PARADIGM pathway analysis of mRNASeq expression data - Pan-kidney cohort (KICH+KIRC+KIRP) (Primary solid tumor)

Pathway.Name	Avg.Num.Perturbations
HIF-1-alpha transcription factor network	196
VEGFR1 specific signals	188
Endothelins	187
FOXA2 and FOXA3 transcription factor networks	178
Signaling events mediated by VEGFR1 and VEGFR2	158
Syndecan-1-mediated signaling events	142
Syndecan-4-mediated signaling events	140
Angiopoietin receptor Tie2-mediated signaling	131
Nephrin/Neph1 signaling in the kidney podocyte	130
Ephrin A reverse signaling	130

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
HIF-1-alpha transcription factor network	0.2205	196	14968	76	-0.76	0.026	1000	-1000	-0.13	-1000
VEGFR1 specific signals	0.2115	188	10531	56	-0.4	0.016	1000	-1000	-0.095	-1000
Endothelins	0.2103	187	18031	96	-0.42	0.016	1000	-1000	-0.09	-1000
FOXA2 and FOXA3 transcription factor networks	0.2002	178	8225	46	-0.74	0.025	1000	-1000	-0.075	-1000
Signaling events mediated by VEGFR1 and VEGFR2	0.1777	158	19773	125	-0.48	0.016	1000	-1000	-0.13	-1000
Syndecan-1-mediated signaling events	0.1597	142	4854	34	-0.29	0.016	1000	-1000	-0.078	-1000
Syndecan-4-mediated signaling events	0.1575	140	9439	67	-0.39	0.087	1000	-1000	-0.12	-1000
Angiopoietin receptor Tie2-mediated signaling	0.1474	131	11552	88	-0.41	0.038	1000	-1000	-0.14	-1000
Nephrin/Neph1 signaling in the kidney podocyte	0.1462	130	4431	34	-0.25	0.016	1000	-1000	-0.088	-1000
Ephrin A reverse signaling	0.1462	130	910	7	-0.13	0	1000	-1000	-0.048	-1000
IL4-mediated signaling events	0.1462	130	11856	91	-0.79	0.54	1000	-1000	-0.15	-1000
IL23-mediated signaling events	0.1451	129	7755	60	-0.48	0.017	1000	-1000	-0.16	-1000
HIF-2-alpha transcription factor network	0.1440	128	5517	43	-0.44	0.31	1000	-1000	-0.11	-1000
PDGFR-alpha signaling pathway	0.1406	125	5514	44	-0.21	0.032	1000	-1000	-0.091	-1000
S1P1 pathway	0.1327	118	4266	36	-0.32	0.016	1000	-1000	-0.077	-1000
p75(NTR)-mediated signaling	0.1249	111	13898	125	-0.42	0.016	1000	-1000	-0.14	-1000
Signaling events mediated by the Hedgehog family	0.1215	108	5654	52	-0.4	0.15	1000	-1000	-0.1	-1000
LPA4-mediated signaling events	0.1181	105	1270	12	-0.17	0.023	1000	-1000	-0.033	-1000
TCR signaling in naïve CD8+ T cells	0.1102	98	9170	93	-0.23	0.052	1000	-1000	-0.11	-1000
amb2 Integrin signaling	0.1080	96	7952	82	-0.28	0.016	1000	-1000	-0.11	-1000
EGFR-dependent Endothelin signaling events	0.1080	96	2021	21	-0.28	0.016	1000	-1000	-0.098	-1000
IL12-mediated signaling events	0.1069	95	8312	87	-0.34	0.097	1000	-1000	-0.14	-1000
Glypican 2 network	0.1035	92	370	4	-0.081	-0.028	1000	-1000	-0.051	-1000
BMP receptor signaling	0.1024	91	7382	81	-0.4	0.034	1000	-1000	-0.11	-1000
Thromboxane A2 receptor signaling	0.1001	89	9434	105	-0.15	0.054	1000	-1000	-0.096	-1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	0.0990	88	5993	68	-0.39	0.11	1000	-1000	-0.14	-1000
Integrins in angiogenesis	0.0956	85	7149	84	-0.32	0.026	1000	-1000	-0.14	-1000
Wnt signaling	0.0956	85	597	7	-0.11	-0.072	1000	-1000	-0.042	-1000
Glypican 1 network	0.0889	79	3818	48	-0.29	0.036	1000	-1000	-0.06	-1000
PDGFR-beta signaling pathway	0.0866	77	7472	97	-0.16	0.016	1000	-1000	-0.12	-1000
Class IB PI3K non-lipid kinase events	0.0832	74	222	3	-0.045	-1000	1000	-1000	-0.015	-1000
IL6-mediated signaling events	0.0787	70	5298	75	-0.38	0.064	1000	-1000	-0.11	-1000
Reelin signaling pathway	0.0776	69	3877	56	-0.35	0.016	1000	-1000	-0.11	-1000
Calcium signaling in the CD4+ TCR pathway	0.0765	68	2122	31	-0.27	0.016	1000	-1000	-0.11	-1000
Neurotrophic factor-mediated Trk receptor signaling	0.0765	68	8248	120	-0.26	0.18	1000	-1000	-0.1	-1000
Signaling events regulated by Ret tyrosine kinase	0.0709	63	5208	82	-0.21	0.016	1000	-1000	-0.11	-1000
Arf6 signaling events	0.0697	62	3864	62	-0.22	0.016	1000	-1000	-0.082	-1000
Effects of Botulinum toxin	0.0664	59	1544	26	-0.21	0.016	1000	-1000	-0.082	-1000
Signaling mediated by p38-alpha and p38-beta	0.0652	58	2592	44	-0.23	0.016	1000	-1000	-0.066	-1000
TCGA08_retinoblastoma	0.0652	58	464	8	-0.041	0.023	1000	-1000	-0.02	-1000
Visual signal transduction: Rods	0.0652	58	3032	52	-0.17	0.016	1000	-1000	-0.1	-1000
BCR signaling pathway	0.0641	57	5673	99	-0.19	0.042	1000	-1000	-0.12	-1000
Noncanonical Wnt signaling pathway	0.0619	55	1440	26	-0.15	0.016	1000	-1000	-0.12	-1000
Fc-epsilon receptor I signaling in mast cells	0.0619	55	5418	97	-0.2	0.037	1000	-1000	-0.12	-1000
Caspase cascade in apoptosis	0.0607	54	4005	74	-0.1	0.043	1000	-1000	-0.073	-1000
Glucocorticoid receptor regulatory network	0.0607	54	6189	114	-0.45	0.12	1000	-1000	-0.093	-1000
Paxillin-independent events mediated by a4b1 and a4b7	0.0607	54	2015	37	-0.22	0.016	1000	-1000	-0.077	-1000
S1P3 pathway	0.0607	54	2299	42	-0.3	0.018	1000	-1000	-0.076	-1000
a4b1 and a4b7 Integrin signaling	0.0585	52	263	5	-0.066	0.008	1000	-1000	-0.048	-1000
Ephrin B reverse signaling	0.0585	52	2521	48	-0.13	0.12	1000	-1000	-0.096	-1000
Signaling events mediated by Stem cell factor receptor (c-Kit)	0.0585	52	4071	78	-0.22	0.069	1000	-1000	-0.11	-1000
E-cadherin signaling events	0.0562	50	251	5	-0.054	0.016	1000	-1000	-0.052	-1000
FOXM1 transcription factor network	0.0551	49	2545	51	-0.16	0.15	1000	-1000	-0.19	-1000
Nongenotropic Androgen signaling	0.0540	48	2512	52	-0.097	0.016	1000	-1000	-0.081	-1000
EPHB forward signaling	0.0529	47	4077	85	-0.14	0.1	1000	-1000	-0.12	-1000
Plasma membrane estrogen receptor signaling	0.0529	47	4075	86	-0.14	0.027	1000	-1000	-0.11	-1000
Visual signal transduction: Cones	0.0517	46	1750	38	-0.12	0.015	1000	-1000	-0.085	-1000
JNK signaling in the CD4+ TCR pathway	0.0517	46	789	17	-0.12	0.016	1000	-1000	-0.1	-1000
IL27-mediated signaling events	0.0517	46	2361	51	-0.19	0.064	1000	-1000	-0.11	-1000
Syndecan-2-mediated signaling events	0.0495	44	3063	69	-0.18	0.042	1000	-1000	-0.082	-1000
LPA receptor mediated events	0.0495	44	4538	102	-0.15	0.021	1000	-1000	-0.12	-1000
EPO signaling pathway	0.0461	41	2255	55	-0.21	0.016	1000	-1000	-0.13	-1000
Osteopontin-mediated events	0.0450	40	1524	38	-0.12	0.016	1000	-1000	-0.14	-1000
Signaling events mediated by PTP1B	0.0450	40	3110	76	-0.15	0.025	1000	-1000	-0.1	-1000
IL2 signaling events mediated by STAT5	0.0450	40	880	22	-0.097	0.017	1000	-1000	-0.052	-1000
Canonical Wnt signaling pathway	0.0439	39	1998	51	-0.16	0.04	1000	-1000	-0.074	-1000
Coregulation of Androgen receptor activity	0.0427	38	2893	76	-0.29	0.034	1000	-1000	-0.063	-1000
IL2 signaling events mediated by PI3K	0.0427	38	2211	58	-0.1	0.035	1000	-1000	-0.1	-1000
ErbB4 signaling events	0.0405	36	2484	69	-0.17	0.088	1000	-1000	-0.11	-1000
Lissencephaly gene (LIS1) in neuronal migration and development	0.0405	36	1981	54	-0.27	0.034	1000	-1000	-0.13	-1000
Cellular roles of Anthrax toxin	0.0405	36	1423	39	-0.1	0.019	1000	-1000	-0.05	-1000
IL1-mediated signaling events	0.0394	35	2175	62	-0.18	0.077	1000	-1000	-0.13	-1000
Sphingosine 1-phosphate (S1P) pathway	0.0382	34	969	28	-0.086	0.016	1000	-1000	-0.079	-1000
Paxillin-dependent events mediated by a4b1	0.0371	33	1203	36	-0.11	0.045	1000	-1000	-0.092	-1000
Ras signaling in the CD4+ TCR pathway	0.0371	33	561	17	-0.037	0.016	1000	-1000	-0.057	-1000
Aurora B signaling	0.0371	33	2276	67	-0.17	0.016	1000	-1000	-0.095	-1000
Presenilin action in Notch and Wnt signaling	0.0360	32	1978	61	-0.11	0.047	1000	-1000	-0.092	-1000
FAS signaling pathway (CD95)	0.0360	32	1506	47	-0.23	0.017	1000	-1000	-0.069	-1000
Signaling mediated by p38-gamma and p38-delta	0.0360	32	483	15	-0.031	0.02	1000	-1000	-0.038	-1000
TRAIL signaling pathway	0.0337	30	1487	48	-0.076	0.028	1000	-1000	-0.1	-1000
Stabilization and expansion of the E-cadherin adherens junction	0.0326	29	2158	74	-0.15	0.066	1000	-1000	-0.13	-1000
S1P5 pathway	0.0315	28	476	17	-0.057	0.055	1000	-1000	-0.071	-1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha	0.0304	27	908	33	-0.21	0.032	1000	-1000	-0.085	-1000
Regulation of p38-alpha and p38-beta	0.0292	26	1427	54	-0.14	0.019	1000	-1000	-0.074	-1000
ErbB2/ErbB3 signaling events	0.0270	24	1575	65	-0.1	0.032	1000	-1000	-0.087	-1000
Regulation of nuclear SMAD2/3 signaling	0.0270	24	3295	136	-0.32	0.31	1000	-1000	-0.097	-1000
Nectin adhesion pathway	0.0270	24	1535	63	-0.12	0.055	1000	-1000	-0.11	-1000
Syndecan-3-mediated signaling events	0.0270	24	847	35	-0.16	0.016	1000	-1000	-0.09	-1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha	0.0270	24	1106	45	-0.14	0.042	1000	-1000	-0.12	-1000
Regulation of Androgen receptor activity	0.0270	24	1686	70	-0.3	0.038	1000	-1000	-0.089	-1000
Signaling events mediated by PRL	0.0259	23	790	34	-0.1	0.024	1000	-1000	-0.056	-1000
p38 MAPK signaling pathway	0.0259	23	1014	44	-0.25	0.021	1000	-1000	-0.084	-1000
Insulin-mediated glucose transport	0.0236	21	674	32	-0.23	0.039	1000	-1000	-0.081	-1000
Ceramide signaling pathway	0.0236	21	1616	76	-0.15	0.039	1000	-1000	-0.087	-1000
RXR and RAR heterodimerization with other nuclear receptor	0.0236	21	1134	52	-0.12	0.051	1000	-1000	-0.089	-1000
S1P4 pathway	0.0236	21	542	25	-0.052	0.02	1000	-1000	-0.071	-1000
BARD1 signaling events	0.0225	20	1173	57	-0.043	0.055	1000	-1000	-0.098	-1000
Aurora A signaling	0.0225	20	1215	60	-0.2	0.043	1000	-1000	-0.084	-1000
Class I PI3K signaling events	0.0225	20	1501	73	-0.1	0.032	1000	-1000	-0.099	-1000
Regulation of Telomerase	0.0225	20	2118	102	-0.26	0.048	1000	-1000	-0.13	-1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes	0.0214	19	1617	83	-0.23	0.064	1000	-1000	-0.096	-1000
IGF1 pathway	0.0214	19	1139	57	-0.06	0.032	1000	-1000	-0.12	-1000
PLK2 and PLK4 events	0.0202	18	56	3	-0.008	0.014	1000	-1000	-0.034	-1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)	0.0202	18	1565	85	-0.094	0.036	1000	-1000	-0.1	-1000
TCGA08_rtk_signaling	0.0202	18	484	26	-0.18	0.042	1000	-1000	-0.026	-1000
E-cadherin signaling in keratinocytes	0.0202	18	774	43	-0.094	0.035	1000	-1000	-0.089	-1000
IFN-gamma pathway	0.0191	17	1217	68	-0.25	0.05	1000	-1000	-0.12	-1000
TCGA08_p53	0.0191	17	122	7	-0.031	0.023	1000	-1000	-0.023	-1000
E-cadherin signaling in the nascent adherens junction	0.0191	17	1330	76	-0.056	0.047	1000	-1000	-0.11	-1000
FoxO family signaling	0.0180	16	1030	64	-0.31	0.14	1000	-1000	-0.073	-1000
Hedgehog signaling events mediated by Gli proteins	0.0169	15	1010	65	-0.12	0.051	1000	-1000	-0.079	-1000
Insulin Pathway	0.0169	15	1159	74	-0.12	0.042	1000	-1000	-0.12	-1000
Rapid glucocorticoid signaling	0.0169	15	319	20	-0.031	0.016	1000	-1000	-0.05	-1000
Aurora C signaling	0.0157	14	102	7	-0.036	0.001	1000	-1000	-0.06	-1000
PLK1 signaling events	0.0157	14	1236	85	-0.038	0.038	1000	-1000	-0.068	-1000
Signaling events mediated by HDAC Class III	0.0157	14	571	40	-0.071	0.028	1000	-1000	-0.057	-1000
ceramide signaling pathway	0.0157	14	734	49	-0.066	0.037	1000	-1000	-0.052	-1000
Atypical NF-kappaB pathway	0.0157	14	434	31	-0.08	0.033	1000	-1000	-0.057	-1000
Signaling events mediated by HDAC Class II	0.0135	12	920	75	-0.07	0.037	1000	-1000	-0.082	-1000
Retinoic acid receptors-mediated signaling	0.0135	12	721	58	-0.042	0.047	1000	-1000	-0.094	-1000
Circadian rhythm pathway	0.0124	11	248	22	-0.05	0.041	1000	-1000	-0.076	-1000
Class I PI3K signaling events mediated by Akt	0.0101	9	612	68	-0.23	0.06	1000	-1000	-0.087	-1000
Signaling events mediated by HDAC Class I	0.0101	9	946	104	-0.07	0.069	1000	-1000	-0.082	-1000
Canonical NF-kappaB pathway	0.0090	8	330	39	-0.062	0.095	1000	-1000	-0.1	-1000
Arf6 downstream pathway	0.0090	8	374	43	-0.03	0.03	1000	-1000	-0.045	-1000
Arf6 trafficking events	0.0090	8	621	71	-0.071	0.054	1000	-1000	-0.097	-1000
Alternative NF-kappaB pathway	0.0079	7	92	13	-0.021	0.016	1000	-1000	-0.088	-1000
mTOR signaling pathway	0.0067	6	333	53	-0.014	0.036	1000	-1000	-0.078	-1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling	0.0022	2	66	23	-0.018	0.058	1000	-1000	-0.094	-1000
Arf1 pathway	0.0022	2	140	54	-0.016	0.036	1000	-1000	-0.063	-1000
Sumoylation by RanBP2 regulates transcriptional repression	0.0000	0	12	27	-0.001	0.037	1000	-1000	-0.081	-1000
Total	NA	6846	404941	7203	-25	-990	131000	-131000	-12	-131000

HIF-1-alpha transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PKM2	-0.46	0.76	-9999	-1.4	277	277
HDAC7	0.015	0.041	-9999	-0.85	2	2
HIF1A/ARNT/Cbp/p300/Src-1	-0.41	0.48	-9999	-1	292	292
SMAD4	0.018	0.003	-9999	-10000	0	0
ID2	-0.46	0.76	-9999	-1.4	278	278
AP1	-0.076	0.21	-9999	-0.58	123	123
ABCG2	-0.49	0.77	-9999	-1.5	285	285
HIF1A	-0.043	0.12	-9999	-0.81	9	9
TFF3	-0.51	0.8	-9999	-1.5	302	302
GATA2	-0.072	0.25	-9999	-0.75	103	103
AKT1	-0.032	0.11	-9999	-1	1	1
response to hypoxia	-0.055	0.12	-9999	-10000	0	0
MCL1	-0.46	0.76	-9999	-1.4	277	277
NDRG1	-0.47	0.77	-9999	-1.5	277	277
SERPINE1	-0.54	0.81	-9999	-1.5	301	301
FECH	-0.46	0.76	-9999	-1.4	276	276
FURIN	-0.46	0.76	-9999	-1.4	277	277
NCOA2	-0.046	0.21	-9999	-0.85	57	57
EP300	-0.015	0.17	-9999	-0.42	7	7
HMOX1	-0.49	0.79	-9999	-1.5	283	283
BHLHE40	-0.46	0.76	-9999	-1.4	276	276
BHLHE41	-0.48	0.78	-9999	-1.5	281	281
HIF1A/ARNT/SMAD3/SMAD4/SP1	-0.049	0.094	-9999	-0.54	14	14
ENG	0.021	0.17	-9999	-0.86	11	11
JUN	0.009	0.07	-9999	-0.77	7	7
RORA	-0.46	0.76	-9999	-1.4	279	279
ABCB1	-0.33	0.55	-9999	-1.3	190	190
TFRC	-0.47	0.76	-9999	-1.4	278	278
CXCR4	-0.48	0.78	-9999	-1.5	279	279
TF	-0.54	0.77	-9999	-1.4	301	301
CITED2	-0.46	0.76	-9999	-1.4	278	278
HIF1A/ARNT	-0.76	1	-9999	-2	301	301
LDHA	-0.066	0.16	-9999	-1.6	9	9
ETS1	-0.47	0.77	-9999	-1.4	284	284
PGK1	-0.46	0.76	-9999	-1.4	276	276
NOS2	-0.51	0.78	-9999	-1.5	292	292
ITGB2	-0.47	0.77	-9999	-1.5	279	279
ALDOA	-0.46	0.76	-9999	-1.4	278	278
Cbp/p300/CITED2	-0.52	0.74	-9999	-1.5	288	288
FOS	-0.088	0.26	-9999	-0.74	120	120
HK2	-0.48	0.78	-9999	-1.5	285	285
SP1	0.018	0.029	-9999	-10000	0	0
GCK	-0.1	0.36	-9999	-0.99	46	46
HK1	-0.46	0.76	-9999	-1.4	277	277
NPM1	-0.46	0.76	-9999	-1.4	277	277
EGLN1	-0.46	0.76	-9999	-1.4	278	278
CREB1	0.026	0.003	-9999	-10000	0	0
PGM1	-0.46	0.76	-9999	-1.4	277	277
SMAD3	0.018	0.003	-9999	-10000	0	0
EDN1	-0.22	0.54	-9999	-1.4	139	139
IGFBP1	-0.56	0.78	-9999	-1.5	305	305
VEGFA	-0.4	0.62	-9999	-1.2	277	277
HIF1A/JAB1	-0.032	0.071	-9999	-0.62	9	9
CP	-0.68	0.83	-9999	-1.5	372	372
CXCL12	-0.48	0.78	-9999	-1.5	282	282
COPS5	0.01	0.014	-9999	-10000	0	0
SMAD3/SMAD4	0	0.003	-9999	-10000	0	0
BNIP3	-0.46	0.76	-9999	-1.4	278	278
EGLN3	-0.54	0.84	-9999	-1.5	319	319
CA9	-0.57	0.85	-9999	-1.5	341	341
TERT	-0.5	0.76	-9999	-1.4	291	291
ENO1	-0.46	0.76	-9999	-1.4	277	277
PFKL	-0.46	0.76	-9999	-1.4	277	277
NCOA1	0.013	0.008	-9999	-10000	0	0
ADM	-0.51	0.81	-9999	-1.5	301	301
ARNT	-0.033	0.093	-9999	-10000	0	0
HNF4A	-0.13	0.32	-9999	-0.85	150	150
ADFP	-0.5	0.72	-9999	-1.4	288	288
SLC2A1	-0.34	0.56	-9999	-1.1	233	233
LEP	-0.51	0.76	-9999	-1.4	304	304
HIF1A/ARNT/Cbp/p300	-0.41	0.52	-9999	-1	295	295
EPO	-0.35	0.5	-9999	-1.1	165	165
CREBBP	-0.014	0.17	-9999	-0.44	3	3
HIF1A/ARNT/Cbp/p300/HDAC7	-0.48	0.56	-9999	-1.2	316	316
PFKFB3	-0.47	0.77	-9999	-1.5	277	277
NT5E	-0.47	0.77	-9999	-1.5	281	281

×

VEGFR1 specific signals

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer	-0.23	0.44	-9999	-0.95	243	243
VEGFR1 homodimer/NRP1	-0.26	0.43	-9999	-0.95	246	246
mol:DAG	-0.35	0.51	-9999	-1.1	259	259
VEGFR1 homodimer/NRP1/VEGFR 121	-0.37	0.58	-9999	-1.2	270	270
CaM/Ca2+	-0.33	0.49	-9999	-1.1	239	239
HIF1A	-0.092	0.2	-9999	-0.4	241	241
GAB1	0.014	0.041	-9999	-0.85	2	2
AKT1	-0.28	0.45	-9999	-0.96	242	242
PLCG1	-0.36	0.53	-9999	-1.1	259	259
NOS3	-0.3	0.5	-9999	-1	243	243
CBL	0.015	0.029	-9999	-0.85	1	1
mol:NO	-0.27	0.45	-9999	-0.95	243	243
FLT1	-0.26	0.49	-9999	-1.1	246	246
PGF	-0.26	0.37	-9999	-0.75	321	321
VEGFR1 homodimer/NRP2/VEGFR121	-0.4	0.63	-9999	-1.3	270	270
CALM1	0.016	0	-9999	-10000	0	0
PIK3CA	0.01	0.071	-9999	-0.85	6	6
eNOS/Hsp90	-0.25	0.43	-9999	-0.9	243	243
endothelial cell proliferation	-0.33	0.49	-9999	-1	260	260
mol:Ca2+	-0.34	0.5	-9999	-1.1	259	259
MAPK3	-0.29	0.45	-9999	-0.97	240	240
MAPK1	-0.29	0.45	-9999	-0.97	240	240
PIK3R1	0.011	0.066	-9999	-0.78	6	6
PLGF homodimer	-0.26	0.37	-9999	-0.75	321	321
PRKACA	0.016	0	-9999	-10000	0	0
RP11-342D11.1	0	0	-9999	-10000	0	0
CAV1	-0.081	0.27	-9999	-0.84	101	101
VEGFA homodimer	-0.21	0.38	-9999	-0.84	236	236
VEGFR1 homodimer/VEGFA homodimer	-0.36	0.63	-9999	-1.3	270	270
platelet activating factor biosynthetic process	-0.27	0.43	-9999	-0.93	240	240
PI3K	-0.37	0.49	-9999	-1.1	241	241
PRKCA	-0.32	0.47	-9999	-1	240	240
PRKCB	-0.34	0.48	-9999	-0.99	277	277
VEGFR1 homodimer/PLGF homodimer	-0.4	0.56	-9999	-1.2	263	263
VEGFA	-0.21	0.38	-9999	-0.84	236	236
VEGFB	0.016	0	-9999	-10000	0	0
mol:IP3	-0.35	0.51	-9999	-1.1	259	259
RASA1	-0.21	0.42	-9999	-0.89	238	238
NRP2	-0.047	0.22	-9999	-0.84	66	66
VEGFR1 homodimer	-0.26	0.49	-9999	-1	246	246
VEGFB homodimer	0.016	0	-9999	-10000	0	0
NCK1	0.014	0.041	-9999	-0.85	2	2
eNOS/Caveolin-1	-0.28	0.48	-9999	-0.99	250	250
PTPN11	0.015	0.029	-9999	-0.85	1	1
mol:PI-3-4-5-P3	-0.36	0.47	-9999	-1.1	241	241
mol:L-citrulline	-0.27	0.45	-9999	-0.95	243	243
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP	-0.35	0.55	-9999	-1.2	238	238
VEGFR1 homodimer/VEGFA homodimer/NCK1	-0.37	0.58	-9999	-1.2	265	265
CD2AP	0.015	0.022	-9999	-0.65	1	1
PI3K/GAB1	-0.35	0.45	-9999	-1	241	241
PDPK1	-0.3	0.46	-9999	-1	241	241
VEGFR1 homodimer/VEGFA homodimer/SHP2	-0.37	0.58	-9999	-1.2	265	265
mol:NADP	-0.27	0.45	-9999	-0.95	243	243
HSP90AA1	0.016	0	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	-0.34	0.53	-9999	-1.2	238	238
VEGFR1 homodimer/NRP2	-0.27	0.51	-9999	-1.1	249	249

×

Endothelins

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	-0.31	0.56	-10000	0	-1	265	265
PTK2B	0.016	0.001	-10000	0	-10000	0	0
mol:Ca2+	-0.26	0.52	-10000	0	-1	257	257
EDN1	-0.14	0.35	-10000	0	-0.87	147	147
EDN3	-0.044	0.18	-10000	0	-0.65	72	72
EDN2	-0.18	0.35	-10000	0	-0.77	226	226
HRAS/GDP	-0.2	0.42	-10000	0	-0.83	231	231
ETA receptor/Endothelin-1/Gq/GTP/PLC beta	-0.23	0.46	-10000	0	-0.83	264	264
ADCY4	-0.31	0.52	-10000	0	-1.1	248	248
ADCY5	-0.33	0.52	-10000	0	-1	262	262
ADCY6	-0.27	0.47	-10000	0	-0.97	231	231
ADCY7	-0.27	0.47	-10000	0	-0.97	232	232
ADCY1	-0.38	0.57	-10000	0	-1.1	300	300
ADCY2	-0.42	0.5	-10000	0	-0.87	397	397
ADCY3	-0.28	0.49	-10000	0	-1	231	231
ADCY8	-0.41	0.46	-10000	0	-0.88	351	351
ADCY9	-0.27	0.47	-10000	0	-0.98	231	231
arachidonic acid secretion	-0.17	0.37	-10000	0	-0.7	237	237
ETB receptor/Endothelin-1/Gq/GTP	-0.11	0.28	-10000	0	-0.52	221	221
GNAO1	-0.052	0.22	-10000	0	-0.76	79	79
HRAS	0.011	0.059	-10000	0	-0.77	5	5
ETA receptor/Endothelin-1/G12/GTP	-0.28	0.55	0.36	109	-1	263	372
ETA receptor/Endothelin-1/Gs/GTP	-0.28	0.53	0.34	109	-0.97	271	380
mol:GTP	0	0.006	-10000	0	-10000	0	0
COL3A1	-0.38	0.64	-10000	0	-1.2	285	285
EDNRB	-0.053	0.23	-10000	0	-0.83	72	72
response to oxidative stress	0	0	-10000	0	-10000	0	0
CYSLTR2	-0.42	0.63	-10000	0	-1.2	307	307
CYSLTR1	-0.35	0.62	-10000	0	-1.2	243	243
SLC9A1	-0.12	0.2	0.22	40	-0.42	213	253
mol:GDP	-0.23	0.48	-10000	0	-0.9	255	255
SLC9A3	-0.29	0.48	-10000	0	-0.98	236	236
RAF1	-0.2	0.43	-10000	0	-0.85	222	222
JUN	-0.18	0.41	-10000	0	-0.85	202	202
JAK2	-0.31	0.56	-10000	0	-1	265	265
mol:IP3	-0.22	0.44	-10000	0	-0.81	256	256
ETA receptor/Endothelin-1	-0.34	0.63	0.42	114	-1.2	270	384
PLCB1	-0.14	0.33	-10000	0	-0.84	160	160
PLCB2	-0.016	0.16	-10000	0	-0.83	32	32
ETA receptor/Endothelin-3	-0.21	0.38	-10000	0	-0.78	248	248
FOS	-0.16	0.36	-10000	0	-0.79	157	157
Gai/GDP	-0.043	0.26	-10000	0	-1.1	44	44
CRK	0.015	0.022	-10000	0	-0.65	1	1
mol:Ca ++	-0.37	0.64	-10000	0	-1.2	296	296
BCAR1	0.013	0.05	-10000	0	-0.85	3	3
PRKCB1	-0.21	0.41	-10000	0	-0.76	260	260
GNAQ	0.014	0.009	-10000	0	-10000	0	0
GNAZ	0.007	0.085	-10000	0	-0.79	10	10
GNAL	-0.006	0.13	-10000	0	-0.72	27	27
Gs family/GDP	-0.25	0.36	-10000	0	-0.77	251	251
ETA receptor/Endothelin-1/Gq/GTP	-0.22	0.48	-10000	0	-0.86	252	252
MAPK14	-0.13	0.32	-10000	0	-0.7	160	160
TRPC6	-0.29	0.57	-10000	0	-1.1	255	255
GNAI2	0.015	0.029	-10000	0	-0.85	1	1
GNAI3	0.016	0	-10000	0	-10000	0	0
GNAI1	0.004	0.1	-10000	0	-0.85	12	12
ETB receptor/Endothelin-1/Gq/GTP/PLC beta	-0.15	0.34	-10000	0	-0.63	226	226
ETB receptor/Endothelin-2	-0.2	0.32	-10000	0	-0.66	263	263
ETB receptor/Endothelin-3	-0.087	0.22	-10000	0	-0.59	136	136
ETB receptor/Endothelin-1	-0.16	0.35	-10000	0	-0.77	185	185
MAPK3	-0.18	0.41	-10000	0	-0.86	190	190
MAPK1	-0.18	0.41	-10000	0	-0.86	190	190
Rac1/GDP	-0.19	0.42	-10000	0	-0.82	234	234
cAMP biosynthetic process	-0.37	0.46	-10000	0	-0.93	309	309
MAPK8	-0.27	0.57	-10000	0	-1.1	239	239
SRC	0.015	0.022	-10000	0	-0.65	1	1
ETB receptor/Endothelin-1/Gi/GTP	-0.064	0.22	-10000	0	-0.58	91	91
p130Cas/CRK/Src/PYK2	-0.22	0.46	-10000	0	-0.86	265	265
mol:K +	0	0	-10000	0	-10000	0	0
G12/GDP	-0.19	0.42	-10000	0	-0.82	232	232
COL1A2	-0.33	0.61	-10000	0	-1.1	265	265
EntrezGene:2778	0	0	-10000	0	-10000	0	0
ETA receptor/Endothelin-2	-0.32	0.42	-10000	0	-0.76	382	382
mol:DAG	-0.22	0.44	-10000	0	-0.82	256	256
MAP2K2	-0.18	0.4	-10000	0	-0.84	195	195
MAP2K1	-0.18	0.4	-10000	0	-0.84	190	190
EDNRA	-0.22	0.45	-10000	0	-1	198	198
positive regulation of muscle contraction	-0.27	0.5	-10000	0	-1	233	233
Gq family/GDP	-0.24	0.39	-10000	0	-0.87	214	214
HRAS/GTP	-0.22	0.45	-10000	0	-0.86	248	248
PRKCH	-0.22	0.46	-10000	0	-0.9	235	235
RAC1	0.016	0	-10000	0	-10000	0	0
PRKCA	-0.2	0.41	-10000	0	-0.81	230	230
PRKCB	-0.22	0.45	-10000	0	-0.87	236	236
PRKCE	-0.2	0.41	-10000	0	-0.81	229	229
PRKCD	-0.22	0.43	-10000	0	-0.83	245	245
PRKCG	-0.23	0.44	-10000	0	-0.85	243	243
regulation of vascular smooth muscle contraction	-0.19	0.43	-10000	0	-0.97	158	158
PRKCQ	-0.22	0.44	-10000	0	-0.86	241	241
PLA2G4A	-0.19	0.42	-10000	0	-0.8	238	238
GNA14	-0.079	0.27	-10000	0	-0.85	97	97
GNA15	-0.016	0.16	-10000	0	-0.81	33	33
GNA12	0.016	0	-10000	0	-10000	0	0
GNA11	-0.012	0.14	-10000	0	-0.75	31	31
Rac1/GTP	-0.28	0.54	0.36	109	-1	263	372
MMP1	-0.29	0.61	-10000	0	-1	313	313

×

FOXA2 and FOXA3 transcription factor networks

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ACADVL	-0.54	0.59	-10000	0	-1.3	285	285
PCK1	-0.55	0.65	-10000	0	-1.4	251	251
HNF4A	-0.71	0.74	-10000	0	-1.5	331	331
KCNJ11	-0.58	0.68	-10000	0	-1.4	284	284
AKT1	-0.16	0.2	-10000	0	-0.5	20	20
response to starvation	-0.017	0.041	-10000	0	-10000	0	0
DLK1	-0.56	0.63	-10000	0	-1.4	273	273
NKX2-1	-0.12	0.24	0.68	2	-0.82	5	7
ACADM	-0.54	0.59	-10000	0	-1.3	273	273
TAT	-0.31	0.32	-10000	0	-0.9	119	119
CEBPB	-0.007	0.077	-10000	0	-0.68	10	10
CEBPA	-0.032	0.16	-10000	0	-0.78	37	37
TTR	-0.38	0.39	-10000	0	-0.94	214	214
PKLR	-0.65	0.72	-10000	0	-1.5	325	325
APOA1	-0.64	0.67	-10000	0	-1.4	303	303
CPT1C	-0.62	0.65	-10000	0	-1.3	335	335
ALAS1	-0.18	0.22	-10000	0	-1	2	2
TFRC	-0.36	0.4	-10000	0	-1	137	137
FOXF1	-0.085	0.27	-10000	0	-0.81	109	109
NF1	0.025	0.003	-10000	0	-10000	0	0
HNF1A (dimer)	-0.075	0.24	-10000	0	-0.88	72	72
CPT1A	-0.54	0.59	-10000	0	-1.3	273	273
HMGCS1	-0.54	0.59	-10000	0	-1.3	282	282
NR3C1	-0.013	0.083	-10000	0	-0.83	4	4
CPT1B	-0.59	0.65	-10000	0	-1.4	297	297
chromatin remodeling	0	0	-10000	0	-10000	0	0
SP1	0.016	0.01	-10000	0	-10000	0	0
GCK	-0.56	0.61	-10000	0	-1.3	282	282
CREB1	-0.023	0.064	-10000	0	-10000	0	0
IGFBP1	-0.41	0.53	-10000	0	-1.2	228	228
PDX1	-0.26	0.36	-10000	0	-1.1	89	89
UCP2	-0.55	0.61	-10000	0	-1.3	281	281
ALDOB	-0.73	0.74	-10000	0	-1.5	365	365
AFP	-0.18	0.26	-10000	0	-0.71	116	116
BDH1	-0.62	0.66	-10000	0	-1.3	345	345
HADH	-0.54	0.62	-10000	0	-1.3	265	265
F2	-0.74	0.73	-10000	0	-1.5	340	340
HNF1A	-0.075	0.25	-10000	0	-0.88	72	72
G6PC	-0.43	0.6	-10000	0	-1.3	242	242
SLC2A2	-0.54	0.76	-10000	0	-1.8	208	208
INS	0.021	0.074	-10000	0	-0.59	3	3
FOXA1	-0.15	0.28	-10000	0	-0.7	169	169
FOXA3	-0.2	0.32	-10000	0	-0.73	197	197
FOXA2	-0.64	0.74	-10000	0	-1.5	313	313
ABCC8	-0.56	0.63	-10000	0	-1.4	278	278
ALB	-0.28	0.44	-10000	0	-0.98	189	189

×

Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin	-0.05	0.17	-9999	-0.6	74	74
AKT1	-0.18	0.42	-9999	-0.82	255	255
PTK2B	-0.31	0.56	-9999	-1.2	242	242
VEGFR2 homodimer/Frs2	-0.23	0.46	-9999	-1	233	233
CAV1	-0.081	0.27	-9999	-0.84	101	101
CALM1	0.016	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2	-0.37	0.59	-9999	-1.3	233	233
endothelial cell proliferation	-0.16	0.39	-9999	-0.75	258	258
mol:Ca2+	-0.28	0.54	-9999	-1.2	234	234
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac	-0.35	0.56	-9999	-1.3	233	233
RP11-342D11.1	-0.29	0.54	-9999	-1.2	234	234
CDH5	-0.13	0.32	-9999	-0.84	148	148
VEGFA homodimer	-0.14	0.24	-9999	-0.52	236	236
SHC1	0.015	0.022	-9999	-0.65	1	1
SHC2	-0.021	0.17	-9999	-0.8	40	40
HRAS/GDP	-0.27	0.41	-9999	-0.94	235	235
SH2D2A	-0.073	0.25	-9999	-0.76	101	101
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS	-0.25	0.38	-9999	-0.87	236	236
VEGFR2 homodimer/VEGFA homodimer/TsAd	-0.42	0.61	-9999	-1.4	238	238
VEGFR1 homodimer	-0.22	0.38	-9999	-0.84	240	240
SHC/GRB2/SOS1	-0.32	0.5	-9999	-1.1	234	234
GRB10	-0.28	0.54	-9999	-1.1	235	235
PTPN11	0.015	0.029	-9999	-0.85	1	1
GRB2	0.016	0	-9999	-10000	0	0
PAK1	0.016	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin	-0.4	0.64	-9999	-1.4	235	235
HRAS	0.012	0.059	-9999	-0.77	5	5
VEGF/Rho/ROCK1/Integrin Complex	-0.16	0.35	-9999	-0.72	222	222
HIF1A	0.008	0.076	-9999	-0.74	9	9
FRS2	0.016	0	-9999	-10000	0	0
oxygen and reactive oxygen species metabolic process	-0.34	0.54	-9999	-1.2	233	233
mol:GTP	0	0	-9999	-10000	0	0
FLT4	-0.12	0.32	-9999	-0.84	144	144
Nck/Pak	-0.001	0.031	-9999	-0.65	2	2
VEGFR2 homodimer/VEGFA homodimer/Fyn	-0.38	0.6	-9999	-1.3	233	233
mol:GDP	-0.3	0.46	-9999	-1.1	234	234
mol:NADP	-0.14	0.36	-9999	-0.71	235	235
eNOS/Hsp90	-0.12	0.33	-9999	-0.65	235	235
PIK3R1	0.011	0.066	-9999	-0.78	6	6
mol:IP3	-0.29	0.56	-9999	-1.2	234	234
HIF1A/ARNT	-0.006	0.056	-9999	-0.56	9	9
SHB	0.015	0.029	-9999	-0.85	1	1
VEGFA	-0.21	0.38	-9999	-0.84	236	236
VEGFC	-0.013	0.15	-9999	-0.82	31	31
FAK1/Vinculin	-0.26	0.53	-9999	-1.1	243	243
mol:Ca ++	0	0	-9999	-10000	0	0
RHOA	0.016	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	-0.39	0.58	-9999	-1.3	242	242
PTPN6	0.014	0.041	-9999	-0.85	2	2
EPAS1	-0.11	0.26	-9999	-1.2	25	25
mol:L-citrulline	-0.14	0.36	-9999	-0.71	235	235
ITGAV	0.009	0.074	-9999	-0.82	7	7
PIK3CA	0.01	0.071	-9999	-0.85	6	6
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2	-0.35	0.56	-9999	-1.3	233	233
VEGFR2 homodimer/VEGFA homodimer	-0.38	0.59	-9999	-1.3	234	234
VEGFR2/3 heterodimer	-0.31	0.6	-9999	-1.3	238	238
VEGFB	0.016	0	-9999	-10000	0	0
MAPK11	-0.29	0.56	-9999	-1.2	238	238
VEGFR2 homodimer	-0.26	0.51	-9999	-1.1	242	242
FLT1	-0.22	0.38	-9999	-0.84	240	240
NEDD4	-0.001	0.13	-9999	-0.84	20	20
MAPK3	-0.24	0.48	-9999	-0.99	242	242
MAPK1	-0.24	0.48	-9999	-0.99	243	243
VEGFA145/NRP2	-0.21	0.36	-9999	-0.75	251	251
VEGFR1/2 heterodimer	-0.36	0.66	-9999	-1.4	257	257
KDR	-0.26	0.52	-9999	-1.1	242	242
VEGFA165/NRP1/VEGFR2 homodimer	-0.38	0.58	-9999	-1.3	240	240
SRC	0.015	0.022	-9999	-0.65	1	1
platelet activating factor biosynthetic process	-0.25	0.5	-9999	-1	242	242
PI3K	-0.37	0.55	-9999	-1.2	254	254
VEGFR2 homodimer/VEGFA homodimer/NCK1	-0.37	0.59	-9999	-1.3	233	233
FES	-0.31	0.59	-9999	-1.3	234	234
GAB1	-0.38	0.57	-9999	-1.3	251	251
VEGFR2 homodimer/VEGFA homodimer/Src	-0.37	0.59	-9999	-1.3	233	233
CTNNB1	0.016	0	-9999	-10000	0	0
SOS1	0.016	0	-9999	-10000	0	0
ARNT	0.016	0	-9999	-10000	0	0
eNOS/Caveolin-1	-0.15	0.37	-9999	-0.71	244	244
VEGFR2 homodimer/VEGFA homodimer/Yes	-0.37	0.59	-9999	-1.3	233	233
PI3K/GAB1	-0.18	0.43	-9999	-0.85	253	253
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak	-0.34	0.54	-9999	-1.2	233	233
PRKACA	0.016	0	-9999	-10000	0	0
VEGFR2/3 heterodimer/VEGFC homodimer	-0.34	0.57	-9999	-1.3	235	235
HSP90AA1	0.016	0	-9999	-10000	0	0
CDC42	-0.3	0.58	-9999	-1.2	234	234
actin cytoskeleton reorganization	-0.41	0.58	-9999	-1.3	238	238
PTK2	-0.31	0.61	-9999	-1.3	243	243
EDG1	-0.29	0.54	-9999	-1.2	234	234
mol:DAG	-0.29	0.56	-9999	-1.2	234	234
CaM/Ca2+	-0.3	0.47	-9999	-1.1	234	234
MAP2K3	-0.28	0.55	-9999	-1.1	237	237
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4	-0.36	0.56	-9999	-1.3	235	235
PLCG1	-0.3	0.58	-9999	-1.2	234	234
VEGFR2 homodimer/VEGFA homodimer/Src/Shb	-0.36	0.56	-9999	-1.3	233	233
IQGAP1	0.016	0	-9999	-10000	0	0
YES1	0.016	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/SHP2	-0.37	0.59	-9999	-1.3	233	233
VEGFR2 homodimer/VEGFA homodimer/SHP1	-0.37	0.59	-9999	-1.3	234	234
cell migration	-0.17	0.43	-9999	-0.85	243	243
mol:PI-3-4-5-P3	-0.31	0.46	-9999	-1	254	254
FYN	0.007	0.086	-9999	-0.85	9	9
VEGFB/NRP1	-0.26	0.5	-9999	-1.1	234	234
mol:NO	-0.14	0.36	-9999	-0.71	235	235
PXN	0.016	0	-9999	-10000	0	0
HRAS/GTP	-0.27	0.42	-9999	-0.95	235	235
VEGFR2 homodimer/VEGFA homodimer/GRB10	-0.31	0.6	-9999	-1.3	235	235
VHL	0.012	0.058	-9999	-0.85	4	4
ITGB3	-0.046	0.21	-9999	-0.76	71	71
NOS3	-0.18	0.43	-9999	-0.86	235	235
VEGFR2 homodimer/VEGFA homodimer/Sck	-0.39	0.6	-9999	-1.3	239	239
RAC1	0.016	0	-9999	-10000	0	0
PRKCA	-0.25	0.5	-9999	-1.1	234	234
PRKCB	-0.28	0.51	-9999	-1.1	244	244
VCL	0.016	0	-9999	-10000	0	0
VEGFA165/NRP1	-0.31	0.57	-9999	-1.2	234	234
VEGFR1/2 heterodimer/VEGFA homodimer	-0.48	0.75	-9999	-1.7	249	249
VEGFA165/NRP2	-0.21	0.36	-9999	-0.75	251	251
MAPKKK cascade	-0.28	0.42	-9999	-0.96	236	236
NRP2	-0.047	0.22	-9999	-0.84	66	66
VEGFC homodimer	-0.013	0.15	-9999	-0.82	31	31
NCK1	0.014	0.041	-9999	-0.85	2	2
ROCK1	0.013	0.05	-9999	-0.85	3	3
FAK1/Paxillin	-0.26	0.53	-9999	-1.1	243	243
MAP3K13	-0.31	0.59	-9999	-1.2	237	237
PDPK1	-0.18	0.42	-9999	-0.82	254	254

×

Syndecan-1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	-0.003	0.12	-9999	-0.83	20	20
CCL5	-0.071	0.25	-9999	-0.75	101	101
SDCBP	0.016	0	-9999	-10000	0	0
FGFR/FGF2/Syndecan-1	-0.26	0.31	-9999	-0.65	254	254
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
Syndecan-1/Laminin-5	-0.25	0.31	-9999	-0.67	222	222
Syndecan-1/Syntenin	-0.24	0.3	-9999	-0.69	196	196
MAPK3	-0.21	0.27	-9999	-0.72	133	133
HGF/MET	-0.087	0.21	-9999	-0.6	129	129
TGFB1/TGF beta receptor Type II	-0.003	0.12	-9999	-0.83	20	20
BSG	0.011	0.058	-9999	-0.68	6	6
keratinocyte migration	-0.24	0.3	-9999	-0.65	222	222
Syndecan-1/RANTES	-0.29	0.34	-9999	-0.74	239	239
Syndecan-1/CD147	-0.23	0.3	-9999	-0.66	198	198
Syndecan-1/Syntenin/PIP2	-0.25	0.28	-9999	-0.67	196	196
LAMA5	0.009	0.074	-9999	-0.82	7	7
positive regulation of cell-cell adhesion	-0.24	0.26	-9999	-0.65	196	196
MMP7	-0.25	0.37	-9999	-0.75	312	312
HGF	-0.094	0.28	-9999	-0.78	122	122
Syndecan-1/CASK	-0.25	0.3	-9999	-0.63	251	251
Syndecan-1/HGF/MET	-0.29	0.35	-9999	-0.81	200	200
regulation of cell adhesion	-0.19	0.26	-9999	-0.77	93	93
HPSE	-0.048	0.22	-9999	-0.81	69	69
positive regulation of cell migration	-0.26	0.31	-9999	-0.65	254	254
SDC1	-0.27	0.32	-9999	-0.66	251	251
Syndecan-1/Collagen	-0.26	0.31	-9999	-0.65	254	254
PPIB	0.016	0	-9999	-10000	0	0
MET	0.009	0.075	-9999	-0.77	8	8
PRKACA	0.016	0	-9999	-10000	0	0
MMP9	-0.15	0.31	-9999	-0.73	194	194
MAPK1	-0.21	0.27	-9999	-0.71	134	134
homophilic cell adhesion	-0.26	0.31	-9999	-0.64	254	254
MMP1	-0.27	0.38	-9999	-0.77	319	319

×

Syndecan-4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.1	0.24	-9999	-0.65	131	131
Syndecan-4/Syndesmos	-0.33	0.34	-9999	-0.8	234	234
positive regulation of JNK cascade	-0.35	0.31	-9999	-0.74	281	281
Syndecan-4/ADAM12	-0.39	0.38	-9999	-0.83	311	311
CCL5	-0.071	0.25	-9999	-0.75	101	101
Rac1/GDP	0	0	-9999	-10000	0	0
DNM2	0.016	0	-9999	-10000	0	0
ITGA5	-0.009	0.14	-9999	-0.81	27	27
SDCBP	0.016	0	-9999	-10000	0	0
PLG	-0.27	0.36	-9999	-0.72	347	347
ADAM12	-0.11	0.28	-9999	-0.71	154	154
mol:GTP	0	0	-9999	-10000	0	0
NUDT16L1	0.014	0.037	-9999	-0.75	2	2
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
Syndecan-4/PKC alpha	-0.085	0.055	-9999	-10000	0	0
Syndecan-4/Laminin alpha1	-0.37	0.36	-9999	-0.82	269	269
Syndecan-4/CXCL12/CXCR4	-0.36	0.37	-9999	-0.85	256	256
Syndecan-4/Laminin alpha3	-0.36	0.35	-9999	-0.79	278	278
MDK	-0.051	0.22	-9999	-0.76	77	77
Syndecan-4/FZD7	-0.35	0.35	-9999	-0.8	257	257
Syndecan-4/Midkine	-0.37	0.35	-9999	-0.82	265	265
FZD7	-0.017	0.16	-9999	-0.77	37	37
Syndecan-4/FGFR1/FGF	-0.34	0.3	-9999	-0.78	226	226
THBS1	-0.05	0.23	-9999	-0.84	69	69
integrin-mediated signaling pathway	-0.36	0.34	-9999	-0.77	285	285
positive regulation of MAPKKK cascade	-0.35	0.31	-9999	-0.74	281	281
Syndecan-4/TACI	-0.36	0.35	-9999	-0.78	288	288
CXCR4	-0.04	0.21	-9999	-0.84	58	58
cell adhesion	-0.036	0.17	-9999	-0.47	99	99
Syndecan-4/Dynamin	-0.33	0.34	-9999	-0.77	260	260
Syndecan-4/TSP1	-0.37	0.36	-9999	-0.8	289	289
Syndecan-4/GIPC	-0.33	0.34	-9999	-0.8	235	235
Syndecan-4/RANTES	-0.37	0.36	-9999	-0.82	288	288
ITGB1	0.016	0	-9999	-10000	0	0
LAMA1	-0.059	0.24	-9999	-0.8	82	82
LAMA3	-0.039	0.19	-9999	-0.67	71	71
RAC1	0.016	0	-9999	-10000	0	0
PRKCA	0.087	0.064	-9999	-0.54	2	2
Syndecan-4/alpha-Actinin	-0.34	0.34	-9999	-0.81	236	236
TFPI	-0.1	0.3	-9999	-0.84	124	124
F2	-0.21	0.34	-9999	-0.72	268	268
alpha5/beta1 Integrin	-0.019	0.11	-9999	-0.62	27	27
positive regulation of cell adhesion	-0.37	0.35	-9999	-0.8	285	285
ACTN1	0.005	0.098	-9999	-0.83	12	12
TNC	-0.08	0.26	-9999	-0.75	112	112
Syndecan-4/CXCL12	-0.36	0.36	-9999	-0.81	278	278
FGF6	0	0.022	-9999	-0.65	1	1
RHOA	0.016	0	-9999	-10000	0	0
CXCL12	-0.047	0.22	-9999	-0.8	69	69
TNFRSF13B	-0.032	0.16	-9999	-0.65	58	58
FGF2	-0.033	0.2	-9999	-0.84	51	51
FGFR1	0.011	0.062	-9999	-0.81	5	5
Syndecan-4/PI-4-5-P2	-0.34	0.34	-9999	-0.78	260	260
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.1	0.28	-9999	-0.76	137	137
cell migration	-0.025	0.021	-9999	-10000	0	0
PRKCD	-0.024	0.16	-9999	-0.65	57	57
vasculogenesis	-0.35	0.33	-9999	-0.76	289	289
SDC4	-0.37	0.37	-9999	-0.85	260	260
Syndecan-4/Tenascin C	-0.38	0.37	-9999	-0.84	273	273
Syndecan-4/PI-4-5-P2/PKC alpha	-0.067	0.043	-9999	-10000	0	0
Syndecan-4/Syntenin	-0.33	0.34	-9999	-0.8	234	234
MMP9	-0.15	0.31	-9999	-0.73	194	194
Rac1/GTP	-0.053	0.18	-9999	-0.49	99	99
cytoskeleton organization	-0.32	0.32	-9999	-0.74	246	246
GIPC1	0.012	0.055	-9999	-0.8	4	4
Syndecan-4/TFPI	-0.39	0.37	-9999	-0.83	300	300

×

Angiopoietin receptor Tie2-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	-0.22	0.54	-10000	0	-1.1	195	195
NCK1/PAK1/Dok-R	-0.14	0.19	-10000	0	-0.47	196	196
NCK1/Dok-R	-0.34	0.6	-10000	0	-1.4	189	189
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
mol:beta2-estradiol	0.038	0.099	0.26	107	-10000	0	107
RELA	0.016	0	-10000	0	-10000	0	0
SHC1	0.014	0.023	-10000	0	-0.65	1	1
Rac/GDP	0	0	-10000	0	-10000	0	0
F2	-0.17	0.37	-10000	0	-0.72	258	258
TNIP2	0.014	0.041	-10000	0	-0.85	2	2
NF kappa B/RelA	-0.29	0.52	-10000	0	-1.3	183	183
FN1	-0.11	0.29	-10000	0	-0.79	137	137
PLD2	-0.26	0.67	-10000	0	-1.5	187	187
PTPN11	0.015	0.029	-10000	0	-0.85	1	1
GRB14	-0.087	0.25	-10000	0	-0.7	128	128
ELK1	-0.19	0.57	-10000	0	-1.2	188	188
GRB7	-0.002	0.12	-10000	0	-0.76	21	21
PAK1	0.016	0	-10000	0	-10000	0	0
Tie2/Ang1/alpha5/beta1 Integrin	-0.34	0.58	-10000	0	-1.4	189	189
CDKN1A	-0.15	0.41	-10000	0	-0.71	277	277
ITGA5	-0.009	0.14	-10000	0	-0.81	27	27
mol:GTP	0	0	-10000	0	-10000	0	0
RasGAP/Dok-R	-0.34	0.6	-10000	0	-1.4	189	189
CRK	0.015	0.022	-10000	0	-0.65	1	1
mol:NO	-0.14	0.41	-10000	0	-0.8	199	199
PLG	-0.41	0.65	-10000	0	-1.5	193	193
mol:GDP	0	0	-10000	0	-10000	0	0
chemokinesis	-0.22	0.45	-10000	0	-1	188	188
GRB2	0.016	0	-10000	0	-10000	0	0
PIK3R1	0.009	0.066	-10000	0	-0.78	6	6
ANGPT2	-0.36	0.66	0.47	2	-1.3	269	271
BMX	-0.32	0.68	-10000	0	-1.5	188	188
ANGPT1	-0.24	0.66	-10000	0	-1.6	157	157
tube development	-0.19	0.46	-10000	0	-0.83	278	278
ANGPT4	-0.054	0.21	-10000	0	-0.73	77	77
response to hypoxia	-0.016	0.031	-10000	0	-10000	0	0
Tie2/Ang1/GRB14	-0.33	0.71	-10000	0	-1.6	195	195
alpha5/beta1 Integrin	-0.019	0.11	-10000	0	-0.62	27	27
FGF2	-0.031	0.2	-10000	0	-0.84	51	51
STAT5A (dimer)	-0.23	0.53	-10000	0	-0.98	278	278
mol:L-citrulline	-0.14	0.41	-10000	0	-0.8	199	199
AGTR1	-0.22	0.35	-10000	0	-0.73	275	275
MAPK14	-0.26	0.66	-10000	0	-1.5	183	183
Tie2/SHP2	-0.24	0.51	-10000	0	-1.4	131	131
TEK	-0.24	0.6	-10000	0	-1.6	137	137
RPS6KB1	-0.18	0.49	-10000	0	-1.1	189	189
Angiotensin II/AT1	-0.17	0.27	-10000	0	-0.56	275	275
Tie2/Ang1/GRB2	-0.28	0.71	-10000	0	-1.6	182	182
MAPK3	-0.21	0.59	-10000	0	-1.3	188	188
MAPK1	-0.21	0.59	-10000	0	-1.3	187	187
Tie2/Ang1/GRB7	-0.29	0.71	-10000	0	-1.6	184	184
NFKB1	0.015	0.029	-10000	0	-0.85	1	1
MAPK8	-0.26	0.68	-10000	0	-1.5	182	182
PI3K	-0.26	0.62	-10000	0	-1.4	189	189
FES	-0.27	0.66	-10000	0	-1.5	185	185
Crk/Dok-R	-0.34	0.6	-10000	0	-1.4	189	189
Tie2/Ang1/ABIN2	-0.28	0.71	-10000	0	-1.6	183	183
blood circulation	0	0	-10000	0	-10000	0	0
negative regulation of caspase activity	-0.18	0.47	-10000	0	-0.97	195	195
STAT5A	0.013	0.05	-10000	0	-0.85	3	3
mol:ROS	0	0	-10000	0	-10000	0	0
PTK2	-0.18	0.49	-10000	0	-1.1	189	189
Tie2/Ang2	-0.33	0.66	-10000	0	-1.3	278	278
Tie2/Ang1	-0.32	0.8	-10000	0	-1.8	182	182
FOXO1	-0.2	0.5	-10000	0	-1	207	207
ELF1	0.008	0.064	-10000	0	-0.87	3	3
ELF2	-0.26	0.68	-10000	0	-1.5	182	182
mol:Choline	-0.23	0.62	-10000	0	-1.4	187	187
cell migration	-0.078	0.1	-10000	0	-10000	0	0
FYN	-0.24	0.53	-10000	0	-0.98	278	278
DOK2	-0.041	0.21	-10000	0	-0.84	59	59
negative regulation of cell cycle	-0.13	0.38	-10000	0	-0.64	277	277
ETS1	-0.054	0.22	-10000	0	-0.91	43	43
PXN	-0.13	0.4	-10000	0	-0.82	188	188
ITGB1	0.016	0	-10000	0	-10000	0	0
NOS3	-0.18	0.47	-10000	0	-0.96	199	199
RAC1	0.016	0	-10000	0	-10000	0	0
TNF	-0.098	0.26	-10000	0	-0.77	99	99
MAPKKK cascade	-0.23	0.62	-10000	0	-1.4	187	187
RASA1	0.013	0.05	-10000	0	-0.85	3	3
Tie2/Ang1/Shc	-0.28	0.71	-10000	0	-1.6	182	182
NCK1	0.014	0.041	-10000	0	-0.85	2	2
vasculogenesis	-0.11	0.36	-10000	0	-0.7	199	199
mol:Phosphatidic acid	-0.23	0.62	-10000	0	-1.4	187	187
mol:Angiotensin II	-0.006	0.015	-10000	0	-10000	0	0
mol:NADP	-0.14	0.41	-10000	0	-0.8	199	199
Rac1/GTP	-0.26	0.38	-10000	0	-0.96	189	189
MMP2	-0.28	0.68	-10000	0	-1.5	186	186

×

Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity	0.17	0.27	0.6	241	-10000	0	241
KIRREL	-0.078	0.25	-10000	0	-0.86	82	82
Nephrin/NEPH1Par3/Par6/Atypical PKCs	-0.17	0.27	-10000	0	-0.6	241	241
PLCG1	0.016	0	-10000	0	-10000	0	0
ARRB2	0.016	0	-10000	0	-10000	0	0
WASL	0.016	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/CD2AP	-0.16	0.25	-10000	0	-0.58	189	189
ChemicalAbstracts:57-88-5	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP	-0.081	0.19	-10000	0	-0.41	188	188
FYN	-0.14	0.25	-10000	0	-0.55	193	193
mol:Ca2+	-0.16	0.24	-10000	0	-0.57	188	188
mol:DAG	-0.16	0.24	-10000	0	-0.58	188	188
NPHS2	-0.093	0.23	-10000	0	-0.68	113	113
mol:IP3	-0.16	0.24	-10000	0	-0.58	188	188
regulation of endocytosis	-0.14	0.22	-10000	0	-0.51	188	188
Nephrin/NEPH1/podocin/Cholesterol	-0.17	0.25	-10000	0	-0.59	188	188
establishment of cell polarity	-0.17	0.27	-10000	0	-0.6	241	241
Nephrin/NEPH1/podocin/NCK1-2	-0.15	0.23	-10000	0	-0.56	150	150
Nephrin/NEPH1/beta Arrestin2	-0.13	0.23	-10000	0	-0.52	188	188
NPHS1	-0.14	0.29	-10000	0	-0.73	166	166
Nephrin/NEPH1/podocin	-0.16	0.24	-10000	0	-0.55	193	193
TJP1	0.016	0	-10000	0	-10000	0	0
NCK1	0.014	0.041	-10000	0	-0.85	2	2
NCK2	0.016	0	-10000	0	-10000	0	0
heterophilic cell adhesion	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/PLCgamma1	-0.16	0.25	-10000	0	-0.58	188	188
CD2AP	0.015	0.022	-10000	0	-0.65	1	1
Nephrin/NEPH1/podocin/GRB2	-0.16	0.25	-10000	0	-0.58	188	188
GRB2	0.016	0	-10000	0	-10000	0	0
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
TRPC6	-0.25	0.33	-10000	0	-0.62	333	333
cytoskeleton organization	-0.11	0.24	-10000	0	-0.53	167	167
Nephrin/NEPH1	-0.12	0.21	-10000	0	-0.45	241	241
Nephrin/NEPH1/ZO-1	-0.14	0.22	-10000	0	-0.53	186	186

