-0.32	1	1
GRB2/SHC	0.018	0	-10000	0	-10000	0	0
E4ICDs/TAB2/NCoR1	0.024	0.032	-10000	0	-0.62	1	1
STAT5A (dimer)	-0.016	0.067	-10000	0	-0.67	1	1
MAP3K7IP2	0	0	-10000	0	-10000	0	0
STAT5B (dimer)	0.064	0.067	-10000	0	-0.69	1	1
LRIG1	0.012	0	-10000	0	-10000	0	0
EREG	-0.28	0.35	-10000	0	-0.68	175	175
BTC	0.006	0.043	-10000	0	-0.32	7	7
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta	0.063	0.077	-10000	0	-0.74	1	1
ERBB4	0.026	0.037	-10000	0	-0.72	1	1
STAT5B	0.012	0	-10000	0	-10000	0	0
YAP1	0.015	0.008	-10000	0	-10000	0	0
GRB2	0.012	0	-10000	0	-10000	0	0
ErbB4/ErbB2/neuregulin 4	0.021	0.063	-10000	0	-0.43	7	7
glial cell differentiation	-0.024	0.031	0.61	1	-10000	0	1
WWOX	0.012	0	-10000	0	-10000	0	0
cell proliferation	0.029	0.086	-10000	0	-0.48	3	3

×

Signaling mediated by p38-alpha and p38-beta

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTGS2	-0.02	0.19	-9999	-0.74	21	21
MKNK1	0.012	0	-9999	-10000	0	0
MAPK14	-0.003	0.085	-9999	-10000	0	0
ATF2/c-Jun	0.011	0.068	-9999	-10000	0	0
MAPK11	-0.007	0.1	-9999	-0.79	2	2
MITF	-0.011	0.13	-9999	-0.59	7	7
MAPKAPK5	0.001	0.1	-9999	-0.49	1	1
KRT8	0.001	0.1	-9999	-0.31	34	34
MAPKAPK3	0.012	0	-9999	-10000	0	0
MAPKAPK2	0.012	0	-9999	-10000	0	0
p38alpha-beta/CK2	-0.007	0.13	-9999	-0.65	2	2
CEBPB	0.001	0.1	-9999	-0.31	34	34
SLC9A1	0	0.11	-9999	-0.32	34	34
mol:GDP	0	0	-9999	-10000	0	0
ATF2	0.006	0.1	-9999	-0.48	1	1
p38alpha-beta/MNK1	0.006	0.1	-9999	-0.54	2	2
JUN	0.011	0.067	-9999	-10000	0	0
PPARGC1A	-0.028	0.14	-9999	-0.59	11	11
USF1	0.001	0.1	-9999	-0.31	34	34
RAB5/GDP/GDI1	0.003	0.073	-9999	-0.36	1	1
NOS2	-0.032	0.22	-9999	-0.76	30	30
DDIT3	0.001	0.1	-9999	-0.49	1	1
RAB5A	0.012	0	-9999	-10000	0	0
HSPB1	0.006	0.084	-9999	-0.4	1	1
p38alpha-beta/HBP1	0.006	0.1	-9999	-0.54	2	2
CREB1	0.003	0.11	-9999	-0.33	34	34
RAB5/GDP	0.009	0	-9999	-10000	0	0
EIF4E	0.006	0.089	-9999	-0.62	1	1
RPS6KA4	0.001	0.1	-9999	-0.31	34	34
PLA2G4A	-0.001	0.098	-9999	-0.43	8	8
GDI1	0.001	0.1	-9999	-0.49	1	1
TP53	-0.005	0.12	-9999	-0.38	35	35
RPS6KA5	0.001	0.1	-9999	-0.31	34	34
ESR1	-0.022	0.14	-9999	-0.38	36	36
HBP1	0.012	0	-9999	-10000	0	0
MEF2C	-0.004	0.11	-9999	-0.32	35	35
MEF2A	0.001	0.1	-9999	-0.49	1	1
EIF4EBP1	0.002	0.11	-9999	-0.34	34	34
KRT19	0.001	0.1	-9999	-0.31	34	34
ELK4	0.001	0.1	-9999	-0.49	1	1
ATF6	0.001	0.1	-9999	-0.49	1	1
ATF1	0.003	0.11	-9999	-0.33	34	34
p38alpha-beta/MAPKAPK2	0.006	0.1	-9999	-0.54	2	2
p38alpha-beta/MAPKAPK3	0.006	0.1	-9999	-0.54	2	2

×

S1P3 pathway

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
PDGFRB	0.008	0.05	-9999	-0.71	2	2
mol:S1P	0.001	0.003	-9999	-10000	0	0
S1P1/S1P/Gi	-0.056	0.1	-9999	-0.31	26	26
GNAO1	-0.12	0.16	-9999	-0.32	170	170
S1P/S1P3/G12/G13	0.024	0.004	-9999	-10000	0	0
AKT1	0.008	0.039	-9999	-10000	0	0
AKT3	-0.033	0.16	-9999	-1.1	8	8
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.008	0.049	-9999	-0.7	2	2
GNAI2	0.013	0.004	-9999	-10000	0	0
GNAI3	0.013	0.002	-9999	-10000	0	0
GNAI1	0.001	0.06	-9999	-0.32	14	14
mol:GDP	0	0	-9999	-10000	0	0
S1PR3	0.013	0.004	-9999	-10000	0	0
S1PR2	0.012	0	-9999	-10000	0	0
EDG1	0	0	-9999	-10000	0	0
mol:Ca2+	-0.055	0.12	-9999	-0.34	26	26
MAPK3	-0.047	0.11	-9999	-0.32	26	26
MAPK1	-0.047	0.11	-9999	-0.32	26	26
JAK2	-0.049	0.12	-9999	-0.34	26	26
CXCR4	-0.048	0.11	-9999	-0.32	27	27
FLT1	0.013	0.005	-9999	-10000	0	0
RhoA/GDP	0.009	0	-9999	-10000	0	0
Rac1/GDP	0.009	0	-9999	-10000	0	0
SRC	-0.047	0.11	-9999	-0.32	26	26
S1P/S1P3/Gi	-0.055	0.12	-9999	-0.35	26	26
RAC1	0.012	0	-9999	-10000	0	0
RhoA/GTP	-0.045	0.11	-9999	-0.31	26	26
VEGFA	0.007	0.07	-9999	-0.7	4	4
S1P/S1P2/Gi	-0.056	0.11	-9999	-0.31	26	26
VEGFR1 homodimer/VEGFA homodimer	0.018	0.054	-9999	-0.53	4	4
RHOA	0.012	0	-9999	-10000	0	0
S1P/S1P3/Gq	0.019	0.04	-9999	-0.24	8	8
GNAQ	0.01	0.023	-9999	-0.32	2	2
GNAZ	0.005	0.048	-9999	-0.32	9	9
G12/G13	0.018	0	-9999	-10000	0	0
GNA14	0.01	0.023	-9999	-0.32	2	2
GNA15	0	0.092	-9999	-0.71	7	7
GNA12	0.012	0	-9999	-10000	0	0
GNA13	0.012	0	-9999	-10000	0	0
GNA11	0.011	0.016	-9999	-0.32	1	1
Rac1/GTP	-0.045	0.11	-9999	-0.31	26	26

×

Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.012	0	-10000	0	-10000	0	0
RAS family/GTP/Tiam1	-0.022	0.08	-10000	0	-0.28	16	16
NT3 (dimer)/TRKC	-0.044	0.1	-10000	0	-0.4	5	5
NT3 (dimer)/TRKB	-0.1	0.14	-10000	0	-0.36	67	67
SHC/Grb2/SOS1/GAB1/PI3K	0.029	0	-10000	0	-10000	0	0
RAPGEF1	0.011	0.016	-10000	0	-0.32	1	1
BDNF	0	0.092	-10000	0	-0.71	7	7
PIK3CA	0.012	0.001	-10000	0	-10000	0	0
DYNLT1	0.012	0	-10000	0	-10000	0	0
NTRK1	0.003	0.072	-10000	0	-0.63	5	5
NTRK2	-0.089	0.16	-10000	0	-0.34	121	121
NTRK3	-0.07	0.14	-10000	0	-0.32	100	100
NT-4/5 (dimer)/TRKB	-0.12	0.16	-10000	0	-0.39	82	82
neuron apoptosis	0.12	0.16	0.37	92	-10000	0	92
SHC 2-3/Grb2	-0.13	0.17	-10000	0	-0.4	92	92
SHC1	0.012	0	-10000	0	-10000	0	0
SHC2	-0.11	0.16	-10000	0	-0.39	77	77
SHC3	-0.13	0.17	-10000	0	-0.41	93	93
STAT3 (dimer)	0.014	0.036	-10000	0	-0.28	6	6
NT3 (dimer)/TRKA	-0.053	0.1	-10000	0	-0.39	9	9
RIN/GDP	-0.012	0.061	-10000	0	-0.25	1	1
GIPC1	0.011	0.016	-10000	0	-0.32	1	1
KRAS	0.012	0	-10000	0	-10000	0	0
DNAJA3	-0.072	0.12	-10000	0	-0.4	11	11
RIN/GTP	-0.001	0.026	-10000	0	-0.54	1	1
CCND1	0.015	0.073	-10000	0	-0.59	6	6
MAGED1	0.012	0	-10000	0	-10000	0	0
PTPN11	0.012	0	-10000	0	-10000	0	0
RICS	0	0	-10000	0	-10000	0	0
NT-4/5 (dimer)	-0.026	0.14	-10000	0	-0.7	18	18
SHC/GRB2/SOS1	0.024	0	-10000	0	-10000	0	0
GRB2	0.012	0	-10000	0	-10000	0	0
NGF (dimer)/TRKA/MATK	-0.008	0.083	-10000	0	-0.41	7	7
TRKA/NEDD4-2	0.011	0.055	-10000	0	-0.53	4	4
ELMO1	0.011	0.016	-10000	0	-0.32	1	1
RhoG/GTP/ELMO1/DOCK1	0.016	0.009	-10000	0	-10000	0	0
NGF	-0.006	0.072	-10000	0	-0.32	21	21
HRAS	0.011	0.016	-10000	0	-0.32	1	1
DOCK1	0.012	0	-10000	0	-10000	0	0
GAB2	0.012	0	-10000	0	-10000	0	0
RIT2	-0.001	0.035	-10000	0	-0.71	1	1
RIT1	0.012	0	-10000	0	-10000	0	0
FRS2	0.012	0.001	-10000	0	-10000	0	0
DNM1	0.007	0.061	-10000	0	-0.71	3	3
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.012	0	-10000	0	-10000	0	0
SH2B1 (homopentamer)	0	0	-10000	0	-10000	0	0
RhoG/GTP	-0.069	0.12	-10000	0	-0.38	12	12
mol:GDP	-0.017	0.083	-10000	0	-10000	0	0
NGF (dimer)	-0.006	0.072	-10000	0	-0.32	21	21
RhoG/GDP	0.008	0.011	-10000	0	-0.22	1	1
RIT1/GDP	-0.007	0.061	-10000	0	-10000	0	0
TIAM1	-0.016	0.092	-10000	0	-0.32	35	35
PIK3R1	0.012	0	-10000	0	-10000	0	0
BDNF (dimer)/TRKB	-0.043	0.11	-10000	0	-0.47	12	12
KIDINS220/CRKL/C3G	0.017	0.011	-10000	0	-10000	0	0
SHC/RasGAP	0.018	0	-10000	0	-10000	0	0
FRS2 family/SHP2	0.024	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1/GAB1	0.031	0	-10000	0	-10000	0	0
RIT1/GTP	0.009	0	-10000	0	-10000	0	0
NT3 (dimer)	0.004	0.051	-10000	0	-0.32	10	10
RAP1/GDP	-0.023	0.037	-10000	0	-10000	0	0
KIDINS220/CRKL	0.012	0	-10000	0	-10000	0	0
BDNF (dimer)	0	0.092	-10000	0	-0.7	7	7
ubiquitin-dependent protein catabolic process	0.008	0.063	-10000	0	-0.43	5	5
Schwann cell development	-0.026	0.026	-10000	0	-10000	0	0
EHD4	0.012	0	-10000	0	-10000	0	0
FRS2 family/GRB2/SOS1	0.031	0	-10000	0	-10000	0	0
FRS2 family/SHP2/CRK family/C3G/GAB2	0.031	0.008	-10000	0	-10000	0	0
RAP1B	0.012	0	-10000	0	-10000	0	0
RAP1A	0.012	0	-10000	0	-10000	0	0
CDC42/GTP	-0.071	0.096	-10000	0	-0.47	4	4
ABL1	0.012	0	-10000	0	-10000	0	0
SH2B family/GRB2/SOS1	0.018	0	-10000	0	-10000	0	0
Rap1/GTP	0.008	0.053	-10000	0	-10000	0	0
STAT3	0.014	0.036	-10000	0	-10000	0	0
axon guidance	-0.069	0.093	-10000	0	-0.45	4	4
MAPK3	-0.004	0.074	-10000	0	-0.36	7	7
MAPK1	-0.004	0.074	-10000	0	-0.36	7	7
CDC42/GDP	-0.007	0.061	-10000	0	-10000	0	0
NTF3	0.004	0.051	-10000	0	-0.32	10	10
NTF4	-0.026	0.14	-10000	0	-0.71	18	18
NGF (dimer)/TRKA/FAIM	0.008	0.064	-10000	0	-0.43	5	5
PI3K	0.018	0	-10000	0	-10000	0	0
FRS3	0.012	0	-10000	0	-10000	0	0
FAIM	0.012	0.001	-10000	0	-10000	0	0
GAB1	0.012	0	-10000	0	-10000	0	0
RASGRF1	-0.098	0.15	-10000	0	-0.41	41	41
SOS1	0.012	0	-10000	0	-10000	0	0
MCF2L	-0.03	0.087	-10000	0	-0.34	5	5
RGS19	0.012	0	-10000	0	-10000	0	0
CDC42	0.011	0.016	-10000	0	-0.32	1	1
RAS family/GTP	-0.002	0.06	-10000	0	-10000	0	0
Rac1/GDP	-0.007	0.061	-10000	0	-10000	0	0
NGF (dimer)/TRKA/GRIT	0	0.063	-10000	0	-0.44	5	5
neuron projection morphogenesis	-0.067	0.13	-10000	0	-0.4	11	11
NGF (dimer)/TRKA/NEDD4-2	0.008	0.064	-10000	0	-0.43	5	5
MAP2K1	0.029	0	-10000	0	-10000	0	0
NGFR	-0.1	0.16	-10000	0	-0.32	145	145
NGF (dimer)/TRKA/GIPC/GAIP	0.014	0.054	-10000	0	-0.34	1	1
RAS family/GTP/PI3K	0.024	0.013	-10000	0	-10000	0	0
FRS2 family/SHP2/GRB2/SOS1	0.035	0	-10000	0	-10000	0	0
NRAS	0.011	0.016	-10000	0	-0.32	1	1
GRB2/SOS1	0.018	0	-10000	0	-10000	0	0
PRKCI	0.01	0.023	-10000	0	-0.32	2	2
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
RAC1	0.012	0	-10000	0	-10000	0	0
PRKCZ	0.012	0	-10000	0	-10000	0	0
MAPKKK cascade	-0.05	0.13	-10000	0	-0.57	21	21
RASA1	0.012	0.001	-10000	0	-10000	0	0
TRKA/c-Abl	0.011	0.055	-10000	0	-0.53	4	4
SQSTM1	0.012	0	-10000	0	-10000	0	0
BDNF (dimer)/TRKB/GIPC	-0.031	0.1	-10000	0	-0.42	12	12
NGF (dimer)/TRKA/p62/Atypical PKCs	0.021	0.059	-10000	0	-0.42	4	4
MATK	-0.017	0.093	-10000	0	-0.32	36	36
NEDD4L	0.012	0	-10000	0	-10000	0	0
RAS family/GDP	-0.019	0.034	-10000	0	-10000	0	0
NGF (dimer)/TRKA	-0.082	0.13	-10000	0	-0.24	149	149
Rac1/GTP	-0.077	0.09	-10000	0	-0.29	27	27
FRS2 family/SHP2/CRK family	0.035	0	-10000	0	-10000	0	0

×

IFN-gamma pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2	-0.01	0.12	-9999	-0.33	49	49
positive regulation of NF-kappaB transcription factor activity	0	0.001	-9999	-10000	0	0
CRKL	0.012	0	-9999	-10000	0	0
STAT1 (dimer)/Cbp/p300	0.011	0.12	-9999	-0.63	2	2
IFN-gammaR/JAK1/JAK1/JAK2/JAK2	0.014	0.033	-9999	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class I	-0.026	0.048	-9999	-0.28	2	2
CaM/Ca2+	-0.007	0.11	-9999	-0.31	49	49
RAP1A	0.012	0	-9999	-10000	0	0
STAT1 (dimer)/SHP2	-0.008	0.12	-9999	-0.34	39	39
AKT1	0.001	0.1	-9999	-10000	0	0
MAP2K1	-0.004	0.11	-9999	-0.34	1	1
MAP3K11	-0.009	0.11	-9999	-0.32	39	39
IFNGR1	0.008	0.013	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKII	-0.049	0.14	-9999	-0.42	24	24
Rap1/GTP	-0.029	0.077	-9999	-10000	0	0
CRKL/C3G	0.017	0.011	-9999	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP	-0.012	0.13	-9999	-0.37	49	49
CEBPB	0.012	0.12	-9999	-0.51	2	2
STAT3	0.012	0	-9999	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1	-0.022	0.16	-9999	-0.73	10	10
STAT1	-0.01	0.12	-9999	-0.34	39	39
CALM1	0.012	0	-9999	-10000	0	0
IFN-gamma (dimer)	-0.072	0.23	-9999	-0.7	49	49
PIK3CA	0.012	0.001	-9999	-10000	0	0
STAT1 (dimer)/PIAS1	-0.002	0.11	-9999	-0.66	2	2
CEBPB/PTGES2/Cbp/p300	-0.027	0.064	-9999	-10000	0	0
mol:Ca2+	-0.012	0.12	-9999	-0.33	49	49
MAPK3	0.007	0.098	-9999	-10000	0	0
STAT1 (dimer)	-0.033	0.063	-9999	-0.4	2	2
MAPK1	0.007	0.098	-9999	-10000	0	0
JAK2	0.006	0.031	-9999	-0.32	3	3
PIK3R1	0.012	0	-9999	-10000	0	0
JAK1	0.008	0.013	-9999	-10000	0	0
CAMK2D	0.012	0	-9999	-10000	0	0
DAPK1	0.011	0.13	-9999	-0.55	16	16
SMAD7	0.016	0.043	-9999	-10000	0	0
CBL/CRKL/C3G	0.003	0.1	-9999	-10000	0	0
PI3K	-0.036	0.097	-9999	-0.33	1	1
IFNG	-0.072	0.23	-9999	-0.7	49	49
apoptosis	0.006	0.1	-9999	-0.42	16	16
CAMK2G	0.012	0	-9999	-10000	0	0
STAT3 (dimer)	0.012	0	-9999	-10000	0	0
CAMK2A	-0.021	0.097	-9999	-0.32	40	40
CAMK2B	-0.052	0.14	-9999	-0.34	75	75
FRAP1	0.001	0.095	-9999	-10000	0	0
PRKCD	0.002	0.1	-9999	-10000	0	0
RAP1B	0.012	0	-9999	-10000	0	0
negative regulation of cell growth	-0.026	0.048	-9999	-0.28	2	2
PTPN2	0.012	0.001	-9999	-10000	0	0
EP300	0.012	0	-9999	-10000	0	0
IRF1	0.011	0.11	-9999	-0.43	12	12
STAT1 (dimer)/PIASy	-0.003	0.11	-9999	-0.66	2	2
SOCS1	-0.015	0.1	-9999	-0.5	17	17
mol:GDP	0.001	0.1	-9999	-10000	0	0
CASP1	0.016	0.044	-9999	-0.22	1	1
PTGES2	0.012	0	-9999	-10000	0	0
IRF9	0.027	0.043	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.035	0.094	-9999	-0.32	1	1
RAP1/GDP	-0.029	0.077	-9999	-10000	0	0
CBL	-0.01	0.11	-9999	-0.32	39	39
MAP3K1	-0.009	0.11	-9999	-0.32	39	39
PIAS1	0.012	0	-9999	-10000	0	0
PIAS4	0.012	0.001	-9999	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class II	-0.026	0.048	-9999	-0.28	2	2
PTPN11	-0.016	0.12	-9999	-0.33	49	49
CREBBP	0.012	0	-9999	-10000	0	0
RAPGEF1	0.011	0.016	-9999	-0.32	1	1

×

HIF-2-alpha transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MMP14	-0.013	0.072	-10000	0	-0.59	6	6
oxygen homeostasis	-0.008	0.012	-10000	0	-10000	0	0
TCEB2	0.007	0.061	-10000	0	-0.71	3	3
TCEB1	0.01	0.035	-10000	0	-0.71	1	1
VHL/Elongin B/Elongin C/HIF2A	-0.004	0.076	-10000	0	-0.4	3	3
EPO	-0.09	0.19	-10000	0	-0.6	25	25
FIH (dimer)	0.005	0.012	-10000	0	-10000	0	0
APEX1	0	0.015	-10000	0	-10000	0	0
SERPINE1	-0.14	0.3	-10000	0	-0.8	58	58
FLT1	-0.002	0.022	-10000	0	-10000	0	0
ADORA2A	-0.093	0.21	-10000	0	-0.68	22	22
germ cell development	-0.098	0.22	-10000	0	-0.67	29	29
SLC11A2	-0.095	0.21	-10000	0	-0.71	21	21
BHLHE40	-0.096	0.22	-10000	0	-0.73	21	21
HIF1AN	0.005	0.012	-10000	0	-10000	0	0
HIF2A/ARNT/SIRT1	-0.04	0.12	-10000	0	-0.39	3	3
ETS1	0.024	0.005	-10000	0	-10000	0	0
CITED2	-0.006	0.021	-10000	0	-10000	0	0
KDR	-0.004	0.049	-10000	0	-0.9	1	1
PGK1	-0.095	0.21	-10000	0	-0.71	21	21
SIRT1	0.012	0.001	-10000	0	-10000	0	0
response to hypoxia	0	0.001	-10000	0	-10000	0	0
HIF2A/ARNT	-0.11	0.25	-10000	0	-0.85	22	22
EPAS1	-0.022	0.076	-10000	0	-10000	0	0
SP1	0.018	0.002	-10000	0	-10000	0	0
ABCG2	-0.24	0.26	-10000	0	-0.66	71	71
EFNA1	-0.095	0.21	-10000	0	-0.71	21	21
FXN	-0.092	0.21	-10000	0	-0.68	22	22
POU5F1	-0.1	0.23	-10000	0	-0.7	29	29
neuron apoptosis	0.11	0.24	0.81	22	-10000	0	22
EP300	0.012	0	-10000	0	-10000	0	0
EGLN3	0.005	0.012	-10000	0	-10000	0	0
EGLN2	0.004	0.02	-10000	0	-0.33	1	1
EGLN1	0.005	0.012	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C	0.02	0.047	-10000	0	-0.46	4	4
VHL	0.012	0	-10000	0	-10000	0	0
ARNT	0	0.023	-10000	0	-0.35	1	1
SLC2A1	-0.11	0.25	-10000	0	-0.73	38	38
TWIST1	-0.11	0.25	-10000	0	-0.83	27	27
ELK1	0.018	0	-10000	0	-10000	0	0
HIF2A/ARNT/Cbp/p300	-0.036	0.12	-10000	0	-0.4	1	1
VEGFA	-0.098	0.22	-10000	0	-0.71	24	24
CREBBP	0.012	0	-10000	0	-10000	0	0

×

IL27-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	-0.048	0.1	-10000	0	-0.71	1	1
CD4-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
cytokine production during immune response	0.005	0.1	0.46	4	-10000	0	4
IL27/IL27R/JAK1	0.019	0.12	-10000	0	-0.52	3	3
TBX21	0.021	0.13	-10000	0	-0.52	4	4
IL12B	0.002	0.061	-10000	0	-0.72	3	3
IL12A	0.005	0.033	-10000	0	-0.3	4	4
IL6ST	0.003	0.057	-10000	0	-0.33	12	12
IL27RA/JAK1	0.021	0.02	-10000	0	-10000	0	0
IL27	-0.031	0.17	-10000	0	-0.71	24	24
TYK2	0.012	0.005	-10000	0	-10000	0	0
T-helper cell lineage commitment	-0.14	0.24	-10000	0	-0.51	119	119
T-helper 2 cell differentiation	0.005	0.1	0.46	4	-10000	0	4
T cell proliferation during immune response	0.005	0.1	0.46	4	-10000	0	4
MAPKKK cascade	-0.005	0.1	-10000	0	-0.46	4	4
STAT3	0.012	0	-10000	0	-10000	0	0
STAT2	0.012	0	-10000	0	-10000	0	0
STAT1	0.01	0.05	-10000	0	-0.71	2	2
IL12RB1	-0.002	0.083	-10000	0	-0.45	12	12
positive regulation of tyrosine phosphorylation of STAT protein	0	0	-10000	0	-10000	0	0
IL12RB2	0.023	0.13	-10000	0	-0.65	3	3
IL27/IL27R/JAK2/TYK2	-0.005	0.1	-10000	0	-0.46	4	4
positive regulation of T cell mediated cytotoxicity	-0.005	0.1	-10000	0	-0.46	4	4
STAT1 (dimer)	0.016	0.17	-10000	0	-0.65	3	3
JAK2	0.01	0.029	-10000	0	-0.32	3	3
JAK1	0.013	0.002	-10000	0	-10000	0	0
STAT2 (dimer)	0	0.098	-10000	0	-0.47	3	3
T cell proliferation	-0.039	0.13	-10000	0	-0.47	18	18
IL12/IL12R/TYK2/JAK2	0.004	0.082	-10000	0	-10000	0	0
IL17A	-0.15	0.24	-10000	0	-0.51	119	119
mast cell activation	0.005	0.1	0.46	4	-10000	0	4
IFNG	-0.003	0.034	-10000	0	-0.087	49	49
T cell differentiation	-0.002	0.005	-10000	0	-0.019	11	11
STAT3 (dimer)	0	0.098	-10000	0	-0.47	3	3
STAT5A (dimer)	0	0.098	-10000	0	-0.47	3	3
STAT4 (dimer)	-0.003	0.1	-10000	0	-0.41	6	6
STAT4	0.002	0.055	-10000	0	-0.32	12	12
T cell activation	-0.007	0.003	-10000	0	-10000	0	0
IL27R/JAK2/TYK2	0.024	0.052	-10000	0	-10000	0	0
GATA3	0.002	0.1	-10000	0	-0.97	4	4
IL18	0.007	0.016	-10000	0	-0.22	2	2
positive regulation of mast cell cytokine production	0	0.096	-10000	0	-0.46	3	3
IL27/EBI3	-0.028	0.14	-10000	0	-0.48	29	29
IL27RA	0.012	0.019	-10000	0	-10000	0	0
IL6	-0.081	0.17	-10000	0	-0.59	26	26
STAT5A	0.012	0	-10000	0	-10000	0	0
monocyte differentiation	0	0.002	-10000	0	-10000	0	0
IL2	-0.004	0.013	-10000	0	-10000	0	0
IL1B	-0.063	0.18	-10000	0	-0.52	56	56
EBI3	-0.009	0.082	-10000	0	-0.32	27	27
TNF	0.008	0.011	-10000	0	-0.22	1	1

×

Arf6 signaling events

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CENTA1/KIF3B	0.015	0.013	-9999	-10000	0	0
ARNO/beta Arrestin1-2	0	0.05	-9999	-10000	0	0
EGFR	0.012	0	-9999	-10000	0	0
EPHA2	0.008	0.05	-9999	-0.71	2	2
USP6	0.01	0.035	-9999	-0.71	1	1
IQSEC1	0.012	0	-9999	-10000	0	0
EGFR/EGFR/EGF/EGF	-0.044	0.14	-9999	-0.53	23	23
ARRB2	0.007	0.002	-9999	-10000	0	0
mol:GTP	0.012	0.016	-9999	-10000	0	0
ARRB1	0.011	0.016	-9999	-0.32	1	1
FBXO8	0.011	0.016	-9999	-0.32	1	1
TSHR	0.005	0.05	-9999	-0.71	2	2
EGF	-0.073	0.19	-9999	-0.43	79	79
somatostatin receptor activity	0	0	-9999	-0.001	11	11
ARAP2	0.011	0.016	-9999	-0.32	1	1
mol:GDP	-0.057	0.082	-9999	-0.22	43	43
mol:PI-3-4-5-P3	0	0	-9999	-0.001	2	2
ITGA2B	-0.015	0.13	-9999	-0.71	15	15
ARF6	0.012	0	-9999	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	0.029	0.031	-9999	-0.41	2	2
ADAP1	0.012	0	-9999	-10000	0	0
KIF13B	0.01	0.023	-9999	-0.32	2	2
HGF/MET	-0.001	0.09	-9999	-0.55	9	9
PXN	0.012	0	-9999	-10000	0	0
ARF6/GTP	-0.045	0.078	-9999	-0.24	14	14
EGFR/EGFR/EGF/EGF/ARFGEP100	-0.029	0.12	-9999	-0.46	23	23
ADRB2	-0.038	0.12	-9999	-0.32	62	62
receptor agonist activity	0	0	-9999	0	15	15
actin filament binding	0	0	-9999	0	13	13
SRC	0.012	0	-9999	-10000	0	0
ITGB3	0.005	0.048	-9999	-0.32	9	9
GNAQ	0.01	0.023	-9999	-0.32	2	2
EFA6/PI-4-5-P2	0	0	-9999	-0.001	4	4
ARF6/GDP	0.004	0.061	-9999	-0.28	8	8
ARF6/GDP/GULP/ACAP1	-0.046	0.086	-9999	-0.45	2	2
alphaIIb/beta3 Integrin/paxillin/GIT1	0.01	0.086	-9999	-0.41	15	15
ACAP1	0.001	0.058	-9999	-0.32	13	13
ACAP2	0.011	0.016	-9999	-0.32	1	1
LHCGR/beta Arrestin2	0.001	0.004	-9999	-10000	0	0
EFNA1	0.012	0	-9999	-10000	0	0
HGF	0	0.065	-9999	-0.35	13	13
CYTH3	0.008	0	-9999	-10000	0	0
CYTH2	0.008	0.001	-9999	-10000	0	0
NCK1	0.012	0	-9999	-10000	0	0
fibronectin binding	0	0	-9999	0	3	3
endosomal lumen acidification	0	0	-9999	0	5	5
microtubule-based process	0	0	-9999	-10000	0	0
GULP1	-0.002	0.067	-9999	-0.32	18	18
GNAQ/ARNO	0.014	0.003	-9999	-10000	0	0
mol:Phosphatidic acid	0	0	-9999	-10000	0	0
PIP3-E	0	0	-9999	0	3	3
MET	-0.002	0.098	-9999	-0.71	8	8
GNA14	0.01	0.023	-9999	-0.32	2	2
GNA15	0	0.092	-9999	-0.71	7	7
GIT1	0.012	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-0.001	5	5
GNA11	0.011	0.016	-9999	-0.32	1	1
LHCGR	0.001	0.004	-9999	-10000	0	0
AGTR1	-0.15	0.16	-9999	-0.32	202	202
desensitization of G-protein coupled receptor protein signaling pathway	0.001	0.004	-9999	-10000	0	0
IPCEF1/ARNO	-0.021	0.094	-9999	-0.35	23	23
alphaIIb/beta3 Integrin	-0.008	0.11	-9999	-0.53	15	15