×

Ephrin A reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAPKKK cascade	-0.12	0.23	-9999	-0.54	191	191
EFNA5	-0.13	0.32	-9999	-0.79	166	166
FYN	-0.091	0.23	-9999	-0.56	132	132
neuron projection morphogenesis	-0.12	0.23	-9999	-0.54	191	191
cell-cell signaling	0	0	-9999	-10000	0	0
Ephrin A5/EPHA5	-0.12	0.23	-9999	-0.54	191	191
EPHA5	-0.024	0.13	-9999	-0.65	39	39

×

IL4-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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.47	0.59	-10000	0	-1.3	224	224
STAT6 (cleaved dimer)	-0.55	0.58	-10000	0	-1.3	303	303
IGHG1	-0.14	0.2	-10000	0	-0.52	14	14
IGHG3	-0.46	0.56	-10000	0	-1.2	286	286
AKT1	-0.24	0.38	-10000	0	-1	115	115
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1	-0.22	0.43	-10000	0	-1.2	99	99
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1	-0.26	0.42	-10000	0	-1.1	105	105
THY1	-0.55	0.7	-10000	0	-1.5	261	261
MYB	-0.035	0.19	-10000	0	-0.72	61	61
HMGA1	-0.008	0.13	-10000	0	-0.68	31	31
IL4/IL4R/JAK1/IL2R gamma/JAK3	-0.34	0.53	-10000	0	-1.1	190	190
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP	-0.25	0.42	-10000	0	-1.1	101	101
SP1	0.023	0.012	-10000	0	-10000	0	0
INPP5D	0.009	0.076	-10000	0	-0.85	7	7
SOCS5	0.026	0.017	-10000	0	-10000	0	0
STAT6 (dimer)/ETS1	-0.55	0.6	-10000	0	-1.3	308	308
SOCS1	-0.3	0.4	-10000	0	-0.85	209	209
SOCS3	-0.27	0.42	-10000	0	-1.1	113	113
FCER2	-0.38	0.5	-10000	0	-1.1	204	204
PARP14	0.016	0.005	-10000	0	-10000	0	0
CCL17	-0.53	0.65	-10000	0	-1.4	265	265
GRB2	0.016	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP	-0.2	0.34	-10000	0	-1	83	83
T cell proliferation	-0.49	0.63	-10000	0	-1.3	247	247
IL4R/JAK1	-0.48	0.6	-10000	0	-1.3	228	228
EGR2	-0.5	0.63	-10000	0	-1.4	240	240
JAK2	0.001	0.045	-10000	0	-0.89	1	1
JAK3	-0.025	0.19	-10000	0	-0.81	48	48
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
JAK1	0.01	0.017	-10000	0	-10000	0	0
COL1A2	-0.24	0.47	-10000	0	-1.3	111	111
CCL26	-0.49	0.61	-10000	0	-1.3	235	235
IL4R	-0.52	0.66	-10000	0	-1.4	232	232
PTPN6	0.024	0.043	-10000	0	-0.83	2	2
IL13RA2	-0.6	0.7	-10000	0	-1.4	307	307
IL13RA1	0.002	0.033	-10000	0	-10000	0	0
IRF4	-0.24	0.53	-10000	0	-1.3	135	135
ARG1	-0.1	0.2	-10000	0	-0.9	19	19
CBL	-0.3	0.46	-10000	0	-1	162	162
GTF3A	0.021	0.015	-10000	0	-10000	0	0
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
IL13RA1/JAK2	-0.001	0.057	-10000	0	-0.7	1	1
IRF4/BCL6	-0.23	0.47	-10000	0	-1.2	129	129
CD40LG	-0.055	0.25	-10000	0	-0.84	81	81
MAPK14	-0.31	0.5	-10000	0	-1.2	148	148
mitosis	-0.22	0.35	-10000	0	-0.91	115	115
STAT6	-0.58	0.78	-10000	0	-1.5	277	277
SPI1	0.005	0.11	-10000	0	-0.8	15	15
RPS6KB1	-0.2	0.34	-10000	0	-0.89	105	105
STAT6 (dimer)	-0.58	0.79	-10000	0	-1.5	277	277
STAT6 (dimer)/PARP14	-0.52	0.66	-10000	0	-1.4	263	263
mast cell activation	0.01	0.015	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2	-0.28	0.48	-10000	0	-1.2	120	120
FRAP1	-0.24	0.38	-10000	0	-1	115	115
LTA	-0.51	0.64	-10000	0	-1.4	236	236
FES	0	0.12	-10000	0	-0.85	17	17
T-helper 1 cell differentiation	0.54	0.71	1.4	278	-10000	0	278
CCL11	-0.53	0.62	-10000	0	-1.3	287	287
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES	-0.27	0.46	-10000	0	-1.2	117	117
IL2RG	-0.057	0.24	-10000	0	-0.78	85	85
IL10	-0.51	0.63	-10000	0	-1.4	244	244
IRS1	-0.01	0.14	-10000	0	-0.72	31	31
IRS2	-0.019	0.15	-10000	0	-0.66	46	46
IL4	-0.088	0.14	-10000	0	-10000	0	0
IL5	-0.47	0.59	-10000	0	-1.3	221	221
IL4/IL4R/JAK1/IL13RA1/JAK2	-0.35	0.44	-10000	0	-0.91	247	247
COL1A1	-0.25	0.47	-10000	0	-1.2	118	118
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1	-0.5	0.63	-10000	0	-1.4	215	215
IL2R gamma/JAK3	-0.063	0.26	-10000	0	-0.75	104	104
TFF3	-0.56	0.69	-10000	0	-1.5	269	269
ALOX15	-0.47	0.6	-10000	0	-1.3	235	235
MYBL1	0	0.1	-10000	0	-0.65	21	21
T-helper 2 cell differentiation	-0.41	0.52	-10000	0	-1.1	258	258
SHC1	0.015	0.022	-10000	0	-0.65	1	1
CEBPB	0.012	0.074	-10000	0	-0.66	10	10
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2	-0.25	0.42	-10000	0	-1.1	109	109
mol:PI-3-4-5-P3	-0.24	0.38	-10000	0	-1	115	115
PI3K	-0.26	0.43	-10000	0	-1.1	116	116
DOK2	-0.041	0.21	-10000	0	-0.84	59	59
ETS1	-0.01	0.17	-10000	0	-0.81	38	38
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2	-0.18	0.32	-10000	0	-0.97	81	81
ITGB3	-0.51	0.64	-10000	0	-1.4	233	233
PIGR	-0.79	0.72	-10000	0	-1.4	430	430
IGHE	0.03	0.062	-10000	0	-10000	0	0
MAPKKK cascade	-0.17	0.31	-10000	0	-0.93	82	82
BCL6	0.012	0.058	-10000	0	-0.84	4	4
OPRM1	-0.48	0.59	-10000	0	-1.3	220	220
RETNLB	-0.48	0.59	-10000	0	-1.3	235	235
SELP	-0.5	0.64	-10000	0	-1.4	238	238
AICDA	-0.5	0.61	-10000	0	-1.3	252	252

×

IL23-mediated signaling events

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
CCL2	-0.36	0.57	-10000	0	-1.2	197	197
IL23A	-0.34	0.56	-10000	0	-1.2	188	188
NF kappa B1 p50/RelA/I kappa B alpha	-0.4	0.49	-10000	0	-1.2	216	216
positive regulation of T cell mediated cytotoxicity	-0.4	0.64	-10000	0	-1.3	220	220
ITGA3	-0.34	0.55	-10000	0	-1.2	186	186
IL17F	-0.2	0.36	-10000	0	-0.76	153	153
IL12B	-0.044	0.19	-10000	0	-0.7	67	67
STAT1 (dimer)	-0.38	0.6	-10000	0	-1.3	215	215
CD4	-0.33	0.54	-10000	0	-1.2	187	187
IL23	-0.36	0.54	-10000	0	-1.2	191	191
IL23R	-0.032	0.13	-10000	0	-0.64	15	15
IL1B	-0.36	0.59	-10000	0	-1.3	199	199
T-helper cell lineage commitment	0	0	-10000	0	-10000	0	0
IL24	-0.32	0.53	-10000	0	-1.2	168	168
TYK2	0.011	0.047	-10000	0	-0.88	2	2
STAT4	-0.052	0.23	-10000	0	-0.84	71	71
STAT3	0.016	0.001	-10000	0	-10000	0	0
IL18RAP	-0.04	0.21	-10000	0	-0.8	60	60
IL12RB1	-0.042	0.21	-10000	0	-0.84	58	58
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
IL12Rbeta1/TYK2	-0.035	0.17	-10000	0	-0.66	60	60
IL23R/JAK2	-0.037	0.15	-10000	0	-0.63	14	14
positive regulation of chronic inflammatory response	-0.4	0.64	-10000	0	-1.3	220	220
natural killer cell activation	0.004	0.011	0.054	18	-10000	0	18
JAK2	0.017	0.042	-10000	0	-0.87	1	1
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
NFKB1	0.014	0.029	-10000	0	-0.85	1	1
RELA	0.015	0.004	-10000	0	-10000	0	0
positive regulation of dendritic cell antigen processing and presentation	-0.34	0.51	-10000	0	-1.1	193	193
ALOX12B	-0.38	0.59	-10000	0	-1.3	208	208
CXCL1	-0.48	0.65	-10000	0	-1.3	271	271
T cell proliferation	-0.4	0.64	-10000	0	-1.3	220	220
NFKBIA	0.015	0.004	-10000	0	-10000	0	0
IL17A	-0.14	0.3	-10000	0	-0.6	101	101
PI3K	-0.41	0.51	-10000	0	-1.2	220	220
IFNG	-0.026	0.056	0.12	8	-0.12	141	149
STAT3 (dimer)	-0.39	0.47	-10000	0	-1.1	211	211
IL18R1	-0.065	0.25	-10000	0	-0.84	82	82
IL23/IL23R/JAK2/TYK2/SOCS3	-0.2	0.38	-10000	0	-0.95	101	101
IL18/IL18R	-0.09	0.27	-10000	0	-0.68	133	133
macrophage activation	-0.019	0.018	-10000	0	-0.044	168	168
TNF	-0.37	0.6	-10000	0	-1.3	208	208
STAT3/STAT4	-0.42	0.53	-10000	0	-1.2	224	224
STAT4 (dimer)	-0.39	0.62	-10000	0	-1.3	223	223
IL18	-0.02	0.16	-10000	0	-0.72	42	42
IL19	-0.33	0.52	-10000	0	-1.1	195	195
STAT5A (dimer)	-0.38	0.6	-10000	0	-1.3	213	213
STAT1	0.009	0.074	-10000	0	-0.72	9	9
SOCS3	-0.033	0.19	-10000	0	-0.78	55	55
CXCL9	-0.47	0.66	-10000	0	-1.3	268	268
MPO	-0.35	0.55	-10000	0	-1.2	192	192
positive regulation of humoral immune response	-0.4	0.64	-10000	0	-1.3	220	220
IL23/IL23R/JAK2/TYK2	-0.45	0.79	-10000	0	-1.5	218	218
IL6	-0.44	0.62	-10000	0	-1.3	250	250
STAT5A	0.013	0.05	-10000	0	-0.85	3	3
IL2	-0.001	0.078	-10000	0	-0.66	12	12
positive regulation of tyrosine phosphorylation of STAT protein	0.004	0.011	0.054	18	-10000	0	18
CD3E	-0.37	0.59	-10000	0	-1.3	179	179
keratinocyte proliferation	-0.4	0.64	-10000	0	-1.3	220	220
NOS2	-0.39	0.59	-10000	0	-1.2	230	230

×

HIF-2-alpha transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MMP14	-0.039	0.18	-10000	0	-1.2	17	17
oxygen homeostasis	-0.002	0.021	-10000	0	-10000	0	0
TCEB2	0.009	0.071	-10000	0	-0.72	8	8
TCEB1	0.016	0	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C/HIF2A	-0.14	0.21	-10000	0	-0.52	161	161
EPO	-0.31	0.43	-10000	0	-0.82	262	262
FIH (dimer)	0.015	0.019	-10000	0	-10000	0	0
APEX1	0.01	0.019	-10000	0	-10000	0	0
SERPINE1	-0.34	0.55	-10000	0	-1.1	247	247
FLT1	-0.44	0.72	-10000	0	-1.6	244	244
ADORA2A	-0.24	0.47	-10000	0	-0.9	232	232
germ cell development	-0.28	0.49	-10000	0	-0.93	269	269
SLC11A2	-0.25	0.47	-10000	0	-0.94	221	221
BHLHE40	-0.25	0.48	-10000	0	-0.94	219	219
HIF1AN	0.015	0.019	-10000	0	-10000	0	0
HIF2A/ARNT/SIRT1	-0.22	0.27	-10000	0	-0.64	206	206
ETS1	-0.013	0.18	-10000	0	-0.86	38	38
CITED2	-0.018	0.057	-10000	0	-1.4	1	1
KDR	-0.44	0.71	-10000	0	-1.6	239	239
PGK1	-0.25	0.48	-10000	0	-0.94	223	223
SIRT1	0.013	0.029	-10000	0	-0.85	1	1
response to hypoxia	-0.004	0.008	-10000	0	-10000	0	0
HIF2A/ARNT	-0.34	0.64	-10000	0	-1.2	254	254
EPAS1	-0.12	0.29	-10000	0	-0.55	225	225
SP1	0.026	0.004	-10000	0	-10000	0	0
ABCG2	-0.28	0.5	-10000	0	-0.98	239	239
EFNA1	-0.26	0.48	-10000	0	-0.95	223	223
FXN	-0.23	0.47	-10000	0	-0.88	242	242
POU5F1	-0.3	0.52	-10000	0	-0.98	281	281
neuron apoptosis	0.31	0.58	1.1	254	-10000	0	254
EP300	0.014	0.041	-10000	0	-0.85	2	2
EGLN3	-0.22	0.39	-10000	0	-0.87	236	236
EGLN2	0.012	0.051	-10000	0	-0.8	3	3
EGLN1	0.015	0.019	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C	-0.007	0.062	-10000	0	-0.62	7	7
VHL	0.012	0.058	-10000	0	-0.85	4	4
ARNT	0.01	0.02	-10000	0	-10000	0	0
SLC2A1	-0.26	0.51	-10000	0	-0.98	237	237
TWIST1	-0.27	0.51	-10000	0	-0.96	245	245
ELK1	0.026	0.001	-10000	0	-10000	0	0
HIF2A/ARNT/Cbp/p300	-0.2	0.27	-10000	0	-0.64	192	192
VEGFA	-0.34	0.58	-10000	0	-1.1	285	285
CREBBP	0.016	0	-10000	0	-10000	0	0

×

PDGFR-alpha signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.18	0.34	-9999	-0.75	228	228
PDGF/PDGFRA/CRKL	-0.14	0.25	-9999	-0.55	228	228
positive regulation of JUN kinase activity	-0.11	0.19	-9999	-0.49	116	116
CRKL	0.016	0	-9999	-10000	0	0
PDGF/PDGFRA/Caveolin-3	-0.15	0.26	-9999	-0.57	233	233
AP1	-0.21	0.37	-9999	-1.2	78	78
mol:IP3	-0.13	0.27	-9999	-0.57	228	228
PLCG1	-0.13	0.27	-9999	-0.57	228	228
PDGF/PDGFRA/alphaV Integrin	-0.15	0.25	-9999	-0.56	232	232
RAPGEF1	0.016	0	-9999	-10000	0	0
CRK	0.015	0.022	-9999	-0.65	1	1
mol:Ca2+	-0.13	0.26	-9999	-0.57	228	228
CAV3	-0.004	0.073	-9999	-0.65	11	11
CAV1	-0.081	0.27	-9999	-0.84	101	101
SHC/Grb2/SOS1	-0.11	0.19	-9999	-0.5	116	116
PDGF/PDGFRA/Shf	-0.15	0.25	-9999	-0.56	232	232
FOS	-0.16	0.38	-9999	-1.2	78	78
JUN	-0.019	0.058	-9999	-0.63	7	7
oligodendrocyte development	-0.15	0.25	-9999	-0.56	232	232
GRB2	0.016	0	-9999	-10000	0	0
PIK3R1	0.011	0.066	-9999	-0.78	6	6
mol:DAG	-0.13	0.27	-9999	-0.57	228	228
PDGF/PDGFRA	-0.18	0.34	-9999	-0.75	228	228
actin cytoskeleton reorganization	-0.14	0.25	-9999	-0.56	228	228
SRF	0.032	0.01	-9999	-10000	0	0
SHC1	0.015	0.022	-9999	-0.65	1	1
PI3K	-0.13	0.22	-9999	-0.54	141	141
PDGF/PDGFRA/Crk/C3G	-0.12	0.21	-9999	-0.54	133	133
JAK1	-0.12	0.26	-9999	-0.55	228	228
ELK1/SRF	-0.065	0.2	-9999	-0.55	25	25
SHB	0.015	0.029	-9999	-0.85	1	1
SHF	0.011	0.066	-9999	-0.78	6	6
CSNK2A1	0.017	0.024	-9999	-10000	0	0
GO:0007205	-0.12	0.26	-9999	-0.56	228	228
SOS1	0.016	0	-9999	-10000	0	0
Ras protein signal transduction	-0.11	0.19	-9999	-0.49	116	116
PDGF/PDGFRA/SHB	-0.14	0.25	-9999	-0.56	228	228
PDGF/PDGFRA/Caveolin-1	-0.21	0.31	-9999	-0.62	307	307
ITGAV	0.009	0.074	-9999	-0.82	7	7
ELK1	-0.1	0.24	-9999	-0.58	132	132
PIK3CA	0.01	0.071	-9999	-0.85	6	6
PDGF/PDGFRA/Crk	-0.14	0.25	-9999	-0.56	228	228
JAK-STAT cascade	-0.12	0.26	-9999	-0.55	228	228
cell proliferation	-0.15	0.25	-9999	-0.56	232	232

×

S1P1 pathway

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
VEGFR2 homodimer/VEGFA homodimer	-0.32	0.5	-9999	-1	276	276
PDGFRB	-0.12	0.31	-9999	-0.84	140	140
SPHK1	-0.057	0.15	-9999	-0.51	57	57
mol:S1P	-0.056	0.14	-9999	-0.55	39	39
S1P1/S1P/Gi	-0.15	0.34	-9999	-0.7	186	186
GNAO1	-0.053	0.22	-9999	-0.76	79	79
PDGFB-D/PDGFRB/PLCgamma1	-0.15	0.37	-9999	-0.87	155	155
PLCG1	-0.13	0.32	-9999	-0.73	148	148
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	-0.12	0.31	-9999	-0.84	140	140
GNAI2	0.014	0.03	-9999	-0.86	1	1
GNAI3	0.013	0.008	-9999	-10000	0	0
GNAI1	0.001	0.1	-9999	-0.85	12	12
mol:GDP	0	0	-9999	-10000	0	0
EDG1	-0.27	0.46	-9999	-0.92	276	276
S1P1/S1P	-0.26	0.38	-9999	-0.8	279	279
negative regulation of cAMP metabolic process	-0.14	0.32	-9999	-0.66	186	186
MAPK3	-0.15	0.35	-9999	-0.9	113	113
calcium-dependent phospholipase C activity	-0.002	0.004	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
RhoA/GDP	0	0	-9999	-10000	0	0
KDR	-0.22	0.38	-9999	-0.84	242	242
PLCB2	-0.2	0.35	-9999	-0.71	258	258
RAC1	0.016	0	-9999	-10000	0	0
RhoA/GTP	-0.2	0.29	-9999	-0.65	249	249
receptor internalization	-0.23	0.34	-9999	-0.71	279	279
PTGS2	-0.16	0.38	-9999	-1	112	112
Rac1/GTP	-0.2	0.29	-9999	-0.65	249	249
RHOA	0.016	0	-9999	-10000	0	0
VEGFA	-0.21	0.38	-9999	-0.85	236	236
negative regulation of T cell proliferation	-0.14	0.32	-9999	-0.66	186	186
GO:0007205	0	0	-9999	-10000	0	0
GNAZ	0.004	0.086	-9999	-0.79	10	10
MAPK1	-0.15	0.35	-9999	-0.9	113	113
S1P1/S1P/PDGFB-D/PDGFRB	-0.27	0.48	-9999	-1	244	244
ABCC1	0.014	0.029	-9999	-0.86	1	1

×

p75(NTR)-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Sortilin/TRAF6	-0.002	0.038	-9999	-0.65	3	3
Necdin/E2F1	-0.063	0.19	-9999	-0.65	87	87
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E	-0.19	0.31	-9999	-0.93	94	94
NGF (dimer)/p75(NTR)/BEX1	-0.37	0.39	-9999	-0.66	501	501
NT-4/5 (dimer)/p75(NTR)	-0.15	0.28	-9999	-0.65	202	202
IKBKB	0.016	0	-9999	-10000	0	0
AKT1	-0.15	0.33	-9999	-0.66	219	219
IKBKG	0.013	0.05	-9999	-0.85	3	3
BDNF	-0.11	0.29	-9999	-0.78	140	140
MGDIs/NGR/p75(NTR)/LINGO1	-0.21	0.35	-9999	-0.77	215	215
FURIN	0.014	0.041	-9999	-0.85	2	2
proBDNF (dimer)/p75(NTR)/Sortilin	-0.18	0.28	-9999	-0.63	220	220
LINGO1	-0.14	0.33	-9999	-0.82	166	166
Sortilin/TRAF6/NRIF	-0.006	0.051	-9999	-0.84	1	1
proBDNF (dimer)	-0.11	0.29	-9999	-0.77	140	140
NTRK1	-0.033	0.18	-9999	-0.69	60	60
RTN4R	0.002	0.1	-9999	-0.73	17	17
neuron apoptosis	-0.14	0.31	-9999	-0.76	124	124
IRAK1	0.015	0.029	-9999	-0.85	1	1
SHC1	-0.19	0.36	-9999	-0.68	278	278
ARHGDIA	0.014	0.041	-9999	-0.85	2	2
RhoA/GTP	0	0	-9999	-10000	0	0
Gamma Secretase	-0.004	0.045	-9999	-0.48	8	8
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1	-0.2	0.33	-9999	-0.72	212	212
MAGEH1	0.011	0.062	-9999	-0.81	5	5
proNGF (dimer)/p75(NTR)/Sortilin/Necdin	-0.24	0.39	-9999	-0.81	236	236
Mammalian IAPs/DIABLO	-0.048	0.14	-9999	-0.51	70	70
proNGF (dimer)	-0.16	0.34	-9999	-0.8	189	189
MAGED1	0.015	0.032	-9999	-0.65	2	2
APP	0.014	0.041	-9999	-0.85	2	2
NT-4/5 (dimer)	-0.031	0.15	-9999	-0.65	50	50
ZNF274	0.015	0.029	-9999	-0.85	1	1
RhoA/GDP/RHOGDI	-0.18	0.31	-9999	-0.68	210	210
NGF	-0.16	0.34	-9999	-0.8	189	189
cell cycle arrest	-0.13	0.34	-9999	-0.66	211	211
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK	-0.1	0.24	-9999	-0.48	219	219
NT-4/5 (dimer)/p75(NTR)/TRAF6	-0.13	0.25	-9999	-0.56	202	202
NCSTN	0.015	0.029	-9999	-0.85	1	1
mol:GTP	-0.21	0.35	-9999	-0.68	277	277
PSENEN	0.016	0	-9999	-10000	0	0
mol:ceramide	-0.16	0.34	-9999	-0.71	211	211
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs	-0.067	0.2	-9999	-0.55	94	94
p75(NTR)/beta APP	-0.12	0.25	-9999	-0.62	178	178
BEX1	-0.25	0.36	-9999	-0.74	311	311
mol:GDP	-0.2	0.36	-9999	-0.69	277	277
NGF (dimer)	-0.42	0.35	-9999	-0.73	402	402
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI	-0.2	0.33	-9999	-0.71	215	215
PIK3R1	0.011	0.066	-9999	-0.78	6	6
RAC1/GTP	-0.19	0.31	-9999	-0.6	277	277
MYD88	0.002	0.11	-9999	-0.85	14	14
CHUK	0.015	0.029	-9999	-0.85	1	1
NGF (dimer)/p75(NTR)/PKA	-0.21	0.35	-9999	-0.68	277	277
RHOB	-0.005	0.13	-9999	-0.82	22	22
RHOA	0.016	0	-9999	-10000	0	0
MAGE-G1/E2F1	-0.004	0.047	-9999	-0.5	8	8
NT3 (dimer)	-0.074	0.26	-9999	-0.79	99	99
TP53	-0.11	0.26	-9999	-0.82	34	34
PRDM4	-0.17	0.34	-9999	-0.71	211	211
BDNF (dimer)	-0.42	0.35	-9999	-0.76	368	368
PIK3CA	0.01	0.071	-9999	-0.85	6	6
SORT1	0.013	0.05	-9999	-0.85	3	3
activation of caspase activity	-0.18	0.3	-9999	-0.91	94	94
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.2	0.33	-9999	-0.72	210	210
RHOC	0.016	0	-9999	-10000	0	0
XIAP	0.016	0	-9999	-10000	0	0
MAPK10	-0.14	0.29	-9999	-0.71	127	127
DIABLO	0.016	0	-9999	-10000	0	0
SMPD2	-0.17	0.34	-9999	-0.71	211	211
APH1B	0.009	0.076	-9999	-0.85	7	7
APH1A	0.016	0	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin	-0.21	0.35	-9999	-0.78	210	210
PSEN1	0.016	0	-9999	-10000	0	0
APAF-1/Pro-Caspase 9	-0.001	0.022	-9999	-0.65	1	1
NT3 (dimer)/p75(NTR)	-0.18	0.34	-9999	-0.72	226	226
MAPK8	-0.13	0.29	-9999	-0.72	121	121
MAPK9	-0.13	0.29	-9999	-0.71	119	119
APAF1	0.015	0.029	-9999	-0.85	1	1
NTF3	-0.074	0.26	-9999	-0.79	99	99
NTF4	-0.031	0.15	-9999	-0.65	50	50
NDN	-0.062	0.25	-9999	-0.84	81	81
RAC1/GDP	0	0	-9999	-10000	0	0
RhoA-B-C/GDP	-0.18	0.3	-9999	-0.88	100	100
p75 CTF/Sortilin/TRAF6/NRIF	-0.005	0.048	-9999	-0.51	8	8
RhoA-B-C/GTP	-0.21	0.34	-9999	-0.67	277	277
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.16	0.24	-9999	-0.86	34	34
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.17	0.26	-9999	-0.57	220	220
PRKACB	0.016	0	-9999	-10000	0	0
proBDNF (dimer)/p75 ECD	-0.095	0.22	-9999	-0.59	143	143
ChemicalAbstracts:86-01-1	0	0	-9999	-10000	0	0
BIRC3	-0.066	0.25	-9999	-0.81	89	89
BIRC2	0.016	0	-9999	-10000	0	0
neuron projection morphogenesis	-0.14	0.38	-9999	-0.77	185	185
BAD	-0.12	0.28	-9999	-0.68	122	122
RIPK2	0.015	0.022	-9999	-0.65	1	1
NGFR	-0.15	0.33	-9999	-0.81	177	177
CYCS	-0.16	0.33	-9999	-0.68	217	217
ADAM17	0.012	0.058	-9999	-0.85	4	4
NGF (dimer)/p75(NTR)/TRAF6/RIP2	-0.2	0.32	-9999	-0.72	209	209
BCL2L11	-0.12	0.28	-9999	-0.68	122	122
BDNF (dimer)/p75(NTR)	-0.21	0.32	-9999	-0.66	287	287
PI3K	-0.2	0.33	-9999	-0.71	218	218
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1	-0.2	0.33	-9999	-0.72	210	210
NDNL2	0.016	0	-9999	-10000	0	0
YWHAE	0.016	0	-9999	-10000	0	0
PRKCI	0.015	0.022	-9999	-0.65	1	1
NGF (dimer)/p75(NTR)	-0.24	0.39	-9999	-0.77	277	277
ChemicalAbstracts:146-91-8	0	0	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE	-0.2	0.33	-9999	-0.72	210	210
TRAF6	0.016	0	-9999	-10000	0	0
RAC1	0.016	0	-9999	-10000	0	0
PRKCZ	0.008	0.082	-9999	-0.85	8	8
PLG	-0.28	0.36	-9999	-0.72	347	347
oligodendrocyte cell fate commitment	0	0	-9999	-10000	0	0
CASP6	-0.22	0.37	-9999	-0.85	176	176
SQSTM1	0.009	0.067	-9999	-0.65	9	9
NGFRAP1	0.011	0.065	-9999	-0.85	5	5
CASP3	-0.1	0.26	-9999	-0.61	119	119
E2F1	0.01	0.066	-9999	-0.68	8	8
CASP9	0.016	0	-9999	-10000	0	0
IKK complex	-0.15	0.25	-9999	-0.63	158	158
NGF (dimer)/TRKA	-0.16	0.28	-9999	-0.62	234	234
MMP7	-0.25	0.37	-9999	-0.75	312	312
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.19	0.31	-9999	-0.93	94	94
MMP3	-0.043	0.17	-9999	-0.65	67	67
APAF-1/Caspase 9	-0.17	0.25	-9999	-0.7	120	120

×

Signaling events mediated by the Hedgehog family

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB2	-0.23	0.34	-10000	0	-0.88	101	101
IHH	-0.17	0.32	-10000	0	-0.81	176	176
SHH Np/Cholesterol/GAS1	-0.081	0.19	-10000	0	-0.58	76	76
LRPAP1	0.014	0.041	-10000	0	-0.85	2	2
dorsoventral neural tube patterning	0.081	0.19	0.58	76	-10000	0	76
SMO/beta Arrestin2	-0.15	0.25	-10000	0	-0.66	95	95
SMO	-0.16	0.26	-10000	0	-0.64	142	142
AKT1	-0.053	0.13	-10000	0	-0.69	8	8
ARRB2	0.016	0	-10000	0	-10000	0	0
BOC	-0.004	0.13	-10000	0	-0.84	21	21
ADRBK1	0.014	0.041	-10000	0	-0.85	2	2
heart looping	-0.16	0.26	-10000	0	-0.62	142	142
STIL	-0.16	0.25	-10000	0	-0.66	103	103
DHH N/PTCH2	-0.068	0.19	-10000	0	-0.6	101	101
DHH N/PTCH1	-0.17	0.26	-10000	0	-0.66	121	121
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
DHH	-0.04	0.2	-10000	0	-0.77	63	63
PTHLH	-0.4	0.54	-10000	0	-1.2	215	215
determination of left/right symmetry	-0.16	0.26	-10000	0	-0.62	142	142
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
skeletal system development	-0.39	0.52	-10000	0	-1.2	215	215
IHH N/Hhip	-0.21	0.32	-10000	0	-0.63	292	292
DHH N/Hhip	-0.15	0.26	-10000	0	-0.57	227	227
mol:Cholesterol	0	0	-10000	0	-10000	0	0
heart development	-0.16	0.26	-10000	0	-0.62	142	142
pancreas development	-0.13	0.29	-10000	0	-0.7	180	180
HHAT	0.009	0.076	-10000	0	-0.85	7	7
PI3K	-0.008	0.072	-10000	0	-0.62	12	12
EntrezGene:84976	0	0	-10000	0	-10000	0	0
GAS1	-0.011	0.14	-10000	0	-0.71	33	33
somite specification	-0.16	0.26	-10000	0	-0.62	142	142
SHH Np/Cholesterol/PTCH1	-0.17	0.26	-10000	0	-0.66	125	125
SHH Np/Cholesterol/PTCH2	-0.088	0.2	-10000	0	-0.57	88	88
SHH Np/Cholesterol/Megalin	-0.15	0.28	-10000	0	-0.65	177	177
SHH	-0.06	0.22	-10000	0	-0.58	128	128
catabolic process	-0.16	0.25	-10000	0	-0.59	151	151
SMO/Vitamin D3	-0.18	0.28	-10000	0	-0.69	127	127
SHH Np/Cholesterol/Hhip	-0.15	0.25	-10000	0	-0.64	132	132
LRP2	-0.13	0.32	-10000	0	-0.84	153	153
receptor-mediated endocytosis	-0.25	0.29	-10000	0	-0.76	163	163
SHH Np/Cholesterol/BOC	-0.078	0.18	-10000	0	-0.48	146	146
SHH Np/Cholesterol/CDO	-0.091	0.2	-10000	0	-0.57	99	99
mesenchymal cell differentiation	0.15	0.25	0.63	132	-10000	0	132
mol:Vitamin D3	-0.17	0.27	-10000	0	-0.67	125	125
IHH N/PTCH2	-0.12	0.26	-10000	0	-0.57	208	208
CDON	-0.026	0.18	-10000	0	-0.8	46	46
IHH N/PTCH1	-0.16	0.25	-10000	0	-0.6	151	151
Megalin/LRPAP1	-0.11	0.25	-10000	0	-0.65	155	155
PTCH2	-0.021	0.17	-10000	0	-0.78	41	41
SHH Np/Cholesterol	-0.068	0.17	-10000	0	-0.47	128	128
PTCH1	-0.16	0.25	-10000	0	-0.6	151	151
HHIP	-0.13	0.29	-10000	0	-0.71	180	180

×

LPA4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ADCY4	-0.038	0.18	-9999	-0.56	96	96
ADCY5	-0.05	0.2	-9999	-0.58	110	110
ADCY6	0.023	0.047	-9999	-0.74	3	3
ADCY7	0.023	0.047	-9999	-0.74	3	3
ADCY1	-0.12	0.25	-9999	-0.53	239	239
ADCY2	-0.16	0.26	-9999	-0.52	304	304
ADCY3	0.008	0.1	-9999	-0.57	26	26
ADCY8	-0.15	0.24	-9999	-0.47	316	316
PRKCE	0.012	0.039	-9999	-0.66	3	3
ADCY9	0.023	0.04	-9999	-0.57	4	4
mol:DAG	0	0	-9999	-10000	0	0
cAMP biosynthetic process	-0.17	0.2	-9999	-0.5	166	166

×

TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC	-0.15	0.26	-10000	0	-0.66	161	161
FYN	-0.14	0.4	-10000	0	-0.9	172	172
LAT/GRAP2/SLP76	-0.17	0.31	-10000	0	-0.77	160	160
IKBKB	0.016	0	-10000	0	-10000	0	0
AKT1	-0.059	0.25	-10000	0	-0.52	168	168
B2M	0.012	0.051	-10000	0	-0.85	3	3
IKBKG	-0.035	0.058	-10000	0	-0.19	40	40
MAP3K8	0.012	0.059	-10000	0	-0.77	5	5
mol:Ca2+	-0.024	0.048	-10000	0	-0.13	131	131
integrin-mediated signaling pathway	-0.02	0.1	-10000	0	-0.57	31	31
LAT/GRAP2/SLP76/VAV1/PI3K Class IA	-0.12	0.38	-10000	0	-0.83	173	173
TRPV6	-0.095	0.24	-10000	0	-0.67	129	129
CD28	-0.038	0.21	-10000	0	-0.81	58	58
SHC1	-0.14	0.4	-10000	0	-0.9	168	168
receptor internalization	-0.18	0.45	-10000	0	-0.95	194	194
PRF1	-0.17	0.47	-10000	0	-1.2	133	133
KRAS	0.016	0	-10000	0	-10000	0	0
GRB2	0.016	0	-10000	0	-10000	0	0
COT/AKT1	-0.034	0.2	-10000	0	-0.41	151	151
LAT	-0.16	0.41	-10000	0	-0.92	174	174
EntrezGene:6955	0	0.004	-10000	0	-10000	0	0
CD3D	-0.11	0.3	-10000	0	-0.8	141	141
CD3E	-0.096	0.28	-10000	0	-0.8	123	123
CD3G	-0.14	0.32	-10000	0	-0.79	175	175
RASGRP2	-0.003	0.049	-10000	0	-0.19	41	41
RASGRP1	-0.056	0.25	-10000	0	-0.52	158	158
HLA-A	0.012	0.051	-10000	0	-0.86	3	3
RASSF5	-0.014	0.16	-10000	0	-0.84	31	31
RAP1A/GTP/RAPL	-0.02	0.1	-10000	0	-0.57	31	31
mol:GTP	0	0	-10000	0	-10000	0	0
mol:GDP	0.013	0.078	-10000	0	-0.15	48	48
PDK1/CARD11/BCL10/MALT1/TRAF6	-0.064	0.1	-10000	0	-0.34	49	49
PRKCA	-0.066	0.12	-10000	0	-0.32	130	130
GRAP2	-0.039	0.21	-10000	0	-0.85	57	57
mol:IP3	-0.097	0.22	0.27	65	-0.53	143	208
EntrezGene:6957	0	0.005	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.23	0.58	-10000	0	-1.2	189	189
ORAI1	0.052	0.13	0.35	125	-0.66	2	127
CSK	-0.15	0.41	-10000	0	-0.94	169	169
B7 family/CD28	-0.23	0.4	-10000	0	-0.98	174	174
CHUK	0.015	0.029	-10000	0	-0.85	1	1
TCR/CD3/MHC I/CD8/LCK/ZAP-70	-0.2	0.5	-10000	0	-1.1	194	194
PTPN6	-0.16	0.42	-10000	0	-0.95	173	173
VAV1	-0.15	0.42	-10000	0	-0.94	170	170
Monovalent TCR/CD3	-0.19	0.5	-10000	0	-0.99	192	192
CBL	0.015	0.029	-10000	0	-0.85	1	1
LCK	-0.17	0.46	-10000	0	-1	176	176
PAG1	-0.16	0.42	-10000	0	-0.95	173	173
RAP1A	0.016	0	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8/LCK	-0.2	0.5	-10000	0	-1.1	193	193
CD80	-0.054	0.23	-10000	0	-0.78	78	78
CD86	-0.019	0.17	-10000	0	-0.85	36	36
PDK1/CARD11/BCL10/MALT1	-0.079	0.13	-10000	0	-0.35	110	110
HRAS	0.012	0.059	-10000	0	-0.77	5	5
GO:0035030	-0.12	0.34	-10000	0	-0.75	172	172
CD8A	-0.15	0.32	-10000	0	-0.76	188	188
CD8B	-0.15	0.32	-10000	0	-0.76	197	197
PTPRC	-0.03	0.19	-10000	0	-0.83	47	47
PDK1/PKC theta	-0.08	0.31	-10000	0	-0.67	161	161
CSK/PAG1	-0.15	0.41	-10000	0	-0.91	173	173
SOS1	0.016	0	-10000	0	-10000	0	0
peptide-MHC class I	0.015	0.063	-10000	0	-0.77	5	5
GRAP2/SLP76	-0.19	0.36	-10000	0	-0.89	168	168
STIM1	0.027	0.074	-10000	0	-0.55	4	4
RAS family/GTP	0.012	0.1	-10000	0	-0.2	19	19
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin	-0.21	0.52	-10000	0	-1.1	194	194
mol:DAG	-0.098	0.18	0.19	2	-0.46	151	153
RAP1A/GDP	0.008	0.034	-10000	0	-10000	0	0
PLCG1	0.016	0	-10000	0	-10000	0	0
CD247	-0.052	0.23	-10000	0	-0.82	73	73
cytotoxic T cell degranulation	-0.15	0.43	-10000	0	-1.1	134	134
RAP1A/GTP	-0.005	0.015	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	-0.084	0.3	-10000	0	-0.64	172	172
LAT/GRAP2/SLP76/VAV1/PLCgamma1	-0.14	0.3	0.29	63	-0.72	149	212
NRAS	0.016	0	-10000	0	-10000	0	0
ZAP70	-0.054	0.23	-10000	0	-0.79	77	77
GRB2/SOS1	0	0	-10000	0	-10000	0	0
LAT/GRAP2/SLP76/VAV1	-0.15	0.28	-10000	0	-0.72	155	155
MALT1	0.015	0.029	-10000	0	-0.85	1	1
TRAF6	0.016	0	-10000	0	-10000	0	0
CD8 heterodimer	-0.21	0.42	-10000	0	-0.9	225	225
CARD11	-0.052	0.22	-10000	0	-0.74	81	81
PRKCB	-0.077	0.15	-10000	0	-0.4	124	124
PRKCE	-0.066	0.13	-10000	0	-0.32	124	124
PRKCQ	-0.11	0.36	-10000	0	-0.78	172	172
LCP2	-0.028	0.19	-10000	0	-0.84	46	46
BCL10	0.016	0	-10000	0	-10000	0	0
regulation of survival gene product expression	-0.043	0.21	-10000	0	-0.43	166	166
IKK complex	0.025	0.078	-10000	0	-0.13	44	44
RAS family/GDP	-0.006	0.012	-10000	0	-0.098	4	4
MAP3K14	-0.02	0.17	-10000	0	-0.37	115	115
PDPK1	-0.051	0.24	-10000	0	-0.5	157	157
TCR/CD3/MHC I/CD8/Fyn	-0.22	0.53	-10000	0	-1.1	200	200

×

amb2 Integrin 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
alphaM/beta2 Integrin/proMMP-2	-0.088	0.26	-9999	-0.74	97	97
alphaM/beta2 Integrin/GPIbA	-0.07	0.23	-9999	-0.82	65	65
alphaM/beta2 Integrin/proMMP-9	-0.16	0.31	-9999	-0.69	164	164
PLAUR	-0.01	0.14	-9999	-0.72	31	31
HMGB1	0.006	0.021	-9999	-10000	0	0
alphaM/beta2 Integrin/Talin	-0.059	0.22	-9999	-0.9	50	50
AGER	-0.03	0.16	-9999	-0.76	41	41
RAP1A	0.016	0	-9999	-10000	0	0
SELPLG	-0.005	0.13	-9999	-0.85	22	22
mol:LDL	0	0	-9999	-10000	0	0
alphaM/beta2 Integrin/RAGE/HMGB1	-0.12	0.26	-9999	-0.92	65	65
mol:GTP	0	0	-9999	-10000	0	0
MMP9	-0.15	0.31	-9999	-0.73	194	194
CYR61	-0.051	0.22	-9999	-0.79	74	74
TLN1	0.015	0.029	-9999	-0.85	1	1
Rap1/GTP	-0.18	0.23	-9999	-0.6	140	140
RHOA	0.016	0	-9999	-10000	0	0
P-selectin oligomer	-0.044	0.22	-9999	-0.8	65	65
MYH2	-0.23	0.28	-9999	-0.64	198	198
MST1R	-0.091	0.26	-9999	-0.7	133	133
leukocyte activation during inflammatory response	-0.22	0.28	-9999	-0.63	195	195
APOB	-0.26	0.37	-9999	-0.74	322	322
mol:GDP	0	0	-9999	-10000	0	0
complement component iC3b receptor activity	0	0	-9999	-10000	0	0
MMP2	-0.032	0.18	-9999	-0.73	57	57
JAM3	-0.06	0.24	-9999	-0.84	79	79
GP1BA	-0.002	0.12	-9999	-0.79	20	20
alphaM/beta2 Integrin/CTGF	-0.074	0.24	-9999	-0.86	65	65
alphaM/beta2 Integrin	-0.21	0.31	-9999	-0.62	205	205
JAM3 homodimer	-0.06	0.24	-9999	-0.84	79	79
ICAM2	0.009	0.074	-9999	-0.82	7	7
ICAM1	-0.028	0.19	-9999	-0.84	46	46
phagocytosis triggered by activation of immune response cell surface activating receptor	-0.2	0.29	-9999	-0.61	205	205
cell adhesion	-0.069	0.22	-9999	-0.81	65	65
NFKB1	-0.12	0.33	-9999	-0.99	71	71
THY1	-0.11	0.3	-9999	-0.83	130	130
RhoA/GDP	0	0	-9999	-10000	0	0
Lipoprotein(a)	-0.2	0.25	-9999	-0.5	364	364
alphaM/beta2 Integrin/LRP/tPA	-0.067	0.24	-9999	-0.86	63	63
IL6	-0.21	0.43	-9999	-1	143	143
ITGB2	-0.031	0.18	-9999	-0.85	38	38
elevation of cytosolic calcium ion concentration	-0.08	0.26	-9999	-0.98	55	55
alphaM/beta2 Integrin/JAM2/JAM3	-0.11	0.28	-9999	-0.71	135	135
JAM2	-0.013	0.15	-9999	-0.82	31	31
alphaM/beta2 Integrin/ICAM1	-0.15	0.32	-9999	-0.98	80	80
alphaM/beta2 Integrin/uPA/Plg	-0.23	0.31	-9999	-0.69	176	176
RhoA/GTP	-0.24	0.3	-9999	-0.68	198	198
positive regulation of phagocytosis	-0.16	0.24	-9999	-0.83	77	77
Ron/MSP	-0.11	0.23	-9999	-0.56	174	174
alphaM/beta2 Integrin/uPAR/uPA	-0.082	0.27	-9999	-1	55	55
alphaM/beta2 Integrin/uPAR	-0.073	0.25	-9999	-0.89	62	62
PLAU	-0.019	0.16	-9999	-0.7	43	43
PLAT	-0.005	0.13	-9999	-0.78	24	24
actin filament polymerization	-0.22	0.26	-9999	-0.6	202	202
MST1	-0.03	0.18	-9999	-0.76	53	53
alphaM/beta2 Integrin/lipoprotein(a)	-0.22	0.29	-9999	-0.64	195	195
TNF	-0.13	0.36	-9999	-1	90	90
RAP1B	0.016	0	-9999	-10000	0	0
alphaM/beta2 Integrin/uPA	-0.079	0.26	-9999	-0.89	64	64
fibrinolysis	-0.23	0.3	-9999	-0.68	176	176
HCK	-0.005	0.13	-9999	-0.83	22	22
dendritic cell antigen processing and presentation	-0.2	0.29	-9999	-0.61	205	205
VTN	-0.11	0.27	-9999	-0.69	161	161
alphaM/beta2 Integrin/CYR61	-0.1	0.29	-9999	-0.85	93	93
LPA	-0.034	0.16	-9999	-0.65	54	54
LRP1	0.005	0.095	-9999	-0.85	11	11
cell migration	-0.17	0.32	-9999	-0.79	133	133
FN1	-0.11	0.29	-9999	-0.79	137	137
alphaM/beta2 Integrin/Thy1	-0.14	0.29	-9999	-0.7	168	168
MPO	-0.045	0.2	-9999	-0.7	75	75
KNG1	-0.18	0.32	-9999	-0.71	238	238
RAP1/GDP	0	0	-9999	-10000	0	0
ROCK1	-0.22	0.28	-9999	-0.64	190	190
ELA2	0	0	-9999	-10000	0	0
PLG	-0.28	0.36	-9999	-0.72	347	347
CTGF	-0.01	0.14	-9999	-0.72	31	31
alphaM/beta2 Integrin/Hck	-0.07	0.26	-9999	-1	55	55
ITGAM	-0.035	0.18	-9999	-0.84	42	42
alphaM/beta2 Integrin/P-Selectin/PSGL1	-0.095	0.3	-9999	-0.9	86	86
HP	-0.24	0.35	-9999	-0.72	307	307
leukocyte adhesion	-0.21	0.35	-9999	-0.91	148	148
SELP	-0.044	0.22	-9999	-0.8	65	65

×

EGFR-dependent Endothelin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HRAS	0.012	0.059	-9999	-0.77	5	5
EGFR	-0.021	0.17	-9999	-0.78	41	41
EGF/EGFR	-0.28	0.34	-9999	-0.64	341	341
EGF/EGFR dimer/SHC/GRB2/SOS1	-0.1	0.19	-9999	-0.53	104	104
mol:GTP	0	0	-9999	-10000	0	0
EDNRA	-0.18	0.36	-9999	-0.84	198	198
response to oxidative stress	0	0	-9999	-10000	0	0
EGF	-0.15	0.31	-9999	-0.73	196	196
EGF/EGFR dimer/SHC	-0.13	0.23	-9999	-0.5	223	223
mol:GDP	-0.1	0.19	-9999	-0.52	104	104
mol:Ca2+	0	0	-9999	-10000	0	0
EDN1	-0.12	0.31	-9999	-0.81	147	147
GRB2/SOS1	0	0	-9999	-10000	0	0
HRAS/GTP	-0.097	0.18	-9999	-0.76	16	16
SHC1	0.015	0.022	-9999	-0.65	1	1
HRAS/GDP	-0.099	0.18	-9999	-0.77	16	16
FRAP1	-0.065	0.2	-9999	-0.5	104	104
EGF/EGFR dimer	-0.15	0.26	-9999	-0.58	222	222
SOS1	0.016	0	-9999	-10000	0	0
GRB2	0.016	0	-9999	-10000	0	0
ETA receptor/Endothelin-1	-0.24	0.35	-9999	-0.71	303	303

×

IL12-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1	-0.098	0.24	-10000	0	-0.58	112	112
TBX21	-0.19	0.56	-10000	0	-1.3	147	147
B2M	0.012	0.051	-10000	0	-0.85	3	3
TYK2	0.018	0.047	-10000	0	-0.86	2	2
IL12RB1	-0.034	0.21	-10000	0	-0.84	58	58
GADD45B	-0.13	0.45	-10000	0	-1	128	128
IL12RB2	-0.2	0.33	-10000	0	-0.69	275	275
GADD45G	-0.16	0.48	-10000	0	-1.1	141	141
natural killer cell activation	0.006	0.027	-10000	0	-10000	0	0
RELB	0.015	0.029	-10000	0	-0.85	1	1
RELA	0.016	0	-10000	0	-10000	0	0
IL18	-0.016	0.16	-10000	0	-0.72	42	42
IL2RA	-0.1	0.28	-10000	0	-0.76	137	137
IFNG	-0.11	0.27	-10000	0	-0.7	151	151
STAT3 (dimer)	-0.13	0.41	-10000	0	-0.89	158	158
HLA-DRB5	-0.059	0.23	-10000	0	-0.77	84	84
FASLG	-0.23	0.6	-10000	0	-1.3	175	175
NF kappa B2 p52/RelB	-0.27	0.45	-10000	0	-1.1	166	166
CD4	-0.009	0.14	-10000	0	-0.85	25	25
SOCS1	-0.038	0.19	-10000	0	-0.7	68	68
EntrezGene:6955	-0.002	0.011	-10000	0	-10000	0	0
CD3D	-0.11	0.3	-10000	0	-0.79	141	141
CD3E	-0.097	0.28	-10000	0	-0.79	123	123
CD3G	-0.14	0.32	-10000	0	-0.8	175	175
IL12Rbeta2/JAK2	-0.14	0.26	-10000	0	-0.51	276	276
CCL3	-0.2	0.56	-10000	0	-1.2	157	157
CCL4	-0.19	0.56	-10000	0	-1.3	156	156
HLA-A	0.012	0.051	-10000	0	-0.85	3	3
IL18/IL18R	-0.05	0.29	-10000	0	-0.69	137	137
NOS2	-0.22	0.59	-10000	0	-1.3	173	173
IL12/IL12R/TYK2/JAK2/SPHK2	-0.077	0.21	-10000	0	-0.55	85	85
IL1R1	-0.18	0.53	-10000	0	-1.2	147	147
IL4	-0.002	0.028	-10000	0	-10000	0	0
JAK2	0.019	0.038	-10000	0	-0.89	1	1
EntrezGene:6957	-0.002	0.011	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.34	0.78	-10000	0	-1.5	220	220
RAB7A	-0.083	0.37	-10000	0	-0.85	107	107
lysosomal transport	-0.074	0.35	-10000	0	-0.78	110	110
FOS	-0.21	0.53	-10000	0	-1.2	158	158
STAT4 (dimer)	-0.17	0.51	-10000	0	-1.1	160	160
STAT5A (dimer)	-0.31	0.48	-10000	0	-1.1	212	212
GZMA	-0.21	0.57	-10000	0	-1.3	158	158
GZMB	-0.23	0.61	-10000	0	-1.4	168	168
HLX	-0.042	0.21	-10000	0	-0.81	62	62
LCK	-0.23	0.63	-10000	0	-1.3	182	182
TCR/CD3/MHC II/CD4	-0.2	0.51	-10000	0	-1.1	169	169
IL2/IL2R	-0.16	0.33	-10000	0	-0.81	143	143
MAPK14	-0.13	0.47	-10000	0	-1	145	145
CCR5	-0.17	0.51	-10000	0	-1.2	147	147
IL1B	-0.039	0.22	-10000	0	-0.8	65	65
STAT6	-0.014	0.14	-10000	0	-10000	0	0
STAT4	-0.052	0.23	-10000	0	-0.84	71	71
STAT3	0.016	0	-10000	0	-10000	0	0
STAT1	0.009	0.074	-10000	0	-0.72	9	9
NFKB1	0.015	0.029	-10000	0	-0.85	1	1
NFKB2	0.016	0	-10000	0	-10000	0	0
IL12B	-0.032	0.19	-10000	0	-0.69	67	67
CD8A	-0.15	0.32	-10000	0	-0.76	188	188
CD8B	-0.16	0.32	-10000	0	-0.76	197	197
T-helper 1 cell differentiation	0	0	-10000	0	-10000	0	0
natural killer cell mediated cytotoxicity	0.097	0.24	0.57	112	-10000	0	112
IL2RB	-0.051	0.23	-10000	0	-0.82	72	72
proteasomal ubiquitin-dependent protein catabolic process	-0.14	0.44	-10000	0	-0.94	160	160
IL2RG	-0.061	0.24	-10000	0	-0.79	85	85
IL12	-0.022	0.17	-10000	0	-0.53	86	86
STAT5A	0.013	0.05	-10000	0	-0.85	3	3
CD247	-0.054	0.23	-10000	0	-0.82	73	73
IL2	-0.001	0.076	-10000	0	-0.65	12	12
SPHK2	0.013	0.05	-10000	0	-0.85	3	3
FRAP1	0	0	-10000	0	-10000	0	0
IL12A	0.002	0.12	-10000	0	-0.77	19	19
IL12/IL12R/TYK2/JAK2	-0.27	0.77	-10000	0	-1.5	176	176
MAP2K3	-0.14	0.48	-10000	0	-1	152	152
RIPK2	0.015	0.022	-10000	0	-0.65	1	1
MAP2K6	-0.14	0.48	-10000	0	-1	156	156
regulation of dendritic cell antigen processing and presentation	0	0	-10000	0	-10000	0	0
HLA-DRA	-0.022	0.18	-10000	0	-0.85	39	39
IL18RAP	-0.037	0.21	-10000	0	-0.8	60	60
IL12Rbeta1/TYK2	-0.018	0.18	-10000	0	-0.66	60	60
EOMES	-0.21	0.52	-10000	0	-1.2	149	149
STAT1 (dimer)	-0.17	0.43	-10000	0	-0.89	182	182
T cell proliferation	-0.083	0.36	0.53	2	-0.73	151	153
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
IL18R1	-0.061	0.25	-10000	0	-0.85	82	82
CD8-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.22	0.32	-10000	0	-0.84	154	154
ATF2	-0.12	0.43	-10000	0	-0.93	137	137

×

Glypican 2 network

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
MDK	-0.051	0.22	-9999	-0.76	77	77
GPC2	-0.028	0.18	-9999	-0.74	51	51
GPC2/Midkine	-0.081	0.21	-9999	-0.6	121	121
neuron projection morphogenesis	-0.081	0.21	-9999	-0.6	121	121

×

BMP receptor 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS	-0.36	0.34	-9999	-0.8	250	250
SMAD6-7/SMURF1	-0.003	0.042	-9999	-0.56	5	5
NOG	-0.16	0.32	-9999	-0.73	209	209
SMAD9	-0.11	0.23	-9999	-0.71	100	100
SMAD4	0.016	0	-9999	-10000	0	0
SMAD5	-0.084	0.19	-9999	-0.53	59	59
BMP7/USAG1	-0.4	0.36	-9999	-0.67	541	541
SMAD5/SKI	-0.072	0.18	-9999	-0.55	44	44
SMAD1	0.026	0.056	-9999	-0.69	2	2
BMP2	-0.015	0.16	-9999	-0.84	32	32
SMAD1/SMAD1/SMAD4	-0.004	0.042	-9999	-0.84	1	1
BMPR1A	0.015	0.029	-9999	-0.85	1	1
BMPR1B	-0.25	0.36	-9999	-0.73	317	317
BMPR1A-1B/BAMBI	-0.21	0.27	-9999	-0.52	359	359
AHSG	-0.03	0.15	-9999	-0.65	50	50
CER1	0	0.058	-9999	-0.65	7	7
BMP2-4/CER1	-0.053	0.18	-9999	-0.6	78	78
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA	-0.07	0.19	-9999	-0.6	53	53
BMP2-4 (homodimer)	-0.057	0.2	-9999	-0.69	73	73
RGMB	0.014	0.039	-9999	-0.65	3	3
BMP6/BMPR2/BMPR1A-1B	-0.16	0.22	-9999	-0.55	150	150
RGMA	-0.044	0.22	-9999	-0.8	65	65
SMURF1	0.016	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP	-0.084	0.19	-9999	-0.53	75	75
BMP2-4/USAG1	-0.24	0.3	-9999	-0.66	200	200
SMAD6/SMURF1/SMAD5	-0.071	0.18	-9999	-0.54	42	42
SOSTDC1	-0.3	0.37	-9999	-0.73	376	376
BMP7/BMPR2/BMPR1A-1B	-0.29	0.3	-9999	-0.67	266	266
SKI	0.014	0.041	-9999	-0.85	2	2
BMP6 (homodimer)	-0.008	0.14	-9999	-0.75	28	28
HFE2	-0.016	0.13	-9999	-0.65	37	37
ZFYVE16	0.016	0	-9999	-10000	0	0
MAP3K7	0.016	0	-9999	-10000	0	0
BMP2-4/CHRD	-0.12	0.27	-9999	-0.62	179	179
SMAD5/SMAD5/SMAD4	-0.071	0.18	-9999	-0.54	42	42
MAPK1	0.015	0.029	-9999	-0.85	1	1
TAK1/TAB family	-0.09	0.14	-9999	-0.49	56	56
BMP7 (homodimer)	-0.24	0.35	-9999	-0.71	316	316
NUP214	0.016	0	-9999	-10000	0	0
BMP6/FETUA	-0.045	0.15	-9999	-0.52	77	77
SMAD1/SKI	0.033	0.059	-9999	-0.57	4	4
SMAD6	0.012	0.058	-9999	-0.85	4	4
CTDSP2	0.016	0	-9999	-10000	0	0
BMP2-4/FETUA	-0.072	0.19	-9999	-0.63	71	71
MAP3K7IP1	0	0	-9999	-10000	0	0
GREM1	-0.26	0.37	-9999	-0.74	318	318
BMPR2 (homodimer)	0.015	0.029	-9999	-0.85	1	1
GADD34/PP1CA	-0.002	0.041	-9999	-0.82	2	2
BMPR1A-1B (homodimer)	-0.2	0.27	-9999	-0.55	318	318
CHRDL1	-0.29	0.38	-9999	-0.74	358	358
ENDOFIN/SMAD1	0.034	0.054	-9999	-0.64	2	2
SMAD6-7/SMURF1/SMAD1	-0.003	0.05	-9999	-0.62	4	4
SMAD6/SMURF1	0.016	0	-9999	-10000	0	0
BAMBI	-0.052	0.23	-9999	-0.8	74	74
SMURF2	0.014	0.037	-9999	-0.75	2	2
BMP2-4/CHRDL1	-0.24	0.3	-9999	-0.53	399	399
BMP2-4/GREM1	-0.22	0.29	-9999	-0.66	191	191
SMAD7	0.015	0.029	-9999	-0.85	1	1
SMAD8A/SMAD8A/SMAD4	-0.075	0.23	-9999	-0.66	99	99
SMAD1/SMAD6	0.034	0.054	-9999	-0.64	2	2
TAK1/SMAD6	0	0	-9999	-10000	0	0
BMP7	-0.24	0.35	-9999	-0.71	316	316
BMP6	-0.008	0.14	-9999	-0.75	28	28
MAP3K7IP2	0	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1	-0.063	0.17	-9999	-0.48	70	70
PPM1A	0.016	0	-9999	-10000	0	0
SMAD1/SMURF2	0.033	0.062	-9999	-0.86	2	2
SMAD7/SMURF1	-0.001	0.022	-9999	-0.65	1	1
CTDSPL	0.015	0.022	-9999	-0.65	1	1
PPP1CA	0.014	0.041	-9999	-0.85	2	2
XIAP	0.016	0	-9999	-10000	0	0
CTDSP1	0.015	0.029	-9999	-0.85	1	1
PPP1R15A	0.015	0.029	-9999	-0.85	1	1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS	-0.16	0.26	-9999	-0.63	144	144
CHRD	-0.1	0.29	-9999	-0.82	127	127
BMPR2	0.015	0.029	-9999	-0.85	1	1
BMP2-4/BMPR2/BMPR1A-1B/RGM	-0.092	0.2	-9999	-0.58	72	72
BMP4	-0.03	0.19	-9999	-0.81	50	50
FST	-0.15	0.31	-9999	-0.73	195	195
BMP2-4/NOG	-0.16	0.26	-9999	-0.52	267	267
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1	-0.27	0.28	-9999	-0.73	158	158