×

Signaling events mediated by PTP1B

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
PDGFRB	0.008	0.05	-10000	0	-0.71	2	2
Jak2/Leptin Receptor	-0.029	0.068	-10000	0	-0.32	8	8
PTP1B/AKT1	-0.038	0.066	-10000	0	-0.25	1	1
FYN	0.012	0	-10000	0	-10000	0	0
p210 bcr-abl/PTP1B	-0.049	0.073	-10000	0	-0.28	1	1
EGFR	0.009	0.005	-10000	0	-10000	0	0
EGF/EGFR	-0.073	0.12	-10000	0	-0.33	53	53
CSF1	0.011	0.016	-10000	0	-0.32	1	1
AKT1	0.012	0.001	-10000	0	-10000	0	0
INSR	0.012	0.001	-10000	0	-10000	0	0
PTP1B/N-cadherin	-0.046	0.08	-10000	0	-0.57	2	2
Insulin Receptor/Insulin	-0.032	0.042	-10000	0	-10000	0	0
HCK	0.009	0.032	-10000	0	-0.32	4	4
CRK	0.012	0	-10000	0	-10000	0	0
TYK2	-0.041	0.07	-10000	0	-0.26	1	1
EGF	-0.075	0.19	-10000	0	-0.44	79	79
YES1	0.011	0.016	-10000	0	-0.32	1	1
CAV1	-0.048	0.081	-10000	0	-0.29	3	3
TXN	0.01	0.003	-10000	0	-10000	0	0
PTP1B/IRS1/GRB2	-0.033	0.069	-10000	0	-0.25	1	1
cell migration	0.049	0.073	0.28	1	-10000	0	1
STAT3	0.012	0.001	-10000	0	-10000	0	0
PRLR	0.004	0.048	-10000	0	-0.32	9	9
ITGA2B	-0.015	0.13	-10000	0	-0.7	15	15
CSF1R	0.002	0.058	-10000	0	-0.32	13	13
Prolactin Receptor/Prolactin	-0.007	0.092	-10000	0	-0.53	11	11
FGR	0.009	0.039	-10000	0	-0.51	2	2
PTP1B/p130 Cas	-0.041	0.071	-10000	0	-0.25	2	2
Crk/p130 Cas	-0.034	0.069	-10000	0	-10000	0	0
DOK1	-0.03	0.065	-10000	0	-0.4	1	1
JAK2	-0.031	0.07	-10000	0	-0.3	13	13
Jak2/Leptin Receptor/Leptin	-0.053	0.073	-10000	0	-0.42	5	5
PIK3R1	0.012	0	-10000	0	-10000	0	0
PTPN1	-0.049	0.074	-10000	0	-0.28	1	1
LYN	0.012	0	-10000	0	-10000	0	0
CDH2	-0.007	0.084	-10000	0	-0.36	21	21
SRC	-0.007	0.031	-10000	0	-10000	0	0
ITGB3	0.004	0.048	-10000	0	-0.32	9	9
CAT1/PTP1B	-0.079	0.1	-10000	0	-0.32	22	22
CAPN1	0.011	0.001	-10000	0	-10000	0	0
CSK	0.012	0	-10000	0	-10000	0	0
PI3K	-0.028	0.032	-10000	0	-10000	0	0
mol:H2O2	0.001	0.005	-10000	0	-10000	0	0
STAT3 (dimer)	-0.048	0.066	-10000	0	-0.38	3	3
negative regulation of transcription	-0.031	0.069	-10000	0	-0.3	13	13
FCGR2A	0.008	0.05	-10000	0	-0.71	2	2
FER	0.009	0.017	-10000	0	-0.33	1	1
alphaIIb/beta3 Integrin	-0.009	0.11	-10000	0	-0.53	15	15
BLK	-0.11	0.16	-10000	0	-0.32	155	155
Insulin Receptor/Insulin/Shc	0.016	0.001	-10000	0	-10000	0	0
RHOA	0.011	0.001	-10000	0	-10000	0	0
LEPR	0.005	0.048	-10000	0	-0.32	9	9
BCAR1	0.011	0.016	-10000	0	-0.32	1	1
p210 bcr-abl/Grb2	0.012	0	-10000	0	-10000	0	0
mol:NADPH	-0.001	0.002	-10000	0	-10000	0	0
TRPV6	-0.074	0.12	-10000	0	-0.35	29	29
PRL	-0.014	0.11	-10000	0	-0.7	11	11
SOCS3	0.014	0.011	-10000	0	-10000	0	0
SPRY2	0.014	0.004	-10000	0	-10000	0	0
Insulin Receptor/Insulin/IRS1	0.016	0.001	-10000	0	-10000	0	0
CSF1/CSF1R	-0.038	0.073	-10000	0	-0.3	1	1
Ras protein signal transduction	0.026	0.023	-10000	0	-10000	0	0
IRS1	0.012	0	-10000	0	-10000	0	0
INS	0	0.001	-10000	0	-10000	0	0
LEP	-0.037	0.13	-10000	0	-0.39	46	46
STAT5B	-0.038	0.067	-10000	0	-0.22	5	5
STAT5A	-0.038	0.067	-10000	0	-0.22	5	5
GRB2	0.012	0	-10000	0	-10000	0	0
PDGFB-D/PDGFRB	-0.042	0.078	-10000	0	-0.56	2	2
CSN2	0.009	0.041	-10000	0	-0.49	1	1
PIK3CA	0.012	0.001	-10000	0	-10000	0	0
LAT	-0.01	0.05	-10000	0	-0.53	2	2
YBX1	0.018	0.002	-10000	0	-10000	0	0
LCK	-0.003	0.1	-10000	0	-0.66	9	9
SHC1	0.012	0	-10000	0	-10000	0	0
NOX4	-0.33	0.36	-10000	0	-0.7	197	197

×

Integrins in angiogenesis

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	0.012	0.055	-9999	-0.53	4	4
alphaV beta3 Integrin	-0.001	0.07	-9999	-0.34	5	5
PTK2	0.006	0.092	-9999	-0.38	8	8
IGF1R	0.012	0	-9999	-10000	0	0
PI4KB	0.012	0	-9999	-10000	0	0
MFGE8	0.012	0	-9999	-10000	0	0
SRC	0.012	0	-9999	-10000	0	0
CDKN1B	0.003	0.056	-9999	-0.3	9	9
VEGFA	0.005	0.07	-9999	-0.71	4	4
ILK	0.003	0.056	-9999	-0.3	9	9
ROCK1	0.011	0.016	-9999	-0.32	1	1
AKT1	0.009	0.052	-9999	-0.27	9	9
PTK2B	0.021	0.046	-9999	-0.38	4	4
alphaV/beta3 Integrin/JAM-A	0.003	0.083	-9999	-0.39	9	9
CBL	0.012	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
alphaV beta3 Integrin/ANGPTL3	0.015	0.028	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.011	0.075	-9999	-10000	0	0
VEGF/Rho/ROCK/alphaV/beta3 Integrin	0.022	0.045	-9999	-0.37	1	1
alphaV/beta3 Integrin/Syndecan-1	0.02	0.028	-9999	-10000	0	0
PI4KA	0.012	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.058	0.1	-9999	-0.36	22	22
PI4 Kinase	0.018	0	-9999	-10000	0	0
PIK3CA	0.012	0.001	-9999	-10000	0	0
alphaV/beta3 Integrin/Osteopontin	-0.18	0.23	-9999	-0.46	172	172
RPS6KB1	-0.027	0.11	-9999	-0.36	7	7
TLN1	0.012	0	-9999	-10000	0	0
MAPK3	-0.036	0.16	-9999	-0.43	50	50
GPR124	0.012	0	-9999	-10000	0	0
MAPK1	-0.036	0.16	-9999	-0.45	42	42
PXN	0.012	0	-9999	-10000	0	0
PIK3R1	0.012	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Tumstatin	-0.003	0.078	-9999	-0.44	6	6
cell adhesion	0.022	0.029	-9999	-10000	0	0
ANGPTL3	0.004	0.006	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Src	0.019	0.048	-9999	-0.46	4	4
IGF-1R heterotetramer	0.012	0	-9999	-10000	0	0
Rac1/GDP	0.009	0	-9999	-10000	0	0
TGFBR2	0.012	0	-9999	-10000	0	0
ITGB3	0.005	0.048	-9999	-0.32	9	9
IGF1	-0.067	0.14	-9999	-0.32	99	99
RAC1	0.012	0	-9999	-10000	0	0
regulation of cell-matrix adhesion	0.02	0.028	-9999	-10000	0	0
apoptosis	0.012	0	-9999	-10000	0	0
CD47	0.012	0	-9999	-10000	0	0
alphaV/beta3 Integrin/CD47	0.02	0.028	-9999	-10000	0	0
VCL	0.012	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Del1	-0.015	0.086	-9999	-0.34	9	9
CSF1	0.011	0.016	-9999	-0.32	1	1
PIK3C2A	0.002	0.061	-9999	-0.32	10	10
PI4 Kinase/Pyk2	-0.024	0.067	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.022	0.051	-9999	-0.41	4	4
FAK1/Vinculin	0.012	0.078	-9999	-0.33	2	2
alphaV beta3/Integrin/ppsTEM5	0.02	0.028	-9999	-10000	0	0
RHOA	0.012	0	-9999	-10000	0	0
VTN	-0.005	0.1	-9999	-0.71	9	9
BCAR1	0.011	0.016	-9999	-0.32	1	1
FGF2	-0.025	0.1	-9999	-0.32	46	46
F11R	-0.008	0.072	-9999	-10000	0	0
alphaV/beta3 Integrin/Lactadherin	0.02	0.028	-9999	-10000	0	0
alphaV/beta3 Integrin/TGFBR2	0.02	0.028	-9999	-10000	0	0
alphaV/beta3 Integrin/c-FMS/Cbl/Cas	0.03	0.012	-9999	-10000	0	0
HSP90AA1	0.012	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Talin	0.019	0.025	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.018	0.14	-9999	-0.61	20	20
alphaV/beta3 Integrin/Pyk2	0.025	0.047	-9999	-0.38	4	4
SDC1	0.012	0	-9999	-10000	0	0
VAV3	0.025	0.014	-9999	-10000	0	0
PTPN11	0.012	0	-9999	-10000	0	0
IRS1	0.012	0	-9999	-10000	0	0
FAK1/Paxillin	0.012	0.078	-9999	-0.33	2	2
cell migration	0.018	0.074	-9999	-0.31	1	1
ITGAV	0.012	0	-9999	-10000	0	0
PI3K	0.009	0.076	-9999	-10000	0	0
SPP1	-0.28	0.35	-9999	-0.7	174	174
KDR	0.011	0.016	-9999	-0.32	1	1
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Caspase 8	0.012	0	-9999	-10000	0	0
COL4A3	-0.026	0.12	-9999	-0.37	39	39
angiogenesis	-0.034	0.16	-9999	-0.47	37	37
Rac1/GTP	0.018	0.045	-9999	-10000	0	0
EDIL3	-0.049	0.13	-9999	-0.32	77	77
cell proliferation	0.02	0.028	-9999	-10000	0	0

×

Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HIF3A	-0.079	0.15	-9999	-0.32	114	114
oxygen homeostasis	0	0	-9999	-10000	0	0
TCEB2	0.007	0.061	-9999	-0.71	3	3
TCEB1	0.01	0.035	-9999	-0.71	1	1
HIF1A/p53	0.025	0.003	-9999	-10000	0	0
HIF1A	0.019	0.003	-9999	-10000	0	0
COPS5	0.012	0	-9999	-10000	0	0
VHL/Elongin B/Elongin C/RBX1/CUL2	0.031	0.042	-9999	-0.39	4	4
FIH (dimer)	0.012	0	-9999	-10000	0	0
CDKN2A	-0.17	0.31	-9999	-0.71	105	105
ARNT/IPAS	-0.045	0.1	-9999	-10000	0	0
HIF1AN	0.012	0	-9999	-10000	0	0
GNB2L1	0.012	0	-9999	-10000	0	0
HIF1A/ARNT	0.025	0.003	-9999	-10000	0	0
CUL2	0.012	0	-9999	-10000	0	0
OS9	0.012	0	-9999	-10000	0	0
RACK1/Elongin B/Elongin C	0.02	0.047	-9999	-0.46	4	4
response to hypoxia	0	0	-9999	-10000	0	0
HIF1A/Hsp90	0.025	0.003	-9999	-10000	0	0
PHD1-3/OS9	0.03	0.009	-9999	-10000	0	0
HIF1A/RACK1/Elongin B/Elongin C	0.031	0.036	-9999	-0.33	4	4
VHL	0.012	0	-9999	-10000	0	0
HSP90AA1	0.012	0	-9999	-10000	0	0
HIF1A/JAB1	0.025	0.003	-9999	-10000	0	0
EGLN3	0.012	0	-9999	-10000	0	0
EGLN2	0.011	0.016	-9999	-0.32	1	1
EGLN1	0.012	0	-9999	-10000	0	0
TP53	0.012	0	-9999	-10000	0	0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A	0.029	0.02	-9999	-10000	0	0
ARNT	0.011	0.016	-9999	-0.32	1	1
ARD1A	0	0	-9999	-10000	0	0
RBX1	0.011	0.016	-9999	-0.32	1	1
HIF1A/p19ARF	-0.071	0.17	-9999	-0.36	105	105

×

Aurora A 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
Aurora A/GADD45A	0.021	0.013	-9999	-10000	0	0
BIRC5	0.01	0.035	-9999	-0.71	1	1
NFKBIA	0.021	0.013	-9999	-10000	0	0
CPEB1	-0.11	0.16	-9999	-0.32	148	148
AKT1	0.021	0.013	-9999	-10000	0	0
NDEL1	0.012	0	-9999	-10000	0	0
Aurora A/BRCA1	0.019	0.012	-9999	-10000	0	0
NDEL1/TACC3	0.026	0.011	-9999	-10000	0	0
GADD45A	0.012	0	-9999	-10000	0	0
GSK3B	0.011	0.001	-9999	-10000	0	0
PAK1/Aurora A	0.021	0.013	-9999	-10000	0	0
MDM2	0.011	0.016	-9999	-0.32	1	1
JUB	-0.18	0.32	-9999	-0.71	112	112
TPX2	0.004	0.084	-9999	-0.53	10	10
TP53	0.022	0.016	-9999	-0.25	1	1
DLG7	0.014	0.013	-9999	-0.25	1	1
AURKAIP1	0.012	0	-9999	-10000	0	0
ARHGEF7	0.012	0	-9999	-10000	0	0
G2 phase of mitotic cell cycle	0	0	-9999	-10000	0	0
Aurora A/NDEL1/TACC3	0.027	0.012	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	0.019	0.012	-9999	-10000	0	0
AURKA	0.017	0.015	-9999	-0.29	1	1
AURKB	0.012	0.004	-9999	-10000	0	0
CDC25B	-0.026	0.082	-9999	-0.27	23	23
G2/M transition checkpoint	-0.098	0.19	-9999	-0.41	112	112
mRNA polyadenylation	-0.044	0.078	-9999	-10000	0	0
Aurora A/CPEB	-0.045	0.079	-9999	-10000	0	0
Aurora A/TACC1/TRAP/chTOG	0.033	0.011	-9999	-10000	0	0
BRCA1	0.012	0	-9999	-10000	0	0
centrosome duplication	0.021	0.013	-9999	-10000	0	0
regulation of centrosome cycle	0.025	0.011	-9999	-10000	0	0
spindle assembly	0.032	0.011	-9999	-10000	0	0
TDRD7	0.012	0	-9999	-10000	0	0
Aurora A/RasGAP/Survivin	0.03	0.022	-9999	-0.37	1	1
CENPA	0.015	0.007	-9999	-10000	0	0
Aurora A/PP2A	0.021	0.013	-9999	-10000	0	0
meiosis	0	0	-9999	-10000	0	0
protein catabolic process	0.026	0.01	-9999	-10000	0	0
negative regulation of DNA binding	0.022	0.016	-9999	-0.25	1	1
prophase	0	0	-9999	-10000	0	0
GIT1/beta-PIX	0.018	0	-9999	-10000	0	0
RASA1	0.012	0.001	-9999	-10000	0	0
Ajuba/Aurora A	-0.098	0.19	-9999	-0.42	112	112
mitotic prometaphase	0	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.017	0.015	-9999	-0.29	1	1
TACC1	0.012	0	-9999	-10000	0	0
TACC3	0.012	0	-9999	-10000	0	0
Aurora A/Antizyme1	0.027	0.012	-9999	-10000	0	0
Aurora A/RasGAP	0.021	0.013	-9999	-0.24	1	1
OAZ1	0.012	0	-9999	-10000	0	0
RAN	0.012	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
PRKACA	0.011	0.001	-9999	-10000	0	0
GIT1	0.012	0	-9999	-10000	0	0
GIT1/beta-PIX/PAK1	0.024	0	-9999	-10000	0	0
Importin alpha/Importin beta/TPX2	0.004	0.084	-9999	-0.53	10	10
PPP2R5D	0.012	0	-9999	-10000	0	0
Aurora A/TPX2	0.015	0.071	-9999	-0.43	10	10
PAK1	0.012	0	-9999	-10000	0	0
CKAP5	0.012	0	-9999	-10000	0	0

×

Signaling mediated by p38-gamma and p38-delta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EEF2K	0.021	0	-9999	-10000	0	0
SNTA1	0.011	0.016	-9999	-0.32	1	1
response to hypoxia	0	0	-9999	-10000	0	0
STMN1	0.02	0.009	-9999	-10000	0	0
MAPK12	0.015	0.054	-9999	-0.47	5	5
CCND1	0.012	0.03	-9999	-0.18	8	8
p38 gamma/SNTA1	0.021	0.052	-9999	-0.44	5	5
MAP2K3	0.012	0	-9999	-10000	0	0
PKN1	0.012	0	-9999	-10000	0	0
G2/M transition checkpoint	0.015	0.054	-9999	-0.46	5	5
MAP2K6	0.016	0.015	-9999	-10000	0	0
MAPT	-0.046	0.12	-9999	-0.23	112	112
MAPK13	0.017	0	-9999	-10000	0	0
hyperosmotic response	0	0	-9999	-10000	0	0
ZAK	0.014	0	-9999	-10000	0	0

×

Regulation of nuclear SMAD2/3 signaling

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
EP300	0.014	0.013	-10000	0	-10000	0	0
HSPA8	0.011	0.003	-10000	0	-10000	0	0
SMAD3/SMAD4/ER alpha	0.007	0.085	-10000	0	-10000	0	0
AKT1	-0.003	0.033	-10000	0	-10000	0	0
GSC	-0.022	0.13	-10000	0	-0.49	28	28
NKX2-5	-0.015	0.11	-10000	0	-0.7	10	10
muscle cell differentiation	0.019	0.048	-10000	0	-10000	0	0
SMAD2-3/SMAD4/SP1	0.01	0.085	-10000	0	-10000	0	0
SMAD4	0.005	0.035	-10000	0	-10000	0	0
CBFB	0.012	0	-10000	0	-10000	0	0
SAP18	0.012	0.001	-10000	0	-10000	0	0
Cbp/p300/MSG1	-0.093	0.21	-10000	0	-0.45	105	105
SMAD3/SMAD4/VDR	0.042	0.029	-10000	0	-10000	0	0
MYC	0.02	0.072	-10000	0	-0.64	4	4
CDKN2B	-0.24	0.52	-10000	0	-1.2	91	91
AP1	0.035	0.039	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1	0.038	0.028	-10000	0	-10000	0	0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1	-0.05	0.15	-10000	0	-0.37	35	35
SP3	0.014	0	-10000	0	-10000	0	0
CREB1	0.012	0	-10000	0	-10000	0	0
FOXH1	-0.003	0.08	-10000	0	-0.42	12	12
SMAD3/SMAD4/GR	0.016	0.079	-10000	0	-10000	0	0
GATA3	0.004	0.054	-10000	0	-0.44	4	4
SKI/SIN3/HDAC complex/NCoR1	0.035	0.01	-10000	0	-10000	0	0
MEF2C/TIF2	0.002	0.094	-10000	0	-0.46	2	2
endothelial cell migration	0.058	0.19	0.5	66	-10000	0	66
MAX	0.016	0.013	-10000	0	-10000	0	0
RBBP7	0.012	0.001	-10000	0	-10000	0	0
RBBP4	0.012	0.001	-10000	0	-10000	0	0
RUNX2	0.012	0	-10000	0	-10000	0	0
RUNX3	0.011	0.016	-10000	0	-0.32	1	1
RUNX1	0.012	0	-10000	0	-10000	0	0
CTBP1	0.012	0	-10000	0	-10000	0	0
NR3C1	-0.007	0.087	-10000	0	-0.32	29	29
VDR	0.012	0	-10000	0	-10000	0	0
CDKN1A	0.034	0.057	-10000	0	-10000	0	0
KAT2B	-0.001	0.065	-10000	0	-0.31	17	17
SMAD2/SMAD2/SMAD4/FOXH1	0	0.076	-10000	0	-0.5	3	3
DCP1A	0.012	0	-10000	0	-10000	0	0
SKI	0.012	0.001	-10000	0	-10000	0	0
SERPINE1	-0.059	0.19	-10000	0	-0.5	66	66
SMAD3/SMAD4/ATF2	0.021	0.039	-10000	0	-10000	0	0
SMAD3/SMAD4/ATF3	0.018	0.057	-10000	0	-0.48	3	3
SAP30	0.012	0.001	-10000	0	-10000	0	0
Cbp/p300/PIAS3	0.032	0.03	-10000	0	-10000	0	0
JUN	0.032	0.039	-10000	0	-10000	0	0
SMAD3/SMAD4/IRF7	0.022	0.04	-10000	0	-10000	0	0
TFE3	0.011	0.014	-10000	0	-10000	0	0
COL1A2	-0.023	0.13	-10000	0	-0.55	24	24
mesenchymal cell differentiation	-0.021	0.039	-10000	0	-10000	0	0
DLX1	-0.016	0.13	-10000	0	-0.63	16	16
TCF3	0.012	0	-10000	0	-10000	0	0
FOS	0.01	0.044	-10000	0	-0.32	7	7
SMAD3/SMAD4/Max	0.03	0.047	-10000	0	-10000	0	0
Cbp/p300/SNIP1	0.025	0.011	-10000	0	-10000	0	0
ZBTB17	0.022	0.029	-10000	0	-0.32	1	1
LAMC1	0.025	0.034	-10000	0	-10000	0	0
TGIF2/HDAC complex/SMAD3/SMAD4	0.015	0.068	-10000	0	-0.49	5	5
IRF7	0.011	0.016	-10000	0	-0.32	1	1
ESR1	-0.017	0.094	-10000	0	-0.32	36	36
HNF4A	0.012	0	-10000	0	-10000	0	0
MEF2C	-0.004	0.098	-10000	0	-0.41	7	7
SMAD2-3/SMAD4	0.007	0.065	-10000	0	-10000	0	0
Cbp/p300/Src-1	0.027	0.019	-10000	0	-10000	0	0
IGHV3OR16-13	0.001	0.006	-10000	0	-10000	0	0
TGIF2/HDAC complex	0.003	0.078	-10000	0	-0.7	5	5
CREBBP	0.013	0.009	-10000	0	-10000	0	0
SKIL	0.011	0.016	-10000	0	-0.32	1	1
HDAC1	0.012	0.001	-10000	0	-10000	0	0
HDAC2	0.012	0.001	-10000	0	-10000	0	0
SNIP1	0.011	0.003	-10000	0	-10000	0	0
GCN5L2	0.002	0.011	-10000	0	-10000	0	0
SMAD3/SMAD4/TFE3	0.027	0.043	-10000	0	-10000	0	0
MSG1/HSC70	-0.12	0.24	-10000	0	-0.53	105	105
SMAD2	-0.006	0.043	-10000	0	-0.35	2	2
SMAD3	0.01	0.032	-10000	0	-10000	0	0
SMAD3/E2F4-5/DP1/p107/SMAD4	0.026	0.041	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4	-0.001	0.055	-10000	0	-0.25	17	17
NCOR1	0.012	0.001	-10000	0	-10000	0	0
NCOA2	0.011	0.016	-10000	0	-0.32	1	1
NCOA1	0.012	0	-10000	0	-10000	0	0
MYOD/E2A	0.009	0	-10000	0	-10000	0	0
SMAD2-3/SMAD4/SP1/MIZ-1	0.022	0.086	-10000	0	-10000	0	0
IFNB1	0.02	0.034	-10000	0	-10000	0	0
SMAD3/SMAD4/MEF2C	0.001	0.1	-10000	0	-0.44	3	3
CITED1	-0.17	0.31	-10000	0	-0.71	105	105
SMAD2-3/SMAD4/ARC105	0.015	0.059	-10000	0	-10000	0	0
RBL1	0.012	0.001	-10000	0	-10000	0	0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB	-0.062	0.22	-10000	0	-0.47	91	91
RUNX1-3/PEBPB2	0.024	0.009	-10000	0	-10000	0	0
SMAD7	0.031	0.063	-10000	0	-10000	0	0
MYC/MIZ-1	0.038	0.076	-10000	0	-0.45	4	4
SMAD3/SMAD4	0.022	0.11	0.32	1	-10000	0	1
IL10	0.011	0.1	-10000	0	-0.51	3	3
PIASy/HDAC complex	0.011	0.01	-10000	0	-10000	0	0
PIAS3	0.012	0.005	-10000	0	-10000	0	0
CDK2	0.013	0.009	-10000	0	-10000	0	0
IL5	0.013	0.091	-10000	0	-0.59	6	6
CDK4	0.012	0.036	-10000	0	-0.69	1	1
PIAS4	0.011	0.01	-10000	0	-10000	0	0
ATF3	0.007	0.061	-10000	0	-0.71	3	3
SMAD3/SMAD4/SP1	0.016	0.063	-10000	0	-10000	0	0
FOXG1	-0.089	0.24	-10000	0	-0.71	53	53
FOXO3	-0.001	0.042	-10000	0	-10000	0	0
FOXO1	-0.001	0.042	-10000	0	-10000	0	0
FOXO4	-0.001	0.042	-10000	0	-10000	0	0
heart looping	-0.004	0.097	-10000	0	-0.41	7	7
CEBPB	0.004	0.018	-10000	0	-10000	0	0
SMAD3/SMAD4/DLX1	0.003	0.094	-10000	0	-0.46	13	13
MYOD1	0	0	-10000	0	-10000	0	0
SMAD3/SMAD4/HNF4	0.022	0.039	-10000	0	-10000	0	0
SMAD3/SMAD4/GATA3	0.015	0.075	-10000	0	-0.43	2	2
SnoN/SIN3/HDAC complex/NCoR1	0.011	0.016	-10000	0	-0.32	1	1
SMAD3/SMAD4/RUNX1-3/PEBPB2	0.032	0.036	-10000	0	-10000	0	0
SMAD3/SMAD4/SP1-3	0.028	0.058	-10000	0	-10000	0	0
MED15	0.011	0.016	-10000	0	-0.32	1	1
SP1	0.006	0.032	-10000	0	-10000	0	0
SIN3B	0.012	0.001	-10000	0	-10000	0	0
SIN3A	0.012	0.001	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5	-0.002	0.098	-10000	0	-0.42	13	13
ITGB5	0.031	0.049	-10000	0	-10000	0	0
TGIF/SIN3/HDAC complex/CtBP	0.036	0.004	-10000	0	-10000	0	0
SMAD3/SMAD4/AR	-0.008	0.088	-10000	0	-0.46	1	1
AR	-0.037	0.12	-10000	0	-0.33	58	58
negative regulation of cell growth	0.028	0.046	-10000	0	-10000	0	0
SMAD3/SMAD4/MYOD	0.015	0.038	-10000	0	-10000	0	0
E2F5	0	0.092	-10000	0	-0.71	7	7
E2F4	0.012	0	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF	0.018	0.062	-10000	0	-0.42	3	3
SMAD2-3/SMAD4/FOXO1-3a-4	-0.032	0.15	-10000	0	-0.32	91	91
TFDP1	0.012	0	-10000	0	-10000	0	0
SMAD3/SMAD4/AP1	0.034	0.044	-10000	0	-10000	0	0
SMAD3/SMAD4/RUNX2	0.022	0.039	-10000	0	-10000	0	0
TGIF2	0.003	0.078	-10000	0	-0.71	5	5
TGIF1	0.012	0	-10000	0	-10000	0	0
ATF2	0.012	0.001	-10000	0	-10000	0	0

×

Signaling events mediated by PRL

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCNE1	0.007	0.061	-10000	0	-0.71	3	3
mol:Halofuginone	0.004	0	-10000	0	-10000	0	0
ITGA1	0.012	0	-10000	0	-10000	0	0
CDKN1A	0.026	0.001	-10000	0	-10000	0	0
PRL-3/alpha Tubulin	-0.011	0.12	-10000	0	-0.53	22	22
mol:Ca2+	-0.056	0.2	0.31	20	-0.54	55	75
AGT	-0.083	0.24	-10000	0	-0.71	55	55
CCNA2	0.03	0.001	-10000	0	-10000	0	0
TUBA1B	0.012	0	-10000	0	-10000	0	0
EGR1	0.018	0.011	-10000	0	-10000	0	0
CDK2/Cyclin E1	0.033	0.034	-10000	0	-0.37	3	3
MAPK3	-0.012	0.12	-10000	0	-0.53	22	22
PRL-2 /Rab GGTase beta	0.018	0	-10000	0	-10000	0	0
MAPK1	-0.012	0.12	-10000	0	-0.53	22	22
PTP4A1	0.027	0.001	-10000	0	-10000	0	0
PTP4A3	-0.026	0.16	-10000	0	-0.71	22	22
PTP4A2	0.012	0	-10000	0	-10000	0	0
ITGB1	-0.012	0.12	-10000	0	-0.53	22	22
SRC	0.012	0	-10000	0	-10000	0	0
RAC1	0.016	0.042	-10000	0	-10000	0	0
Rab GGTase beta/Rab GGTase alpha	0.018	0	-10000	0	-10000	0	0
PRL-1/ATF-5	0.031	0.008	-10000	0	-10000	0	0
RABGGTA	0.012	0	-10000	0	-10000	0	0
BCAR1	0.016	0.07	0.31	22	-0.22	1	23
RHOC	0.016	0.042	-10000	0	-10000	0	0
RHOA	0.016	0.042	-10000	0	-10000	0	0
cell motility	0.019	0.044	-10000	0	-10000	0	0
PRL-1/alpha Tubulin	0.031	0.008	-10000	0	-10000	0	0
PRL-3/alpha1 Integrin	-0.011	0.12	-10000	0	-0.53	22	22
ROCK1	0.019	0.044	-10000	0	-10000	0	0
RABGGTB	0.012	0	-10000	0	-10000	0	0
CDK2	0.012	0	-10000	0	-10000	0	0
mitosis	0.026	0.008	-10000	0	-10000	0	0
ATF5	0.012	0	-10000	0	-10000	0	0

×

Coregulation of Androgen receptor activity

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NRIP1	0	0.035	-9999	-0.32	2	2
SVIL	0.001	0.032	-9999	-0.32	2	2
ZNF318	0.033	0.055	-9999	-10000	0	0
JMJD2C	0.003	0.023	-9999	-0.11	14	14
T-DHT/AR/Ubc9	-0.004	0.072	-9999	-0.28	5	5
CARM1	0.011	0.003	-9999	-10000	0	0
PRDX1	0.013	0.004	-9999	-10000	0	0
PELP1	0.015	0.009	-9999	-10000	0	0
CTNNB1	0.004	0.019	-9999	-10000	0	0
AKT1	0.018	0.016	-9999	-10000	0	0
PTK2B	0.005	0.017	-9999	-10000	0	0
MED1	0.017	0.04	-9999	-0.71	1	1
MAK	0.017	0.12	-9999	-0.7	9	9
response to oxidative stress	0.001	0.004	-9999	-10000	0	0
HIP1	0.002	0.028	-9999	-0.32	1	1
GSN	-0.004	0.052	-9999	-0.35	7	7
NCOA2	0.01	0.017	-9999	-0.32	1	1
NCOA6	0.003	0.023	-9999	-10000	0	0
DNA-PK	0.044	0.052	-9999	-10000	0	0
NCOA4	0.01	0.016	-9999	-0.32	1	1
PIAS3	0.004	0.019	-9999	-10000	0	0
cell proliferation	0.009	0.075	-9999	-0.34	9	9
XRCC5	0.017	0.012	-9999	-10000	0	0
UBE3A	-0.002	0.037	-9999	-10000	0	0
T-DHT/AR/SNURF	-0.026	0.099	-9999	-0.38	13	13
FHL2	0.034	0.053	-9999	-10000	0	0
RANBP9	0.003	0.023	-9999	-10000	0	0
JMJD1A	0.006	0.024	-9999	-0.13	12	12
CDK6	0.013	0.003	-9999	-10000	0	0
TGFB1I1	0.002	0.028	-9999	-0.32	1	1
T-DHT/AR/CyclinD1	-0.017	0.093	-9999	-0.48	7	7
XRCC6	0.017	0.012	-9999	-10000	0	0
T-DHT/AR	0.008	0.083	-9999	-0.32	5	5
CTDSP1	0.009	0.008	-9999	-10000	0	0
CTDSP2	0.026	0.038	-9999	-10000	0	0
BRCA1	0.003	0.024	-9999	-10000	0	0
TCF4	0.021	0.036	-9999	-0.32	2	2
CDKN2A	-0.16	0.31	-9999	-0.7	105	105
SRF	0.025	0.017	-9999	-10000	0	0
NKX3-1	-0.008	0.13	-9999	-0.74	11	11
KLK3	-0.17	0.46	-9999	-1.2	65	65
TMF1	0.009	0.017	-9999	-0.32	1	1
HNRNPA1	0.02	0.02	-9999	-10000	0	0
AOF2	-0.009	0.024	-9999	-0.066	62	62
APPL1	0.029	0.038	-9999	-10000	0	0
T-DHT/AR/Caspase 8	0.003	0.077	-9999	-0.45	1	1
AR	-0.034	0.12	-9999	-0.32	58	58
UBA3	0.009	0.008	-9999	-10000	0	0
PATZ1	0.02	0.02	-9999	-10000	0	0
PAWR	0.01	0.004	-9999	-10000	0	0
PRKDC	0.017	0.012	-9999	-10000	0	0
PA2G4	0.021	0.025	-9999	-10000	0	0
UBE2I	0.012	0	-9999	-10000	0	0
T-DHT/AR/Cyclin D3/CDK11 p58	0.003	0.068	-9999	-0.41	1	1
RPS6KA3	0.002	0.027	-9999	-10000	0	0
T-DHT/AR/ARA70	-0.009	0.072	-9999	-0.44	1	1
LATS2	0.02	0.02	-9999	-10000	0	0
T-DHT/AR/PRX1	0.008	0.073	-9999	-0.26	5	5
Cyclin D3/CDK11 p58	0.01	0.004	-9999	-10000	0	0
VAV3	-0.028	0.1	-9999	-0.33	41	41
KLK2	-0.013	0.11	-9999	-0.55	14	14
CASP8	0.015	0.008	-9999	-10000	0	0
T-DHT/AR/TIF2/CARM1	-0.002	0.068	-9999	-0.4	1	1
TMPRSS2	0.005	0.061	-9999	-0.74	1	1
CCND1	-0.003	0.086	-9999	-0.71	6	6
PIAS1	-0.002	0.037	-9999	-10000	0	0
mol:T-DHT	0.003	0.014	-9999	-0.056	20	20
CDC2L1	0.001	0.002	-9999	-10000	0	0
PIAS4	-0.009	0.054	-9999	-10000	0	0
T-DHT/AR/CDK6	-0.001	0.073	-9999	-0.45	1	1
CMTM2	-0.021	0.15	-9999	-0.71	20	20
SNURF	-0.024	0.11	-9999	-0.36	37	37
ZMIZ1	0.014	0.014	-9999	-10000	0	0
CCND3	0.013	0.002	-9999	-10000	0	0
TGIF1	0.02	0.02	-9999	-10000	0	0
FKBP4	0.001	0.042	-9999	-0.7	1	1

×

Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.013	0.054	-9999	-0.39	2	2
CRKL	0.012	0	-9999	-10000	0	0
Rac1/GDP	0.009	0	-9999	-10000	0	0
DOCK1	0.012	0	-9999	-10000	0	0
ITGA4	0.003	0.053	-9999	-0.32	11	11
alpha4/beta7 Integrin/MAdCAM1	-0.06	0.1	-9999	-0.32	15	15
EPO	-0.002	0.078	-9999	-0.71	5	5
alpha4/beta7 Integrin	0.006	0.054	-9999	-0.4	2	2
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.012	0	-9999	-10000	0	0
alpha4/beta1 Integrin	0.012	0.037	-9999	-10000	0	0
EPO/EPOR (dimer)	0.006	0.071	-9999	-0.62	5	5
lamellipodium assembly	0.028	0.002	-9999	-10000	0	0
PIK3CA	0.012	0.001	-9999	-10000	0	0
PI3K	0.018	0	-9999	-10000	0	0
ARF6	0.012	0	-9999	-10000	0	0
JAK2	0.014	0.053	-9999	-0.37	3	3
PXN	0.012	0	-9999	-10000	0	0
PIK3R1	0.012	0	-9999	-10000	0	0
MADCAM1	-0.14	0.16	-9999	-0.32	194	194
cell adhesion	-0.06	0.099	-9999	-0.32	15	15
CRKL/CBL	0.018	0	-9999	-10000	0	0
ITGB1	0.012	0	-9999	-10000	0	0
SRC	0.017	0.043	-9999	-0.3	5	5
ITGB7	0.003	0.053	-9999	-0.32	11	11
RAC1	0.012	0	-9999	-10000	0	0
alpha4/beta1 Integrin/VCAM1	0.016	0.048	-9999	-0.34	5	5
p130Cas/Crk/Dock1	0.033	0.038	-9999	-10000	0	0
VCAM1	0.005	0.046	-9999	-0.32	8	8
RHOA	0.012	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/GIT1	0.026	0.028	-9999	-10000	0	0
BCAR1	0.021	0.04	-9999	-10000	0	0
EPOR	0.01	0.035	-9999	-0.71	1	1
mol:GDP	0	0	-9999	-10000	0	0
CBL	0.012	0	-9999	-10000	0	0
GIT1	0.012	0	-9999	-10000	0	0
Rac1/GTP	0.029	0.002	-9999	-10000	0	0

×

Regulation of Telomerase

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Telomerase catalytic core complex	-0.064	0.18	-9999	-0.58	35	35
RAD9A	0.012	0	-9999	-10000	0	0
AP1	0.014	0.03	-9999	-10000	0	0
IFNAR2	0.012	0.004	-9999	-10000	0	0
AKT1	-0.001	0.044	-9999	-10000	0	0
ER alpha/Oestrogen	-0.011	0.064	-9999	-0.22	36	36
NFX1/SIN3/HDAC complex	0.034	0.012	-9999	-10000	0	0
EGF	-0.074	0.19	-9999	-0.43	79	79
SMG5	0.012	0	-9999	-10000	0	0
SMG6	0.012	0	-9999	-10000	0	0
SP3/HDAC2	0.018	0.008	-9999	-10000	0	0
TERT/c-Abl	-0.055	0.17	-9999	-0.55	33	33
SAP18	0.012	0.001	-9999	-10000	0	0
MRN complex	0.024	0.009	-9999	-10000	0	0
WT1	-0.32	0.36	-9999	-0.71	192	192
WRN	0.011	0.016	-9999	-0.32	1	1
SP1	0.012	0.007	-9999	-10000	0	0
SP3	0.012	0.003	-9999	-10000	0	0
TERF2IP	0.012	0	-9999	-10000	0	0
Telomerase/Nucleolin	-0.063	0.15	-9999	-0.57	12	12
Mad/Max	0.017	0.013	-9999	-10000	0	0
TERT	-0.065	0.19	-9999	-0.6	33	33
CCND1	-0.056	0.17	-9999	-0.68	8	8
MAX	0.012	0.003	-9999	-10000	0	0
RBBP7	0.012	0.001	-9999	-10000	0	0
RBBP4	0.012	0.001	-9999	-10000	0	0
TERF2	0.011	0	-9999	-10000	0	0
PTGES3	0.012	0	-9999	-10000	0	0
SIN3A	0.012	0.001	-9999	-10000	0	0
Telomerase/911	0.021	0.028	-9999	-10000	0	0
CDKN1B	-0.028	0.15	-9999	-0.44	49	49
RAD1	0.01	0.035	-9999	-0.71	1	1
XRCC5	0.012	0	-9999	-10000	0	0
XRCC6	0.012	0	-9999	-10000	0	0
SAP30	0.012	0.001	-9999	-10000	0	0
TRF2/PARP2	0.017	0	-9999	-10000	0	0
UBE3A	0.012	0.003	-9999	-10000	0	0
JUN	0.012	0.003	-9999	-10000	0	0
E6	0	0.003	-9999	-10000	0	0
HPV-16 E6/E6AP	0.009	0.005	-9999	-10000	0	0
FOS	0.006	0.043	-9999	-0.32	7	7
IFN-gamma/IRF1	-0.04	0.18	-9999	-0.52	49	49
PARP2	0.012	0	-9999	-10000	0	0
BLM	0.008	0.05	-9999	-0.71	2	2
Telomerase	0.004	0.055	-9999	-0.28	4	4
IRF1	0.015	0.003	-9999	-10000	0	0
ESR1	-0.017	0.093	-9999	-0.32	36	36
KU/TER	0.018	0	-9999	-10000	0	0
ATM/TRF2	0.018	0	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	0.038	0.012	-9999	-10000	0	0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex	0.038	0.013	-9999	-10000	0	0
HDAC1	0.012	0.001	-9999	-10000	0	0
HDAC2	0.011	0.007	-9999	-10000	0	0
ATM	0	0	-9999	-10000	0	0
SMAD3	0.016	0.027	-9999	-0.53	1	1
ABL1	0.012	0	-9999	-10000	0	0
MXD1	0.011	0.016	-9999	-0.32	1	1
MRE11A	0.012	0.001	-9999	-10000	0	0
HUS1	0.012	0	-9999	-10000	0	0
RPS6KB1	0.011	0.016	-9999	-0.32	1	1
TERT/NF kappa B1/14-3-3	-0.039	0.17	-9999	-0.61	13	13
NR2F2	0.012	0.006	-9999	-10000	0	0
MAPK3	0.011	0.006	-9999	-10000	0	0
MAPK1	0.011	0.006	-9999	-10000	0	0
TGFB1/TGF beta receptor Type II	0.01	0.035	-9999	-0.71	1	1
NFKB1	0.012	0	-9999	-10000	0	0
HNRNPC	0.012	0	-9999	-10000	0	0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis	0	0	-9999	-10000	0	0
NBN	0.011	0.016	-9999	-0.32	1	1
EGFR	0.012	0.002	-9999	-10000	0	0
mol:Oestrogen	0	0.002	-9999	-10000	0	0
EGF/EGFR	-0.044	0.14	-9999	-0.52	24	24
MYC	0.005	0.07	-9999	-0.71	4	4
IL2	0.003	0.009	-9999	-10000	0	0
KU	0.018	0	-9999	-10000	0	0
RAD50	0.012	0	-9999	-10000	0	0
HSP90AA1	0.012	0	-9999	-10000	0	0
TGFB1	0.01	0.035	-9999	-0.71	1	1
TRF2/BLM	0.015	0.036	-9999	-0.5	2	2
FRAP1	0	0	-9999	-10000	0	0
KU/TERT	-0.05	0.17	-9999	-0.56	28	28
SP1/HDAC2	0.018	0.012	-9999	-10000	0	0
PINX1	0.012	0	-9999	-10000	0	0
Telomerase/EST1A	-0.063	0.15	-9999	-0.57	12	12
Smad3/Myc	0.016	0.052	-9999	-0.46	5	5
911 complex	0.023	0.023	-9999	-0.46	1	1
IFNG	-0.07	0.23	-9999	-0.7	49	49
Telomerase/PinX1	-0.063	0.15	-9999	-0.57	12	12
Telomerase/AKT1/mTOR/p70S6K	0.006	0.049	-9999	-10000	0	0
SIN3B	0.012	0.001	-9999	-10000	0	0
YWHAE	0.012	0	-9999	-10000	0	0
Telomerase/EST1B	-0.063	0.15	-9999	-0.56	14	14
response to DNA damage stimulus	0.003	0	-9999	-10000	0	0
MRN complex/TRF2/Rap1	0.034	0.008	-9999	-10000	0	0
TRF2/WRN	0.017	0.01	-9999	-10000	0	0
Telomerase/hnRNP C1/C2	-0.063	0.15	-9999	-0.57	12	12
E2F1	-0.005	0.11	-9999	-0.71	10	10
ZNFX1	0.012	0.001	-9999	-10000	0	0
PIF1	-0.009	0.12	-9999	-0.71	12	12
NCL	0.012	0	-9999	-10000	0	0
DKC1	0.012	0	-9999	-10000	0	0
telomeric DNA binding	0	0	-9999	-10000	0	0

×

Regulation of Androgen receptor activity

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.016	0.003	-9999	-10000	0	0
SMARCC1	0.004	0.008	-9999	-10000	0	0
REL	0.014	0.007	-9999	-10000	0	0
HDAC7	0.016	0.074	-9999	-10000	0	0
JUN	0.01	0.004	-9999	-10000	0	0
EP300	0.012	0.001	-9999	-10000	0	0
KAT2B	-0.002	0.066	-9999	-0.32	17	17
KAT5	0.012	0.001	-9999	-10000	0	0
MAPK14	0.013	0.024	-9999	-10000	0	0
FOXO1	0.012	0.001	-9999	-10000	0	0
T-DHT/AR	0.015	0.08	-9999	-10000	0	0
MAP2K6	0.008	0.03	-9999	-0.34	3	3
BRM/BAF57	0.013	0.017	-9999	-10000	0	0
MAP2K4	0.009	0.017	-9999	-0.32	1	1
SMARCA2	0.009	0.018	-9999	-0.34	1	1
PDE9A	-0.11	0.35	-9999	-0.91	66	66
NCOA2	0.011	0.016	-9999	-0.32	1	1
CEBPA	0.011	0.023	-9999	-0.32	2	2
EHMT2	0.009	0.035	-9999	-0.71	1	1
cell proliferation	0.019	0.095	-9999	-0.44	1	1
NR0B1	0.001	0.049	-9999	-0.71	2	2
EGR1	0.009	0.017	-9999	-0.32	1	1
RXRs/9cRA	-0.056	0.085	-9999	-10000	0	0
AR/RACK1/Src	0.016	0.05	-9999	-10000	0	0
AR/GR	-0.008	0.08	-9999	-0.34	6	6
GNB2L1	0.012	0.001	-9999	-10000	0	0
PKN1	0.012	0.001	-9999	-10000	0	0
RCHY1	0.012	0	-9999	-10000	0	0
epidermal growth factor receptor activity	0	0.002	-9999	-10000	0	0
MAPK8	0.015	0.016	-9999	-10000	0	0
T-DHT/AR/TIF2/CARM1	0.021	0.048	-9999	-10000	0	0
SRC	0.021	0.03	-9999	-10000	0	0
NR3C1	-0.011	0.084	-9999	-0.32	29	29
KLK3	-0.18	0.4	-9999	-1.1	65	65
APPBP2	0.01	0.017	-9999	-0.32	1	1
TRIM24	0.01	0.006	-9999	-10000	0	0
T-DHT/AR/TIP60	0.015	0.045	-9999	-10000	0	0
TMPRSS2	0.01	0.082	-9999	-1	1	1
RXRG	-0.13	0.16	-9999	-0.32	176	176
mol:9cRA	-0.001	0.002	-9999	-10000	0	0
RXRA	0.011	0.016	-9999	-0.32	1	1
RXRB	0.011	0.001	-9999	-10000	0	0
CARM1	0.012	0.001	-9999	-10000	0	0
NR2C2	0.012	0.001	-9999	-10000	0	0
KLK2	0.013	0.099	-9999	-0.48	14	14
AR	-0.009	0.079	-9999	-0.26	8	8
SENP1	0.011	0.001	-9999	-10000	0	0
HSP90AA1	0.012	0	-9999	-10000	0	0
MDM2	0.015	0.02	-9999	-0.32	1	1
SRY	0.002	0.037	-9999	-0.71	1	1
GATA2	0.005	0.048	-9999	-0.32	9	9
MYST2	0.012	0.001	-9999	-10000	0	0
HOXB13	-0.023	0.099	-9999	-0.32	40	40
T-DHT/AR/RACK1/Src	0.019	0.046	-9999	-10000	0	0
positive regulation of transcription	0.005	0.048	-9999	-0.32	9	9
DNAJA1	0.011	0.006	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.023	0.014	-9999	-0.26	1	1
NCOA1	0.013	0.006	-9999	-10000	0	0
SPDEF	-0.053	0.13	-9999	-0.32	81	81
T-DHT/AR/TIF2	0.017	0.051	-9999	-10000	0	0
T-DHT/AR/Hsp90	0.014	0.045	-9999	-10000	0	0
GSK3B	0.011	0.003	-9999	-10000	0	0
NR2C1	0.013	0.002	-9999	-10000	0	0
mol:T-DHT	0.017	0.032	-9999	-10000	0	0
SIRT1	0.012	0.001	-9999	-10000	0	0
ZMIZ2	0.016	0.011	-9999	-10000	0	0
POU2F1	0.011	0.035	-9999	-10000	0	0
T-DHT/AR/DAX-1	0.008	0.052	-9999	-0.37	2	2
CREBBP	0.012	0.001	-9999	-10000	0	0
SMARCE1	0.01	0.007	-9999	-10000	0	0

×

Aurora B signaling

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
Condensin I complex	0.029	0.02	-9999	-0.32	1	1
STMN1	0.021	0.012	-9999	-10000	0	0
Aurora B/RasGAP/Survivin	0.034	0.024	-9999	-0.43	1	1
Chromosomal passenger complex/Cul3 protein complex	0.011	0.057	-9999	-10000	0	0
BIRC5	0.013	0.035	-9999	-0.69	1	1
DES	-0.38	0.22	-9999	-0.51	316	316
Aurora C/Aurora B/INCENP	0.033	0.006	-9999	-10000	0	0
Aurora B/TACC1	0.022	0.004	-9999	-10000	0	0
Aurora B/PP2A	0.024	0.004	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CBX5	0.014	0.001	-9999	-10000	0	0
mitotic metaphase/anaphase transition	0	0	-9999	-10000	0	0
NDC80	0.022	0.003	-9999	-10000	0	0
Cul3 protein complex	-0.002	0.07	-9999	-0.46	2	2
KIF2C	0.025	0.005	-9999	-10000	0	0
PEBP1	0.013	0	-9999	-10000	0	0
KIF20A	0.012	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
Aurora B/RasGAP	0.024	0.004	-9999	-10000	0	0
SEPT1	0.009	0.032	-9999	-0.32	4	4
SMC2	0.011	0.016	-9999	-0.32	1	1
SMC4	0.01	0.023	-9999	-0.32	2	2
NSUN2/NPM1/Nucleolin	0.007	0.013	-9999	-10000	0	0
PSMA3	0.012	0	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	0	0.001	-9999	-10000	0	0
H3F3B	0.017	0.002	-9999	-10000	0	0
AURKB	0.021	0.005	-9999	-10000	0	0
AURKC	0.011	0.002	-9999	-10000	0	0
CDCA8	0.015	0.001	-9999	-10000	0	0
cytokinesis	0.008	0.023	-9999	-10000	0	0
Aurora B/Septin1	0.038	0.022	-9999	-10000	0	0
AURKA	0.01	0.035	-9999	-0.71	1	1
INCENP	0.015	0.001	-9999	-10000	0	0
KLHL13	-0.032	0.12	-9999	-0.34	53	53
BUB1	0.012	0	-9999	-10000	0	0
hSgo1/Aurora B/Survivin	0.032	0.031	-9999	-0.41	2	2
EVI5	0.014	0.001	-9999	-10000	0	0
RhoA/GTP	0.008	0.023	-9999	-0.3	1	1
SGOL1	0.01	0.035	-9999	-0.71	1	1
CENPA	0.028	0.012	-9999	-10000	0	0
NCAPG	0.012	0.001	-9999	-10000	0	0
Aurora B/HC8 Proteasome	0.024	0.004	-9999	-10000	0	0
NCAPD2	0.012	0	-9999	-10000	0	0
Aurora B/PP1-gamma	0.024	0.004	-9999	-10000	0	0
RHOA	0.012	0	-9999	-10000	0	0
NCAPH	0.012	0	-9999	-10000	0	0
NPM1	0.004	0.008	-9999	-10000	0	0
RASA1	0.012	0.001	-9999	-10000	0	0
KLHL9	0.012	0	-9999	-10000	0	0
mitotic prometaphase	0.001	0.001	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.024	0.004	-9999	-10000	0	0
PPP1CC	0.012	0	-9999	-10000	0	0
Centraspindlin	0.048	0.021	-9999	-0.32	1	1
RhoA/GDP	0.009	0	-9999	-10000	0	0
NSUN2	0.004	0.008	-9999	-10000	0	0
MYLK	-0.036	0.1	-9999	-0.23	89	89
KIF23	0.012	0.035	-9999	-0.7	1	1
VIM	0.022	0.003	-9999	-10000	0	0
RACGAP1	0.014	0.001	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
NCL	0.004	0.008	-9999	-10000	0	0
Chromosomal passenger complex	0.037	0.01	-9999	-10000	0	0
Chromosomal passenger complex/EVI5	0.077	0.034	-9999	-0.35	1	1
TACC1	0.012	0	-9999	-10000	0	0
PPP2R5D	0.012	0	-9999	-10000	0	0
CUL3	0.012	0	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0

×

Cellular roles of Anthrax toxin

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ANTXR1	0.006	0.063	-10000	0	-0.61	4	4
ANTXR2	0.011	0.016	-10000	0	-0.32	1	1
negative regulation of myeloid dendritic cell antigen processing and presentation	-0.001	0.008	-10000	0	-0.085	3	3
monocyte activation	0.006	0.054	-10000	0	-0.36	9	9
MAP2K2	0.01	0.004	-10000	0	-10000	0	0
MAP2K1	0.008	0.008	-10000	0	-10000	0	0
MAP2K7	0.007	0.011	-10000	0	-0.15	1	1
MAP2K6	0.006	0.015	-10000	0	-0.15	3	3
CYAA	0.007	0.036	-10000	0	-0.4	3	3
MAP2K4	0.007	0.011	-10000	0	-0.15	1	1
IL1B	-0.042	0.14	-10000	0	-0.38	55	55
Channel	0.011	0.039	-10000	0	-0.42	3	3
NLRP1	0.005	0.025	-10000	0	-0.4	1	1
CALM1	0.012	0	-10000	0	-10000	0	0
negative regulation of phagocytosis	0.01	0.01	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
regulation of endothelial cell proliferation	0.001	0.008	0.085	3	-10000	0	3
MAPK3	0.008	0.008	-10000	0	-10000	0	0
MAPK1	0.008	0.008	-10000	0	-10000	0	0
PGR	-0.037	0.071	-10000	0	-0.15	118	118
PA/Cellular Receptors	0.012	0.042	-10000	0	-0.46	3	3
apoptosis	-0.001	0.008	-10000	0	-0.085	3	3
LOC728358	0	0	-10000	0	-10000	0	0
Lethal toxin (unfolded)	0.011	0.035	-10000	0	-0.38	3	3
macrophage activation	0.012	0.007	-10000	0	-10000	0	0
TNF	0.011	0.016	-10000	0	-0.32	1	1
VCAM1	0.006	0.054	-10000	0	-0.36	9	9
platelet activation	0.01	0.01	-10000	0	-10000	0	0
MAPKKK cascade	-0.01	0.009	-10000	0	-10000	0	0
IL18	0.01	0.017	-10000	0	-0.18	1	1
negative regulation of macrophage activation	-0.001	0.008	-10000	0	-0.085	3	3
LEF	-0.001	0.008	-10000	0	-0.086	3	3
CASP1	0.006	0.012	-10000	0	-0.2	1	1
mol:cAMP	0.01	0.01	-10000	0	-10000	0	0
necrosis	-0.001	0.008	-10000	0	-0.085	3	3
intracellular pH reduction	0	0	-10000	0	-10000	0	0
PAGA	0	0	-10000	0	-10000	0	0
Edema toxin (unfolded)	0.011	0.037	-10000	0	-0.4	3	3
mol:Epigallocatechin-3-gallate (EGCG)	0	0	-10000	0	-10000	0	0

×

Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.012	0	-10000	0	-10000	0	0
NFATC1	0.04	0.028	-10000	0	-10000	0	0
NFATC2	0.028	0.021	-10000	0	-10000	0	0
NFATC3	0.019	0.002	-10000	0	-10000	0	0
YWHAE	0.012	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/CABIN1	-0.072	0.1	-10000	0	-0.32	35	35
Exportin 1/Ran/NUP214	0.025	0.001	-10000	0	-10000	0	0
mol:DAG	0	0.001	-10000	0	-10000	0	0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV	-0.055	0.1	-10000	0	-0.38	12	12
BCL2/BAX	0.01	0.041	-10000	0	-10000	0	0
CaM/Ca2+/Calcineurin A alpha-beta B1	0.01	0.002	-10000	0	-10000	0	0
CaM/Ca2+	0.01	0.002	-10000	0	-10000	0	0
BAX	0.012	0	-10000	0	-10000	0	0
MAPK14	0.012	0.001	-10000	0	-10000	0	0
BAD	0.011	0.016	-10000	0	-0.32	1	1
CABIN1/MEF2D	-0.062	0.1	-10000	0	-0.3	35	35
Calcineurin A alpha-beta B1/BCL2	0.001	0.06	-10000	0	-0.32	14	14
FKBP8	0.011	0.016	-10000	0	-0.32	1	1
activation-induced cell death of T cells	0.061	0.099	0.29	35	-10000	0	35
KPNB1	0.012	0	-10000	0	-10000	0	0
KPNA2	0.008	0.05	-10000	0	-0.71	2	2
XPO1	0.012	0	-10000	0	-10000	0	0
SFN	0.011	0.016	-10000	0	-0.32	1	1
MAP3K8	0.012	0.001	-10000	0	-10000	0	0
NFAT4/CK1 alpha	0.027	0.008	-10000	0	-10000	0	0
MEF2D/NFAT1/Cbp/p300	0.049	0.04	-10000	0	-10000	0	0
CABIN1	-0.072	0.11	-10000	0	-0.32	35	35
CALM1	0.012	0.001	-10000	0	-10000	0	0
RAN	0.012	0	-10000	0	-10000	0	0
MAP3K1	0.011	0.016	-10000	0	-0.32	1	1
CAMK4	-0.007	0.076	-10000	0	-0.32	23	23
mol:Ca2+	0.001	0.002	-10000	0	-10000	0	0
MAPK3	0.012	0	-10000	0	-10000	0	0
YWHAH	0.012	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/AKAP79/PKA	0.007	0.049	-10000	0	-10000	0	0
YWHAB	0.012	0	-10000	0	-10000	0	0
MAPK8	0.012	0.001	-10000	0	-10000	0	0
MAPK9	0.012	0	-10000	0	-10000	0	0
YWHAG	0.012	0	-10000	0	-10000	0	0
FKBP1A	0.012	0	-10000	0	-10000	0	0
NFAT1-c-4/YWHAQ	0.055	0.026	-10000	0	-10000	0	0
PRKCH	0.012	0	-10000	0	-10000	0	0
CABIN1/Cbp/p300	0.018	0.004	-10000	0	-10000	0	0
CASP3	0.012	0.001	-10000	0	-10000	0	0
PIM1	0.012	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0.008	0.001	-10000	0	-10000	0	0
apoptosis	0	0.005	-10000	0	-10000	0	0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1	0.033	0.018	-10000	0	-0.33	1	1
PRKCB	-0.053	0.13	-10000	0	-0.32	82	82
PRKCE	0.012	0	-10000	0	-10000	0	0
JNK2/NFAT4	0.024	0.002	-10000	0	-10000	0	0
BAD/BCL-XL	0.017	0.011	-10000	0	-10000	0	0
PRKCD	0.012	0	-10000	0	-10000	0	0
NUP214	0.012	0	-10000	0	-10000	0	0
PRKCZ	0.012	0.001	-10000	0	-10000	0	0
PRKCA	0.012	0	-10000	0	-10000	0	0
PRKCG	-0.3	0.36	-10000	0	-0.71	183	183
PRKCQ	0.008	0.045	-10000	0	-0.42	4	4
FKBP38/BCL2	0.009	0.043	-10000	0	-10000	0	0
EP300	0.012	0.002	-10000	0	-10000	0	0
PRKCB1	0	0	-10000	0	-10000	0	0
CSNK2A1	0.012	0	-10000	0	-10000	0	0
NFATc/JNK1	0.046	0.027	-10000	0	-10000	0	0
CaM/Ca2+/FKBP38	0.017	0.01	-10000	0	-10000	0	0
FKBP12/FK506	0.009	0	-10000	0	-10000	0	0
CSNK1A1	0.016	0.003	-10000	0	-10000	0	0
CaM/Ca2+/CAMK IV	0.006	0.044	-10000	0	-10000	0	0
NFATc/ERK1	0.046	0.027	-10000	0	-10000	0	0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV	-0.056	0.1	-10000	0	-0.41	9	9
NR4A1	0.044	0.066	-10000	0	-0.54	5	5
GSK3B	0.012	0.001	-10000	0	-10000	0	0
positive T cell selection	0.019	0.002	-10000	0	-10000	0	0
NFAT1/CK1 alpha	0.026	0.017	-10000	0	-10000	0	0
RCH1/ KPNB1	0.015	0.038	-10000	0	-0.53	2	2
YWHAQ	0.012	0	-10000	0	-10000	0	0
PRKACA	0.012	0.001	-10000	0	-10000	0	0
AKAP5	-0.004	0.071	-10000	0	-0.32	20	20
MEF2D	0.012	0.002	-10000	0	-10000	0	0
mol:FK506	0	0	-10000	0	-10000	0	0
YWHAZ	0.012	0	-10000	0	-10000	0	0
NFATc/p38 alpha	0.046	0.027	-10000	0	-10000	0	0
CREBBP	0.012	0.002	-10000	0	-10000	0	0
BCL2	0.001	0.06	-10000	0	-0.32	14	14

×

Rapid glucocorticoid signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma	0.002	0.059	-10000	0	-0.29	6	6
MAPK9	0.007	0	-10000	0	-10000	0	0
adrenocorticotropin secretion	-0.002	0.037	-10000	0	-0.54	2	2
GNB1/GNG2	0.007	0.04	-10000	0	-10000	0	0
GNB1	0.012	0	-10000	0	-10000	0	0
regulation of calcium ion transport via voltage-gated calcium channel activity	0	0	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
MAPK14	0.007	0	-10000	0	-10000	0	0
Gs family/GTP	-0.005	0.045	-10000	0	-0.16	32	32
EntrezGene:2778	0	0	-10000	0	-10000	0	0
vasopressin secretion	0	0	-10000	0	-10000	0	0
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
ChemicalAbstracts:86-01-1	0	0	-10000	0	-10000	0	0
glutamate secretion	0.004	0.012	0.047	32	-10000	0	32
GNAL	-0.014	0.088	-10000	0	-0.32	32	32
GNG2	-0.003	0.069	-10000	0	-0.32	19	19
CRH	-0.003	0.049	-10000	0	-0.71	2	2
mol:cortisol	0	0	-10000	0	-10000	0	0
MAPK8	0.007	0	-10000	0	-10000	0	0
MAPK11	0.005	0.021	-10000	0	-0.3	2	2

×

FAS signaling pathway (CD95)

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
SPTAN1	0.011	0.045	0.34	2	-10000	0	2
RFC1	0.011	0.045	0.34	2	-10000	0	2
PRKDC	0.011	0.045	0.34	2	-10000	0	2
RIPK1	0.012	0.002	-10000	0	-10000	0	0
CASP7	0.018	0.036	0.2	8	-10000	0	8
FASLG/FAS/FADD/FAF1	0.007	0.057	0.22	4	-0.26	5	9
MAP2K4	0.023	0.073	-10000	0	-0.33	2	2
mol:ceramide	0.017	0.065	-10000	0	-0.34	2	2
GSN	0.008	0.044	0.34	2	-10000	0	2
FASLG/FAS/FADD/FAF1/Caspase 8	0.016	0.06	-10000	0	-0.39	1	1
FAS	0.009	0.029	-10000	0	-0.32	3	3
BID	0.013	0.048	0.26	12	-0.47	1	13
MAP3K1	0.025	0.049	0.24	1	-10000	0	1
MAP3K7	0.012	0.002	-10000	0	-10000	0	0
RB1	0.011	0.045	0.34	2	-10000	0	2
CFLAR	0.012	0.002	-10000	0	-10000	0	0
HGF/MET	0	0.1	-10000	0	-0.49	15	15
ARHGDIB	0.011	0.045	0.34	2	-10000	0	2
FADD	0.012	0.004	-10000	0	-10000	0	0
actin filament polymerization	-0.013	0.043	-10000	0	-0.34	2	2
NFKB1	-0.011	0.04	-10000	0	-10000	0	0
MAPK8	0.022	0.098	-10000	0	-0.41	11	11
DFFA	0.011	0.045	0.34	2	-10000	0	2
DNA fragmentation during apoptosis	0.016	0.043	0.2	12	-10000	0	12
FAS/FADD/MET	0.013	0.068	-10000	0	-0.46	8	8
CFLAR/RIP1	0.017	0.004	-10000	0	-10000	0	0
FAIM3	0.002	0.055	-10000	0	-0.32	12	12
FAF1	0.012	0.005	-10000	0	-10000	0	0
PARP1	0.011	0.045	0.34	2	-10000	0	2
DFFB	0.011	0.045	0.2	12	-10000	0	12
CHUK	0.01	0.041	-10000	0	-10000	0	0
FASLG	-0.006	0.086	-10000	0	-0.38	18	18
FAS/FADD	0.016	0.021	-10000	0	-10000	0	0
HGF	0	0.065	-10000	0	-0.35	13	13
LMNA	0.02	0.039	0.3	2	-10000	0	2
CASP6	0.011	0.045	0.34	2	-10000	0	2
CASP10	0.012	0.004	-10000	0	-10000	0	0
CASP3	0.012	0.052	0.21	24	-10000	0	24
PTPN13	-0.002	0.088	-10000	0	-0.48	12	12
CASP8	0.008	0.05	0.3	12	-10000	0	12
IL6	-0.02	0.21	-10000	0	-0.78	26	26
MET	-0.002	0.098	-10000	0	-0.71	8	8
ICAD/CAD	0.01	0.041	0.3	2	-10000	0	2
FASLG/FAS/FADD/FAF1/Caspase 10	0.017	0.066	-10000	0	-0.35	2	2
activation of caspase activity by cytochrome c	0.013	0.048	0.26	12	-0.46	1	13
PAK2	0.016	0.043	0.34	2	-10000	0	2
BCL2	0.001	0.06	-10000	0	-0.32	14	14