×

Thromboxane A2 receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGM2	-0.052	0.22	-10000	0	-0.82	69	69
GNB1/GNG2	-0.075	0.094	-10000	0	-0.23	154	154
AKT1	-0.02	0.14	-10000	0	-0.29	6	6
EGF	-0.15	0.31	-10000	0	-0.73	196	196
mol:TXA2	0	0.001	-10000	0	-10000	0	0
FGR	-0.027	0.2	-10000	0	-0.66	58	58
mol:Ca2+	-0.06	0.2	-10000	0	-0.35	193	193
LYN	-0.017	0.18	-10000	0	-0.61	54	54
RhoA/GTP	-0.046	0.059	-10000	0	-0.21	1	1
mol:PGI2	0	0	-10000	0	-10000	0	0
SYK	-0.067	0.22	-10000	0	-0.4	189	189
GNG2	-0.016	0.16	-10000	0	-0.85	33	33
ARRB2	0.016	0	-10000	0	-10000	0	0
TP alpha/Gq family/GDP/G beta5/gamma2	-0.034	0.22	-10000	0	-0.72	62	62
G beta5/gamma2	-0.1	0.13	-10000	0	-0.32	158	158
PRKCH	-0.085	0.24	-10000	0	-0.45	192	192
DNM1	-0.1	0.28	-10000	0	-0.76	136	136
TXA2/TP beta/beta Arrestin3	-0.048	0.099	-10000	0	-0.3	98	98
mol:GTP	0	0.002	-10000	0	-10000	0	0
PTGDR	-0.053	0.23	-10000	0	-0.83	73	73
G12 family/GTP	-0.11	0.15	-10000	0	-0.34	197	197
ADRBK1	0.014	0.041	-10000	0	-0.85	2	2
ADRBK2	0.015	0.029	-10000	0	-0.85	1	1
RhoA/GTP/ROCK1	-0.002	0.033	-10000	0	-0.57	3	3
mol:GDP	0.054	0.19	0.46	110	-10000	0	110
mol:NADP	-0.063	0.25	-10000	0	-0.84	82	82
RAB11A	0.016	0	-10000	0	-10000	0	0
PRKG1	-0.14	0.33	-10000	0	-0.84	158	158
mol:IP3	-0.085	0.24	-10000	0	-0.45	201	201
cell morphogenesis	-0.002	0.033	-10000	0	-0.57	3	3
PLCB2	-0.14	0.32	-10000	0	-0.63	201	201
mol:cGMP	0	0.001	-10000	0	-10000	0	0
BLK	-0.062	0.22	-10000	0	-0.61	74	74
mol:PDG2	0	0	-10000	0	-10000	0	0
HCK	-0.023	0.2	-10000	0	-0.66	55	55
RHOA	0.016	0	-10000	0	-10000	0	0
PTGIR	-0.038	0.2	-10000	0	-0.8	59	59
PRKCB1	-0.082	0.23	-10000	0	-0.42	235	235
GNAQ	0.016	0	-10000	0	-10000	0	0
mol:L-citrulline	-0.063	0.25	-10000	0	-0.84	82	82
TXA2/TXA2-R family	-0.13	0.32	-10000	0	-0.59	260	260
LCK	-0.055	0.25	-10000	0	-0.67	96	96
TXA2/TP beta/beta Arrestin3/RAB11/GDP	-0.089	0.23	-10000	0	-0.67	91	91
TXA2-R family/G12 family/GDP/G beta/gamma	0.009	0.084	-10000	0	-0.37	22	22
TXA2/TP beta/beta Arrestin2/RAB11/GDP	-0.088	0.22	-10000	0	-0.66	91	91
MAPK14	-0.029	0.16	-10000	0	-0.32	19	19
TGM2/GTP	-0.11	0.29	-10000	0	-0.55	194	194
MAPK11	-0.032	0.16	-10000	0	-0.37	33	33
ARHGEF1	-0.022	0.12	-10000	0	-0.28	3	3
GNAI2	0.015	0.029	-10000	0	-0.85	1	1
JNK cascade	-0.083	0.24	-10000	0	-0.42	256	256
RAB11/GDP	0.016	0.002	-10000	0	-10000	0	0
ICAM1	-0.053	0.19	-10000	0	-0.39	78	78
cAMP biosynthetic process	-0.085	0.23	-10000	0	-0.42	207	207
Gq family/GTP/EBP50	-0.018	0.14	-10000	0	-0.43	51	51
actin cytoskeleton reorganization	-0.002	0.033	-10000	0	-0.57	3	3
SRC	-0.016	0.18	-10000	0	-0.6	51	51
GNB5	0.015	0.029	-10000	0	-0.85	1	1
GNB1	0.016	0	-10000	0	-10000	0	0
EGF/EGFR	-0.032	0.17	-10000	0	-0.45	80	80
VCAM1	-0.069	0.21	-10000	0	-0.4	192	192
TP beta/Gq family/GDP/G beta5/gamma2	-0.034	0.22	-10000	0	-0.72	62	62
platelet activation	-0.042	0.21	-10000	0	-0.35	151	151
PGI2/IP	-0.041	0.16	-10000	0	-0.62	59	59
PRKACA	-0.037	0.19	-10000	0	-0.54	91	91
Gq family/GDP/G beta5/gamma2	-0.03	0.21	-10000	0	-0.67	66	66
TXA2/TP beta/beta Arrestin2	-0.082	0.2	-10000	0	-0.67	83	83
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TBXA2R	-0.074	0.28	-10000	0	-0.65	133	133
mol:DAG	-0.096	0.26	-10000	0	-0.48	235	235
EGFR	-0.021	0.17	-10000	0	-0.78	41	41
TXA2/TP alpha	-0.13	0.32	-10000	0	-0.6	210	210
Gq family/GTP	-0.044	0.12	-10000	0	-0.31	127	127
YES1	-0.016	0.18	-10000	0	-0.6	51	51
GNAI2/GTP	-0.078	0.2	-10000	0	-0.74	52	52
PGD2/DP	-0.053	0.18	-10000	0	-0.64	73	73
SLC9A3R1	0.005	0.095	-10000	0	-0.85	11	11
FYN	-0.019	0.19	-10000	0	-0.63	54	54
mol:NO	-0.063	0.25	-10000	0	-0.84	82	82
GNA15	-0.014	0.16	-10000	0	-0.81	33	33
PGK/cGMP	-0.15	0.3	-10000	0	-0.68	196	196
RhoA/GDP	0.016	0.002	-10000	0	-10000	0	0
TP alpha/TGM2/GDP/G beta/gamma	-0.13	0.29	-10000	0	-0.94	77	77
NOS3	-0.063	0.25	-10000	0	-0.84	82	82
RAC1	0.016	0	-10000	0	-10000	0	0
PRKCA	-0.07	0.22	-10000	0	-0.4	178	178
PRKCB	-0.084	0.24	-10000	0	-0.45	193	193
PRKCE	-0.069	0.22	-10000	0	-0.4	176	176
PRKCD	-0.088	0.25	-10000	0	-0.44	244	244
PRKCG	-0.095	0.25	-10000	0	-0.47	204	204
muscle contraction	-0.12	0.3	-10000	0	-0.55	250	250
PRKCZ	-0.066	0.22	-10000	0	-0.39	199	199
ARR3	0.004	0.007	-10000	0	-10000	0	0
TXA2/TP beta	-0.091	0.23	-10000	0	-0.73	80	80
PRKCQ	-0.087	0.24	-10000	0	-0.45	200	200
MAPKKK cascade	-0.12	0.3	-10000	0	-0.56	216	216
SELE	-0.078	0.22	-10000	0	-0.4	217	217
TP beta/GNAI2/GDP/G beta/gamma	-0.099	0.26	-10000	0	-0.98	57	57
ROCK1	0.013	0.05	-10000	0	-0.85	3	3
GNA14	-0.078	0.27	-10000	0	-0.84	97	97
chemotaxis	-0.15	0.35	-10000	0	-0.65	255	255
GNA12	0.016	0	-10000	0	-10000	0	0
GNA13	0.015	0.022	-10000	0	-0.65	1	1
GNA11	-0.011	0.14	-10000	0	-0.75	31	31
Rac1/GTP	0.006	0.007	-10000	0	-10000	0	0

×

Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FOXP3	-0.081	0.25	-10000	0	-0.78	96	96
NFATC2	-0.12	0.37	-10000	0	-0.87	139	139
NFATC3	-0.015	0.1	-10000	0	-0.85	1	1
CD40LG	-0.28	0.54	-10000	0	-1.2	162	162
ITCH	0.027	0.1	-10000	0	-10000	0	0
CBLB	0.027	0.1	-10000	0	-10000	0	0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment	-0.39	0.54	-10000	0	-1.3	209	209
JUNB	0.001	0.11	-10000	0	-0.78	17	17
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.035	0.1	-10000	0	-10000	0	0
T cell anergy	-0.028	0.18	-10000	0	-0.56	78	78
TLE4	-0.067	0.29	-10000	0	-0.88	65	65
Jun/NFAT1-c-4/p21SNFT	-0.27	0.45	-10000	0	-1.3	114	114
AP-1/NFAT1-c-4	-0.34	0.66	-10000	0	-1.5	151	151
IKZF1	-0.097	0.38	-10000	0	-1.1	84	84
T-helper 2 cell differentiation	-0.18	0.36	-10000	0	-0.9	131	131
AP-1/NFAT1	-0.18	0.32	-10000	0	-0.83	121	121
CALM1	0.013	0.063	-10000	0	-10000	0	0
EGR2	-0.18	0.51	-10000	0	-1.3	106	106
EGR3	-0.19	0.54	-10000	0	-1.4	97	97
NFAT1/FOXP3	-0.17	0.38	-10000	0	-0.86	151	151
EGR1	-0.072	0.24	-10000	0	-0.74	102	102
JUN	0.005	0.074	-10000	0	-0.77	7	7
EGR4	-0.027	0.15	-10000	0	-0.65	49	49
mol:Ca2+	-0.004	0.069	-10000	0	-10000	0	0
GBP3	-0.13	0.41	-10000	0	-1	118	118
FOSL1	-0.055	0.22	-10000	0	-0.73	84	84
NFAT1-c-4/MAF/IRF4	-0.29	0.47	-10000	0	-1.3	123	123
DGKA	-0.086	0.35	-10000	0	-1	77	77
CREM	0.015	0.022	-10000	0	-0.65	1	1
NFAT1-c-4/PPARG	-0.24	0.42	-10000	0	-1.2	106	106
CTLA4	-0.2	0.45	-10000	0	-1	166	166
NFAT1-c-4 (dimer)/EGR1	-0.29	0.48	-10000	0	-1.3	137	137
NFAT1-c-4 (dimer)/EGR4	-0.26	0.44	-10000	0	-1.2	118	118
FOS	-0.092	0.26	-10000	0	-0.75	120	120
IFNG	-0.29	0.45	-10000	0	-1.1	164	164
T cell activation	-0.11	0.32	-10000	0	-0.88	78	78
MAF	-0.013	0.16	-10000	0	-0.85	30	30
T-helper 2 cell lineage commitment	0	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	0.11	0.34	0.93	80	-10000	0	80
TNF	-0.24	0.48	-10000	0	-1.1	165	165
FASLG	-0.31	0.67	-10000	0	-1.6	147	147
TBX21	-0.054	0.22	-10000	0	-0.84	65	65
BATF3	-0.028	0.19	-10000	0	-0.8	48	48
PRKCQ	-0.044	0.21	-10000	0	-0.79	62	62
PTPN1	-0.066	0.29	-10000	0	-0.9	62	62
NFAT1-c-4/ICER1	-0.24	0.42	-10000	0	-1.2	106	106
GATA3	-0.12	0.29	-10000	0	-0.72	159	159
T-helper 1 cell differentiation	-0.25	0.46	-10000	0	-1	166	166
IL2RA	-0.34	0.47	-10000	0	-1.1	189	189
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
CASP3	-0.065	0.29	-10000	0	-0.83	75	75
E2F1	0.018	0.066	-10000	0	-0.67	8	8
PPARG	0.011	0.066	-10000	0	-0.78	6	6
SLC3A2	-0.07	0.3	-10000	0	-0.87	74	74
IRF4	-0.091	0.27	-10000	0	-0.75	124	124
PTGS2	-0.3	0.55	-10000	0	-1.2	176	176
CSF2	-0.26	0.5	-10000	0	-1.2	152	152
JunB/Fra1/NFAT1-c-4	-0.26	0.44	-10000	0	-1.2	110	110
IL4	-0.19	0.38	-10000	0	-0.97	129	129
IL5	-0.26	0.49	-10000	0	-1.2	145	145
IL2	-0.12	0.32	-10000	0	-0.9	78	78
IL3	-0.055	0.088	-10000	0	-1.2	3	3
RNF128	-0.039	0.29	-10000	0	-0.88	94	94
NFATC1	-0.11	0.35	-10000	0	-0.94	79	79
CDK4	0.085	0.23	0.7	30	-10000	0	30
PTPRK	-0.067	0.29	-10000	0	-0.86	72	72
IL8	-0.31	0.54	-10000	0	-1.2	184	184
POU2F1	0.014	0.05	-10000	0	-0.85	3	3

×

Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer	-0.32	0.5	-9999	-1	276	276
alphaV beta3 Integrin	-0.075	0.21	-9999	-0.58	115	115
PTK2	-0.25	0.39	-9999	-0.79	274	274
IGF1R	0.013	0.05	-9999	-0.85	3	3
PI4KB	0.016	0	-9999	-10000	0	0
MFGE8	-0.027	0.19	-9999	-0.84	45	45
SRC	0.015	0.022	-9999	-0.65	1	1
CDKN1B	-0.09	0.18	-9999	-0.64	49	49
VEGFA	-0.21	0.38	-9999	-0.84	236	236
ILK	-0.09	0.18	-9999	-0.64	49	49
ROCK1	0.013	0.05	-9999	-0.85	3	3
AKT1	-0.049	0.18	-9999	-0.61	46	46
PTK2B	-0.25	0.45	-9999	-0.87	286	286
alphaV/beta3 Integrin/JAM-A	-0.13	0.23	-9999	-0.86	39	39
CBL	0.015	0.029	-9999	-0.85	1	1
mol:GTP	0	0	-9999	-10000	0	0
alphaV beta3 Integrin/ANGPTL3	-0.22	0.27	-9999	-0.63	173	173
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.058	0.16	-9999	-0.56	51	51
VEGF/Rho/ROCK/alphaV/beta3 Integrin	-0.18	0.31	-9999	-0.64	240	240
alphaV/beta3 Integrin/Syndecan-1	-0.057	0.18	-9999	-0.54	94	94
PI4KA	0.015	0.029	-9999	-0.85	1	1
IGF-1R heterotetramer/IGF1/IRS1	-0.17	0.29	-9999	-0.86	89	89
PI4 Kinase	-0.001	0.022	-9999	-0.65	1	1
PIK3CA	0.01	0.071	-9999	-0.85	6	6
alphaV/beta3 Integrin/Osteopontin	-0.079	0.21	-9999	-0.69	75	75
RPS6KB1	-0.1	0.29	-9999	-0.78	89	89
TLN1	0.015	0.029	-9999	-0.85	1	1
MAPK3	-0.13	0.27	-9999	-0.87	87	87
GPR124	-0.11	0.3	-9999	-0.84	129	129
MAPK1	-0.13	0.27	-9999	-0.87	86	86
PXN	0.016	0	-9999	-10000	0	0
PIK3R1	0.011	0.066	-9999	-0.78	6	6
alphaV/beta3 Integrin/Tumstatin	-0.08	0.21	-9999	-0.63	90	90
cell adhesion	-0.19	0.26	-9999	-0.81	74	74
ANGPTL3	-0.26	0.36	-9999	-0.72	334	334
VEGFR2 homodimer/VEGFA homodimer/Src	-0.29	0.45	-9999	-0.96	262	262
IGF-1R heterotetramer	0.013	0.05	-9999	-0.85	3	3
Rac1/GDP	0	0	-9999	-10000	0	0
TGFBR2	0.012	0.058	-9999	-0.85	4	4
ITGB3	-0.046	0.21	-9999	-0.76	71	71
IGF1	-0.058	0.22	-9999	-0.72	89	89
RAC1	0.016	0	-9999	-10000	0	0
regulation of cell-matrix adhesion	-0.12	0.25	-9999	-0.59	184	184
apoptosis	0.009	0.074	-9999	-0.82	7	7
CD47	0.016	0	-9999	-10000	0	0
alphaV/beta3 Integrin/CD47	-0.043	0.15	-9999	-0.61	42	42
VCL	0.016	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Del1	-0.14	0.28	-9999	-0.6	217	217
CSF1	0	0.12	-9999	-0.82	17	17
PIK3C2A	-0.092	0.18	-9999	-0.66	51	51
PI4 Kinase/Pyk2	-0.31	0.38	-9999	-0.85	264	264
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	-0.31	0.46	-9999	-0.93	286	286
FAK1/Vinculin	-0.17	0.29	-9999	-0.57	261	261
alphaV beta3/Integrin/ppsTEM5	-0.12	0.26	-9999	-0.6	184	184
RHOA	0.016	0	-9999	-10000	0	0
VTN	-0.11	0.27	-9999	-0.69	161	161
BCAR1	0.013	0.05	-9999	-0.85	3	3
FGF2	-0.033	0.2	-9999	-0.84	51	51
F11R	-0.01	0.16	-9999	-0.65	51	51
alphaV/beta3 Integrin/Lactadherin	-0.071	0.21	-9999	-0.66	77	77
alphaV/beta3 Integrin/TGFBR2	-0.046	0.16	-9999	-0.62	45	45
alphaV/beta3 Integrin/c-FMS/Cbl/Cas	-0.016	0.095	-9999	-0.57	23	23
HSP90AA1	0.016	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Talin	-0.041	0.14	-9999	-0.58	43	43
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.11	0.29	-9999	-0.79	137	137
alphaV/beta3 Integrin/Pyk2	-0.29	0.43	-9999	-0.94	240	240
SDC1	-0.006	0.13	-9999	-0.73	26	26
VAV3	0.026	0.12	-9999	-0.51	37	37
PTPN11	0.015	0.029	-9999	-0.85	1	1
IRS1	-0.01	0.14	-9999	-0.72	31	31
FAK1/Paxillin	-0.17	0.29	-9999	-0.57	261	261
cell migration	-0.14	0.26	-9999	-0.51	239	239
ITGAV	0.009	0.074	-9999	-0.82	7	7
PI3K	-0.12	0.22	-9999	-0.82	42	42
SPP1	-0.042	0.2	-9999	-0.75	68	68
KDR	-0.22	0.38	-9999	-0.84	242	242
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Caspase 8	0.009	0.074	-9999	-0.82	7	7
COL4A3	-0.042	0.21	-9999	-0.82	61	61
angiogenesis	-0.096	0.29	-9999	-0.85	86	86
Rac1/GTP	-0.02	0.096	-9999	-0.82	3	3
EDIL3	-0.14	0.33	-9999	-0.82	171	171
cell proliferation	-0.046	0.16	-9999	-0.62	45	45

×

Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Noncanonical Wnts/FZD	-0.11	0.2	-9999	-0.56	81	81
FZD6	0.014	0.043	-9999	-0.72	3	3
WNT6	-0.098	0.27	-9999	-0.73	134	134
WNT4	-0.089	0.26	-9999	-0.72	127	127
FZD3	0.016	0	-9999	-10000	0	0
WNT5A	-0.072	0.23	-9999	-0.69	112	112
WNT11	-0.096	0.26	-9999	-0.69	140	140

×

Glypican 1 network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer	-0.039	0.16	-10000	0	-0.61	57	57
fibroblast growth factor receptor signaling pathway	-0.039	0.16	-10000	0	-0.61	57	57
LAMA1	-0.059	0.24	-10000	0	-0.8	82	82
PRNP	0.012	0.055	-10000	0	-0.8	4	4
GPC1/SLIT2	-0.12	0.24	-10000	0	-0.56	192	192
SMAD2	0.036	0.06	-10000	0	-0.51	9	9
GPC1/PrPc/Cu2+	-0.007	0.061	-10000	0	-0.52	12	12
GPC1/Laminin alpha1	-0.061	0.19	-10000	0	-0.62	88	88
TDGF1	-0.093	0.24	-10000	0	-0.66	140	140
CRIPTO/GPC1	-0.081	0.18	-10000	0	-0.49	148	148
APP/GPC1	-0.007	0.064	-10000	0	-0.6	10	10
mol:NO	0	0	-10000	0	-10000	0	0
YES1	-0.041	0.17	-10000	0	-0.56	11	11
FLT1	-0.22	0.38	-10000	0	-0.84	240	240
GPC1/TGFB/TGFBR1/TGFBR2	-0.007	0.061	-10000	0	-0.52	12	12
SERPINC1	-0.029	0.16	-10000	0	-0.66	57	57
FYN	-0.047	0.17	-10000	0	-0.42	157	157
FGR	-0.06	0.2	-10000	0	-0.46	169	169
positive regulation of MAPKKK cascade	-0.066	0.22	-10000	0	-0.7	55	55
SLIT2	-0.14	0.31	-10000	0	-0.74	186	186
GPC1/NRG	-0.063	0.19	-10000	0	-0.62	90	90
NRG1	-0.062	0.24	-10000	0	-0.8	85	85
GPC1/VEGF165 homodimer/VEGFR1 homodimer	-0.29	0.45	-10000	0	-0.94	278	278
LYN	-0.044	0.17	-10000	0	-0.42	150	150
mol:Spermine	0.009	0.058	-10000	0	-0.6	8	8
cell growth	-0.039	0.16	-10000	0	-0.61	57	57
BMP signaling pathway	-0.009	0.075	0.77	8	-10000	0	8
SRC	-0.041	0.17	-10000	0	-0.58	12	12
TGFBR1	0.016	0	-10000	0	-10000	0	0
mol:Cu2+	0	0	-10000	0	-10000	0	0
PLA2G2A	-0.081	0.23	-10000	0	-0.66	120	120
GPC1	0.009	0.075	-10000	0	-0.77	8	8
TGFBR1 (dimer)	0.016	0	-10000	0	-10000	0	0
VEGFA	-0.21	0.38	-10000	0	-0.84	236	236
BLK	-0.1	0.23	-10000	0	-0.59	88	88
HCK	-0.055	0.19	-10000	0	-0.44	166	166
FGF2	-0.033	0.2	-10000	0	-0.84	51	51
FGFR1	0.011	0.062	-10000	0	-0.81	5	5
VEGFR1 homodimer	-0.22	0.38	-10000	0	-0.84	240	240
TGFBR2	0.012	0.058	-10000	0	-0.85	4	4
cell death	-0.007	0.064	-10000	0	-0.6	10	10
ATIII/GPC1	-0.036	0.13	-10000	0	-0.5	65	65
PLA2G2A/GPC1	-0.07	0.17	-10000	0	-0.49	127	127
LCK	-0.1	0.25	-10000	0	-0.51	224	224
neuron differentiation	-0.063	0.19	-10000	0	-0.62	90	90
PrPc/Cu2+	-0.003	0.042	-10000	0	-0.62	4	4
APP	0.014	0.041	-10000	0	-0.85	2	2
TGFBR2 (dimer)	0.012	0.058	-10000	0	-0.85	4	4

×

PDGFR-beta signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate	-0.13	0.26	-9999	-0.68	149	149
PDGFB-D/PDGFRB/SLAP	-0.13	0.27	-9999	-0.67	169	169
PDGFB-D/PDGFRB/APS/CBL	-0.098	0.22	-9999	-0.58	147	147
AKT1	-0.005	0.18	-9999	-0.72	8	8
mol:PI-4-5-P2	0	0.001	-9999	-10000	0	0
mol:Sphingosine-1-phosphate	-0.1	0.3	-9999	-0.72	149	149
PIK3CA	0.01	0.071	-9999	-0.85	6	6
FGR	-0.11	0.26	-9999	-0.63	152	152
mol:Ca2+	-0.087	0.28	-9999	-0.73	134	134
MYC	-0.055	0.26	-9999	-0.7	78	78
SHC1	0.015	0.022	-9999	-0.65	1	1
HRAS/GDP	-0.068	0.18	-9999	-0.48	79	79
LRP1/PDGFRB/PDGFB	-0.098	0.22	-9999	-0.59	143	143
GRB10	0.014	0.041	-9999	-0.85	2	2
PTPN11	0.015	0.029	-9999	-0.85	1	1
GO:0007205	-0.09	0.29	-9999	-0.75	134	134
PTEN	0.016	0	-9999	-10000	0	0
GRB2	0.016	0	-9999	-10000	0	0
GRB7	-0.002	0.12	-9999	-0.76	21	21
PDGFB-D/PDGFRB/SHP2	-0.1	0.24	-9999	-0.64	141	141
PDGFB-D/PDGFRB/GRB10	-0.1	0.24	-9999	-0.64	142	142
cell cycle arrest	-0.13	0.27	-9999	-0.67	169	169
HRAS	0.012	0.059	-9999	-0.77	5	5
HIF1A	0.005	0.17	-9999	-0.64	11	11
GAB1	-0.099	0.3	-9999	-0.74	143	143
mol:GTP	0	0	-9999	-10000	0	0
DNM2	-0.086	0.28	-9999	-0.68	141	141
PDGFB-D/PDGFRB	-0.084	0.21	-9999	-0.57	134	134
mol:GDP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/LMW-PTP	-0.1	0.24	-9999	-0.64	140	140
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB	-0.14	0.27	-9999	-0.68	150	150
positive regulation of MAPKKK cascade	-0.1	0.24	-9999	-0.64	141	141
PIK3R1	0.011	0.066	-9999	-0.78	6	6
mol:IP3	-0.091	0.29	-9999	-0.76	134	134
E5	-0.001	0.003	-9999	-10000	0	0
CSK	0.014	0.041	-9999	-0.84	2	2
PDGFB-D/PDGFRB/GRB7	-0.11	0.25	-9999	-0.65	157	157
SHB	0.015	0.029	-9999	-0.85	1	1
BLK	-0.14	0.26	-9999	-0.64	166	166
PTPN2	0.014	0.006	-9999	-10000	0	0
PDGFB-D/PDGFRB/SNX15	-0.1	0.24	-9999	-0.64	140	140
BCAR1	0.013	0.05	-9999	-0.85	3	3
VAV2	-0.093	0.3	-9999	-0.72	144	144
CBL	0.015	0.029	-9999	-0.85	1	1
PDGFB-D/PDGFRB/DEP1	-0.1	0.24	-9999	-0.64	146	146
LCK	-0.16	0.35	-9999	-0.78	178	178
PDGFRB	-0.12	0.31	-9999	-0.84	140	140
ACP1	0.016	0	-9999	-10000	0	0
HCK	-0.1	0.26	-9999	-0.63	143	143
ABL1	-0.088	0.27	-9999	-0.68	140	140
PDGFB-D/PDGFRB/CBL	-0.11	0.32	-9999	-0.81	139	139
PTPN1	0.013	0.03	-9999	-0.85	1	1
SNX15	0.016	0	-9999	-10000	0	0
STAT3	0.016	0	-9999	-10000	0	0
STAT1	0.009	0.074	-9999	-0.72	9	9
cell proliferation	-0.045	0.23	-9999	-0.56	101	101
SLA	-0.02	0.17	-9999	-0.82	39	39
actin cytoskeleton reorganization	-0.021	0.18	-9999	-0.87	1	1
SRC	-0.085	0.2	-9999	-0.56	134	134
PI3K	-0.075	0.16	-9999	-0.83	7	7
PDGFB-D/PDGFRB/GRB7/SHC	-0.099	0.22	-9999	-0.56	158	158
SH2B2	0	0.12	-9999	-0.82	17	17
PLCgamma1/SPHK1	-0.11	0.32	-9999	-0.76	149	149
LYN	-0.087	0.21	-9999	-0.56	138	138
LRP1	0.005	0.095	-9999	-0.85	11	11
SOS1	0.016	0	-9999	-10000	0	0
STAT5B	0.016	0	-9999	-10000	0	0
STAT5A	0.013	0.05	-9999	-0.85	3	3
NCK1-2/p130 Cas	-0.071	0.17	-9999	-0.93	1	1
SPHK1	-0.062	0.22	-9999	-0.69	97	97
EDG1	-0.001	0.005	-9999	-10000	0	0
mol:DAG	-0.091	0.29	-9999	-0.76	134	134
PLCG1	-0.095	0.3	-9999	-0.79	134	134
NHERF/PDGFRB	-0.097	0.21	-9999	-0.57	146	146
YES1	-0.084	0.2	-9999	-0.56	134	134
cell migration	-0.097	0.21	-9999	-0.56	146	146
SHC/Grb2/SOS1	-0.069	0.16	-9999	-10000	0	0
SLC9A3R2	0.011	0.063	-9999	-0.75	6	6
SLC9A3R1	0.005	0.095	-9999	-0.85	11	11
NHERF1-2/PDGFRB/PTEN	-0.088	0.19	-9999	-0.52	146	146
FYN	-0.092	0.23	-9999	-0.6	135	135
DOK1	-0.049	0.2	-9999	-0.51	140	140
HRAS/GTP	-0.003	0.045	-9999	-0.59	5	5
PDGFB	0.009	0.076	-9999	-0.85	7	7
RAC1	-0.075	0.28	-9999	-0.64	154	154
PRKCD	-0.071	0.22	-9999	-0.53	134	134
FER	-0.047	0.2	-9999	-0.52	136	136
MAPKKK cascade	-0.068	0.16	-9999	-10000	0	0
RASA1	-0.047	0.21	-9999	-0.52	135	135
NCK1	0.014	0.041	-9999	-0.85	2	2
NCK2	0.016	0	-9999	-10000	0	0
p62DOK/Csk	-0.066	0.18	-9999	-0.47	141	141
PDGFB-D/PDGFRB/SHB	-0.1	0.24	-9999	-0.64	141	141
chemotaxis	-0.083	0.26	-9999	-0.65	140	140
STAT1-3-5/STAT1-3-5	-0.072	0.16	-9999	-0.76	3	3
Bovine Papilomavirus E5/PDGFRB	-0.1	0.24	-9999	-0.66	140	140
PTPRJ	0.011	0.063	-9999	-0.75	6	6

×

Class IB PI3K non-lipid kinase events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
cAMP biosynthetic process	0.045	0.2	0.71	74	-10000	0	74
PI3K Class IB/PDE3B	-0.045	0.2	-10000	0	-0.71	74	74
PDE3B	-0.045	0.2	-10000	0	-0.71	74	74

×

IL6-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.19	0.29	-9999	-0.74	77	77
CRP	-0.22	0.33	-9999	-0.8	140	140
cell cycle arrest	-0.23	0.33	-9999	-0.8	133	133
TIMP1	-0.18	0.32	-9999	-0.84	98	98
IL6ST	-0.082	0.27	-9999	-0.85	97	97
Rac1/GDP	-0.13	0.26	-9999	-0.71	91	91
AP1	-0.04	0.17	-9999	-0.61	28	28
GAB2	0.013	0.061	-9999	-0.72	6	6
TNFSF11	-0.24	0.34	-9999	-0.86	120	120
HSP90B1	-0.001	0.062	-9999	-10000	0	0
GAB1	0.015	0.041	-9999	-0.85	2	2
MAPK14	-0.1	0.26	-9999	-0.73	89	89
AKT1	0.056	0.061	-9999	-0.77	2	2
FOXO1	0.061	0.064	-9999	-0.99	1	1
MAP2K6	-0.12	0.25	-9999	-0.65	103	103
mol:GTP	-0.001	0.003	-9999	-10000	0	0
MAP2K4	-0.14	0.26	-9999	-0.72	79	79
MITF	-0.12	0.23	-9999	-0.6	102	102
positive regulation of NF-kappaB transcription factor activity	0	0	-9999	-10000	0	0
TYK2	0.014	0.041	-9999	-0.85	2	2
A2M	-0.053	0.36	-9999	-1.6	44	44
CEBPB	0.016	0.071	-9999	-0.65	10	10
GRB2/SOS1/GAB family/SHP2	-0.017	0.1	-9999	-0.7	6	6
STAT3	-0.24	0.35	-9999	-0.85	138	138
STAT1	-0.017	0.082	-9999	-0.76	7	7
CEBPD	-0.19	0.3	-9999	-0.77	72	72
PIK3CA	0.012	0.071	-9999	-0.85	6	6
PI3K	0.018	0.075	-9999	-0.62	12	12
JUN	0.009	0.069	-9999	-0.76	7	7
PIAS3/MITF	-0.1	0.22	-9999	-0.69	61	61
MAPK11	-0.11	0.27	-9999	-0.72	101	101
STAT3 (dimer)/FOXO1	-0.14	0.28	-9999	-0.72	66	66
GRB2/SOS1/GAB family	-0.1	0.19	-9999	-0.7	49	49
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK	-0.12	0.24	-9999	-0.56	132	132
GRB2	0.017	0.003	-9999	-10000	0	0
JAK2	0.015	0.029	-9999	-0.85	1	1
LBP	-0.29	0.39	-9999	-0.83	237	237
PIK3R1	0.012	0.066	-9999	-0.78	6	6
JAK1	0.015	0.007	-9999	-10000	0	0
MYC	-0.21	0.34	-9999	-0.95	87	87
FGG	-0.38	0.47	-9999	-1	258	258
macrophage differentiation	-0.23	0.33	-9999	-0.8	133	133
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4	-0.18	0.27	-9999	-0.58	197	197
JUNB	-0.19	0.3	-9999	-0.78	82	82
FOS	-0.087	0.26	-9999	-0.74	120	120
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4	-0.14	0.24	-9999	-0.56	141	141
STAT1/PIAS1	-0.13	0.22	-9999	-0.57	102	102
GRB2/SOS1/GAB family/SHP2/PI3K	0.033	0.064	-9999	-1.2	1	1
STAT3 (dimer)	-0.24	0.35	-9999	-0.84	134	134
PRKCD	-0.16	0.3	-9999	-0.78	97	97
IL6R	-0.009	0.14	-9999	-0.84	25	25
SOCS3	-0.11	0.33	-9999	-1	77	77
gp130 (dimer)/JAK1/JAK1/LMO4	-0.045	0.18	-9999	-0.56	98	98
Rac1/GTP	-0.15	0.26	-9999	-0.71	95	95
HCK	-0.005	0.13	-9999	-0.83	22	22
MAPKKK cascade	0.008	0.097	-9999	-0.91	4	4
bone resorption	-0.22	0.32	-9999	-0.8	121	121
IRF1	-0.19	0.29	-9999	-0.76	69	69
mol:GDP	-0.14	0.27	-9999	-0.7	107	107
SOS1	0.017	0.006	-9999	-10000	0	0
VAV1	-0.15	0.27	-9999	-0.72	107	107
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3	-0.1	0.27	-9999	-0.71	92	92
PTPN11	-0.011	0.045	-9999	-1.2	1	1
IL6/IL6RA	-0.16	0.28	-9999	-0.57	268	268
gp130 (dimer)/TYK2/TYK2/LMO4	-0.049	0.18	-9999	-0.56	100	100
gp130 (dimer)/JAK2/JAK2/LMO4	-0.048	0.18	-9999	-0.57	98	98
IL6	-0.2	0.34	-9999	-0.74	247	247
PIAS3	0.016	0	-9999	-10000	0	0
PTPRE	0.013	0.077	-9999	-0.84	7	7
PIAS1	0.016	0	-9999	-10000	0	0
RAC1	0.016	0.002	-9999	-10000	0	0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4	-0.12	0.22	-9999	-0.49	155	155
LMO4	0.011	0.025	-9999	-0.63	1	1
STAT3 (dimer)/PIAS3	-0.26	0.28	-9999	-0.8	126	126
MCL1	0.064	0.054	-9999	-0.88	1	1

×

Reelin signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDK5R1/CDK5	-0.003	0.041	-9999	-0.55	5	5
VLDLR	0.01	0.067	-9999	-0.74	7	7
CRKL	0.016	0	-9999	-10000	0	0
LRPAP1	0.014	0.041	-9999	-0.85	2	2
FYN	0.007	0.086	-9999	-0.85	9	9
ITGA3	-0.009	0.14	-9999	-0.75	29	29
RELN/VLDLR/Fyn	-0.18	0.24	-9999	-0.47	349	349
MAPK8IP1/MKK7/MAP3K11/JNK1	-0.014	0.097	-9999	-0.6	18	18
AKT1	-0.082	0.15	-9999	-0.46	27	27
MAP2K7	0.014	0.041	-9999	-0.85	2	2
RAPGEF1	0.016	0	-9999	-10000	0	0
DAB1	-0.036	0.17	-9999	-0.65	60	60
RELN/LRP8/DAB1	-0.2	0.23	-9999	-0.58	140	140
LRPAP1/LRP8	-0.018	0.093	-9999	-0.5	32	32
RELN/LRP8/DAB1/Fyn	-0.19	0.22	-9999	-0.55	148	148
DAB1/alpha3/beta1 Integrin	-0.18	0.21	-9999	-0.69	47	47
long-term memory	-0.35	0.32	-9999	-0.8	223	223
DAB1/LIS1	-0.17	0.2	-9999	-0.71	30	30
DAB1/CRLK/C3G	-0.17	0.2	-9999	-0.68	30	30
PIK3CA	0.01	0.071	-9999	-0.85	6	6
DAB1/NCK2	-0.18	0.2	-9999	-0.71	30	30
ARHGEF2	0.014	0.041	-9999	-0.85	2	2
mol:Src family inhibitors PP1 and PP2	0	0	-9999	-10000	0	0
GRIN2A	-0.28	0.38	-9999	-0.75	337	337
CDK5R1	0.013	0.048	-9999	-0.7	4	4
RELN	-0.27	0.36	-9999	-0.72	343	343
PIK3R1	0.011	0.066	-9999	-0.78	6	6
RELN/LRP8/Fyn	-0.2	0.24	-9999	-0.6	136	136
GRIN2A/RELN/LRP8/DAB1/Fyn	-0.34	0.32	-9999	-0.68	338	338
MAPK8	0.005	0.095	-9999	-0.85	11	11
RELN/VLDLR/DAB1	-0.19	0.23	-9999	-0.48	259	259
ITGB1	0.016	0	-9999	-10000	0	0
MAP1B	-0.17	0.24	-9999	-0.56	151	151
RELN/LRP8	-0.19	0.24	-9999	-0.58	130	130
GRIN2B/RELN/LRP8/DAB1/Fyn	-0.21	0.24	-9999	-0.57	167	167
PI3K	-0.008	0.072	-9999	-0.62	12	12
mol:PP2	0	0	-9999	-10000	0	0
alpha3/beta1 Integrin	-0.018	0.1	-9999	-0.56	29	29
RAP1A	-0.12	0.21	-9999	-0.63	30	30
PAFAH1B1	0.016	0	-9999	-10000	0	0
MAPK8IP1	0.007	0.081	-9999	-0.75	10	10
CRLK/C3G	0	0	-9999	-10000	0	0
GRIN2B	-0.031	0.16	-9999	-0.65	54	54
NCK2	0.016	0	-9999	-10000	0	0
neuron differentiation	-0.05	0.14	-9999	-0.5	28	28
neuron adhesion	-0.11	0.22	-9999	-0.69	19	19
LRP8	-0.007	0.12	-9999	-0.66	30	30
GSK3B	-0.068	0.15	-9999	-0.51	12	12
RELN/VLDLR/DAB1/Fyn	-0.18	0.22	-9999	-0.54	146	146
MAP3K11	0.014	0.041	-9999	-0.85	2	2
RELN/VLDLR/DAB1/P13K	-0.097	0.16	-9999	-0.37	148	148
CDK5	0.015	0.029	-9999	-0.85	1	1
MAPT	-0.061	0.25	-9999	-0.78	95	95
neuron migration	-0.083	0.2	-9999	-0.58	22	22
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1	-0.051	0.14	-9999	-0.5	28	28
RELN/VLDLR	-0.18	0.22	-9999	-0.54	133	133

×

Calcium signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC1	0.004	0.083	-9999	-0.61	13	13
NFATC2	-0.056	0.19	-9999	-0.58	102	102
NFATC3	0.013	0.042	-9999	-0.58	1	1
CD40LG	-0.2	0.41	-9999	-0.88	169	169
PTGS2	-0.22	0.42	-9999	-0.89	189	189
JUNB	0.001	0.11	-9999	-0.78	17	17
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.007	0.014	-9999	-10000	0	0
CaM/Ca2+	-0.007	0.014	-9999	-10000	0	0
CALM1	0.013	0.01	-9999	-10000	0	0
JUN	0.007	0.071	-9999	-0.77	7	7
mol:Ca2+	-0.008	0.014	-9999	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0	0.003	-9999	-10000	0	0
FOSL1	-0.055	0.22	-9999	-0.73	84	84
CREM	0.015	0.022	-9999	-0.65	1	1
Jun/NFAT1-c-4/p21SNFT	-0.15	0.24	-9999	-0.72	89	89
FOS	-0.09	0.26	-9999	-0.75	120	120
IFNG	-0.22	0.42	-9999	-0.82	231	231
AP-1/NFAT1-c-4	-0.27	0.46	-9999	-1	174	174
FASLG	-0.22	0.44	-9999	-0.88	222	222
NFAT1-c-4/ICER1	-0.094	0.17	-9999	-0.59	66	66
IL2RA	-0.22	0.42	-9999	-0.9	184	184
FKBP12/FK506	0	0	-9999	-10000	0	0
CSF2	-0.18	0.37	-9999	-0.82	144	144
JunB/Fra1/NFAT1-c-4	-0.13	0.22	-9999	-0.66	92	92
IL4	-0.18	0.36	-9999	-0.79	151	151
IL2	-0.01	0.068	-9999	-0.57	12	12
IL3	-0.024	0.07	-9999	-1.1	3	3
FKBP1A	0.016	0	-9999	-10000	0	0
BATF3	-0.028	0.19	-9999	-0.8	48	48
mol:FK506	0	0	-9999	-10000	0	0
POU2F1	0.014	0.05	-9999	-0.85	3	3

×

Neurotrophic factor-mediated Trk receptor 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
CRKL	0.016	0	-10000	0	-10000	0	0
RAS family/GTP/Tiam1	-0.053	0.11	-10000	0	-0.61	8	8
NT3 (dimer)/TRKC	-0.15	0.29	-10000	0	-0.68	195	195
NT3 (dimer)/TRKB	-0.26	0.37	-10000	0	-0.66	357	357
SHC/Grb2/SOS1/GAB1/PI3K	0.042	0.046	-10000	0	-10000	0	0
RAPGEF1	0.016	0	-10000	0	-10000	0	0
BDNF	-0.11	0.29	-10000	0	-0.78	140	140
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
DYNLT1	0.016	0	-10000	0	-10000	0	0
NTRK1	-0.033	0.18	-10000	0	-0.69	60	60
NTRK2	-0.16	0.32	-10000	0	-0.76	196	196
NTRK3	-0.099	0.28	-10000	0	-0.76	132	132
NT-4/5 (dimer)/TRKB	-0.24	0.32	-10000	0	-0.6	348	348
neuron apoptosis	0.18	0.23	0.56	197	-10000	0	197
SHC 2-3/Grb2	-0.2	0.27	-10000	0	-0.63	196	196
SHC1	0.015	0.022	-10000	0	-0.65	1	1
SHC2	-0.19	0.29	-10000	0	-0.67	182	182
SHC3	-0.18	0.24	-10000	0	-0.57	190	190
STAT3 (dimer)	0.007	0.086	-10000	0	-10000	0	0
NT3 (dimer)/TRKA	-0.19	0.32	-10000	0	-0.62	269	269
RIN/GDP	-0.005	0.11	-10000	0	-0.32	10	10
GIPC1	0.012	0.055	-10000	0	-0.8	4	4
KRAS	0.016	0	-10000	0	-10000	0	0
DNAJA3	-0.16	0.25	-10000	0	-0.63	161	161
RIN/GTP	-0.002	0.028	-10000	0	-0.49	3	3
CCND1	-0.012	0.23	-10000	0	-1	42	42
MAGED1	0.015	0.032	-10000	0	-0.65	2	2
PTPN11	0.015	0.029	-10000	0	-0.85	1	1
RICS	0	0	-10000	0	-10000	0	0
NT-4/5 (dimer)	-0.031	0.15	-10000	0	-0.65	50	50
SHC/GRB2/SOS1	0	0.013	-10000	0	-10000	0	0
GRB2	0.016	0	-10000	0	-10000	0	0
NGF (dimer)/TRKA/MATK	-0.18	0.29	-10000	0	-0.58	266	266
TRKA/NEDD4-2	-0.063	0.17	-10000	0	-0.51	109	109
ELMO1	-0.032	0.2	-10000	0	-0.85	49	49
RhoG/GTP/ELMO1/DOCK1	-0.033	0.14	-10000	0	-0.58	50	50
NGF	-0.16	0.34	-10000	0	-0.8	189	189
HRAS	0.012	0.059	-10000	0	-0.77	5	5
DOCK1	0.014	0.041	-10000	0	-0.85	2	2
GAB2	0.011	0.06	-10000	0	-0.72	6	6
RIT2	0.001	0.038	-10000	0	-0.65	3	3
RIT1	0.015	0.029	-10000	0	-0.85	1	1
FRS2	0.016	0	-10000	0	-10000	0	0
DNM1	-0.1	0.28	-10000	0	-0.76	136	136
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.015	0.022	-10000	0	-0.65	1	1
SH2B1 (homopentamer)	0	0	-10000	0	-10000	0	0
RhoG/GTP	-0.18	0.29	-10000	0	-0.69	178	178
mol:GDP	-0.014	0.16	-10000	0	-0.5	16	16
NGF (dimer)	-0.16	0.34	-10000	0	-0.8	189	189
RhoG/GDP	-0.037	0.15	-10000	0	-0.66	49	49
RIT1/GDP	0.002	0.11	-10000	0	-0.33	12	12
TIAM1	0.005	0.098	-10000	0	-0.83	12	12
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
BDNF (dimer)/TRKB	-0.19	0.29	-10000	0	-0.56	292	292
KIDINS220/CRKL/C3G	0	0	-10000	0	-10000	0	0
SHC/RasGAP	-0.003	0.041	-10000	0	-0.61	4	4
FRS2 family/SHP2	-0.004	0.042	-10000	0	-0.56	3	3
SHC/GRB2/SOS1/GAB1	-0.002	0.027	-10000	0	-0.51	2	2
RIT1/GTP	-0.001	0.022	-10000	0	-0.66	1	1
NT3 (dimer)	-0.074	0.26	-10000	0	-0.79	99	99
RAP1/GDP	-0.036	0.069	-10000	0	-10000	0	0
KIDINS220/CRKL	0.016	0	-10000	0	-10000	0	0
BDNF (dimer)	-0.11	0.29	-10000	0	-0.77	140	140
ubiquitin-dependent protein catabolic process	-0.16	0.26	-10000	0	-0.53	276	276
Schwann cell development	-0.042	0.041	-10000	0	-10000	0	0
EHD4	0.016	0	-10000	0	-10000	0	0
FRS2 family/GRB2/SOS1	-0.003	0.034	-10000	0	-0.51	2	2
FRS2 family/SHP2/CRK family/C3G/GAB2	0.048	0.036	-10000	0	-0.5	1	1
RAP1B	0.016	0	-10000	0	-10000	0	0
RAP1A	0.016	0	-10000	0	-10000	0	0
CDC42/GTP	-0.24	0.31	-10000	0	-0.86	129	129
ABL1	0.016	0	-10000	0	-10000	0	0
SH2B family/GRB2/SOS1	0	0	-10000	0	-10000	0	0
Rap1/GTP	-0.056	0.086	-10000	0	-10000	0	0
STAT3	0.007	0.086	-10000	0	-10000	0	0
axon guidance	-0.22	0.29	-10000	0	-0.79	129	129
MAPK3	-0.13	0.29	-10000	0	-0.62	175	175
MAPK1	-0.13	0.29	-10000	0	-0.62	176	176
CDC42/GDP	0.002	0.11	-10000	0	-0.31	14	14
NTF3	-0.074	0.26	-10000	0	-0.79	99	99
NTF4	-0.031	0.15	-10000	0	-0.65	50	50
NGF (dimer)/TRKA/FAIM	-0.14	0.25	-10000	0	-0.61	154	154
PI3K	-0.008	0.072	-10000	0	-0.62	12	12
FRS3	0.011	0.06	-10000	0	-0.72	6	6
FAIM	0.015	0.032	-10000	0	-0.65	2	2
GAB1	0.014	0.041	-10000	0	-0.85	2	2
RASGRF1	-0.18	0.27	-10000	0	-0.63	191	191
SOS1	0.016	0	-10000	0	-10000	0	0
MCF2L	-0.1	0.27	-10000	0	-0.65	150	150
RGS19	0.014	0.041	-10000	0	-0.85	2	2
CDC42	0.016	0	-10000	0	-10000	0	0
RAS family/GTP	0.008	0.098	-10000	0	-0.56	2	2
Rac1/GDP	0.002	0.11	-10000	0	-0.32	11	11
NGF (dimer)/TRKA/GRIT	-0.14	0.25	-10000	0	-0.54	234	234
neuron projection morphogenesis	-0.12	0.26	-10000	0	-0.68	111	111
NGF (dimer)/TRKA/NEDD4-2	-0.16	0.26	-10000	0	-0.53	276	276
MAP2K1	0.049	0.028	-10000	0	-0.47	2	2
NGFR	-0.15	0.33	-10000	0	-0.81	177	177
NGF (dimer)/TRKA/GIPC/GAIP	-0.096	0.21	-10000	0	-0.41	227	227
RAS family/GTP/PI3K	0.033	0.053	-10000	0	-0.38	13	13
FRS2 family/SHP2/GRB2/SOS1	-0.003	0.035	-10000	0	-10000	0	0
NRAS	0.016	0	-10000	0	-10000	0	0
GRB2/SOS1	0	0	-10000	0	-10000	0	0
PRKCI	0.015	0.022	-10000	0	-0.65	1	1
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
RAC1	0.016	0	-10000	0	-10000	0	0
PRKCZ	0.008	0.082	-10000	0	-0.85	8	8
MAPKKK cascade	-0.16	0.3	-10000	0	-0.77	154	154
RASA1	0.013	0.05	-10000	0	-0.85	3	3
TRKA/c-Abl	-0.034	0.13	-10000	0	-0.51	60	60
SQSTM1	0.009	0.067	-10000	0	-0.65	9	9
BDNF (dimer)/TRKB/GIPC	-0.17	0.27	-10000	0	-0.61	187	187
NGF (dimer)/TRKA/p62/Atypical PKCs	-0.13	0.22	-10000	0	-0.52	162	162
MATK	-0.04	0.21	-10000	0	-0.79	62	62
NEDD4L	-0.023	0.16	-10000	0	-0.66	52	52
RAS family/GDP	-0.033	0.065	-10000	0	-10000	0	0
NGF (dimer)/TRKA	-0.17	0.27	-10000	0	-0.59	219	219
Rac1/GTP	-0.12	0.16	-10000	0	-0.43	135	135
FRS2 family/SHP2/CRK family	-0.003	0.042	-10000	0	-0.59	3	3

×

Signaling events regulated by Ret tyrosine kinase

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
PTK2	-0.036	0.055	-9999	-10000	0	0
Crk/p130 Cas/Paxillin	-0.1	0.15	-9999	-0.49	51	51
JUN	-0.053	0.19	-9999	-0.63	41	41
HRAS	0.012	0.059	-9999	-0.77	5	5
RET51/GFRalpha1/GDNF/GRB10	-0.16	0.24	-9999	-0.59	151	151
RAP1A	0.016	0	-9999	-10000	0	0
FRS2	0.016	0	-9999	-10000	0	0
RAP1A/GDP	0	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/DOK1	-0.16	0.25	-9999	-0.6	153	153
EntrezGene:5979	0	0	-9999	-10000	0	0
PTPN11	0.015	0.029	-9999	-0.85	1	1
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.015	0.022	-9999	-0.65	1	1
RET9/GFRalpha1/GDNF/Enigma	-0.12	0.21	-9999	-0.55	124	124
RHOA	0.016	0	-9999	-10000	0	0
RAP1A/GTP	-0.15	0.24	-9999	-0.58	157	157
GRB7	-0.002	0.12	-9999	-0.76	21	21
RET51/GFRalpha1/GDNF	-0.16	0.24	-9999	-0.59	150	150
MAPKKK cascade	-0.13	0.2	-9999	-0.7	42	42
BCAR1	0.013	0.05	-9999	-0.85	3	3
RET9/GFRalpha1/GDNF/IRS1	-0.13	0.22	-9999	-0.57	130	130
lamellipodium assembly	-0.093	0.14	-9999	-0.45	49	49
RET51/GFRalpha1/GDNF/SHC	-0.16	0.24	-9999	-0.59	151	151
PIK3CA	0.01	0.071	-9999	-0.85	6	6
RET9/GFRalpha1/GDNF/SHC	-0.12	0.21	-9999	-0.54	122	122
RET9/GFRalpha1/GDNF/Shank3	-0.13	0.22	-9999	-0.56	132	132
MAPK3	-0.11	0.25	-9999	-0.8	46	46
DOK1	0.01	0.071	-9999	-0.85	6	6
DOK6	-0.11	0.3	-9999	-0.83	128	128
PXN	0.016	0	-9999	-10000	0	0
neurite development	-0.11	0.25	-9999	-0.71	79	79
DOK5	-0.076	0.25	-9999	-0.76	105	105
GFRA1	-0.18	0.34	-9999	-0.76	221	221
MAPK8	-0.063	0.19	-9999	-0.65	37	37
HRAS/GTP	-0.14	0.23	-9999	-0.81	39	39
tube development	-0.12	0.2	-9999	-0.52	132	132
MAPK1	-0.11	0.25	-9999	-0.8	46	46
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.047	0.14	-9999	-0.51	6	6
Rac1/GDP	0	0	-9999	-10000	0	0
SRC	0.015	0.022	-9999	-0.65	1	1
PDLIM7	0.012	0.055	-9999	-0.8	4	4
RET51/GFRalpha1/GDNF/Dok6	-0.21	0.31	-9999	-0.67	219	219
SHC1	0.015	0.022	-9999	-0.65	1	1
RET51/GFRalpha1/GDNF/Dok4	-0.17	0.27	-9999	-0.64	157	157
RET51/GFRalpha1/GDNF/Dok5	-0.21	0.31	-9999	-0.72	179	179
PRKCA	0.015	0.032	-9999	-0.65	2	2
HRAS/GDP	-0.003	0.045	-9999	-0.59	5	5
CREB1	-0.055	0.16	-9999	-0.4	128	128
PIK3R1	0.011	0.066	-9999	-0.78	6	6
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.049	0.15	-9999	-0.36	122	122
RET51/GFRalpha1/GDNF/Grb7	-0.17	0.26	-9999	-0.62	156	156
mol:GDP	0	0	-9999	-10000	0	0
RET	-0.052	0.22	-9999	-0.72	83	83
DOK4	-0.007	0.14	-9999	-0.85	24	24
JNK cascade	-0.051	0.18	-9999	-0.61	41	41
RET9/GFRalpha1/GDNF/FRS2	-0.12	0.21	-9999	-0.54	122	122
SHANK3	0.003	0.1	-9999	-0.8	14	14
RASA1	0.013	0.05	-9999	-0.85	3	3
NCK1	0.014	0.041	-9999	-0.85	2	2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.048	0.14	-9999	-0.36	122	122
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.066	0.17	-9999	-0.55	30	30
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK	-0.071	0.19	-9999	-0.63	35	35
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.068	0.18	-9999	-0.63	30	30
PI3K	-0.096	0.26	-9999	-0.6	133	133
SOS1	0.016	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/Shank3/Grb2	-0.12	0.2	-9999	-0.52	132	132
GRB10	0.014	0.041	-9999	-0.85	2	2
activation of MAPKK activity	-0.058	0.16	-9999	-0.51	26	26
RET51/GFRalpha1/GDNF/FRS2	-0.16	0.24	-9999	-0.59	150	150
GAB1	0.014	0.041	-9999	-0.85	2	2
IRS1	-0.01	0.14	-9999	-0.72	31	31
IRS2	-0.019	0.15	-9999	-0.66	46	46
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.07	0.19	-9999	-0.64	33	33
RET51/GFRalpha1/GDNF/PKC alpha	-0.16	0.24	-9999	-0.59	150	150
GRB2	0.016	0	-9999	-10000	0	0
PRKACA	0.016	0	-9999	-10000	0	0
GDNF	-0.005	0.082	-9999	-0.65	14	14
RAC1	0.016	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/IRS1	-0.17	0.26	-9999	-0.61	161	161
Rac1/GTP	-0.11	0.17	-9999	-0.56	49	49
RET9/GFRalpha1/GDNF	-0.13	0.23	-9999	-0.51	229	229
GFRalpha1/GDNF	-0.15	0.26	-9999	-0.59	229	229

×

Arf6 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CENTA1/KIF3B	-0.039	0.14	-9999	-0.51	68	68
ARNO/beta Arrestin1-2	-0.04	0.11	-9999	-0.81	7	7
EGFR	-0.021	0.17	-9999	-0.78	41	41
EPHA2	0.006	0.094	-9999	-0.83	11	11
USP6	0.004	0.09	-9999	-0.66	16	16
IQSEC1	0.016	0	-9999	-10000	0	0
EGFR/EGFR/EGF/EGF	-0.15	0.26	-9999	-0.58	222	222
ARRB2	-0.011	0.085	-9999	-0.29	77	77
mol:GTP	0.014	0.048	-9999	-0.33	9	9
ARRB1	0.003	0.11	-9999	-0.83	14	14
FBXO8	0.016	0	-9999	-10000	0	0
TSHR	-0.12	0.3	-9999	-0.79	152	152
EGF	-0.15	0.31	-9999	-0.73	196	196
somatostatin receptor activity	0	0	-9999	-0.001	115	115
ARAP2	0.011	0.065	-9999	-0.85	5	5
mol:GDP	-0.086	0.14	-9999	-0.35	135	135
mol:PI-3-4-5-P3	0	0	-9999	-0.001	58	58
ITGA2B	-0.058	0.22	-9999	-0.73	88	88
ARF6	0.016	0	-9999	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	-0.018	0.1	-9999	-0.55	28	28
ADAP1	-0.009	0.13	-9999	-0.69	31	31
KIF13B	-0.023	0.16	-9999	-0.65	52	52
HGF/MET	-0.087	0.21	-9999	-0.6	129	129
PXN	0.016	0	-9999	-10000	0	0
ARF6/GTP	-0.086	0.14	-9999	-0.34	120	120
EGFR/EGFR/EGF/EGF/ARFGEP100	-0.12	0.23	-9999	-0.62	104	104
ADRB2	-0.024	0.16	-9999	-0.69	50	50
receptor agonist activity	0	0	-9999	0	102	102
actin filament binding	0	0	-9999	-0.001	119	119
SRC	0.015	0.022	-9999	-0.65	1	1
ITGB3	-0.046	0.21	-9999	-0.76	71	71
GNAQ	0.016	0	-9999	-10000	0	0
EFA6/PI-4-5-P2	0	0.001	-9999	-0.001	82	82
ARF6/GDP	-0.009	0.14	-9999	-0.49	45	45
ARF6/GDP/GULP/ACAP1	-0.12	0.19	-9999	-0.56	110	110
alphaIIb/beta3 Integrin/paxillin/GIT1	-0.078	0.18	-9999	-0.57	76	76
ACAP1	-0.04	0.21	-9999	-0.79	62	62
ACAP2	0.015	0.029	-9999	-0.85	1	1
LHCGR/beta Arrestin2	-0.031	0.12	-9999	-0.42	77	77
EFNA1	0.001	0.12	-9999	-0.85	16	16
HGF	-0.094	0.28	-9999	-0.78	122	122
CYTH3	0.014	0	-9999	-10000	0	0
CYTH2	0.007	0.061	-9999	-1.3	2	2
NCK1	0.014	0.041	-9999	-0.85	2	2
fibronectin binding	0	0	-9999	-0.001	109	109
endosomal lumen acidification	0	0	-9999	-0.001	127	127
microtubule-based process	0	0	-9999	-10000	0	0
GULP1	-0.028	0.18	-9999	-0.79	49	49
GNAQ/ARNO	0.012	0.057	-9999	-1.2	2	2
mol:Phosphatidic acid	0	0	-9999	-10000	0	0
PIP3-E	0	0	-9999	0	17	17
MET	0.009	0.075	-9999	-0.77	8	8
GNA14	-0.078	0.27	-9999	-0.84	97	97
GNA15	-0.015	0.16	-9999	-0.81	33	33
GIT1	0.014	0.041	-9999	-0.85	2	2
mol:PI-4-5-P2	0	0	-9999	-0.001	91	91
GNA11	-0.011	0.14	-9999	-0.75	31	31
LHCGR	-0.052	0.18	-9999	-0.65	77	77
AGTR1	-0.22	0.35	-9999	-0.73	275	275
desensitization of G-protein coupled receptor protein signaling pathway	-0.03	0.12	-9999	-0.42	77	77
IPCEF1/ARNO	-0.087	0.2	-9999	-0.51	106	106
alphaIIb/beta3 Integrin	-0.099	0.23	-9999	-0.6	147	147