×

Class I PI3K signaling events

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
ARF5/GTP	0.028	0.012	-9999	-10000	0	0
DAPP1	-0.028	0.086	-9999	-0.28	13	13
Src family/SYK family/BLNK-LAT/BTK-ITK	-0.039	0.12	-9999	-0.38	14	14
mol:DAG	-0.003	0.068	-9999	-0.22	4	4
HRAS	0.012	0.016	-9999	-0.32	1	1
RAP1A	0.012	0.001	-9999	-10000	0	0
ARF5/GDP	0.009	0.085	-9999	-0.39	11	11
PLCG2	-0.012	0.086	-9999	-0.32	30	30
PLCG1	0.012	0	-9999	-10000	0	0
ARF5	0.012	0	-9999	-10000	0	0
mol:GTP	0	0.013	-9999	-10000	0	0
ARF1/GTP	0.028	0.013	-9999	-10000	0	0
RHOA	0.012	0	-9999	-10000	0	0
YES1	0.011	0.016	-9999	-0.32	1	1
RAP1A/GTP	0.021	0.013	-9999	-10000	0	0
ADAP1	0	0.012	-9999	-10000	0	0
ARAP3	0	0.013	-9999	-10000	0	0
INPPL1	0.012	0	-9999	-10000	0	0
PREX1	0.011	0.016	-9999	-0.32	1	1
ARHGEF6	0.004	0.051	-9999	-0.32	10	10
ARHGEF7	0.012	0	-9999	-10000	0	0
ARF1	0.012	0	-9999	-10000	0	0
NRAS	0.012	0.016	-9999	-0.32	1	1
FYN	0.012	0	-9999	-10000	0	0
ARF6	0.012	0	-9999	-10000	0	0
FGR	0.009	0.039	-9999	-0.51	2	2
mol:Ca2+	0.004	0.039	-9999	-10000	0	0
mol:IP4	0	0	-9999	-10000	0	0
TIAM1	-0.016	0.092	-9999	-0.32	35	35
ZAP70	0.002	0.061	-9999	-0.36	11	11
mol:IP3	0.002	0.052	-9999	-10000	0	0
LYN	0.012	0	-9999	-10000	0	0
ARF1/GDP	0.009	0.085	-9999	-0.39	11	11
RhoA/GDP	0.028	0.038	-9999	-10000	0	0
PDK1/Src/Hsp90	0.024	0	-9999	-10000	0	0
BLNK	0.008	0.036	-9999	-0.32	5	5
actin cytoskeleton reorganization	0.031	0.055	-9999	-0.32	3	3
SRC	0.012	0	-9999	-10000	0	0
PLEKHA2	0.021	0	-9999	-10000	0	0
RAC1	0.012	0	-9999	-10000	0	0
PTEN	0.008	0.015	-9999	-0.3	1	1
HSP90AA1	0.012	0	-9999	-10000	0	0
ARF6/GTP	0.028	0.012	-9999	-10000	0	0
RhoA/GTP	0.025	0.012	-9999	-10000	0	0
Src family/SYK family/BLNK-LAT	-0.027	0.095	-9999	-0.38	7	7
BLK	-0.11	0.16	-9999	-0.32	155	155
PDPK1	0.012	0	-9999	-10000	0	0
CYTH1	0	0.012	-9999	-10000	0	0
HCK	0.009	0.032	-9999	-0.32	4	4
CYTH3	0	0.012	-9999	-10000	0	0
CYTH2	0	0.012	-9999	-10000	0	0
KRAS	0.012	0.001	-9999	-10000	0	0
GO:0030676	0	0	-9999	-10000	0	0
FOXO3	0.025	0.056	-9999	-0.37	8	8
SGK1	-0.007	0.056	-9999	-0.4	8	8
INPP5D	0.012	0	-9999	-10000	0	0
mol:GDP	0.002	0.088	-9999	-0.42	11	11
SOS1	0.012	0	-9999	-10000	0	0
SYK	0.012	0	-9999	-10000	0	0
ARF6/GDP	0.027	0.037	-9999	-10000	0	0
mol:PI-3-4-5-P3	0	0.013	-9999	-10000	0	0
ARAP3/RAP1A/GTP	0.021	0.013	-9999	-10000	0	0
VAV1	0.002	0.058	-9999	-0.32	13	13
mol:PI-3-4-P2	0.017	0	-9999	-10000	0	0
RAS family/GTP/PI3K Class I	0.025	0.011	-9999	-10000	0	0
PLEKHA1	0.021	0	-9999	-10000	0	0
Rac1/GDP	0.009	0.085	-9999	-0.39	11	11
LAT	0.009	0.042	-9999	-0.45	3	3
Rac1/GTP	0	0.11	-9999	-0.49	12	12
ITK	-0.001	0.022	-9999	-0.36	1	1
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma	-0.008	0.089	-9999	-0.29	9	9
LCK	-0.003	0.1	-9999	-0.66	9	9
BTK	-0.001	0.008	-9999	-10000	0	0

×

ErbB2/ErbB3 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
USP8	0.013	0.013	-10000	0	-10000	0	0
RAS family/GTP	0.02	0.064	-10000	0	-10000	0	0
NFATC4	0.015	0.056	-10000	0	-0.34	1	1
ERBB2IP	0.008	0.032	-10000	0	-0.32	4	4
HSP90 (dimer)	0.012	0	-10000	0	-10000	0	0
mammary gland morphogenesis	0.008	0.067	-10000	0	-0.38	2	2
JUN	0.032	0.062	-10000	0	-0.26	7	7
HRAS	0.011	0.016	-10000	0	-0.32	1	1
DOCK7	0.012	0.065	-10000	0	-0.42	1	1
ErbB2/ErbB3/neuregulin 1 beta/SHC	0.001	0.071	-10000	0	-0.42	5	5
AKT1	0.009	0.002	-10000	0	-10000	0	0
BAD	0.014	0.009	-10000	0	-10000	0	0
MAPK10	0.01	0.052	-10000	0	-0.25	1	1
mol:GTP	0	0.001	-10000	0	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta	0.01	0.072	-10000	0	-0.41	2	2
RAF1	0.027	0.069	-10000	0	-10000	0	0
ErbB2/ErbB3/neuregulin 2	-0.018	0.078	-10000	0	-0.45	5	5
STAT3	0.018	0.004	-10000	0	-10000	0	0
cell migration	0.008	0.06	0.16	1	-0.23	1	2
mol:PI-3-4-5-P3	0	0.001	-10000	0	-10000	0	0
cell proliferation	0.028	0.17	-10000	0	-0.6	22	22
FOS	0.035	0.12	-10000	0	-0.36	29	29
NRAS	0.011	0.016	-10000	0	-0.32	1	1
mol:Ca2+	0.008	0.067	-10000	0	-0.38	2	2
MAPK3	0.029	0.13	-10000	0	-0.47	22	22
MAPK1	0.029	0.13	-10000	0	-0.47	22	22
JAK2	0.012	0.065	-10000	0	-0.42	1	1
NF2	0	0.003	-10000	0	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1	0	0.068	-10000	0	-0.3	1	1
NRG1	-0.027	0.11	-10000	0	-0.32	49	49
GRB2/SOS1	0.018	0.001	-10000	0	-10000	0	0
MAPK8	0.01	0.077	-10000	0	-0.36	1	1
MAPK9	0.018	0.038	-10000	0	-10000	0	0
ERBB2	-0.004	0.066	0.3	4	-0.54	5	9
ERBB3	0.012	0.002	-10000	0	-10000	0	0
SHC1	0.012	0.001	-10000	0	-10000	0	0
RAC1	0.012	0	-10000	0	-10000	0	0
apoptosis	-0.01	0.013	-10000	0	-10000	0	0
STAT3 (dimer)	0.017	0.004	-10000	0	-10000	0	0
RNF41	0.018	0.005	-10000	0	-10000	0	0
FRAP1	0.007	0.002	-10000	0	-10000	0	0
RAC1-CDC42/GTP	-0.014	0.039	-10000	0	-0.3	1	1
ErbB2/ErbB2/HSP90 (dimer)	0.003	0.051	-10000	0	-0.46	5	5
CHRNA1	0.022	0.16	-10000	0	-0.59	23	23
myelination	0.015	0.055	-10000	0	-0.33	1	1
PPP3CB	0.011	0.061	-10000	0	-0.39	1	1
KRAS	0.012	0.001	-10000	0	-10000	0	0
RAC1-CDC42/GDP	0.013	0.06	-10000	0	-10000	0	0
NRG2	-0.043	0.12	-10000	0	-0.32	65	65
mol:GDP	0	0.068	-10000	0	-0.3	1	1
SOS1	0.012	0.001	-10000	0	-10000	0	0
MAP2K2	0.03	0.074	-10000	0	-10000	0	0
SRC	0.012	0	-10000	0	-10000	0	0
mol:cAMP	0	0.001	-10000	0	-10000	0	0
PTPN11	0.011	0.065	-10000	0	-0.42	1	1
MAP2K1	0.022	0.13	-10000	0	-0.52	10	10
heart morphogenesis	0.008	0.067	-10000	0	-0.38	2	2
RAS family/GDP	0.02	0.063	-10000	0	-10000	0	0
GRB2	0.012	0.001	-10000	0	-10000	0	0
PRKACA	-0.001	0.004	-10000	0	-10000	0	0
CHRNE	0.013	0.031	-10000	0	-0.2	7	7
HSP90AA1	0.012	0	-10000	0	-10000	0	0
activation of caspase activity	-0.009	0.002	-10000	0	-10000	0	0
nervous system development	0.008	0.067	-10000	0	-0.38	2	2
CDC42	0.011	0.016	-10000	0	-0.32	1	1

×

PLK2 and PLK4 events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLK2	0.002	0.085	-9999	-0.71	6	6
PLK4	0.012	0.001	-9999	-10000	0	0
regulation of centriole replication	0.009	0.065	-9999	-0.53	6	6

×

a4b1 and a4b7 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ITGB1	0.012	0	-9999	-10000	0	0
ITGB7	0.003	0.053	-9999	-0.32	11	11
ITGA4	0.003	0.053	-9999	-0.32	11	11
alpha4/beta7 Integrin	0.006	0.054	-9999	-0.4	2	2
alpha4/beta1 Integrin	0.012	0.037	-9999	-10000	0	0

×

Hedgehog signaling events mediated by Gli proteins

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.012	0	-9999	-10000	0	0
HDAC2	0.012	0	-9999	-10000	0	0
GNB1/GNG2	0.016	0.04	-9999	-10000	0	0
forebrain development	0.008	0.071	-9999	-0.46	4	4
GNAO1	-0.12	0.16	-9999	-0.32	170	170
SMO/beta Arrestin2	0.02	0.003	-9999	-10000	0	0
SMO	0.013	0.002	-9999	-10000	0	0
ARRB2	0.012	0.002	-9999	-10000	0	0
GLI3/SPOP	0.017	0.065	-9999	-10000	0	0
mol:GTP	0	0.001	-9999	-10000	0	0
GSK3B	0.012	0	-9999	-10000	0	0
GNAI2	0.012	0.001	-9999	-10000	0	0
SIN3/HDAC complex	0.03	0.001	-9999	-10000	0	0
GNAI1	0.001	0.06	-9999	-0.32	14	14
XPO1	0.014	0.002	-9999	-10000	0	0
GLI1/Su(fu)	0.019	0.057	-9999	-0.45	2	2
SAP30	0.012	0	-9999	-10000	0	0
mol:GDP	0.013	0.002	-9999	-10000	0	0
MIM/GLI2A	0.013	0.035	-9999	-0.32	4	4
IFT88	0.012	0.001	-9999	-10000	0	0
GNAI3	0.012	0.001	-9999	-10000	0	0
GLI2	0.034	0.014	-9999	-10000	0	0
GLI3	0.011	0.068	-9999	-10000	0	0
CSNK1D	0.012	0	-9999	-10000	0	0
CSNK1E	0.012	0	-9999	-10000	0	0
SAP18	0.012	0	-9999	-10000	0	0
embryonic digit morphogenesis	0.012	0.001	-9999	-10000	0	0
GNG2	-0.003	0.069	-9999	-0.32	19	19
Gi family/GTP	-0.055	0.11	-9999	-0.32	20	20
SIN3B	0.012	0	-9999	-10000	0	0
SIN3A	0.012	0	-9999	-10000	0	0
GLI3/Su(fu)	0.033	0.05	-9999	-10000	0	0
GLI2/Su(fu)	0.047	0.014	-9999	-10000	0	0
FOXA2	-0.014	0.12	-9999	-0.62	14	14
neural tube patterning	0.008	0.071	-9999	-0.46	4	4
SPOP	0.012	0	-9999	-10000	0	0
Su(fu)/PIAS1	0.028	0.003	-9999	-10000	0	0
GNB1	0.012	0	-9999	-10000	0	0
CSNK1G2	0.011	0.016	-9999	-0.32	1	1
CSNK1G3	0.012	0	-9999	-10000	0	0
MTSS1	0.013	0.035	-9999	-0.32	4	4
embryonic limb morphogenesis	0.008	0.071	-9999	-0.46	4	4
SUFU	0.024	0.004	-9999	-10000	0	0
LGALS3	0.011	0.016	-9999	-0.32	1	1
catabolic process	0.038	0.06	-9999	-10000	0	0
GLI3A/CBP	0.017	0.025	-9999	-10000	0	0
KIF3A	0.012	0.001	-9999	-10000	0	0
GLI1	0.008	0.072	-9999	-0.47	4	4
RAB23	0.01	0.023	-9999	-0.32	2	2
CSNK1A1	0.012	0	-9999	-10000	0	0
IFT172	0.012	0	-9999	-10000	0	0
RBBP7	0.012	0	-9999	-10000	0	0
Su(fu)/Galectin3	0.028	0.009	-9999	-10000	0	0
GNAZ	0.005	0.048	-9999	-0.32	9	9
RBBP4	0.012	0	-9999	-10000	0	0
CSNK1G1	0.011	0.016	-9999	-0.32	1	1
PIAS1	0.012	0	-9999	-10000	0	0
PRKACA	0.012	0	-9999	-10000	0	0
GLI2/SPOP	0.038	0.013	-9999	-10000	0	0
STK36	0.014	0.002	-9999	-10000	0	0
Gi family/GNB1/GNG2/GDP	-0.052	0.12	-9999	-0.36	27	27
PTCH1	0.013	0.081	-9999	-0.81	2	2
MIM/GLI1	0.015	0.093	-9999	-0.54	4	4
CREBBP	0.017	0.025	-9999	-10000	0	0
Su(fu)/SIN3/HDAC complex	0.038	0.002	-9999	-10000	0	0

×

Ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.017	0.011	-10000	0	-10000	0	0
MAP4K4	0.033	0.025	-10000	0	-10000	0	0
BAG4	0.012	0.001	-10000	0	-10000	0	0
PKC zeta/ceramide	-0.01	0.028	-10000	0	-10000	0	0
NFKBIA	0.012	0	-10000	0	-10000	0	0
BIRC3	0.005	0.055	-10000	0	-0.37	8	8
BAX	-0.002	0.013	-10000	0	-10000	0	0
RIPK1	0.012	0	-10000	0	-10000	0	0
AKT1	0.014	0.006	-10000	0	-10000	0	0
BAD	-0.012	0.026	-10000	0	-10000	0	0
SMPD1	0.02	0.02	-10000	0	-0.23	2	2
RB1	-0.012	0.027	-10000	0	-10000	0	0
FADD/Caspase 8	0.04	0.024	-10000	0	-10000	0	0
MAP2K4	-0.007	0.027	-10000	0	-10000	0	0
NSMAF	0.012	0	-10000	0	-10000	0	0
response to UV	0	0	-10000	0	-10000	0	0
RAF1	-0.006	0.025	-10000	0	-10000	0	0
EGF	-0.073	0.19	-10000	0	-0.43	79	79
mol:ceramide	-0.019	0.029	-10000	0	-10000	0	0
MADD	0.012	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
mol:Free Fatty acid	0.017	0	-10000	0	-10000	0	0
ASAH1	0.012	0	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.012	0.026	-10000	0	-10000	0	0
cell proliferation	-0.018	0.061	-10000	0	-10000	0	0
BID	0.023	0.027	-10000	0	-10000	0	0
MAP3K1	-0.012	0.028	-10000	0	-0.16	1	1
EIF2A	-0.002	0.025	-10000	0	-10000	0	0
TRADD	0.012	0	-10000	0	-10000	0	0
CRADD	0.012	0	-10000	0	-10000	0	0
MAPK3	0.002	0.024	-10000	0	-10000	0	0
response to heat	0	0	-10000	0	-10000	0	0
MAPK1	0.002	0.024	-10000	0	-10000	0	0
Cathepsin D/ceramide	-0.01	0.027	-10000	0	-10000	0	0
FADD	0.033	0.025	-10000	0	-10000	0	0
KSR1	-0.012	0.027	-10000	0	-10000	0	0
MAPK8	-0.002	0.026	-10000	0	-10000	0	0
PRKRA	-0.012	0.027	-10000	0	-10000	0	0
PDGFA	0.012	0	-10000	0	-10000	0	0
TRAF2	0.011	0.016	-10000	0	-0.32	1	1
IGF1	-0.067	0.14	-10000	0	-0.32	99	99
mol:GD3	0	0	-10000	0	-10000	0	0
ganglioside biosynthetic process	-0.019	0.028	-10000	0	-10000	0	0
CTSD	0.011	0.016	-10000	0	-0.32	1	1
regulation of nitric oxide biosynthetic process	0.018	0	-10000	0	-10000	0	0
response to radiation	0	0	-10000	0	-10000	0	0
ERK1/PKC delta	-0.018	0.065	-10000	0	-10000	0	0
PRKCD	0.012	0	-10000	0	-10000	0	0
PRKCZ	0.012	0	-10000	0	-10000	0	0
mol:GW4869	0	0	-10000	0	-10000	0	0
mol:sphingosine	0.017	0	-10000	0	-10000	0	0
RelA/NF kappa B1	0.018	0	-10000	0	-10000	0	0
mol:glutathione	0	0	-10000	0	-10000	0	0
PAWR	0.012	0	-10000	0	-10000	0	0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD	0.029	0.027	-10000	0	-10000	0	0
TNFR1A/BAG4/TNF-alpha	0.024	0.009	-10000	0	-10000	0	0
mol:Sphingosine-1-phosphate	0.017	0.011	-10000	0	-10000	0	0
MAP2K1	-0.001	0.024	-10000	0	-10000	0	0
mol:C11AG	0	0	-10000	0	-10000	0	0
RELA	0.012	0	-10000	0	-10000	0	0
CYCS	-0.002	0.029	0.13	11	-10000	0	11
TNFRSF1A	0.012	0	-10000	0	-10000	0	0
NFKB1	0.012	0	-10000	0	-10000	0	0
TNFR1A/BAG4	0.018	0.001	-10000	0	-10000	0	0
EIF2AK2	-0.007	0.026	-10000	0	-10000	0	0
TNF-alpha/TNFR1A/FAN	0.024	0.009	-10000	0	-10000	0	0
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
CASP8	0.033	0.016	-10000	0	-10000	0	0
MAP2K2	-0.001	0.024	-10000	0	-10000	0	0
SMPD3	0.019	0.043	-10000	0	-0.28	8	8
TNF	0.011	0.016	-10000	0	-0.32	1	1
PKC zeta/PAR4	0.018	0	-10000	0	-10000	0	0
mol:PHOSPHOCHOLINE	0.029	0.074	0.18	78	-10000	0	78
NF kappa B1/RelA/I kappa B alpha	0.035	0	-10000	0	-10000	0	0
AIFM1	-0.002	0.029	0.13	12	-10000	0	12
BCL2	0.001	0.06	-10000	0	-0.32	14	14

×

Signaling events mediated by HDAC Class III

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
EP300	0.012	0	-10000	0	-10000	0	0
HDAC4	0.012	0	-10000	0	-10000	0	0
induction of apoptosis	0	0	-10000	0	-10000	0	0
regulation of S phase of mitotic cell cycle	-0.007	0.065	0.53	6	-10000	0	6
CDKN1A	0	0	-10000	0	-10000	0	0
KAT2B	-0.002	0.066	-10000	0	-0.32	17	17
BAX	0.012	0	-10000	0	-10000	0	0
FOXO3	0	0	-10000	0	-10000	0	0
FOXO1	0.012	0	-10000	0	-10000	0	0
FOXO4	0.018	0	-10000	0	-10000	0	0
response to UV	0	0	-10000	0	-10000	0	0
XRCC6	0.012	0	-10000	0	-10000	0	0
TAT	-0.049	0.12	-10000	0	-0.32	73	73
mol:Lysophosphatidic acid	0	0	-10000	0	-10000	0	0
MYOD1	-0.001	0.045	-10000	0	-10000	0	0
PPARGC1A	-0.025	0.1	-10000	0	-0.32	46	46
FHL2	0.012	0	-10000	0	-10000	0	0
response to nutrient levels	0	0	-10000	0	-10000	0	0
KU70/SIRT1	0.015	0	-10000	0	-10000	0	0
HIST2H4A	0.007	0.065	-10000	0	-0.53	6	6
SIRT1/FOXO3a	0.001	0	-10000	0	-10000	0	0
SIRT1	0.008	0.001	-10000	0	-10000	0	0
response to hypoxia	0	0	-10000	0	-10000	0	0
SIRT1/MEF2D/HDAC4	0.022	0	-10000	0	-10000	0	0
SIRT1/Histone H1b	0.004	0.053	-10000	0	-10000	0	0
apoptosis	-0.021	0	-10000	0	-10000	0	0
SIRT1/PGC1A	-0.007	0.059	-10000	0	-10000	0	0
p53/SIRT1	0	0	-10000	0	-10000	0	0
SIRT1/FOXO4	0.018	0.001	-10000	0	-10000	0	0
FOXO1/FHL2/SIRT1	0.02	0	-10000	0	-10000	0	0
HIST1H1E	0	0.063	-10000	0	-0.23	28	28
SIRT1/p300	0.015	0	-10000	0	-10000	0	0
muscle cell differentiation	-0.006	0.037	-10000	0	-10000	0	0
TP53	0.008	0	-10000	0	-10000	0	0
KU70/SIRT1/BAX	0.022	0	-10000	0	-10000	0	0
CREBBP	0.012	0	-10000	0	-10000	0	0
MEF2D	0.012	0	-10000	0	-10000	0	0
HIV-1 Tat/SIRT1	-0.027	0.085	-10000	0	-10000	0	0
ACSS2	0.015	0	-10000	0	-10000	0	0
SIRT1/PCAF/MYOD	0.006	0.037	-10000	0	-10000	0	0

×

FoxO family signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G6PC	-0.054	0.3	-9999	-1.2	29	29
PLK1	0.054	0.11	-9999	-0.72	2	2
CDKN1B	0.078	0.069	-9999	-10000	0	0
FOXO3	0.054	0.11	-9999	-0.52	3	3
KAT2B	0.007	0.067	-9999	-0.32	17	17
FOXO1/SIRT1	-0.015	0.099	-9999	-0.37	29	29
CAT	0.055	0.1	-9999	-10000	0	0
CTNNB1	0.012	0	-9999	-10000	0	0
AKT1	0.019	0.016	-9999	-10000	0	0
FOXO1	0.001	0.11	-9999	-0.4	29	29
MAPK10	0.024	0.021	-9999	-10000	0	0
mol:GTP	0.002	0	-9999	-10000	0	0
FOXO4	0.059	0.048	-9999	-10000	0	0
response to oxidative stress	0.008	0.016	-9999	-10000	0	0
FOXO3A/SIRT1	0.043	0.094	-9999	-0.49	3	3
XPO1	0.012	0	-9999	-10000	0	0
EP300	0.009	0.015	-9999	-10000	0	0
BCL2L11	0.025	0.023	-9999	-10000	0	0
FOXO1/SKP2	0.006	0.1	-9999	-0.37	29	29
mol:GDP	0.008	0.016	-9999	-10000	0	0
RAN	0.013	0	-9999	-10000	0	0
GADD45A	0.073	0.05	-9999	-10000	0	0
YWHAQ	0.012	0	-9999	-10000	0	0
FOXO1/14-3-3 family	0.051	0.031	-9999	-10000	0	0
MST1	-0.075	0.24	-9999	-0.7	56	56
CSNK1D	0.012	0	-9999	-10000	0	0
CSNK1E	0.012	0	-9999	-10000	0	0
FOXO4/14-3-3 family	0.045	0.013	-9999	-10000	0	0
YWHAB	0.012	0	-9999	-10000	0	0
MAPK8	0.03	0.006	-9999	-10000	0	0
MAPK9	0.03	0.006	-9999	-10000	0	0
YWHAG	0.012	0	-9999	-10000	0	0
YWHAE	0.012	0	-9999	-10000	0	0
YWHAZ	0.012	0	-9999	-10000	0	0
SIRT1	0.012	0.012	-9999	-10000	0	0
SOD2	0.079	0.079	-9999	-10000	0	0
RBL2	0.064	0.08	-9999	-10000	0	0
RAL/GDP	0.026	0.01	-9999	-10000	0	0
CHUK	0.021	0.007	-9999	-10000	0	0
Ran/GTP	0.012	0	-9999	-10000	0	0
CSNK1G2	0.011	0.016	-9999	-0.32	1	1
RAL/GTP	0.031	0.01	-9999	-10000	0	0
CSNK1G1	0.011	0.016	-9999	-0.32	1	1
FASLG	-0.021	0.24	-9999	-1.1	18	18
SKP2	0.012	0	-9999	-10000	0	0
USP7	0.013	0	-9999	-10000	0	0
IKBKB	0.021	0.007	-9999	-10000	0	0
CCNB1	0.055	0.1	-9999	-10000	0	0
FOXO1-3a-4/beta catenin	0.086	0.083	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.006	0.1	-9999	-0.36	29	29
CSNK1A1	0.012	0	-9999	-10000	0	0
SGK1	0.014	0.047	-9999	-0.32	8	8
CSNK1G3	0.012	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.021	0	-9999	-10000	0	0
ZFAND5	0.061	0.044	-9999	-10000	0	0
SFN	0.011	0.016	-9999	-0.32	1	1
CDK2	0.006	0.023	-9999	-10000	0	0
FOXO3A/14-3-3	0.051	0.025	-9999	-10000	0	0
CREBBP	0.006	0.023	-9999	-10000	0	0
FBXO32	0.054	0.12	-9999	-1.2	1	1
BCL6	0.064	0.08	-9999	-10000	0	0
RALB	0.013	0	-9999	-10000	0	0
RALA	0.013	0	-9999	-10000	0	0
YWHAH	0.012	0	-9999	-10000	0	0

×

Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3	0.016	0	-9999	-10000	0	0
response to insulin stimulus	0	0	-9999	-10000	0	0
RIPK1	0.012	0	-9999	-10000	0	0
response to stress	0	0	-9999	-10000	0	0
MAP2K6	0.009	0.028	-9999	-0.32	3	3
mol:GTP	0	0	-9999	-10000	0	0
MAP2K4	0.011	0.016	-9999	-0.32	1	1
RAC1-CDC42/GTP/PAK family	0.019	0.009	-9999	-10000	0	0
response to UV	0	0	-9999	-10000	0	0
YES1	0.011	0.016	-9999	-0.32	1	1
interleukin-1 receptor activity	0	0	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
MAP3K3	0.012	0	-9999	-10000	0	0
FYN	0.012	0	-9999	-10000	0	0
MAP3K12	0.011	0.016	-9999	-0.32	1	1
FGR	0.009	0.039	-9999	-0.51	2	2
p38 alpha/TAB1	-0.028	0.039	-9999	-10000	0	0
PRKG1	-0.01	0.082	-9999	-0.32	27	27
DUSP8	0.011	0.016	-9999	-0.32	1	1
PGK/cGMP/p38 alpha	-0.033	0.051	-9999	-0.28	3	3
apoptosis	-0.027	0.037	-9999	-10000	0	0
RAL/GTP	0.016	0	-9999	-10000	0	0
LYN	0.012	0	-9999	-10000	0	0
DUSP1	0.01	0.023	-9999	-0.32	2	2
PAK1	0.012	0	-9999	-10000	0	0
SRC	0.012	0	-9999	-10000	0	0
RAC1/OSM/MEKK3/MKK3	0.031	0	-9999	-10000	0	0
TRAF6	0.012	0	-9999	-10000	0	0
RAC1	0.012	0	-9999	-10000	0	0
epidermal growth factor receptor activity	0	0	-9999	-10000	0	0
mol:LPS	0	0	-9999	-10000	0	0
mol:cGMP	0	0	-9999	-10000	0	0
CCM2	0.012	0	-9999	-10000	0	0
RAC1-CDC42/GTP	0.016	0.009	-9999	-10000	0	0
MAPK11	-0.013	0.08	-9999	-0.28	3	3
BLK	-0.11	0.16	-9999	-0.32	155	155
HCK	0.009	0.032	-9999	-0.32	4	4
MAP2K3	0.012	0	-9999	-10000	0	0
DUSP16	0.012	0	-9999	-10000	0	0
DUSP10	0.012	0	-9999	-10000	0	0
TRAF6/MEKK3	0.015	0	-9999	-10000	0	0
MAP3K7IP1	0	0	-9999	-10000	0	0
MAPK14	-0.002	0.063	-9999	-10000	0	0
positive regulation of innate immune response	-0.009	0.086	-9999	-0.29	3	3
LCK	-0.003	0.1	-9999	-0.66	9	9
p38alpha-beta/MKP7	-0.003	0.084	-9999	-10000	0	0
p38alpha-beta/MKP5	-0.003	0.084	-9999	-10000	0	0
PGK/cGMP	-0.006	0.056	-9999	-0.22	27	27
PAK2	0.012	0	-9999	-10000	0	0
p38alpha-beta/MKP1	-0.004	0.085	-9999	-10000	0	0
CDC42	0.011	0.016	-9999	-0.32	1	1
RALB	0.012	0	-9999	-10000	0	0
RALA	0.012	0	-9999	-10000	0	0
PAK3	0.007	0.006	-9999	-10000	0	0

×

IL6-mediated signaling events

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
BCL2L1	0.026	0.14	-9999	-0.64	2	2
CRP	0.021	0.14	-9999	-0.62	4	4
cell cycle arrest	0.019	0.15	-9999	-0.68	3	3
TIMP1	0.023	0.15	-9999	-0.57	8	8
IL6ST	0.006	0.056	-9999	-0.32	12	12
Rac1/GDP	0.001	0.11	-9999	-0.44	4	4
AP1	0.043	0.047	-9999	-10000	0	0
GAB2	0.013	0.002	-9999	-10000	0	0
TNFSF11	0.01	0.18	-9999	-0.74	9	9
HSP90B1	0.031	0.032	-9999	-10000	0	0
GAB1	0.012	0.001	-9999	-10000	0	0
MAPK14	0.001	0.092	-9999	-0.44	2	2
AKT1	0.045	0.009	-9999	-10000	0	0
FOXO1	0.049	0.008	-9999	-10000	0	0
MAP2K6	-0.004	0.099	-9999	-0.42	4	4
mol:GTP	0	0.002	-9999	-10000	0	0
MAP2K4	0.013	0.12	-9999	-0.46	4	4
MITF	-0.008	0.11	-9999	-0.4	10	10
positive regulation of NF-kappaB transcription factor activity	0	0	-9999	-10000	0	0
TYK2	0.012	0	-9999	-10000	0	0
A2M	0.01	0.086	-9999	-1.2	2	2
CEBPB	0.018	0.003	-9999	-10000	0	0
GRB2/SOS1/GAB family/SHP2	0.021	0.045	-9999	-10000	0	0
STAT3	0.017	0.15	-9999	-0.72	3	3
STAT1	-0.001	0.016	-9999	-0.2	1	1
CEBPD	0.025	0.14	-9999	-0.84	2	2
PIK3CA	0.013	0.001	-9999	-10000	0	0
PI3K	0.02	0.001	-9999	-10000	0	0
JUN	0.012	0.001	-9999	-10000	0	0
PIAS3/MITF	-0.005	0.11	-9999	-0.44	6	6
MAPK11	-0.001	0.096	-9999	-0.44	2	2
STAT3 (dimer)/FOXO1	0.05	0.13	-9999	-0.55	3	3
GRB2/SOS1/GAB family	-0.029	0.074	-9999	-0.43	3	3
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK	-0.012	0.11	-9999	-0.37	15	15
GRB2	0.012	0.001	-9999	-10000	0	0
JAK2	0.009	0.028	-9999	-0.32	3	3
LBP	0.016	0.17	-9999	-0.56	13	13
PIK3R1	0.013	0	-9999	-10000	0	0
JAK1	0.014	0.004	-9999	-10000	0	0
MYC	0.024	0.14	-9999	-0.63	3	3
FGG	-0.003	0.18	-9999	-0.61	7	7
macrophage differentiation	0.019	0.15	-9999	-0.68	3	3
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4	-0.008	0.11	-9999	-0.39	15	15
JUNB	0.023	0.14	-9999	-0.83	3	3
FOS	0.006	0.043	-9999	-0.32	7	7
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4	-0.009	0.11	-9999	-0.34	17	17
STAT1/PIAS1	0.006	0.098	-9999	-0.37	7	7
GRB2/SOS1/GAB family/SHP2/PI3K	0.038	0.009	-9999	-10000	0	0
STAT3 (dimer)	0.016	0.15	-9999	-0.71	3	3
PRKCD	0.024	0.13	-9999	-0.51	3	3
IL6R	-0.039	0.12	-9999	-0.32	67	67
SOCS3	0	0.09	-9999	-10000	0	0
gp130 (dimer)/JAK1/JAK1/LMO4	0.027	0.037	-9999	-10000	0	0
Rac1/GTP	0.003	0.11	-9999	-0.46	4	4
HCK	0.008	0.032	-9999	-0.32	4	4
MAPKKK cascade	0.032	0.035	-9999	-10000	0	0
bone resorption	0.011	0.17	-9999	-0.69	9	9
IRF1	0.026	0.14	-9999	-0.64	2	2
mol:GDP	-0.006	0.11	-9999	-0.43	5	5
SOS1	0.012	0.002	-9999	-10000	0	0
VAV1	-0.006	0.11	-9999	-0.44	5	5
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3	-0.028	0.14	-9999	-0.45	13	13
PTPN11	0	0.009	-9999	-10000	0	0
IL6/IL6RA	-0.038	0.13	-9999	-0.5	19	19
gp130 (dimer)/TYK2/TYK2/LMO4	0.023	0.035	-9999	-10000	0	0
gp130 (dimer)/JAK2/JAK2/LMO4	0.022	0.04	-9999	-0.35	1	1
IL6	-0.018	0.14	-9999	-0.53	26	26
PIAS3	0.012	0	-9999	-10000	0	0
PTPRE	0.006	0.009	-9999	-10000	0	0
PIAS1	0.012	0	-9999	-10000	0	0
RAC1	0.012	0.001	-9999	-10000	0	0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4	-0.02	0.1	-9999	-0.33	18	18
LMO4	0.015	0.018	-9999	-0.33	1	1
STAT3 (dimer)/PIAS3	0.018	0.15	-9999	-0.68	3	3
MCL1	0.049	0.008	-9999	-10000	0	0