×

Effects of Botulinum toxin

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
STX1A	0.004	0.075	-9999	-0.54	16	16
UniProt:P19321	0	0	-9999	-10000	0	0
RIMS1/UNC13B	-0.054	0.15	-9999	-0.48	100	100
STXBP1	0.014	0.037	-9999	-0.75	2	2
ACh/CHRNA1	-0.15	0.24	-9999	-0.51	264	264
RAB3GAP2/RIMS1/UNC13B	-0.046	0.13	-9999	-0.67	2	2
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	-0.064	0.21	-9999	-0.65	100	100
mol:ACh	-0.011	0.057	-9999	-0.15	127	127
RAB3GAP2	0.016	0	-9999	-10000	0	0
STX1A/SNAP25/VAMP2	-0.062	0.13	-9999	-0.5	43	43
UniProt:P10844	0	0	-9999	-10000	0	0
muscle contraction	-0.15	0.24	-9999	-0.51	264	264
UNC13B	0.015	0.022	-9999	-0.65	1	1
CHRNA1	-0.21	0.34	-9999	-0.73	264	264
UniProt:P10845	0	0	-9999	-10000	0	0
ACh/Synaptotagmin 1	-0.051	0.17	-9999	-0.52	93	93
SNAP25	-0.041	0.13	-9999	-0.39	114	114
VAMP2	0.009	0	-9999	-10000	0	0
SYT1	-0.062	0.23	-9999	-0.73	93	93
UniProt:Q00496	0	0	-9999	-10000	0	0
STXIA/STXBP1	0.013	0.069	-9999	-0.46	18	18
STX1A/SNAP25 fragment 1/VAMP2	-0.062	0.13	-9999	-0.5	43	43

×

Signaling mediated by p38-alpha and p38-beta

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
PTGS2	-0.14	0.42	-9999	-0.96	145	145
MKNK1	0.016	0	-9999	-10000	0	0
MAPK14	-0.039	0.14	-9999	-0.47	19	19
ATF2/c-Jun	-0.024	0.16	-9999	-0.76	20	20
MAPK11	-0.054	0.18	-9999	-0.68	34	34
MITF	-0.044	0.18	-9999	-0.56	43	43
MAPKAPK5	-0.041	0.18	-9999	-0.57	38	38
KRT8	-0.045	0.19	-9999	-0.59	43	43
MAPKAPK3	0.015	0.029	-9999	-0.85	1	1
MAPKAPK2	0.016	0	-9999	-10000	0	0
p38alpha-beta/CK2	-0.072	0.23	-9999	-0.53	140	140
CEBPB	-0.045	0.18	-9999	-0.56	43	43
SLC9A1	-0.041	0.18	-9999	-0.57	38	38
mol:GDP	0	0	-9999	-10000	0	0
ATF2	-0.042	0.2	-9999	-0.6	49	49
p38alpha-beta/MNK1	-0.044	0.19	-9999	-0.68	35	35
JUN	-0.023	0.16	-9999	-0.74	20	20
PPARGC1A	-0.089	0.23	-9999	-0.56	108	108
USF1	-0.041	0.18	-9999	-0.4	139	139
RAB5/GDP/GDI1	-0.06	0.11	-9999	-0.48	26	26
NOS2	-0.15	0.44	-9999	-1.1	130	130
DDIT3	-0.052	0.2	-9999	-0.59	52	52
RAB5A	0.016	0	-9999	-10000	0	0
HSPB1	-0.027	0.16	-9999	-0.55	35	35
p38alpha-beta/HBP1	-0.044	0.19	-9999	-0.68	35	35
CREB1	-0.042	0.19	-9999	-0.59	42	42
RAB5/GDP	0	0	-9999	-10000	0	0
EIF4E	-0.03	0.17	-9999	-0.62	33	33
RPS6KA4	-0.041	0.18	-9999	-0.57	38	38
PLA2G4A	-0.056	0.22	-9999	-0.68	57	57
GDI1	-0.041	0.18	-9999	-0.56	40	40
TP53	-0.06	0.23	-9999	-0.52	139	139
RPS6KA5	-0.05	0.2	-9999	-0.62	45	45
ESR1	-0.078	0.26	-9999	-0.71	77	77
HBP1	0.016	0	-9999	-10000	0	0
MEF2C	-0.071	0.26	-9999	-0.76	74	74
MEF2A	-0.043	0.18	-9999	-0.56	42	42
EIF4EBP1	-0.047	0.2	-9999	-0.43	143	143
KRT19	-0.23	0.3	-9999	-0.59	280	280
ELK4	-0.042	0.18	-9999	-0.56	40	40
ATF6	-0.041	0.18	-9999	-0.4	139	139
ATF1	-0.042	0.19	-9999	-0.42	140	140
p38alpha-beta/MAPKAPK2	-0.044	0.19	-9999	-0.68	35	35
p38alpha-beta/MAPKAPK3	-0.044	0.2	-9999	-0.69	35	35

×

TCGA08_retinoblastoma

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
CDKN2B	-0.004	0.12	-10000	0	-0.81	20	20
CDKN2C	0.001	0.13	-10000	0	-0.82	20	20
CDKN2A	-0.041	0.21	-10000	0	-0.79	63	63
CCND2	0.015	0.091	0.28	66	-0.18	33	99
RB1	-0.021	0.096	0.2	1	-0.31	64	65
CDK4	0.023	0.099	0.32	64	-10000	0	64
CDK6	0.022	0.1	0.32	66	-0.25	2	68
G1/S progression	0.002	0.1	0.31	64	-0.2	1	65

×

Visual signal transduction: Rods

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:K +	0.015	0.022	-9999	-0.65	1	1
GNAT1/GTP	-0.006	0.054	-9999	-0.49	11	11
Metarhodopsin II/Arrestin	-0.01	0.063	-9999	-0.42	21	21
PDE6G/GNAT1/GTP	-0.045	0.14	-9999	-0.46	88	88
mol:GTP	0	0	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
GNAT1	-0.003	0.073	-9999	-0.65	11	11
GRK1	-0.004	0.073	-9999	-0.65	11	11
CNG Channel	-0.16	0.27	-9999	-0.67	146	146
mol:Na +	-0.13	0.22	-9999	-0.7	62	62
mol:ADP	-0.004	0.073	-9999	-0.65	11	11
RGS9-1/Gbeta5/R9AP	-0.12	0.23	-9999	-0.6	119	119
mol:GDP	0	0	-9999	-10000	0	0
cGMP/CNG Channel	-0.14	0.23	-9999	-0.73	62	62
CNGB1	-0.055	0.2	-9999	-0.65	87	87
RDH5	-0.1	0.29	-9999	-0.81	124	124
SAG	0	0.031	-9999	-0.65	2	2
mol:Ca2+	-0.091	0.23	-9999	-0.68	62	62
Na + (4 Units)	-0.12	0.2	-9999	-0.65	62	62
RGS9	-0.12	0.3	-9999	-0.76	160	160
GNB1/GNGT1	-0.095	0.22	-9999	-0.62	137	137
GNAT1/GDP	-0.11	0.2	-9999	-0.53	123	123
GUCY2D	-0.023	0.15	-9999	-0.66	47	47
GNGT1	-0.12	0.3	-9999	-0.81	137	137
GUCY2F	0.002	0.005	-9999	-10000	0	0
GNB5	0.015	0.029	-9999	-0.85	1	1
mol:GMP (4 units)	-0.056	0.21	-9999	-0.6	81	81
mol:11-cis-retinal	-0.099	0.29	-9999	-0.81	124	124
mol:cGMP	-0.05	0.14	-9999	-0.57	30	30
GNB1	0.016	0	-9999	-10000	0	0
Rhodopsin	-0.098	0.23	-9999	-0.62	141	141
SLC24A1	0.015	0.022	-9999	-0.65	1	1
CNGA1	-0.096	0.27	-9999	-0.75	129	129
Metarhodopsin II	-0.013	0.071	-9999	-0.39	29	29
mol:Ca ++	0	0	-9999	-10000	0	0
GC1/GCAP Family	-0.056	0.15	-9999	-0.6	30	30
RGS9BP	-0.041	0.2	-9999	-0.73	68	68
Metarhodopsin II/Transducin	-0.041	0.14	-9999	-0.37	114	114
GCAP Family/Ca ++	-0.037	0.13	-9999	-0.44	75	75
PDE6A/B	-0.06	0.19	-9999	-0.62	87	87
mol:Pi	-0.12	0.23	-9999	-0.6	119	119
mol:all-trans-retinal	0	0	-9999	-10000	0	0
Transducin	-0.081	0.19	-9999	-0.5	146	146
PDE6B	-0.045	0.22	-9999	-0.84	63	63
PDE6A	-0.007	0.11	-9999	-0.65	27	27
PDE6G	-0.046	0.2	-9999	-0.7	77	77
RHO	-0.005	0.096	-9999	-0.65	19	19
PDE6	-0.17	0.28	-9999	-0.88	81	81
GUCA1A	-0.009	0.1	-9999	-0.65	21	21
GC2/GCAP Family	-0.037	0.13	-9999	-0.57	26	26
GUCA1C	-0.018	0.12	-9999	-0.65	31	31
GUCA1B	-0.01	0.14	-9999	-0.8	28	28

×

BCR signaling pathway

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
JUN	-0.038	0.18	-10000	0	-0.47	79	79
IKBKB	-0.007	0.095	-10000	0	-0.28	22	22
AKT1	-0.029	0.13	-10000	0	-0.29	52	52
IKBKG	-0.006	0.1	-10000	0	-0.32	24	24
CALM1	-0.051	0.18	-10000	0	-0.58	59	59
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
MAP3K1	-0.077	0.25	-10000	0	-0.68	92	92
MAP3K7	0.016	0	-10000	0	-10000	0	0
mol:Ca2+	-0.065	0.19	-10000	0	-0.57	73	73
DOK1	0.01	0.071	-10000	0	-0.85	6	6
AP-1	-0.022	0.12	0.21	17	-0.29	57	74
LYN	0.012	0.058	-10000	0	-0.85	4	4
BLNK	-0.011	0.14	-10000	0	-0.74	32	32
SHC1	0.015	0.022	-10000	0	-0.65	1	1
BCR complex	-0.15	0.29	-10000	0	-0.63	214	214
CD22	-0.16	0.31	-10000	0	-0.81	121	121
CAMK2G	-0.038	0.16	-10000	0	-0.6	42	42
CSNK2A1	0.016	0	-10000	0	-10000	0	0
INPP5D	0.009	0.076	-10000	0	-0.85	7	7
SHC/GRB2/SOS1	-0.12	0.22	-10000	0	-0.83	52	52
GO:0007205	-0.066	0.19	-10000	0	-0.59	73	73
SYK	-0.001	0.12	-10000	0	-0.8	19	19
ELK1	-0.053	0.18	-10000	0	-0.59	59	59
NFATC1	-0.07	0.22	-10000	0	-0.61	80	80
B-cell antigen/BCR complex	-0.15	0.29	-10000	0	-0.63	214	214
PAG1/CSK	-0.023	0.12	-10000	0	-0.66	31	31
NFKBIB	0.011	0.037	0.099	20	-0.14	1	21
HRAS	-0.051	0.19	-10000	0	-0.56	74	74
NFKBIA	0.011	0.037	0.099	20	-0.14	1	21
NF-kappa-B/RelA/I kappa B beta	0.018	0.031	-10000	0	-0.2	1	1
RasGAP/Csk	-0.16	0.28	-10000	0	-0.91	64	64
mol:GDP	-0.061	0.18	-10000	0	-0.55	73	73
PTEN	0.016	0	-10000	0	-10000	0	0
CD79B	-0.049	0.22	-10000	0	-0.81	70	70
NF-kappa-B/RelA/I kappa B alpha	0.018	0.031	-10000	0	-0.2	1	1
GRB2	0.016	0	-10000	0	-10000	0	0
PI3K/BCAP/CD19	-0.092	0.25	-10000	0	-0.6	107	107
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
mol:IP3	-0.076	0.19	-10000	0	-0.6	73	73
CSK	0.014	0.041	-10000	0	-0.85	2	2
FOS	-0.091	0.23	-10000	0	-0.61	101	101
CHUK	-0.006	0.1	-10000	0	-0.31	23	23
IBTK	0.016	0	-10000	0	-10000	0	0
CARD11/BCL10/MALT1/TAK1	-0.085	0.17	-10000	0	-0.6	65	65
PTPN6	-0.15	0.28	-10000	0	-0.86	92	92
RELA	0.016	0	-10000	0	-10000	0	0
BCL2A1	0.008	0.048	-10000	0	-0.13	63	63
VAV2	-0.16	0.29	-10000	0	-0.71	159	159
ubiquitin-dependent protein catabolic process	0.016	0.036	0.1	20	-0.13	1	21
BTK	-0.044	0.23	0.46	4	-1.3	29	33
CD19	-0.17	0.32	-10000	0	-0.75	170	170
MAP4K1	-0.049	0.22	-10000	0	-0.8	71	71
CD72	-0.016	0.16	-10000	0	-0.74	38	38
PAG1	-0.013	0.15	-10000	0	-0.84	30	30
MAPK14	-0.052	0.21	-10000	0	-0.56	84	84
SH3BP5	-0.05	0.23	-10000	0	-0.84	68	68
PIK3AP1	-0.074	0.24	-10000	0	-0.66	94	94
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72	-0.093	0.28	-10000	0	-0.76	90	90
RAF1	-0.038	0.17	-10000	0	-0.61	48	48
RasGAP/p62DOK/SHIP	-0.16	0.28	-10000	0	-0.92	66	66
CD79A	-0.13	0.3	-10000	0	-0.72	177	177
re-entry into mitotic cell cycle	-0.022	0.12	0.21	17	-0.29	59	76
RASA1	0.013	0.05	-10000	0	-0.85	3	3
MAPK3	-0.013	0.14	-10000	0	-0.52	35	35
MAPK1	-0.013	0.14	-10000	0	-0.5	40	40
CD72/SHP1	-0.11	0.29	-10000	0	-0.77	112	112
NFKB1	0.015	0.029	-10000	0	-0.85	1	1
MAPK8	-0.057	0.22	-10000	0	-0.56	92	92
actin cytoskeleton organization	-0.091	0.26	-10000	0	-0.68	89	89
NF-kappa-B/RelA	0.042	0.06	0.2	20	-0.26	2	22
Calcineurin	-0.056	0.13	-10000	0	-0.54	41	41
PI3K	-0.14	0.22	-10000	0	-0.65	78	78
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2	-0.081	0.21	0.29	24	-0.65	74	98
SOS1	0.016	0	-10000	0	-10000	0	0
Bam32/HPK1	-0.14	0.35	-10000	0	-0.96	118	118
DAPP1	-0.17	0.37	-10000	0	-1.1	103	103
cytokine secretion	-0.063	0.2	-10000	0	-0.55	80	80
mol:DAG	-0.076	0.19	-10000	0	-0.6	73	73
PLCG2	-0.054	0.21	-10000	0	-0.68	90	90
MAP2K1	-0.025	0.16	-10000	0	-0.57	41	41
B-cell antigen/BCR complex/FcgammaRIIB	-0.19	0.32	-10000	0	-0.74	162	162
mol:PI-3-4-5-P3	-0.099	0.15	-10000	0	-0.43	72	72
ETS1	-0.043	0.18	-10000	0	-0.56	64	64
B-cell antigen/BCR complex/LYN/SYK/BLNK	-0.14	0.26	-10000	0	-0.7	112	112
B-cell antigen/BCR complex/LYN	-0.14	0.31	-10000	0	-0.85	108	108
MALT1	0.015	0.029	-10000	0	-0.85	1	1
TRAF6	0.016	0	-10000	0	-10000	0	0
RAC1	-0.1	0.28	-10000	0	-0.75	89	89
B-cell antigen/BCR complex/LYN/SYK	-0.16	0.3	-10000	0	-0.87	99	99
CARD11	-0.088	0.23	-10000	0	-0.65	97	97
FCGR2B	-0.08	0.26	-10000	0	-0.79	106	106
PPP3CA	0.016	0	-10000	0	-10000	0	0
BCL10	0.016	0	-10000	0	-10000	0	0
IKK complex	0.01	0.046	-10000	0	-0.13	2	2
PTPRC	-0.028	0.19	-10000	0	-0.82	47	47
PDPK1	-0.031	0.12	-10000	0	-0.29	52	52
PPP3CB	0.016	0	-10000	0	-10000	0	0
PPP3CC	0.016	0	-10000	0	-10000	0	0
POU2F2	0.016	0.035	-10000	0	-0.13	28	28

×

Noncanonical Wnt signaling pathway

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
NFATC2	-0.081	0.27	-9999	-0.83	102	102
GNB1/GNG2	-0.14	0.19	-9999	-0.6	83	83
mol:DAG	-0.085	0.2	-9999	-0.61	50	50
PLCG1	-0.088	0.2	-9999	-0.64	50	50
YES1	-0.097	0.19	-9999	-0.6	53	53
FZD3	0.016	0	-9999	-10000	0	0
FZD6	0.014	0.043	-9999	-0.72	3	3
G protein	-0.09	0.2	-9999	-0.65	50	50
MAP3K7	-0.071	0.18	-9999	-0.54	44	44
mol:Ca2+	-0.082	0.19	-9999	-0.58	50	50
mol:IP3	-0.085	0.2	-9999	-0.61	50	50
NLK	-0.004	0.008	-9999	-10000	0	0
GNB1	0.016	0	-9999	-10000	0	0
CAMK2A	-0.087	0.2	-9999	-0.59	49	49
MAP3K7IP1	0	0	-9999	-10000	0	0
Noncanonical Wnts/FZD	-0.11	0.2	-9999	-0.56	81	81
CSNK1A1	0.016	0	-9999	-10000	0	0
GNAS	-0.097	0.19	-9999	-0.6	53	53
GO:0007205	-0.083	0.19	-9999	-0.6	50	50
WNT6	-0.098	0.27	-9999	-0.73	134	134
WNT4	-0.089	0.26	-9999	-0.72	127	127
NFAT1/CK1 alpha	-0.15	0.2	-9999	-0.63	73	73
GNG2	-0.016	0.16	-9999	-0.85	33	33
WNT5A	-0.072	0.23	-9999	-0.69	112	112
WNT11	-0.096	0.26	-9999	-0.69	140	140
CDC42	-0.083	0.18	-9999	-0.56	53	53

×

Fc-epsilon receptor I signaling in mast cells

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
PPAP2A	0.01	0.071	-9999	-0.85	6	6
LAT2	-0.067	0.28	-9999	-0.86	66	66
AP1	-0.13	0.23	-9999	-0.7	98	98
mol:PIP3	-0.068	0.28	-9999	-0.76	85	85
IKBKB	-0.014	0.15	-9999	-0.38	78	78
AKT1	-0.052	0.24	-9999	-0.76	52	52
IKBKG	-0.015	0.15	-9999	-0.38	78	78
MS4A2	-0.11	0.29	-9999	-0.8	133	133
mol:Sphingosine-1-phosphate	0	0	-9999	-10000	0	0
PIK3CA	0.01	0.071	-9999	-0.85	6	6
MAP3K1	-0.022	0.22	-9999	-0.63	73	73
mol:Ca2+	-0.038	0.2	-9999	-0.51	85	85
LYN	0.011	0.06	-9999	-0.88	4	4
CBLB	-0.058	0.24	-9999	-0.76	64	64
SHC1	0.015	0.022	-9999	-0.65	1	1
RasGAP/p62DOK	-0.063	0.17	-9999	-0.53	102	102
positive regulation of cell migration	0	0	-9999	-10000	0	0
INPP5D	0.009	0.076	-9999	-0.85	7	7
PLD2	-0.098	0.28	-9999	-0.68	118	118
PTPN13	-0.051	0.24	-9999	-0.72	67	67
PTPN11	0.013	0.031	-9999	-0.86	1	1
GO:0007205	0	0	-9999	-10000	0	0
regulation of mast cell degranulation	-0.002	0.18	-9999	-0.44	58	58
SYK	-0.003	0.12	-9999	-0.82	19	19
GRB2	0.016	0.001	-9999	-10000	0	0
LAT/PLCgamma1/GRB2/SLP76/GADs	-0.14	0.25	-9999	-0.78	90	90
LAT	-0.079	0.27	-9999	-0.79	79	79
PAK2	-0.04	0.25	-9999	-0.74	74	74
NFATC2	-0.13	0.28	-9999	-0.84	102	102
HRAS	-0.06	0.29	-9999	-0.85	79	79
GAB2	0.011	0.06	-9999	-0.72	6	6
PLA2G1B	0.037	0.033	-9999	-0.41	1	1
Fc epsilon R1	-0.16	0.3	-9999	-0.67	193	193
Antigen/IgE/Fc epsilon R1	-0.15	0.28	-9999	-0.66	167	167
mol:GDP	-0.07	0.3	-9999	-0.9	78	78
JUN	0.01	0.069	-9999	-0.76	7	7
mol:Ca++	0	0	-9999	-10000	0	0
PIK3R1	0.01	0.066	-9999	-0.78	6	6
FOS	-0.086	0.26	-9999	-0.74	120	120
Antigen/IgE/Fc epsilon R1/LYN/SYK	-0.11	0.24	-9999	-0.58	129	129
CHUK	-0.014	0.15	-9999	-0.38	77	77
KLRG1	-0.065	0.25	-9999	-0.75	71	71
VAV1	-0.079	0.3	-9999	-0.9	78	78
calcium-dependent protein kinase C activity	0	0	-9999	-10000	0	0
CBL	-0.059	0.24	-9999	-0.76	65	65
negative regulation of mast cell degranulation	-0.053	0.23	-9999	-0.7	72	72
BTK	-0.12	0.28	-9999	-0.85	81	81
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK	-0.12	0.34	-9999	-1	84	84
GAB2/PI3K/SHP2	-0.12	0.24	-9999	-0.85	57	57
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP	-0.063	0.24	-9999	-0.77	63	63
RAF1	0.024	0.028	-9999	-10000	0	0
Fc epsilon R1/FcgammaRIIB/SHIP	-0.19	0.35	-9999	-0.83	147	147
FCER1G	-0.008	0.15	-9999	-0.83	27	27
FCER1A	-0.091	0.28	-9999	-0.8	117	117
Antigen/IgE/Fc epsilon R1/Fyn	-0.14	0.27	-9999	-0.63	170	170
MAPK3	0.036	0.035	-9999	-0.6	1	1
MAPK1	0.037	0.029	-9999	-10000	0	0
NFKB1	0.015	0.029	-9999	-0.85	1	1
MAPK8	0.008	0.096	-9999	-0.59	13	13
DUSP1	-0.081	0.27	-9999	-0.84	101	101
NF-kappa-B/RelA	-0.038	0.068	-9999	-0.29	1	1
actin cytoskeleton reorganization	-0.052	0.22	-9999	-0.69	64	64
mol:Glucocorticoid Dexamethasone	0	0	-9999	-10000	0	0
PI3K	-0.11	0.24	-9999	-0.82	74	74
FER	-0.06	0.24	-9999	-0.76	67	67
RELA	0.016	0	-9999	-10000	0	0
ITK	-0.085	0.21	-9999	-0.67	91	91
SOS1	0.016	0	-9999	-10000	0	0
PLCG1	-0.065	0.3	-9999	-0.89	78	78
cytokine secretion	-0.028	0.049	-9999	-10000	0	0
SPHK1	-0.099	0.28	-9999	-0.76	96	96
PTK2	-0.057	0.24	-9999	-0.74	64	64
NTAL/PLCgamma1/GRB2/SLP76/GADs	-0.14	0.26	-9999	-0.83	85	85
EDG1	0	0	-9999	-10000	0	0
mol:DAG	-0.056	0.26	-9999	-0.73	80	80
MAP2K2	0.031	0.041	-9999	-0.54	3	3
MAP2K1	0.033	0.024	-9999	-10000	0	0
MAP2K7	0.014	0.041	-9999	-0.85	2	2
KLRG1/SHP2	-0.095	0.22	-9999	-0.71	72	72
MAP2K4	0.021	0.055	-9999	-1.1	2	2
Fc epsilon R1/FcgammaRIIB	-0.2	0.36	-9999	-0.76	198	198
mol:Choline	-0.095	0.28	-9999	-0.66	119	119
SHC/Grb2/SOS1	-0.089	0.2	-9999	-0.75	54	54
FYN	0.007	0.086	-9999	-0.85	9	9
DOK1	0.01	0.071	-9999	-0.85	6	6
PXN	-0.041	0.21	-9999	-0.68	59	59
HCLS1	-0.074	0.29	-9999	-0.84	77	77
PRKCB	-0.043	0.22	-9999	-0.56	88	88
FCGR2B	-0.08	0.26	-9999	-0.79	106	106
IGHE	-0.002	0.009	-9999	-10000	0	0
KLRG1/SHIP	-0.055	0.24	-9999	-0.73	72	72
LCP2	-0.029	0.19	-9999	-0.85	46	46
PLA2G4A	-0.081	0.27	-9999	-0.77	85	85
RASA1	0.013	0.05	-9999	-0.85	3	3
mol:Phosphatidic acid	-0.095	0.28	-9999	-0.66	119	119
IKK complex	0.01	0.12	-9999	-0.29	41	41
WIPF1	0.016	0	-9999	-10000	0	0

×

Caspase cascade in apoptosis

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TOP1	-0.032	0.21	0.28	1	-0.53	109	110
ACTA1	-0.063	0.27	0.3	5	-0.71	109	114
NUMA1	-0.032	0.21	0.28	1	-0.53	108	109
SPTAN1	-0.055	0.27	-10000	0	-0.71	107	107
LIMK1	-0.058	0.27	0.32	1	-0.7	110	111
BIRC3	-0.066	0.25	-10000	0	-0.81	89	89
BIRC2	0.016	0	-10000	0	-10000	0	0
BAX	0.014	0.041	-10000	0	-0.85	2	2
CASP10	-0.085	0.3	-10000	0	-0.69	150	150
CRMA	0	0	-10000	0	-10000	0	0
XIAP	0.016	0	-10000	0	-10000	0	0
PTK2	-0.032	0.21	0.28	1	-0.53	108	109
DIABLO	0.016	0	-10000	0	-10000	0	0
apoptotic nuclear changes	-0.053	0.26	-10000	0	-0.69	107	107
response to UV	0	0	-10000	0	-10000	0	0
CRADD	0.016	0	-10000	0	-10000	0	0
GSN	-0.056	0.27	0.32	1	-0.72	107	108
MADD	0.016	0	-10000	0	-10000	0	0
TFAP2A	-0.1	0.26	-10000	0	-0.78	81	81
BID	-0.022	0.13	-10000	0	-0.32	116	116
MAP3K1	-0.003	0.082	-10000	0	-0.23	41	41
TRADD	0.015	0.029	-10000	0	-0.85	1	1
mol:Ca2+	0	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0.001	0.023	-10000	0	-0.65	1	1
mol:Activated DNA	0	0	-10000	0	-10000	0	0
ARHGDIB	-0.065	0.3	0.32	1	-0.76	111	112
CASP9	0.016	0	-10000	0	-10000	0	0
DNA repair	-0.009	0.076	-10000	0	-0.24	44	44
neuron apoptosis	0.021	0.046	-10000	0	-0.58	3	3
mol:NAD	0	0	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	-0.045	0.26	-10000	0	-0.68	107	107
APAF1	0.015	0.029	-10000	0	-0.85	1	1
CASP6	-0.001	0.13	-10000	0	-0.54	22	22
TRAF2	0.014	0.041	-10000	0	-0.85	2	2
ICAD/CAD	-0.045	0.26	-10000	0	-0.68	107	107
CASP7	0.025	0.11	0.34	89	-10000	0	89
KRT18	0.012	0.042	-10000	0	-0.42	2	2
apoptosis	-0.052	0.24	0.31	1	-0.61	110	111
DFFA	-0.055	0.27	0.32	1	-0.71	107	108
DFFB	-0.055	0.27	-10000	0	-0.71	107	107
PARP1	0.009	0.076	0.24	43	-10000	0	43
actin filament polymerization	0.043	0.25	0.64	110	-10000	0	110
TNF	-0.062	0.23	-10000	0	-0.75	90	90
CYCS	-0.018	0.1	-10000	0	-0.29	57	57
SATB1	0.005	0.13	-10000	0	-0.51	26	26
SLK	-0.057	0.27	0.32	1	-0.7	109	110
p15 BID/BAX	-0.013	0.12	-10000	0	-0.37	43	43
CASP2	0.016	0.12	-10000	0	-0.5	18	18
JNK cascade	0.003	0.082	0.23	41	-10000	0	41
CASP3	-0.068	0.28	0.32	6	-0.75	109	115
LMNB2	0.019	0.095	-10000	0	-0.42	18	18
RIPK1	0.016	0	-10000	0	-10000	0	0
CASP4	0.011	0.065	-10000	0	-0.85	5	5
Mammalian IAPs/DIABLO	-0.048	0.14	-10000	0	-0.51	70	70
negative regulation of DNA binding	-0.099	0.25	-10000	0	-0.76	82	82
stress fiber formation	-0.054	0.26	0.32	1	-0.69	109	110
GZMB	-0.1	0.32	-10000	0	-0.77	146	146
CASP1	-0.001	0.12	-10000	0	-0.57	34	34
LMNB1	0.016	0.1	-10000	0	-0.45	24	24
APP	0.021	0.046	-10000	0	-0.59	3	3
TNFRSF1A	0.016	0	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
CASP8	0.014	0.023	-10000	0	-0.66	1	1
VIM	-0.056	0.23	0.31	1	-0.6	108	109
LMNA	0.019	0.1	-10000	0	-0.46	18	18
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD	0.006	0.12	-10000	0	-0.54	18	18
LRDD	0.011	0.066	-10000	0	-0.78	6	6
SREBF1	-0.057	0.27	-10000	0	-0.71	109	109
APAF-1/Caspase 9	0.001	0.052	-10000	0	-10000	0	0
nuclear fragmentation during apoptosis	-0.031	0.2	0.28	1	-0.52	109	110
CFL2	-0.046	0.26	-10000	0	-0.66	110	110
GAS2	-0.1	0.28	-10000	0	-0.72	117	117
positive regulation of apoptosis	0.021	0.1	-10000	0	-0.41	22	22
PRF1	-0.048	0.22	-10000	0	-0.81	69	69

×

Glucocorticoid receptor regulatory network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PCK2	-0.002	0.11	0.46	1	-1	4	5
SMARCC2	0.016	0.014	-10000	0	-10000	0	0
SMARCC1	0.016	0.014	-10000	0	-10000	0	0
TBX21	-0.074	0.33	-10000	0	-1.1	67	67
SUMO2	0.014	0.01	-10000	0	-10000	0	0
STAT1 (dimer)	0.019	0.076	-10000	0	-0.72	9	9
FKBP4	0.016	0	-10000	0	-10000	0	0
FKBP5	-0.066	0.24	-10000	0	-0.74	96	96
GR alpha/HSP90/FKBP51/HSP90	0.002	0.19	0.36	19	-0.51	68	87
PRL	-0.014	0.13	-10000	0	-0.74	3	3
cortisol/GR alpha (dimer)/TIF2	0.067	0.31	0.59	104	-0.58	27	131
RELA	-0.056	0.1	-10000	0	-10000	0	0
FGG	-0.15	0.43	0.56	36	-0.73	247	283
GR beta/TIF2	0.01	0.2	0.38	34	-0.6	61	95
IFNG	-0.28	0.41	-10000	0	-0.96	151	151
apoptosis	-0.04	0.18	0.62	12	-0.66	14	26
CREB1	0.008	0.046	-10000	0	-10000	0	0
histone acetylation	0.008	0.16	0.41	8	-0.51	40	48
BGLAP	0.002	0.14	-10000	0	-0.69	7	7
GR/PKAc	0.06	0.11	0.37	10	-0.54	1	11
NF kappa B1 p50/RelA	-0.1	0.2	-10000	0	-0.54	46	46
SMARCD1	0.016	0.014	-10000	0	-10000	0	0
MDM2	0.045	0.097	0.32	31	-10000	0	31
GATA3	-0.11	0.29	-10000	0	-0.72	159	159
AKT1	0.001	0.033	-10000	0	-0.86	1	1
CSF2	-0.02	0.14	-10000	0	-0.69	7	7
GSK3B	0.014	0.01	-10000	0	-10000	0	0
NR1I3	-0.006	0.18	0.62	10	-0.79	8	18
CSN2	0.046	0.2	0.48	18	-0.56	2	20
BRG1/BAF155/BAF170/BAF60A	0.037	0.053	-10000	0	-0.51	1	1
NFATC1	0.006	0.1	-10000	0	-0.85	13	13
POU2F1	0.014	0.053	-10000	0	-0.85	3	3
CDKN1A	0.034	0.15	-10000	0	-1.7	6	6
response to stress	0	0	-10000	0	-10000	0	0
response to UV	-0.001	0.008	-10000	0	-10000	0	0
SFN	-0.23	0.35	-10000	0	-0.72	299	299
GR alpha/HSP90/FKBP51/HSP90/14-3-3	-0.14	0.28	0.36	7	-0.66	98	105
prolactin receptor activity	0	0	-10000	0	-10000	0	0
EGR1	-0.048	0.28	0.6	10	-0.93	50	60
JUN	-0.16	0.22	-10000	0	-0.63	71	71
IL4	-0.023	0.16	-10000	0	-0.6	27	27
CDK5R1	0.012	0.049	-10000	0	-0.7	4	4
PRKACA	0.016	0	-10000	0	-10000	0	0
cortisol/GR alpha (monomer)/AP-1	-0.26	0.3	0.29	4	-0.69	200	204
GR alpha/HSP90/FKBP51/HSP90/PP5C	0.014	0.18	0.36	19	-0.5	37	56
cortisol/GR alpha (monomer)	0.12	0.34	0.68	129	-0.58	5	134
NCOA2	-0.039	0.21	-10000	0	-0.85	57	57
response to hypoxia	0	0	-10000	0	-10000	0	0
FOS	-0.15	0.27	-10000	0	-0.81	120	120
AP-1/NFAT1-c-4	-0.36	0.38	-10000	0	-0.85	239	239
AFP	-0.13	0.24	-10000	0	-0.8	48	48
SUV420H1	0.015	0.022	-10000	0	-0.65	1	1
IRF1	0.079	0.16	0.53	19	-0.6	1	20
TP53	0.039	0.058	-10000	0	-0.52	9	9
PPP5C	0.016	0	-10000	0	-10000	0	0
KRT17	-0.39	0.54	-10000	0	-1.1	261	261
KRT14	-0.11	0.26	-10000	0	-0.77	79	79
TBP	0.028	0.013	-10000	0	-10000	0	0
CREBBP	0.035	0.078	0.36	3	-10000	0	3
HDAC1	0.012	0.01	-10000	0	-10000	0	0
HDAC2	0.016	0.007	-10000	0	-10000	0	0
AP-1	-0.36	0.38	-10000	0	-0.85	243	243
MAPK14	0.014	0.009	-10000	0	-10000	0	0
MAPK10	-0.008	0.13	-10000	0	-0.85	22	22
MAPK11	-0.001	0.11	-10000	0	-0.83	15	15
KRT5	-0.3	0.43	-10000	0	-0.95	196	196
interleukin-1 receptor activity	0	0.007	-10000	0	-10000	0	0
NCOA1	0.019	0.008	-10000	0	-10000	0	0
STAT1	0.019	0.076	-10000	0	-0.73	9	9
CGA	-0.041	0.19	-10000	0	-0.73	31	31
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2	0.038	0.14	0.43	24	-0.44	1	25
MAPK3	0.013	0.03	-10000	0	-0.85	1	1
MAPK1	0.013	0.03	-10000	0	-0.85	1	1
ICAM1	-0.16	0.41	-10000	0	-1.3	68	68
NFKB1	-0.057	0.11	-10000	0	-0.96	1	1
MAPK8	-0.11	0.2	-10000	0	-0.56	74	74
MAPK9	0.014	0.009	-10000	0	-10000	0	0
cortisol/GR alpha (dimer)	-0.045	0.18	0.62	12	-0.7	14	26
BAX	0.04	0.091	-10000	0	-1.7	2	2
POMC	-0.12	0.32	-10000	0	-1.2	34	34
EP300	0.033	0.087	0.4	1	-0.79	2	3
cortisol/GR alpha (dimer)/p53	0.12	0.28	0.6	119	-0.73	2	121
proteasomal ubiquitin-dependent protein catabolic process	0.025	0.076	0.26	6	-10000	0	6
SGK1	0.043	0.28	-10000	0	-1.6	23	23
IL13	-0.21	0.31	-10000	0	-0.83	117	117
IL6	-0.3	0.53	-10000	0	-1.1	200	200
PRKACG	0.002	0.032	-10000	0	-0.65	2	2
IL5	-0.18	0.25	-10000	0	-0.84	56	56
IL2	-0.19	0.25	-10000	0	-0.71	79	79
CDK5	0.014	0.029	-10000	0	-0.84	1	1
PRKACB	0.016	0	-10000	0	-10000	0	0
HSP90AA1	0.016	0	-10000	0	-10000	0	0
IL8	-0.22	0.45	-10000	0	-1	162	162
CDK5R1/CDK5	-0.001	0.043	-10000	0	-0.55	5	5
NF kappa B1 p50/RelA/PKAc	-0.047	0.15	-10000	0	-0.59	2	2
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90	0.12	0.26	0.58	101	-0.55	2	103
SMARCA4	0.015	0.032	-10000	0	-0.85	1	1
chromatin remodeling	0.084	0.16	0.43	49	-0.5	2	51
NF kappa B1 p50/RelA/Cbp	-0.039	0.19	0.45	1	-0.69	12	13
JUN (dimer)	-0.16	0.22	-10000	0	-0.63	71	71
YWHAH	0.016	0	-10000	0	-10000	0	0
VIPR1	-0.078	0.29	-10000	0	-0.77	106	106
NR3C1	0.07	0.2	0.52	63	-0.75	4	67
NR4A1	-0.12	0.3	-10000	0	-0.73	166	166
TIF2/SUV420H1	-0.042	0.16	-10000	0	-0.65	58	58
MAPKKK cascade	-0.04	0.18	0.62	12	-0.66	14	26
cortisol/GR alpha (dimer)/Src-1	0.12	0.28	0.59	119	-0.64	2	121
PBX1	0.005	0.1	-10000	0	-0.85	13	13
POU1F1	0.007	0.018	-10000	0	-10000	0	0
SELE	-0.31	0.57	-10000	0	-1.3	196	196
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A	0.084	0.16	0.43	49	-0.51	2	51
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90	0.12	0.26	0.58	101	-0.55	2	103
mol:cortisol	0.054	0.2	0.41	119	-0.27	11	130
MMP1	-0.45	0.64	-10000	0	-1.3	267	267

×

Paxillin-independent events mediated by a4b1 and a4b7

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.023	0.19	-9999	-0.59	87	87
CRKL	0.016	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
DOCK1	0.014	0.041	-9999	-0.85	2	2
ITGA4	-0.064	0.25	-9999	-0.84	83	83
alpha4/beta7 Integrin/MAdCAM1	-0.073	0.18	-9999	-0.56	88	88
EPO	-0.22	0.34	-9999	-0.7	285	285
alpha4/beta7 Integrin	-0.066	0.2	-9999	-0.66	89	89
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.015	0.022	-9999	-0.65	1	1
alpha4/beta1 Integrin	-0.06	0.19	-9999	-0.65	83	83
EPO/EPOR (dimer)	-0.17	0.25	-9999	-0.52	287	287
lamellipodium assembly	0.001	0.057	-9999	-0.49	10	10
PIK3CA	0.01	0.071	-9999	-0.85	6	6
PI3K	-0.008	0.072	-9999	-0.62	12	12
ARF6	0.016	0	-9999	-10000	0	0
JAK2	-0.098	0.19	-9999	-0.51	40	40
PXN	0.016	0	-9999	-10000	0	0
PIK3R1	0.011	0.066	-9999	-0.78	6	6
MADCAM1	-0.026	0.16	-9999	-0.65	53	53
cell adhesion	-0.073	0.18	-9999	-0.56	88	88
CRKL/CBL	-0.001	0.022	-9999	-0.65	1	1
ITGB1	0.016	0	-9999	-10000	0	0
SRC	-0.083	0.26	-9999	-0.58	177	177
ITGB7	0.008	0.082	-9999	-0.85	8	8
RAC1	0.016	0	-9999	-10000	0	0
alpha4/beta1 Integrin/VCAM1	-0.13	0.27	-9999	-0.64	177	177
p130Cas/Crk/Dock1	-0.047	0.24	-9999	-0.84	30	30
VCAM1	-0.1	0.3	-9999	-0.85	123	123
RHOA	0.016	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/GIT1	-0.048	0.15	-9999	-0.52	82	82
BCAR1	-0.069	0.25	-9999	-0.54	180	180
EPOR	0.013	0.048	-9999	-0.7	4	4
mol:GDP	0	0	-9999	-10000	0	0
CBL	0.015	0.029	-9999	-0.85	1	1
GIT1	0.014	0.041	-9999	-0.85	2	2
Rac1/GTP	0.001	0.059	-9999	-0.51	10	10

×

S1P3 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
PDGFRB	-0.12	0.31	-9999	-0.84	140	140
mol:S1P	0.002	0.003	-9999	-10000	0	0
S1P1/S1P/Gi	0.011	0.096	-9999	-0.35	23	23
GNAO1	-0.051	0.22	-9999	-0.75	79	79
S1P/S1P3/G12/G13	-0.061	0.16	-9999	-0.52	92	92
AKT1	-0.13	0.3	-9999	-0.78	134	134
AKT3	-0.11	0.31	-9999	-0.78	113	113
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	-0.12	0.31	-9999	-0.84	140	140
GNAI2	0.017	0.029	-9999	-0.85	1	1
GNAI3	0.018	0.002	-9999	-10000	0	0
GNAI1	0.006	0.1	-9999	-0.85	12	12
mol:GDP	0	0	-9999	-10000	0	0
S1PR3	-0.084	0.28	-9999	-0.82	109	109
S1PR2	0.012	0.056	-9999	-0.73	5	5
EDG1	0	0	-9999	-10000	0	0
mol:Ca2+	-0.03	0.2	-9999	-0.84	32	32
MAPK3	-0.02	0.2	-9999	-0.82	31	31
MAPK1	-0.02	0.2	-9999	-0.82	31	31
JAK2	-0.03	0.22	-9999	-0.75	50	50
CXCR4	-0.051	0.26	-9999	-0.76	74	74
FLT1	-0.21	0.38	-9999	-0.84	240	240
RhoA/GDP	0	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
SRC	-0.019	0.2	-9999	-0.82	31	31
S1P/S1P3/Gi	-0.031	0.21	-9999	-0.85	32	32
RAC1	0.016	0	-9999	-10000	0	0
RhoA/GTP	-0.068	0.17	-9999	-0.8	30	30
VEGFA	-0.21	0.38	-9999	-0.84	236	236
S1P/S1P2/Gi	0.014	0.11	-9999	-0.39	25	25
VEGFR1 homodimer/VEGFA homodimer	-0.3	0.51	-9999	-1	272	272
RHOA	0.016	0	-9999	-10000	0	0
S1P/S1P3/Gq	-0.072	0.25	-9999	-0.52	164	164
GNAQ	0.016	0	-9999	-10000	0	0
GNAZ	0.009	0.085	-9999	-0.79	10	10
G12/G13	-0.001	0.016	-9999	-0.48	1	1
GNA14	-0.078	0.27	-9999	-0.84	97	97
GNA15	-0.014	0.16	-9999	-0.81	33	33
GNA12	0.016	0	-9999	-10000	0	0
GNA13	0.015	0.022	-9999	-0.65	1	1
GNA11	-0.011	0.14	-9999	-0.75	31	31
Rac1/GTP	-0.068	0.17	-9999	-0.8	30	30

×

a4b1 and a4b7 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ITGB1	0.016	0	-9999	-10000	0	0
ITGB7	0.008	0.082	-9999	-0.85	8	8
ITGA4	-0.064	0.25	-9999	-0.84	83	83
alpha4/beta7 Integrin	-0.066	0.2	-9999	-0.66	89	89
alpha4/beta1 Integrin	-0.06	0.19	-9999	-0.65	83	83

×

Ephrin B reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EFNB2	-0.02	0.17	-10000	0	-0.85	37	37
EPHB2	-0.025	0.17	-10000	0	-0.72	50	50
EFNB1	-0.065	0.22	-10000	0	-0.58	136	136
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	-0.12	0.22	-10000	0	-0.81	40	40
Ephrin B2/EPHB1-2	-0.087	0.2	-10000	0	-0.48	161	161
neuron projection morphogenesis	-0.11	0.21	-10000	0	-0.76	40	40
Ephrin B1/EPHB1-2/Tiam1	-0.12	0.24	-10000	0	-0.69	78	78
DNM1	-0.1	0.28	-10000	0	-0.77	136	136
cell-cell signaling	-0.001	0.003	-10000	0	-10000	0	0
MAP2K4	0.003	0.14	-10000	0	-0.86	23	23
YES1	-0.027	0.18	-10000	0	-1.1	23	23
Ephrin B1/EPHB1-2/NCK2	-0.12	0.23	-10000	0	-0.58	124	124
PI3K	-0.004	0.16	-10000	0	-0.81	31	31
mol:GDP	-0.13	0.24	-10000	0	-0.59	129	129
ITGA2B	-0.058	0.22	-10000	0	-0.73	88	88
endothelial cell proliferation	-0.028	0.12	-10000	0	-0.57	44	44
FYN	-0.029	0.18	-10000	0	-1.1	23	23
MAP3K7	-0.024	0.15	-10000	0	-0.91	23	23
FGR	-0.032	0.18	-10000	0	-1.1	23	23
TIAM1	0.005	0.098	-10000	0	-0.83	12	12
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
RGS3	0.015	0.032	-10000	0	-0.65	2	2
cell adhesion	-0.058	0.23	-10000	0	-0.66	78	78
LYN	-0.028	0.18	-10000	0	-1.1	23	23
Ephrin B1/EPHB1-2/Src Family Kinases	-0.028	0.17	-10000	0	-1	23	23
Ephrin B1/EPHB1-2	-0.031	0.16	-10000	0	-0.98	23	23
SRC	-0.027	0.18	-10000	0	-1.1	23	23
ITGB3	-0.046	0.21	-10000	0	-0.76	71	71
EPHB1	-0.06	0.22	-10000	0	-0.71	93	93
EPHB4	0.009	0.076	-10000	0	-0.85	7	7
RAC1	0.016	0	-10000	0	-10000	0	0
Ephrin B2/EPHB4	-0.028	0.12	-10000	0	-0.58	44	44
alphaIIb/beta3 Integrin	-0.099	0.23	-10000	0	-0.6	147	147
BLK	-0.043	0.18	-10000	0	-1.1	23	23
HCK	-0.031	0.18	-10000	0	-1.1	23	23
regulation of stress fiber formation	0.12	0.22	0.57	124	-10000	0	124
MAPK8	0.006	0.15	-10000	0	-0.72	33	33
Ephrin B1/EPHB1-2/RGS3	-0.12	0.23	-10000	0	-0.58	126	126
endothelial cell migration	-0.042	0.17	-10000	0	-0.61	65	65
NCK2	0.016	0	-10000	0	-10000	0	0
PTPN13	-0.015	0.16	-10000	0	-0.96	24	24
regulation of focal adhesion formation	0.12	0.22	0.57	124	-10000	0	124
chemotaxis	0.12	0.22	0.57	126	-10000	0	126
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
Rac1/GTP	-0.12	0.22	-10000	0	-0.8	40	40
angiogenesis	-0.03	0.16	-10000	0	-0.97	23	23
LCK	-0.045	0.19	-10000	0	-1.1	23	23

×

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K1	-0.052	0.21	-10000	0	-0.64	67	67
CRKL	-0.029	0.16	-10000	0	-0.48	57	57
HRAS	-0.038	0.22	-10000	0	-0.68	65	65
mol:PIP3	-0.046	0.15	-10000	0	-0.46	62	62
SPRED1	0.013	0.05	-10000	0	-0.85	3	3
SPRED2	0.014	0.041	-10000	0	-0.85	2	2
GAB1	-0.04	0.16	-10000	0	-0.5	60	60
FOXO3	-0.019	0.14	-10000	0	-0.52	19	19
AKT1	-0.031	0.15	-10000	0	-0.46	56	56
BAD	-0.021	0.14	-10000	0	-0.42	60	60
megakaryocyte differentiation	-0.074	0.22	-10000	0	-0.59	114	114
GSK3B	-0.019	0.14	-10000	0	-0.42	52	52
RAF1	-0.015	0.18	-10000	0	-0.52	57	57
SHC1	0.015	0.022	-10000	0	-0.65	1	1
STAT3	-0.039	0.16	-10000	0	-0.5	55	55
STAT1	-0.098	0.32	-10000	0	-1.1	57	57
HRAS/SPRED1	-0.06	0.16	-10000	0	-0.51	65	65
cell proliferation	-0.044	0.17	-10000	0	-0.49	67	67
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
TEC	0.016	0	-10000	0	-10000	0	0
RPS6KB1	-0.038	0.16	-10000	0	-0.47	68	68
HRAS/SPRED2	-0.06	0.16	-10000	0	-0.51	64	64
LYN/TEC/p62DOK	-0.058	0.15	-10000	0	-0.72	18	18
MAPK3	0.008	0.13	-10000	0	-0.38	34	34
STAP1	-0.11	0.25	-10000	0	-0.57	168	168
GRAP2	-0.039	0.21	-10000	0	-0.85	57	57
JAK2	-0.13	0.26	-10000	0	-0.93	60	60
STAT1 (dimer)	-0.095	0.32	-10000	0	-1.1	57	57
mol:Gleevec	0	0.006	-10000	0	-10000	0	0
GRB2/SOCS1/VAV1	-0.1	0.22	-10000	0	-0.7	73	73
actin filament polymerization	-0.047	0.18	-10000	0	-0.53	71	71
LYN	0.012	0.058	-10000	0	-0.85	4	4
STAP1/STAT5A (dimer)	-0.11	0.28	-10000	0	-0.67	148	148
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
CBL/CRKL/GRB2	-0.046	0.12	-10000	0	-0.61	12	12
PI3K	-0.025	0.16	-10000	0	-0.48	64	64
PTEN	0.016	0	-10000	0	-10000	0	0
SCF/KIT/EPO/EPOR	-0.19	0.41	-10000	0	-1.3	73	73
MAPK8	-0.045	0.17	-10000	0	-0.5	67	67
STAT3 (dimer)	-0.038	0.16	-10000	0	-0.49	55	55
positive regulation of transcription	0.013	0.11	-10000	0	-0.32	14	14
mol:GDP	-0.1	0.22	-10000	0	-0.72	74	74
PIK3C2B	-0.042	0.17	-10000	0	-0.52	60	60
CBL/CRKL	-0.018	0.15	-10000	0	-0.62	13	13
FER	-0.041	0.16	-10000	0	-0.5	59	59
SH2B3	-0.04	0.16	-10000	0	-0.51	57	57
PDPK1	-0.035	0.14	-10000	0	-0.43	62	62
SNAI2	-0.1	0.24	-10000	0	-0.57	139	139
positive regulation of cell proliferation	-0.066	0.25	-10000	0	-0.79	61	61
KITLG	-0.029	0.18	-10000	0	-0.73	54	54
cell motility	-0.066	0.25	-10000	0	-0.79	61	61
PTPN6	0.01	0.042	-10000	0	-0.84	2	2
EPOR	0.007	0.12	-10000	0	-1	3	3
STAT5A (dimer)	-0.054	0.21	-10000	0	-0.66	61	61
SOCS1	-0.038	0.19	-10000	0	-0.7	68	68
cell migration	0.069	0.21	0.56	99	-10000	0	99
SOS1	0.016	0	-10000	0	-10000	0	0
EPO	-0.22	0.33	-10000	0	-0.7	285	285
VAV1	-0.026	0.18	-10000	0	-0.83	44	44
GRB10	-0.04	0.16	-10000	0	-0.5	60	60
PTPN11	0.016	0.029	-10000	0	-0.84	1	1
SCF/KIT	-0.052	0.17	-10000	0	-0.5	70	70
GO:0007205	0.001	0.008	-10000	0	-10000	0	0
MAP2K1	0.003	0.14	-10000	0	-0.42	31	31
CBL	0.015	0.029	-10000	0	-0.85	1	1
KIT	-0.1	0.39	-10000	0	-1.5	53	53
MAP2K2	0.002	0.14	-10000	0	-0.42	41	41
SHC/Grb2/SOS1	-0.053	0.14	-10000	0	-0.65	12	12
STAT5A	-0.056	0.22	-10000	0	-0.68	61	61
GRB2	0.016	0	-10000	0	-10000	0	0
response to radiation	-0.097	0.23	-10000	0	-0.55	139	139
SHC/GRAP2	-0.042	0.16	-10000	0	-0.65	58	58
PTPRO	-0.076	0.23	-10000	0	-0.61	114	114
SH2B2	-0.048	0.18	-10000	0	-0.54	71	71
DOK1	0.01	0.071	-10000	0	-0.85	6	6
MATK	-0.071	0.21	-10000	0	-0.57	99	99
CREBBP	0.038	0.018	-10000	0	-10000	0	0
BCL2	-0.008	0.21	-10000	0	-1.5	14	14

×

E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin	-0.048	0.16	-9999	-0.51	84	84
E-cadherin/beta catenin	-0.052	0.17	-9999	-0.57	80	80
CTNNB1	0.016	0	-9999	-10000	0	0
JUP	0.009	0.076	-9999	-0.85	7	7
CDH1	-0.054	0.22	-9999	-0.76	80	80

×

FOXM1 transcription factor 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC3	0.15	0.48	-10000	0	-1.2	57	57
PLK1	0.048	0.2	-10000	0	-1.7	6	6
BIRC5	0.01	0.31	-10000	0	-0.94	68	68
HSPA1B	0.15	0.49	-10000	0	-1.2	57	57
MAP2K1	0.06	0.046	-10000	0	-10000	0	0
BRCA2	0.13	0.53	-10000	0	-1.3	77	77
FOXM1	0.11	0.62	-10000	0	-1.6	71	71
XRCC1	0.15	0.48	-10000	0	-1.2	56	56
FOXM1B/p19	-0.16	0.37	0.48	5	-1.2	81	86
Cyclin D1/CDK4	0.1	0.5	-10000	0	-1.1	77	77
CDC2	0.15	0.51	-10000	0	-1.2	66	66
TGFA	0.078	0.55	-10000	0	-1.1	103	103
SKP2	0.15	0.49	-10000	0	-1.2	58	58
CCNE1	0.008	0.11	-10000	0	-0.67	21	21
CKS1B	0.15	0.48	-10000	0	-1.2	56	56
RB1	-0.071	0.16	-10000	0	-0.79	19	19
FOXM1C/SP1	0.12	0.54	-10000	0	-1.3	68	68
AURKB	0.023	0.28	-10000	0	-1.7	17	17
CENPF	0.14	0.52	-10000	0	-1.3	67	67
CDK4	0.031	0.021	-10000	0	-10000	0	0
MYC	0.14	0.48	-10000	0	-1.1	76	76
CHEK2	0.053	0.093	-10000	0	-0.86	7	7
ONECUT1	0.11	0.5	-10000	0	-1.1	69	69
CDKN2A	-0.052	0.21	-10000	0	-0.81	63	63
LAMA4	0.075	0.61	-10000	0	-1.3	125	125
FOXM1B/HNF6	0.085	0.6	-10000	0	-1.5	73	73
FOS	0.085	0.58	-10000	0	-1.3	95	95
SP1	0.017	0.004	-10000	0	-10000	0	0
CDC25B	0.15	0.48	-10000	0	-1.2	56	56
response to radiation	0.037	0.044	-10000	0	-10000	0	0
CENPB	0.15	0.48	-10000	0	-1.2	57	57
CENPA	0.14	0.51	-10000	0	-1.3	61	61
NEK2	0.13	0.52	-10000	0	-1.3	70	70
HIST1H2BA	0.15	0.48	-10000	0	-1.2	57	57
CCNA2	0.014	0.087	-10000	0	-0.69	13	13
EP300	0.014	0.041	-10000	0	-0.85	2	2
CCNB1/CDK1	0.13	0.55	-10000	0	-1.4	58	58
CCNB2	0.14	0.51	-10000	0	-1.2	63	63
CCNB1	0.15	0.51	-10000	0	-1.3	58	58
ETV5	0.15	0.48	-10000	0	-1.2	55	55
ESR1	0.11	0.56	-10000	0	-1.3	94	94
CCND1	0.11	0.52	-10000	0	-1.1	80	80
GSK3A	0.055	0.038	-10000	0	-10000	0	0
Cyclin A-E1/CDK1-2	0.054	0.12	-10000	0	-0.72	8	8
CDK2	0.024	0.012	-10000	0	-10000	0	0
G2/M transition of mitotic cell cycle	0.043	0.051	-10000	0	-10000	0	0
FOXM1B/Cbp/p300	-0.15	0.36	-10000	0	-1.2	71	71
GAS1	0.14	0.51	-10000	0	-1.2	63	63
MMP2	0.13	0.53	-10000	0	-1.2	74	74
RB1/FOXM1C	0.12	0.51	-10000	0	-1.2	67	67
CREBBP	0.016	0	-10000	0	-10000	0	0

×

Nongenotropic Androgen signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.014	0	-10000	0	-10000	0	0
GNB1/GNG2	-0.087	0.2	-10000	0	-0.54	139	139
regulation of S phase of mitotic cell cycle	-0.015	0.14	-10000	0	-0.53	21	21
GNAO1	-0.053	0.22	-10000	0	-0.76	79	79
HRAS	0.011	0.059	-10000	0	-0.77	5	5
SHBG/T-DHT	-0.042	0.14	-10000	0	-0.48	78	78
PELP1	0.016	0.001	-10000	0	-10000	0	0
AKT1	0.014	0.023	-10000	0	-0.66	1	1
MAP2K1	-0.013	0.16	-10000	0	-0.56	16	16
T-DHT/AR	-0.086	0.22	-10000	0	-0.64	120	120
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
mol:GTP	-0.001	0.002	-10000	0	-0.007	114	114
GNAI2	0.015	0.029	-10000	0	-0.85	1	1
GNAI3	0.016	0	-10000	0	-10000	0	0
GNAI1	0.004	0.1	-10000	0	-0.85	12	12
mol:GDP	-0.085	0.22	-10000	0	-0.67	104	104
cell proliferation	-0.016	0.2	-10000	0	-0.67	24	24
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
FOS	-0.045	0.26	-10000	0	-0.85	63	63
mol:Ca2+	-0.014	0.028	-10000	0	-0.1	36	36
MAPK3	-0.014	0.18	-10000	0	-0.62	24	24
MAPK1	0.001	0.096	-10000	0	-0.33	18	18
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
mol:IP3	0	0.002	-10000	0	-0.004	120	120
cAMP biosynthetic process	-0.027	0.14	-10000	0	-0.45	78	78
GNG2	-0.016	0.16	-10000	0	-0.85	33	33
potassium channel inhibitor activity	0	0.002	-10000	0	-0.004	120	120
HRAS/GTP	-0.065	0.16	-10000	0	-0.48	106	106
actin cytoskeleton reorganization	-0.006	0.05	-10000	0	-0.46	10	10
SRC	0.015	0.022	-10000	0	-0.65	1	1
voltage-gated calcium channel activity	0	0.002	-10000	0	-0.004	120	120
PI3K	-0.007	0.063	-10000	0	-0.55	12	12
apoptosis	0.011	0.16	0.45	62	-10000	0	62
T-DHT/AR/PELP1	-0.073	0.19	-10000	0	-0.55	120	120
HRAS/GDP	-0.081	0.21	-10000	0	-0.63	107	107
CREB1	-0.015	0.18	-10000	0	-0.49	62	62
RAC1-CDC42/GTP	-0.006	0.051	-10000	0	-0.47	10	10
AR	-0.097	0.29	-10000	0	-0.82	120	120
GNB1	0.016	0	-10000	0	-10000	0	0
RAF1	-0.022	0.17	-10000	0	-0.56	18	18
RAC1-CDC42/GDP	-0.076	0.2	-10000	0	-0.6	104	104
T-DHT/AR/PELP1/Src	-0.067	0.18	-10000	0	-0.53	104	104
MAP2K2	-0.015	0.17	-10000	0	-0.61	18	18
T-DHT/AR/PELP1/Src/PI3K	-0.016	0.14	-10000	0	-0.54	21	21
GNAZ	0.007	0.085	-10000	0	-0.79	10	10
SHBG	-0.049	0.21	-10000	0	-0.72	78	78
Gi family/GNB1/GNG2/GDP	-0.006	0.16	-10000	0	-0.56	45	45
mol:T-DHT	0	0.001	0.002	1	-0.003	100	101
RAC1	0.016	0	-10000	0	-10000	0	0
GNRH1	-0.016	0.14	-10000	0	-0.61	43	43
Gi family/GTP	-0.053	0.11	-10000	0	-0.51	22	22
CDC42	0.016	0	-10000	0	-10000	0	0