×

VEGFR1 specific signals

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer	0.027	0	-9999	-10000	0	0
VEGFR1 homodimer/NRP1	0.018	0	-9999	-10000	0	0
mol:DAG	0.019	0.066	-9999	-0.4	10	10
VEGFR1 homodimer/NRP1/VEGFR 121	0.02	0.043	-9999	-0.41	4	4
CaM/Ca2+	0.025	0.063	-9999	-0.38	10	10
HIF1A	0.019	0	-9999	-10000	0	0
GAB1	0.012	0	-9999	-10000	0	0
AKT1	0.034	0.054	-9999	-10000	0	0
PLCG1	0.019	0.067	-9999	-0.41	10	10
NOS3	0.036	0.058	-9999	-10000	0	0
CBL	0.012	0	-9999	-10000	0	0
mol:NO	0.035	0.056	-9999	-10000	0	0
FLT1	0.024	0	-9999	-10000	0	0
PGF	-0.005	0.11	-9999	-0.71	10	10
VEGFR1 homodimer/NRP2/VEGFR121	0.027	0.045	-9999	-0.41	4	4
CALM1	0.012	0	-9999	-10000	0	0
PIK3CA	0.012	0.001	-9999	-10000	0	0
eNOS/Hsp90	0.041	0.055	-9999	-10000	0	0
endothelial cell proliferation	0.002	0.078	-9999	-0.44	1	1
mol:Ca2+	0.019	0.066	-9999	-0.4	10	10
MAPK3	0.026	0.059	-9999	-0.35	10	10
MAPK1	0.026	0.059	-9999	-0.35	10	10
PIK3R1	0.012	0	-9999	-10000	0	0
PLGF homodimer	-0.005	0.11	-9999	-0.7	10	10
PRKACA	0.012	0	-9999	-10000	0	0
RP11-342D11.1	0	0	-9999	-10000	0	0
CAV1	-0.002	0.066	-9999	-0.32	17	17
VEGFA homodimer	0.005	0.07	-9999	-0.7	4	4
VEGFR1 homodimer/VEGFA homodimer	0.022	0.047	-9999	-0.45	4	4
platelet activating factor biosynthetic process	0.03	0.057	-9999	-10000	0	0
PI3K	0.028	0.064	-9999	-0.38	10	10
PRKCA	0.023	0.062	-9999	-0.37	10	10
PRKCB	0.016	0.065	-9999	-0.39	10	10
VEGFR1 homodimer/PLGF homodimer	0.015	0.073	-9999	-0.45	10	10
VEGFA	0.005	0.07	-9999	-0.71	4	4
VEGFB	0.012	0	-9999	-10000	0	0
mol:IP3	0.019	0.066	-9999	-0.4	10	10
RASA1	0.03	0	-9999	-10000	0	0
NRP2	0.01	0.023	-9999	-0.32	2	2
VEGFR1 homodimer	0.024	0	-9999	-10000	0	0
VEGFB homodimer	0.012	0	-9999	-10000	0	0
NCK1	0.012	0	-9999	-10000	0	0
eNOS/Caveolin-1	0.039	0.056	-9999	-10000	0	0
PTPN11	0.012	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	0.027	0.063	-9999	-0.38	10	10
mol:L-citrulline	0.035	0.056	-9999	-10000	0	0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP	0.03	0.052	-9999	-0.42	4	4
VEGFR1 homodimer/VEGFA homodimer/NCK1	0.028	0.043	-9999	-0.41	4	4
CD2AP	0.002	0.055	-9999	-0.32	12	12
PI3K/GAB1	0.033	0.061	-9999	-0.36	10	10
PDPK1	0.027	0.06	-9999	-0.35	10	10
VEGFR1 homodimer/VEGFA homodimer/SHP2	0.028	0.043	-9999	-0.41	4	4
mol:NADP	0.035	0.056	-9999	-10000	0	0
HSP90AA1	0.012	0	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	0.029	0.051	-9999	-0.41	4	4
VEGFR1 homodimer/NRP2	0.026	0.013	-9999	-10000	0	0

×

PDGFR-beta signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate	-0.002	0.096	-9999	-0.33	31	31
PDGFB-D/PDGFRB/SLAP	0.013	0.042	-9999	-0.34	5	5
PDGFB-D/PDGFRB/APS/CBL	0.015	0.066	-9999	-0.46	8	8
AKT1	0.038	0.026	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
mol:Sphingosine-1-phosphate	-0.005	0.1	-9999	-0.34	31	31
PIK3CA	0.012	0.001	-9999	-10000	0	0
FGR	-0.002	0.038	-9999	-0.4	3	3
mol:Ca2+	0.008	0.036	-9999	-0.3	2	2
MYC	0.016	0.062	-9999	-0.43	4	4
SHC1	0.012	0	-9999	-10000	0	0
HRAS/GDP	0.026	0.029	-9999	-0.37	2	2
LRP1/PDGFRB/PDGFB	0.021	0.035	-9999	-0.45	2	2
GRB10	0.012	0	-9999	-10000	0	0
PTPN11	0.012	0	-9999	-10000	0	0
GO:0007205	0.008	0.037	-9999	-0.3	2	2
PTEN	0.011	0.016	-9999	-0.32	1	1
GRB2	0.012	0	-9999	-10000	0	0
GRB7	-0.007	0.12	-9999	-0.71	11	11
PDGFB-D/PDGFRB/SHP2	0.015	0.038	-9999	-0.53	2	2
PDGFB-D/PDGFRB/GRB10	0.015	0.038	-9999	-0.53	2	2
cell cycle arrest	0.013	0.042	-9999	-0.34	5	5
HRAS	0.011	0.016	-9999	-0.32	1	1
HIF1A	0.041	0.023	-9999	-10000	0	0
GAB1	0.002	0.054	-9999	-0.36	2	2
mol:GTP	0	0	-9999	-10000	0	0
DNM2	0.005	0.057	-9999	-0.38	2	2
PDGFB-D/PDGFRB	0.023	0.034	-9999	-0.46	2	2
mol:GDP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/LMW-PTP	0.015	0.038	-9999	-0.53	2	2
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB	-0.016	0.089	-9999	-0.38	11	11
positive regulation of MAPKKK cascade	0.015	0.038	-9999	-0.53	2	2
PIK3R1	0.012	0	-9999	-10000	0	0
mol:IP3	0.008	0.037	-9999	-0.3	2	2
E5	0	0.001	-9999	-10000	0	0
CSK	0.012	0.001	-9999	-10000	0	0
PDGFB-D/PDGFRB/GRB7	0.001	0.096	-9999	-0.54	13	13
SHB	0.012	0	-9999	-10000	0	0
BLK	-0.17	0.22	-9999	-0.45	156	156
PTPN2	0.012	0.001	-9999	-10000	0	0
PDGFB-D/PDGFRB/SNX15	0.015	0.038	-9999	-0.53	2	2
BCAR1	0.011	0.016	-9999	-0.32	1	1
VAV2	0.005	0.057	-9999	-0.36	2	2
CBL	0.012	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/DEP1	0.015	0.038	-9999	-0.53	2	2
LCK	-0.005	0.047	-9999	-0.4	3	3
PDGFRB	0.009	0.05	-9999	-0.71	2	2
ACP1	0.012	0	-9999	-10000	0	0
HCK	0.002	0.053	-9999	-0.42	6	6
ABL1	-0.003	0.052	-9999	-0.37	2	2
PDGFB-D/PDGFRB/CBL	-0.001	0.054	-9999	-0.34	2	2
PTPN1	0.012	0.001	-9999	-10000	0	0
SNX15	0.012	0	-9999	-10000	0	0
STAT3	0.012	0	-9999	-10000	0	0
STAT1	0.008	0.05	-9999	-0.71	2	2
cell proliferation	0.016	0.058	-9999	-0.4	4	4
SLA	0.009	0.028	-9999	-0.32	3	3
actin cytoskeleton reorganization	0.035	0.028	-9999	-0.35	2	2
SRC	0	0.028	-9999	-0.37	2	2
PI3K	-0.002	0.024	-9999	-10000	0	0
PDGFB-D/PDGFRB/GRB7/SHC	0.009	0.084	-9999	-0.46	13	13
SH2B2	0.001	0.085	-9999	-0.71	6	6
PLCgamma1/SPHK1	-0.005	0.1	-9999	-0.36	31	31
LYN	0.001	0.028	-9999	-0.37	2	2
LRP1	0.01	0.023	-9999	-0.32	2	2
SOS1	0.012	0	-9999	-10000	0	0
STAT5B	0.012	0	-9999	-10000	0	0
STAT5A	0.012	0	-9999	-10000	0	0
NCK1-2/p130 Cas	0.034	0.029	-9999	-0.37	2	2
SPHK1	-0.041	0.19	-9999	-0.7	31	31
EDG1	0	0.002	-9999	-10000	0	0
mol:DAG	0.008	0.037	-9999	-0.3	2	2
PLCG1	0.008	0.037	-9999	-0.31	2	2
NHERF/PDGFRB	0.022	0.034	-9999	-0.45	2	2
YES1	-0.001	0.035	-9999	-0.39	3	3
cell migration	0.021	0.034	-9999	-0.45	2	2
SHC/Grb2/SOS1	0.035	0.028	-9999	-0.37	2	2
SLC9A3R2	0.011	0.016	-9999	-0.32	1	1
SLC9A3R1	0.012	0	-9999	-10000	0	0
NHERF1-2/PDGFRB/PTEN	0.028	0.033	-9999	-0.41	2	2
FYN	0.001	0.028	-9999	-0.37	2	2
DOK1	0.022	0.03	-9999	-0.41	2	2
HRAS/GTP	0.008	0.011	-9999	-0.22	1	1
PDGFB	0.012	0	-9999	-10000	0	0
RAC1	0.015	0.058	-9999	-0.35	1	1
PRKCD	0.022	0.031	-9999	-0.42	2	2
FER	0.022	0.031	-9999	-0.42	2	2
MAPKKK cascade	-0.002	0.025	-9999	-0.36	2	2
RASA1	0.022	0.031	-9999	-0.42	2	2
NCK1	0.012	0	-9999	-10000	0	0
NCK2	0.012	0	-9999	-10000	0	0
p62DOK/Csk	0.029	0.028	-9999	-0.38	2	2
PDGFB-D/PDGFRB/SHB	0.015	0.038	-9999	-0.53	2	2
chemotaxis	-0.003	0.051	-9999	-0.36	2	2
STAT1-3-5/STAT1-3-5	-0.003	0.035	-9999	-0.36	2	2
Bovine Papilomavirus E5/PDGFRB	0.006	0.038	-9999	-0.54	2	2
PTPRJ	0.012	0	-9999	-10000	0	0

×

EPO signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.044	0.073	-9999	-0.51	1	1
CRKL	0.026	0.054	-9999	-0.54	2	2
mol:DAG	0.031	0.051	-9999	-0.47	2	2
HRAS	0.041	0.047	-9999	-0.53	1	1
MAPK8	0.02	0.056	-9999	-0.46	5	5
RAP1A	0.026	0.054	-9999	-0.4	5	5
GAB1	0.026	0.054	-9999	-0.4	5	5
MAPK14	0.02	0.056	-9999	-0.46	5	5
EPO	0	0.079	-9999	-0.72	5	5
PLCG1	0.031	0.052	-9999	-0.48	2	2
EPOR/TRPC2/IP3 Receptors	0.012	0.037	-9999	-0.75	1	1
RAPGEF1	0.011	0.016	-9999	-0.32	1	1
EPO/EPOR (dimer)/SOCS3	0.018	0.062	-9999	-0.52	5	5
GAB1/SHC/GRB2/SOS1	0.036	0.049	-9999	-0.47	2	2
EPO/EPOR (dimer)	0.01	0.072	-9999	-0.62	5	5
IRS2	0.025	0.058	-9999	-0.48	3	3
STAT1	0.035	0.067	-9999	-0.52	2	2
STAT5B	0.034	0.058	-9999	-0.5	2	2
cell proliferation	0.023	0.053	-9999	-0.43	5	5
GAB1/SHIP/PIK3R1/SHP2/SHC	-0.006	0.04	-9999	-0.54	1	1
TEC	0.026	0.054	-9999	-0.54	2	2
SOCS3	0.012	0	-9999	-10000	0	0
STAT1 (dimer)	0.035	0.066	-9999	-0.51	2	2
JAK2	0.01	0.029	-9999	-0.32	3	3
PIK3R1	0.012	0	-9999	-10000	0	0
EPO/EPOR (dimer)/JAK2	0.036	0.059	-9999	-0.43	5	5
EPO/EPOR	0.01	0.072	-9999	-0.62	5	5
LYN	0.013	0.003	-9999	-10000	0	0
TEC/VAV2	0.033	0.054	-9999	-0.52	2	2
elevation of cytosolic calcium ion concentration	0.012	0.037	-9999	-0.74	1	1
SHC1	0.012	0	-9999	-10000	0	0
EPO/EPOR (dimer)/LYN	0.022	0.063	-9999	-0.52	5	5
mol:IP3	0.031	0.051	-9999	-0.47	2	2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP	0.036	0.054	-9999	-0.49	2	2
SH2B3	0.013	0.006	-9999	-10000	0	0
NFKB1	0.02	0.056	-9999	-0.46	5	5
EPO/EPOR (dimer)/JAK2/SOCS3	0.002	0.035	-9999	-0.26	5	5
PTPN6	0.022	0.056	-9999	-0.42	5	5
TEC/VAV2/GRB2	0.037	0.053	-9999	-0.5	2	2
EPOR	0.012	0.038	-9999	-0.75	1	1
INPP5D	0.012	0	-9999	-10000	0	0
mol:GDP	0.036	0.05	-9999	-0.48	2	2
SOS1	0.012	0	-9999	-10000	0	0
PLCG2	-0.012	0.086	-9999	-0.32	30	30
CRKL/CBL/C3G	0.038	0.053	-9999	-0.5	2	2
VAV2	0.026	0.054	-9999	-0.54	2	2
CBL	0.026	0.054	-9999	-0.54	2	2
SHC/Grb2/SOS1	-0.007	0.045	-9999	-0.5	2	2
STAT5A	0.034	0.058	-9999	-0.5	2	2
GRB2	0.012	0	-9999	-10000	0	0
STAT5 (dimer)	0.045	0.075	-9999	-0.56	2	2
LYN/PLCgamma2	0.002	0.059	-9999	-10000	0	0
PTPN11	0.012	0	-9999	-10000	0	0
BTK	0.021	0.061	-9999	-0.4	5	5
BCL2	0.029	0.15	-9999	-0.72	15	15

×

PLK1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
regulation of centriole-centriole cohesion	-0.008	0.01	0.19	1	-10000	0	1
BUB1B	0.014	0.019	-10000	0	-10000	0	0
PLK1	0.012	0.011	-10000	0	-0.095	1	1
PLK1S1	0.011	0.006	-10000	0	-10000	0	0
KIF2A	0.017	0.01	-10000	0	-10000	0	0
regulation of mitotic centrosome separation	0.012	0.011	-10000	0	-0.095	1	1
GOLGA2	0.012	0	-10000	0	-10000	0	0
Hec1/SPC24	-0.004	0.11	-10000	0	-0.39	29	29
WEE1	0.015	0.022	-10000	0	-10000	0	0
cytokinesis	0.024	0.014	-10000	0	-0.2	1	1
PP2A-alpha B56	0.029	0.013	-10000	0	-10000	0	0
AURKA	0.011	0.01	-10000	0	-0.15	1	1
PICH/PLK1	0.004	0.091	-10000	0	-0.32	30	30
CENPE	0.014	0.037	-10000	0	-0.41	3	3
RhoA/GTP	0.009	0	-10000	0	-10000	0	0
positive regulation of microtubule depolymerization	0.017	0.01	-10000	0	-10000	0	0
PPP2CA	0.012	0	-10000	0	-10000	0	0
FZR1	0.011	0.016	-10000	0	-0.32	1	1
TPX2	0.008	0.023	-10000	0	-0.14	10	10
PAK1	0.011	0.001	-10000	0	-10000	0	0
SPC24	-0.038	0.18	-10000	0	-0.71	29	29
FBXW11	0.012	0	-10000	0	-10000	0	0
CLSPN	0.007	0.028	-10000	0	-0.15	12	12
GORASP1	0.012	0	-10000	0	-10000	0	0
metaphase	0	0.001	-10000	0	-0.011	2	2
mol:GTP	0	0	-10000	0	-10000	0	0
NLP	0.007	0.006	-10000	0	-10000	0	0
G2 phase of mitotic cell cycle	0	0.001	-10000	0	-0.012	1	1
STAG2	0.012	0	-10000	0	-10000	0	0
GRASP65/GM130/RAB1/GTP	0.017	0.011	-10000	0	-10000	0	0
spindle elongation	0.012	0.011	-10000	0	-0.095	1	1
ODF2	0.012	0.001	-10000	0	-10000	0	0
BUB1	-0.002	0.009	-10000	0	-10000	0	0
TPT1	0.011	0.006	-10000	0	-10000	0	0
CDC25C	0.013	0.006	-10000	0	-10000	0	0
CDC25B	-0.027	0.16	-10000	0	-0.7	23	23
SGOL1	0.008	0.011	-10000	0	-0.19	1	1
RHOA	0.012	0	-10000	0	-10000	0	0
CCNB1/CDK1	-0.018	0.072	-10000	0	-0.31	24	24
CDC14B	0.008	0.011	-10000	0	-0.22	1	1
CDC20	0.008	0.05	-10000	0	-0.71	2	2
PLK1/PBIP1	0.014	0.009	-10000	0	-10000	0	0
mitosis	0	0.002	0.028	1	-10000	0	1
FBXO5	0.013	0.017	-10000	0	-10000	0	0
CDC2	0	0.003	-10000	0	-0.014	24	24
NDC80	0.012	0.001	-10000	0	-10000	0	0
metaphase plate congression	0.012	0.007	-10000	0	-10000	0	0
ERCC6L	0.004	0.086	-10000	0	-0.3	30	30
NLP/gamma Tubulin	0.01	0.007	-10000	0	-10000	0	0
microtubule cytoskeleton organization	0.011	0.006	-10000	0	-10000	0	0
G2/M transition DNA damage checkpoint	0	0.001	-10000	0	-10000	0	0
PPP1R12A	0.01	0.023	-10000	0	-0.32	2	2
interphase	0	0.001	-10000	0	-10000	0	0
PLK1/PRC1-2	0.025	0.01	-10000	0	-10000	0	0
GRASP65/GM130/RAB1/GTP/PLK1	0.028	0.008	-10000	0	-10000	0	0
RAB1A	0.012	0	-10000	0	-10000	0	0
prophase	0	0	-10000	0	-10000	0	0
Aurora A/BORA	0.014	0.01	-10000	0	-10000	0	0
mitotic prometaphase	0	0.001	-10000	0	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.026	0.015	-10000	0	-10000	0	0
microtubule-based process	0.018	0.01	-10000	0	-10000	0	0
Golgi organization	0.012	0.011	-10000	0	-0.095	1	1
Cohesin/SA2	0.015	0.01	-10000	0	-10000	0	0
PPP1CB/MYPT1	0.016	0.024	-10000	0	-0.41	1	1
KIF20A	0.012	0	-10000	0	-10000	0	0
APC/C/CDC20	0.016	0.031	-10000	0	-0.41	2	2
PPP2R1A	0.012	0	-10000	0	-10000	0	0
chromosome segregation	0.014	0.009	-10000	0	-10000	0	0
PRC1	0.012	0	-10000	0	-10000	0	0
ECT2	0.01	0.053	-10000	0	-0.38	7	7
C13orf34	0.014	0.009	-10000	0	-10000	0	0
NUDC	0.012	0.007	-10000	0	-10000	0	0
regulation of attachment of spindle microtubules to kinetochore	0.014	0.019	-10000	0	-10000	0	0
spindle assembly	0.012	0.009	-10000	0	-10000	0	0
spindle stabilization	0.011	0.006	-10000	0	-10000	0	0
APC/C/HCDH1	0.014	0.013	-10000	0	-10000	0	0
MKLP2/PLK1	0.018	0.01	-10000	0	-10000	0	0
CCNB1	0.01	0.035	-10000	0	-0.7	1	1
PPP1CB	0.011	0.017	-10000	0	-0.33	1	1
BTRC	0.012	0	-10000	0	-10000	0	0
ROCK2	0.017	0.022	-10000	0	-0.4	1	1
TUBG1	0.011	0.006	-10000	0	-10000	0	0
G2/M transition of mitotic cell cycle	-0.018	0.071	-10000	0	-0.3	24	24
MLF1IP	0.009	0.001	-10000	0	-10000	0	0
INCENP	0.012	0	-10000	0	-10000	0	0

×

TCGA08_rtk_signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	0.002	0.058	-10000	0	-0.32	13	13
HRAS	0.011	0.016	-10000	0	-0.32	1	1
EGFR	0.012	0	-10000	0	-10000	0	0
AKT	0.031	0.014	-10000	0	-10000	0	0
FOXO3	0.012	0	-10000	0	-10000	0	0
AKT1	0.012	0	-10000	0	-10000	0	0
FOXO1	0.012	0	-10000	0	-10000	0	0
AKT3	0.005	0.046	-10000	0	-0.32	8	8
FOXO4	0.012	0	-10000	0	-10000	0	0
MET	-0.002	0.098	-10000	0	-0.71	8	8
PIK3CA	0.012	0.001	-10000	0	-10000	0	0
PIK3CB	0.012	0.001	-10000	0	-10000	0	0
NRAS	0.011	0.016	-10000	0	-0.32	1	1
PIK3CG	-0.031	0.11	-10000	0	-0.32	54	54
PIK3R3	0.012	0	-10000	0	-10000	0	0
PIK3R2	0.012	0	-10000	0	-10000	0	0
NF1	0.012	0	-10000	0	-10000	0	0
RAS	0.016	0.03	-10000	0	-0.24	2	2
ERBB2	0.003	0.078	-10000	0	-0.71	5	5
proliferation/survival/translation	-0.018	0.037	0.19	6	-10000	0	6
PI3K	0.02	0.032	-10000	0	-0.25	3	3
PIK3R1	0.012	0	-10000	0	-10000	0	0
KRAS	0.012	0	-10000	0	-10000	0	0
FOXO	0.037	0.017	-10000	0	-10000	0	0
AKT2	0.012	0	-10000	0	-10000	0	0
PTEN	0.011	0.016	-10000	0	-0.32	1	1

×

Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
adherens junction organization	0.024	0.013	-9999	-10000	0	0
epithelial cell differentiation	0.026	0	-9999	-10000	0	0
CYFIP2	0.012	0	-9999	-10000	0	0
ENAH	0.043	0.019	-9999	-10000	0	0
EGFR	0.012	0	-9999	-10000	0	0
EPHA2	0.008	0.05	-9999	-0.71	2	2
MYO6	0.028	0	-9999	-10000	0	0
CTNNB1	0.012	0	-9999	-10000	0	0
ABI1/Sra1/Nap1	0.024	0	-9999	-10000	0	0
AQP5	-0.022	0.1	-9999	-10000	0	0
CTNND1	0.012	0	-9999	-10000	0	0
mol:PI-4-5-P2	0.027	0.001	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	0.026	0.005	-9999	-10000	0	0
EGF	-0.073	0.19	-9999	-0.43	79	79
NCKAP1	0.012	0	-9999	-10000	0	0
AQP3	0.025	0.056	-9999	-10000	0	0
cortical microtubule organization	0.026	0	-9999	-10000	0	0
GO:0000145	0.025	0.001	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.028	0	-9999	-10000	0	0
MLLT4	0.011	0.016	-9999	-0.32	1	1
ARF6/GDP	-0.001	0.021	-9999	-10000	0	0
ARF6	0.012	0	-9999	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	0.029	0.031	-9999	-0.41	2	2
mol:Ca2+	0	0	-9999	-10000	0	0
VASP	0.035	0.002	-9999	-10000	0	0
PVRL2	0.012	0	-9999	-10000	0	0
ZYX	0.028	0	-9999	-10000	0	0
ARF6/GTP	0.032	0.029	-9999	-0.38	2	2
CDH1	0.012	0	-9999	-10000	0	0
EGFR/EGFR/EGF/EGF	-0.035	0.087	-9999	-0.36	23	23
RhoA/GDP	0.026	0	-9999	-10000	0	0
actin cytoskeleton organization	0.031	0	-9999	-10000	0	0
IGF-1R heterotetramer	0.012	0	-9999	-10000	0	0
GIT1	0.012	0	-9999	-10000	0	0
IGF1R	0.012	0	-9999	-10000	0	0
IGF1	-0.067	0.14	-9999	-0.32	99	99
DIAPH1	0	0.001	-9999	-10000	0	0
Wnt receptor signaling pathway	-0.026	0	-9999	-10000	0	0
RHOA	0.012	0	-9999	-10000	0	0
RhoA/GTP	-0.001	0.021	-9999	-10000	0	0
CTNNA1	0.012	0	-9999	-10000	0	0
VCL	0.031	0	-9999	-10000	0	0
EFNA1	0.012	0	-9999	-10000	0	0
LPP	0.031	0.002	-9999	-10000	0	0
Ephrin A1/EPHA2	-0.002	0.025	-9999	-0.36	2	2
SEC6/SEC8	0	0.005	-9999	-10000	0	0
MGAT3	0.027	0.005	-9999	-10000	0	0
HGF/MET	-0.011	0.057	-9999	-0.37	9	9
HGF	0	0.065	-9999	-0.35	13	13
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN	0.024	0.013	-9999	-10000	0	0
actin cable formation	0.057	0.016	-9999	-10000	0	0
KIAA1543	0.031	0.002	-9999	-10000	0	0
KIFC3	0.019	0.058	-9999	-0.37	9	9
NCK1	0.012	0	-9999	-10000	0	0
EXOC3	0.012	0	-9999	-10000	0	0
ACTN1	0.028	0	-9999	-10000	0	0
NCK1/GIT1	0.018	0	-9999	-10000	0	0
mol:GDP	0.026	0	-9999	-10000	0	0
EXOC4	0.012	0	-9999	-10000	0	0
STX4	0.028	0	-9999	-10000	0	0
PIP5K1C	0.028	0.001	-9999	-10000	0	0
LIMA1	0.01	0.023	-9999	-0.32	2	2
ABI1	0.012	0	-9999	-10000	0	0
ROCK1	0.042	0.022	-9999	-10000	0	0
adherens junction assembly	0.036	0.045	-9999	-0.43	1	1
IGF-1R heterotetramer/IGF1	-0.027	0.049	-9999	-10000	0	0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.017	0.011	-9999	-10000	0	0
MET	-0.002	0.098	-9999	-0.71	8	8
PLEKHA7	0.028	0	-9999	-10000	0	0
mol:GTP	0.027	0.03	-9999	-0.41	2	2
establishment of epithelial cell apical/basal polarity	0.043	0.007	-9999	-10000	0	0
cortical actin cytoskeleton stabilization	0.024	0.013	-9999	-10000	0	0
regulation of cell-cell adhesion	0.031	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton	0.024	0.013	-9999	-10000	0	0

×

IGF1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NCK2	0.012	0	-9999	-10000	0	0
PTK2	0.012	0	-9999	-10000	0	0
CRKL	-0.02	0.072	-9999	-10000	0	0
GRB2/SOS1/SHC	0.024	0	-9999	-10000	0	0
HRAS	0.011	0.016	-9999	-0.32	1	1
IRS1/Crk	-0.019	0.073	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/PTP1B	-0.021	0.078	-9999	-10000	0	0
AKT1	-0.003	0.062	-9999	-10000	0	0
BAD	0.002	0.059	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CRK	-0.02	0.072	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.019	0.073	-9999	-10000	0	0
RAF1	0.007	0.059	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos	-0.009	0.071	-9999	-10000	0	0
YWHAZ	0.012	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.027	0.08	-9999	-10000	0	0
PIK3CA	0.012	0.001	-9999	-10000	0	0
RPS6KB1	-0.003	0.062	-9999	-10000	0	0
GNB2L1	0.012	0	-9999	-10000	0	0
positive regulation of MAPKKK cascade	0.004	0.053	-9999	-10000	0	0
PXN	0.012	0	-9999	-10000	0	0
PIK3R1	0.012	0	-9999	-10000	0	0
cell adhesion	0	0	-9999	-10000	0	0
GRB2/SOS1	0.018	0	-9999	-10000	0	0
HRAS/GTP	-0.027	0.049	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc	0	0.063	-9999	-10000	0	0
IGF-1R heterotetramer	0.001	0.021	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS/Nck	-0.017	0.074	-9999	-10000	0	0
Crk/p130 Cas/Paxillin	-0.005	0.068	-9999	-10000	0	0
IGF1R	0.001	0.021	-9999	-10000	0	0
IGF1	-0.069	0.15	-9999	-0.33	99	99
IRS2/Crk	-0.013	0.071	-9999	-0.38	1	1
PI3K	-0.009	0.07	-9999	-10000	0	0
apoptosis	-0.008	0.055	-9999	-10000	0	0
HRAS/GDP	0.008	0.011	-9999	-0.22	1	1
PRKCD	-0.036	0.12	-9999	-10000	0	0
RAF1/14-3-3 E	0.013	0.054	-9999	-10000	0	0
BAD/14-3-3	0.008	0.057	-9999	-10000	0	0
PRKCZ	-0.003	0.062	-9999	-10000	0	0
Crk/p130 Cas/Paxillin/FAK1	-0.021	0.037	-9999	-10000	0	0
PTPN1	0.012	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1	-0.043	0.13	-9999	-0.27	99	99
BCAR1	0.011	0.016	-9999	-0.32	1	1
IGF-1R heterotetramer/IGF1/SHC/GRB10	-0.009	0.068	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
SOS1	0.012	0	-9999	-10000	0	0
IRS1/NCK2	-0.018	0.073	-9999	-10000	0	0
GRB10	0.012	0	-9999	-10000	0	0
PTPN11	-0.02	0.072	-9999	-10000	0	0
IRS1	-0.028	0.079	-9999	-10000	0	0
IRS2	-0.021	0.074	-9999	-0.41	1	1
IGF-1R heterotetramer/IGF1	-0.041	0.1	-9999	-10000	0	0
GRB2	0.012	0	-9999	-10000	0	0
PDPK1	-0.007	0.065	-9999	-10000	0	0
YWHAE	0.012	0	-9999	-10000	0	0
PRKD1	-0.037	0.12	-9999	-0.4	4	4
SHC1	0.012	0	-9999	-10000	0	0

×

FOXM1 transcription factor network

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
NFATC3	0.11	0.25	-9999	-0.95	1	1
PLK1	0.049	0.056	-9999	-0.51	2	2
BIRC5	0.05	0.05	-9999	-0.52	1	1
HSPA1B	0.089	0.28	-9999	-1.2	1	1
MAP2K1	0.033	0.028	-9999	-10000	0	0
BRCA2	0.11	0.26	-9999	-0.95	1	1
FOXM1	0.11	0.27	-9999	-1.1	1	1
XRCC1	0.11	0.25	-9999	-0.95	1	1
FOXM1B/p19	-0.14	0.21	-9999	-1.1	4	4
Cyclin D1/CDK4	0.1	0.25	-9999	-0.88	1	1
CDC2	0.11	0.26	-9999	-1	1	1
TGFA	0.11	0.24	-9999	-10000	0	0
SKP2	0.11	0.25	-9999	-0.95	1	1
CCNE1	0.011	0.061	-9999	-0.71	3	3
CKS1B	0.11	0.25	-9999	-1.2	1	1
RB1	-0.027	0.072	-9999	-10000	0	0
FOXM1C/SP1	0.11	0.26	-9999	-1.1	1	1
AURKB	0.051	0.042	-9999	-10000	0	0
CENPF	0.11	0.25	-9999	-0.96	2	2
CDK4	0.018	0.037	-9999	-0.7	1	1
MYC	0.11	0.24	-9999	-0.84	1	1
CHEK2	0.033	0.028	-9999	-10000	0	0
ONECUT1	0.1	0.25	-9999	-0.92	1	1
CDKN2A	-0.17	0.31	-9999	-0.71	105	105
LAMA4	0.11	0.25	-9999	-0.95	1	1
FOXM1B/HNF6	0.1	0.26	-9999	-1.1	1	1
FOS	0.1	0.28	-9999	-1.1	5	5
SP1	0.013	0.003	-9999	-10000	0	0
CDC25B	0.098	0.27	-9999	-0.95	1	1
response to radiation	0.018	0.025	-9999	-10000	0	0
CENPB	0.11	0.25	-9999	-0.95	1	1
CENPA	0.11	0.25	-9999	-0.95	1	1
NEK2	0.11	0.25	-9999	-0.96	2	2
HIST1H2BA	0.11	0.25	-9999	-0.96	1	1
CCNA2	0.016	0.006	-9999	-10000	0	0
EP300	0.012	0	-9999	-10000	0	0
CCNB1/CDK1	0.11	0.26	-9999	-1.1	1	1
CCNB2	0.11	0.25	-9999	-0.95	1	1
CCNB1	0.11	0.26	-9999	-1	1	1
ETV5	0.1	0.26	-9999	-0.95	1	1
ESR1	0.053	0.39	-9999	-1.1	21	21
CCND1	0.11	0.25	-9999	-0.88	2	2
GSK3A	0.03	0.024	-9999	-10000	0	0
Cyclin A-E1/CDK1-2	0.04	0.051	-9999	-0.45	3	3
CDK2	0.016	0.006	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	0.021	0.029	-9999	-10000	0	0
FOXM1B/Cbp/p300	-0.059	0.16	-9999	-1	1	1
GAS1	0.015	0.44	-9999	-1.1	27	27
MMP2	0.11	0.26	-9999	-0.95	1	1
RB1/FOXM1C	0.11	0.25	-9999	-0.92	1	1
CREBBP	0.012	0	-9999	-10000	0	0

×

Signaling events mediated by HDAC Class II

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G beta1gamma2/HDAC5	0.022	0.038	-9999	-10000	0	0
HDAC3	0.012	0	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	-0.001	0.017	-9999	-0.34	1	1
GATA1/HDAC4	0.014	0.004	-9999	-10000	0	0
GATA1/HDAC5	0.014	0.012	-9999	-10000	0	0
GATA2/HDAC5	0.012	0.035	-9999	-10000	0	0
HDAC5/BCL6/BCoR	0.024	0.009	-9999	-10000	0	0
HDAC9	-0.022	0.1	-9999	-0.32	43	43
Glucocorticoid receptor/Hsp90/HDAC6	0.011	0.049	-9999	-10000	0	0
HDAC4/ANKRA2	0.018	0	-9999	-10000	0	0
HDAC5/YWHAB	0.017	0.011	-9999	-10000	0	0
NPC/RanGAP1/SUMO1/Ubc9	0.016	0.015	-9999	-10000	0	0
GATA2	0.005	0.048	-9999	-0.32	9	9
HDAC4/RFXANK	0.018	0	-9999	-10000	0	0
BCOR	0.012	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
HDAC10	0.011	0.016	-9999	-0.32	1	1
HDAC5	0.011	0.016	-9999	-0.32	1	1
GNB1/GNG2	0.007	0.048	-9999	-10000	0	0
Histones	0.013	0.055	-9999	-0.32	1	1
ADRBK1	0.012	0	-9999	-10000	0	0
HDAC4	0.012	0	-9999	-10000	0	0
XPO1	0.012	0	-9999	-10000	0	0
HDAC5/ANKRA2	0.017	0.011	-9999	-10000	0	0
HDAC4/Ubc9	0.018	0	-9999	-10000	0	0
HDAC7	0.012	0	-9999	-10000	0	0
HDAC5/14-3-3 E	0.017	0.011	-9999	-10000	0	0
TUBA1B	0.012	0	-9999	-10000	0	0
HDAC6	0.012	0	-9999	-10000	0	0
HDAC5/RFXANK	0.017	0.011	-9999	-10000	0	0
CAMK4	-0.007	0.076	-9999	-0.32	23	23
Tubulin/HDAC6	0.018	0.052	-9999	-0.46	5	5
SUMO1	0.01	0.023	-9999	-0.32	2	2
EntrezGene:9972	0	0	-9999	-10000	0	0
YWHAB	0.012	0	-9999	-10000	0	0
GATA1	0.008	0.006	-9999	-10000	0	0
EntrezGene:8021	0	0	-9999	-10000	0	0
YWHAE	0.012	0	-9999	-10000	0	0
NR3C1	-0.011	0.084	-9999	-0.32	29	29
SUMO1/HDAC4	0.024	0.019	-9999	-10000	0	0
SRF	0.012	0	-9999	-10000	0	0
HDAC4/YWHAB	0.018	0	-9999	-10000	0	0
Tubulin	0.011	0.06	-9999	-0.53	5	5
HDAC4/14-3-3 E	0.018	0	-9999	-10000	0	0
GNB1	0.012	0	-9999	-10000	0	0
RANGAP1	0.012	0	-9999	-10000	0	0
BCL6/BCoR	0.018	0	-9999	-10000	0	0
HDAC4/HDAC3/SMRT (N-CoR2)	0.024	0.009	-9999	-10000	0	0
HDAC4/SRF	0.013	0.044	-9999	-10000	0	0
HDAC4/ER alpha	-0.002	0.064	-9999	-10000	0	0
EntrezGene:23225	0	0	-9999	-10000	0	0
positive regulation of chromatin silencing	0.013	0.055	-9999	-0.32	1	1
cell motility	0.018	0.052	-9999	-0.45	5	5
EntrezGene:23636	0	0	-9999	-10000	0	0
UBE2I	0.012	0	-9999	-10000	0	0
HDAC7/HDAC3	0.018	0	-9999	-10000	0	0
BCL6	0.012	0	-9999	-10000	0	0
HDAC4/CaMK II delta B	0.012	0	-9999	-10000	0	0
Hsp90/HDAC6	0.018	0	-9999	-10000	0	0
ESR1	-0.017	0.093	-9999	-0.32	36	36
HDAC6/HDAC11	0.018	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.027	0.014	-9999	-10000	0	0
NPC	0.006	0.02	-9999	-0.4	1	1
MEF2C	0.005	0.048	-9999	-0.32	9	9
RAN	0.012	0	-9999	-10000	0	0
HDAC4/MEF2C	0.031	0.025	-9999	-10000	0	0
GNG2	-0.003	0.069	-9999	-0.32	19	19
NCOR2	0.011	0.016	-9999	-0.32	1	1
TUBB2A	0.003	0.078	-9999	-0.71	5	5
HDAC11	0.012	0	-9999	-10000	0	0
HSP90AA1	0.012	0	-9999	-10000	0	0
RANBP2	0.01	0.035	-9999	-0.71	1	1
ANKRA2	0.012	0	-9999	-10000	0	0
RFXANK	0.012	0	-9999	-10000	0	0
nuclear import	-0.024	0.011	-9999	-10000	0	0

×

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

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
MET/RANBP9	0.007	0.075	-10000	0	-0.53	8	8
CRKL	0.022	0.042	-10000	0	-0.33	1	1
mol:PIP3	-0.014	0.016	0.31	1	-10000	0	1
AKT1	0	0.012	0.24	1	-10000	0	1
PTK2B	0.012	0	-10000	0	-10000	0	0
RAPGEF1	0.025	0.04	-10000	0	-0.31	1	1
RANBP10	0.012	0	-10000	0	-10000	0	0
PIK3CA	0.012	0.001	-10000	0	-10000	0	0
HGF/MET/SHIP2	0.008	0.078	-10000	0	-0.47	9	9
MAP3K5	0.014	0.076	-10000	0	-0.33	6	6
HGF/MET/CIN85/CBL/ENDOPHILINS	0.016	0.072	-10000	0	-0.43	9	9
AP1	0.01	0.033	-10000	0	-10000	0	0
mol:SU11274	0	0	-10000	0	-10000	0	0
SHC1	0.012	0	-10000	0	-10000	0	0
apoptosis	0.003	0.097	-10000	0	-0.73	7	7
STAT3 (dimer)	0.022	0.046	-10000	0	-0.37	1	1
GAB1/CRKL/SHP2/PI3K	0.036	0.039	-10000	0	-10000	0	0
INPP5D	0.012	0	-10000	0	-10000	0	0
CBL/CRK	0.028	0.04	-10000	0	-0.31	1	1
PTPN11	0.012	0	-10000	0	-10000	0	0
GO:0007205	0	0	-10000	0	-10000	0	0
PLCG1	0.012	0	-10000	0	-10000	0	0
PTEN	0.011	0.016	-10000	0	-0.32	1	1
ELK1	-0.005	0.035	-10000	0	-0.25	8	8
mol:SU5416	0	0	-10000	0	-10000	0	0
SHP2/GRB2/SOS1GAB1	0.018	0.031	-10000	0	-0.24	1	1
PAK1	0.005	0.011	0.23	1	-10000	0	1
HGF/MET/RANBP10	0.008	0.078	-10000	0	-0.47	9	9
HRAS	0.019	0.054	-10000	0	-0.44	1	1
DOCK1	0.026	0.04	-10000	0	-0.31	1	1
GAB1	0.017	0.044	-10000	0	-0.35	1	1
CRK	0.022	0.042	-10000	0	-0.33	1	1
mol:PHA665752	0	0	-10000	0	-10000	0	0
mol:GDP	0.011	0.081	-10000	0	-0.4	12	12
JUN	0.012	0	-10000	0	-10000	0	0
EntrezGene:200958	0	0	-10000	0	-10000	0	0
HGF/MET	0.003	0.044	-10000	0	-0.24	9	9
PIK3R1	0.012	0	-10000	0	-10000	0	0
cell morphogenesis	0.041	0.047	-10000	0	-10000	0	0
GRB2/SHC	0.017	0.041	-10000	0	-0.33	1	1
FOS	0.006	0.043	-10000	0	-0.32	7	7
GLMN	0	0.01	-10000	0	-0.2	1	1
cell motility	-0.005	0.035	-10000	0	-0.25	8	8
HGF/MET/MUC20	0	0.078	-10000	0	-0.48	9	9
cell migration	0.017	0.04	-10000	0	-0.32	1	1
GRB2	0.012	0	-10000	0	-10000	0	0
CBL	0.012	0	-10000	0	-10000	0	0
MET/RANBP10	0.007	0.075	-10000	0	-0.53	8	8
HGF/MET/Paxillin/FAK1/FAK12/RasGAP	0.019	0.049	-10000	0	-0.39	1	1
MET/MUC20	-0.002	0.075	-10000	0	-0.54	8	8
RAP1B	0.029	0.038	-10000	0	-10000	0	0
RAP1A	0.029	0.038	-10000	0	-10000	0	0
HGF/MET/RANBP9	0.008	0.078	-10000	0	-0.47	9	9
RAF1	0.023	0.052	-10000	0	-0.41	1	1
STAT3	0.022	0.047	-10000	0	-0.37	1	1
cell proliferation	0.028	0.06	-10000	0	-0.47	1	1
RPS6KB1	0.007	0.022	-10000	0	-0.27	1	1
MAPK3	-0.01	0.032	-10000	0	-0.24	8	8
MAPK1	-0.01	0.032	-10000	0	-0.24	8	8
RANBP9	0.012	0	-10000	0	-10000	0	0
MAPK8	0.029	0.06	-10000	0	-10000	0	0
SRC	0.023	0.046	-10000	0	-0.36	1	1
PI3K	0.017	0.041	-10000	0	-0.33	1	1
MET/Glomulin	0.001	0.068	-10000	0	-0.48	8	8
SOS1	0.012	0	-10000	0	-10000	0	0
MAP2K1	0.027	0.049	-10000	0	-0.38	1	1
MET	-0.002	0.098	-10000	0	-0.71	8	8
MAP4K1	0.009	0.08	-10000	0	-0.35	6	6
PTK2	0.012	0	-10000	0	-10000	0	0
MAP2K2	0.027	0.049	-10000	0	-0.38	1	1
BAD	0.005	0.013	0.23	1	-10000	0	1
MAP2K4	0.018	0.072	-10000	0	-0.3	5	5
SHP2/GRB2/SOS1/GAB1	-0.009	0.043	-10000	0	-0.4	1	1
INPPL1	0.012	0	-10000	0	-10000	0	0
PXN	0.012	0	-10000	0	-10000	0	0
SH3KBP1	0.012	0	-10000	0	-10000	0	0
HGS	0.008	0.041	-10000	0	-0.23	8	8
PLCgamma1/PKC	0.009	0	-10000	0	-10000	0	0
HGF	0	0.065	-10000	0	-0.35	13	13
RASA1	0.012	0.001	-10000	0	-10000	0	0
NCK1	0.012	0	-10000	0	-10000	0	0
PTPRJ	0.012	0	-10000	0	-10000	0	0
NCK/PLCgamma1	0.018	0.042	-10000	0	-0.34	1	1
PDPK1	-0.006	0.013	0.26	1	-10000	0	1
HGF/MET/SHIP	0.008	0.078	-10000	0	-0.47	9	9

×

PDGFR-alpha signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	0.002	0.058	-9999	-0.32	13	13
PDGF/PDGFRA/CRKL	0.011	0.039	-9999	-10000	0	0
positive regulation of JUN kinase activity	0.025	0.029	-9999	-10000	0	0
CRKL	0.012	0	-9999	-10000	0	0
PDGF/PDGFRA/Caveolin-3	0.001	0.054	-9999	-0.54	2	2
AP1	0.013	0.1	-9999	-0.73	7	7
mol:IP3	0.012	0.041	-9999	-10000	0	0
PLCG1	0.012	0.041	-9999	-10000	0	0
PDGF/PDGFRA/alphaV Integrin	0.011	0.039	-9999	-10000	0	0
RAPGEF1	0.011	0.016	-9999	-0.32	1	1
CRK	0.012	0	-9999	-10000	0	0
mol:Ca2+	0.012	0.041	-9999	-10000	0	0
CAV3	-0.002	0.049	-9999	-0.71	2	2
CAV1	-0.002	0.066	-9999	-0.32	17	17
SHC/Grb2/SOS1	0.026	0.029	-9999	-10000	0	0
PDGF/PDGFRA/Shf	-0.003	0.093	-9999	-0.54	10	10
FOS	0.014	0.1	-9999	-0.72	7	7
JUN	-0.002	0.008	-9999	-10000	0	0
oligodendrocyte development	0.011	0.038	-9999	-10000	0	0
GRB2	0.012	0	-9999	-10000	0	0
PIK3R1	0.012	0	-9999	-10000	0	0
mol:DAG	0.012	0.041	-9999	-10000	0	0
PDGF/PDGFRA	0.002	0.058	-9999	-0.32	13	13
actin cytoskeleton reorganization	0.011	0.038	-9999	-10000	0	0
SRF	0.016	0.003	-9999	-10000	0	0
SHC1	0.012	0	-9999	-10000	0	0
PI3K	0.019	0.032	-9999	-10000	0	0
PDGF/PDGFRA/Crk/C3G	0.019	0.033	-9999	-10000	0	0
JAK1	0.011	0.039	-9999	-10000	0	0
ELK1/SRF	0.023	0.032	-9999	-10000	0	0
SHB	0.012	0	-9999	-10000	0	0
SHF	-0.006	0.11	-9999	-0.67	11	11
CSNK2A1	0.009	0.006	-9999	-10000	0	0
GO:0007205	0.011	0.047	-9999	-10000	0	0
SOS1	0.012	0	-9999	-10000	0	0
Ras protein signal transduction	0.025	0.029	-9999	-10000	0	0
PDGF/PDGFRA/SHB	0.011	0.039	-9999	-10000	0	0
PDGF/PDGFRA/Caveolin-1	0.002	0.066	-9999	-0.4	5	5
ITGAV	0.012	0	-9999	-10000	0	0
ELK1	0.016	0.041	-9999	-10000	0	0
PIK3CA	0.012	0.001	-9999	-10000	0	0
PDGF/PDGFRA/Crk	0.011	0.039	-9999	-10000	0	0
JAK-STAT cascade	0.011	0.038	-9999	-10000	0	0
cell proliferation	-0.003	0.093	-9999	-0.54	10	10

×

IL2 signaling events mediated by PI3K

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
BCL2L1	0.04	0.038	-9999	-10000	0	0
UGCG	0.022	0.014	-9999	-10000	0	0
AKT1/mTOR/p70S6K/Hsp90/TERT	0.038	0.075	-9999	-0.3	2	2
mol:GTP	0	0	-9999	-10000	0	0
mol:glucosylceramide	0.022	0.014	-9999	-10000	0	0
mol:DAG	0.001	0.013	-9999	-10000	0	0
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.016	0.064	-9999	-0.34	14	14
FRAP1	0.05	0.092	-9999	-0.38	14	14
FOXO3	0.056	0.062	-9999	-10000	0	0
AKT1	0.053	0.065	-9999	-0.33	1	1
GAB2	0.012	0.002	-9999	-10000	0	0
SMPD1	0.019	0.042	-9999	-0.55	2	2
SGMS1	0.022	0.014	-9999	-10000	0	0
positive regulation of NF-kappaB transcription factor activity	0	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
mol:GDP	0.016	0.003	-9999	-10000	0	0
CALM1	0.012	0	-9999	-10000	0	0
cell proliferation	0.037	0.034	-9999	-10000	0	0
EIF3A	0.012	0	-9999	-10000	0	0
PI3K	0.022	0.005	-9999	-10000	0	0
RPS6KB1	0.021	0.038	-9999	-0.71	1	1
mol:sphingomyelin	0.001	0.013	-9999	-10000	0	0
natural killer cell activation	0	0.002	-9999	-10000	0	0
JAK3	0.011	0.05	-9999	-0.7	2	2
PIK3R1	0.014	0.002	-9999	-10000	0	0
JAK1	0.014	0.002	-9999	-10000	0	0
NFKB1	0.012	0	-9999	-10000	0	0
MYC	0.054	0.071	-9999	-0.41	4	4
MYB	0.024	0.03	-9999	-10000	0	0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.05	0.053	-9999	-10000	0	0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.032	0.04	-9999	-0.5	2	2
mol:PI-3-4-5-P3	0.049	0.052	-9999	-10000	0	0
Rac1/GDP	0.022	0.005	-9999	-10000	0	0
T cell proliferation	0.052	0.05	-9999	-10000	0	0
SHC1	0.012	0.002	-9999	-10000	0	0
RAC1	0.012	0	-9999	-10000	0	0
positive regulation of cyclin-dependent protein kinase activity	0.004	0	-9999	-10000	0	0
PRKCZ	0.052	0.051	-9999	-10000	0	0
NF kappa B1 p50/RelA	0.056	0.083	-9999	-0.43	2	2
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K	0.035	0.041	-9999	-10000	0	0
HSP90AA1	0.012	0	-9999	-10000	0	0
RELA	0.012	0	-9999	-10000	0	0
IL2RA	0.006	0.046	-9999	-0.32	8	8
IL2RB	0.009	0.04	-9999	-0.32	6	6
TERT	-0.062	0.22	-9999	-0.69	44	44
E2F1	0.02	0.034	-9999	-0.36	1	1
SOS1	0.012	0.002	-9999	-10000	0	0
RPS6	0.01	0.035	-9999	-0.71	1	1
mol:cAMP	-0.002	0	-9999	-10000	0	0
PTPN11	0.012	0.002	-9999	-10000	0	0
IL2RG	0.013	0.023	-9999	-0.32	2	2
actin cytoskeleton organization	0.052	0.05	-9999	-10000	0	0
GRB2	0.012	0.002	-9999	-10000	0	0
IL2	0.005	0.006	-9999	-10000	0	0
PIK3CA	0.014	0.002	-9999	-10000	0	0
Rac1/GTP	0.031	0.007	-9999	-10000	0	0
LCK	0	0.1	-9999	-0.66	9	9
BCL2	0.038	0.16	-9999	-0.79	14	14

×

Arf6 trafficking events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SLC2A4	-0.033	0.11	-10000	0	-0.32	56	56
CLTC	0.02	0.034	-10000	0	-10000	0	0
calcium ion-dependent exocytosis	0.02	0.006	-10000	0	-10000	0	0
Dynamin 2/GTP	0.011	0.06	-10000	0	-0.42	8	8
EXOC4	0.012	0	-10000	0	-10000	0	0
CD59	0.019	0.021	-10000	0	-10000	0	0
CPE	-0.005	0.06	-10000	0	-0.46	1	1
CTNNB1	0.012	0	-10000	0	-10000	0	0
membrane fusion	0.02	0.001	-10000	0	-10000	0	0
CTNND1	0.016	0.056	-10000	0	-0.39	8	8
DNM2	0.012	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.022	0.017	-10000	0	-10000	0	0
TSHR	0.01	0.033	-10000	0	-0.46	2	2
INS	0.008	0.006	-10000	0	-10000	0	0
BIN1	0.011	0.016	-10000	0	-0.32	1	1
mol:Choline	0.02	0.001	-10000	0	-10000	0	0
growth hormone secretagogue receptor activity	0	0	-10000	0	-10000	0	0
mol:GDP	0.006	0.065	-10000	0	-0.46	8	8
membrane depolarization	0	0	-10000	0	-10000	0	0
ARF6	0.012	0	-10000	0	-10000	0	0
mol:Ca2+	0.011	0.06	-10000	0	-0.42	8	8
JUP	0.019	0.023	-10000	0	-10000	0	0
ASAP2/amphiphysin II	0.023	0.008	-10000	0	-10000	0	0
ARF6/GTP	0.009	0	-10000	0	-10000	0	0
CDH1	0.019	0.021	-10000	0	-10000	0	0
clathrin-independent pinocytosis	0.009	0	-10000	0	-10000	0	0
MAPK8IP3	0.009	0.039	-10000	0	-0.51	2	2
positive regulation of endocytosis	0.009	0	-10000	0	-10000	0	0
EXOC2	0.011	0.016	-10000	0	-0.32	1	1
substrate adhesion-dependent cell spreading	0.031	0.03	-10000	0	-0.55	1	1
insulin receptor binding	0	0	-10000	0	-10000	0	0
SPAG9	0.012	0	-10000	0	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.023	0.047	0.32	8	-10000	0	8
positive regulation of phagocytosis	0.015	0	-10000	0	-10000	0	0
ARF6/GTP/JIP3	0.015	0.025	-10000	0	-0.46	1	1
ACAP1	0.016	0.022	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
CHRM2	-0.021	0.07	-10000	0	-0.36	2	2
clathrin heavy chain/ACAP1	0.023	0.031	-10000	0	-10000	0	0
JIP4/KLC1	0.023	0	-10000	0	-10000	0	0
EXOC1	0.011	0.016	-10000	0	-0.32	1	1
exocyst	0.031	0.031	-10000	0	-0.55	1	1
RALA/GTP	0.009	0	-10000	0	-10000	0	0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex	0.016	0	-10000	0	-10000	0	0
receptor recycling	0.009	0	-10000	0	-10000	0	0
CTNNA1	0.016	0.056	-10000	0	-0.39	8	8
NME1	0.006	0.065	-10000	0	-0.46	8	8
clathrin coat assembly	0.02	0.034	-10000	0	-10000	0	0
IL2RA	0.016	0.03	-10000	0	-10000	0	0
VAMP3	0.015	0	-10000	0	-10000	0	0
GLUT4/clathrin heavy chain/ACAP1	-0.018	0.046	-10000	0	-0.31	2	2
EXOC6	0.012	0	-10000	0	-10000	0	0
PLD1	0.017	0.011	-10000	0	-0.21	1	1
PLD2	0.017	0	-10000	0	-10000	0	0
EXOC5	0.009	0.028	-10000	0	-0.32	3	3
PIP5K1C	0.022	0.017	-10000	0	-10000	0	0
SDC1	0.019	0.021	-10000	0	-10000	0	0
ARF6/GDP	0.006	0.065	-10000	0	-0.46	8	8
EXOC7	0.012	0	-10000	0	-10000	0	0
E-cadherin/beta catenin	0.025	0.049	-10000	0	-0.32	8	8
mol:Phosphatidic acid	0.02	0.001	-10000	0	-10000	0	0
endocytosis	-0.022	0.008	-10000	0	-10000	0	0
SCAMP2	0.012	0	-10000	0	-10000	0	0
ADRB2	0.002	0.065	-10000	0	-0.35	4	4
EXOC3	0.012	0	-10000	0	-10000	0	0
ASAP2	0.012	0	-10000	0	-10000	0	0
Dynamin 2/GDP	0.013	0.06	-10000	0	-0.42	8	8
KLC1	0.012	0	-10000	0	-10000	0	0
AVPR2	0.008	0.069	-10000	0	-0.36	9	9
RALA	0.012	0	-10000	0	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.006	0.041	-10000	0	-10000	0	0

×

E-cadherin signaling in keratinocytes

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
keratinocyte differentiation	0.037	0.006	-9999	-10000	0	0
adherens junction organization	0	0.058	-9999	-0.3	1	1
mol:GTP	0	0	-9999	-10000	0	0
Rac1/GDP	0.042	0.005	-9999	-10000	0	0
FMN1	0.033	0.01	-9999	-10000	0	0
mol:IP3	0.032	0.006	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.029	0.011	-9999	-10000	0	0
CTNNB1	0.012	0	-9999	-10000	0	0
AKT1	0.037	0.007	-9999	-10000	0	0
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.032	0.006	-9999	-10000	0	0
CTNND1	0.013	0	-9999	-10000	0	0
mol:PI-4-5-P2	0.032	0.01	-9999	-10000	0	0
VASP	0.033	0.01	-9999	-10000	0	0
ZYX	0.033	0.01	-9999	-10000	0	0
JUB	-0.072	0.18	-9999	-0.36	112	112
EGFR(dimer)	0.034	0.01	-9999	-10000	0	0
E-cadherin/beta catenin-gamma catenin	0.022	0.009	-9999	-10000	0	0
mol:PI-3-4-5-P3	0.033	0.007	-9999	-10000	0	0
PIK3CA	0.013	0.001	-9999	-10000	0	0
PI3K	0.034	0.007	-9999	-10000	0	0
FYN	0.033	0.019	-9999	-10000	0	0
mol:Ca2+	0.031	0.005	-9999	-10000	0	0
JUP	0.011	0.016	-9999	-0.32	1	1
PIK3R1	0.013	0	-9999	-10000	0	0
mol:DAG	0.032	0.006	-9999	-10000	0	0
CDH1	0.012	0	-9999	-10000	0	0
RhoA/GDP	0.042	0.005	-9999	-10000	0	0
establishment of polarity of embryonic epithelium	0.032	0.01	-9999	-10000	0	0
SRC	0.012	0	-9999	-10000	0	0
RAC1	0.012	0	-9999	-10000	0	0
RHOA	0.012	0	-9999	-10000	0	0
EGFR	0.012	0	-9999	-10000	0	0
CASR	0.028	0.021	-9999	-0.34	1	1
RhoA/GTP	0.035	0.005	-9999	-10000	0	0
AKT2	0.037	0.007	-9999	-10000	0	0
actin cable formation	0.036	0.01	-9999	-10000	0	0
apoptosis	-0.035	0.006	-9999	-10000	0	0
CTNNA1	0.013	0	-9999	-10000	0	0
mol:GDP	0.037	0.006	-9999	-10000	0	0
PIP5K1A	0.033	0.01	-9999	-10000	0	0
PLCG1	0.032	0.006	-9999	-10000	0	0
Rac1/GTP	0.036	0.009	-9999	-10000	0	0
homophilic cell adhesion	0.001	0	-9999	-10000	0	0

×

Class IB PI3K non-lipid kinase events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
cAMP biosynthetic process	-0.01	0.023	0.32	2	-10000	0	2
PI3K Class IB/PDE3B	0.01	0.023	-10000	0	-0.32	2	2
PDE3B	0.01	0.023	-10000	0	-0.32	2	2

×

p38 MAPK signaling pathway

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
TRAF6/ASK1	0.012	0	-10000	0	-10000	0	0
TRAF2/ASK1	0.016	0.009	-10000	0	-10000	0	0
ATM	0.012	0	-10000	0	-10000	0	0
MAP2K3	0.021	0.027	-10000	0	-0.29	1	1
response to stress	0	0	-10000	0	-10000	0	0
MAP2K6	0.027	0.027	-10000	0	-10000	0	0
hyperosmotic response	0	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
GADD45G	0.008	0.052	-10000	0	-0.58	3	3
TXN	0.007	0	-10000	0	-10000	0	0
CALM1	0.012	0	-10000	0	-10000	0	0
GADD45A	0.012	0	-10000	0	-10000	0	0
GADD45B	0.012	0	-10000	0	-10000	0	0
MAP3K1	0.011	0.016	-10000	0	-0.32	1	1
MAP3K6	0.01	0.023	-10000	0	-0.32	2	2
MAP3K7	0.012	0	-10000	0	-10000	0	0
MAP3K4	0.012	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
ASK1/ASK2	0.017	0.016	-10000	0	-10000	0	0
TAK1/TAB family	0.001	0.012	0.17	2	-10000	0	2
RAC1/OSM/MEKK3	0.023	0	-10000	0	-10000	0	0
TRAF2	0.011	0.016	-10000	0	-0.32	1	1
RAC1/OSM/MEKK3/MKK3	-0.002	0.012	-10000	0	-10000	0	0
TRAF6	0.007	0	-10000	0	-10000	0	0
RAC1	0.012	0	-10000	0	-10000	0	0
mol:LPS	0	0	-10000	0	-10000	0	0
CAMK2B	-0.052	0.14	-10000	0	-0.34	75	75
CCM2	0.012	0	-10000	0	-10000	0	0
CaM/Ca2+/CAMKIIB	-0.021	0.081	-10000	0	-0.46	3	3
MAPK11	0.008	0.05	-10000	0	-0.71	2	2
response to DNA damage stimulus	0	0	-10000	0	-10000	0	0
CaM/Ca2+/CAMKIIB/ASK1	-0.011	0.074	-10000	0	-0.42	3	3
OSM/MEKK3	0.018	0	-10000	0	-10000	0	0
TAOK1	0.013	0.012	-10000	0	-0.24	1	1
TAOK2	0.014	0	-10000	0	-10000	0	0
TAOK3	0.014	0	-10000	0	-10000	0	0
MAP3K7IP1	0	0	-10000	0	-10000	0	0
MAPK14	0.012	0	-10000	0	-10000	0	0
MAP3K7IP2	0	0	-10000	0	-10000	0	0
MAP3K5	0.012	0	-10000	0	-10000	0	0
MAP3K10	0.012	0	-10000	0	-10000	0	0
MAP3K3	0.012	0	-10000	0	-10000	0	0
TRX/ASK1	0.014	0	-10000	0	-10000	0	0
GADD45/MTK1/MTK1	0.026	0.03	-10000	0	-0.39	2	2

×

LPA4-mediated signaling events

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
ADCY4	0.014	0	-9999	-10000	0	0
ADCY5	-0.078	0.094	-9999	-10000	0	0
ADCY6	0.014	0	-9999	-10000	0	0
ADCY7	0.014	0	-9999	-10000	0	0
ADCY1	0.004	0.066	-9999	-0.46	8	8
ADCY2	-0.016	0.069	-9999	-10000	0	0
ADCY3	0.014	0	-9999	-10000	0	0
ADCY8	0	0.06	-9999	-0.46	7	7
PRKCE	0.009	0	-9999	-10000	0	0
ADCY9	0.013	0.013	-9999	-10000	0	0
mol:DAG	0	0	-9999	-10000	0	0
cAMP biosynthetic process	-0.018	0.051	-9999	-0.25	2	2

×

Canonical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FBXW11	0.014	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.058	0.028	-9999	-10000	0	0
ERC1	0.012	0	-9999	-10000	0	0
RIP2/NOD2	-0.005	0.11	-9999	-0.53	17	17
NFKBIA	0.033	0	-9999	-10000	0	0
BIRC2	0.012	0.001	-9999	-10000	0	0
IKBKB	0.012	0	-9999	-10000	0	0
RIPK2	0.012	0	-9999	-10000	0	0
IKBKG	0.026	0.044	-9999	-0.29	2	2
IKK complex/A20	0.04	0.041	-9999	-10000	0	0
NEMO/A20/RIP2	0.012	0	-9999	-10000	0	0
XPO1	0.012	0	-9999	-10000	0	0
NEMO/ATM	0.031	0.043	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
RAN	0.012	0	-9999	-10000	0	0
Exportin 1/RanGTP	0.016	0	-9999	-10000	0	0
IKK complex/ELKS	-0.006	0.03	-9999	-10000	0	0
BCL10/MALT1/TRAF6	0.024	0.009	-9999	-10000	0	0
NOD2	-0.018	0.14	-9999	-0.68	18	18
NFKB1	0.014	0	-9999	-10000	0	0
RELA	0.014	0	-9999	-10000	0	0
MALT1	0.011	0.016	-9999	-0.32	1	1
cIAP1/UbcH5C	0.018	0	-9999	-10000	0	0
ATM	0.012	0	-9999	-10000	0	0
TNF/TNFR1A	0.017	0.011	-9999	-10000	0	0
TRAF6	0.012	0	-9999	-10000	0	0
PRKCA	0.012	0	-9999	-10000	0	0
CHUK	0.012	0	-9999	-10000	0	0
UBE2D3	0.012	0	-9999	-10000	0	0
TNF	0.011	0.016	-9999	-0.32	1	1
NF kappa B1 p50/RelA	0.033	0	-9999	-10000	0	0
BCL10	0.012	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.033	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.014	0	-9999	-10000	0	0
TNFRSF1A	0.012	0	-9999	-10000	0	0
IKK complex	0.037	0.042	-9999	-10000	0	0
CYLD	0.011	0.016	-9999	-0.32	1	1
IKK complex/PKC alpha	0.041	0.041	-9999	-10000	0	0