×

EPHB forward 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
Ephrin A5/EPHB2	-0.12	0.23	-10000	0	-0.53	206	206
cell-cell adhesion	0.1	0.19	0.7	45	-10000	0	45
Ephrin B/EPHB2/RasGAP	-0.091	0.2	-10000	0	-0.8	25	25
ITSN1	0.016	0	-10000	0	-10000	0	0
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
SHC1	0.015	0.022	-10000	0	-0.65	1	1
Ephrin B1/EPHB3	-0.057	0.17	-10000	0	-0.54	93	93
Ephrin B1/EPHB1	-0.049	0.14	-10000	0	-0.46	94	94
HRAS/GDP	-0.09	0.18	-10000	0	-0.7	39	39
Ephrin B/EPHB1/GRB7	-0.12	0.22	-10000	0	-0.6	115	115
Endophilin/SYNJ1	-0.045	0.2	-10000	0	-0.71	26	26
KRAS	0.016	0	-10000	0	-10000	0	0
Ephrin B/EPHB1/Src	-0.11	0.22	-10000	0	-0.6	100	100
endothelial cell migration	-0.03	0.12	-10000	0	-0.49	53	53
GRB2	0.016	0	-10000	0	-10000	0	0
GRB7	-0.002	0.12	-10000	0	-0.76	21	21
PAK1	-0.043	0.21	-10000	0	-0.8	25	25
HRAS	0.012	0.059	-10000	0	-0.77	5	5
RRAS	-0.047	0.2	-10000	0	-0.54	93	93
DNM1	-0.1	0.28	-10000	0	-0.76	136	136
cell-cell signaling	0	0	-10000	0	-10000	0	0
CRK	-0.064	0.22	-10000	0	-0.57	100	100
lamellipodium assembly	-0.1	0.19	-10000	0	-0.7	45	45
Ephrin B/EPHB1/Src/p52 SHC/GRB2	-0.024	0.16	-10000	0	-0.59	29	29
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
EPHB2	-0.025	0.17	-10000	0	-0.71	50	50
EPHB3	-0.069	0.25	-10000	0	-0.8	93	93
EPHB1	-0.06	0.22	-10000	0	-0.71	93	93
EPHB4	0.009	0.076	-10000	0	-0.85	7	7
mol:GDP	-0.077	0.2	-10000	0	-0.6	70	70
Ephrin B/EPHB2	-0.091	0.2	-10000	0	-0.57	92	92
Ephrin B/EPHB3	-0.12	0.24	-10000	0	-0.62	130	130
JNK cascade	-0.019	0.17	-10000	0	-0.53	51	51
Ephrin B/EPHB1	-0.11	0.22	-10000	0	-0.61	100	100
RAP1/GDP	-0.063	0.16	-10000	0	-0.64	29	29
EFNB2	-0.02	0.17	-10000	0	-0.85	37	37
EFNB3	-0.075	0.24	-10000	0	-0.72	110	110
EFNB1	0.015	0.029	-10000	0	-0.85	1	1
Ephrin B2/EPHB1-2	-0.088	0.2	-10000	0	-0.48	161	161
RAP1B	0.016	0	-10000	0	-10000	0	0
RAP1A	0.016	0	-10000	0	-10000	0	0
CDC42/GTP	-0.11	0.2	-10000	0	-0.75	42	42
Rap1/GTP	-0.1	0.19	-10000	0	-0.7	43	43
axon guidance	-0.12	0.23	-10000	0	-0.53	206	206
MAPK3	-0.002	0.14	-10000	0	-0.64	15	15
MAPK1	-0.002	0.14	-10000	0	-0.64	15	15
Rac1/GDP	-0.024	0.19	-10000	0	-0.58	50	50
actin cytoskeleton reorganization	-0.076	0.14	-10000	0	-0.54	37	37
CDC42/GDP	-0.024	0.19	-10000	0	-0.58	50	50
PI3K	-0.03	0.12	-10000	0	-0.5	53	53
EFNA5	-0.13	0.32	-10000	0	-0.79	166	166
Ephrin B2/EPHB4	-0.028	0.12	-10000	0	-0.57	44	44
Ephrin B/EPHB2/Intersectin/N-WASP	-0.019	0.15	-10000	0	-0.56	21	21
CDC42	0.016	0	-10000	0	-10000	0	0
RAS family/GTP	-0.099	0.18	-10000	0	-0.68	45	45
PTK2	0.015	0.036	-10000	0	-10000	0	0
MAP4K4	-0.019	0.17	-10000	0	-0.53	51	51
SRC	0.015	0.022	-10000	0	-0.65	1	1
KALRN	0.004	0.1	-10000	0	-0.82	13	13
Intersectin/N-WASP	0	0	-10000	0	-10000	0	0
neuron projection morphogenesis	-0.013	0.18	-10000	0	-0.55	41	41
MAP2K1	-0.012	0.15	-10000	0	-0.6	24	24
WASL	0.016	0	-10000	0	-10000	0	0
Ephrin B1/EPHB1-2/NCK1	-0.066	0.16	-10000	0	-0.56	51	51
cell migration	-0.006	0.16	-10000	0	-0.62	24	24
NRAS	0.016	0	-10000	0	-10000	0	0
SYNJ1	-0.047	0.2	-10000	0	-0.79	21	21
PXN	0.016	0	-10000	0	-10000	0	0
TF	-0.12	0.24	-10000	0	-0.75	45	45
HRAS/GTP	-0.11	0.2	-10000	0	-0.76	45	45
Ephrin B1/EPHB1-2	-0.067	0.16	-10000	0	-0.57	49	49
cell adhesion mediated by integrin	0.079	0.19	0.56	88	-10000	0	88
RAC1	0.016	0	-10000	0	-10000	0	0
mol:GTP	-0.12	0.22	-10000	0	-0.83	42	42
RAC1-CDC42/GTP	-0.14	0.23	-10000	0	-0.72	77	77
RASA1	0.013	0.05	-10000	0	-0.85	3	3
RAC1-CDC42/GDP	-0.063	0.16	-10000	0	-0.64	29	29
ruffle organization	-0.046	0.22	-10000	0	-0.72	46	46
NCK1	0.014	0.041	-10000	0	-0.85	2	2
receptor internalization	-0.099	0.26	-10000	0	-0.76	67	67
Ephrin B/EPHB2/KALRN	-0.096	0.2	-10000	0	-0.57	99	99
ROCK1	-0.024	0.16	-10000	0	-0.53	74	74
RAS family/GDP	-0.075	0.14	-10000	0	-0.56	37	37
Rac1/GTP	-0.11	0.21	-10000	0	-0.77	45	45
Ephrin B/EPHB1/Src/Paxillin	-0.034	0.17	-10000	0	-0.64	29	29

×

Plasma membrane estrogen receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.063	0.18	-10000	0	-0.59	75	75
ER alpha/Gai/GDP/Gbeta gamma	-0.018	0.22	-10000	0	-0.68	64	64
AKT1	-0.021	0.24	-10000	0	-0.95	54	54
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
E2/ER alpha (dimer)/PELP1/Src/PI3K	-0.023	0.25	-10000	0	-0.98	53	53
mol:Ca2+	-0.13	0.32	-10000	0	-0.61	230	230
IGF1R	0.013	0.05	-10000	0	-0.85	3	3
E2/ER alpha (dimer)/Striatin	-0.057	0.18	-10000	0	-0.58	88	88
SHC1	0.015	0.022	-10000	0	-0.65	1	1
apoptosis	0.017	0.23	0.89	54	-10000	0	54
RhoA/GTP	-0.029	0.1	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas	-0.061	0.18	-10000	0	-0.69	50	50
regulation of stress fiber formation	-0.026	0.12	0.63	7	-10000	0	7
E2/ERA-ERB (dimer)	-0.054	0.16	-10000	0	-0.52	91	91
KRAS	0.016	0	-10000	0	-10000	0	0
G13/GTP	-0.033	0.13	-10000	0	-0.5	59	59
pseudopodium formation	0.026	0.12	-10000	0	-0.63	7	7
E2/ER alpha (dimer)/PELP1	-0.036	0.14	-10000	0	-0.55	58	58
GRB2	0.016	0	-10000	0	-10000	0	0
GNG2	-0.016	0.16	-10000	0	-0.85	33	33
GNAO1	-0.052	0.22	-10000	0	-0.76	79	79
HRAS	0.012	0.059	-10000	0	-0.77	5	5
mol:GTP	0	0	-10000	0	-10000	0	0
mol:NO	-0.031	0.22	-10000	0	-0.68	74	74
E2/ER beta (dimer)	-0.021	0.1	-10000	0	-0.52	37	37
mol:GDP	-0.048	0.15	-10000	0	-0.59	55	55
mol:NADP	-0.031	0.22	-10000	0	-0.68	74	74
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
mol:IP3	-0.14	0.34	-10000	0	-0.66	230	230
IGF-1R heterotetramer	0.013	0.05	-10000	0	-0.85	3	3
PLCB1	-0.14	0.32	-10000	0	-0.64	227	227
PLCB2	-0.068	0.27	-10000	0	-0.67	126	126
IGF1	-0.058	0.22	-10000	0	-0.72	89	89
mol:L-citrulline	-0.031	0.22	-10000	0	-0.68	74	74
RHOA	0.016	0	-10000	0	-10000	0	0
Gai/GDP	-0.056	0.19	-10000	0	-0.84	43	43
JNK cascade	-0.021	0.1	-10000	0	-0.52	37	37
BCAR1	0.013	0.05	-10000	0	-0.85	3	3
ESR2	-0.013	0.14	-10000	0	-0.68	37	37
GNAQ	0.016	0	-10000	0	-10000	0	0
ESR1	-0.038	0.21	-10000	0	-0.82	58	58
Gq family/GDP/Gbeta gamma	-0.041	0.25	-10000	0	-0.85	61	61
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1	0.023	0.093	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC	-0.06	0.18	-10000	0	-0.69	50	50
GNAZ	0.007	0.085	-10000	0	-0.79	10	10
E2/ER alpha (dimer)	-0.041	0.16	-10000	0	-0.64	58	58
STRN	-0.017	0.17	-10000	0	-0.85	34	34
GNAL	-0.006	0.13	-10000	0	-0.72	27	27
PELP1	0.016	0	-10000	0	-10000	0	0
MAPK11	-0.005	0.12	-10000	0	-0.48	51	51
GNAI2	0.015	0.029	-10000	0	-0.85	1	1
GNAI3	0.016	0	-10000	0	-10000	0	0
GNAI1	0.004	0.1	-10000	0	-0.85	12	12
HBEGF	-0.049	0.23	-10000	0	-0.75	59	59
cAMP biosynthetic process	-0.055	0.15	-10000	0	-0.43	114	114
SRC	-0.006	0.2	-10000	0	-0.78	38	38
PI3K	-0.008	0.072	-10000	0	-0.62	12	12
GNB1	0.016	0	-10000	0	-10000	0	0
G13/GDP/Gbeta gamma	-0.056	0.16	-10000	0	-0.61	53	53
SOS1	0.016	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1	-0.07	0.17	-10000	0	-0.65	48	48
Gs family/GTP	-0.056	0.15	-10000	0	-0.44	114	114
EntrezGene:2778	0	0	-10000	0	-10000	0	0
RAS family/GTP	-0.003	0.035	-10000	0	-0.52	3	3
vasodilation	-0.027	0.21	-10000	0	-0.64	74	74
mol:DAG	-0.14	0.34	-10000	0	-0.66	230	230
Gs family/GDP/Gbeta gamma	-0.059	0.16	-10000	0	-0.57	55	55
MSN	0.025	0.14	-10000	0	-0.71	7	7
Gq family/GTP	-0.1	0.23	-10000	0	-0.66	113	113
mol:PI-3-4-5-P3	-0.02	0.23	-10000	0	-0.91	54	54
NRAS	0.016	0	-10000	0	-10000	0	0
mol:E2	0	0	-10000	0	-10000	0	0
cell adhesion	0.027	0.21	0.64	74	-10000	0	74
GRB2/SOS1	0	0	-10000	0	-10000	0	0
RhoA/GDP	-0.044	0.14	-10000	0	-0.54	55	55
NOS3	-0.036	0.24	-10000	0	-0.74	74	74
GNA11	-0.011	0.14	-10000	0	-0.75	31	31
MAPKKK cascade	-0.004	0.22	-10000	0	-0.74	58	58
E2/ER alpha (dimer)/PELP1/Src	-0.064	0.19	-10000	0	-0.68	63	63
ruffle organization	0.026	0.12	-10000	0	-0.63	7	7
ROCK2	0.016	0.14	-10000	0	-0.81	5	5
GNA14	-0.078	0.27	-10000	0	-0.84	97	97
GNA15	-0.014	0.16	-10000	0	-0.81	33	33
GNA13	0.015	0.022	-10000	0	-0.65	1	1
MMP9	-0.08	0.26	-10000	0	-0.78	63	63
MMP2	-0.019	0.23	-10000	0	-0.8	46	46

×

Visual signal transduction: Cones

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin	-0.067	0.16	-9999	-0.49	88	88
RGS9BP	-0.041	0.2	-9999	-0.73	68	68
mol:GTP	0	0	-9999	-10000	0	0
GRK1	-0.004	0.073	-9999	-0.65	11	11
mol:Na +	-0.036	0.12	-9999	-0.42	77	77
mol:ADP	0.004	0.067	-9999	-0.48	16	16
GNAT2	0.014	0.006	-9999	-10000	0	0
RGS9-1/Gbeta5/R9AP	-0.12	0.23	-9999	-0.6	119	119
mol:GDP	0	0	-9999	-10000	0	0
PDE6H/GNAT2/GTP	-0.001	0.024	-9999	-0.41	3	3
GRK7	0.007	0.05	-9999	-0.65	5	5
CNGB3	-0.036	0.16	-9999	-0.65	57	57
Cone Metarhodopsin II/X-Arrestin	0	0	-9999	-10000	0	0
mol:Ca2+	-0.049	0.17	-9999	-0.5	92	92
Cone PDE6	-0.11	0.2	-9999	-0.53	120	120
Cone Metarhodopsin II	-0.007	0.051	-9999	-0.38	16	16
Na + (4 Units)	-0.056	0.16	-9999	-0.5	89	89
GNAT2/GDP	-0.11	0.2	-9999	-0.52	119	119
GNB5	0.015	0.029	-9999	-0.85	1	1
mol:GMP (4 units)	0.014	0.033	-9999	-0.37	6	6
Cone Transducin	-0.071	0.17	-9999	-0.51	88	88
SLC24A2	-0.039	0.16	-9999	-0.65	57	57
GNB3/GNGT2	-0.09	0.21	-9999	-0.58	137	137
GNB3	-0.076	0.25	-9999	-0.73	108	108
GNAT2/GTP	0	0	-9999	-10000	0	0
CNGA3	-0.01	0.097	-9999	-0.65	20	20
ARR3	0.004	0.007	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
cGMP/Cone CNG Channel	-0.036	0.12	-9999	-0.42	77	77
mol:Pi	-0.12	0.23	-9999	-0.6	119	119
Cone CNG Channel	-0.031	0.099	-9999	-0.66	2	2
mol:all-trans-retinal	0	0	-9999	-10000	0	0
mol:K +	-0.039	0.16	-9999	-0.65	57	57
RGS9	-0.12	0.3	-9999	-0.76	160	160
PDE6C	0.004	0.039	-9999	-0.65	3	3
GNGT2	-0.015	0.16	-9999	-0.84	32	32
mol:cGMP (4 units)	0	0	-9999	-10000	0	0
PDE6H	0.002	0.039	-9999	-0.65	3	3

×

JNK signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1	-0.12	0.32	-9999	-0.9	103	103
MAP4K1	-0.049	0.22	-9999	-0.8	71	71
MAP3K8	0.012	0.059	-9999	-0.77	5	5
PRKCB	-0.035	0.2	-9999	-0.83	54	54
DBNL	0.016	0	-9999	-10000	0	0
CRKL	0.016	0	-9999	-10000	0	0
MAP3K1	-0.025	0.25	-9999	-0.89	56	56
JUN	-0.028	0.26	-9999	-0.91	63	63
MAP3K7	-0.024	0.25	-9999	-0.9	55	55
GRAP2	-0.039	0.21	-9999	-0.85	57	57
CRK	0.015	0.022	-9999	-0.65	1	1
MAP2K4	-0.014	0.24	-9999	-0.86	56	56
LAT	-0.022	0.16	-9999	-0.72	46	46
LCP2	-0.028	0.19	-9999	-0.84	46	46
MAPK8	-0.037	0.27	-9999	-0.99	60	60
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family	-0.037	0.26	-9999	-0.96	55	55
LAT/GRAP2/SLP76/HPK1/HIP-55	-0.11	0.3	-9999	-1.1	61	61

×

IL27-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	-0.002	0.13	-10000	0	-0.83	20	20
CD4-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
cytokine production during immune response	0.064	0.22	0.83	36	-0.36	3	39
IL27/IL27R/JAK1	-0.12	0.29	-10000	0	-1.1	38	38
TBX21	-0.12	0.28	-10000	0	-0.7	113	113
IL12B	-0.041	0.18	-10000	0	-0.68	67	67
IL12A	-0.001	0.089	-10000	0	-0.59	19	19
IL6ST	-0.082	0.27	-10000	0	-0.86	97	97
IL27RA/JAK1	-0.018	0.21	-10000	0	-1.5	18	18
IL27	-0.012	0.12	-10000	0	-0.66	28	28
TYK2	0.012	0.043	-10000	0	-0.87	2	2
T-helper cell lineage commitment	-0.078	0.16	-10000	0	-0.94	6	6
T-helper 2 cell differentiation	0.064	0.22	0.83	36	-0.36	3	39
T cell proliferation during immune response	0.064	0.22	0.83	36	-0.36	3	39
MAPKKK cascade	-0.064	0.22	0.36	3	-0.83	36	39
STAT3	0.016	0	-10000	0	-10000	0	0
STAT2	0.016	0	-10000	0	-10000	0	0
STAT1	0.008	0.074	-10000	0	-0.72	9	9
IL12RB1	-0.04	0.2	-10000	0	-0.81	58	58
positive regulation of tyrosine phosphorylation of STAT protein	0	0	-10000	0	-10000	0	0
IL12RB2	-0.19	0.33	-10000	0	-0.71	158	158
IL27/IL27R/JAK2/TYK2	-0.066	0.23	-10000	0	-0.86	36	36
positive regulation of T cell mediated cytotoxicity	-0.064	0.22	0.36	3	-0.83	36	39
STAT1 (dimer)	-0.17	0.36	0.54	10	-0.99	88	98
JAK2	0.014	0.03	-10000	0	-0.85	1	1
JAK1	0.015	0.003	-10000	0	-10000	0	0
STAT2 (dimer)	-0.053	0.21	-10000	0	-0.85	31	31
T cell proliferation	-0.17	0.29	-10000	0	-0.69	126	126
IL12/IL12R/TYK2/JAK2	-0.05	0.18	-10000	0	-0.74	26	26
IL17A	-0.078	0.16	-10000	0	-0.94	6	6
mast cell activation	0.064	0.22	0.83	36	-0.36	3	39
IFNG	-0.016	0.048	0.099	3	-0.1	163	166
T cell differentiation	-0.007	0.009	0.022	4	-0.026	79	83
STAT3 (dimer)	-0.053	0.21	-10000	0	-0.86	30	30
STAT5A (dimer)	-0.054	0.22	-10000	0	-0.86	32	32
STAT4 (dimer)	-0.09	0.28	-10000	0	-0.81	75	75
STAT4	-0.052	0.23	-10000	0	-0.84	71	71
T cell activation	-0.009	0.021	0.13	19	-10000	0	19
IL27R/JAK2/TYK2	-0.087	0.26	-10000	0	-1.4	20	20
GATA3	-0.14	0.42	-10000	0	-1.6	60	60
IL18	-0.012	0.12	-10000	0	-0.55	42	42
positive regulation of mast cell cytokine production	-0.051	0.2	-10000	0	-0.82	30	30
IL27/EBI3	-0.034	0.16	-10000	0	-0.62	61	61
IL27RA	-0.029	0.23	-10000	0	-1.6	18	18
IL6	-0.19	0.34	-10000	0	-0.73	247	247
STAT5A	0.013	0.05	-10000	0	-0.85	3	3
monocyte differentiation	-0.001	0.002	-10000	0	-10000	0	0
IL2	0.008	0.089	0.51	18	-10000	0	18
IL1B	-0.032	0.16	-10000	0	-0.61	65	65
EBI3	-0.025	0.17	-10000	0	-0.8	40	40
TNF	-0.046	0.18	-10000	0	-0.58	90	90

×

Syndecan-2-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Syndecan-2/Fibronectin	-0.063	0.22	-9999	-0.54	147	147
EPHB2	-0.025	0.17	-9999	-0.71	50	50
Syndecan-2/TACI	-0.015	0.13	-9999	-0.44	73	73
LAMA1	-0.059	0.24	-9999	-0.8	82	82
Syndecan-2/alpha2 ITGB1	-0.048	0.14	-9999	-0.55	38	38
HRAS	0.012	0.059	-9999	-0.77	5	5
Syndecan-2/CASK	-0.01	0.072	-9999	-0.54	16	16
ITGA5	-0.009	0.14	-9999	-0.81	27	27
BAX	0.033	0.12	-9999	-1.3	3	3
EPB41	0.014	0.043	-9999	-0.72	3	3
positive regulation of cell-cell adhesion	-0.009	0.065	-9999	-0.48	16	16
LAMA3	-0.039	0.19	-9999	-0.67	71	71
EZR	0.015	0.029	-9999	-0.85	1	1
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
CAV2	0.001	0.11	-9999	-0.84	16	16
Syndecan-2/MMP2	-0.011	0.15	-9999	-0.51	69	69
RP11-540L11.1	0	0	-9999	-10000	0	0
alpha2 ITGB1	-0.017	0.1	-9999	-0.63	24	24
dendrite morphogenesis	-0.006	0.14	-9999	-0.48	64	64
Syndecan-2/GM-CSF	-0.004	0.093	-9999	-0.46	33	33
determination of left/right symmetry	0.014	0.086	-9999	-0.61	16	16
Syndecan-2/PKC delta	-0.007	0.13	-9999	-0.45	70	70
GNB2L1	0.016	0	-9999	-10000	0	0
MAPK3	0.018	0.092	-9999	-0.56	12	12
MAPK1	0.018	0.089	-9999	-0.52	13	13
Syndecan-2/RACK1	-0.011	0.074	-9999	-0.54	14	14
NF1	0.016	0	-9999	-10000	0	0
FGFR/FGF/Syndecan-2	0.014	0.086	-9999	-0.61	16	16
ITGA2	-0.007	0.14	-9999	-0.82	24	24
MAPK8	0.026	0.11	-9999	-0.56	27	27
Syndecan-2/alpha2/beta1 Integrin	-0.061	0.17	-9999	-0.53	89	89
Syndecan-2/Kininogen	-0.12	0.23	-9999	-0.47	244	244
ITGB1	0.016	0	-9999	-10000	0	0
SRC	0.036	0.078	-9999	-0.51	15	15
Syndecan-2/CASK/Protein 4.1	-0.01	0.07	-9999	-0.48	19	19
extracellular matrix organization	0.008	0.12	-9999	-0.58	33	33
actin cytoskeleton reorganization	-0.063	0.22	-9999	-0.53	147	147
Syndecan-2/Caveolin-2/Ras	-0.02	0.11	-9999	-0.57	28	28
Syndecan-2/Laminin alpha3	-0.015	0.14	-9999	-0.45	85	85
Syndecan-2/RasGAP	-0.012	0.077	-9999	-0.52	17	17
alpha5/beta1 Integrin	-0.019	0.11	-9999	-0.62	27	27
PRKCD	-0.027	0.16	-9999	-0.65	57	57
Syndecan-2 dimer	-0.006	0.14	-9999	-0.48	64	64
GO:0007205	0.004	0.006	-9999	-10000	0	0
DNA mediated transformation	0	0	-9999	-10000	0	0
Syndecan-2/RasGAP/Src	0.042	0.084	-9999	-0.73	4	4
RHOA	0.016	0	-9999	-10000	0	0
SDCBP	0.016	0	-9999	-10000	0	0
TNFRSF13B	-0.032	0.16	-9999	-0.65	58	58
RASA1	0.013	0.05	-9999	-0.85	3	3
alpha2/beta1 Integrin	-0.017	0.1	-9999	-0.63	24	24
Syndecan-2/Synbindin	0.021	0.075	-9999	-0.53	16	16
TGFB1	-0.003	0.12	-9999	-0.83	20	20
CASP3	0.007	0.12	-9999	-0.4	69	69
FN1	-0.11	0.29	-9999	-0.79	137	137
Syndecan-2/IL8	-0.065	0.2	-9999	-0.48	166	166
SDC2	0.014	0.086	-9999	-0.61	16	16
KNG1	-0.18	0.32	-9999	-0.71	238	238
Syndecan-2/Neurofibromin	0.021	0.075	-9999	-0.53	16	16
TRAPPC4	0.016	0	-9999	-10000	0	0
CSF2	-0.006	0.09	-9999	-0.65	17	17
Syndecan-2/TGFB1	0.008	0.12	-9999	-0.59	33	33
Syndecan-2/Syntenin/PI-4-5-P2	-0.009	0.065	-9999	-0.48	16	16
Syndecan-2/Ezrin	-0.009	0.066	-9999	-0.52	13	13
PRKACA	0.032	0.069	-9999	-0.51	12	12
angiogenesis	-0.064	0.2	-9999	-0.48	166	166
MMP2	-0.032	0.18	-9999	-0.73	57	57
IL8	-0.11	0.28	-9999	-0.72	154	154
calcineurin-NFAT signaling pathway	-0.015	0.13	-9999	-0.44	73	73

×

LPA receptor mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.068	0.18	-9999	-0.58	86	86
NF kappa B1 p50/RelA/I kappa B alpha	-0.041	0.1	-9999	-0.61	11	11
AP1	-0.11	0.21	-9999	-0.75	40	40
mol:PIP3	-0.067	0.15	-9999	-0.63	27	27
AKT1	0.017	0.15	-9999	-0.55	22	22
PTK2B	0	0.1	-9999	-0.44	19	19
RHOA	0.018	0.066	-9999	-0.43	5	5
PIK3CB	0.015	0.022	-9999	-0.65	1	1
mol:Ca2+	0.01	0.12	-9999	-0.71	12	12
MAGI3	0.003	0.091	-9999	-0.65	17	17
RELA	0.016	0	-9999	-10000	0	0
apoptosis	-0.02	0.14	-9999	-0.46	57	57
HRAS/GDP	-0.003	0.045	-9999	-0.59	5	5
positive regulation of microtubule depolymerization	-0.03	0.18	-9999	-0.47	100	100
NF kappa B1 p50/RelA	-0.066	0.16	-9999	-0.69	30	30
endothelial cell migration	-0.051	0.24	-9999	-0.68	104	104
ADCY4	-0.058	0.23	-9999	-0.66	91	91
ADCY5	-0.06	0.22	-9999	-0.64	86	86
ADCY6	-0.028	0.19	-9999	-0.6	67	67
ADCY7	-0.028	0.19	-9999	-0.6	67	67
ADCY1	-0.091	0.24	-9999	-0.68	95	95
ADCY2	-0.1	0.24	-9999	-0.66	101	101
ADCY3	-0.036	0.21	-9999	-0.66	72	72
ADCY8	-0.091	0.21	-9999	-0.63	82	82
ADCY9	-0.028	0.19	-9999	-0.6	67	67
GSK3B	0.01	0.1	-9999	-0.48	12	12
arachidonic acid secretion	-0.029	0.2	-9999	-0.58	79	79
GNG2	-0.016	0.16	-9999	-0.85	33	33
TRIP6	0.019	0.083	-9999	-0.64	11	11
GNAO1	-0.068	0.22	-9999	-0.55	140	140
HRAS	0.012	0.059	-9999	-0.77	5	5
NFKBIA	-0.001	0.14	-9999	-0.56	27	27
GAB1	0.014	0.041	-9999	-0.85	2	2
mol:GTP	0	0	-9999	-10000	0	0
lamellipodium assembly	-0.012	0.13	-9999	-1	14	14
JUN	0.01	0.069	-9999	-0.76	7	7
LPA/LPA2/NHERF2	-0.013	0.072	-9999	-0.56	13	13
TIAM1	-0.017	0.16	-9999	-1.3	14	14
PIK3R1	0.011	0.066	-9999	-0.78	6	6
mol:IP3	0.009	0.12	-9999	-0.74	12	12
PLCB3	0.021	0.087	-9999	-0.67	10	10
FOS	-0.086	0.26	-9999	-0.74	120	120
positive regulation of mitosis	-0.029	0.2	-9999	-0.58	79	79
LPA/LPA1-2-3	-0.063	0.16	-9999	-0.57	64	64
mol:Ca ++	0	0	-9999	-10000	0	0
JNK cascade	0	0.001	-9999	-10000	0	0
BCAR1	0.013	0.05	-9999	-0.85	3	3
stress fiber formation	0.002	0.12	-9999	-0.49	20	20
GNAZ	-0.029	0.18	-9999	-0.58	71	71
EGFR/PI3K-beta/Gab1	-0.07	0.16	-9999	-0.67	27	27
positive regulation of dendritic cell cytokine production	-0.062	0.16	-9999	-0.56	64	64
LPA/LPA2/MAGI-3	-0.017	0.08	-9999	-0.47	24	24
ARHGEF1	-0.002	0.15	-9999	-0.51	58	58
GNAI2	-0.023	0.17	-9999	-0.58	63	63
GNAI3	-0.023	0.17	-9999	-0.57	62	62
GNAI1	-0.031	0.18	-9999	-0.59	73	73
LPA/LPA3	-0.019	0.079	-9999	-0.48	22	22
LPA/LPA2	-0.012	0.065	-9999	-0.64	8	8
LPA/LPA1	-0.064	0.18	-9999	-0.6	80	80
HB-EGF/EGFR	-0.11	0.25	-9999	-0.51	231	231
HBEGF	-0.1	0.26	-9999	-0.57	199	199
mol:DAG	0.009	0.12	-9999	-0.74	12	12
cAMP biosynthetic process	-0.072	0.22	-9999	-0.62	102	102
NFKB1	0.015	0.029	-9999	-0.85	1	1
SRC	0.015	0.022	-9999	-0.65	1	1
GNB1	0.016	0.001	-9999	-10000	0	0
LYN	-0.004	0.16	-9999	-0.61	29	29
GNAQ	0.01	0.07	-9999	-0.49	8	8
LPAR2	0.008	0.079	-9999	-0.82	8	8
LPAR3	-0.008	0.1	-9999	-0.65	22	22
LPAR1	-0.048	0.22	-9999	-0.83	62	62
IL8	-0.11	0.23	-9999	-0.51	144	144
PTK2	-0.019	0.17	-9999	-0.53	64	64
Rac1/GDP	0	0	-9999	-10000	0	0
CASP3	-0.02	0.14	-9999	-0.46	57	57
EGFR	-0.022	0.17	-9999	-0.78	41	41
PLCG1	-0.007	0.11	-9999	-0.44	25	25
PLD2	-0.023	0.17	-9999	-0.54	71	71
G12/G13	-0.049	0.14	-9999	-0.55	56	56
PI3K-beta	-0.055	0.14	-9999	-0.61	27	27
cell migration	-0.018	0.064	-9999	-0.31	5	5
SLC9A3R2	0.011	0.063	-9999	-0.75	6	6
PXN	0.002	0.13	-9999	-0.5	19	19
HRAS/GTP	-0.031	0.21	-9999	-0.6	79	79
RAC1	0.016	0	-9999	-10000	0	0
MMP9	-0.15	0.31	-9999	-0.73	194	194
PRKCE	0.013	0.05	-9999	-0.85	3	3
PRKCD	-0.004	0.15	-9999	-0.64	21	21
Gi(beta/gamma)	-0.03	0.2	-9999	-0.59	80	80
mol:LPA	-0.006	0.047	-9999	-10000	0	0
TRIP6/p130 Cas/FAK1/Paxillin	-0.046	0.15	-9999	-0.73	16	16
MAPKKK cascade	-0.029	0.2	-9999	-0.58	79	79
contractile ring contraction involved in cytokinesis	0.018	0.065	-9999	-0.42	5	5
mol:GDP	0	0	-9999	-10000	0	0
GNA14	-0.041	0.16	-9999	-0.46	102	102
GNA15	-0.006	0.12	-9999	-0.52	37	37
GNA12	0.016	0	-9999	-10000	0	0
GNA13	0.015	0.022	-9999	-0.65	1	1
MAPT	-0.032	0.18	-9999	-0.49	100	100
GNA11	-0.004	0.1	-9999	-0.48	26	26
Rac1/GTP	-0.013	0.14	-9999	-1.1	14	14
MMP2	-0.052	0.24	-9999	-0.68	104	104

×

EPO signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.01	0.17	-10000	0	-0.76	2	2
CRKL	-0.056	0.18	-10000	0	-0.73	3	3
mol:DAG	-0.048	0.18	-10000	0	-0.47	72	72
HRAS	-0.017	0.16	-10000	0	-0.86	2	2
MAPK8	-0.094	0.2	-10000	0	-0.5	85	85
RAP1A	-0.056	0.18	-10000	0	-0.73	3	3
GAB1	-0.057	0.18	-10000	0	-0.62	5	5
MAPK14	-0.087	0.2	-10000	0	-0.49	74	74
EPO	-0.21	0.33	-10000	0	-0.69	285	285
PLCG1	-0.049	0.18	-10000	0	-0.48	72	72
EPOR/TRPC2/IP3 Receptors	0.006	0.052	-10000	0	-0.72	4	4
RAPGEF1	0.016	0	-10000	0	-10000	0	0
EPO/EPOR (dimer)/SOCS3	-0.16	0.24	-10000	0	-0.59	122	122
GAB1/SHC/GRB2/SOS1	-0.081	0.12	-10000	0	-0.92	1	1
EPO/EPOR (dimer)	-0.15	0.26	-10000	0	-0.51	287	287
IRS2	-0.074	0.19	-10000	0	-0.68	19	19
STAT1	-0.043	0.19	-10000	0	-0.66	8	8
STAT5B	-0.044	0.18	-10000	0	-0.85	3	3
cell proliferation	-0.078	0.19	-10000	0	-0.46	85	85
GAB1/SHIP/PIK3R1/SHP2/SHC	-0.081	0.12	-10000	0	-0.78	4	4
TEC	-0.056	0.18	-10000	0	-0.73	3	3
SOCS3	-0.033	0.19	-10000	0	-0.78	55	55
STAT1 (dimer)	-0.042	0.18	-10000	0	-0.63	8	8
JAK2	0.008	0.035	-10000	0	-0.91	1	1
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
EPO/EPOR (dimer)/JAK2	-0.059	0.19	-10000	0	-0.45	75	75
EPO/EPOR	-0.15	0.26	-10000	0	-0.51	287	287
LYN	0.014	0.058	-10000	0	-0.85	4	4
TEC/VAV2	-0.044	0.17	-10000	0	-0.81	2	2
elevation of cytosolic calcium ion concentration	0.006	0.052	-10000	0	-0.72	4	4
SHC1	0.015	0.022	-10000	0	-0.65	1	1
EPO/EPOR (dimer)/LYN	-0.1	0.22	-10000	0	-0.55	79	79
mol:IP3	-0.048	0.18	-10000	0	-0.47	72	72
PI3K regualtory subunit polypeptide 1/IRS2/SHIP	-0.1	0.16	-10000	0	-0.65	22	22
SH2B3	0.007	0.043	-10000	0	-0.84	2	2
NFKB1	-0.088	0.2	-10000	0	-0.5	74	74
EPO/EPOR (dimer)/JAK2/SOCS3	-0.098	0.14	0.34	1	-0.41	82	83
PTPN6	-0.069	0.18	-10000	0	-0.45	75	75
TEC/VAV2/GRB2	-0.035	0.17	-10000	0	-0.77	2	2
EPOR	0.006	0.052	-10000	0	-0.72	4	4
INPP5D	0.009	0.076	-10000	0	-0.85	7	7
mol:GDP	-0.082	0.12	-10000	0	-0.73	2	2
SOS1	0.016	0	-10000	0	-10000	0	0
PLCG2	-0.054	0.21	-10000	0	-0.68	90	90
CRKL/CBL/C3G	-0.035	0.17	-10000	0	-0.92	2	2
VAV2	-0.056	0.18	-10000	0	-0.73	3	3
CBL	-0.056	0.18	-10000	0	-0.86	3	3
SHC/Grb2/SOS1	-0.087	0.13	-10000	0	-0.77	2	2
STAT5A	-0.046	0.19	-10000	0	-0.85	4	4
GRB2	0.016	0	-10000	0	-10000	0	0
STAT5 (dimer)	-0.023	0.18	-10000	0	-0.71	7	7
LYN/PLCgamma2	-0.053	0.16	-10000	0	-0.52	90	90
PTPN11	0.015	0.029	-10000	0	-0.85	1	1
BTK	-0.073	0.2	-10000	0	-0.59	33	33
BCL2	-0.02	0.21	-10000	0	-1	16	16

×

Osteopontin-mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IKK alpha homodimer	-0.021	0.23	-9999	-0.77	47	47
NF kappa B1 p50/RelA/I kappa B alpha	-0.071	0.19	-9999	-0.8	33	33
alphaV/beta3 Integrin/Osteopontin/Src	-0.047	0.16	-9999	-0.56	74	74
AP1	-0.12	0.24	-9999	-0.88	55	55
ILK	-0.015	0.21	-9999	-0.74	34	34
bone resorption	-0.085	0.22	-9999	-0.81	44	44
PTK2B	0.016	0	-9999	-10000	0	0
PYK2/p130Cas	-0.072	0.19	-9999	-0.82	33	33
ITGAV	0.014	0.074	-9999	-0.82	7	7
mol:GTP	0	0	-9999	-10000	0	0
CD44/Rho Family GTPase/ROCK2	-0.045	0.16	-9999	-0.6	66	66
alphaV/beta3 Integrin/Osteopontin	-0.076	0.21	-9999	-0.65	81	81
MAP3K1	-0.017	0.21	-9999	-0.61	76	76
JUN	0.01	0.07	-9999	-0.76	7	7
MAPK3	-0.017	0.23	-9999	-0.81	42	42
MAPK1	-0.017	0.23	-9999	-0.81	43	43
Rac1/GDP	0	0	-9999	-10000	0	0
NFKB1	0.015	0.029	-9999	-0.85	1	1
MAPK8	-0.01	0.21	-9999	-0.73	40	40
ITGB3	-0.041	0.21	-9999	-0.76	71	71
NFKBIA	-0.007	0.24	-9999	-0.8	46	46
FOS	-0.086	0.26	-9999	-0.74	120	120
CD44	-0.016	0.15	-9999	-0.75	37	37
CHUK	0.015	0.029	-9999	-0.85	1	1
PLAU	-0.015	0.28	-9999	-0.97	43	43
NF kappa B1 p50/RelA	-0.071	0.18	-9999	-0.8	28	28
BCAR1	0.013	0.05	-9999	-0.85	3	3
RELA	0.016	0	-9999	-10000	0	0
alphaV beta3 Integrin	-0.049	0.17	-9999	-0.6	74	74
mol:GDP	0	0	-9999	-10000	0	0
SYK	-0.027	0.23	-9999	-0.64	88	88
VAV3	-0.022	0.23	-9999	-0.8	39	39
MAP3K14	-0.031	0.24	-9999	-0.65	93	93
ROCK2	-0.012	0.15	-9999	-0.85	29	29
SPP1	-0.037	0.2	-9999	-0.74	68	68
RAC1	0.016	0	-9999	-10000	0	0
Rac1/GTP	-0.071	0.19	-9999	-0.76	34	34
MMP2	-0.036	0.26	-9999	-0.74	67	67

×

Signaling events mediated by PTP1B

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
PDGFRB	-0.12	0.31	-10000	0	-0.84	140	140
Jak2/Leptin Receptor	-0.046	0.13	-10000	0	-0.51	35	35
PTP1B/AKT1	0.003	0.098	-10000	0	-0.46	17	17
FYN	0.007	0.086	-10000	0	-0.85	9	9
p210 bcr-abl/PTP1B	-0.006	0.11	-10000	0	-0.39	40	40
EGFR	-0.024	0.17	-10000	0	-0.79	41	41
EGF/EGFR	-0.12	0.21	-10000	0	-0.56	126	126
CSF1	0	0.12	-10000	0	-0.82	17	17
AKT1	0.015	0.029	-10000	0	-0.86	1	1
INSR	0.014	0.041	-10000	0	-0.85	2	2
PTP1B/N-cadherin	-0.06	0.22	-10000	0	-0.59	119	119
Insulin Receptor/Insulin	-0.022	0.071	-10000	0	-0.53	4	4
HCK	-0.005	0.13	-10000	0	-0.83	22	22
CRK	0.015	0.022	-10000	0	-0.65	1	1
TYK2	0.003	0.11	-10000	0	-0.45	24	24
EGF	-0.15	0.31	-10000	0	-0.73	196	196
YES1	0.016	0	-10000	0	-10000	0	0
CAV1	-0.035	0.16	-10000	0	-0.49	50	50
TXN	0.008	0.059	-10000	0	-0.65	7	7
PTP1B/IRS1/GRB2	-0.003	0.13	-10000	0	-0.54	30	30
cell migration	0.006	0.11	0.39	40	-10000	0	40
STAT3	0.016	0.001	-10000	0	-10000	0	0
PRLR	-0.13	0.29	-10000	0	-0.72	172	172
ITGA2B	-0.059	0.22	-10000	0	-0.73	88	88
CSF1R	-0.009	0.14	-10000	0	-0.82	26	26
Prolactin Receptor/Prolactin	-0.11	0.22	-10000	0	-0.54	181	181
FGR	-0.012	0.15	-10000	0	-0.83	30	30
PTP1B/p130 Cas	0.002	0.11	-10000	0	-0.47	23	23
Crk/p130 Cas	0.009	0.11	-10000	0	-0.53	15	15
DOK1	-0.036	0.15	-10000	0	-0.41	59	59
JAK2	-0.025	0.13	-10000	0	-0.4	48	48
Jak2/Leptin Receptor/Leptin	-0.086	0.18	-10000	0	-0.64	61	61
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
PTPN1	-0.006	0.11	-10000	0	-0.39	40	40
LYN	0.012	0.058	-10000	0	-0.85	4	4
CDH2	-0.092	0.29	-10000	0	-0.85	111	111
SRC	0.018	0.053	-10000	0	-0.56	3	3
ITGB3	-0.047	0.21	-10000	0	-0.76	71	71
CAT1/PTP1B	-0.041	0.2	-10000	0	-0.62	62	62
CAPN1	0.014	0.041	-10000	0	-0.86	2	2
CSK	0.014	0.041	-10000	0	-0.85	2	2
PI3K	-0.02	0.087	-10000	0	-0.6	9	9
mol:H2O2	-0.002	0.004	-10000	0	-10000	0	0
STAT3 (dimer)	-0.08	0.18	-10000	0	-0.66	58	58
negative regulation of transcription	-0.024	0.12	-10000	0	-0.4	49	49
FCGR2A	-0.003	0.13	-10000	0	-0.84	20	20
FER	0.01	0.051	-10000	0	-0.86	3	3
alphaIIb/beta3 Integrin	-0.098	0.23	-10000	0	-0.6	147	147
BLK	-0.081	0.25	-10000	0	-0.72	115	115
Insulin Receptor/Insulin/Shc	-0.003	0.038	-10000	0	-0.52	3	3
RHOA	0.016	0.002	-10000	0	-10000	0	0
LEPR	0.002	0.11	-10000	0	-0.82	15	15
BCAR1	0.013	0.05	-10000	0	-0.85	3	3
p210 bcr-abl/Grb2	0.016	0	-10000	0	-10000	0	0
mol:NADPH	-0.001	0.004	-10000	0	-10000	0	0
TRPV6	-0.057	0.23	-10000	0	-0.7	65	65
PRL	-0.002	0.066	-10000	0	-0.65	9	9
SOCS3	-0.059	0.32	-10000	0	-1.2	55	55
SPRY2	0.011	0.051	-10000	0	-0.86	3	3
Insulin Receptor/Insulin/IRS1	-0.019	0.096	-10000	0	-0.61	13	13
CSF1/CSF1R	-0.012	0.16	-10000	0	-0.62	43	43
Ras protein signal transduction	0.02	0.031	-10000	0	-10000	0	0
IRS1	-0.01	0.14	-10000	0	-0.72	31	31
INS	-0.001	0.038	-10000	0	-0.65	3	3
LEP	-0.058	0.2	-10000	0	-0.65	92	92
STAT5B	-0.009	0.11	-10000	0	-0.36	45	45
STAT5A	-0.01	0.11	-10000	0	-0.37	45	45
GRB2	0.016	0	-10000	0	-10000	0	0
PDGFB-D/PDGFRB	-0.076	0.21	-10000	0	-0.5	157	157
CSN2	-0.029	0.071	-10000	0	-10000	0	0
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
LAT	-0.012	0.14	-10000	0	-0.6	38	38
YBX1	0.025	0.014	-10000	0	-0.4	1	1
LCK	-0.08	0.26	-10000	0	-0.8	104	104
SHC1	0.015	0.022	-10000	0	-0.65	1	1
NOX4	-0.036	0.2	-10000	0	-0.83	52	52

×

IL2 signaling events mediated by STAT5

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
GAB2	0.012	0.06	-9999	-0.72	6	6
ELF1	-0.031	0.14	-9999	-0.4	76	76
CCNA2	0.006	0.084	-9999	-0.68	13	13
PIK3CA	0.011	0.071	-9999	-0.85	6	6
JAK3	-0.029	0.19	-9999	-0.83	48	48
PIK3R1	0.012	0.066	-9999	-0.78	6	6
JAK1	0.017	0.001	-9999	-10000	0	0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	-0.033	0.3	-9999	-0.87	83	83
SHC1	0.016	0.022	-9999	-0.65	1	1
SP1	0.003	0.095	-9999	-0.38	50	50
IL2RA	-0.097	0.33	-9999	-0.83	140	140
IL2RB	-0.051	0.23	-9999	-0.82	72	72
SOS1	0.017	0.001	-9999	-10000	0	0
IL2RG	-0.06	0.24	-9999	-0.79	85	85
G1/S transition of mitotic cell cycle	-0.01	0.24	-9999	-0.93	54	54
PTPN11	0.016	0.029	-9999	-0.85	1	1
CCND2	-0.024	0.26	-9999	-1.1	51	51
LCK	-0.079	0.26	-9999	-0.8	104	104
GRB2	0.017	0.001	-9999	-10000	0	0
IL2	0	0.076	-9999	-0.65	12	12
CDK6	0.012	0.059	-9999	-0.77	5	5
CCND3	-0.008	0.24	-9999	-0.74	67	67

×

Canonical Wnt signaling pathway

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
HDAC1	0.009	0.027	-10000	0	-10000	0	0
AES	0.008	0.038	-10000	0	-0.85	1	1
FBXW11	0.016	0	-10000	0	-10000	0	0
mol:GTP	0	0.001	-10000	0	-10000	0	0
LRP6/FZD1	-0.052	0.18	-10000	0	-0.65	71	71
SMAD4	0.016	0	-10000	0	-10000	0	0
DKK2	-0.11	0.29	-10000	0	-0.75	149	149
TLE1	0.007	0.047	-10000	0	-0.85	2	2
MACF1	0.016	0.001	-10000	0	-10000	0	0
CTNNB1	0.005	0.12	0.32	1	-0.46	19	20
WIF1	-0.023	0.14	-10000	0	-0.65	42	42
beta catenin/RanBP3	0.002	0.14	0.39	52	-0.48	5	57
KREMEN2	-0.031	0.17	-10000	0	-0.67	60	60
DKK1	-0.094	0.27	-10000	0	-0.75	126	126
beta catenin/beta TrCP1	0.015	0.12	0.31	1	-0.44	12	13
FZD1	-0.051	0.23	-10000	0	-0.85	70	70
AXIN2	0.009	0.17	-10000	0	-1	14	14
AXIN1	0.014	0.041	-10000	0	-0.85	2	2
RAN	0.016	0.001	-10000	0	-10000	0	0
Axin1/APC/GSK3/beta catenin	0.002	0.042	-10000	0	-0.68	2	2
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4	-0.067	0.25	-10000	0	-0.69	93	93
Axin1/APC/GSK3	0.002	0.065	0.26	1	-0.56	2	3
Axin1/APC/GSK3/beta catenin/Macf1	0.02	0.15	-10000	0	-0.47	54	54
HNF1A	-0.06	0.23	-10000	0	-0.84	72	72
CTBP1	0.01	0.024	-10000	0	-10000	0	0
MYC	-0.037	0.35	-10000	0	-1.7	37	37
RANBP3	0.015	0.029	-10000	0	-0.85	1	1
DKK2/LRP6/Kremen 2	-0.11	0.21	-10000	0	-0.58	97	97
NKD1	-0.043	0.2	-10000	0	-0.7	73	73
TCF4	-0.087	0.27	-10000	0	-0.82	102	102
TCF3	0.01	0.023	-10000	0	-10000	0	0
WNT1/LRP6/FZD1/Axin1	-0.048	0.15	-10000	0	-0.52	74	74
Ran/GTP	0.001	0.005	-10000	0	-10000	0	0
CtBP/CBP/TCF/TLE1/AES	-0.056	0.22	0.48	42	-0.64	49	91
LEF1	-0.16	0.32	-10000	0	-0.76	200	200
DVL1	0.01	0.047	-10000	0	-0.37	3	3
CSNK2A1	0.016	0.001	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES	-0.075	0.27	-10000	0	-0.78	80	80
DKK1/LRP6/Kremen 2	-0.097	0.2	-10000	0	-0.57	82	82
LRP6	0.015	0.029	-10000	0	-0.85	1	1
CSNK1A1	0.01	0.027	-10000	0	-10000	0	0
NLK	0.016	0.005	-10000	0	-10000	0	0
CCND1	-0.042	0.36	-10000	0	-1.7	40	40
WNT1	0.002	0.09	-10000	0	-0.66	16	16
GSK3A	0.016	0.001	-10000	0	-10000	0	0
GSK3B	0.016	0.001	-10000	0	-10000	0	0
FRAT1	0.015	0.022	-10000	0	-0.65	1	1
PPP2R5D	0.04	0.085	0.31	73	-10000	0	73
APC	-0.001	0.16	-10000	0	-0.49	74	74
WNT1/LRP6/FZD1	-0.002	0.12	0.22	33	-0.35	69	102
CREBBP	0.01	0.023	-10000	0	-10000	0	0

×

Coregulation of Androgen receptor activity

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
NRIP1	0.009	0.064	-9999	-0.83	5	5
SVIL	0.012	0.041	-9999	-0.85	2	2
ZNF318	0.024	0.043	-9999	-0.76	1	1
JMJD2C	-0.003	0.025	-9999	-0.089	57	57
T-DHT/AR/Ubc9	-0.081	0.22	-9999	-0.62	120	120
CARM1	0.015	0.029	-9999	-0.85	1	1
PRDX1	0.015	0.032	-9999	-0.65	2	2
PELP1	0.018	0.004	-9999	-10000	0	0
CTNNB1	0.014	0.006	-9999	-10000	0	0
AKT1	0.018	0.03	-9999	-0.85	1	1
PTK2B	0.015	0.004	-9999	-10000	0	0
MED1	0.017	0.029	-9999	-0.83	1	1
MAK	-0.004	0.15	-9999	-0.7	35	35
response to oxidative stress	0	0.002	-9999	-10000	0	0
HIP1	-0.002	0.12	-9999	-0.86	16	16
GSN	0.013	0.03	-9999	-0.85	1	1
NCOA2	-0.04	0.21	-9999	-0.85	57	57
NCOA6	0.014	0.006	-9999	-10000	0	0
DNA-PK	0.016	0.042	-9999	-10000	0	0
NCOA4	0.015	0.029	-9999	-0.85	1	1
PIAS3	0.014	0.006	-9999	-10000	0	0
cell proliferation	-0.029	0.12	-9999	-0.53	34	34
XRCC5	0.019	0.007	-9999	-10000	0	0
UBE3A	0.011	0.016	-9999	-10000	0	0
T-DHT/AR/SNURF	-0.11	0.26	-9999	-0.66	152	152
FHL2	-0.1	0.36	-9999	-1.3	66	66
RANBP9	0.014	0.006	-9999	-10000	0	0
JMJD1A	-0.022	0.066	-9999	-0.13	224	224
CDK6	0.012	0.059	-9999	-0.77	5	5
TGFB1I1	-0.055	0.23	-9999	-0.84	71	71
T-DHT/AR/CyclinD1	-0.11	0.26	-9999	-0.63	157	157
XRCC6	0.019	0.007	-9999	-10000	0	0
T-DHT/AR	-0.1	0.27	-9999	-0.66	140	140
CTDSP1	0.013	0.029	-9999	-0.85	1	1
CTDSP2	0.023	0.02	-9999	-10000	0	0
BRCA1	0.005	0.087	-9999	-0.85	9	9
TCF4	-0.076	0.27	-9999	-0.83	102	102
CDKN2A	-0.039	0.21	-9999	-0.81	63	63
SRF	0.021	0.03	-9999	-10000	0	0
NKX3-1	-0.095	0.17	-9999	-1.2	9	9
KLK3	-0.053	0.19	-9999	-0.63	6	6
TMF1	0.011	0.058	-9999	-0.85	4	4
HNRNPA1	0.02	0.011	-9999	-10000	0	0
AOF2	-0.004	0.013	-9999	-10000	0	0
APPL1	0.034	0.029	-9999	-0.65	1	1
T-DHT/AR/Caspase 8	-0.085	0.22	-9999	-0.62	121	121
AR	-0.12	0.3	-9999	-0.87	120	120
UBA3	0.013	0.03	-9999	-0.86	1	1
PATZ1	0.02	0.011	-9999	-10000	0	0
PAWR	0.013	0.041	-9999	-0.85	2	2
PRKDC	0.019	0.007	-9999	-10000	0	0
PA2G4	0.021	0.013	-9999	-10000	0	0
UBE2I	0.016	0	-9999	-10000	0	0
T-DHT/AR/Cyclin D3/CDK11 p58	-0.073	0.21	-9999	-0.57	122	122
RPS6KA3	0.013	0.031	-9999	-0.87	1	1
T-DHT/AR/ARA70	-0.082	0.23	-9999	-0.62	121	121
LATS2	0.019	0.03	-9999	-0.83	1	1
T-DHT/AR/PRX1	-0.074	0.21	-9999	-0.57	121	121
Cyclin D3/CDK11 p58	-0.002	0.028	-9999	-0.48	3	3
VAV3	0.001	0.11	-9999	-0.85	14	14
KLK2	-0.092	0.19	-9999	-0.67	78	78
CASP8	0.016	0.029	-9999	-0.83	1	1
T-DHT/AR/TIF2/CARM1	-0.1	0.27	-9999	-0.66	147	147
TMPRSS2	-0.29	0.45	-9999	-0.91	270	270
CCND1	-0.025	0.18	-9999	-0.84	42	42
PIAS1	0.011	0.016	-9999	-10000	0	0
mol:T-DHT	-0.018	0.044	-9999	-0.093	169	169
CDC2L1	0	0.001	-9999	-10000	0	0
PIAS4	0.004	0.05	-9999	-0.85	2	2
T-DHT/AR/CDK6	-0.086	0.23	-9999	-0.63	122	122
CMTM2	-0.017	0.15	-9999	-0.7	42	42
SNURF	-0.029	0.19	-9999	-0.85	45	45
ZMIZ1	0.001	0.047	-9999	-0.84	1	1
CCND3	0.014	0.039	-9999	-0.65	3	3
TGIF1	0.02	0.011	-9999	-10000	0	0
FKBP4	0.014	0.006	-9999	-10000	0	0

×

IL2 signaling events mediated by PI3K

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.028	0.28	-10000	0	-0.89	70	70
UGCG	-0.017	0.13	-10000	0	-0.82	19	19
AKT1/mTOR/p70S6K/Hsp90/TERT	0.006	0.18	-10000	0	-0.46	84	84
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucosylceramide	-0.001	0.13	-10000	0	-0.8	19	19
mol:DAG	-0.003	0.011	-10000	0	-10000	0	0
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.082	0.19	-10000	0	-0.61	85	85
FRAP1	-0.011	0.28	-10000	0	-0.73	89	89
FOXO3	-0.005	0.27	-10000	0	-0.75	81	81
AKT1	-0.022	0.3	-10000	0	-0.84	84	84
GAB2	0.012	0.061	-10000	0	-0.72	6	6
SMPD1	0	0.043	-10000	0	-10000	0	0
SGMS1	0	0.044	-10000	0	-0.38	1	1
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
mol:GDP	0.02	0.067	-10000	0	-0.54	12	12
CALM1	0.016	0	-10000	0	-10000	0	0
cell proliferation	0.01	0.14	-10000	0	-0.41	37	37
EIF3A	0.016	0	-10000	0	-10000	0	0
PI3K	0.02	0.076	-10000	0	-0.62	12	12
RPS6KB1	0.015	0.056	-10000	0	-10000	0	0
mol:sphingomyelin	-0.003	0.011	-10000	0	-10000	0	0
natural killer cell activation	0.001	0.002	-10000	0	-0.013	10	10
JAK3	-0.026	0.19	-10000	0	-0.83	48	48
PIK3R1	0.014	0.066	-10000	0	-0.78	6	6
JAK1	0.019	0.004	-10000	0	-10000	0	0
NFKB1	0.015	0.029	-10000	0	-0.85	1	1
MYC	-0.016	0.3	-10000	0	-0.86	79	79
MYB	-0.018	0.24	-10000	0	-0.79	62	62
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	-0.038	0.32	-10000	0	-0.81	105	105
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.032	0.054	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	-0.033	0.3	-10000	0	-0.77	105	105
Rac1/GDP	0.027	0.062	-10000	0	-0.52	10	10
T cell proliferation	-0.02	0.28	-10000	0	-0.78	82	82
SHC1	0.016	0.023	-10000	0	-0.65	1	1
RAC1	0.016	0	-10000	0	-10000	0	0
positive regulation of cyclin-dependent protein kinase activity	0.003	0.016	-10000	0	-0.054	61	61
PRKCZ	-0.026	0.3	-10000	0	-0.84	82	82
NF kappa B1 p50/RelA	-0.08	0.19	-10000	0	-0.64	72	72
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K	-0.047	0.32	-10000	0	-0.91	91	91
HSP90AA1	0.016	0	-10000	0	-10000	0	0
RELA	0.016	0	-10000	0	-10000	0	0
IL2RA	-0.1	0.28	-10000	0	-0.76	137	137
IL2RB	-0.048	0.23	-10000	0	-0.82	72	72
TERT	-0.057	0.2	-10000	0	-0.65	87	87
E2F1	0.009	0.099	-10000	0	-0.33	62	62
SOS1	0.017	0.003	-10000	0	-10000	0	0
RPS6	0.015	0.032	-10000	0	-0.65	2	2
mol:cAMP	-0.002	0.008	0.026	61	-10000	0	61
PTPN11	0.016	0.029	-10000	0	-0.85	1	1
IL2RG	-0.057	0.24	-10000	0	-0.79	85	85
actin cytoskeleton organization	-0.02	0.28	-10000	0	-0.78	82	82
GRB2	0.017	0.003	-10000	0	-10000	0	0
IL2	0.002	0.076	-10000	0	-0.65	12	12
PIK3CA	0.014	0.071	-10000	0	-0.85	6	6
Rac1/GTP	0.035	0.061	-10000	0	-0.49	10	10
LCK	-0.077	0.27	-10000	0	-0.8	104	104
BCL2	0.007	0.24	-10000	0	-0.64	76	76

×

ErbB4 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF	-0.01	0.11	-10000	0	-0.62	9	9
epithelial cell differentiation	-0.082	0.15	-10000	0	-0.6	14	14
ITCH	0.028	0.019	-10000	0	-10000	0	0
WWP1	0	0.086	-10000	0	-0.99	1	1
FYN	0.007	0.086	-10000	0	-0.85	9	9
EGFR	-0.021	0.17	-10000	0	-0.78	41	41
PRL	-0.002	0.066	-10000	0	-0.65	9	9
neuron projection morphogenesis	0.007	0.16	-10000	0	-0.68	12	12
PTPRZ1	-0.045	0.18	-10000	0	-0.65	74	74
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC	-0.061	0.15	-10000	0	-0.66	17	17
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta	-0.04	0.18	-10000	0	-0.57	75	75
ADAM17	0.024	0.061	-10000	0	-0.84	4	4
ErbB4/ErbB4	-0.01	0.1	-10000	0	-0.44	12	12
ErbB4/ErbB4/neuregulin 3/neuregulin 3	-0.049	0.18	-10000	0	-0.58	78	78
NCOR1	0.015	0.029	-10000	0	-0.85	1	1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn	-0.068	0.17	-10000	0	-0.55	75	75
GRIN2B	-0.047	0.19	-10000	0	-0.6	48	48
ErbB4/ErbB2/betacellulin	-0.056	0.14	-10000	0	-0.54	50	50
STAT1	0.009	0.074	-10000	0	-0.72	9	9
HBEGF	0.004	0.094	-10000	0	-0.74	14	14
PRLR	-0.13	0.29	-10000	0	-0.72	172	172
E4ICDs/ETO2	-0.016	0.13	-10000	0	-0.63	20	20
axon guidance	0.012	0.09	-10000	0	-0.63	2	2
NEDD4	0.008	0.13	-10000	0	-0.84	20	20
Prolactin receptor/Prolactin receptor/Prolactin	-0.11	0.22	-10000	0	-0.54	181	181
CBFA2T3	-0.005	0.13	-10000	0	-0.82	22	22
ErbB4/ErbB2/HBEGF	-0.028	0.086	-10000	0	-0.56	14	14
MAPK3	-0.003	0.16	-10000	0	-0.69	11	11
STAT1 (dimer)	-0.007	0.1	-10000	0	-0.73	5	5
MAPK1	-0.003	0.16	-10000	0	-0.7	11	11
JAK2	0.015	0.029	-10000	0	-0.85	1	1
ErbB4/ErbB2/neuregulin 1 beta	-0.066	0.16	-10000	0	-0.54	73	73
NRG1	-0.029	0.2	-10000	0	-0.61	89	89
NRG3	-0.057	0.24	-10000	0	-0.81	78	78
NRG2	-0.059	0.22	-10000	0	-0.71	92	92
NRG4	-0.074	0.23	-10000	0	-0.67	115	115
heart development	0.012	0.09	-10000	0	-0.63	2	2
neural crest cell migration	-0.031	0.17	-10000	0	-0.53	73	73
ERBB2	0.031	0.064	-10000	0	-0.62	8	8
WWOX/E4ICDs	-0.003	0.09	-10000	0	-1	1	1
SHC1	0.015	0.022	-10000	0	-0.65	1	1
ErbB4/EGFR/neuregulin 4	-0.1	0.19	-10000	0	-0.67	48	48
apoptosis	0.088	0.17	0.56	70	-10000	0	70
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta	-0.049	0.18	-10000	0	-0.54	86	86
ErbB4/ErbB2/epiregulin	-0.12	0.18	-10000	0	-0.51	88	88
ErbB4/ErbB4/betacellulin/betacellulin	-0.043	0.17	-10000	0	-0.54	67	67
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2	-0.1	0.18	-10000	0	-0.6	41	41
MDM2	0.002	0.091	-10000	0	-1	1	1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta	-0.061	0.15	-10000	0	-0.54	68	68
STAT5A	0.019	0.091	-10000	0	-0.6	4	4
ErbB4/EGFR/neuregulin 1 beta	-0.084	0.19	-10000	0	-0.65	54	54
DLG4	0.005	0.096	-10000	0	-0.82	12	12
GRB2/SHC	-0.001	0.016	-10000	0	-0.48	1	1
E4ICDs/TAB2/NCoR1	-0.033	0.07	-10000	0	-0.88	2	2
STAT5A (dimer)	-0.087	0.16	-10000	0	-0.67	13	13
MAP3K7IP2	0	0	-10000	0	-10000	0	0
STAT5B (dimer)	0.019	0.083	-10000	0	-0.77	1	1
LRIG1	0.012	0.055	-10000	0	-0.8	4	4
EREG	-0.17	0.31	-10000	0	-0.7	228	228
BTC	-0.046	0.21	-10000	0	-0.78	69	69
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta	0.012	0.09	-10000	0	-0.64	2	2
ERBB4	-0.01	0.1	-10000	0	-1.1	1	1
STAT5B	0.016	0	-10000	0	-10000	0	0
YAP1	-0.011	0.033	-10000	0	-0.79	1	1
GRB2	0.016	0	-10000	0	-10000	0	0
ErbB4/ErbB2/neuregulin 4	-0.07	0.15	-10000	0	-0.54	29	29
glial cell differentiation	0.033	0.069	0.87	2	-10000	0	2
WWOX	0.015	0.022	-10000	0	-0.65	1	1
cell proliferation	-0.04	0.21	-10000	0	-0.67	48	48

×

Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
DYNC1H1	0.016	0	-10000	0	-10000	0	0
VLDLR	0.01	0.067	-10000	0	-0.74	7	7
LRPAP1	0.014	0.041	-10000	0	-0.85	2	2
NUDC	0.016	0	-10000	0	-10000	0	0
RELN/LRP8	-0.19	0.24	-10000	0	-0.58	130	130
CaM/Ca2+	0	0	-10000	0	-10000	0	0
KATNA1	0.016	0.001	-10000	0	-10000	0	0
GO:0030286	0	0	-10000	0	-10000	0	0
ABL1	-0.15	0.23	-10000	0	-0.53	129	129
IQGAP1/CaM	0	0	-10000	0	-10000	0	0
DAB1	-0.036	0.17	-10000	0	-0.65	60	60
IQGAP1	0.016	0	-10000	0	-10000	0	0
PLA2G7	-0.071	0.25	-10000	0	-0.77	99	99
CALM1	0.016	0	-10000	0	-10000	0	0
DYNLT1	0.016	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
LRPAP1/LRP8	-0.018	0.093	-10000	0	-0.5	32	32
UniProt:Q4QZ09	0	0	-10000	0	-10000	0	0
CLIP1	0.016	0	-10000	0	-10000	0	0
CDK5R1	0.013	0.048	-10000	0	-0.7	4	4
LIS1/Poliovirus Protein 3A	0	0	-10000	0	-10000	0	0
CDK5R2	-0.055	0.2	-10000	0	-0.65	89	89
mol:PP1	0	0	-10000	0	-10000	0	0
RELN/VLDLR/DAB1	-0.21	0.25	-10000	0	-0.48	389	389
YWHAE	0.016	0	-10000	0	-10000	0	0
NDEL1/14-3-3 E	-0.1	0.2	-10000	0	-0.61	19	19
MAP1B	-0.012	0.067	0.24	2	-0.39	23	25
RAC1	0	0	-10000	0	-10000	0	0
p35/CDK5	-0.11	0.21	-10000	0	-0.71	11	11
RELN	-0.27	0.36	-10000	0	-0.72	343	343
PAFAH/LIS1	-0.026	0.17	-10000	0	-0.56	60	60
LIS1/CLIP170	0.034	0	-10000	0	-10000	0	0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain	-0.1	0.13	-10000	0	-0.53	4	4
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3	-0.087	0.17	-10000	0	-0.65	21	21
GO:0005869	0	0	-10000	0	-10000	0	0
NDEL1	-0.12	0.21	-10000	0	-0.66	19	19
LIS1/IQGAP1	0.034	0	-10000	0	-10000	0	0
RHOA	0	0	-10000	0	-10000	0	0
PAFAH1B1	0.029	0	-10000	0	-10000	0	0
PAFAH1B3	0.009	0.071	-10000	0	-0.72	8	8
PAFAH1B2	0.001	0.12	-10000	0	-0.85	16	16
MAP1B/LIS1/Dynein heavy chain	0.024	0.047	-10000	0	-10000	0	0
NDEL1/Katanin 60/Dynein heavy chain	-0.13	0.16	-10000	0	-0.59	17	17
LRP8	-0.007	0.12	-10000	0	-0.66	30	30
NDEL1/Katanin 60	-0.1	0.2	-10000	0	-0.61	19	19
P39/CDK5	-0.15	0.24	-10000	0	-0.7	46	46
LIS1/NudC/Dynein intermediate chain/microtubule organizing center	0.034	0	-10000	0	-10000	0	0
CDK5	-0.13	0.22	-10000	0	-0.49	129	129
PPP2R5D	0.015	0.032	-10000	0	-0.65	2	2
LIS1/CLIP170/Dynein Complex/Dynactin Complex	0	0	-10000	0	-10000	0	0
CSNK2A1	0.016	0	-10000	0	-10000	0	0
RELN/VLDLR/DAB1/LIS1	-0.17	0.21	-10000	0	-0.52	138	138
RELN/VLDLR	-0.18	0.22	-10000	0	-0.54	133	133
CDC42	0	0	-10000	0	-10000	0	0

×

Cellular roles of Anthrax toxin

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ANTXR1	0.001	0.11	-10000	0	-0.84	16	16
ANTXR2	-0.02	0.17	-10000	0	-0.84	38	38
negative regulation of myeloid dendritic cell antigen processing and presentation	-0.006	0.025	-10000	0	-0.11	49	49
monocyte activation	-0.09	0.24	-10000	0	-0.56	155	155
MAP2K2	-0.005	0.054	-10000	0	-0.91	3	3
MAP2K1	-0.005	0.021	-10000	0	-10000	0	0
MAP2K7	-0.006	0.032	-10000	0	-0.51	2	2
MAP2K6	-0.011	0.061	-10000	0	-0.52	11	11
CYAA	-0.011	0.13	-10000	0	-0.54	49	49
MAP2K4	-0.005	0.021	-10000	0	-10000	0	0
IL1B	-0.031	0.16	-10000	0	-0.52	76	76
Channel	-0.032	0.14	-10000	0	-0.57	49	49
NLRP1	-0.025	0.11	-10000	0	-0.52	37	37
CALM1	0.016	0	-10000	0	-10000	0	0
negative regulation of phagocytosis	-0.007	0.029	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
regulation of endothelial cell proliferation	0.006	0.025	0.11	49	-10000	0	49
MAPK3	-0.005	0.027	-10000	0	-0.51	1	1
MAPK1	-0.005	0.027	-10000	0	-0.51	1	1
PGR	-0.1	0.2	-10000	0	-0.48	191	191
PA/Cellular Receptors	-0.034	0.14	-10000	0	-0.62	49	49
apoptosis	-0.006	0.025	-10000	0	-0.11	49	49
LOC728358	0	0	-10000	0	-10000	0	0
Lethal toxin (unfolded)	-0.01	0.13	-10000	0	-0.54	49	49
macrophage activation	0.019	0.033	-10000	0	-0.48	2	2
TNF	-0.062	0.23	-10000	0	-0.75	90	90
VCAM1	-0.091	0.24	-10000	0	-0.56	155	155
platelet activation	-0.007	0.029	-10000	0	-10000	0	0
MAPKKK cascade	-0.013	0.032	0.21	7	-10000	0	7
IL18	-0.017	0.13	-10000	0	-0.48	55	55
negative regulation of macrophage activation	-0.006	0.025	-10000	0	-0.11	49	49
LEF	-0.006	0.025	-10000	0	-0.11	49	49
CASP1	-0.02	0.082	-10000	0	-0.32	44	44
mol:cAMP	-0.007	0.029	-10000	0	-10000	0	0
necrosis	-0.006	0.025	-10000	0	-0.11	49	49
intracellular pH reduction	0	0	-10000	0	-10000	0	0
PAGA	0	0	-10000	0	-10000	0	0
Edema toxin (unfolded)	-0.03	0.13	-10000	0	-0.55	49	49
mol:Epigallocatechin-3-gallate (EGCG)	0	0	-10000	0	-10000	0	0

×

IL1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
UBC13/UEV1A	-0.001	0.023	-10000	0	-0.48	2	2
PRKCZ	0.008	0.082	-10000	0	-0.85	8	8
MAP3K7IP2	0	0	-10000	0	-10000	0	0
ERC1	0.016	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4	-0.047	0.18	-10000	0	-0.82	29	29
IRAK/TOLLIP	0.034	0.027	-10000	0	-0.52	1	1
IKBKB	0.016	0	-10000	0	-10000	0	0
IKBKG	0.013	0.05	-10000	0	-0.85	3	3
IL1 alpha/IL1R2	-0.15	0.25	-10000	0	-0.55	248	248
IL1A	-0.013	0.13	-10000	0	-0.66	36	36
IL1B	-0.04	0.23	-10000	0	-0.71	84	84
IRAK/TRAF6/p62/Atypical PKCs	-0.008	0.059	-10000	0	-0.89	1	1
IL1R2	-0.17	0.32	-10000	0	-0.72	221	221
IL1R1	-0.005	0.13	-10000	0	-0.84	22	22
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	0.011	0.16	0.25	16	-0.8	21	37
TOLLIP	0.016	0	-10000	0	-10000	0	0
TICAM2	0.008	0.082	-10000	0	-0.85	8	8
MAP3K3	0.016	0	-10000	0	-10000	0	0
TAK1/TAB1/TAB2	0	0	-10000	0	-10000	0	0
IKK complex/ELKS	0.077	0.051	-10000	0	-0.76	2	2
JUN	0.043	0.08	-10000	0	-0.7	1	1
MAP3K7	0.016	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/PI3K	-0.076	0.23	-10000	0	-1	33	33
IL1 alpha/IL1R1/IL1RAP/MYD88	-0.049	0.17	-10000	0	-0.66	43	43
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4	-0.046	0.16	-10000	0	-0.62	43	43
IL1 beta fragment/IL1R1/IL1RAP	-0.079	0.23	-10000	0	-0.69	88	88
NFKB1	0.015	0.029	-10000	0	-0.85	1	1
MAPK8	0.038	0.074	-10000	0	-0.44	11	11
IRAK1	0.027	0.029	-10000	0	-0.46	3	3
IL1RN/IL1R1	-0.062	0.18	-10000	0	-0.58	95	95
IRAK4	0.016	0	-10000	0	-10000	0	0
PRKCI	0.015	0.022	-10000	0	-0.65	1	1
TRAF6	0.016	0	-10000	0	-10000	0	0
PI3K	-0.008	0.072	-10000	0	-0.62	12	12
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.007	0.2	-10000	0	-0.92	28	28
CHUK	0.015	0.029	-10000	0	-0.85	1	1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s	-0.079	0.23	-10000	0	-0.69	88	88
IL1 beta/IL1R2	-0.17	0.29	-10000	0	-0.55	275	275
IRAK/TRAF6/TAK1/TAB1/TAB2	-0.001	0.021	-10000	0	-0.45	1	1
NF kappa B1 p50/RelA	-0.067	0.2	-10000	0	-0.91	33	33
IRAK3	-0.017	0.16	-10000	0	-0.83	35	35
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4	-0.074	0.22	-10000	0	-1.1	26	26
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	0.011	0.13	-10000	0	-0.63	19	19
IL1 alpha/IL1R1/IL1RAP	-0.046	0.15	-10000	0	-0.6	41	41
RELA	0.016	0	-10000	0	-10000	0	0
MAP3K7IP1	0	0	-10000	0	-10000	0	0
SQSTM1	0.009	0.067	-10000	0	-0.65	9	9
MYD88	0.002	0.11	-10000	0	-0.85	14	14
IRAK/TRAF6/MEKK3	0.024	0.031	-10000	0	-0.48	1	1
IL1RAP	-0.009	0.14	-10000	0	-0.8	27	27
UBE2N	0.016	0	-10000	0	-10000	0	0
IRAK/TRAF6	-0.06	0.17	-10000	0	-0.83	26	26
CASP1	-0.017	0.17	-10000	0	-0.85	34	34
IL1RN/IL1R2	-0.18	0.28	-10000	0	-0.58	270	270
IL1 beta fragment/IL1R1/IL1RAP/MYD88	-0.081	0.25	-10000	0	-0.71	89	89
TMEM189-UBE2V1	0.005	0.032	-10000	0	-0.65	2	2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	0.019	0.14	-10000	0	-0.63	27	27
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
IL1RN	-0.047	0.21	-10000	0	-0.72	76	76
TRAF6/TAK1/TAB1/TAB2	-0.001	0.015	-10000	0	-10000	0	0
MAP2K6	0.035	0.054	-10000	0	-0.46	8	8

×

Sphingosine 1-phosphate (S1P) pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.013	0.05	-9999	-0.85	3	3
SPHK1	-0.061	0.22	-9999	-0.69	97	97
GNAI2	0.015	0.029	-9999	-0.85	1	1
mol:S1P	-0.004	0.1	-9999	-0.46	19	19
GNAO1	-0.052	0.22	-9999	-0.76	79	79
mol:Sphinganine-1-P	-0.031	0.18	-9999	-0.52	97	97
growth factor activity	0	0	-9999	-10000	0	0
S1P/S1P2/G12/G13	-0.021	0.075	-9999	-0.66	6	6
GNAI3	0.016	0	-9999	-10000	0	0
G12/G13	-0.001	0.016	-9999	-0.48	1	1
S1PR3	-0.086	0.27	-9999	-0.82	109	109
S1PR2	0.012	0.056	-9999	-0.73	5	5
EDG1	0	0	-9999	-10000	0	0
S1P1/S1P	-0.025	0.083	-9999	-0.41	19	19
S1PR5	-0.052	0.23	-9999	-0.81	73	73
S1PR4	-0.018	0.17	-9999	-0.83	36	36
GNAI1	0.004	0.1	-9999	-0.85	12	12
S1P/S1P5/G12	-0.06	0.15	-9999	-0.56	61	61
S1P/S1P3/Gq	-0.072	0.26	-9999	-0.58	139	139
S1P/S1P4/Gi	-0.01	0.17	-9999	-0.62	39	39
GNAQ	0.016	0	-9999	-10000	0	0
GNAZ	0.007	0.085	-9999	-0.79	10	10
GNA14	-0.078	0.27	-9999	-0.84	97	97
GNA15	-0.014	0.16	-9999	-0.81	33	33
GNA12	0.016	0	-9999	-10000	0	0
GNA13	0.015	0.022	-9999	-0.65	1	1
GNA11	-0.011	0.14	-9999	-0.75	31	31
ABCC1	0.015	0.029	-9999	-0.85	1	1

×

Paxillin-dependent events mediated by a4b1

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.016	0	-10000	0	-10000	0	0
Rac1/GDP	0.007	0.021	-10000	0	-10000	0	0
DOCK1	0.014	0.041	-10000	0	-0.85	2	2
ITGA4	-0.064	0.25	-10000	0	-0.84	83	83
RAC1	0.016	0	-10000	0	-10000	0	0
alpha4/beta7 Integrin	-0.066	0.2	-10000	0	-0.66	89	89
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.015	0.022	-10000	0	-0.65	1	1
alpha4/beta1 Integrin	-0.052	0.16	-10000	0	-0.56	83	83
alpha4/beta7 Integrin/Paxillin	-0.052	0.16	-10000	0	-0.52	87	87
lamellipodium assembly	-0.002	0.071	-10000	0	-0.56	12	12
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
PI3K	-0.008	0.072	-10000	0	-0.62	12	12
ARF6	0.016	0	-10000	0	-10000	0	0
TLN1	0.015	0.029	-10000	0	-0.85	1	1
PXN	0.029	0	-10000	0	-10000	0	0
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
ARF6/GTP	-0.041	0.13	-10000	0	-0.75	2	2
cell adhesion	-0.044	0.14	-10000	0	-0.48	81	81
CRKL/CBL	-0.001	0.022	-10000	0	-0.65	1	1
alpha4/beta1 Integrin/Paxillin	-0.047	0.15	-10000	0	-0.51	80	80
ITGB1	0.016	0	-10000	0	-10000	0	0
ITGB7	0.008	0.082	-10000	0	-0.85	8	8
ARF6/GDP	0.007	0.021	-10000	0	-10000	0	0
alpha4/beta1 Integrin/Paxillin/VCAM1	-0.11	0.23	-10000	0	-0.55	177	177
p130Cas/Crk/Dock1	-0.004	0.049	-10000	0	-0.64	5	5
VCAM1	-0.1	0.3	-10000	0	-0.85	123	123
alpha4/beta1 Integrin/Paxillin/Talin	-0.045	0.14	-10000	0	-0.48	81	81
alpha4/beta1 Integrin/Paxillin/GIT1	-0.045	0.14	-10000	0	-0.49	82	82
BCAR1	0.013	0.05	-10000	0	-0.85	3	3
mol:GDP	0.045	0.14	0.48	82	-10000	0	82
CBL	0.015	0.029	-10000	0	-0.85	1	1
PRKACA	0.016	0	-10000	0	-10000	0	0
GIT1	0.014	0.041	-10000	0	-0.85	2	2
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton	-0.045	0.14	-10000	0	-0.48	81	81
Rac1/GTP	-0.003	0.082	-10000	0	-0.64	12	12

×

Ras signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ERK1-2/ELK1	-0.021	0.23	-9999	-0.81	46	46
MAP3K8	0.01	0.059	-9999	-0.77	5	5
FOS	-0.014	0.21	-9999	-0.76	46	46
PRKCA	0.014	0.032	-9999	-0.65	2	2
PTPN7	-0.037	0.2	-9999	-0.77	61	61
HRAS	0.011	0.059	-9999	-0.77	5	5
PRKCB	-0.036	0.2	-9999	-0.83	54	54
NRAS	0.016	0.001	-9999	-10000	0	0
RAS family/GTP	-0.003	0.035	-9999	-0.52	3	3
MAPK3	-0.01	0.18	-9999	-0.74	39	39
MAP2K1	0.011	0.14	-9999	-0.54	50	50
ELK1	0.015	0.006	-9999	-10000	0	0
BRAF	-0.033	0.13	-9999	-0.55	49	49
mol:GTP	0	0.002	-9999	-0.006	113	113
MAPK1	-0.01	0.18	-9999	-0.74	39	39
RAF1	-0.033	0.13	-9999	-0.55	49	49
KRAS	0.016	0.001	-9999	-10000	0	0

×

Aurora B signaling

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
Condensin I complex	0.005	0.14	-9999	-0.55	38	38
STMN1	-0.007	0.15	-9999	-0.56	57	57
Aurora B/RasGAP/Survivin	-0.047	0.21	-9999	-0.73	65	65
Chromosomal passenger complex/Cul3 protein complex	-0.001	0.14	-9999	-0.45	57	57
BIRC5	-0.04	0.2	-9999	-0.73	68	68
DES	-0.17	0.27	-9999	-0.67	168	168
Aurora C/Aurora B/INCENP	-0.021	0.13	-9999	-0.47	42	42
Aurora B/TACC1	-0.02	0.12	-9999	-0.47	60	60
Aurora B/PP2A	-0.022	0.14	-9999	-0.52	59	59
mol:GTP	0	0	-9999	-10000	0	0
CBX5	0.01	0.042	-9999	-0.21	17	17
mitotic metaphase/anaphase transition	0	0.004	-9999	-10000	0	0
NDC80	-0.038	0.21	-9999	-0.64	91	91
Cul3 protein complex	-0.023	0.11	-9999	-0.51	40	40
KIF2C	-0.002	0.11	-9999	-0.42	45	45
PEBP1	0.015	0.005	-9999	-10000	0	0
KIF20A	-0.039	0.2	-9999	-0.74	64	64
mol:GDP	0	0	-9999	-10000	0	0
Aurora B/RasGAP	-0.023	0.14	-9999	-0.54	59	59
SEPT1	0.002	0.1	-9999	-0.71	17	17
SMC2	0.015	0.029	-9999	-0.85	1	1
SMC4	0.011	0.065	-9999	-0.85	5	5
NSUN2/NPM1/Nucleolin	0.004	0.15	-9999	-0.93	17	17
PSMA3	0.016	0	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	-0.001	0.003	-9999	-10000	0	0
H3F3B	0	0.091	-9999	-0.34	57	57
AURKB	-0.027	0.18	-9999	-0.72	57	57
AURKC	0.001	0.1	-9999	-0.7	19	19
CDCA8	0.002	0.097	-9999	-0.68	18	18
cytokinesis	-0.071	0.19	-9999	-0.7	60	60
Aurora B/Septin1	-0.045	0.2	-9999	-0.73	54	54
AURKA	0.008	0.071	-9999	-0.66	10	10
INCENP	0.014	0.042	-9999	-0.86	2	2
KLHL13	-0.018	0.16	-9999	-0.76	39	39
BUB1	-0.023	0.16	-9999	-0.69	49	49
hSgo1/Aurora B/Survivin	-0.06	0.23	-9999	-0.73	82	82
EVI5	0.016	0.002	-9999	-10000	0	0
RhoA/GTP	-0.051	0.16	-9999	-0.68	44	44
SGOL1	-0.016	0.15	-9999	-0.71	39	39
CENPA	-0.009	0.15	-9999	-0.54	56	56
NCAPG	-0.017	0.16	-9999	-0.76	38	38
Aurora B/HC8 Proteasome	-0.021	0.14	-9999	-0.53	57	57
NCAPD2	0.015	0.032	-9999	-0.65	2	2
Aurora B/PP1-gamma	-0.021	0.14	-9999	-0.53	57	57
RHOA	0.016	0	-9999	-10000	0	0
NCAPH	-0.012	0.14	-9999	-0.73	33	33
NPM1	-0.022	0.13	-9999	-0.78	17	17
RASA1	0.013	0.05	-9999	-0.85	3	3
KLHL9	0.014	0.041	-9999	-0.85	2	2
mitotic prometaphase	-0.001	0.005	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	-0.021	0.13	-9999	-0.52	57	57
PPP1CC	0.016	0	-9999	-10000	0	0
Centraspindlin	-0.057	0.18	-9999	-0.74	47	47
RhoA/GDP	0	0	-9999	-10000	0	0
NSUN2	-0.022	0.13	-9999	-0.73	19	19
MYLK	-0.035	0.16	-9999	-0.46	87	87
KIF23	-0.003	0.12	-9999	-0.7	24	24
VIM	-0.055	0.24	-9999	-0.66	110	110
RACGAP1	0.013	0.039	-9999	-0.66	3	3
mitosis	0	0	-9999	-10000	0	0
NCL	-0.022	0.13	-9999	-0.78	17	17
Chromosomal passenger complex	-0.013	0.18	-9999	-0.55	73	73
Chromosomal passenger complex/EVI5	-0.03	0.22	-9999	-0.71	68	68
TACC1	0.012	0.058	-9999	-0.85	4	4
PPP2R5D	0.015	0.032	-9999	-0.65	2	2
CUL3	0.016	0	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0

×

Presenilin action in Notch and Wnt 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved)	-0.078	0.19	-10000	0	-0.52	117	117
HDAC1	0.005	0.014	-10000	0	-10000	0	0
AES	0.015	0.029	-10000	0	-0.85	1	1
FBXW11	0.016	0	-10000	0	-10000	0	0
DTX1	-0.03	0.19	-10000	0	-0.78	52	52
LRP6/FZD1	-0.052	0.18	-10000	0	-0.65	71	71
TLE1	0.014	0.041	-10000	0	-0.85	2	2
AP1	-0.038	0.15	-10000	0	-0.42	77	77
NCSTN	0.015	0.029	-10000	0	-0.85	1	1
ADAM10	0.006	0.089	-10000	0	-0.83	10	10
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4	0.009	0.13	-10000	0	-0.62	13	13
NICD/RBPSUH	-0.009	0.08	-10000	0	-0.78	9	9
WIF1	-0.022	0.14	-10000	0	-0.65	42	42
NOTCH1	-0.01	0.085	-10000	0	-0.83	9	9
PSENEN	0.016	0	-10000	0	-10000	0	0
KREMEN2	-0.031	0.17	-10000	0	-0.67	60	60
DKK1	-0.094	0.27	-10000	0	-0.75	126	126
beta catenin/beta TrCP1	0.04	0.06	0.33	1	-10000	0	1
APH1B	0.009	0.076	-10000	0	-0.85	7	7
APH1A	0.016	0	-10000	0	-10000	0	0
AXIN1	0	0.04	-10000	0	-0.45	3	3
CtBP/CBP/TCF1/TLE1/AES	0.007	0.12	-10000	0	-0.87	2	2
PSEN1	0.016	0	-10000	0	-10000	0	0
FOS	-0.086	0.26	-10000	0	-0.74	120	120
JUN	0.01	0.069	-10000	0	-0.76	7	7
MAP3K7	0.015	0.005	-10000	0	-10000	0	0
CTNNB1	0.032	0.064	0.26	14	-10000	0	14
MAPK3	0.015	0.029	-10000	0	-0.85	1	1
DKK2/LRP6/Kremen 2	-0.11	0.21	-10000	0	-0.58	97	97
HNF1A	-0.054	0.24	-10000	0	-0.85	72	72
CTBP1	0.016	0.003	-10000	0	-10000	0	0
MYC	-0.041	0.33	-10000	0	-1.6	37	37
NKD1	-0.044	0.2	-10000	0	-0.7	73	73
FZD1	-0.052	0.23	-10000	0	-0.85	70	70
NOTCH1 precursor/Deltex homolog 1	-0.033	0.13	-10000	0	-0.54	44	44
apoptosis	-0.037	0.15	-10000	0	-0.42	77	77
Delta 1/NOTCHprecursor	-0.077	0.19	-10000	0	-0.52	117	117
DLL1	-0.11	0.3	-10000	0	-0.82	137	137
PPARD	0.022	0.084	-10000	0	-1.6	2	2
Gamma Secretase	-0.004	0.045	-10000	0	-0.48	8	8
APC	0	0.036	-10000	0	-0.41	2	2
DVL1	-0.009	0.039	-10000	0	-0.54	3	3
CSNK2A1	0.015	0.004	-10000	0	-10000	0	0
MAP3K7IP1	-0.001	0.006	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	-0.097	0.2	-10000	0	-0.57	83	83
LRP6	0.015	0.029	-10000	0	-0.85	1	1
CSNK1A1	0.015	0.004	-10000	0	-10000	0	0
NLK	0.02	0.013	-10000	0	-10000	0	0
CCND1	-0.046	0.34	-10000	0	-1.6	40	40
WNT1	0.002	0.09	-10000	0	-0.66	16	16
Axin1/APC/beta catenin	0.047	0.059	0.32	1	-0.48	3	4
DKK2	-0.11	0.29	-10000	0	-0.75	149	149
NOTCH1 precursor/DVL1	-0.012	0.076	-10000	0	-0.7	9	9
GSK3B	0.016	0.001	-10000	0	-10000	0	0
FRAT1	0.015	0.023	-10000	0	-0.65	1	1
NOTCH/Deltex homolog 1	-0.034	0.13	-10000	0	-0.54	44	44
PPP2R5D	0.021	0.092	0.32	73	-10000	0	73
MAPK1	0.015	0.029	-10000	0	-0.85	1	1
WNT1/LRP6/FZD1	-0.065	0.16	-10000	0	-0.54	73	73
RBPJ	0.016	0	-10000	0	-10000	0	0
CREBBP	0.019	0.006	-10000	0	-10000	0	0

×

FAS signaling pathway (CD95)

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
SPTAN1	0.01	0.053	0.31	14	-0.33	1	15
RFC1	0.01	0.053	0.31	14	-0.33	1	15
PRKDC	0.01	0.053	0.31	14	-0.33	1	15
RIPK1	0.017	0.005	-10000	0	-10000	0	0
CASP7	-0.019	0.055	0.26	2	-0.56	1	3
FASLG/FAS/FADD/FAF1	-0.057	0.14	0.27	9	-0.4	80	89
MAP2K4	-0.045	0.17	-10000	0	-0.52	45	45
mol:ceramide	-0.061	0.2	-10000	0	-0.53	93	93
GSN	0.01	0.056	0.31	14	-0.44	2	16
FASLG/FAS/FADD/FAF1/Caspase 8	-0.05	0.16	-10000	0	-0.49	67	67
FAS	-0.013	0.14	-10000	0	-0.85	26	26
BID	0.008	0.057	0.34	20	-0.49	2	22
MAP3K1	-0.011	0.1	0.24	1	-0.35	7	8
MAP3K7	0.012	0.007	-10000	0	-10000	0	0
RB1	0.008	0.065	0.31	14	-0.51	5	19
CFLAR	0.017	0.005	-10000	0	-10000	0	0
HGF/MET	-0.089	0.21	-10000	0	-0.6	104	104
ARHGDIB	-0.003	0.092	0.31	14	-0.5	21	35
FADD	0.013	0.008	-10000	0	-10000	0	0
actin filament polymerization	-0.01	0.056	0.44	2	-0.31	14	16
NFKB1	-0.062	0.095	-10000	0	-0.88	2	2
MAPK8	-0.072	0.22	-10000	0	-0.5	112	112
DFFA	0.01	0.053	0.31	14	-0.33	1	15
DNA fragmentation during apoptosis	0.01	0.052	0.31	14	-0.33	1	15
FAS/FADD/MET	-0.021	0.11	-10000	0	-0.57	31	31
CFLAR/RIP1	0	0	-10000	0	-10000	0	0
FAIM3	-0.008	0.14	-10000	0	-0.8	27	27
FAF1	0.012	0.03	-10000	0	-0.85	1	1
PARP1	0.01	0.053	0.31	14	-0.33	1	15
DFFB	0.01	0.053	0.31	14	-0.33	1	15
CHUK	-0.053	0.085	-10000	0	-0.92	2	2
FASLG	-0.12	0.3	-10000	0	-0.76	153	153
FAS/FADD	-0.019	0.11	-10000	0	-0.66	26	26
HGF	-0.094	0.28	-10000	0	-0.78	122	122
LMNA	0.008	0.055	0.43	1	-0.51	2	3
CASP6	0.01	0.053	0.31	14	-0.33	1	15
CASP10	0.004	0.087	-10000	0	-0.85	9	9
CASP3	0.012	0.063	0.38	14	-0.38	1	15
PTPN13	-0.007	0.14	-10000	0	-0.84	24	24
CASP8	0.013	0.08	0.44	27	-0.68	1	28
IL6	-0.23	0.48	-10000	0	-1.3	122	122
MET	0.009	0.075	-10000	0	-0.77	8	8
ICAD/CAD	0.01	0.049	0.29	14	-10000	0	14
FASLG/FAS/FADD/FAF1/Caspase 10	-0.062	0.2	-10000	0	-0.54	93	93
activation of caspase activity by cytochrome c	0.008	0.057	0.34	20	-0.48	2	22
PAK2	0.01	0.052	0.31	14	-0.33	1	15
BCL2	0.003	0.11	-10000	0	-0.85	14	14

×

Signaling mediated by p38-gamma and p38-delta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EEF2K	0.018	0.11	-9999	-0.55	31	31
SNTA1	0.003	0.098	-9999	-0.71	16	16
response to hypoxia	0	0	-9999	-10000	0	0
STMN1	0.018	0.11	-9999	-0.57	30	30
MAPK12	-0.002	0.14	-9999	-0.43	76	76
CCND1	-0.011	0.12	-9999	-0.46	45	45
p38 gamma/SNTA1	-0.001	0.14	-9999	-0.53	33	33
MAP2K3	0.015	0.029	-9999	-0.85	1	1
PKN1	0.014	0.041	-9999	-0.85	2	2
G2/M transition checkpoint	-0.001	0.14	-9999	-0.43	76	76
MAP2K6	0.02	0.076	-9999	-0.48	19	19
MAPT	-0.031	0.17	-9999	-0.43	117	117
MAPK13	0.008	0.12	-9999	-0.65	27	27
hyperosmotic response	0	0	-9999	-10000	0	0
ZAK	0.017	0.049	-9999	-0.44	10	10

×

TRAIL signaling pathway

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
TNFSF10	-0.045	0.22	-10000	0	-0.84	63	63
positive regulation of NF-kappaB transcription factor activity	-0.054	0.19	-10000	0	-0.68	70	70
MAP2K4	0.025	0.12	-10000	0	-0.49	19	19
IKBKB	0.016	0	-10000	0	-10000	0	0
TNFRSF10B	0.014	0.041	-10000	0	-0.85	2	2
TNFRSF10A	-0.027	0.19	-10000	0	-0.85	44	44
SMPD1	-0.022	0.079	-10000	0	-0.6	1	1
IKBKG	0.013	0.05	-10000	0	-0.85	3	3
mol:GTP	0	0	-10000	0	-10000	0	0
TNFRSF10D	0.005	0.098	-10000	0	-0.83	12	12
TRAIL/TRAILR2	-0.048	0.17	-10000	0	-0.65	65	65
TRAIL/TRAILR3	-0.062	0.2	-10000	0	-0.67	82	82
TRAIL/TRAILR1	-0.076	0.24	-10000	0	-0.76	89	89
TRAIL/TRAILR4	-0.054	0.19	-10000	0	-0.68	70	70
TRAIL/TRAILR1/DAP3/GTP	-0.062	0.2	-10000	0	-0.62	88	88
IKK complex	-0.022	0.078	-10000	0	-0.76	4	4
RIPK1	0.016	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
DAP3/GTP	0	0	-10000	0	-10000	0	0
MAPK3	-0.02	0.18	-10000	0	-0.65	64	64
MAP3K1	-0.032	0.11	-10000	0	-0.53	19	19
TRAILR4 (trimer)	0.005	0.098	-10000	0	-0.83	12	12
TRADD	0.015	0.029	-10000	0	-0.85	1	1
TRAILR1 (trimer)	-0.027	0.19	-10000	0	-0.85	44	44
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2	0.001	0.15	-10000	0	-0.72	19	19
CFLAR	0.016	0	-10000	0	-10000	0	0
MAPK1	-0.02	0.18	-10000	0	-0.65	64	64
TRAIL/TRAILR1/FADD/TRADD/RIP	-0.058	0.18	-10000	0	-0.96	19	19
mol:ceramide	0.002	0.085	-10000	0	-0.3	64	64
FADD	0.016	0	-10000	0	-10000	0	0
MAPK8	0.028	0.13	-10000	0	-0.72	6	6
TRAF2	0.014	0.041	-10000	0	-0.85	2	2
TRAILR3 (trimer)	-0.007	0.13	-10000	0	-0.76	26	26
CHUK	0.015	0.029	-10000	0	-0.85	1	1
TRAIL/TRAILR1/FADD	-0.067	0.21	-10000	0	-0.67	88	88
DAP3	0.016	0	-10000	0	-10000	0	0
CASP10	-0.054	0.19	0.33	5	-0.68	61	66
JNK cascade	-0.054	0.19	-10000	0	-0.68	70	70
TRAIL (trimer)	-0.045	0.22	-10000	0	-0.84	63	63
TNFRSF10C	-0.007	0.13	-10000	0	-0.76	26	26
TRAIL/TRAILR1/DAP3/GTP/FADD	-0.058	0.19	-10000	0	-0.58	88	88
TRAIL/TRAILR2/FADD	-0.041	0.15	-10000	0	-0.56	64	64
cell death	0.002	0.085	-10000	0	-0.3	64	64
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2	0.019	0.1	-10000	0	-0.68	1	1
TRAILR2 (trimer)	0.014	0.041	-10000	0	-0.85	2	2
CASP8	0.009	0.056	0.31	1	-1.1	1	2
negative regulation of caspase activity	0	0	-10000	0	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP	-0.035	0.12	-10000	0	-10000	0	0

×

Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization	0.007	0.1	-10000	0	-0.35	53	53
epithelial cell differentiation	-0.037	0.12	-10000	0	-0.48	44	44
CYFIP2	0.008	0.078	-10000	0	-0.76	9	9
ENAH	0.045	0.12	-10000	0	-0.51	13	13
EGFR	-0.021	0.17	-10000	0	-0.78	41	41
EPHA2	0.006	0.094	-10000	0	-0.83	11	11
MYO6	0.008	0.13	-10000	0	-0.48	45	45
CTNNB1	0.016	0	-10000	0	-10000	0	0
ABI1/Sra1/Nap1	-0.005	0.05	-10000	0	-0.49	9	9
AQP5	-0.057	0.12	-10000	0	-0.58	14	14
CTNND1	0.016	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.008	0.13	-10000	0	-0.45	46	46
regulation of calcium-dependent cell-cell adhesion	-0.1	0.25	-10000	0	-0.53	169	169
EGF	-0.15	0.31	-10000	0	-0.73	196	196
NCKAP1	0.016	0	-10000	0	-10000	0	0
AQP3	-0.084	0.21	-10000	0	-0.69	77	77
cortical microtubule organization	-0.037	0.12	-10000	0	-0.48	44	44
GO:0000145	0.009	0.12	-10000	0	-0.43	46	46
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.038	0.12	-10000	0	-0.49	44	44
MLLT4	0.016	0	-10000	0	-10000	0	0
ARF6/GDP	-0.041	0.13	-10000	0	-0.74	14	14
ARF6	0.016	0	-10000	0	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	-0.018	0.1	-10000	0	-0.55	28	28
mol:Ca2+	0	0	-10000	0	-10000	0	0
VASP	0.02	0.13	-10000	0	-0.58	7	7
PVRL2	0.015	0.029	-10000	0	-0.85	1	1
ZYX	0.007	0.13	-10000	0	-0.46	4	4
ARF6/GTP	-0.016	0.092	-10000	0	-0.5	28	28
CDH1	-0.054	0.22	-10000	0	-0.76	80	80
EGFR/EGFR/EGF/EGF	-0.13	0.22	-10000	0	-0.73	49	49
RhoA/GDP	-0.035	0.11	-10000	0	-10000	0	0
actin cytoskeleton organization	0.017	0.13	-10000	0	-0.84	2	2
IGF-1R heterotetramer	0.013	0.05	-10000	0	-0.85	3	3
GIT1	0.014	0.041	-10000	0	-0.85	2	2
IGF1R	0.013	0.05	-10000	0	-0.85	3	3
IGF1	-0.058	0.22	-10000	0	-0.72	89	89
DIAPH1	-0.007	0.068	-10000	0	-0.89	5	5
Wnt receptor signaling pathway	0.037	0.12	0.48	44	-10000	0	44
RHOA	0.016	0	-10000	0	-10000	0	0
RhoA/GTP	-0.041	0.13	-10000	0	-0.73	14	14
CTNNA1	0.016	0	-10000	0	-10000	0	0
VCL	0.017	0.13	-10000	0	-0.88	2	2
EFNA1	0.001	0.12	-10000	0	-0.85	16	16
LPP	0.011	0.14	-10000	0	-0.78	7	7
Ephrin A1/EPHA2	-0.047	0.15	-10000	0	-0.84	14	14
SEC6/SEC8	-0.031	0.099	-10000	0	-10000	0	0
MGAT3	-0.11	0.25	-10000	0	-0.54	169	169
HGF/MET	-0.091	0.19	-10000	0	-0.84	24	24
HGF	-0.094	0.28	-10000	0	-0.78	122	122
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN	0.007	0.1	-10000	0	-0.35	53	53
actin cable formation	0.066	0.11	-10000	0	-0.44	11	11
KIAA1543	0.007	0.17	-10000	0	-1.1	8	8
KIFC3	-0.006	0.16	-10000	0	-0.5	72	72
NCK1	0.014	0.041	-10000	0	-0.85	2	2
EXOC3	0.015	0.029	-10000	0	-0.85	1	1
ACTN1	0.003	0.14	-10000	0	-0.49	55	55
NCK1/GIT1	-0.003	0.044	-10000	0	-0.65	4	4
mol:GDP	-0.037	0.12	-10000	0	-0.48	44	44
EXOC4	0.016	0	-10000	0	-10000	0	0
STX4	0.009	0.13	-10000	0	-0.46	1	1
PIP5K1C	0.008	0.13	-10000	0	-0.46	46	46
LIMA1	0.002	0.096	-10000	0	-0.66	18	18
ABI1	0.016	0	-10000	0	-10000	0	0
ROCK1	-0.036	0.11	-10000	0	-0.62	15	15
adherens junction assembly	0.013	0.19	-10000	0	-0.88	21	21
IGF-1R heterotetramer/IGF1	-0.07	0.17	-10000	0	-0.73	22	22
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	-0.001	0.022	-10000	0	-0.65	1	1
MET	0.009	0.075	-10000	0	-0.77	8	8
PLEKHA7	0.002	0.15	-10000	0	-0.51	51	51
mol:GTP	-0.017	0.1	-10000	0	-0.54	28	28
establishment of epithelial cell apical/basal polarity	0.043	0.12	-10000	0	-0.76	1	1
cortical actin cytoskeleton stabilization	0.007	0.1	-10000	0	-0.35	53	53
regulation of cell-cell adhesion	0.017	0.13	-10000	0	-0.84	2	2
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton	0.007	0.1	-10000	0	-0.35	53	53

×

S1P5 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	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	0.055	0.16	0.79	27	-10000	0	27
GNAI2	0.015	0.029	-10000	0	-0.85	1	1
S1P/S1P5/G12	-0.044	0.15	-10000	0	-0.54	73	73
mol:GDP	0	0	-10000	0	-10000	0	0
GNAO1	-0.052	0.22	-10000	0	-0.76	79	79
RhoA/GTP	-0.057	0.16	-10000	0	-0.82	27	27
negative regulation of cAMP metabolic process	-0.025	0.19	-10000	0	-0.51	87	87
GNAZ	0.007	0.085	-10000	0	-0.79	10	10
GNAI3	0.016	0	-10000	0	-10000	0	0
GNA12	0.016	0	-10000	0	-10000	0	0
S1PR5	-0.052	0.23	-10000	0	-0.81	73	73
mol:GTP	0	0	-10000	0	-10000	0	0
S1P/S1P5/Gi	-0.026	0.19	-10000	0	-0.51	87	87
RhoA/GDP	0	0	-10000	0	-10000	0	0
RHOA	0.016	0	-10000	0	-10000	0	0
GNAI1	0.004	0.1	-10000	0	-0.85	12	12

×

Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HIF3A	-0.093	0.27	-9999	-0.75	126	126
oxygen homeostasis	0	0	-9999	-10000	0	0
TCEB2	0.009	0.071	-9999	-0.72	8	8
TCEB1	0.016	0	-9999	-10000	0	0
HIF1A/p53	0	0.069	-9999	-0.38	5	5
HIF1A	-0.009	0.071	-9999	-0.38	4	4
COPS5	0.016	0	-9999	-10000	0	0
VHL/Elongin B/Elongin C/RBX1/CUL2	-0.007	0.061	-9999	-0.58	9	9
FIH (dimer)	0.016	0	-9999	-10000	0	0
CDKN2A	-0.043	0.21	-9999	-0.81	63	63
ARNT/IPAS	-0.08	0.2	-9999	-0.57	126	126
HIF1AN	0.016	0	-9999	-10000	0	0
GNB2L1	0.016	0	-9999	-10000	0	0
HIF1A/ARNT	0.001	0.068	-9999	-0.36	4	4
CUL2	0.015	0.029	-9999	-0.85	1	1
OS9	0.016	0	-9999	-10000	0	0
RACK1/Elongin B/Elongin C	-0.004	0.044	-9999	-0.56	3	3
response to hypoxia	0	0	-9999	-10000	0	0
HIF1A/Hsp90	0.001	0.068	-9999	-0.41	2	2
PHD1-3/OS9	-0.14	0.23	-9999	-0.51	237	237
HIF1A/RACK1/Elongin B/Elongin C	-0.026	0.057	-9999	-0.53	6	6
VHL	0.012	0.058	-9999	-0.85	4	4
HSP90AA1	0.016	0	-9999	-10000	0	0
HIF1A/JAB1	0.001	0.068	-9999	-0.36	4	4
EGLN3	-0.21	0.38	-9999	-0.85	236	236
EGLN2	0.013	0.047	-9999	-0.78	3	3
EGLN1	0.016	0	-9999	-10000	0	0
TP53	0.015	0.029	-9999	-0.85	1	1
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A	0.032	0.067	-9999	-0.68	6	6
ARNT	0.016	0	-9999	-10000	0	0
ARD1A	0	0	-9999	-10000	0	0
RBX1	0.015	0.022	-9999	-0.65	1	1
HIF1A/p19ARF	-0.031	0.15	-9999	-0.54	59	59

×

Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3	0	0	-9999	-10000	0	0
response to insulin stimulus	0	0	-9999	-10000	0	0
RIPK1	0.016	0	-9999	-10000	0	0
response to stress	0	0	-9999	-10000	0	0
MAP2K6	0.006	0.09	-9999	-0.79	11	11
mol:GTP	0	0	-9999	-10000	0	0
MAP2K4	0.016	0	-9999	-10000	0	0
RAC1-CDC42/GTP/PAK family	-0.006	0.096	-9999	-0.28	74	74
response to UV	0	0	-9999	-10000	0	0
YES1	0.016	0	-9999	-10000	0	0
interleukin-1 receptor activity	0	0	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
MAP3K3	0.016	0	-9999	-10000	0	0
FYN	0.007	0.086	-9999	-0.85	9	9
MAP3K12	0.011	0.062	-9999	-0.81	5	5
FGR	-0.012	0.15	-9999	-0.83	30	30
p38 alpha/TAB1	-0.034	0.089	-9999	-0.42	28	28
PRKG1	-0.14	0.33	-9999	-0.84	158	158
DUSP8	-0.014	0.14	-9999	-0.68	38	38
PGK/cGMP/p38 alpha	-0.1	0.19	-9999	-0.46	164	164
apoptosis	-0.033	0.085	-9999	-0.4	28	28
RAL/GTP	0	0	-9999	-10000	0	0
LYN	0.012	0.058	-9999	-0.85	4	4
DUSP1	-0.081	0.27	-9999	-0.84	101	101
PAK1	0.016	0	-9999	-10000	0	0
SRC	0.015	0.022	-9999	-0.65	1	1
RAC1/OSM/MEKK3/MKK3	-0.001	0.024	-9999	-0.51	2	2
TRAF6	0.016	0	-9999	-10000	0	0
RAC1	0.016	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	0.015	0.029	-9999	-0.85	1	1
RAC1-CDC42/GTP	0	0	-9999	-10000	0	0
MAPK11	0.003	0.16	-9999	-0.53	39	39
BLK	-0.081	0.25	-9999	-0.72	115	115
HCK	-0.005	0.13	-9999	-0.83	22	22
MAP2K3	0.015	0.029	-9999	-0.85	1	1
DUSP16	0.016	0	-9999	-10000	0	0
DUSP10	0.007	0.083	-9999	-0.77	10	10
TRAF6/MEKK3	0	0	-9999	-10000	0	0
MAP3K7IP1	0	0	-9999	-10000	0	0
MAPK14	0.016	0.12	-9999	-0.45	29	29
positive regulation of innate immune response	0.01	0.16	-9999	-0.57	36	36
LCK	-0.08	0.26	-9999	-0.8	104	104
p38alpha-beta/MKP7	0.019	0.16	-9999	-0.6	25	25
p38alpha-beta/MKP5	0.015	0.16	-9999	-0.63	29	29
PGK/cGMP	-0.12	0.25	-9999	-0.66	158	158
PAK2	0.016	0	-9999	-10000	0	0
p38alpha-beta/MKP1	-0.028	0.22	-9999	-0.62	66	66
CDC42	0.016	0	-9999	-10000	0	0
RALB	0.016	0	-9999	-10000	0	0
RALA	0.016	0	-9999	-10000	0	0
PAK3	-0.11	0.28	-9999	-0.76	139	139

×

ErbB2/ErbB3 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
USP8	0.024	0.029	-10000	0	-0.58	2	2
RAS family/GTP	-0.013	0.16	-10000	0	-0.84	19	19
NFATC4	-0.015	0.15	-10000	0	-0.54	25	25
ERBB2IP	0.015	0.029	-10000	0	-0.84	1	1
HSP90 (dimer)	0.016	0	-10000	0	-10000	0	0
mammary gland morphogenesis	-0.029	0.16	-10000	0	-0.72	18	18
JUN	0.015	0.12	-10000	0	-0.44	30	30
HRAS	0.011	0.059	-10000	0	-0.77	5	5
DOCK7	-0.018	0.16	-10000	0	-0.67	19	19
ErbB2/ErbB3/neuregulin 1 beta/SHC	-0.069	0.19	-10000	0	-0.59	92	92
AKT1	0.014	0.023	-10000	0	-0.66	1	1
BAD	0.022	0.049	-10000	0	-0.67	4	4
MAPK10	-0.031	0.082	-10000	0	-0.32	38	38
mol:GTP	-0.001	0.002	-10000	0	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta	-0.028	0.18	-10000	0	-0.82	18	18
RAF1	0.002	0.16	-10000	0	-0.77	19	19
ErbB2/ErbB3/neuregulin 2	-0.07	0.2	-10000	0	-0.57	94	94
STAT3	0.001	0.009	-10000	0	-10000	0	0
cell migration	0.028	0.093	-10000	0	-0.3	22	22
mol:PI-3-4-5-P3	0	0.002	-10000	0	-10000	0	0
cell proliferation	-0.086	0.28	-10000	0	-0.63	120	120
FOS	-0.057	0.23	-10000	0	-0.5	92	92
NRAS	0.016	0.001	-10000	0	-10000	0	0
mol:Ca2+	-0.029	0.16	-10000	0	-0.72	18	18
MAPK3	-0.058	0.24	-10000	0	-0.64	41	41
MAPK1	-0.058	0.23	-10000	0	-0.63	42	42
JAK2	-0.018	0.16	-10000	0	-0.67	19	19
NF2	-0.003	0.02	-10000	0	-0.48	1	1
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1	-0.022	0.18	-10000	0	-0.49	90	90
NRG1	-0.062	0.24	-10000	0	-0.8	85	85
GRB2/SOS1	0	0	-10000	0	-10000	0	0
MAPK8	-0.009	0.14	-10000	0	-0.44	30	30
MAPK9	-0.025	0.067	-10000	0	-0.29	18	18
ERBB2	-0.002	0.045	0.47	1	-0.63	4	5
ERBB3	-0.026	0.18	-10000	0	-0.85	42	42
SHC1	0.015	0.022	-10000	0	-0.65	1	1
RAC1	0.016	0	-10000	0	-10000	0	0
apoptosis	0.005	0.044	0.68	3	-10000	0	3
STAT3 (dimer)	0.001	0.009	-10000	0	-10000	0	0
RNF41	0.032	0.028	-10000	0	-0.53	2	2
FRAP1	0.012	0.02	-10000	0	-0.58	1	1
RAC1-CDC42/GTP	-0.036	0.097	-10000	0	-0.43	19	19
ErbB2/ErbB2/HSP90 (dimer)	-0.002	0.038	0.31	1	-0.54	4	5
CHRNA1	-0.1	0.29	-10000	0	-0.67	128	128
myelination	-0.003	0.15	-10000	0	-0.5	25	25
PPP3CB	-0.015	0.15	-10000	0	-0.61	18	18
KRAS	0.016	0.001	-10000	0	-10000	0	0
RAC1-CDC42/GDP	-0.031	0.15	-10000	0	-0.89	17	17
NRG2	-0.059	0.22	-10000	0	-0.71	92	92
mol:GDP	-0.022	0.18	-10000	0	-0.48	90	90
SOS1	0.016	0.001	-10000	0	-10000	0	0
MAP2K2	0.005	0.16	-10000	0	-0.74	19	19
SRC	0.015	0.022	-10000	0	-0.65	1	1
mol:cAMP	-0.001	0.002	-10000	0	-10000	0	0
PTPN11	-0.018	0.16	-10000	0	-0.67	19	19
MAP2K1	-0.051	0.21	-10000	0	-0.63	39	39
heart morphogenesis	-0.029	0.16	-10000	0	-0.72	18	18
RAS family/GDP	-0.013	0.16	-10000	0	-0.84	19	19
GRB2	0.016	0.001	-10000	0	-10000	0	0
PRKACA	-0.003	0.009	-10000	0	-10000	0	0
CHRNE	0.012	0.052	-10000	0	-0.24	30	30
HSP90AA1	0.016	0	-10000	0	-10000	0	0
activation of caspase activity	-0.014	0.023	0.66	1	-10000	0	1
nervous system development	-0.029	0.16	-10000	0	-0.72	18	18
CDC42	0.016	0	-10000	0	-10000	0	0