×

Arf6 downstream pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLAUR	0.029	0.012	-10000	0	-10000	0	0
regulation of axonogenesis	-0.022	0.001	-10000	0	-10000	0	0
myoblast fusion	-0.019	0.012	-10000	0	-10000	0	0
mol:GTP	0.009	0.003	-10000	0	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.006	0.087	0.51	8	-10000	0	8
ARF1/GTP	0.016	0.005	-10000	0	-10000	0	0
mol:GM1	0.008	0.003	-10000	0	-10000	0	0
mol:Choline	0.021	0.009	-10000	0	-10000	0	0
lamellipodium assembly	0.025	0.016	-10000	0	-10000	0	0
MAPK3	0.021	0.007	-10000	0	-10000	0	0
ARF6/GTP/NME1/Tiam1	0.007	0.088	-10000	0	-0.51	8	8
ARF1	0.012	0	-10000	0	-10000	0	0
ARF6/GDP	0.02	0.012	-10000	0	-10000	0	0
ARF1/GDP	0.027	0.014	-10000	0	-10000	0	0
ARF6	0.012	0.001	-10000	0	-10000	0	0
RAB11A	0.012	0	-10000	0	-10000	0	0
TIAM1	-0.015	0.092	-10000	0	-0.32	35	35
fibronectin binding	0	0	-10000	0	-10000	0	0
MAPK1	0.021	0.007	-10000	0	-10000	0	0
actin filament bundle formation	-0.02	0.007	-10000	0	-10000	0	0
KALRN	0.006	0.018	-10000	0	-10000	0	0
RAB11FIP3/RAB11A	0.018	0	-10000	0	-10000	0	0
RhoA/GDP	0.021	0.007	-10000	0	-10000	0	0
NME1	-0.001	0.098	-10000	0	-0.7	8	8
Rac1/GDP	0.021	0.007	-10000	0	-10000	0	0
substrate adhesion-dependent cell spreading	0.009	0.003	-10000	0	-10000	0	0
cortical actin cytoskeleton organization	0.025	0.016	-10000	0	-10000	0	0
RAC1	0.012	0	-10000	0	-10000	0	0
liver development	0.009	0.003	-10000	0	-10000	0	0
ARF6/GTP	0.009	0.003	-10000	0	-10000	0	0
RhoA/GTP	0.016	0.005	-10000	0	-10000	0	0
mol:GDP	0.023	0.017	-10000	0	-10000	0	0
ARF6/GTP/RAB11FIP3/RAB11A	0.023	0.003	-10000	0	-10000	0	0
RHOA	0.012	0	-10000	0	-10000	0	0
PLD1	0.017	0.01	-10000	0	-10000	0	0
RAB11FIP3	0.012	0	-10000	0	-10000	0	0
tube morphogenesis	0.025	0.016	-10000	0	-10000	0	0
ruffle organization	0.022	0.001	-10000	0	-10000	0	0
regulation of epithelial cell migration	0.009	0.003	-10000	0	-10000	0	0
PLD2	0.017	0.001	-10000	0	-10000	0	0
PIP5K1A	0.022	0.001	-10000	0	-10000	0	0
mol:Phosphatidic acid	0.021	0.009	-10000	0	-10000	0	0
Rac1/GTP	0.025	0.016	-10000	0	-10000	0	0

×

TRAIL signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TNFSF10	0.011	0.016	-9999	-0.32	1	1
positive regulation of NF-kappaB transcription factor activity	0.017	0.011	-9999	-10000	0	0
MAP2K4	0.035	0.014	-9999	-10000	0	0
IKBKB	0.012	0	-9999	-10000	0	0
TNFRSF10B	0.012	0	-9999	-10000	0	0
TNFRSF10A	0.012	0	-9999	-10000	0	0
SMPD1	0.013	0.028	-9999	-0.38	2	2
IKBKG	0.011	0.016	-9999	-0.32	1	1
mol:GTP	0	0	-9999	-10000	0	0
TNFRSF10D	0.012	0	-9999	-10000	0	0
TRAIL/TRAILR2	0.017	0.011	-9999	-10000	0	0
TRAIL/TRAILR3	-0.013	0.13	-9999	-0.53	23	23
TRAIL/TRAILR1	0.017	0.011	-9999	-10000	0	0
TRAIL/TRAILR4	0.017	0.011	-9999	-10000	0	0
TRAIL/TRAILR1/DAP3/GTP	0.023	0.008	-9999	-10000	0	0
IKK complex	-0.001	0.014	-9999	-10000	0	0
RIPK1	0.012	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
DAP3/GTP	0.009	0	-9999	-10000	0	0
MAPK3	0.017	0.011	-9999	-10000	0	0
MAP3K1	0.031	0.014	-9999	-10000	0	0
TRAILR4 (trimer)	0.012	0	-9999	-10000	0	0
TRADD	0.012	0	-9999	-10000	0	0
TRAILR1 (trimer)	0.012	0	-9999	-10000	0	0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2	0.028	0.013	-9999	-10000	0	0
CFLAR	0.012	0	-9999	-10000	0	0
MAPK1	0.017	0.011	-9999	-10000	0	0
TRAIL/TRAILR1/FADD/TRADD/RIP	0.035	0.008	-9999	-10000	0	0
mol:ceramide	0.013	0.028	-9999	-0.38	2	2
FADD	0.012	0	-9999	-10000	0	0
MAPK8	0.038	0.015	-9999	-10000	0	0
TRAF2	0.011	0.016	-9999	-0.32	1	1
TRAILR3 (trimer)	-0.028	0.16	-9999	-0.7	23	23
CHUK	0.012	0	-9999	-10000	0	0
TRAIL/TRAILR1/FADD	0.024	0.009	-9999	-10000	0	0
DAP3	0.012	0	-9999	-10000	0	0
CASP10	0	0.009	-9999	-10000	0	0
JNK cascade	0.017	0.011	-9999	-10000	0	0
TRAIL (trimer)	0.011	0.016	-9999	-0.32	1	1
TNFRSF10C	-0.028	0.16	-9999	-0.71	23	23
TRAIL/TRAILR1/DAP3/GTP/FADD	0.028	0.008	-9999	-10000	0	0
TRAIL/TRAILR2/FADD	0.024	0.009	-9999	-10000	0	0
cell death	0.013	0.028	-9999	-0.37	2	2
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2	0.028	0.013	-9999	-10000	0	0
TRAILR2 (trimer)	0.012	0	-9999	-10000	0	0
CASP8	0	0	-9999	-10000	0	0
negative regulation of caspase activity	0	0	-9999	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP	0.035	0.008	-9999	-10000	0	0

×

ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K4	0.036	0.035	-10000	0	-10000	0	0
BAG4	0.012	0.001	-10000	0	-10000	0	0
BAD	0.023	0.019	-10000	0	-0.28	1	1
NFKBIA	0.012	0	-10000	0	-10000	0	0
BIRC3	0.004	0.055	-10000	0	-0.37	8	8
BAX	0.023	0.014	-10000	0	-10000	0	0
EnzymeConsortium:3.1.4.12	0.012	0.009	-10000	0	-10000	0	0
IKBKB	0.039	0.033	-10000	0	-10000	0	0
MAP2K2	0.031	0.012	-10000	0	-10000	0	0
MAP2K1	0.031	0.012	-10000	0	-10000	0	0
SMPD1	0.015	0.016	-10000	0	-0.18	2	2
GO:0005551	0	0	-10000	0	-10000	0	0
FADD/Caspase 8	0.041	0.034	-10000	0	-10000	0	0
MAP2K4	0.027	0.018	-10000	0	-10000	0	0
protein ubiquitination	0.04	0.035	-10000	0	-10000	0	0
EnzymeConsortium:2.7.1.37	0.035	0.012	-10000	0	-10000	0	0
response to UV	0	0	-10000	0	-10000	0	0
RAF1	0.028	0.013	-10000	0	-10000	0	0
CRADD	0.012	0	-10000	0	-10000	0	0
mol:ceramide	0.019	0.015	-10000	0	-0.15	1	1
I-kappa-B-alpha/RELA/p50/ubiquitin	0.016	0	-10000	0	-10000	0	0
MADD	0.012	0	-10000	0	-10000	0	0
MAP3K1	0.023	0.017	-10000	0	-0.19	1	1
TRADD	0.012	0	-10000	0	-10000	0	0
RELA/p50	0.012	0	-10000	0	-10000	0	0
MAPK3	0.033	0.012	-10000	0	-10000	0	0
MAPK1	0.033	0.012	-10000	0	-10000	0	0
p50/RELA/I-kappa-B-alpha	0.018	0	-10000	0	-10000	0	0
FADD	0.036	0.035	-10000	0	-10000	0	0
KSR1	0.024	0.014	-10000	0	-10000	0	0
MAPK8	0.03	0.017	-10000	0	-10000	0	0
TRAF2	0.011	0.016	-10000	0	-0.32	1	1
response to radiation	0	0	-10000	0	-10000	0	0
CHUK	0.039	0.033	-10000	0	-10000	0	0
TNF R/SODD	0.018	0.001	-10000	0	-10000	0	0
TNF	0.011	0.016	-10000	0	-0.32	1	1
CYCS	0.026	0.022	0.12	12	-0.21	1	13
IKBKG	0.039	0.036	-10000	0	-0.33	1	1
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD	0.032	0.036	-10000	0	-10000	0	0
RELA	0.012	0	-10000	0	-10000	0	0
RIPK1	0.012	0	-10000	0	-10000	0	0
AIFM1	0.026	0.023	0.12	13	-0.21	1	14
TNF/TNF R/SODD	0.024	0.009	-10000	0	-10000	0	0
TNFRSF1A	0.012	0	-10000	0	-10000	0	0
response to heat	0	0	-10000	0	-10000	0	0
CASP8	0.025	0.01	-10000	0	-10000	0	0
NSMAF	0.036	0.034	-10000	0	-10000	0	0
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
BCL2	0.001	0.06	-10000	0	-0.32	14	14

×

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

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
BAG4	0.012	0.001	-9999	-10000	0	0
Caspase 8 (4 units)	0.026	0.044	-9999	-0.32	1	1
NEF	-0.003	0.031	-9999	-10000	0	0
NFKBIA	0.013	0.012	-9999	-10000	0	0
BIRC3	0.025	0.059	-9999	-0.65	1	1
CYCS	0.026	0.052	-9999	-0.34	2	2
RIPK1	0.012	0	-9999	-10000	0	0
CD247	0.003	0.056	-9999	-0.33	8	8
MAP2K7	0.032	0.051	-9999	-0.62	1	1
protein ubiquitination	0.05	0.018	-9999	-10000	0	0
CRADD	0.012	0	-9999	-10000	0	0
DAXX	0.012	0	-9999	-10000	0	0
FAS	0.009	0.028	-9999	-0.32	3	3
BID	0.022	0.055	-9999	-0.36	2	2
NF-kappa-B/RelA/I kappa B alpha	0.029	0.033	-9999	-10000	0	0
TRADD	0.012	0	-9999	-10000	0	0
MAP3K5	0.012	0	-9999	-10000	0	0
CFLAR	0.012	0	-9999	-10000	0	0
FADD	0.012	0	-9999	-10000	0	0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin	0.029	0.033	-9999	-10000	0	0
MAPK8	0.036	0.048	-9999	-0.58	1	1
APAF1	0.012	0.001	-9999	-10000	0	0
TRAF1	0.012	0	-9999	-10000	0	0
TRAF2	0.011	0.016	-9999	-0.32	1	1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG	0.019	0.054	-9999	-0.38	1	1
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD	0.046	0.02	-9999	-10000	0	0
CHUK	0.051	0.018	-9999	-10000	0	0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8	0.034	0.014	-9999	-10000	0	0
TCRz/NEF	0.001	0.062	-9999	-0.25	20	20
TNF	0.011	0.016	-9999	-0.32	1	1
FASLG	-0.002	0.1	-9999	-0.46	18	18
NFKB1	0.013	0.012	-9999	-10000	0	0
TNFR1A/BAG4/TNF-alpha	0.024	0.009	-9999	-10000	0	0
CASP6	0.038	0.032	-9999	-10000	0	0
CASP7	0.048	0.07	-9999	-0.39	7	7
RELA	0.013	0.012	-9999	-10000	0	0
CASP2	0.012	0	-9999	-10000	0	0
CASP3	0.048	0.07	-9999	-0.39	7	7
TNFRSF1A	0.012	0	-9999	-10000	0	0
TNFR1A/BAG4	0.018	0.001	-9999	-10000	0	0
CASP8	0.012	0	-9999	-10000	0	0
CASP9	0.012	0	-9999	-10000	0	0
MAP3K14	0.049	0.019	-9999	-10000	0	0
APAF-1/Caspase 9	-0.011	0.045	-9999	-0.41	2	2
BCL2	0.035	0.053	-9999	-0.52	1	1

×

Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin	0.013	0.033	-9999	-10000	0	0
AKT1	0.061	0.034	-9999	-0.42	1	1
PTK2B	0.034	0.048	-9999	-0.38	1	1
VEGFR2 homodimer/Frs2	0.028	0.025	-9999	-0.48	1	1
CAV1	-0.002	0.066	-9999	-0.32	17	17
CALM1	0.012	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2	0.032	0.049	-9999	-0.41	5	5
endothelial cell proliferation	0.047	0.058	-9999	-0.43	1	1
mol:Ca2+	0.037	0.045	-9999	-0.4	1	1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac	0.038	0.046	-9999	-0.38	5	5
RP11-342D11.1	0.029	0.045	-9999	-0.38	5	5
CDH5	0.012	0	-9999	-10000	0	0
VEGFA homodimer	0.027	0.047	-9999	-0.45	4	4
SHC1	0.012	0	-9999	-10000	0	0
SHC2	0	0.084	-9999	-0.54	9	9
HRAS/GDP	-0.004	0.035	-9999	-10000	0	0
SH2D2A	0.012	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS	0.056	0.045	-9999	-0.5	1	1
VEGFR2 homodimer/VEGFA homodimer/TsAd	0.032	0.049	-9999	-0.41	5	5
VEGFR1 homodimer	0.012	0	-9999	-10000	0	0
SHC/GRB2/SOS1	0.044	0.043	-9999	-10000	0	0
GRB10	0.037	0.045	-9999	-10000	0	0
PTPN11	0.012	0	-9999	-10000	0	0
GRB2	0.012	0	-9999	-10000	0	0
PAK1	0.012	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin	0.042	0.045	-9999	-0.39	1	1
HRAS	0.011	0.016	-9999	-0.32	1	1
VEGF/Rho/ROCK1/Integrin Complex	0.033	0.046	-9999	-0.68	1	1
HIF1A	0.012	0	-9999	-10000	0	0
FRS2	0.012	0.001	-9999	-10000	0	0
oxygen and reactive oxygen species metabolic process	0.037	0.046	-9999	-0.38	5	5
mol:GTP	0	0	-9999	-10000	0	0
FLT4	0.009	0.032	-9999	-0.32	4	4
Nck/Pak	0.018	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Fyn	0.032	0.049	-9999	-0.41	5	5
mol:GDP	-0.004	0.036	-9999	-10000	0	0
mol:NADP	0.052	0.042	-9999	-0.46	1	1
eNOS/Hsp90	0.055	0.04	-9999	-0.43	1	1
PIK3R1	0.012	0	-9999	-10000	0	0
mol:IP3	0.037	0.045	-9999	-0.4	1	1
HIF1A/ARNT	0.017	0.011	-9999	-10000	0	0
SHB	0.012	0	-9999	-10000	0	0
VEGFA	0.007	0.07	-9999	-0.7	4	4
VEGFC	0.009	0.032	-9999	-0.32	4	4
FAK1/Vinculin	0.048	0.048	-9999	-0.56	1	1
mol:Ca ++	0	0	-9999	-10000	0	0
RHOA	0.012	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.035	0.052	-9999	-0.38	5	5
PTPN6	0.012	0	-9999	-10000	0	0
EPAS1	0.02	0.015	-9999	-10000	0	0
mol:L-citrulline	0.052	0.042	-9999	-0.46	1	1
ITGAV	0.012	0	-9999	-10000	0	0
PIK3CA	0.012	0.001	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2	0.038	0.046	-9999	-0.38	5	5
VEGFR2 homodimer/VEGFA homodimer	0.037	0.049	-9999	-0.41	5	5
VEGFR2/3 heterodimer	0.027	0.031	-9999	-0.48	1	1
VEGFB	0.012	0	-9999	-10000	0	0
MAPK11	0.037	0.046	-9999	-0.43	2	2
VEGFR2 homodimer	0.027	0.029	-9999	-0.56	1	1
FLT1	0.012	0	-9999	-10000	0	0
NEDD4	0.014	0.001	-9999	-10000	0	0
MAPK3	0.03	0.047	-9999	-0.41	2	2
MAPK1	0.03	0.047	-9999	-0.41	2	2
VEGFA145/NRP2	0.013	0.055	-9999	-0.53	4	4
VEGFR1/2 heterodimer	0.028	0.025	-9999	-0.48	1	1
KDR	0.027	0.029	-9999	-0.56	1	1
VEGFA165/NRP1/VEGFR2 homodimer	0.039	0.046	-9999	-0.4	1	1
SRC	0.012	0	-9999	-10000	0	0
platelet activating factor biosynthetic process	0.026	0.053	-9999	-0.4	3	3
PI3K	0.055	0.039	-9999	-0.44	1	1
VEGFR2 homodimer/VEGFA homodimer/NCK1	0.032	0.049	-9999	-0.41	5	5
FES	0.037	0.046	-9999	-0.41	1	1
GAB1	0.047	0.039	-9999	-0.45	1	1
VEGFR2 homodimer/VEGFA homodimer/Src	0.032	0.049	-9999	-0.41	5	5
CTNNB1	0.012	0	-9999	-10000	0	0
SOS1	0.012	0	-9999	-10000	0	0
ARNT	0.011	0.016	-9999	-0.32	1	1
eNOS/Caveolin-1	0.052	0.043	-9999	-0.43	1	1
VEGFR2 homodimer/VEGFA homodimer/Yes	0.032	0.052	-9999	-0.44	5	5
PI3K/GAB1	0.064	0.034	-9999	-0.43	1	1
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak	0.042	0.045	-9999	-0.39	1	1
PRKACA	0.012	0	-9999	-10000	0	0
VEGFR2/3 heterodimer/VEGFC homodimer	0.031	0.033	-9999	-0.44	1	1
HSP90AA1	0.012	0	-9999	-10000	0	0
CDC42	0.037	0.049	-9999	-0.46	2	2
actin cytoskeleton reorganization	0.032	0.048	-9999	-0.41	5	5
PTK2	0.043	0.05	-9999	-0.6	1	1
EDG1	0.029	0.045	-9999	-0.38	5	5
mol:DAG	0.037	0.045	-9999	-0.4	1	1
CaM/Ca2+	0.04	0.042	-9999	-10000	0	0
MAP2K3	0.04	0.044	-9999	-0.39	1	1
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4	0.042	0.047	-9999	-10000	0	0
PLCG1	0.037	0.046	-9999	-0.41	1	1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb	0.038	0.046	-9999	-0.38	5	5
IQGAP1	0.012	0	-9999	-10000	0	0
YES1	0.011	0.016	-9999	-0.32	1	1
VEGFR2 homodimer/VEGFA homodimer/SHP2	0.032	0.049	-9999	-0.41	5	5
VEGFR2 homodimer/VEGFA homodimer/SHP1	0.032	0.049	-9999	-0.41	5	5
cell migration	0.063	0.042	-9999	-0.49	1	1
mol:PI-3-4-5-P3	0.054	0.037	-9999	-0.41	1	1
FYN	0.012	0	-9999	-10000	0	0
VEGFB/NRP1	0.035	0.043	-9999	-0.36	2	2
mol:NO	0.052	0.042	-9999	-0.46	1	1
PXN	0.012	0	-9999	-10000	0	0
HRAS/GTP	-0.004	0.034	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/GRB10	0.041	0.046	-9999	-0.41	1	1
VHL	0.012	0	-9999	-10000	0	0
ITGB3	0.005	0.048	-9999	-0.32	9	9
NOS3	0.053	0.045	-9999	-0.52	1	1
VEGFR2 homodimer/VEGFA homodimer/Sck	0.025	0.07	-9999	-0.41	10	10
RAC1	0.012	0	-9999	-10000	0	0
PRKCA	0.04	0.043	-9999	-10000	0	0
PRKCB	0.031	0.051	-9999	-0.48	2	2
VCL	0.012	0	-9999	-10000	0	0
VEGFA165/NRP1	0.032	0.046	-9999	-0.38	5	5
VEGFR1/2 heterodimer/VEGFA homodimer	0.032	0.049	-9999	-0.41	5	5
VEGFA165/NRP2	0.013	0.055	-9999	-0.53	4	4
MAPKKK cascade	0.053	0.04	-9999	-10000	0	0
NRP2	0.01	0.023	-9999	-0.32	2	2
VEGFC homodimer	0.009	0.032	-9999	-0.32	4	4
NCK1	0.012	0	-9999	-10000	0	0
ROCK1	0.011	0.016	-9999	-0.32	1	1
FAK1/Paxillin	0.048	0.048	-9999	-0.56	1	1
MAP3K13	0.037	0.046	-9999	-0.41	1	1
PDPK1	0.055	0.035	-9999	-10000	0	0

×

E-cadherin signaling in the nascent adherens junction

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
CTTN	0.032	0.003	-9999	-10000	0	0
KLHL20	0.029	0.044	-9999	-0.23	1	1
CYFIP2	0.012	0	-9999	-10000	0	0
Rac1/GDP	0.046	0.013	-9999	-10000	0	0
ENAH	0.032	0.003	-9999	-10000	0	0
AP1M1	0.012	0	-9999	-10000	0	0
RAP1B	0.012	0	-9999	-10000	0	0
RAP1A	0.012	0	-9999	-10000	0	0
CTNNB1	0.012	0	-9999	-10000	0	0
CDC42/GTP	0	0.006	-9999	-10000	0	0
ABI1/Sra1/Nap1	-0.006	0.022	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin	0.026	0.028	-9999	-10000	0	0
RAPGEF1	0.039	0.004	-9999	-10000	0	0
CTNND1	0.012	0	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	0.028	0.003	-9999	-10000	0	0
CRK	0.036	0.003	-9999	-10000	0	0
E-cadherin/gamma catenin/alpha catenin	0.024	0.009	-9999	-10000	0	0
alphaE/beta7 Integrin	0.012	0.037	-9999	-10000	0	0
IQGAP1	0.012	0	-9999	-10000	0	0
NCKAP1	0.012	0	-9999	-10000	0	0
Rap1/GTP/I-afadin	0.023	0.008	-9999	-10000	0	0
DLG1	0.032	0.003	-9999	-10000	0	0
ChemicalAbstracts:7440-70-2	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	0	0.004	-9999	-10000	0	0
MLLT4	0.011	0.016	-9999	-0.32	1	1
ARF6/GTP/NME1/Tiam1	0	0.083	-9999	-0.49	8	8
PI3K	0	0.004	-9999	-10000	0	0
ARF6	0.012	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
E-cadherin/gamma catenin	0.017	0.011	-9999	-10000	0	0
TIAM1	-0.016	0.092	-9999	-0.32	35	35
E-cadherin(dimer)/Ca2+	0.028	0.001	-9999	-10000	0	0
AKT1	0	0.003	-9999	-10000	0	0
PIK3R1	0.012	0	-9999	-10000	0	0
CDH1	0.012	0	-9999	-10000	0	0
RhoA/GDP	0.046	0.012	-9999	-10000	0	0
actin cytoskeleton organization	0.024	0.033	-9999	-0.16	1	1
CDC42/GDP	0.046	0.013	-9999	-10000	0	0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin	0.019	0.009	-9999	-10000	0	0
ITGB7	0.003	0.053	-9999	-0.32	11	11
RAC1	0.012	0	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/p120 catenin	0.031	0.001	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin	0.021	0.001	-9999	-10000	0	0
mol:GDP	0.043	0.013	-9999	-10000	0	0
CDC42/GTP/IQGAP1	0.016	0.009	-9999	-10000	0	0
JUP	0.011	0.016	-9999	-0.32	1	1
p120 catenin/RhoA/GDP	0.046	0.012	-9999	-10000	0	0
RAC1/GTP/IQGAP1	0.016	0	-9999	-10000	0	0
PIP5K1C/AP1M1	0.017	0.011	-9999	-10000	0	0
RHOA	0.012	0	-9999	-10000	0	0
CDC42	0.011	0.016	-9999	-0.32	1	1
CTNNA1	0.012	0	-9999	-10000	0	0
positive regulation of S phase of mitotic cell cycle	0.018	0.036	-9999	-0.24	6	6
NME1	-0.002	0.098	-9999	-0.71	8	8
clathrin coat assembly	0	0	-9999	-10000	0	0
TJP1	0.032	0.003	-9999	-10000	0	0
regulation of cell-cell adhesion	0	0.005	-9999	-10000	0	0
WASF2	-0.003	0.012	-9999	-10000	0	0
Rap1/GTP	0	0.005	-9999	-10000	0	0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin	0.031	0.028	-9999	-10000	0	0
CCND1	0.02	0.044	-9999	-0.3	6	6
VAV2	0.037	0.045	-9999	-0.61	2	2
RAP1/GDP	0.039	0.015	-9999	-10000	0	0
adherens junction assembly	0.032	0.003	-9999	-10000	0	0
homophilic cell adhesion	0	0	-9999	-10000	0	0
ABI1	0.012	0	-9999	-10000	0	0
PIP5K1C	0.011	0.016	-9999	-0.32	1	1
regulation of heterotypic cell-cell adhesion	0.034	0.026	-9999	-10000	0	0
E-cadherin/beta catenin	0	0.006	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
SRC	0.032	0.005	-9999	-10000	0	0
PIK3CA	0.012	0.001	-9999	-10000	0	0
Rac1/GTP	-0.014	0.053	-9999	-0.34	2	2
E-cadherin/beta catenin/alpha catenin	0.024	0.001	-9999	-10000	0	0
ITGAE	0.012	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.028	0.003	-9999	-10000	0	0

×

IL2 signaling events mediated by STAT5

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GAB2	0.012	0	-9999	-10000	0	0
ELF1	0.013	0.041	-9999	-0.28	8	8
CCNA2	0.012	0	-9999	-10000	0	0
PIK3CA	0.012	0.001	-9999	-10000	0	0
JAK3	0.009	0.05	-9999	-0.71	2	2
PIK3R1	0.012	0	-9999	-10000	0	0
JAK1	0.012	0	-9999	-10000	0	0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.05	0.046	-9999	-10000	0	0
SHC1	0.012	0	-9999	-10000	0	0
SP1	0.016	0.029	-9999	-10000	0	0
IL2RA	0.014	0.081	-9999	-0.57	8	8
IL2RB	0.008	0.04	-9999	-0.32	6	6
SOS1	0.012	0	-9999	-10000	0	0
IL2RG	0.011	0.023	-9999	-0.32	2	2
G1/S transition of mitotic cell cycle	0.031	0.054	-9999	-0.56	3	3
PTPN11	0.012	0	-9999	-10000	0	0
CCND2	0.018	0.058	-9999	-0.57	4	4
LCK	-0.002	0.1	-9999	-0.66	9	9
GRB2	0.012	0	-9999	-10000	0	0
IL2	0.004	0.005	-9999	-10000	0	0
CDK6	0.012	0	-9999	-10000	0	0
CCND3	0.053	0.042	-9999	-10000	0	0

×

Insulin Pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CBL/APS/CAP	-0.01	0.051	-9999	-0.38	6	6
TC10/GTP	-0.01	0.05	-9999	-0.37	6	6
Insulin Receptor/Insulin/IRS1/Shp2	0.025	0	-9999	-10000	0	0
HRAS	0.011	0.016	-9999	-0.32	1	1
APS homodimer	0.001	0.085	-9999	-0.7	6	6
GRB14	-0.021	0.12	-9999	-0.44	29	29
FOXO3	0.009	0.078	-9999	-0.53	8	8
AKT1	0.021	0.059	-9999	-10000	0	0
INSR	0.013	0	-9999	-10000	0	0
Insulin Receptor/Insulin	0.03	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
GRB10	0.012	0	-9999	-10000	0	0
SORBS1	-0.002	0.066	-9999	-0.32	17	17
CRK	0.012	0	-9999	-10000	0	0
PTPN1	0.024	0	-9999	-10000	0	0
CAV1	0.02	0.004	-9999	-10000	0	0
CBL/APS/CAP/Crk-II/C3G	0.022	0.062	-9999	-0.41	6	6
Insulin Receptor/Insulin/IRS1/NCK2	0.025	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	0	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B	0.03	0	-9999	-10000	0	0
RPS6KB1	0.025	0.055	-9999	-10000	0	0
PARD6A	0.008	0.05	-9999	-0.71	2	2
CBL	0.012	0	-9999	-10000	0	0
tumor necrosis factor-mediated signaling pathway	0	0	-9999	-10000	0	0
DOK1	0	0	-9999	-10000	0	0
PIK3R1	0.012	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/Shc	-0.011	0.045	-9999	-10000	0	0
HRAS/GTP	0	0.005	-9999	-10000	0	0
Insulin Receptor	0.013	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC	0.031	0	-9999	-10000	0	0
PRKCI	-0.005	0.029	-9999	-0.38	2	2
Insulin Receptor/Insulin/GRB14/PDK1	-0.013	0.055	-9999	-0.35	9	9
SHC1	0.012	0	-9999	-10000	0	0
negative regulation of MAPKKK cascade	0.023	0	-9999	-10000	0	0
PI3K	0.026	0	-9999	-10000	0	0
NCK2	0.012	0	-9999	-10000	0	0
RHOQ	0.012	0	-9999	-10000	0	0
mol:H2O2	0	0	-9999	-10000	0	0
HRAS/GDP	0.008	0.011	-9999	-0.22	1	1
AKT2	0.021	0.059	-9999	-10000	0	0
PRKCZ	-0.003	0.013	-9999	-10000	0	0
SH2B2	0.001	0.085	-9999	-0.71	6	6
SHC/SHIP	0.027	0	-9999	-10000	0	0
F2RL2	-0.014	0.13	-9999	-0.62	17	17
TRIP10	0.012	0	-9999	-10000	0	0
Insulin Receptor/Insulin/Shc	0.018	0	-9999	-10000	0	0
TC10/GTP/CIP4/Exocyst	0.016	0	-9999	-10000	0	0
Insulin Receptor/Insulin/SHC/GRB2/Sos1	0.031	0	-9999	-10000	0	0
RAPGEF1	0.011	0.016	-9999	-0.32	1	1
RASA1	0.012	0.001	-9999	-10000	0	0
NCK1	0.012	0	-9999	-10000	0	0
CBL/APS/CAP/Crk-II	0.017	0.065	-9999	-0.44	6	6
TC10/GDP	0.009	0	-9999	-10000	0	0
Insulin Receptor/Insulin/SHC/GRB10	0.025	0	-9999	-10000	0	0
INPP5D	0.02	0	-9999	-10000	0	0
SOS1	0.012	0	-9999	-10000	0	0
SGK1	-0.016	0.11	-9999	-0.77	8	8
mol:cAMP	0	0	-9999	-10000	0	0
PTPN11	0.012	0	-9999	-10000	0	0
IRS1	0.012	0	-9999	-10000	0	0
p62DOK/RasGAP	0.023	0	-9999	-10000	0	0
INS	0.002	0	-9999	-10000	0	0
mol:PI-3-4-P2	0.02	0	-9999	-10000	0	0
GRB2	0.012	0	-9999	-10000	0	0
EIF4EBP1	0.023	0.06	-9999	-10000	0	0
PTPRA	0.013	0	-9999	-10000	0	0
PIK3CA	0.012	0.001	-9999	-10000	0	0
TC10/GTP/CIP4	0.016	0	-9999	-10000	0	0
PDPK1	0.012	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos	0.026	0	-9999	-10000	0	0
Insulin Receptor/Insulin/IRS1	0.018	0	-9999	-10000	0	0
Insulin Receptor/Insulin/IRS3	0.012	0	-9999	-10000	0	0
Par3/Par6	0.012	0.079	-9999	-0.39	15	15

×

Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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
SMAD4	0.012	0	-9999	-10000	0	0
SMAD2	0.011	0.008	-9999	-10000	0	0
SMAD3	0.031	0	-9999	-10000	0	0
SMAD3/SMAD4	0.036	0.011	-9999	-10000	0	0
SMAD4/Ubc9/PIASy	0.024	0	-9999	-10000	0	0
SMAD2/SMAD2/SMAD4	0.032	0.027	-9999	-0.35	2	2
PPM1A	0.012	0	-9999	-10000	0	0
CALM1	0.012	0	-9999	-10000	0	0
SMAD2/SMAD4	0.018	0.007	-9999	-10000	0	0
MAP3K1	0.011	0.016	-9999	-0.32	1	1
TRAP-1/SMAD4	0.018	0	-9999	-10000	0	0
MAPK3	0.012	0	-9999	-10000	0	0
MAPK1	0.012	0	-9999	-10000	0	0
NUP214	0.012	0	-9999	-10000	0	0
CTDSP1	0.012	0	-9999	-10000	0	0
CTDSP2	0.012	0	-9999	-10000	0	0
CTDSPL	0.012	0	-9999	-10000	0	0
KPNB1	0.012	0	-9999	-10000	0	0
TGFBRAP1	0.012	0	-9999	-10000	0	0
UBE2I	0.012	0	-9999	-10000	0	0
NUP153	0.012	0.001	-9999	-10000	0	0
KPNA2	0.008	0.05	-9999	-0.71	2	2
PIAS4	0.012	0	-9999	-10000	0	0