×

Regulation of nuclear SMAD2/3 signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EP300	0.009	0.043	-10000	0	-0.85	2	2
HSPA8	0.016	0.041	-10000	0	-0.84	2	2
SMAD3/SMAD4/ER alpha	-0.018	0.16	-10000	0	-0.59	49	49
AKT1	0.018	0.031	-10000	0	-0.84	1	1
GSC	0	0.23	-10000	0	-1.3	20	20
NKX2-5	-0.024	0.14	-10000	0	-0.65	39	39
muscle cell differentiation	0.03	0.09	0.5	9	-10000	0	9
SMAD2-3/SMAD4/SP1	0.048	0.098	-10000	0	-0.44	3	3
SMAD4	0.018	0.045	-10000	0	-10000	0	0
CBFB	0.015	0.029	-10000	0	-0.85	1	1
SAP18	0.017	0.002	-10000	0	-10000	0	0
Cbp/p300/MSG1	-0.013	0.087	-10000	0	-0.64	5	5
SMAD3/SMAD4/VDR	-0.019	0.091	-10000	0	-0.53	2	2
MYC	-0.024	0.18	-10000	0	-0.82	40	40
CDKN2B	0.031	0.24	-10000	0	-1.5	19	19
AP1	0.005	0.17	-10000	0	-0.64	21	21
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1	0.069	0.067	-10000	0	-10000	0	0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1	0.044	0.077	-10000	0	-0.47	5	5
SP3	0.018	0.041	-10000	0	-0.84	2	2
CREB1	0.016	0	-10000	0	-10000	0	0
FOXH1	-0.018	0.15	-10000	0	-0.7	41	41
SMAD3/SMAD4/GR	0.004	0.053	-10000	0	-0.47	3	3
GATA3	-0.12	0.29	-10000	0	-0.74	159	159
SKI/SIN3/HDAC complex/NCoR1	0.054	0.055	-10000	0	-0.42	1	1
MEF2C/TIF2	-0.059	0.26	-10000	0	-0.83	65	65
endothelial cell migration	0.31	0.59	1.6	147	-10000	0	147
MAX	0.026	0.022	-10000	0	-10000	0	0
RBBP7	0.017	0.002	-10000	0	-10000	0	0
RBBP4	0.016	0.029	-10000	0	-0.85	1	1
RUNX2	-0.013	0.15	-10000	0	-0.82	31	31
RUNX3	-0.029	0.19	-10000	0	-0.83	48	48
RUNX1	-0.013	0.15	-10000	0	-0.84	30	30
CTBP1	0.016	0	-10000	0	-10000	0	0
NR3C1	0.023	0.055	-10000	0	-0.73	4	4
VDR	-0.028	0.17	-10000	0	-0.66	58	58
CDKN1A	0.059	0.15	-10000	0	-1.5	6	6
KAT2B	0.013	0.029	-10000	0	-0.84	1	1
SMAD2/SMAD2/SMAD4/FOXH1	-0.023	0.12	-10000	0	-0.54	25	25
DCP1A	0.016	0	-10000	0	-10000	0	0
SKI	0.015	0.041	-10000	0	-0.85	2	2
SERPINE1	-0.32	0.6	-10000	0	-1.6	147	147
SMAD3/SMAD4/ATF2	-0.01	0.081	-10000	0	-0.58	14	14
SMAD3/SMAD4/ATF3	-0.044	0.14	-10000	0	-0.57	33	33
SAP30	-0.013	0.16	-10000	0	-0.85	31	31
Cbp/p300/PIAS3	0	0.036	-10000	0	-0.57	2	2
JUN	0.018	0.17	-10000	0	-0.65	19	19
SMAD3/SMAD4/IRF7	-0.009	0.077	-10000	0	-0.6	10	10
TFE3	0.014	0.02	-10000	0	-10000	0	0
COL1A2	-0.11	0.34	-10000	0	-0.9	118	118
mesenchymal cell differentiation	0.021	0.11	0.61	28	-10000	0	28
DLX1	-0.1	0.29	-10000	0	-0.8	131	131
TCF3	0.016	0	-10000	0	-10000	0	0
FOS	-0.077	0.26	-10000	0	-0.73	120	120
SMAD3/SMAD4/Max	0.006	0.043	-10000	0	-10000	0	0
Cbp/p300/SNIP1	0.001	0.029	-10000	0	-0.57	2	2
ZBTB17	0.011	0.051	-10000	0	-0.85	3	3
LAMC1	0.048	0.055	-10000	0	-10000	0	0
TGIF2/HDAC complex/SMAD3/SMAD4	-0.001	0.036	-10000	0	-10000	0	0
IRF7	0.006	0.097	-10000	0	-0.78	13	13
ESR1	-0.034	0.2	-10000	0	-0.8	58	58
HNF4A	-0.13	0.32	-10000	0	-0.84	150	150
MEF2C	-0.007	0.23	-10000	0	-0.82	52	52
SMAD2-3/SMAD4	-0.004	0.043	-10000	0	-10000	0	0
Cbp/p300/Src-1	0.002	0.031	-10000	0	-0.57	2	2
IGHV3OR16-13	-0.009	0.031	-10000	0	-10000	0	0
TGIF2/HDAC complex	0.016	0	-10000	0	-10000	0	0
CREBBP	0.012	0.009	-10000	0	-10000	0	0
SKIL	0.008	0.085	-10000	0	-0.83	9	9
HDAC1	0.017	0.002	-10000	0	-10000	0	0
HDAC2	0.017	0.002	-10000	0	-10000	0	0
SNIP1	0.018	0.004	-10000	0	-10000	0	0
GCN5L2	-0.006	0.013	-10000	0	-10000	0	0
SMAD3/SMAD4/TFE3	0	0.043	-10000	0	-10000	0	0
MSG1/HSC70	-0.008	0.097	-10000	0	-0.5	32	32
SMAD2	0.019	0.027	-10000	0	-10000	0	0
SMAD3	0.019	0.039	-10000	0	-10000	0	0
SMAD3/E2F4-5/DP1/p107/SMAD4	0.041	0.061	-10000	0	-0.43	2	2
SMAD2/SMAD2/SMAD4	0.014	0.038	-10000	0	-0.6	1	1
NCOR1	0.016	0.029	-10000	0	-0.85	1	1
NCOA2	-0.039	0.21	-10000	0	-0.85	57	57
NCOA1	0.016	0	-10000	0	-10000	0	0
MYOD/E2A	-0.01	0.069	-10000	0	-0.48	19	19
SMAD2-3/SMAD4/SP1/MIZ-1	0.055	0.1	-10000	0	-0.51	3	3
IFNB1	0.042	0.089	-10000	0	-0.57	10	10
SMAD3/SMAD4/MEF2C	-0.003	0.22	-10000	0	-0.79	51	51
CITED1	-0.007	0.12	-10000	0	-0.67	30	30
SMAD2-3/SMAD4/ARC105	0.001	0.047	-10000	0	-0.53	2	2
RBL1	0.006	0.091	-10000	0	-0.85	10	10
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB	0.058	0.11	-10000	0	-0.58	19	19
RUNX1-3/PEBPB2	-0.048	0.18	-10000	0	-0.66	61	61
SMAD7	0.041	0.16	-10000	0	-0.68	12	12
MYC/MIZ-1	-0.028	0.14	-10000	0	-0.63	43	43
SMAD3/SMAD4	-0.085	0.18	0.31	7	-0.48	63	70
IL10	-0.074	0.31	-10000	0	-0.81	92	92
PIASy/HDAC complex	0.021	0.043	-10000	0	-0.85	2	2
PIAS3	0.012	0.008	-10000	0	-10000	0	0
CDK2	0.012	0.008	-10000	0	-10000	0	0
IL5	-0.043	0.22	-10000	0	-0.7	42	42
CDK4	0.012	0.009	-10000	0	-10000	0	0
PIAS4	0.021	0.043	-10000	0	-0.85	2	2
ATF3	-0.052	0.21	-10000	0	-0.7	84	84
SMAD3/SMAD4/SP1	-0.013	0.072	-10000	0	-10000	0	0
FOXG1	-0.016	0.12	-10000	0	-0.65	30	30
FOXO3	0.032	0.028	-10000	0	-0.65	1	1
FOXO1	0.029	0.05	-10000	0	-0.5	7	7
FOXO4	0.032	0.028	-10000	0	-0.65	1	1
heart looping	-0.006	0.23	-10000	0	-0.8	52	52
CEBPB	0.01	0.07	-10000	0	-0.65	10	10
SMAD3/SMAD4/DLX1	-0.081	0.2	-10000	0	-0.57	110	110
MYOD1	-0.01	0.095	-10000	0	-0.65	19	19
SMAD3/SMAD4/HNF4	-0.099	0.22	-10000	0	-0.59	150	150
SMAD3/SMAD4/GATA3	-0.1	0.22	-10000	0	-0.66	81	81
SnoN/SIN3/HDAC complex/NCoR1	0.008	0.084	-10000	0	-0.82	9	9
SMAD3/SMAD4/RUNX1-3/PEBPB2	-0.039	0.17	-10000	0	-0.67	40	40
SMAD3/SMAD4/SP1-3	0.017	0.081	-10000	0	-0.54	2	2
MED15	0.014	0.041	-10000	0	-0.85	2	2
SP1	0.011	0.053	-10000	0	-10000	0	0
SIN3B	0.015	0.041	-10000	0	-0.85	2	2
SIN3A	0.017	0.002	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5	-0.016	0.16	-10000	0	-0.64	29	29
ITGB5	0.068	0.081	-10000	0	-0.53	1	1
TGIF/SIN3/HDAC complex/CtBP	0.053	0.051	-10000	0	-10000	0	0
SMAD3/SMAD4/AR	-0.076	0.2	-10000	0	-0.58	110	110
AR	-0.097	0.29	-10000	0	-0.82	120	120
negative regulation of cell growth	0.035	0.083	-10000	0	-0.47	2	2
SMAD3/SMAD4/MYOD	-0.012	0.07	-10000	0	-0.47	7	7
E2F5	0.01	0.068	-10000	0	-0.82	6	6
E2F4	0.016	0	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF	-0.019	0.099	-10000	0	-0.59	9	9
SMAD2-3/SMAD4/FOXO1-3a-4	0.052	0.079	-10000	0	-0.5	5	5
TFDP1	0.016	0	-10000	0	-10000	0	0
SMAD3/SMAD4/AP1	0.007	0.17	-10000	0	-0.67	19	19
SMAD3/SMAD4/RUNX2	-0.021	0.11	-10000	0	-0.61	28	28
TGIF2	0.016	0	-10000	0	-10000	0	0
TGIF1	0.016	0	-10000	0	-10000	0	0
ATF2	0.002	0.11	-10000	0	-0.85	14	14

×

Nectin adhesion pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	-0.12	0.31	-9999	-0.84	140	140
alphaV beta3 Integrin	-0.05	0.17	-9999	-0.6	74	74
PTK2	-0.034	0.12	-9999	-0.64	25	25
positive regulation of JNK cascade	-0.012	0.059	-9999	-0.35	25	25
CDC42/GDP	0.053	0.095	-9999	-0.48	24	24
Rac1/GDP	0.055	0.094	-9999	-0.47	24	24
RAP1B	0.016	0	-9999	-10000	0	0
RAP1A	0.016	0	-9999	-10000	0	0
CTNNB1	0.016	0	-9999	-10000	0	0
CDC42/GTP	-0.014	0.073	-9999	-0.43	25	25
nectin-3/I-afadin	-0.018	0.11	-9999	-0.65	24	24
RAPGEF1	0.046	0.11	-9999	-0.55	24	24
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.037	0.12	-9999	-0.65	24	24
PDGFB-D/PDGFRB	-0.12	0.31	-9999	-0.84	140	140
TLN1	0.029	0.08	-9999	-0.56	10	10
Rap1/GTP	-0.012	0.062	-9999	-0.45	6	6
IQGAP1	0.016	0	-9999	-10000	0	0
Rap1/GTP/I-afadin	0	0	-9999	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin	-0.018	0.11	-9999	-0.65	24	24
PVR	0.015	0.022	-9999	-0.65	1	1
Necl-5(dimer)	0.015	0.022	-9999	-0.65	1	1
mol:GDP	0.05	0.12	-9999	-0.61	24	24
MLLT4	0.016	0	-9999	-10000	0	0
PIK3CA	0.01	0.071	-9999	-0.85	6	6
PI3K	-0.093	0.21	-9999	-0.52	155	155
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin	-0.005	0.052	-9999	-0.54	8	8
positive regulation of lamellipodium assembly	-0.012	0.06	-9999	-0.37	24	24
PVRL1	0.009	0.071	-9999	-0.72	8	8
PVRL3	-0.007	0.14	-9999	-0.85	24	24
PVRL2	0.015	0.029	-9999	-0.85	1	1
PIK3R1	0.011	0.066	-9999	-0.78	6	6
CDH1	-0.054	0.22	-9999	-0.76	80	80
CLDN1	-0.09	0.27	-9999	-0.76	121	121
JAM-A/CLDN1	-0.074	0.18	-9999	-0.53	89	89
SRC	-0.026	0.12	-9999	-0.75	24	24
ITGB3	-0.046	0.21	-9999	-0.76	71	71
nectin-1(dimer)/I-afadin/I-afadin	-0.005	0.052	-9999	-0.54	8	8
FARP2	0.042	0.12	-9999	-0.6	25	25
RAC1	0.016	0	-9999	-10000	0	0
CTNNA1	0.016	0	-9999	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer)	-0.016	0.092	-9999	-0.56	24	24
nectin-1/I-afadin	-0.005	0.052	-9999	-0.54	8	8
nectin-2/I-afadin	-0.001	0.022	-9999	-0.65	1	1
RAC1/GTP/IQGAP1/filamentous actin	0	0	-9999	-10000	0	0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin	-0.019	0.1	-9999	-0.58	27	27
CDC42/GTP/IQGAP1/filamentous actin	0	0	-9999	-10000	0	0
F11R	0.016	0	-9999	-10000	0	0
positive regulation of filopodium formation	-0.012	0.059	-9999	-0.35	25	25
alphaV/beta3 Integrin/Talin	0.007	0.16	-9999	-0.89	10	10
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	-0.001	0.022	-9999	-0.65	1	1
nectin-2(dimer)/I-afadin/I-afadin	-0.001	0.022	-9999	-0.65	1	1
PIP5K1C	0.021	0.079	-9999	-0.55	10	10
VAV2	0.042	0.11	-9999	-0.61	24	24
RAP1/GDP	-0.014	0.073	-9999	-0.44	24	24
ITGAV	0.009	0.074	-9999	-0.82	7	7
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin	-0.016	0.093	-9999	-0.56	25	25
nectin-3(dimer)/I-afadin/I-afadin	-0.018	0.11	-9999	-0.65	24	24
Rac1/GTP	-0.014	0.075	-9999	-0.45	24	24
PTPRM	-0.013	0.076	-9999	-0.38	31	31
E-cadherin/beta catenin/alpha catenin	-0.038	0.12	-9999	-0.72	4	4
adherens junction assembly	0	0	-9999	-10000	0	0
CDC42	0.016	0	-9999	-10000	0	0

×

Syndecan-3-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	0.016	0	-9999	-10000	0	0
Syndecan-3/Src/Cortactin	-0.091	0.18	-9999	-0.71	13	13
Syndecan-3/Neurocan	-0.015	0.081	-9999	-0.77	5	5
POMC	-0.014	0.15	-9999	-0.72	36	36
EGFR	-0.021	0.17	-9999	-0.78	41	41
Syndecan-3/EGFR	-0.025	0.11	-9999	-0.54	32	32
AGRP	-0.01	0.12	-9999	-0.65	28	28
NCSTN	0.015	0.029	-9999	-0.85	1	1
PSENEN	0.016	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
APH1B	0.009	0.076	-9999	-0.85	7	7
APH1A	0.016	0	-9999	-10000	0	0
NCAN	-0.009	0.11	-9999	-0.65	27	27
long-term memory	-0.009	0.069	-9999	-0.54	14	14
Syndecan-3/IL8	-0.072	0.17	-9999	-0.52	63	63
PSEN1	0.016	0	-9999	-10000	0	0
Src/Cortactin	-0.001	0.016	-9999	-0.48	1	1
FYN	0.007	0.086	-9999	-0.85	9	9
limb bud formation	-0.006	0.06	-9999	-0.78	5	5
MC4R	-0.007	0.087	-9999	-0.65	16	16
SRC	0.015	0.022	-9999	-0.65	1	1
PTN	-0.16	0.33	-9999	-0.77	201	201
FGFR/FGF/Syndecan-3	-0.006	0.061	-9999	-0.8	5	5
neuron projection morphogenesis	-0.096	0.18	-9999	-0.68	21	21
Syndecan-3/AgRP	-0.016	0.082	-9999	-0.71	6	6
Syndecan-3/AgRP/MC4R	-0.021	0.088	-9999	-0.68	6	6
Fyn/Cortactin	-0.007	0.065	-9999	-0.65	9	9
SDC3	-0.006	0.062	-9999	-0.81	5	5
GO:0007205	0	0	-9999	-10000	0	0
positive regulation of leukocyte migration	-0.071	0.16	-9999	-0.52	63	63
IL8	-0.11	0.28	-9999	-0.72	154	154
Syndecan-3/Fyn/Cortactin	-0.01	0.071	-9999	-0.55	14	14
Syndecan-3/CASK	-0.005	0.059	-9999	-0.77	5	5
alpha-MSH/MC4R	-0.031	0.13	-9999	-0.54	51	51
Gamma Secretase	-0.004	0.045	-9999	-0.48	8	8

×

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

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
BAG4	0.011	0.065	-9999	-0.85	5	5
Caspase 8 (4 units)	-0.044	0.093	-9999	-0.49	11	11
NEF	-0.02	0.065	-9999	-10000	0	0
NFKBIA	0.008	0.038	-9999	-10000	0	0
BIRC3	-0.028	0.26	-9999	-0.79	90	90
CYCS	0	0.15	-9999	-0.6	20	20
RIPK1	0.016	0	-9999	-10000	0	0
CD247	-0.08	0.28	-9999	-0.97	73	73
MAP2K7	0.012	0.12	-9999	-0.54	11	11
protein ubiquitination	0.042	0.12	-9999	-0.51	23	23
CRADD	0.016	0	-9999	-10000	0	0
DAXX	0.016	0	-9999	-10000	0	0
FAS	-0.009	0.15	-9999	-0.85	26	26
BID	-0.003	0.13	-9999	-0.58	10	10
NF-kappa-B/RelA/I kappa B alpha	-0.033	0.099	-9999	-0.55	1	1
TRADD	0.015	0.029	-9999	-0.85	1	1
MAP3K5	0.014	0.041	-9999	-0.85	2	2
CFLAR	0.016	0	-9999	-10000	0	0
FADD	0.016	0	-9999	-10000	0	0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin	-0.033	0.1	-9999	-0.55	1	1
MAPK8	0.016	0.12	-9999	-0.48	19	19
APAF1	0.015	0.029	-9999	-0.85	1	1
TRAF1	0.008	0.082	-9999	-0.8	9	9
TRAF2	0.014	0.041	-9999	-0.85	2	2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG	-0.014	0.14	-9999	-0.57	10	10
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD	0.036	0.1	-9999	-0.54	5	5
CHUK	0.041	0.13	-9999	-0.57	23	23
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8	-0.016	0.085	-9999	-0.48	29	29
TCRz/NEF	-0.11	0.26	-9999	-0.73	111	111
TNF	-0.062	0.23	-9999	-0.75	90	90
FASLG	-0.14	0.4	-9999	-0.91	169	169
NFKB1	0.007	0.047	-9999	-0.84	1	1
TNFR1A/BAG4/TNF-alpha	-0.052	0.15	-9999	-0.49	95	95
CASP6	-0.027	0.069	-9999	-0.52	3	3
CASP7	0.012	0.22	-9999	-0.65	74	74
RELA	0.008	0.038	-9999	-10000	0	0
CASP2	0.016	0	-9999	-10000	0	0
CASP3	0.012	0.22	-9999	-0.65	74	74
TNFRSF1A	0.016	0	-9999	-10000	0	0
TNFR1A/BAG4	-0.004	0.049	-9999	-0.65	5	5
CASP8	0.015	0.029	-9999	-0.85	1	1
CASP9	0.016	0	-9999	-10000	0	0
MAP3K14	0.032	0.14	-9999	-0.67	22	22
APAF-1/Caspase 9	-0.071	0.16	-9999	-0.56	78	78
BCL2	0.018	0.13	-9999	-0.52	11	11

×

Regulation of Androgen receptor activity

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
HDAC1	0.028	0.002	-9999	-10000	0	0
SMARCC1	0.009	0.013	-9999	-10000	0	0
REL	-0.01	0.15	-9999	-0.83	29	29
HDAC7	0.006	0.15	-9999	-0.59	23	23
JUN	0.008	0.069	-9999	-0.76	7	7
EP300	0.014	0.041	-9999	-0.85	2	2
KAT2B	0.015	0.029	-9999	-0.85	1	1
KAT5	0.016	0.001	-9999	-10000	0	0
MAPK14	0.016	0.074	-9999	-0.62	11	11
FOXO1	0.011	0.055	-9999	-0.66	6	6
T-DHT/AR	0	0.16	-9999	-0.64	21	21
MAP2K6	0.003	0.092	-9999	-0.81	11	11
BRM/BAF57	0	0	-9999	-10000	0	0
MAP2K4	0.014	0.008	-9999	-10000	0	0
SMARCA2	0.014	0.006	-9999	-10000	0	0
PDE9A	-0.084	0.19	-9999	-1.3	8	8
NCOA2	-0.04	0.21	-9999	-0.85	57	57
CEBPA	-0.016	0.16	-9999	-0.77	37	37
EHMT2	0.011	0.05	-9999	-0.85	3	3
cell proliferation	-0.002	0.19	-9999	-0.6	15	15
NR0B1	-0.06	0.2	-9999	-0.65	90	90
EGR1	-0.073	0.24	-9999	-0.74	102	102
RXRs/9cRA	-0.013	0.071	-9999	-0.4	21	21
AR/RACK1/Src	-0.021	0.11	-9999	-0.6	18	18
AR/GR	-0.014	0.16	-9999	-0.54	44	44
GNB2L1	0.016	0.001	-9999	-10000	0	0
PKN1	0.014	0.041	-9999	-0.85	2	2
RCHY1	0.016	0	-9999	-10000	0	0
epidermal growth factor receptor activity	-0.001	0.002	-9999	-10000	0	0
MAPK8	0.016	0.077	-9999	-0.66	11	11
T-DHT/AR/TIF2/CARM1	-0.047	0.18	-9999	-0.72	39	39
SRC	0.027	0.09	-9999	-0.5	19	19
NR3C1	0.012	0.055	-9999	-0.8	4	4
KLK3	-0.12	0.26	-9999	-0.76	92	92
APPBP2	0.012	0.03	-9999	-0.86	1	1
TRIM24	0.014	0.005	-9999	-10000	0	0
T-DHT/AR/TIP60	0.01	0.12	-9999	-0.6	22	22
TMPRSS2	-0.3	0.47	-9999	-1.1	194	194
RXRG	-0.01	0.11	-9999	-0.65	27	27
mol:9cRA	-0.001	0.002	-9999	-10000	0	0
RXRA	0.014	0.041	-9999	-0.85	2	2
RXRB	0.015	0.029	-9999	-0.85	1	1
CARM1	0.014	0.029	-9999	-0.85	1	1
NR2C2	0.007	0.087	-9999	-0.85	9	9
KLK2	-0.025	0.2	-9999	-0.64	43	43
AR	-0.02	0.17	-9999	-0.43	104	104
SENP1	0.016	0.001	-9999	-10000	0	0
HSP90AA1	0.016	0	-9999	-10000	0	0
MDM2	0.019	0.008	-9999	-10000	0	0
SRY	0.004	0.009	-9999	-10000	0	0
GATA2	-0.07	0.24	-9999	-0.73	103	103
MYST2	0.015	0.029	-9999	-0.85	1	1
HOXB13	-0.14	0.28	-9999	-0.67	187	187
T-DHT/AR/RACK1/Src	0.016	0.12	-9999	-0.62	17	17
positive regulation of transcription	-0.07	0.24	-9999	-0.73	103	103
DNAJA1	0.013	0.008	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.038	0.003	-9999	-10000	0	0
NCOA1	0.019	0.006	-9999	-10000	0	0
SPDEF	-0.062	0.21	-9999	-0.66	99	99
T-DHT/AR/TIF2	0.017	0.14	-9999	-0.64	21	21
T-DHT/AR/Hsp90	0.009	0.12	-9999	-0.6	22	22
GSK3B	0.014	0.006	-9999	-10000	0	0
NR2C1	0.017	0.002	-9999	-10000	0	0
mol:T-DHT	0.02	0.094	-9999	-0.52	22	22
SIRT1	0.015	0.029	-9999	-0.85	1	1
ZMIZ2	0.017	0.042	-9999	-0.85	2	2
POU2F1	0.022	0.055	-9999	-0.87	3	3
T-DHT/AR/DAX-1	-0.055	0.16	-9999	-0.66	28	28
CREBBP	0.016	0.001	-9999	-10000	0	0
SMARCE1	0.014	0.006	-9999	-10000	0	0

×

Signaling events mediated by PRL

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCNE1	0	0.1	-10000	0	-0.66	21	21
mol:Halofuginone	0.006	0.001	-10000	0	-10000	0	0
ITGA1	-0.08	0.27	-10000	0	-0.85	99	99
CDKN1A	0.017	0.073	-10000	0	-0.44	6	6
PRL-3/alpha Tubulin	-0.005	0.056	-10000	0	-0.59	8	8
mol:Ca2+	-0.089	0.23	0.4	6	-0.65	126	132
AGT	-0.1	0.3	-10000	0	-0.83	126	126
CCNA2	-0.001	0.15	-10000	0	-0.8	2	2
TUBA1B	0.016	0	-10000	0	-10000	0	0
EGR1	-0.036	0.19	-10000	0	-0.55	102	102
CDK2/Cyclin E1	0.024	0.085	-10000	0	-0.47	4	4
MAPK3	0.023	0.063	-10000	0	-0.59	9	9
PRL-2 /Rab GGTase beta	0	0	-10000	0	-10000	0	0
MAPK1	0.023	0.063	-10000	0	-0.59	9	9
PTP4A1	-0.006	0.15	-10000	0	-0.5	47	47
PTP4A3	0.009	0.075	-10000	0	-0.77	8	8
PTP4A2	0.016	0	-10000	0	-10000	0	0
ITGB1	0.024	0.059	-10000	0	-0.59	8	8
SRC	0.015	0.022	-10000	0	-0.65	1	1
RAC1	0.017	0.072	-10000	0	-0.44	5	5
Rab GGTase beta/Rab GGTase alpha	-0.001	0.031	-10000	0	-0.65	2	2
PRL-1/ATF-5	-0.002	0.15	-10000	0	-0.76	3	3
RABGGTA	0.014	0.041	-10000	0	-0.85	2	2
BCAR1	0.001	0.046	0.4	6	-0.53	3	9
RHOC	0.017	0.072	-10000	0	-0.44	5	5
RHOA	0.017	0.072	-10000	0	-0.44	5	5
cell motility	0.021	0.078	-10000	0	-0.44	6	6
PRL-1/alpha Tubulin	0.002	0.14	-10000	0	-10000	0	0
PRL-3/alpha1 Integrin	-0.078	0.21	-10000	0	-0.65	107	107
ROCK1	0.021	0.078	-10000	0	-0.45	6	6
RABGGTB	0.016	0	-10000	0	-10000	0	0
CDK2	0.016	0	-10000	0	-10000	0	0
mitosis	-0.005	0.15	-10000	0	-0.49	47	47
ATF5	0.008	0.074	-10000	0	-0.65	11	11

×

p38 MAPK signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TRAF6/ASK1	-0.001	0.024	-10000	0	-0.5	2	2
TRAF2/ASK1	-0.003	0.038	-10000	0	-0.57	4	4
ATM	0.014	0.041	-10000	0	-0.85	2	2
MAP2K3	0.009	0.073	-10000	0	-0.64	3	3
response to stress	0	0	-10000	0	-10000	0	0
MAP2K6	0.015	0.085	-10000	0	-0.61	7	7
hyperosmotic response	0	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
GADD45G	-0.052	0.2	-10000	0	-0.67	89	89
TXN	0.009	0.027	-10000	0	-0.3	7	7
CALM1	0.016	0	-10000	0	-10000	0	0
GADD45A	0.015	0.022	-10000	0	-0.65	1	1
GADD45B	-0.003	0.12	-10000	0	-0.72	23	23
MAP3K1	0.015	0.022	-10000	0	-0.65	1	1
MAP3K6	0.014	0.041	-10000	0	-0.85	2	2
MAP3K7	0.016	0	-10000	0	-10000	0	0
MAP3K4	0.014	0.041	-10000	0	-0.85	2	2
mol:Ca2+	0	0	-10000	0	-10000	0	0
ASK1/ASK2	-0.003	0.044	-10000	0	-0.65	4	4
TAK1/TAB family	0.004	0.028	0.22	15	-10000	0	15
RAC1/OSM/MEKK3	-0.001	0.017	-10000	0	-0.52	1	1
TRAF2	0.014	0.041	-10000	0	-0.85	2	2
RAC1/OSM/MEKK3/MKK3	-0.011	0.039	-10000	0	-0.53	3	3
TRAF6	0.011	0	-10000	0	-10000	0	0
RAC1	0.016	0	-10000	0	-10000	0	0
mol:LPS	0	0	-10000	0	-10000	0	0
CAMK2B	-0.25	0.35	-10000	0	-0.7	326	326
CCM2	0.015	0.029	-10000	0	-0.85	1	1
CaM/Ca2+/CAMKIIB	-0.17	0.22	-10000	0	-0.45	326	326
MAPK11	0.002	0.11	-10000	0	-0.84	15	15
response to DNA damage stimulus	0	0	-10000	0	-10000	0	0
CaM/Ca2+/CAMKIIB/ASK1	-0.15	0.2	-10000	0	-0.53	88	88
OSM/MEKK3	-0.001	0.022	-10000	0	-0.65	1	1
TAOK1	-0.011	0.13	-10000	0	-0.49	57	57
TAOK2	0.021	0.023	-10000	0	-0.46	2	2
TAOK3	0.02	0.028	-10000	0	-0.46	3	3
MAP3K7IP1	0	0	-10000	0	-10000	0	0
MAPK14	0.016	0	-10000	0	-10000	0	0
MAP3K7IP2	0	0	-10000	0	-10000	0	0
MAP3K5	0.014	0.041	-10000	0	-0.85	2	2
MAP3K10	0.013	0.05	-10000	0	-0.85	3	3
MAP3K3	0.016	0	-10000	0	-10000	0	0
TRX/ASK1	0.017	0.039	-10000	0	-0.67	2	2
GADD45/MTK1/MTK1	-0.046	0.14	-10000	0	-0.62	20	20

×

Insulin-mediated glucose transport

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Insulin responsive Vesicles	-0.028	0.086	-10000	0	-0.41	23	23
CaM/Ca2+	0	0	-10000	0	-10000	0	0
AKT1	0.015	0.029	-10000	0	-0.85	1	1
AKT2	0.015	0.029	-10000	0	-0.85	1	1
STXBP4	0.015	0.029	-10000	0	-0.85	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucose	0.032	0.13	0.3	70	-0.48	13	83
YWHAZ	0.016	0	-10000	0	-10000	0	0
CALM1	0.016	0	-10000	0	-10000	0	0
YWHAQ	0.016	0	-10000	0	-10000	0	0
TBC1D4	0.026	0.044	-10000	0	-0.51	6	6
mol:Ca2+	0	0	-10000	0	-10000	0	0
YWHAH	0.016	0	-10000	0	-10000	0	0
YWHAB	0.016	0	-10000	0	-10000	0	0
SNARE/Synip	-0.001	0.027	-10000	0	-0.56	2	2
YWHAG	0.016	0	-10000	0	-10000	0	0
ASIP	-0.085	0.25	-10000	0	-0.71	120	120
PRKCI	0.015	0.022	-10000	0	-0.65	1	1
AS160/CaM/Ca2+	0	0	-10000	0	-10000	0	0
RHOQ	0.016	0	-10000	0	-10000	0	0
GYS1	0.039	0.038	-10000	0	-1.1	1	1
PRKCZ	0.008	0.082	-10000	0	-0.85	8	8
TRIP10	0.006	0.091	-10000	0	-0.85	10	10
TC10/GTP/CIP4/Exocyst	-0.006	0.061	-10000	0	-0.57	10	10
AS160/14-3-3	-0.017	0.11	-10000	0	-0.43	3	3
VAMP2	0.016	0	-10000	0	-10000	0	0
SLC2A4	0.03	0.14	0.3	70	-0.54	13	83
STX4	0.015	0.029	-10000	0	-0.85	1	1
GSK3B	0.032	0.041	-10000	0	-1.2	1	1
SFN	-0.23	0.35	-10000	0	-0.72	299	299
LNPEP	-0.003	0.13	-10000	0	-0.85	20	20
YWHAE	0.016	0	-10000	0	-10000	0	0

×

Ceramide 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.015	0.094	-10000	0	-0.6	20	20
MAP4K4	0.006	0.14	-10000	0	-0.7	20	20
BAG4	0.011	0.065	-10000	0	-0.85	5	5
PKC zeta/ceramide	-0.024	0.067	0.2	1	-0.52	8	9
NFKBIA	0.016	0	-10000	0	-10000	0	0
BIRC3	-0.066	0.25	-10000	0	-0.81	89	89
BAX	-0.006	0.029	-10000	0	-0.36	2	2
RIPK1	0.016	0	-10000	0	-10000	0	0
AKT1	0.027	0.029	-10000	0	-0.78	1	1
BAD	-0.02	0.052	-10000	0	-0.36	4	4
SMPD1	0.007	0.082	-10000	0	-0.28	47	47
RB1	-0.02	0.061	-10000	0	-0.56	4	4
FADD/Caspase 8	0.02	0.14	-10000	0	-0.7	18	18
MAP2K4	-0.008	0.047	-10000	0	-0.35	1	1
NSMAF	0.016	0	-10000	0	-10000	0	0
response to UV	0	0	-10000	0	-10000	0	0
RAF1	-0.017	0.078	-10000	0	-0.48	16	16
EGF	-0.15	0.31	-10000	0	-0.73	196	196
mol:ceramide	-0.031	0.052	0.19	8	-10000	0	8
MADD	0.016	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
mol:Free Fatty acid	0.013	0.096	-10000	0	-0.56	24	24
ASAH1	0.011	0.059	-10000	0	-0.65	7	7
negative regulation of cell cycle	-0.021	0.06	-10000	0	-0.55	4	4
cell proliferation	-0.066	0.15	-10000	0	-0.5	75	75
BID	0.003	0.1	-10000	0	-0.48	19	19
MAP3K1	-0.018	0.05	0.21	2	-0.38	1	3
EIF2A	0.002	0.044	-10000	0	-10000	0	0
TRADD	0.015	0.029	-10000	0	-0.85	1	1
CRADD	0.016	0	-10000	0	-10000	0	0
MAPK3	-0.002	0.073	-10000	0	-0.44	16	16
response to heat	0	0	-10000	0	-10000	0	0
MAPK1	-0.002	0.072	-10000	0	-0.43	16	16
Cathepsin D/ceramide	-0.021	0.054	-10000	0	-0.37	5	5
FADD	0.007	0.14	-10000	0	-0.72	18	18
KSR1	-0.027	0.082	0.21	2	-0.51	16	18
MAPK8	-0.008	0.061	0.21	1	-0.3	17	18
PRKRA	-0.018	0.049	0.22	1	-10000	0	1
PDGFA	0.001	0.11	-10000	0	-0.78	17	17
TRAF2	0.014	0.041	-10000	0	-0.85	2	2
IGF1	-0.058	0.22	-10000	0	-0.72	89	89
mol:GD3	0	0	-10000	0	-10000	0	0
ganglioside biosynthetic process	-0.031	0.052	0.19	8	-10000	0	8
CTSD	0.012	0.056	-10000	0	-0.73	5	5
regulation of nitric oxide biosynthetic process	-0.001	0.022	-10000	0	-0.65	1	1
response to radiation	0	0	-10000	0	-10000	0	0
ERK1/PKC delta	-0.043	0.18	-10000	0	-0.56	72	72
PRKCD	-0.027	0.16	-10000	0	-0.65	57	57
PRKCZ	0.008	0.082	-10000	0	-0.85	8	8
mol:GW4869	0	0	-10000	0	-10000	0	0
mol:sphingosine	0.013	0.096	-10000	0	-0.56	24	24
RelA/NF kappa B1	-0.001	0.022	-10000	0	-0.65	1	1
mol:glutathione	0	0	-10000	0	-10000	0	0
PAWR	0.014	0.041	-10000	0	-0.85	2	2
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD	-0.004	0.15	-10000	0	-0.75	19	19
TNFR1A/BAG4/TNF-alpha	-0.052	0.15	-10000	0	-0.49	95	95
mol:Sphingosine-1-phosphate	0.015	0.094	-10000	0	-0.6	20	20
MAP2K1	-0.006	0.074	-10000	0	-0.47	13	13
mol:C11AG	0	0	-10000	0	-10000	0	0
RELA	0.016	0	-10000	0	-10000	0	0
CYCS	-0.011	0.049	0.19	8	-0.25	15	23
TNFRSF1A	0.016	0	-10000	0	-10000	0	0
NFKB1	0.015	0.029	-10000	0	-0.85	1	1
TNFR1A/BAG4	-0.004	0.049	-10000	0	-0.65	5	5
EIF2AK2	-0.008	0.046	-10000	0	-10000	0	0
TNF-alpha/TNFR1A/FAN	-0.049	0.15	-10000	0	-0.48	90	90
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
CASP8	0.023	0.087	-10000	0	-0.38	17	17
MAP2K2	-0.008	0.075	-10000	0	-0.46	14	14
SMPD3	0.005	0.093	-10000	0	-0.31	51	51
TNF	-0.062	0.23	-10000	0	-0.75	90	90
PKC zeta/PAR4	-0.007	0.073	-10000	0	-0.71	9	9
mol:PHOSPHOCHOLINE	0.039	0.11	0.24	184	-10000	0	184
NF kappa B1/RelA/I kappa B alpha	-0.006	0.062	-10000	0	-0.58	9	9
AIFM1	-0.008	0.042	0.19	8	-0.31	3	11
BCL2	0.002	0.11	-10000	0	-0.85	14	14

×

RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	-0.024	0.21	-9999	-1.5	18	18
VDR	-0.028	0.17	-9999	-0.66	58	58
FAM120B	0.016	0	-9999	-10000	0	0
RXRs/LXRs/DNA/9cRA	0.042	0.11	-9999	-0.59	7	7
RXRs/LXRs/DNA/Oxysterols	0.041	0.14	-9999	-0.75	7	7
MED1	0.015	0.029	-9999	-0.85	1	1
mol:9cRA	0.004	0.017	-9999	-10000	0	0
RARs/THRs/DNA/Src-1	0.02	0.093	-9999	-0.65	2	2
RXRs/NUR77	-0.047	0.2	-9999	-0.53	80	80
RXRs/PPAR	0.039	0.067	-9999	-0.57	4	4
NCOR2	0.014	0.041	-9999	-0.85	2	2
VDR/VDR/Vit D3	-0.033	0.12	-9999	-0.5	58	58
RARs/VDR/DNA/Vit D3	-0.03	0.1	-9999	-0.53	16	16
RARA	0.013	0.05	-9999	-0.85	3	3
NCOA1	0.016	0	-9999	-10000	0	0
VDR/VDR/DNA	-0.028	0.17	-9999	-0.66	58	58
RARs/RARs/DNA/9cRA	-0.007	0.059	-9999	-0.5	12	12
RARG	0.013	0.047	-9999	-0.78	3	3
RPS6KB1	0	0.067	-9999	-0.42	18	18
RARs/THRs/DNA/SMRT	0.019	0.1	-9999	-0.88	3	3
THRA	0.014	0.041	-9999	-0.85	2	2
mol:Bile acids	0	0	-9999	-10000	0	0
VDR/Vit D3/DNA	-0.033	0.12	-9999	-0.5	58	58
RXRs/PPAR/9cRA/PGJ2/DNA	0.029	0.095	-9999	-0.57	6	6
NR1H4	-0.061	0.24	-9999	-0.84	79	79
RXRs/LXRs/DNA	0.051	0.11	-9999	-0.66	7	7
NR1H2	0.019	0.044	-9999	-0.88	2	2
NR1H3	0.021	0.013	-9999	-10000	0	0
RXRs/VDR/DNA/Vit D3	0.008	0.13	-9999	-0.56	25	25
NR4A1	-0.12	0.29	-9999	-0.73	159	159
mol:ATRA	0	0	-9999	-10000	0	0
RXRs/FXR/9cRA/MED1	0.001	0.13	-9999	-0.38	76	76
RXRG	-0.005	0.12	-9999	-0.65	27	27
RXR alpha/CCPG	0.025	0.035	-9999	-0.68	2	2
RXRA	0.019	0.044	-9999	-0.88	2	2
RXRB	0.02	0.033	-9999	-0.87	1	1
THRB	-0.039	0.2	-9999	-0.72	66	66
PPARG	0.011	0.066	-9999	-0.78	6	6
PPARD	0.014	0.041	-9999	-0.85	2	2
TNF	-0.012	0.33	-9999	-1.2	49	49
mol:Oxysterols	0.004	0.015	-9999	-10000	0	0
cholesterol transport	0.041	0.14	-9999	-0.73	7	7
PPARA	0.016	0	-9999	-10000	0	0
mol:Vit D3	0	0	-9999	-10000	0	0
RARB	0.009	0.076	-9999	-0.85	7	7
RXRs/NUR77/BCL2	-0.028	0.14	-9999	-0.37	82	82
SREBF1	0.047	0.15	-9999	-1.1	5	5
RXRs/RXRs/DNA/9cRA	0.029	0.095	-9999	-0.57	6	6
ABCA1	0.046	0.16	-9999	-0.96	9	9
RARs/THRs	-0.036	0.12	-9999	-0.89	2	2
RXRs/FXR	-0.013	0.19	-9999	-0.56	83	83
BCL2	0.002	0.11	-9999	-0.85	14	14

×

S1P4 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-9999	-10000	0	0
GNAO1	-0.052	0.22	-9999	-0.76	79	79
CDC42/GTP	-0.042	0.13	-9999	-0.82	16	16
PLCG1	0.002	0.15	-9999	-0.84	16	16
mol:GTP	0	0	-9999	-10000	0	0
GNAI2	0.015	0.029	-9999	-0.85	1	1
GNAI3	0.016	0	-9999	-10000	0	0
G12/G13	-0.001	0.016	-9999	-0.48	1	1
cell migration	-0.041	0.13	-9999	-0.78	16	16
S1PR5	-0.052	0.23	-9999	-0.81	73	73
S1PR4	-0.018	0.17	-9999	-0.83	36	36
MAPK3	0.001	0.16	-9999	-0.84	17	17
MAPK1	0.001	0.16	-9999	-0.84	17	17
S1P/S1P5/Gi	-0.026	0.19	-9999	-0.51	87	87
GNAI1	0.004	0.1	-9999	-0.85	12	12
CDC42/GDP	0	0	-9999	-10000	0	0
S1P/S1P5/G12	-0.044	0.15	-9999	-0.54	73	73
RHOA	0.02	0.1	-9999	-0.49	32	32
S1P/S1P4/Gi	-0.009	0.16	-9999	-0.82	19	19
mol:GDP	0	0	-9999	-10000	0	0
GNAZ	0.007	0.085	-9999	-0.79	10	10
S1P/S1P4/G12/G13	-0.021	0.1	-9999	-0.51	36	36
GNA12	0.016	0	-9999	-10000	0	0
GNA13	0.015	0.022	-9999	-0.65	1	1
CDC42	0.016	0	-9999	-10000	0	0

×

BARD1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BARD1/CSTF1	-0.037	0.15	-10000	0	-0.65	51	51
ATM	0.014	0.041	-10000	0	-0.85	2	2
UBE2D3	0.016	0	-10000	0	-10000	0	0
PRKDC	0.016	0	-10000	0	-10000	0	0
ATR	0.015	0.029	-10000	0	-0.85	1	1
UBE2L3	0.016	0	-10000	0	-10000	0	0
FANCD2	0.028	0.053	-10000	0	-0.7	3	3
protein ubiquitination	-0.041	0.14	-10000	0	-0.87	6	6
XRCC5	0.016	0	-10000	0	-10000	0	0
XRCC6	0.016	0	-10000	0	-10000	0	0
M/R/N Complex	-0.003	0.04	-10000	0	-0.56	4	4
MRE11A	0.015	0.029	-10000	0	-0.85	1	1
DNA-PK	0	0	-10000	0	-10000	0	0
FA complex/FANCD2/Ubiquitin	-0.004	0.049	-10000	0	-0.81	2	2
FANCF	0.016	0	-10000	0	-10000	0	0
BRCA1	0.008	0.085	-10000	0	-0.83	9	9
CCNE1	0	0.1	-10000	0	-0.66	21	21
CDK2/Cyclin E1	-0.011	0.074	-10000	0	-0.48	21	21
FANCG	0.015	0.029	-10000	0	-0.85	1	1
BRCA1/BACH1/BARD1	-0.043	0.17	-10000	0	-0.68	57	57
FANCE	0.014	0.037	-10000	0	-0.75	2	2
FANCC	0.014	0.037	-10000	0	-0.75	2	2
NBN	0.015	0.022	-10000	0	-0.65	1	1
FANCA	0.011	0.063	-10000	0	-0.75	6	6
DNA repair	0.055	0.14	-10000	0	-0.74	7	7
BRCA1/BARD1/ubiquitin	-0.043	0.17	-10000	0	-0.68	57	57
BARD1/DNA-PK	-0.029	0.12	-10000	0	-0.51	51	51
FANCL	0.016	0	-10000	0	-10000	0	0
mRNA polyadenylation	0.037	0.15	0.65	51	-10000	0	51
BRCA1/BARD1/CTIP/M/R/N Complex	0.024	0.11	-10000	0	-0.81	5	5
BRCA1/BACH1/BARD1/TopBP1	-0.038	0.15	-10000	0	-0.59	57	57
BRCA1/BARD1/P53	-0.035	0.14	-10000	0	-0.54	58	58
BARD1/CSTF1/BRCA1	-0.038	0.15	-10000	0	-0.59	56	56
BRCA1/BACH1	0.008	0.084	-10000	0	-0.82	9	9
BARD1	-0.034	0.2	-10000	0	-0.85	51	51
PCNA	0.016	0	-10000	0	-10000	0	0
BRCA1/BARD1/UbcH5C	-0.038	0.15	-10000	0	-0.59	56	56
BRCA1/BARD1/UbcH7	-0.038	0.15	-10000	0	-0.59	57	57
BRCA1/BARD1/RAD51/PCNA	-0.039	0.14	-10000	0	-0.55	57	57
BARD1/DNA-PK/P53	-0.028	0.11	-10000	0	-0.48	52	52
BRCA1/BARD1/Ubiquitin	-0.043	0.17	-10000	0	-0.68	57	57
BRCA1/BARD1/CTIP	-0.038	0.14	-10000	0	-0.55	59	59
FA complex	0.047	0.047	-10000	0	-1	1	1
BARD1/EWS	-0.037	0.15	-10000	0	-0.65	51	51
RBBP8	0.025	0.064	-10000	0	-0.88	4	4
TP53	0.015	0.029	-10000	0	-0.85	1	1
TOPBP1	0.015	0.029	-10000	0	-0.85	1	1
G1/S transition of mitotic cell cycle	0.035	0.14	0.53	58	-10000	0	58
BRCA1/BARD1	-0.041	0.14	-10000	0	-0.89	6	6
CSTF1	0.016	0	-10000	0	-10000	0	0
BARD1/EWS-Fli1	-0.038	0.15	-10000	0	-0.66	51	51
CDK2	0.016	0	-10000	0	-10000	0	0
UniProt:Q9BZD1	0	0	-10000	0	-10000	0	0
RAD51	0.008	0.075	-10000	0	-0.69	10	10
RAD50	0.013	0.05	-10000	0	-0.85	3	3
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme	-0.043	0.17	-10000	0	-0.68	57	57
EWSR1	0.016	0	-10000	0	-10000	0	0

×

Aurora A signaling

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
Aurora A/GADD45A	0.031	0.03	-9999	-0.4	1	1
BIRC5	-0.04	0.2	-9999	-0.71	68	68
NFKBIA	0.037	0.027	-9999	-10000	0	0
CPEB1	-0.2	0.34	-9999	-0.74	252	252
AKT1	0.036	0.033	-9999	-0.56	1	1
NDEL1	0.016	0	-9999	-10000	0	0
Aurora A/BRCA1	-0.004	0.055	-9999	-0.5	9	9
NDEL1/TACC3	-0.001	0.044	-9999	-0.52	5	5
GADD45A	0.015	0.022	-9999	-0.65	1	1
GSK3B	0.016	0.007	-9999	-10000	0	0
PAK1/Aurora A	0.032	0.026	-9999	-10000	0	0
MDM2	0.016	0	-9999	-10000	0	0
JUB	-0.014	0.16	-9999	-0.85	31	31
TPX2	0.007	0.11	-9999	-0.53	35	35
TP53	0.036	0.026	-9999	-0.53	1	1
DLG7	0.024	0.027	-9999	-10000	0	0
AURKAIP1	0.013	0.052	-9999	-0.75	4	4
ARHGEF7	0.016	0	-9999	-10000	0	0
G2 phase of mitotic cell cycle	0	0	-9999	-10000	0	0
Aurora A/NDEL1/TACC3	-0.001	0.047	-9999	-0.54	5	5
G2/M transition of mitotic cell cycle	-0.004	0.055	-9999	-0.5	9	9
AURKA	0.029	0.033	-9999	-10000	0	0
AURKB	-0.018	0.066	-9999	-0.28	45	45
CDC25B	-0.005	0.047	-9999	-0.41	4	4
G2/M transition checkpoint	-0.017	0.099	-9999	-0.52	31	31
mRNA polyadenylation	-0.12	0.2	-9999	-0.44	251	251
Aurora A/CPEB	-0.12	0.2	-9999	-0.44	251	251
Aurora A/TACC1/TRAP/chTOG	-0.001	0.042	-9999	-0.47	5	5
BRCA1	0.008	0.085	-9999	-0.83	9	9
centrosome duplication	0.031	0.026	-9999	-10000	0	0
regulation of centrosome cycle	-0.002	0.043	-9999	-0.51	5	5
spindle assembly	-0.001	0.041	-9999	-0.47	5	5
TDRD7	0.016	0	-9999	-10000	0	0
Aurora A/RasGAP/Survivin	-0.034	0.12	-9999	-0.53	34	34
CENPA	-0.015	0.059	-9999	-0.26	37	37
Aurora A/PP2A	0.031	0.033	-9999	-0.4	2	2
meiosis	0	0	-9999	-10000	0	0
protein catabolic process	0.043	0.027	-9999	-10000	0	0
negative regulation of DNA binding	0.036	0.026	-9999	-0.53	1	1
prophase	0	0	-9999	-10000	0	0
GIT1/beta-PIX	-0.001	0.031	-9999	-0.65	2	2
RASA1	0.013	0.05	-9999	-0.85	3	3
Ajuba/Aurora A	-0.017	0.1	-9999	-0.53	31	31
mitotic prometaphase	0.005	0.019	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.029	0.033	-9999	-10000	0	0
TACC1	0.012	0.058	-9999	-0.85	4	4
TACC3	0.012	0.055	-9999	-0.65	6	6
Aurora A/Antizyme1	0	0.04	-9999	-0.51	2	2
Aurora A/RasGAP	0.029	0.043	-9999	-0.56	3	3
OAZ1	0.015	0.022	-9999	-0.65	1	1
RAN	0.016	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
PRKACA	0.016	0.007	-9999	-10000	0	0
GIT1	0.014	0.041	-9999	-0.85	2	2
GIT1/beta-PIX/PAK1	-0.001	0.027	-9999	-0.56	2	2
Importin alpha/Importin beta/TPX2	0.007	0.11	-9999	-0.53	35	35
PPP2R5D	0.015	0.032	-9999	-0.65	2	2
Aurora A/TPX2	0.024	0.096	-9999	-0.52	19	19
PAK1	0.016	0	-9999	-10000	0	0
CKAP5	0.015	0.029	-9999	-0.85	1	1

×

Class I PI3K signaling events

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
ARF5/GTP	-0.051	0.13	-9999	-0.71	2	2
DAPP1	-0.036	0.24	-9999	-0.8	61	61
Src family/SYK family/BLNK-LAT/BTK-ITK	-0.064	0.3	-9999	-0.81	103	103
mol:DAG	-0.007	0.14	-9999	-0.33	78	78
HRAS	0.01	0.06	-9999	-0.77	5	5
RAP1A	0.014	0.008	-9999	-10000	0	0
ARF5/GDP	0.021	0.1	-9999	-0.46	25	25
PLCG2	-0.054	0.21	-9999	-0.68	90	90
PLCG1	0.016	0	-9999	-10000	0	0
ARF5	0.015	0.029	-9999	-0.85	1	1
mol:GTP	-0.055	0.14	-9999	-0.48	4	4
ARF1/GTP	-0.053	0.14	-9999	-0.6	3	3
RHOA	0.016	0	-9999	-10000	0	0
YES1	0.016	0	-9999	-10000	0	0
RAP1A/GTP	-0.054	0.14	-9999	-0.48	4	4
ADAP1	-0.063	0.15	-9999	-0.75	5	5
ARAP3	-0.055	0.14	-9999	-0.43	113	113
INPPL1	0.014	0.041	-9999	-0.85	2	2
PREX1	0.002	0.11	-9999	-0.85	14	14
ARHGEF6	0.003	0.1	-9999	-0.85	13	13
ARHGEF7	0.016	0	-9999	-10000	0	0
ARF1	0.016	0	-9999	-10000	0	0
NRAS	0.014	0.008	-9999	-10000	0	0
FYN	0.007	0.086	-9999	-0.85	9	9
ARF6	0.016	0	-9999	-10000	0	0
FGR	-0.012	0.15	-9999	-0.83	30	30
mol:Ca2+	0.012	0.072	-9999	-10000	0	0
mol:IP4	0	0	-9999	-10000	0	0
TIAM1	0.005	0.098	-9999	-0.83	12	12
ZAP70	-0.054	0.23	-9999	-0.79	77	77
mol:IP3	0.009	0.098	-9999	-10000	0	0
LYN	0.012	0.058	-9999	-0.85	4	4
ARF1/GDP	0.021	0.1	-9999	-0.45	24	24
RhoA/GDP	-0.054	0.13	-9999	-0.59	10	10
PDK1/Src/Hsp90	-0.002	0.03	-9999	-0.51	3	3
BLNK	-0.011	0.14	-9999	-0.74	32	32
actin cytoskeleton reorganization	0.011	0.17	-9999	-0.62	16	16
SRC	0.015	0.022	-9999	-0.65	1	1
PLEKHA2	0.032	0.06	-9999	-0.56	9	9
RAC1	0.016	0	-9999	-10000	0	0
PTEN	0.007	0.017	-9999	-10000	0	0
HSP90AA1	0.016	0	-9999	-10000	0	0
ARF6/GTP	-0.051	0.13	-9999	-0.75	3	3
RhoA/GTP	-0.051	0.13	-9999	-0.58	1	1
Src family/SYK family/BLNK-LAT	-0.06	0.3	-9999	-0.86	84	84
BLK	-0.081	0.25	-9999	-0.72	115	115
PDPK1	0.014	0.041	-9999	-0.85	2	2
CYTH1	-0.051	0.13	-9999	-0.58	1	1
HCK	-0.005	0.13	-9999	-0.83	22	22
CYTH3	-0.051	0.13	-9999	-0.58	1	1
CYTH2	-0.052	0.14	-9999	-0.77	3	3
KRAS	0.014	0.008	-9999	-10000	0	0
GO:0030676	0	0	-9999	-10000	0	0
FOXO3	-0.04	0.11	-9999	-0.6	24	24
SGK1	-0.044	0.13	-9999	-0.67	24	24
INPP5D	0.009	0.076	-9999	-0.85	7	7
mol:GDP	0.012	0.1	-9999	-0.46	28	28
SOS1	0.016	0	-9999	-10000	0	0
SYK	-0.001	0.12	-9999	-0.8	19	19
ARF6/GDP	-0.054	0.13	-9999	-0.53	18	18
mol:PI-3-4-5-P3	-0.055	0.14	-9999	-0.48	4	4
ARAP3/RAP1A/GTP	-0.055	0.14	-9999	-0.48	4	4
VAV1	-0.026	0.18	-9999	-0.83	44	44
mol:PI-3-4-P2	0.022	0.068	-9999	-0.65	9	9
RAS family/GTP/PI3K Class I	-0.021	0.16	-9999	-0.49	4	4
PLEKHA1	0.031	0.063	-9999	-0.56	10	10
Rac1/GDP	0.021	0.1	-9999	-0.45	24	24
LAT	-0.022	0.16	-9999	-0.72	46	46
Rac1/GTP	0.017	0.14	-9999	-0.7	24	24
ITK	-0.1	0.21	-9999	-0.86	33	33
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma	-0.024	0.19	-9999	-0.48	86	86
LCK	-0.08	0.26	-9999	-0.8	104	104
BTK	-0.066	0.16	-9999	-0.88	7	7

×

Regulation of Telomerase

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
Telomerase catalytic core complex	-0.087	0.21	-9999	-0.68	44	44
RAD9A	0.014	0.043	-9999	-0.72	3	3
AP1	-0.07	0.21	-9999	-0.57	123	123
IFNAR2	0.01	0.071	-9999	-0.85	6	6
AKT1	-0.002	0.089	-9999	-0.35	17	17
ER alpha/Oestrogen	-0.038	0.16	-9999	-0.64	58	58
NFX1/SIN3/HDAC complex	0.041	0.062	-9999	-10000	0	0
EGF	-0.15	0.31	-9999	-0.73	196	196
SMG5	0.016	0	-9999	-10000	0	0
SMG6	0.015	0.029	-9999	-0.85	1	1
SP3/HDAC2	0.01	0.035	-9999	-0.65	2	2
TERT/c-Abl	-0.099	0.18	-9999	-0.66	35	35
SAP18	0.016	0.002	-9999	-10000	0	0
MRN complex	-0.003	0.04	-9999	-0.56	4	4
WT1	-0.26	0.36	-9999	-0.74	317	317
WRN	0.015	0.029	-9999	-0.85	1	1
SP1	0.016	0.007	-9999	-10000	0	0
SP3	0.013	0.041	-9999	-0.85	2	2
TERF2IP	0.016	0	-9999	-10000	0	0
Telomerase/Nucleolin	-0.087	0.16	-9999	-0.76	9	9
Mad/Max	0.01	0.027	-9999	-0.48	2	2
TERT	-0.089	0.22	-9999	-0.7	42	42
CCND1	-0.1	0.31	-9999	-1.3	43	43
MAX	0.015	0.006	-9999	-10000	0	0
RBBP7	0.016	0.003	-9999	-10000	0	0
RBBP4	0.015	0.029	-9999	-0.85	1	1
TERF2	0	0.005	-9999	-10000	0	0
PTGES3	0.016	0	-9999	-10000	0	0
SIN3A	0.016	0.002	-9999	-10000	0	0
Telomerase/911	0.036	0.036	-9999	-10000	0	0
CDKN1B	-0.035	0.18	-9999	-0.55	40	40
RAD1	0.016	0	-9999	-10000	0	0
XRCC5	0.016	0	-9999	-10000	0	0
XRCC6	0.016	0	-9999	-10000	0	0
SAP30	-0.014	0.16	-9999	-0.85	31	31
TRF2/PARP2	0	0.005	-9999	-10000	0	0
UBE3A	0.015	0.006	-9999	-10000	0	0
JUN	0.009	0.069	-9999	-0.76	7	7
E6	-0.001	0.004	-9999	-10000	0	0
HPV-16 E6/E6AP	0.008	0.007	-9999	-10000	0	0
FOS	-0.088	0.26	-9999	-0.74	120	120
IFN-gamma/IRF1	-0.086	0.19	-9999	-0.51	151	151
PARP2	0.016	0	-9999	-10000	0	0
BLM	0.005	0.091	-9999	-0.71	14	14
Telomerase	-0.002	0.096	-9999	-0.53	12	12
IRF1	0.018	0.032	-9999	-0.64	2	2
ESR1	-0.039	0.21	-9999	-0.82	58	58
KU/TER	0	0	-9999	-10000	0	0
ATM/TRF2	-0.001	0.027	-9999	-0.58	2	2
ubiquitin-dependent protein catabolic process	0.048	0.058	-9999	-10000	0	0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex	0.048	0.059	-9999	-10000	0	0
HDAC1	0.016	0.002	-9999	-10000	0	0
HDAC2	0.016	0.007	-9999	-10000	0	0
ATM	-0.001	0.027	-9999	-0.58	2	2
SMAD3	0.015	0.099	-9999	-0.63	20	20
ABL1	0.016	0	-9999	-10000	0	0
MXD1	0.013	0.032	-9999	-0.65	2	2
MRE11A	0.015	0.029	-9999	-0.85	1	1
HUS1	0.016	0	-9999	-10000	0	0
RPS6KB1	0.016	0	-9999	-10000	0	0
TERT/NF kappa B1/14-3-3	-0.084	0.18	-9999	-0.76	14	14
NR2F2	0.015	0.042	-9999	-0.85	2	2
MAPK3	0.013	0.063	-9999	-0.49	13	13
MAPK1	0.013	0.063	-9999	-0.49	13	13
TGFB1/TGF beta receptor Type II	-0.003	0.12	-9999	-0.83	20	20
NFKB1	0.015	0.029	-9999	-0.85	1	1
HNRNPC	0.016	0	-9999	-10000	0	0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis	-0.001	0.027	-9999	-0.58	2	2
NBN	0.015	0.022	-9999	-0.65	1	1
EGFR	-0.022	0.17	-9999	-0.79	41	41
mol:Oestrogen	0	0.002	-9999	-10000	0	0
EGF/EGFR	-0.15	0.26	-9999	-0.59	222	222
MYC	-0.023	0.18	-9999	-0.83	40	40
IL2	-0.002	0.077	-9999	-0.65	12	12
KU	0	0	-9999	-10000	0	0
RAD50	0.013	0.05	-9999	-0.85	3	3
HSP90AA1	0.016	0	-9999	-10000	0	0
TGFB1	-0.003	0.12	-9999	-0.83	20	20
TRF2/BLM	-0.008	0.062	-9999	-0.49	14	14
FRAP1	0	0	-9999	-10000	0	0
KU/TERT	-0.08	0.19	-9999	-0.72	20	20
SP1/HDAC2	0.025	0.012	-9999	-10000	0	0
PINX1	0.014	0.041	-9999	-0.85	2	2
Telomerase/EST1A	-0.087	0.16	-9999	-0.74	10	10
Smad3/Myc	-0.005	0.16	-9999	-0.59	55	55
911 complex	-0.002	0.027	-9999	-0.56	1	1
IFNG	-0.1	0.27	-9999	-0.69	151	151
Telomerase/PinX1	-0.088	0.16	-9999	-0.76	9	9
Telomerase/AKT1/mTOR/p70S6K	0.013	0.07	-9999	-10000	0	0
SIN3B	0.014	0.041	-9999	-0.85	2	2
YWHAE	0.016	0	-9999	-10000	0	0
Telomerase/EST1B	-0.087	0.16	-9999	-0.74	10	10
response to DNA damage stimulus	0.004	0.007	-9999	-10000	0	0
MRN complex/TRF2/Rap1	-0.002	0.033	-9999	-0.47	2	2
TRF2/WRN	0	0.021	-9999	-0.61	1	1
Telomerase/hnRNP C1/C2	-0.087	0.16	-9999	-0.7	13	13
E2F1	0.009	0.066	-9999	-0.68	8	8
ZNFX1	0.016	0.002	-9999	-10000	0	0
PIF1	-0.023	0.16	-9999	-0.7	48	48
NCL	0.016	0	-9999	-10000	0	0
DKC1	0.016	0	-9999	-10000	0	0
telomeric DNA binding	0	0	-9999	-10000	0	0