×

BARD1 signaling events

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
BARD1/CSTF1	0.018	0	-9999	-10000	0	0
ATM	0.012	0	-9999	-10000	0	0
UBE2D3	0.012	0	-9999	-10000	0	0
PRKDC	0.012	0	-9999	-10000	0	0
ATR	0.012	0	-9999	-10000	0	0
UBE2L3	0.012	0	-9999	-10000	0	0
FANCD2	0.02	0	-9999	-10000	0	0
protein ubiquitination	0.029	0.035	-9999	-0.38	3	3
XRCC5	0.012	0	-9999	-10000	0	0
XRCC6	0.012	0	-9999	-10000	0	0
M/R/N Complex	0.024	0.009	-9999	-10000	0	0
MRE11A	0.012	0.001	-9999	-10000	0	0
DNA-PK	0.024	0	-9999	-10000	0	0
FA complex/FANCD2/Ubiquitin	0.04	0.005	-9999	-10000	0	0
FANCF	0.012	0	-9999	-10000	0	0
BRCA1	0.012	0	-9999	-10000	0	0
CCNE1	0.007	0.061	-9999	-0.71	3	3
CDK2/Cyclin E1	0.014	0.046	-9999	-0.53	3	3
FANCG	0.012	0	-9999	-10000	0	0
BRCA1/BACH1/BARD1	0.018	0	-9999	-10000	0	0
FANCE	0.012	0	-9999	-10000	0	0
FANCC	0.012	0	-9999	-10000	0	0
NBN	0.011	0.016	-9999	-0.32	1	1
FANCA	0.012	0	-9999	-10000	0	0
DNA repair	0.054	0.009	-9999	-10000	0	0
BRCA1/BARD1/ubiquitin	0.018	0	-9999	-10000	0	0
BARD1/DNA-PK	0.031	0	-9999	-10000	0	0
FANCL	0.012	0	-9999	-10000	0	0
mRNA polyadenylation	-0.018	0	-9999	-10000	0	0
BRCA1/BARD1/CTIP/M/R/N Complex	0.03	0.014	-9999	-10000	0	0
BRCA1/BACH1/BARD1/TopBP1	0.024	0	-9999	-10000	0	0
BRCA1/BARD1/P53	0.031	0	-9999	-10000	0	0
BARD1/CSTF1/BRCA1	0.024	0	-9999	-10000	0	0
BRCA1/BACH1	0.012	0	-9999	-10000	0	0
BARD1	0.012	0	-9999	-10000	0	0
PCNA	0.012	0	-9999	-10000	0	0
BRCA1/BARD1/UbcH5C	0.024	0	-9999	-10000	0	0
BRCA1/BARD1/UbcH7	0.024	0	-9999	-10000	0	0
BRCA1/BARD1/RAD51/PCNA	0.031	0	-9999	-10000	0	0
BARD1/DNA-PK/P53	0.035	0	-9999	-10000	0	0
BRCA1/BARD1/Ubiquitin	0.018	0	-9999	-10000	0	0
BRCA1/BARD1/CTIP	0.027	0.012	-9999	-10000	0	0
FA complex	0.031	0	-9999	-10000	0	0
BARD1/EWS	0.018	0	-9999	-10000	0	0
RBBP8	0.016	0.016	-9999	-10000	0	0
TP53	0.012	0	-9999	-10000	0	0
TOPBP1	0.012	0	-9999	-10000	0	0
G1/S transition of mitotic cell cycle	-0.03	0	-9999	-10000	0	0
BRCA1/BARD1	0.032	0.035	-9999	-0.38	3	3
CSTF1	0.012	0	-9999	-10000	0	0
BARD1/EWS-Fli1	0.009	0	-9999	-10000	0	0
CDK2	0.012	0	-9999	-10000	0	0
UniProt:Q9BZD1	0	0	-9999	-10000	0	0
RAD51	0.012	0	-9999	-10000	0	0
RAD50	0.012	0	-9999	-10000	0	0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme	0.018	0	-9999	-10000	0	0
EWSR1	0.012	0	-9999	-10000	0	0

×

Circadian rhythm pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
chromatin modification	0.039	0.015	-10000	0	-10000	0	0
CLOCK	0.014	0.003	-10000	0	-10000	0	0
TIMELESS/CRY2	0.034	0.015	-10000	0	-10000	0	0
DEC1/BMAL1	0.008	0.053	-10000	0	-0.53	4	4
ATR	0.012	0	-10000	0	-10000	0	0
NR1D1	0.03	0.036	-10000	0	-0.49	2	2
ARNTL	0.014	0.003	-10000	0	-10000	0	0
TIMELESS	0.031	0.017	-10000	0	-10000	0	0
NPAS2	0.014	0.003	-10000	0	-10000	0	0
CRY2	0.012	0	-10000	0	-10000	0	0
mol:CO	-0.01	0.007	0.092	2	-10000	0	2
CHEK1	0.012	0	-10000	0	-10000	0	0
mol:HEME	0.01	0.007	-10000	0	-0.092	2	2
PER1	0.009	0.028	-10000	0	-0.32	3	3
BMAL/CLOCK/NPAS2	0.037	0.007	-10000	0	-10000	0	0
BMAL1/CLOCK	0.037	0.035	-10000	0	-10000	0	0
S phase of mitotic cell cycle	0.039	0.015	-10000	0	-10000	0	0
TIMELESS/CHEK1/ATR	0.039	0.015	-10000	0	-10000	0	0
mol:NADPH	0.01	0.007	-10000	0	-0.092	2	2
PER1/TIMELESS	0.033	0.016	-10000	0	-10000	0	0
PER1-2 / CRY1-2	0	0	-10000	0	-10000	0	0
DEC1	-0.003	0.069	-10000	0	-0.71	4	4

×

Aurora C signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations
INCENP	0.012	0	-9999	-9999
Aurora C/Aurora B/INCENP	0.023	0.002	-9999	-9999
metaphase	0	0	-9999	-9999
mitosis	0	0	-9999	-9999
H3F3B	0.001	0.002	-9999	-9999
AURKB	0.012	0	-9999	-9999
AURKC	0.011	0.002	-9999	-9999

×

Insulin-mediated glucose transport

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Insulin responsive Vesicles	0.017	0.058	-10000	0	-10000	0	0
CaM/Ca2+	0.009	0	-10000	0	-10000	0	0
AKT1	0.012	0	-10000	0	-10000	0	0
AKT2	0.012	0	-10000	0	-10000	0	0
STXBP4	0.011	0.016	-10000	0	-0.32	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucose	0.015	0.068	0.26	6	-10000	0	6
YWHAZ	0.012	0	-10000	0	-10000	0	0
CALM1	0.012	0	-10000	0	-10000	0	0
YWHAQ	0.012	0	-10000	0	-10000	0	0
TBC1D4	0.017	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
YWHAH	0.012	0	-10000	0	-10000	0	0
YWHAB	0.012	0	-10000	0	-10000	0	0
SNARE/Synip	0.024	0.009	-10000	0	-10000	0	0
YWHAG	0.012	0	-10000	0	-10000	0	0
ASIP	-0.005	0.092	-10000	0	-0.71	7	7
PRKCI	0.01	0.023	-10000	0	-0.32	2	2
AS160/CaM/Ca2+	0.009	0	-10000	0	-10000	0	0
RHOQ	0.012	0	-10000	0	-10000	0	0
GYS1	0.023	0	-10000	0	-10000	0	0
PRKCZ	0.012	0	-10000	0	-10000	0	0
TRIP10	0.012	0	-10000	0	-10000	0	0
TC10/GTP/CIP4/Exocyst	0.016	0	-10000	0	-10000	0	0
AS160/14-3-3	0.035	0.008	-10000	0	-10000	0	0
VAMP2	0.012	0	-10000	0	-10000	0	0
SLC2A4	0.015	0.072	0.26	6	-10000	0	6
STX4	0.012	0	-10000	0	-10000	0	0
GSK3B	0.02	0	-10000	0	-10000	0	0
SFN	0.011	0.016	-10000	0	-0.32	1	1
LNPEP	0.012	0.001	-10000	0	-10000	0	0
YWHAE	0.012	0	-10000	0	-10000	0	0

×

mTOR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GBL	0	0	-10000	0	-10000	0	0
MKNK1	0.012	0	-10000	0	-10000	0	0
mol:PIP3	0	0.01	0.2	1	-10000	0	1
FRAP1	0.012	0.005	-10000	0	-10000	0	0
AKT1	0.021	0.009	0.19	1	-10000	0	1
INSR	0.012	0	-10000	0	-10000	0	0
Insulin Receptor/Insulin	0.008	0	-10000	0	-10000	0	0
mol:GTP	0.028	0.005	-10000	0	-10000	0	0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit	-0.001	0.012	-10000	0	-0.23	1	1
TSC2	0.012	0	-10000	0	-10000	0	0
RHEB/GDP	0	0.003	-10000	0	-10000	0	0
TSC1	0.012	0	-10000	0	-10000	0	0
Insulin Receptor/IRS1	0.014	0	-10000	0	-10000	0	0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA	-0.001	0.014	-10000	0	-0.27	1	1
mol:GDP	0	0	-10000	0	-10000	0	0
EIF3A	0.012	0	-10000	0	-10000	0	0
RPS6KB1	0.021	0.017	-10000	0	-0.29	1	1
MAP3K5	0.008	0	-10000	0	-10000	0	0
PIK3R1	0.012	0	-10000	0	-10000	0	0
apoptosis	0.008	0	-10000	0	-10000	0	0
mol:LY294002	0	0	-10000	0	-10000	0	0
EIF4B	0.024	0.015	-10000	0	-0.25	1	1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.027	0.021	-10000	0	-0.29	1	1
eIF4E/eIF4G1/eIF4A1	0	0.006	-10000	0	-10000	0	0
KIAA1303	0	0	-10000	0	-10000	0	0
PI3K	0.021	0.001	-10000	0	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL	0.023	0.007	0.14	1	-10000	0	1
FKBP1A	0.012	0	-10000	0	-10000	0	0
RHEB/GTP	0.028	0.004	-10000	0	-10000	0	0
mol:Amino Acids	0	0	-10000	0	-10000	0	0
FKBP12/Rapamycin	0.009	0	-10000	0	-10000	0	0
PDPK1	0.017	0.009	0.19	1	-10000	0	1
EIF4E	0.01	0.023	-10000	0	-0.32	2	2
ASK1/PP5C	0.02	0.003	-10000	0	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E	0.012	0.026	-10000	0	-0.36	2	2
TSC1/TSC2	0.031	0.005	-10000	0	-10000	0	0
tumor necrosis factor receptor activity	0	0	-10000	0	-10000	0	0
RPS6	0.01	0.035	-10000	0	-0.71	1	1
PPP5C	0.012	0	-10000	0	-10000	0	0
EIF4G1	0.012	0	-10000	0	-10000	0	0
IRS1	0.007	0	-10000	0	-10000	0	0
INS	0	0	-10000	0	-10000	0	0
PTEN	0.011	0.016	-10000	0	-0.32	1	1
PDK2	0.017	0.009	0.19	1	-10000	0	1
EIF4EBP1	0.01	0.017	-10000	0	-10000	0	0
PIK3CA	0.012	0.001	-10000	0	-10000	0	0
PPP2R5D	0.016	0.005	-10000	0	-10000	0	0
peptide biosynthetic process	0.013	0.021	-10000	0	-0.42	1	1
RHEB	0.012	0	-10000	0	-10000	0	0
EIF4A1	0.012	0	-10000	0	-10000	0	0
mol:Rapamycin	0	0	0.003	1	-10000	0	1
EEF2	0.013	0.021	-10000	0	-0.42	1	1
eIF4E/4E-BP1	0.016	0.015	-10000	0	-10000	0	0

×

Class I PI3K signaling events mediated by Akt

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
BCL2L1	0.017	0	-9999	-10000	0	0
BAD/BCL-XL/YWHAZ	0.028	0.008	-9999	-10000	0	0
CDKN1B	0.027	0.005	-9999	-10000	0	0
CDKN1A	0.027	0.005	-9999	-10000	0	0
FRAP1	0	0	-9999	-10000	0	0
PRKDC	0.012	0	-9999	-10000	0	0
FOXO3	0.027	0.005	-9999	-10000	0	0
AKT1	0.023	0.005	-9999	-10000	0	0
BAD	0.011	0.016	-9999	-0.32	1	1
AKT3	0.009	0.035	-9999	-0.24	8	8
mol:GTP	0	0	-9999	-10000	0	0
FOXO4	0.027	0.005	-9999	-10000	0	0
AKT1/ASK1	0.028	0.005	-9999	-10000	0	0
BAD/YWHAZ	0.024	0.009	-9999	-10000	0	0
RICTOR	0.009	0.032	-9999	-0.32	4	4
RAF1	0.012	0	-9999	-10000	0	0
JNK cascade	-0.027	0.004	-9999	-10000	0	0
TSC1	0.027	0.005	-9999	-10000	0	0
YWHAZ	0.012	0	-9999	-10000	0	0
AKT1/RAF1	0.029	0.005	-9999	-10000	0	0
EP300	0.012	0	-9999	-10000	0	0
mol:GDP	0.023	0.005	-9999	-10000	0	0
mol:PI-3-4-5-P3	0	0	-9999	-10000	0	0
TSC2	0.027	0.005	-9999	-10000	0	0
YWHAQ	0.012	0	-9999	-10000	0	0
TBC1D4	0.018	0	-9999	-10000	0	0
MAP3K5	0.012	0	-9999	-10000	0	0
MAPKAP1	0.012	0	-9999	-10000	0	0
negative regulation of cell cycle	-0.034	0.006	-9999	-10000	0	0
YWHAH	0.012	0	-9999	-10000	0	0
AKT1S1	0.027	0.005	-9999	-10000	0	0
CASP9	0.027	0.005	-9999	-10000	0	0
YWHAB	0.012	0	-9999	-10000	0	0
p27Kip1/KPNA1	0.033	0.005	-9999	-10000	0	0
GBL	0	0	-9999	-10000	0	0
PDK1/Src/Hsp90	0.024	0	-9999	-10000	0	0
YWHAE	0.012	0	-9999	-10000	0	0
SRC	0.012	0	-9999	-10000	0	0
AKT2/p21CIP1	0.031	0.004	-9999	-10000	0	0
KIAA1303	0	0	-9999	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL	0.014	0.003	-9999	-10000	0	0
CHUK	0.027	0.005	-9999	-10000	0	0
BAD/BCL-XL	0.039	0.008	-9999	-10000	0	0
mTORC2	0.014	0.017	-9999	-10000	0	0
AKT2	0.014	0	-9999	-10000	0	0
FOXO1-3a-4/14-3-3 family	0.045	0.007	-9999	-10000	0	0
PDPK1	0.012	0	-9999	-10000	0	0
MDM2	0.027	0.009	-9999	-10000	0	0
MAPKKK cascade	-0.029	0.005	-9999	-10000	0	0
MDM2/Cbp/p300	0.039	0.008	-9999	-10000	0	0
TSC1/TSC2	0.031	0.004	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.037	0.008	-9999	-10000	0	0
glucose import	-0.001	0.056	-9999	-10000	0	0
mTOR/RHEB/GDP/Raptor/GBL/PRAS40	0.023	0.005	-9999	-10000	0	0
response to stress	0	0	-9999	-10000	0	0
SLC2A4	-0.001	0.057	-9999	-10000	0	0
GSK3A	0.027	0.005	-9999	-10000	0	0
FOXO1	0.027	0.005	-9999	-10000	0	0
GSK3B	0.027	0.005	-9999	-10000	0	0
SFN	0.011	0.016	-9999	-0.32	1	1
G1/S transition of mitotic cell cycle	0.031	0.004	-9999	-10000	0	0
p27Kip1/14-3-3 family	0.038	0.002	-9999	-10000	0	0
PRKACA	0.012	0	-9999	-10000	0	0
KPNA1	0.012	0	-9999	-10000	0	0
HSP90AA1	0.012	0	-9999	-10000	0	0
YWHAG	0.012	0	-9999	-10000	0	0
RHEB	0.012	0	-9999	-10000	0	0
CREBBP	0.012	0	-9999	-10000	0	0

×

Signaling events mediated by HDAC Class I

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NF kappa B/RelA	0.033	0.011	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC1	-0.001	0.017	-9999	-0.34	1	1
NF kappa B1 p50/RelA/I kappa B alpha	0.038	0.012	-9999	-10000	0	0
SUMO1	0.01	0.023	-9999	-0.32	2	2
ZFPM1	-0.005	0.11	-9999	-0.71	10	10
NPC/RanGAP1/SUMO1/Ubc9	0.016	0.015	-9999	-10000	0	0
FKBP3	0.012	0	-9999	-10000	0	0
Histones	0.039	0.006	-9999	-10000	0	0
YY1/LSF	0.018	0.038	-9999	-10000	0	0
SMG5	0.012	0	-9999	-10000	0	0
RAN	0.012	0	-9999	-10000	0	0
I kappa B alpha/HDAC3	0.026	0.009	-9999	-10000	0	0
I kappa B alpha/HDAC1	0.027	0.006	-9999	-10000	0	0
SAP18	0.012	0	-9999	-10000	0	0
RELA	0.029	0.009	-9999	-10000	0	0
HDAC1/Smad7	0.024	0	-9999	-10000	0	0
RANGAP1	0.012	0	-9999	-10000	0	0
HDAC3/TR2	0.027	0.006	-9999	-10000	0	0
NuRD/MBD3 Complex	0.036	0.008	-9999	-10000	0	0
NF kappa B1 p50/RelA	0.032	0.008	-9999	-10000	0	0
EntrezGene:23225	0	0	-9999	-10000	0	0
GATA2	0.005	0.048	-9999	-0.32	9	9
GATA1	0.008	0.006	-9999	-10000	0	0
Mad/Max	0.017	0.011	-9999	-10000	0	0
NuRD/MBD3 Complex/GATA1/Fog1	0.039	0.028	-9999	-10000	0	0
RBBP7	0.012	0	-9999	-10000	0	0
NPC	0.006	0.02	-9999	-0.4	1	1
RBBP4	0.012	0	-9999	-10000	0	0
MAX	0.012	0	-9999	-10000	0	0
EntrezGene:9972	0	0	-9999	-10000	0	0
FBXW11	0.012	0	-9999	-10000	0	0
NFKBIA	0.022	0.007	-9999	-10000	0	0
KAT2B	-0.002	0.066	-9999	-0.32	17	17
mol:GTP	0	0	-9999	-10000	0	0
SIN3/HDAC complex	0.034	0	-9999	-10000	0	0
SIN3 complex	0.031	0	-9999	-10000	0	0
SMURF1	0.012	0	-9999	-10000	0	0
CHD3	0.012	0	-9999	-10000	0	0
SAP30	0.012	0	-9999	-10000	0	0
EntrezGene:23636	0	0	-9999	-10000	0	0
NCOR1	0.012	0	-9999	-10000	0	0
YY1/HDAC3	0.027	0.033	-9999	-10000	0	0
YY1/HDAC2	0.018	0.038	-9999	-10000	0	0
YY1/HDAC1	0.018	0.038	-9999	-10000	0	0
NuRD/MBD2 Complex (MeCP1)	0.037	0	-9999	-10000	0	0
PPARG	0.029	0.018	-9999	-10000	0	0
HDAC8/hEST1B	0.024	0	-9999	-10000	0	0
UBE2I	0.012	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.012	0	-9999	-10000	0	0
TNFRSF1A	0.012	0	-9999	-10000	0	0
HDAC3/SMRT (N-CoR2)	0.026	0.01	-9999	-10000	0	0
MBD3L2	0	0	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	0.024	0	-9999	-10000	0	0
CREBBP	0.012	0	-9999	-10000	0	0
NuRD/MBD3/MBD3L2 Complex	0.039	0.008	-9999	-10000	0	0
HDAC1	0.012	0	-9999	-10000	0	0
HDAC3	0.022	0.007	-9999	-10000	0	0
HDAC2	0.012	0	-9999	-10000	0	0
YY1	0.014	0.045	-9999	-10000	0	0
HDAC8	0.012	0	-9999	-10000	0	0
SMAD7	0.012	0	-9999	-10000	0	0
NCOR2	0.011	0.016	-9999	-0.32	1	1
MXD1	0.011	0.016	-9999	-0.32	1	1
STAT3	0.02	0	-9999	-10000	0	0
NFKB1	0.012	0	-9999	-10000	0	0
EntrezGene:8021	0	0	-9999	-10000	0	0
RANBP2	0.01	0.035	-9999	-0.71	1	1
YY1/LSF/HDAC1	0.023	0.036	-9999	-10000	0	0
YY1/SAP30/HDAC1	0.024	0.035	-9999	-10000	0	0
EP300	0.012	0	-9999	-10000	0	0
STAT3 (dimer non-phopshorylated)	0.02	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.022	0.007	-9999	-10000	0	0
histone deacetylation	0.037	0	-9999	-10000	0	0
STAT3 (dimer non-phopshorylated)/HDAC3	0.032	0.006	-9999	-10000	0	0
nuclear export	-0.024	0	-9999	-10000	0	0
PRKACA	0.012	0	-9999	-10000	0	0
GATAD2B	0.012	0	-9999	-10000	0	0
GATAD2A	0.012	0	-9999	-10000	0	0
GATA2/HDAC3	0.023	0.025	-9999	-10000	0	0
GATA1/HDAC1	0.014	0.004	-9999	-10000	0	0
GATA1/HDAC3	0.023	0.008	-9999	-10000	0	0
CHD4	0.012	0	-9999	-10000	0	0
TNF-alpha/TNFR1A	0.017	0.011	-9999	-10000	0	0
SIN3/HDAC complex/Mad/Max	0.036	0.008	-9999	-10000	0	0
NuRD Complex	0.043	0.008	-9999	-10000	0	0
positive regulation of chromatin silencing	0.037	0.006	-9999	-10000	0	0
SIN3B	0.012	0	-9999	-10000	0	0
MTA2	0.012	0	-9999	-10000	0	0
SIN3A	0.012	0	-9999	-10000	0	0
XPO1	0.012	0	-9999	-10000	0	0
SUMO1/HDAC1	0.024	0.019	-9999	-0.22	2	2
HDAC complex	0.031	0	-9999	-10000	0	0
GATA1/Fog1	0.001	0.084	-9999	-0.54	10	10
FKBP25/HDAC1/HDAC2	0.024	0	-9999	-10000	0	0
TNF	0.011	0.016	-9999	-0.32	1	1
negative regulation of cell growth	0.036	0.007	-9999	-10000	0	0
NuRD/MBD2/PRMT5 Complex	0.037	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.027	0.014	-9999	-10000	0	0
NF kappa B/RelA/I kappa B alpha	0.032	0.012	-9999	-10000	0	0
SIN3/HDAC complex/NCoR1	0.035	0	-9999	-10000	0	0
TFCP2	0.011	0.016	-9999	-0.32	1	1
NR2C1	0.012	0	-9999	-10000	0	0
MBD3	0.011	0.016	-9999	-0.32	1	1
MBD2	0.012	0	-9999	-10000	0	0

×

Paxillin-dependent events mediated by a4b1

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
CRKL	0.012	0	-9999	-10000	0	0
Rac1/GDP	0.001	0.005	-9999	-10000	0	0
DOCK1	0.012	0	-9999	-10000	0	0
ITGA4	0.003	0.053	-9999	-0.32	11	11
RAC1	0.012	0	-9999	-10000	0	0
alpha4/beta7 Integrin	0.006	0.054	-9999	-0.4	2	2
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.012	0	-9999	-10000	0	0
alpha4/beta1 Integrin	0.019	0.031	-9999	-10000	0	0
alpha4/beta7 Integrin/Paxillin	0.019	0.042	-9999	-10000	0	0
lamellipodium assembly	0.037	0.01	-9999	-10000	0	0
PIK3CA	0.012	0.001	-9999	-10000	0	0
PI3K	0.018	0	-9999	-10000	0	0
ARF6	0.012	0	-9999	-10000	0	0
TLN1	0.012	0	-9999	-10000	0	0
PXN	0.017	0	-9999	-10000	0	0
PIK3R1	0.012	0	-9999	-10000	0	0
ARF6/GTP	0.027	0.023	-9999	-10000	0	0
cell adhesion	0.029	0.026	-9999	-10000	0	0
CRKL/CBL	0.018	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin	0.023	0.028	-9999	-10000	0	0
ITGB1	0.012	0	-9999	-10000	0	0
ITGB7	0.003	0.053	-9999	-0.32	11	11
ARF6/GDP	0.001	0.005	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/VCAM1	0.027	0.041	-9999	-10000	0	0
p130Cas/Crk/Dock1	0.024	0.009	-9999	-10000	0	0
VCAM1	0.005	0.046	-9999	-0.32	8	8
alpha4/beta1 Integrin/Paxillin/Talin	0.03	0.026	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/GIT1	0.03	0.026	-9999	-10000	0	0
BCAR1	0.011	0.016	-9999	-0.32	1	1
mol:GDP	-0.029	0.026	-9999	-10000	0	0
CBL	0.012	0	-9999	-10000	0	0
PRKACA	0.012	0	-9999	-10000	0	0
GIT1	0.012	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton	0.03	0.026	-9999	-10000	0	0
Rac1/GTP	0.001	0.011	-9999	-10000	0	0

×

Atypical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL3/RelA	0.018	0	-9999	-10000	0	0
FBXW11	0.012	0	-9999	-10000	0	0
NF kappa B1 p50/c-Rel	0.022	0.001	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.034	0.025	-9999	-10000	0	0
NFKBIA	0.018	0.028	-9999	-10000	0	0
MAPK14	0.012	0	-9999	-10000	0	0
NF kappa B1 p105/p50	0.022	0	-9999	-10000	0	0
ARRB2	0.014	0	-9999	-10000	0	0
REL	0.012	0.001	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
BCL3/NF kappa B1 p50	0.022	0	-9999	-10000	0	0
response to UV	0	0	-9999	-10000	0	0
NF kappa B1 p105/RelA	0.022	0	-9999	-10000	0	0
PIK3CA	0.012	0.001	-9999	-10000	0	0
NF kappa B1 p50 dimer	0.016	0	-9999	-10000	0	0
PIK3R1	0.012	0	-9999	-10000	0	0
NFKB1	0.017	0	-9999	-10000	0	0
RELA	0.012	0	-9999	-10000	0	0
positive regulation of anti-apoptosis	0.023	0.027	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2	0.037	0.024	-9999	-10000	0	0
SRC	0.012	0	-9999	-10000	0	0
PI3K	0.018	0	-9999	-10000	0	0
NF kappa B1 p50/RelA	0.023	0.027	-9999	-10000	0	0
IKBKB	0.012	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.012	0	-9999	-10000	0	0
SYK	0.012	0	-9999	-10000	0	0
I kappa B alpha/PIK3R1	0.024	0.026	-9999	-10000	0	0
cell death	0.035	0.023	-9999	-10000	0	0
NF kappa B1 p105/c-Rel	0.022	0.001	-9999	-10000	0	0
LCK	-0.003	0.1	-9999	-0.66	9	9
BCL3	0.012	0	-9999	-10000	0	0

×

Sumoylation by RanBP2 regulates transcriptional repression

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.012	0	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	-0.001	0.015	-9999	-0.3	1	1
MDM2/SUMO1	0.024	0.024	-9999	-0.37	1	1
HDAC4	0.012	0	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC1	-0.001	0.015	-9999	-0.3	1	1
SUMO1	0.01	0.023	-9999	-0.32	2	2
NPC/RanGAP1/SUMO1	0.012	0.015	-9999	-0.17	3	3
mol:GTP	0	0	-9999	-10000	0	0
XPO1	0.02	0.014	-9999	-10000	0	0
EntrezGene:23636	0	0	-9999	-10000	0	0
RAN	0.012	0	-9999	-10000	0	0
EntrezGene:8021	0	0	-9999	-10000	0	0
RANBP2	0.01	0.035	-9999	-0.71	1	1
SUMO1/HDAC4	0.024	0.019	-9999	-10000	0	0
SUMO1/HDAC1	0.024	0.019	-9999	-0.22	2	2
RANGAP1	0.012	0	-9999	-10000	0	0
MDM2/SUMO1/SUMO1	0.029	0.019	-9999	-0.31	1	1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9	0.016	0.015	-9999	-0.17	1	1
Ran/GTP	0.021	0.014	-9999	-10000	0	0
EntrezGene:23225	0	0	-9999	-10000	0	0
MDM2	0.011	0.016	-9999	-0.32	1	1
UBE2I	0.012	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.025	0.013	-9999	-10000	0	0
NPC	0.006	0.02	-9999	-0.4	1	1
PIAS2	0.012	0.001	-9999	-10000	0	0
PIAS1	0.012	0	-9999	-10000	0	0
EntrezGene:9972	0	0	-9999	-10000	0	0

×

E-cadherin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin	0.024	0.009	-9999	-10000	0	0
E-cadherin/beta catenin	0.018	0	-9999	-10000	0	0
CTNNB1	0.012	0	-9999	-10000	0	0
JUP	0.011	0.016	-9999	-0.32	1	1
CDH1	0.012	0	-9999	-10000	0	0

×

Arf1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
coatomer protein complex	-0.004	0.035	-9999	-0.32	5	5
EntrezGene:79658	0	0	-9999	-10000	0	0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A	0.016	0	-9999	-10000	0	0
AP2	0.017	0.011	-9999	-10000	0	0
mol:DAG	0	0	-9999	-10000	0	0
Arfaptin 2/Rac/GTP	0.017	0	-9999	-10000	0	0
CLTB	0.012	0	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ER cargo protein	0.02	0	-9999	-10000	0	0
CD4	0.007	0.04	-9999	-0.32	6	6
CLTA	0.012	0	-9999	-10000	0	0
mol:GTP	0.001	0	-9999	-10000	0	0
ARFGAP1	0.003	0.054	-9999	-0.47	5	5
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
ARF1/GTP	0.014	0	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein	0.016	0.039	-9999	-0.36	4	4
mol:Choline	0	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
ARF1	0.012	0	-9999	-10000	0	0
DDEF1	0.01	0	-9999	-10000	0	0
ARF1/GDP	0.002	0.039	-9999	-0.34	5	5
AP2M1	0.012	0	-9999	-10000	0	0
EntrezGene:1313	0	0	-9999	-10000	0	0
actin filament polymerization	0.013	0	-9999	-10000	0	0
Rac/GTP	0.01	0	-9999	-10000	0	0
ARF1/GTP/GGA3/ARF-GAP1	0.017	0.042	-9999	-0.4	4	4
ARFIP2	0.011	0	-9999	-10000	0	0
COPA	0.012	0	-9999	-10000	0	0
RAC1	0.012	0	-9999	-10000	0	0
ARF1/GTP/coatomer protein complex	0.02	0	-9999	-10000	0	0
ARF1/GTP/ARHGAP10	0.009	0	-9999	-10000	0	0
GGA3	0.012	0	-9999	-10000	0	0
ARF1/GTP/Membrin	0.016	0	-9999	-10000	0	0
AP2A1	0.011	0.016	-9999	-0.32	1	1
coatomer protein complex/ARF1/GTP/ARF-GAP1	0.019	0.023	-9999	-0.2	4	4
ARF1/GDP/Membrin	0.016	0	-9999	-10000	0	0
Arfaptin 2/Rac/GDP	0.016	0	-9999	-10000	0	0
CYTH2	0.012	0	-9999	-10000	0	0
ARF1/GTP/GGA3	0.017	0	-9999	-10000	0	0
mol:ATP	0	0	-9999	-10000	0	0
Rac/GDP	0.009	0	-9999	-10000	0	0
mol:Brefeldin A	0	0	-9999	-10000	0	0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP	0.025	0.022	-9999	-10000	0	0
PLD2	0	0	-9999	-10000	0	0
ARF-GAP1/v-SNARE	0.003	0.054	-9999	-0.47	5	5
PIP5K1A	0	0	-9999	-10000	0	0
ARF1/GTP/Membrin/GBF1/p115	0.017	0	-9999	-10000	0	0
mol:Phosphatic acid	0	0	-9999	-10000	0	0
mol:Phosphatidic acid	0	0	-9999	-10000	0	0
KDEL Receptor/Ligand/ARF-GAP1	0.003	0.054	-9999	-0.47	5	5
GOSR2	0.012	0	-9999	-10000	0	0
USO1	0.012	0	-9999	-10000	0	0
GBF1	0.012	0	-9999	-10000	0	0
ARF1/GTP/Arfaptin 2	0.017	0	-9999	-10000	0	0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex	0.021	0.025	-9999	-10000	0	0

×

Alternative NF-kappaB pathway

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

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

Entity	Mean	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations
IKK alpha homodimer	0.018	-9999	-9999
FBXW11	0.012	-9999	-9999
proteasomal ubiquitin-dependent protein catabolic process	0	-9999	-9999
beta TrCP1/SCF ubiquitin ligase complex	0.012	-9999	-9999
CHUK	0.012	-9999	-9999
NF kappa B2 p100/RelB	0.035	-9999	-9999
NFKB1	0.012	-9999	-9999
MAP3K14	0.012	-9999	-9999
NF kappa B1 p50/RelB	0.018	-9999	-9999
RELB	0.012	-9999	-9999
NFKB2	0.012	-9999	-9999
NF kappa B2 p52/RelB	0.016	-9999	-9999
regulation of B cell activation	0.016	-9999	-9999

pid_entity	TCGA.QG.A5Z2	TCGA.QG.A5Z1	TCGA.QG.A5YX	TCGA.QG.A5YW
109_MAP3K5	0.041	0.041	0.041	0.041
47_PPARGC1A	0.012	0.012	0.012	0.012
105_BMP4	0.012	0.012	0.012	0.012
105_BMP6	0.012	0.012	-0.32	0.012
105_BMP7	0.012	0.012	0.012	0.012
105_BMP2	0.012	0.012	0.012	0.012
131_RELN/VLDLR	-0.56	-0.41	-0.56	-0.41
30_TGFB1/TGF beta receptor Type II	0.011	0.011	0.011	0.011
84_STAT5B	0.017	-0.075	-0.034	0.023
84_STAT5A	0.017	-0.075	-0.034	0.023