×

Role of Calcineurin-dependent NFAT signaling in lymphocytes

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
BCL2L1	0.016	0	-10000	0	-10000	0	0
NFATC1	0.057	0.07	-10000	0	-0.47	3	3
NFATC2	0.014	0.079	-10000	0	-0.37	9	9
NFATC3	0.02	0.058	-10000	0	-0.55	9	9
YWHAE	0.016	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/CABIN1	-0.031	0.18	-10000	0	-0.54	68	68
Exportin 1/Ran/NUP214	0	0	-10000	0	-10000	0	0
mol:DAG	-0.001	0.003	-10000	0	-10000	0	0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV	-0.087	0.2	-10000	0	-0.72	62	62
BCL2/BAX	-0.012	0.087	-10000	0	-0.65	16	16
CaM/Ca2+/Calcineurin A alpha-beta B1	0.011	0.008	-10000	0	-10000	0	0
CaM/Ca2+	0.011	0.008	-10000	0	-10000	0	0
BAX	0.014	0.041	-10000	0	-0.85	2	2
MAPK14	0.014	0.006	-10000	0	-10000	0	0
BAD	0.012	0.055	-10000	0	-0.8	4	4
CABIN1/MEF2D	-0.023	0.17	-10000	0	-0.51	68	68
Calcineurin A alpha-beta B1/BCL2	0.002	0.11	-10000	0	-0.85	14	14
FKBP8	0.014	0.041	-10000	0	-0.85	2	2
activation-induced cell death of T cells	0.022	0.16	0.5	68	-10000	0	68
KPNB1	0.015	0.029	-10000	0	-0.85	1	1
KPNA2	0.013	0.045	-10000	0	-0.65	4	4
XPO1	0.016	0.001	-10000	0	-10000	0	0
SFN	-0.23	0.35	-10000	0	-0.72	299	299
MAP3K8	0.009	0.059	-10000	0	-0.77	5	5
NFAT4/CK1 alpha	-0.004	0.037	-10000	0	-10000	0	0
MEF2D/NFAT1/Cbp/p300	-0.062	0.12	-10000	0	-0.49	14	14
CABIN1	-0.032	0.18	-10000	0	-0.55	68	68
CALM1	0.014	0.006	-10000	0	-10000	0	0
RAN	0.016	0.001	-10000	0	-10000	0	0
MAP3K1	0.015	0.022	-10000	0	-0.65	1	1
CAMK4	-0.05	0.23	-10000	0	-0.84	69	69
mol:Ca2+	-0.002	0.008	-10000	0	-10000	0	0
MAPK3	0.015	0.029	-10000	0	-0.85	1	1
YWHAH	0.016	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/AKAP79/PKA	-0.037	0.14	-10000	0	-0.55	60	60
YWHAB	0.016	0	-10000	0	-10000	0	0
MAPK8	0.003	0.096	-10000	0	-0.85	11	11
MAPK9	0.016	0	-10000	0	-10000	0	0
YWHAG	0.016	0	-10000	0	-10000	0	0
FKBP1A	0.016	0	-10000	0	-10000	0	0
NFAT1-c-4/YWHAQ	-0.003	0.06	-10000	0	-0.46	6	6
PRKCH	-0.04	0.21	-10000	0	-0.85	58	58
CABIN1/Cbp/p300	-0.001	0.031	-10000	0	-0.65	2	2
CASP3	0.014	0.006	-10000	0	-10000	0	0
PIM1	0.011	0.062	-10000	0	-0.68	7	7
Calcineurin A alpha-beta B1/FKBP12/FK506	0	0	-10000	0	-10000	0	0
apoptosis	-0.006	0.055	-10000	0	-0.81	3	3
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1	-0.012	0.1	-10000	0	-0.6	2	2
PRKCB	-0.035	0.2	-10000	0	-0.83	54	54
PRKCE	0.013	0.05	-10000	0	-0.85	3	3
JNK2/NFAT4	0.028	0.053	-10000	0	-0.49	9	9
BAD/BCL-XL	-0.003	0.041	-10000	0	-0.61	4	4
PRKCD	-0.027	0.16	-10000	0	-0.65	57	57
NUP214	0.016	0.001	-10000	0	-10000	0	0
PRKCZ	0.006	0.082	-10000	0	-0.85	8	8
PRKCA	0.015	0.032	-10000	0	-0.65	2	2
PRKCG	-0.042	0.18	-10000	0	-0.65	68	68
PRKCQ	-0.04	0.2	-10000	0	-0.78	62	62
FKBP38/BCL2	-0.012	0.087	-10000	0	-0.65	16	16
EP300	0.013	0.041	-10000	0	-0.85	2	2
PRKCB1	0	0	-10000	0	-10000	0	0
CSNK2A1	0.016	0	-10000	0	-10000	0	0
NFATc/JNK1	0.049	0.088	-10000	0	-0.5	1	1
CaM/Ca2+/FKBP38	-0.001	0.028	-10000	0	-0.59	2	2
FKBP12/FK506	0	0	-10000	0	-10000	0	0
CSNK1A1	0.022	0.01	-10000	0	-10000	0	0
CaM/Ca2+/CAMK IV	-0.044	0.15	-10000	0	-0.57	69	69
NFATc/ERK1	0.064	0.071	-10000	0	-0.62	2	2
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV	-0.086	0.2	-10000	0	-0.67	72	72
NR4A1	-0.054	0.28	-10000	0	-0.62	160	160
GSK3B	0.014	0.006	-10000	0	-10000	0	0
positive T cell selection	0.02	0.058	-10000	0	-0.54	9	9
NFAT1/CK1 alpha	-0.02	0.045	-10000	0	-0.35	1	1
RCH1/ KPNB1	-0.003	0.039	-10000	0	-0.51	5	5
YWHAQ	0.016	0	-10000	0	-10000	0	0
PRKACA	0.014	0.006	-10000	0	-10000	0	0
AKAP5	-0.034	0.19	-10000	0	-0.73	60	60
MEF2D	0.015	0.005	-10000	0	-10000	0	0
mol:FK506	0	0	-10000	0	-10000	0	0
YWHAZ	0.016	0	-10000	0	-10000	0	0
NFATc/p38 alpha	0.055	0.072	-10000	0	-0.5	1	1
CREBBP	0.015	0.005	-10000	0	-10000	0	0
BCL2	0.002	0.11	-10000	0	-0.85	14	14

×

IGF1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NCK2	0.016	0	-10000	0	-10000	0	0
PTK2	0.016	0	-10000	0	-10000	0	0
CRKL	-0.017	0.14	-10000	0	-0.52	40	40
GRB2/SOS1/SHC	0	0.013	-10000	0	-10000	0	0
HRAS	0.012	0.059	-10000	0	-0.77	5	5
IRS1/Crk	-0.018	0.14	-10000	0	-0.49	50	50
IGF-1R heterotetramer/IGF1/PTP1B	-0.047	0.14	-10000	0	-0.55	41	41
AKT1	0.007	0.14	-10000	0	-0.66	16	16
BAD	0.015	0.14	-10000	0	-0.72	12	12
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	-0.017	0.14	-10000	0	-0.49	50	50
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.019	0.14	-10000	0	-0.52	41	41
RAF1	0.023	0.13	-10000	0	-0.63	11	11
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos	-0.044	0.12	-10000	0	-0.68	9	9
YWHAZ	0.016	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.031	0.15	-10000	0	-0.53	50	50
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
RPS6KB1	0.007	0.14	-10000	0	-0.66	15	15
GNB2L1	0.016	0	-10000	0	-10000	0	0
positive regulation of MAPKKK cascade	0.02	0.11	-10000	0	-0.52	11	11
PXN	0.016	0	-10000	0	-10000	0	0
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
cell adhesion	0	0	-10000	0	-10000	0	0
GRB2/SOS1	0	0	-10000	0	-10000	0	0
HRAS/GTP	-0.04	0.11	-10000	0	-0.62	11	11
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc	-0.035	0.11	-10000	0	-0.62	4	4
IGF-1R heterotetramer	0.003	0.061	-10000	0	-0.92	3	3
IGF-1R heterotetramer/IGF1/IRS/Nck	-0.047	0.13	-10000	0	-0.52	40	40
Crk/p130 Cas/Paxillin	-0.043	0.12	-10000	0	-0.66	10	10
IGF1R	0.003	0.061	-10000	0	-0.92	3	3
IGF1	-0.06	0.23	-10000	0	-0.73	89	89
IRS2/Crk	-0.026	0.17	-10000	0	-0.54	52	52
PI3K	-0.05	0.14	-10000	0	-0.65	19	19
apoptosis	-0.024	0.12	0.58	12	-10000	0	12
HRAS/GDP	-0.003	0.045	-10000	0	-0.59	5	5
PRKCD	-0.013	0.17	-10000	0	-0.55	65	65
RAF1/14-3-3 E	0.032	0.11	-10000	0	-0.54	8	8
BAD/14-3-3	0.024	0.13	-10000	0	-0.64	12	12
PRKCZ	0.003	0.15	-10000	0	-0.66	19	19
Crk/p130 Cas/Paxillin/FAK1	-0.036	0.1	-10000	0	-0.61	12	12
PTPN1	0.015	0.029	-10000	0	-0.85	1	1
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1	0	0.14	-10000	0	-0.58	34	34
BCAR1	0.013	0.05	-10000	0	-0.85	3	3
IGF-1R heterotetramer/IGF1/SHC/GRB10	-0.041	0.12	-10000	0	-0.5	37	37
mol:GDP	0	0	-10000	0	-10000	0	0
SOS1	0.016	0	-10000	0	-10000	0	0
IRS1/NCK2	-0.018	0.14	-10000	0	-0.51	40	40
GRB10	0.014	0.041	-10000	0	-0.85	2	2
PTPN11	-0.017	0.14	-10000	0	-0.52	41	41
IRS1	-0.03	0.15	-10000	0	-0.53	50	50
IRS2	-0.037	0.17	-10000	0	-0.57	52	52
IGF-1R heterotetramer/IGF1	-0.06	0.17	-10000	0	-0.56	91	91
GRB2	0.016	0	-10000	0	-10000	0	0
PDPK1	-0.004	0.15	-10000	0	-0.65	19	19
YWHAE	0.016	0	-10000	0	-10000	0	0
PRKD1	0.005	0.14	-10000	0	-0.56	41	41
SHC1	0.015	0.022	-10000	0	-0.65	1	1

×

PLK2 and PLK4 events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLK2	-0.008	0.14	-9999	-0.84	25	25
PLK4	0.014	0.039	-9999	-0.65	3	3
regulation of centriole replication	0.008	0.12	-9999	-0.63	28	28

×

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

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
MET/RANBP9	-0.005	0.056	-10000	0	-0.59	8	8
CRKL	0.01	0.11	-10000	0	-0.49	6	6
mol:PIP3	-0.026	0.007	-10000	0	-10000	0	0
AKT1	0	0.031	-10000	0	-0.53	3	3
PTK2B	0.016	0	-10000	0	-10000	0	0
RAPGEF1	0.019	0.1	-10000	0	-0.57	3	3
RANBP10	0.016	0	-10000	0	-10000	0	0
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
HGF/MET/SHIP2	-0.076	0.18	-10000	0	-0.57	90	90
MAP3K5	0.009	0.14	-10000	0	-0.57	27	27
HGF/MET/CIN85/CBL/ENDOPHILINS	-0.071	0.18	-10000	0	-0.56	88	88
AP1	-0.053	0.19	-10000	0	-0.51	123	123
mol:SU11274	0	0	-10000	0	-10000	0	0
SHC1	0.015	0.022	-10000	0	-0.65	1	1
apoptosis	-0.05	0.23	-10000	0	-0.85	60	60
STAT3 (dimer)	0.007	0.12	-10000	0	-0.57	2	2
GAB1/CRKL/SHP2/PI3K	-0.033	0.094	-10000	0	-0.69	7	7
INPP5D	0.009	0.076	-10000	0	-0.85	7	7
CBL/CRK	0.018	0.11	-10000	0	-0.7	4	4
PTPN11	0.015	0.029	-10000	0	-0.85	1	1
GO:0007205	0	0	-10000	0	-10000	0	0
PLCG1	0.016	0	-10000	0	-10000	0	0
PTEN	0.016	0	-10000	0	-10000	0	0
ELK1	-0.002	0.03	0.26	2	-0.27	8	10
mol:SU5416	0	0	-10000	0	-10000	0	0
SHP2/GRB2/SOS1GAB1	-0.025	0.064	-10000	0	-0.37	7	7
PAK1	0.009	0.03	-10000	0	-0.5	3	3
HGF/MET/RANBP10	-0.075	0.18	-10000	0	-0.57	88	88
HRAS	-0.011	0.16	-10000	0	-0.71	9	9
DOCK1	0.018	0.11	-10000	0	-0.61	5	5
GAB1	0	0.11	-10000	0	-0.44	11	11
CRK	0.009	0.11	-10000	0	-0.59	5	5
mol:PHA665752	0	0	-10000	0	-10000	0	0
mol:GDP	-0.069	0.18	-10000	0	-0.6	88	88
JUN	0.01	0.069	-10000	0	-0.76	7	7
EntrezGene:200958	0	0	-10000	0	-10000	0	0
HGF/MET	-0.036	0.091	-10000	0	-0.28	91	91
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
cell morphogenesis	0.036	0.14	-10000	0	-0.68	7	7
GRB2/SHC	0.002	0.089	-10000	0	-0.44	4	4
FOS	-0.086	0.26	-10000	0	-0.74	120	120
GLMN	-0.001	0.016	-10000	0	-0.33	2	2
cell motility	-0.002	0.03	0.26	2	-0.27	8	10
HGF/MET/MUC20	-0.076	0.19	-10000	0	-0.52	129	129
cell migration	0.002	0.087	-10000	0	-0.43	4	4
GRB2	0.016	0	-10000	0	-10000	0	0
CBL	0.015	0.029	-10000	0	-0.85	1	1
MET/RANBP10	-0.005	0.056	-10000	0	-0.59	8	8
HGF/MET/Paxillin/FAK1/FAK12/RasGAP	-0.002	0.12	-10000	0	-0.62	2	2
MET/MUC20	-0.005	0.057	-10000	0	-0.6	8	8
RAP1B	0.028	0.096	-10000	0	-0.6	2	2
RAP1A	0.028	0.096	-10000	0	-0.83	1	1
HGF/MET/RANBP9	-0.075	0.18	-10000	0	-0.57	88	88
RAF1	0	0.15	-10000	0	-0.68	8	8
STAT3	0.007	0.12	-10000	0	-0.58	2	2
cell proliferation	0.008	0.16	-10000	0	-0.53	10	10
RPS6KB1	0.003	0.037	-10000	0	-10000	0	0
MAPK3	-0.008	0.037	0.8	1	-10000	0	1
MAPK1	-0.008	0.039	0.91	1	-0.26	5	6
RANBP9	0.016	0	-10000	0	-10000	0	0
MAPK8	0.028	0.14	-10000	0	-0.61	18	18
SRC	0.008	0.12	-10000	0	-0.57	2	2
PI3K	-0.004	0.11	-10000	0	-0.53	13	13
MET/Glomulin	0.01	0.054	-10000	0	-0.54	8	8
SOS1	0.016	0	-10000	0	-10000	0	0
MAP2K1	0.01	0.14	-10000	0	-0.64	7	7
MET	0.009	0.075	-10000	0	-0.77	8	8
MAP4K1	-0.001	0.15	-10000	0	-0.59	28	28
PTK2	0.016	0	-10000	0	-10000	0	0
MAP2K2	0.009	0.14	-10000	0	-0.66	11	11
BAD	0.007	0.053	-10000	0	-0.67	5	5
MAP2K4	0.019	0.13	-10000	0	-0.5	27	27
SHP2/GRB2/SOS1/GAB1	-0.031	0.085	-10000	0	-0.57	8	8
INPPL1	0.014	0.041	-10000	0	-0.85	2	2
PXN	0.016	0	-10000	0	-10000	0	0
SH3KBP1	0.01	0.071	-10000	0	-0.85	6	6
HGS	-0.009	0.094	-10000	0	-0.39	13	13
PLCgamma1/PKC	0	0	-10000	0	-10000	0	0
HGF	-0.094	0.28	-10000	0	-0.78	122	122
RASA1	0.013	0.05	-10000	0	-0.85	3	3
NCK1	0.014	0.041	-10000	0	-0.85	2	2
PTPRJ	0.011	0.063	-10000	0	-0.75	6	6
NCK/PLCgamma1	0	0.1	-10000	0	-0.51	5	5
PDPK1	-0.012	0.027	-10000	0	-0.58	2	2
HGF/MET/SHIP	-0.079	0.2	-10000	0	-0.6	90	90

×

TCGA08_rtk_signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.18	0.34	-10000	0	-0.75	228	228
HRAS	0.012	0.059	-10000	0	-0.77	5	5
EGFR	-0.021	0.17	-10000	0	-0.78	41	41
AKT	0.033	0.055	-10000	0	-0.51	5	5
FOXO3	0.016	0	-10000	0	-10000	0	0
AKT1	0.015	0.029	-10000	0	-0.85	1	1
FOXO1	0.012	0.055	-10000	0	-0.65	6	6
AKT3	0.008	0.082	-10000	0	-0.85	8	8
FOXO4	0.016	0	-10000	0	-10000	0	0
MET	0.009	0.075	-10000	0	-0.77	8	8
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
PIK3CB	0.015	0.022	-10000	0	-0.65	1	1
NRAS	0.016	0	-10000	0	-10000	0	0
PIK3CG	-0.052	0.23	-10000	0	-0.83	71	71
PIK3R3	0.001	0.11	-10000	0	-0.82	16	16
PIK3R2	0.015	0.029	-10000	0	-0.85	1	1
NF1	0.016	0	-10000	0	-10000	0	0
RAS	-0.021	0.097	-10000	0	-0.39	20	20
ERBB2	0.012	0.055	-10000	0	-0.8	4	4
proliferation/survival/translation	-0.032	0.043	0.27	3	-0.19	1	4
PI3K	-0.017	0.1	-10000	0	-0.28	51	51
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
KRAS	0.016	0	-10000	0	-10000	0	0
FOXO	0.042	0.039	-10000	0	-0.44	1	1
AKT2	0.015	0.029	-10000	0	-0.85	1	1
PTEN	0.016	0	-10000	0	-10000	0	0

×

E-cadherin signaling in keratinocytes

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
keratinocyte differentiation	0.039	0.087	-10000	0	-0.49	15	15
adherens junction organization	0.009	0.12	-10000	0	-0.52	19	19
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.028	0.12	-10000	0	-0.6	11	11
FMN1	-0.017	0.17	-10000	0	-0.52	62	62
mol:IP3	-0.019	0.068	-10000	0	-0.45	14	14
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.017	0.1	-10000	0	-0.75	4	4
CTNNB1	0.017	0.004	-10000	0	-10000	0	0
AKT1	0.035	0.09	-10000	0	-0.59	5	5
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin	-0.005	0.15	-10000	0	-0.59	44	44
CTNND1	0.017	0.003	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.026	0.099	-10000	0	-0.66	5	5
VASP	0.026	0.099	-10000	0	-0.7	4	4
ZYX	0.024	0.11	-10000	0	-0.73	7	7
JUB	0.009	0.14	-10000	0	-0.53	35	35
EGFR(dimer)	0.004	0.14	-10000	0	-0.54	33	33
E-cadherin/beta catenin-gamma catenin	-0.047	0.15	-10000	0	-0.5	84	84
mol:PI-3-4-5-P3	-0.022	0.077	-10000	0	-0.49	14	14
PIK3CA	0.011	0.071	-10000	0	-0.85	6	6
PI3K	-0.023	0.079	-10000	0	-0.5	14	14
FYN	-0.066	0.19	-10000	0	-0.58	34	34
mol:Ca2+	0.029	0.08	-10000	0	-0.44	14	14
JUP	0.01	0.076	-10000	0	-0.85	7	7
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
mol:DAG	-0.019	0.068	-10000	0	-0.45	14	14
CDH1	-0.054	0.22	-10000	0	-0.76	80	80
RhoA/GDP	0.028	0.12	-10000	0	-0.6	11	11
establishment of polarity of embryonic epithelium	0.026	0.097	-10000	0	-0.68	4	4
SRC	0.015	0.022	-10000	0	-0.65	1	1
RAC1	0.016	0	-10000	0	-10000	0	0
RHOA	0.016	0	-10000	0	-10000	0	0
EGFR	-0.021	0.17	-10000	0	-0.78	41	41
CASR	-0.094	0.22	-10000	0	-0.61	35	35
RhoA/GTP	-0.016	0.059	-10000	0	-0.48	4	4
AKT2	0.035	0.09	-10000	0	-0.59	5	5
actin cable formation	-0.007	0.17	-10000	0	-0.5	62	62
apoptosis	0.021	0.075	0.48	15	-10000	0	15
CTNNA1	0.017	0.003	-10000	0	-10000	0	0
mol:GDP	0.019	0.13	-10000	0	-0.63	13	13
PIP5K1A	0.026	0.1	-10000	0	-0.68	5	5
PLCG1	-0.019	0.069	-10000	0	-0.47	14	14
Rac1/GTP	-0.039	0.11	-10000	0	-0.48	33	33
homophilic cell adhesion	0.001	0.002	-10000	0	-10000	0	0

×

IFN-gamma 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2	-0.016	0.15	-9999	-0.46	36	36
positive regulation of NF-kappaB transcription factor activity	0	0.002	-9999	-10000	0	0
CRKL	0.016	0	-9999	-10000	0	0
STAT1 (dimer)/Cbp/p300	-0.046	0.11	-9999	-0.79	4	4
IFN-gammaR/JAK1/JAK1/JAK2/JAK2	-0.008	0.028	-9999	-0.67	1	1
antigen processing and presentation of peptide antigen via MHC class I	-0.05	0.099	-9999	-0.42	27	27
CaM/Ca2+	-0.051	0.12	-9999	-0.85	1	1
RAP1A	0.016	0	-9999	-10000	0	0
STAT1 (dimer)/SHP2	-0.005	0.15	-9999	-0.64	7	7
AKT1	0.009	0.14	-9999	-0.84	2	2
MAP2K1	0.009	0.14	-9999	-0.8	1	1
MAP3K11	-0.005	0.14	-9999	-0.59	5	5
IFNGR1	0.013	0.012	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKII	-0.11	0.14	-9999	-0.61	21	21
Rap1/GTP	-0.036	0.085	-9999	-0.79	1	1
CRKL/C3G	0	0	-9999	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP	-0.059	0.13	-9999	-0.46	39	39
CEBPB	0.031	0.16	-9999	-0.75	4	4
STAT3	0.016	0	-9999	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1	-0.1	0.23	-9999	-1.2	24	24
STAT1	-0.004	0.15	-9999	-0.63	7	7
CALM1	0.016	0	-9999	-10000	0	0
IFN-gamma (dimer)	-0.1	0.27	-9999	-0.69	151	151
PIK3CA	0.01	0.071	-9999	-0.85	6	6
STAT1 (dimer)/PIAS1	0.006	0.14	-9999	-0.66	5	5
CEBPB/PTGES2/Cbp/p300	-0.032	0.074	-9999	-0.49	5	5
mol:Ca2+	-0.055	0.13	-9999	-0.45	36	36
MAPK3	0.022	0.13	-9999	-0.77	2	2
STAT1 (dimer)	-0.067	0.14	-9999	-0.64	27	27
MAPK1	0.023	0.13	-9999	-1.1	1	1
JAK2	0.012	0.033	-9999	-0.9	1	1
PIK3R1	0.011	0.066	-9999	-0.78	6	6
JAK1	0.013	0.012	-9999	-10000	0	0
CAMK2D	0.016	0	-9999	-10000	0	0
DAPK1	0.025	0.18	-9999	-0.67	45	45
SMAD7	0.017	0.078	-9999	-0.4	1	1
CBL/CRKL/C3G	-0.045	0.11	-9999	-1.1	1	1
PI3K	-0.054	0.12	-9999	-1.2	1	1
IFNG	-0.1	0.27	-9999	-0.69	151	151
apoptosis	0.014	0.14	-9999	-0.48	45	45
CAMK2G	0.016	0	-9999	-10000	0	0
STAT3 (dimer)	0.016	0	-9999	-10000	0	0
CAMK2A	-0.022	0.15	-9999	-0.66	46	46
CAMK2B	-0.25	0.35	-9999	-0.7	326	326
FRAP1	0.011	0.13	-9999	-0.74	2	2
PRKCD	-0.01	0.16	-9999	-0.79	5	5
RAP1B	0.016	0	-9999	-10000	0	0
negative regulation of cell growth	-0.05	0.099	-9999	-0.42	27	27
PTPN2	0.016	0	-9999	-10000	0	0
EP300	0.015	0.041	-9999	-0.85	2	2
IRF1	0.028	0.14	-9999	-0.65	8	8
STAT1 (dimer)/PIASy	-0.041	0.13	-9999	-0.67	6	6
SOCS1	-0.054	0.25	-9999	-1.6	16	16
mol:GDP	-0.043	0.1	-9999	-0.98	1	1
CASP1	0.009	0.1	-9999	-0.39	34	34
PTGES2	0.01	0.068	-9999	-0.7	8	8
IRF9	0.05	0.06	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.052	0.12	-9999	-0.78	2	2
RAP1/GDP	-0.037	0.086	-9999	-0.8	1	1
CBL	-0.004	0.14	-9999	-1.3	1	1
MAP3K1	-0.003	0.14	-9999	-0.59	3	3
PIAS1	0.016	0	-9999	-10000	0	0
PIAS4	0.014	0.041	-9999	-0.85	2	2
antigen processing and presentation of peptide antigen via MHC class II	-0.05	0.099	-9999	-0.42	27	27
PTPN11	-0.014	0.14	-9999	-0.45	36	36
CREBBP	0.017	0.001	-9999	-10000	0	0
RAPGEF1	0.016	0	-9999	-10000	0	0

×

TCGA08_p53

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2A	-0.031	0.17	-10000	0	-0.63	63	63
TP53	-0.013	0.051	0.26	1	-0.41	1	2
Senescence	-0.013	0.051	0.26	1	-0.41	1	2
Apoptosis	-0.013	0.051	0.26	1	-0.41	1	2
Activated_Oncogenes	0	0	-10000	0	-10000	0	0
MDM2	0.023	0.085	0.34	52	-10000	0	52
MDM4	0.015	0.022	-10000	0	-0.65	1	1

×

E-cadherin signaling in the nascent adherens junction

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
CTTN	0.009	0.15	-9999	-0.6	44	44
KLHL20	-0.022	0.061	-9999	-0.34	10	10
CYFIP2	0.008	0.078	-9999	-0.76	9	9
Rac1/GDP	0.047	0.1	-9999	-10000	0	0
ENAH	0.007	0.15	-9999	-0.6	47	47
AP1M1	0.015	0.029	-9999	-0.85	1	1
RAP1B	0.016	0	-9999	-10000	0	0
RAP1A	0.016	0	-9999	-10000	0	0
CTNNB1	0.016	0	-9999	-10000	0	0
CDC42/GTP	-0.021	0.07	-9999	-10000	0	0
ABI1/Sra1/Nap1	-0.015	0.042	-9999	-0.23	13	13
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin	-0.045	0.15	-9999	-0.56	50	50
RAPGEF1	0.03	0.13	-9999	-0.5	44	44
CTNND1	0.016	0	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.041	0.14	-9999	-0.63	44	44
CRK	0.02	0.14	-9999	-0.55	44	44
E-cadherin/gamma catenin/alpha catenin	-0.048	0.16	-9999	-0.6	48	48
alphaE/beta7 Integrin	-0.007	0.065	-9999	-0.65	9	9
IQGAP1	0.016	0	-9999	-10000	0	0
NCKAP1	0.016	0	-9999	-10000	0	0
Rap1/GTP/I-afadin	0	0	-9999	-10000	0	0
DLG1	0.009	0.15	-9999	-0.6	44	44
ChemicalAbstracts:7440-70-2	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.018	0.054	-9999	-0.32	1	1
MLLT4	0.016	0	-9999	-10000	0	0
ARF6/GTP/NME1/Tiam1	-0.008	0.061	-9999	-0.49	14	14
PI3K	-0.023	0.07	-9999	-0.44	1	1
ARF6	0.016	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
E-cadherin/gamma catenin	-0.056	0.18	-9999	-0.6	84	84
TIAM1	0.005	0.098	-9999	-0.83	12	12
E-cadherin(dimer)/Ca2+	-0.038	0.12	-9999	-0.49	44	44
AKT1	-0.013	0.04	-9999	-0.28	1	1
PIK3R1	0.011	0.066	-9999	-0.78	6	6
CDH1	-0.054	0.22	-9999	-0.76	80	80
RhoA/GDP	0.047	0.1	-9999	-10000	0	0
actin cytoskeleton organization	-0.015	0.045	-9999	-0.24	9	9
CDC42/GDP	0.047	0.1	-9999	-10000	0	0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin	0.001	0.1	-9999	-0.37	48	48
ITGB7	0.008	0.082	-9999	-0.85	8	8
RAC1	0.016	0	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/p120 catenin	-0.04	0.13	-9999	-0.51	44	44
E-cadherin/Ca2+/beta catenin/alpha catenin	-0.039	0.12	-9999	-0.5	44	44
mol:GDP	0.04	0.12	-9999	-0.44	8	8
CDC42/GTP/IQGAP1	0	0	-9999	-10000	0	0
JUP	0.009	0.076	-9999	-0.85	7	7
p120 catenin/RhoA/GDP	-0.024	0.082	-9999	-10000	0	0
RAC1/GTP/IQGAP1	0	0	-9999	-10000	0	0
PIP5K1C/AP1M1	-0.002	0.045	-9999	-0.92	2	2
RHOA	0.016	0	-9999	-10000	0	0
CDC42	0.016	0	-9999	-10000	0	0
CTNNA1	0.016	0	-9999	-10000	0	0
positive regulation of S phase of mitotic cell cycle	0.024	0.073	-9999	-0.27	42	42
NME1	0.015	0.032	-9999	-0.65	2	2
clathrin coat assembly	0	0	-9999	-10000	0	0
TJP1	0.009	0.15	-9999	-0.6	44	44
regulation of cell-cell adhesion	-0.019	0.061	-9999	-10000	0	0
WASF2	-0.007	0.021	-9999	-10000	0	0
Rap1/GTP	-0.025	0.081	-9999	-10000	0	0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin	-0.045	0.15	-9999	-0.55	53	53
CCND1	0.026	0.091	-9999	-0.35	42	42
VAV2	0.026	0.14	-9999	-0.53	44	44
RAP1/GDP	-0.022	0.082	-9999	-10000	0	0
adherens junction assembly	0.011	0.14	-9999	-0.58	44	44
homophilic cell adhesion	0	0	-9999	-10000	0	0
ABI1	0.016	0	-9999	-10000	0	0
PIP5K1C	0.014	0.041	-9999	-0.85	2	2
regulation of heterotypic cell-cell adhesion	-0.043	0.14	-9999	-1	7	7
E-cadherin/beta catenin	-0.038	0.12	-9999	-0.41	82	82
mol:GTP	0	0	-9999	-10000	0	0
SRC	0.009	0.15	-9999	-0.6	44	44
PIK3CA	0.01	0.071	-9999	-0.85	6	6
Rac1/GTP	-0.035	0.1	-9999	-0.65	9	9
E-cadherin/beta catenin/alpha catenin	-0.044	0.14	-9999	-0.56	44	44
ITGAE	0.015	0.029	-9999	-0.85	1	1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.042	0.14	-9999	-0.64	44	44

×

FoxO family signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G6PC	-0.31	0.58	-9999	-1.5	147	147
PLK1	0.063	0.24	-9999	-1.1	17	17
CDKN1B	0.093	0.13	-9999	-0.38	3	3
FOXO3	0.073	0.2	-9999	-0.84	16	16
KAT2B	0.026	0.035	-9999	-0.9	1	1
FOXO1/SIRT1	-0.088	0.16	-9999	-0.56	5	5
CAT	0.075	0.2	-9999	-1	12	12
CTNNB1	0.016	0	-9999	-10000	0	0
AKT1	0.014	0.041	-9999	-0.86	1	1
FOXO1	-0.077	0.19	-9999	-0.42	147	147
MAPK10	0.032	0.086	-9999	-0.5	22	22
mol:GTP	0.003	0.001	-9999	-10000	0	0
FOXO4	0.11	0.066	-9999	-0.51	1	1
response to oxidative stress	-0.002	0.033	-9999	-10000	0	0
FOXO3A/SIRT1	0.038	0.16	-9999	-0.77	13	13
XPO1	0.017	0	-9999	-10000	0	0
EP300	0.002	0.047	-9999	-0.87	2	2
BCL2L11	0.038	0.038	-9999	-10000	0	0
FOXO1/SKP2	-0.067	0.18	-9999	-0.55	9	9
mol:GDP	-0.002	0.033	-9999	-10000	0	0
RAN	0.018	0.001	-9999	-10000	0	0
GADD45A	0.14	0.088	-9999	-0.63	1	1
YWHAQ	0.016	0	-9999	-10000	0	0
FOXO1/14-3-3 family	0.01	0.098	-9999	-0.48	2	2
MST1	-0.019	0.19	-9999	-0.75	53	53
CSNK1D	0.016	0	-9999	-10000	0	0
CSNK1E	0.016	0	-9999	-10000	0	0
FOXO4/14-3-3 family	-0.011	0.13	-9999	-10000	0	0
YWHAB	0.016	0	-9999	-10000	0	0
MAPK8	0.039	0.062	-9999	-0.49	11	11
MAPK9	0.045	0.015	-9999	-10000	0	0
YWHAG	0.016	0	-9999	-10000	0	0
YWHAE	0.016	0	-9999	-10000	0	0
YWHAZ	0.016	0	-9999	-10000	0	0
SIRT1	0.017	0.038	-9999	-0.84	1	1
SOD2	0.094	0.17	-9999	-0.73	11	11
RBL2	0.099	0.15	-9999	-1.2	3	3
RAL/GDP	0.024	0.024	-9999	-10000	0	0
CHUK	0.026	0.033	-9999	-0.83	1	1
Ran/GTP	0.018	0.003	-9999	-10000	0	0
CSNK1G2	0.013	0.05	-9999	-0.85	3	3
RAL/GTP	0.038	0.021	-9999	-10000	0	0
CSNK1G1	0.016	0	-9999	-10000	0	0
FASLG	-0.15	0.5	-9999	-1.1	153	153
SKP2	0.012	0.055	-9999	-0.8	4	4
USP7	0.018	0.001	-9999	-10000	0	0
IKBKB	0.027	0.016	-9999	-10000	0	0
CCNB1	0.074	0.2	-9999	-0.84	20	20
FOXO1-3a-4/beta catenin	-0.011	0.088	-9999	-0.43	7	7
proteasomal ubiquitin-dependent protein catabolic process	-0.066	0.18	-9999	-0.54	9	9
CSNK1A1	0.016	0	-9999	-10000	0	0
SGK1	0.004	0.14	-9999	-0.84	24	24
CSNK1G3	0.016	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.031	0.005	-9999	-10000	0	0
ZFAND5	0.12	0.062	-9999	-10000	0	0
SFN	-0.23	0.35	-9999	-0.72	299	299
CDK2	-0.006	0.036	-9999	-10000	0	0
FOXO3A/14-3-3	0.006	0.13	-9999	-0.44	9	9
CREBBP	-0.006	0.036	-9999	-10000	0	0
FBXO32	0.073	0.2	-9999	-0.8	17	17
BCL6	0.097	0.16	-9999	-1.1	6	6
RALB	0.018	0.001	-9999	-10000	0	0
RALA	0.018	0.001	-9999	-10000	0	0
YWHAH	0.016	0	-9999	-10000	0	0

×

Hedgehog signaling events mediated by Gli proteins

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.016	0.001	-9999	-10000	0	0
HDAC2	0.016	0.001	-9999	-10000	0	0
GNB1/GNG2	-0.032	0.13	-9999	-0.55	51	51
forebrain development	-0.023	0.19	-9999	-0.57	52	52
GNAO1	-0.054	0.22	-9999	-0.76	79	79
SMO/beta Arrestin2	0.011	0.092	-9999	-0.62	18	18
SMO	-0.002	0.12	-9999	-0.82	18	18
ARRB2	0.015	0.007	-9999	-10000	0	0
GLI3/SPOP	0.043	0.091	-9999	-0.64	4	4
mol:GTP	0	0.003	-9999	-10000	0	0
GSK3B	0.016	0	-9999	-10000	0	0
GNAI2	0.013	0.03	-9999	-0.85	1	1
SIN3/HDAC complex	-0.012	0.1	-9999	-0.51	33	33
GNAI1	0.003	0.1	-9999	-0.85	12	12
XPO1	0.017	0.008	-9999	-10000	0	0
GLI1/Su(fu)	-0.057	0.14	-9999	-0.93	11	11
SAP30	-0.014	0.16	-9999	-0.85	31	31
mol:GDP	-0.002	0.12	-9999	-0.81	18	18
MIM/GLI2A	0.005	0.1	-9999	-0.75	16	16
IFT88	0.01	0.071	-9999	-0.85	6	6
GNAI3	0.015	0.006	-9999	-10000	0	0
GLI2	0.02	0.091	-9999	-10000	0	0
GLI3	0.035	0.096	-9999	-0.49	12	12
CSNK1D	0.016	0	-9999	-10000	0	0
CSNK1E	0.016	0	-9999	-10000	0	0
SAP18	0.016	0.001	-9999	-10000	0	0
embryonic digit morphogenesis	0.01	0.071	-9999	-0.85	6	6
GNG2	-0.016	0.16	-9999	-0.85	33	33
Gi family/GTP	0	0.13	-9999	-0.4	57	57
SIN3B	0.014	0.041	-9999	-0.85	2	2
SIN3A	0.016	0.001	-9999	-10000	0	0
GLI3/Su(fu)	0.048	0.085	-9999	-0.65	4	4
GLI2/Su(fu)	0.029	0.089	-9999	-10000	0	0
FOXA2	-0.12	0.29	-9999	-1.1	49	49
neural tube patterning	-0.023	0.19	-9999	-0.57	52	52
SPOP	0.016	0	-9999	-10000	0	0
Su(fu)/PIAS1	0.03	0.045	-9999	-0.48	1	1
GNB1	0.016	0	-9999	-10000	0	0
CSNK1G2	0.013	0.05	-9999	-0.85	3	3
CSNK1G3	0.016	0	-9999	-10000	0	0
MTSS1	0.005	0.1	-9999	-0.75	16	16
embryonic limb morphogenesis	-0.023	0.19	-9999	-0.57	52	52
SUFU	0.026	0.049	-9999	-0.53	1	1
LGALS3	-0.023	0.16	-9999	-0.68	50	50
catabolic process	0.049	0.11	-9999	-0.49	8	8
GLI3A/CBP	-0.017	0.12	-9999	-0.38	65	65
KIF3A	0.016	0	-9999	-10000	0	0
GLI1	-0.024	0.2	-9999	-0.59	52	52
RAB23	0.015	0.022	-9999	-0.65	1	1
CSNK1A1	0.016	0	-9999	-10000	0	0
IFT172	0.015	0.029	-9999	-0.85	1	1
RBBP7	0.016	0.001	-9999	-10000	0	0
Su(fu)/Galectin3	0.007	0.11	-9999	-0.57	13	13
GNAZ	0.006	0.085	-9999	-0.79	10	10
RBBP4	0.015	0.029	-9999	-0.85	1	1
CSNK1G1	0.016	0	-9999	-10000	0	0
PIAS1	0.016	0	-9999	-10000	0	0
PRKACA	0.016	0	-9999	-10000	0	0
GLI2/SPOP	0.026	0.085	-9999	-10000	0	0
STK36	0.016	0.03	-9999	-0.85	1	1
Gi family/GNB1/GNG2/GDP	0.002	0.14	-9999	-0.57	28	28
PTCH1	-0.011	0.18	-9999	-0.9	11	11
MIM/GLI1	-0.049	0.24	-9999	-0.65	66	66
CREBBP	-0.017	0.12	-9999	-0.38	65	65
Su(fu)/SIN3/HDAC complex	0.051	0.061	-9999	-10000	0	0

×

Insulin Pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CBL/APS/CAP	-0.038	0.13	-9999	-0.79	6	6
TC10/GTP	-0.023	0.1	-9999	-0.81	2	2
Insulin Receptor/Insulin/IRS1/Shp2	-0.018	0.089	-9999	-0.55	14	14
HRAS	0.012	0.059	-9999	-0.77	5	5
APS homodimer	0	0.12	-9999	-0.82	17	17
GRB14	-0.087	0.25	-9999	-0.7	128	128
FOXO3	-0.029	0.13	-9999	-0.83	23	23
AKT1	-0.006	0.17	-9999	-0.67	19	19
INSR	0.016	0.041	-9999	-0.84	2	2
Insulin Receptor/Insulin	-0.002	0.04	-9999	-0.86	1	1
mol:GTP	0	0	-9999	-10000	0	0
GRB10	0.014	0.041	-9999	-0.85	2	2
SORBS1	-0.013	0.16	-9999	-0.85	30	30
CRK	0.015	0.022	-9999	-0.65	1	1
PTPN1	0.042	0.042	-9999	-0.84	1	1
CAV1	-0.043	0.19	-9999	-0.52	107	107
CBL/APS/CAP/Crk-II/C3G	-0.026	0.11	-9999	-0.5	45	45
Insulin Receptor/Insulin/IRS1/NCK2	-0.017	0.087	-9999	-0.55	13	13
mol:GDP	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.021	0.095	-9999	-0.52	21	21
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B	0.038	0.064	-9999	-0.76	2	2
RPS6KB1	0.006	0.15	-9999	-0.59	19	19
PARD6A	0.007	0.082	-9999	-0.72	11	11
CBL	0.015	0.029	-9999	-0.85	1	1
tumor necrosis factor-mediated signaling pathway	0	0	-9999	-10000	0	0
DOK1	-0.006	0.083	-9999	-1	6	6
PIK3R1	0.011	0.066	-9999	-0.78	6	6
Insulin Receptor/Insuli/IRS1/GRB2/Shc	-0.053	0.13	-9999	-0.61	19	19
HRAS/GTP	-0.018	0.078	-9999	-0.65	2	2
Insulin Receptor	0.016	0.041	-9999	-0.84	2	2
Insulin Receptor/Insuli/IRS1/GRB2/SHC	-0.016	0.081	-9999	-0.52	12	12
PRKCI	-0.022	0.085	-9999	-0.75	10	10
Insulin Receptor/Insulin/GRB14/PDK1	-0.066	0.16	-9999	-0.75	19	19
SHC1	0.015	0.022	-9999	-0.65	1	1
negative regulation of MAPKKK cascade	-0.008	0.086	-9999	-0.84	9	9
PI3K	-0.021	0.096	-9999	-0.53	21	21
NCK2	0.016	0	-9999	-10000	0	0
RHOQ	0.016	0	-9999	-10000	0	0
mol:H2O2	0	0.004	-9999	-10000	0	0
HRAS/GDP	-0.003	0.045	-9999	-0.59	5	5
AKT2	-0.006	0.17	-9999	-0.67	19	19
PRKCZ	-0.028	0.12	-9999	-0.86	16	16
SH2B2	0	0.12	-9999	-0.82	17	17
SHC/SHIP	0.022	0.097	-9999	-0.5	19	19
F2RL2	-0.12	0.3	-9999	-0.77	152	152
TRIP10	0.006	0.091	-9999	-0.85	10	10
Insulin Receptor/Insulin/Shc	-0.003	0.033	-9999	-0.46	3	3
TC10/GTP/CIP4/Exocyst	-0.006	0.061	-9999	-0.57	10	10
Insulin Receptor/Insulin/SHC/GRB2/Sos1	-0.002	0.03	-9999	-10000	0	0
RAPGEF1	0.016	0	-9999	-10000	0	0
RASA1	0.013	0.05	-9999	-0.85	3	3
NCK1	0.014	0.041	-9999	-0.85	2	2
CBL/APS/CAP/Crk-II	-0.028	0.12	-9999	-0.53	45	45
TC10/GDP	0	0	-9999	-10000	0	0
Insulin Receptor/Insulin/SHC/GRB10	-0.004	0.041	-9999	-0.51	4	4
INPP5D	0.013	0.1	-9999	-0.53	20	20
SOS1	0.016	0	-9999	-10000	0	0
SGK1	-0.034	0.18	-9999	-1.2	23	23
mol:cAMP	0	0	-9999	-10000	0	0
PTPN11	0.015	0.029	-9999	-0.85	1	1
IRS1	-0.01	0.14	-9999	-0.72	31	31
p62DOK/RasGAP	-0.008	0.087	-9999	-0.86	9	9
INS	0.002	0.038	-9999	-0.64	3	3
mol:PI-3-4-P2	0.013	0.1	-9999	-0.52	20	20
GRB2	0.016	0	-9999	-10000	0	0
EIF4EBP1	-0.007	0.18	-9999	-0.68	32	32
PTPRA	0.018	0.003	-9999	-10000	0	0
PIK3CA	0.01	0.071	-9999	-0.85	6	6
TC10/GTP/CIP4	-0.006	0.061	-9999	-0.57	10	10
PDPK1	0.014	0.041	-9999	-0.85	2	2
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos	0.031	0.06	-9999	-0.56	1	1
Insulin Receptor/Insulin/IRS1	-0.018	0.089	-9999	-0.56	13	13
Insulin Receptor/Insulin/IRS3	-0.003	0.041	-9999	-0.54	5	5
Par3/Par6	-0.083	0.19	-9999	-0.53	101	101

×

Rapid glucocorticoid signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma	-0.031	0.12	-10000	0	-0.45	60	60
MAPK9	0.011	0	-10000	0	-10000	0	0
adrenocorticotropin secretion	-0.019	0.11	-10000	0	-0.49	43	43
GNB1/GNG2	-0.021	0.11	-10000	0	-0.57	33	33
GNB1	0.016	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	0.011	0	-10000	0	-10000	0	0
Gs family/GTP	-0.013	0.077	-10000	0	-0.44	27	27
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	0.003	0.018	0.1	27	-10000	0	27
GNAL	-0.006	0.13	-10000	0	-0.72	27	27
GNG2	-0.016	0.16	-10000	0	-0.85	33	33
CRH	-0.026	0.14	-10000	0	-0.65	43	43
mol:cortisol	0	0	-10000	0	-10000	0	0
MAPK8	0.005	0.053	-10000	0	-0.47	11	11
MAPK11	0.003	0.061	-10000	0	-0.46	15	15

×

Aurora C signaling

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
INCENP	0.014	0.041	-9999	-0.85	2	2
Aurora C/Aurora B/INCENP	-0.036	0.12	-9999	-0.54	24	24
metaphase	0	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
H3F3B	-0.01	0.032	-9999	-10000	0	0
AURKB	-0.03	0.18	-9999	-0.71	57	57
AURKC	0.001	0.1	-9999	-0.7	19	19

×

PLK1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
regulation of centriole-centriole cohesion	-0.004	0.052	0.23	39	-10000	0	39
BUB1B	0.016	0.077	-10000	0	-0.39	27	27
PLK1	0.019	0.03	-10000	0	-0.18	11	11
PLK1S1	0.018	0.015	-10000	0	-10000	0	0
KIF2A	0.021	0.065	-10000	0	-0.42	15	15
regulation of mitotic centrosome separation	0.019	0.029	-10000	0	-0.18	11	11
GOLGA2	0.016	0	-10000	0	-10000	0	0
Hec1/SPC24	-0.012	0.17	-10000	0	-0.52	79	79
WEE1	0.025	0.039	-10000	0	-10000	0	0
cytokinesis	-0.005	0.16	-10000	0	-0.59	49	49
PP2A-alpha B56	0.022	0.11	-10000	0	-0.75	12	12
AURKA	0.017	0.027	-10000	0	-0.2	10	10
PICH/PLK1	0.026	0.12	-10000	0	-0.63	22	22
CENPE	0.005	0.11	-10000	0	-0.46	47	47
RhoA/GTP	0	0	-10000	0	-10000	0	0
positive regulation of microtubule depolymerization	0.021	0.064	-10000	0	-0.42	15	15
PPP2CA	0.016	0	-10000	0	-10000	0	0
FZR1	0.014	0.041	-10000	0	-0.85	2	2
TPX2	0.01	0.051	-10000	0	-0.23	35	35
PAK1	0.016	0.001	-10000	0	-10000	0	0
SPC24	-0.021	0.16	-10000	0	-0.74	43	43
FBXW11	0.016	0	-10000	0	-10000	0	0
CLSPN	0.005	0.07	-10000	0	-0.31	40	40
GORASP1	0.016	0	-10000	0	-10000	0	0
metaphase	0	0.003	-10000	0	-0.017	30	30
mol:GTP	0	0	-10000	0	-10000	0	0
NLP	0.011	0.015	-10000	0	-0.089	9	9
G2 phase of mitotic cell cycle	0	0.001	0.02	1	-0.011	8	9
STAG2	0.012	0.058	-10000	0	-0.85	4	4
GRASP65/GM130/RAB1/GTP	0.001	0.007	-10000	0	-10000	0	0
spindle elongation	0.019	0.029	-10000	0	-0.18	11	11
ODF2	0.015	0.029	-10000	0	-0.86	1	1
BUB1	-0.022	0.11	-10000	0	-0.84	12	12
TPT1	0.018	0.015	-10000	0	-10000	0	0
CDC25C	-0.003	0.093	-10000	0	-0.33	56	56
CDC25B	0.01	0.068	-10000	0	-0.66	9	9
SGOL1	0.004	0.052	-10000	0	-0.24	39	39
RHOA	0.016	0	-10000	0	-10000	0	0
CCNB1/CDK1	-0.012	0.07	-10000	0	-0.47	16	16
CDC14B	0.015	0.002	-10000	0	-10000	0	0
CDC20	-0.012	0.14	-10000	0	-0.67	36	36
PLK1/PBIP1	-0.007	0.041	-10000	0	-0.48	5	5
mitosis	0	0.003	0.03	3	-10000	0	3
FBXO5	0.024	0.028	-10000	0	-0.36	1	1
CDC2	0.001	0.003	-10000	0	-0.018	19	19
NDC80	-0.028	0.19	-10000	0	-0.81	47	47
metaphase plate congression	0.018	0.019	-10000	0	-10000	0	0
ERCC6L	-0.019	0.1	-10000	0	-0.65	19	19
NLP/gamma Tubulin	0.015	0.02	-10000	0	-0.2	3	3
microtubule cytoskeleton organization	0.018	0.015	-10000	0	-10000	0	0
G2/M transition DNA damage checkpoint	0	0.001	-10000	0	-10000	0	0
PPP1R12A	0.016	0.001	-10000	0	-10000	0	0
interphase	0	0.001	-10000	0	-10000	0	0
PLK1/PRC1-2	-0.001	0.15	-10000	0	-0.49	66	66
GRASP65/GM130/RAB1/GTP/PLK1	-0.002	0.014	-10000	0	-10000	0	0
RAB1A	0.016	0	-10000	0	-10000	0	0
prophase	0	0	-10000	0	-10000	0	0
Aurora A/BORA	0.024	0.023	-10000	0	-10000	0	0
mitotic prometaphase	0	0.002	-10000	0	-0.012	8	8
proteasomal ubiquitin-dependent protein catabolic process	0.038	0.043	-10000	0	-0.56	2	2
microtubule-based process	-0.006	0.13	-10000	0	-0.47	64	64
Golgi organization	0.019	0.029	-10000	0	-0.18	11	11
Cohesin/SA2	-0.006	0.039	-10000	0	-0.49	4	4
PPP1CB/MYPT1	0	0.001	-10000	0	-10000	0	0
KIF20A	-0.038	0.2	-10000	0	-0.73	64	64
APC/C/CDC20	0.01	0.098	-10000	0	-0.46	36	36
PPP2R1A	0.015	0.029	-10000	0	-0.85	1	1
chromosome segregation	-0.006	0.041	-10000	0	-0.47	5	5
PRC1	0.007	0.081	-10000	0	-0.75	10	10
ECT2	0.025	0.047	-10000	0	-0.46	6	6
C13orf34	0.024	0.023	-10000	0	-10000	0	0
NUDC	0.018	0.02	-10000	0	-10000	0	0
regulation of attachment of spindle microtubules to kinetochore	0.016	0.076	-10000	0	-0.39	27	27
spindle assembly	0.019	0.026	-10000	0	-0.16	10	10
spindle stabilization	0.018	0.015	-10000	0	-10000	0	0
APC/C/HCDH1	0.021	0.028	-10000	0	-0.58	2	2
MKLP2/PLK1	-0.006	0.13	-10000	0	-0.47	64	64
CCNB1	0.005	0.089	-10000	0	-0.67	15	15
PPP1CB	0.016	0.001	-10000	0	-10000	0	0
BTRC	0.016	0	-10000	0	-10000	0	0
ROCK2	0.01	0.1	-10000	0	-0.53	29	29
TUBG1	0.017	0.024	-10000	0	-0.29	3	3
G2/M transition of mitotic cell cycle	-0.012	0.068	-10000	0	-0.46	16	16
MLF1IP	0.011	0.052	-10000	0	-0.67	5	5
INCENP	0.014	0.041	-10000	0	-0.85	2	2

×

Signaling events mediated by HDAC Class III

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EP300	0.014	0.041	-10000	0	-0.85	2	2
HDAC4	0.015	0.029	-10000	0	-0.85	1	1
induction of apoptosis	0	0	-10000	0	-10000	0	0
regulation of S phase of mitotic cell cycle	-0.024	0.038	0.52	4	-10000	0	4
CDKN1A	-0.007	0.083	-10000	0	-1	6	6
KAT2B	0.015	0.029	-10000	0	-0.85	1	1
BAX	0.014	0.041	-10000	0	-0.85	2	2
FOXO3	0.001	0.03	0.63	2	-10000	0	2
FOXO1	0.012	0.055	-10000	0	-0.65	6	6
FOXO4	0.028	0.019	-10000	0	-0.37	2	2
response to UV	0	0	-10000	0	-10000	0	0
XRCC6	0.016	0	-10000	0	-10000	0	0
TAT	-0.025	0.15	-10000	0	-0.65	50	50
mol:Lysophosphatidic acid	0	0	-10000	0	-10000	0	0
MYOD1	0.007	0.075	-10000	0	-0.49	20	20
PPARGC1A	-0.071	0.25	-10000	0	-0.75	102	102
FHL2	-0.05	0.23	-10000	0	-0.83	69	69
response to nutrient levels	0	0	-10000	0	-10000	0	0
KU70/SIRT1	0	0.026	-10000	0	-0.65	1	1
HIST2H4A	0.024	0.038	-10000	0	-0.52	4	4
SIRT1/FOXO3a	0.001	0.02	0.35	1	-0.32	1	2
SIRT1	0.001	0.034	-10000	0	-0.85	1	1
response to hypoxia	0	0	-10000	0	-10000	0	0
SIRT1/MEF2D/HDAC4	0	0.03	-10000	0	-0.56	2	2
SIRT1/Histone H1b	-0.006	0.047	-10000	0	-0.84	1	1
apoptosis	0.001	0.035	0.56	3	-10000	0	3
SIRT1/PGC1A	-0.056	0.16	-10000	0	-0.49	103	103
p53/SIRT1	0.002	0.048	0.45	6	-0.65	2	8
SIRT1/FOXO4	0	0.034	-10000	0	-0.84	1	1
FOXO1/FHL2/SIRT1	-0.042	0.15	-10000	0	-0.55	64	64
HIST1H1E	0.019	0.05	-10000	0	-0.38	2	2
SIRT1/p300	-0.001	0.047	-10000	0	-0.92	2	2
muscle cell differentiation	0.009	0.065	0.42	21	-10000	0	21
TP53	0.001	0.034	-10000	0	-0.85	1	1
KU70/SIRT1/BAX	-0.001	0.035	-10000	0	-0.56	3	3
CREBBP	0.016	0	-10000	0	-10000	0	0
MEF2D	0.016	0	-10000	0	-10000	0	0
HIV-1 Tat/SIRT1	-0.027	0.11	-10000	0	-0.48	51	51
ACSS2	0.019	0.063	-10000	0	-0.49	13	13
SIRT1/PCAF/MYOD	-0.009	0.065	-10000	0	-0.42	21	21

×

ceramide signaling 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K4	0.01	0.14	-10000	0	-0.55	24	24
BAG4	0.011	0.065	-10000	0	-0.85	5	5
BAD	0.022	0.06	-10000	0	-0.51	4	4
NFKBIA	0.016	0	-10000	0	-10000	0	0
BIRC3	-0.066	0.25	-10000	0	-0.81	89	89
BAX	0.022	0.056	-10000	0	-0.64	2	2
EnzymeConsortium:3.1.4.12	0.007	0.035	-10000	0	-0.12	25	25
IKBKB	0.019	0.13	-10000	0	-0.55	19	19
MAP2K2	0.031	0.083	-10000	0	-0.44	18	18
MAP2K1	0.032	0.077	-10000	0	-0.43	15	15
SMPD1	0.014	0.036	-10000	0	-0.17	2	2
GO:0005551	0	0	-10000	0	-10000	0	0
FADD/Caspase 8	0.02	0.14	-10000	0	-0.58	17	17
MAP2K4	0.031	0.049	-10000	0	-0.34	1	1
protein ubiquitination	0.021	0.14	-10000	0	-0.55	21	21
EnzymeConsortium:2.7.1.37	0.037	0.083	-10000	0	-0.44	16	16
response to UV	0	0.001	-10000	0	-0.003	16	16
RAF1	0.025	0.08	-10000	0	-0.46	15	15
CRADD	0.016	0	-10000	0	-10000	0	0
mol:ceramide	0.015	0.05	-10000	0	-0.17	21	21
I-kappa-B-alpha/RELA/p50/ubiquitin	0	0	-10000	0	-10000	0	0
MADD	0.016	0	-10000	0	-10000	0	0
MAP3K1	0.023	0.05	-10000	0	-0.31	2	2
TRADD	0.015	0.029	-10000	0	-0.85	1	1
RELA/p50	0.016	0	-10000	0	-10000	0	0
MAPK3	0.035	0.081	-10000	0	-0.44	16	16
MAPK1	0.035	0.078	-10000	0	-0.42	16	16
p50/RELA/I-kappa-B-alpha	0	0	-10000	0	-10000	0	0
FADD	0.01	0.14	-10000	0	-0.55	22	22
KSR1	0.016	0.083	-10000	0	-0.47	17	17
MAPK8	0.034	0.068	-10000	0	-0.4	12	12
TRAF2	0.014	0.041	-10000	0	-0.85	2	2
response to radiation	0	0	-10000	0	-0.003	1	1
CHUK	0.019	0.14	-10000	0	-0.56	20	20
TNF R/SODD	-0.004	0.049	-10000	0	-0.65	5	5
TNF	-0.062	0.23	-10000	0	-0.75	90	90
CYCS	0.023	0.063	0.16	10	-0.39	5	15
IKBKG	0.018	0.14	-10000	0	-0.57	21	21
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD	0.001	0.15	-10000	0	-0.58	23	23
RELA	0.016	0	-10000	0	-10000	0	0
RIPK1	0.016	0.001	-10000	0	-10000	0	0
AIFM1	0.025	0.058	0.16	9	-0.51	3	12
TNF/TNF R/SODD	-0.052	0.15	-10000	0	-0.49	95	95
TNFRSF1A	0.016	0.001	-10000	0	-10000	0	0
response to heat	0	0	-10000	0	-0.003	1	1
CASP8	0.024	0.051	-10000	0	-1.1	1	1
NSMAF	0.011	0.14	-10000	0	-0.55	22	22
response to hydrogen peroxide	0	0.001	-10000	0	-0.003	16	16
BCL2	0.002	0.11	-10000	0	-0.85	14	14

×

Atypical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL3/RelA	-0.007	0.064	-9999	-0.6	10	10
FBXW11	0.016	0	-9999	-10000	0	0
NF kappa B1 p50/c-Rel	0.014	0.11	-9999	-0.55	30	30
NF kappa B1 p50/RelA/I kappa B alpha	0.023	0.11	-9999	-0.63	13	13
NFKBIA	-0.005	0.13	-9999	-0.34	85	85
MAPK14	0.016	0	-9999	-10000	0	0
NF kappa B1 p105/p50	0.033	0.02	-9999	-0.56	1	1
ARRB2	0.022	0	-9999	-10000	0	0
REL	-0.012	0.15	-9999	-0.83	29	29
response to oxidative stress	0	0	-9999	-10000	0	0
BCL3/NF kappa B1 p50	0.027	0.062	-9999	-0.52	11	11
response to UV	0	0	-9999	-10000	0	0
NF kappa B1 p105/RelA	0.033	0.02	-9999	-0.56	1	1
PIK3CA	0.01	0.071	-9999	-0.85	6	6
NF kappa B1 p50 dimer	0.025	0.023	-9999	-0.65	1	1
PIK3R1	0.011	0.066	-9999	-0.78	6	6
NFKB1	0.028	0.023	-9999	-0.65	1	1
RELA	0.016	0	-9999	-10000	0	0
positive regulation of anti-apoptosis	0.007	0.11	-9999	-0.53	12	12
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2	0.028	0.11	-9999	-0.63	12	12
SRC	0.015	0.022	-9999	-0.65	1	1
PI3K	-0.008	0.072	-9999	-0.62	12	12
NF kappa B1 p50/RelA	0.006	0.11	-9999	-0.54	12	12
IKBKB	0.016	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.016	0	-9999	-10000	0	0
SYK	-0.001	0.12	-9999	-0.8	19	19
I kappa B alpha/PIK3R1	0.001	0.13	-9999	-0.7	16	16
cell death	0.027	0.11	-9999	-0.59	12	12
NF kappa B1 p105/c-Rel	0.014	0.11	-9999	-0.55	30	30
LCK	-0.08	0.26	-9999	-0.8	104	104
BCL3	0.007	0.085	-9999	-0.79	10	10

×

Signaling events mediated by HDAC Class II

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G beta1gamma2/HDAC5	-0.022	0.11	-10000	0	-0.54	36	36
HDAC3	0.016	0	-10000	0	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	0	0.014	-10000	0	-0.43	1	1
GATA1/HDAC4	-0.017	0.09	-10000	0	-0.48	32	32
GATA1/HDAC5	-0.019	0.095	-10000	0	-0.49	34	34
GATA2/HDAC5	-0.066	0.18	-10000	0	-0.55	106	106
HDAC5/BCL6/BCoR	-0.005	0.058	-10000	0	-0.64	7	7
HDAC9	-0.008	0.14	-10000	0	-0.84	25	25
Glucocorticoid receptor/Hsp90/HDAC6	-0.002	0.035	-10000	0	-0.56	3	3
HDAC4/ANKRA2	-0.001	0.022	-10000	0	-0.65	1	1
HDAC5/YWHAB	-0.002	0.038	-10000	0	-0.65	3	3
NPC/RanGAP1/SUMO1/Ubc9	0.027	0.016	-10000	0	-0.29	2	2
GATA2	-0.07	0.24	-10000	0	-0.73	103	103
HDAC4/RFXANK	-0.003	0.041	-10000	0	-0.61	4	4
BCOR	0.015	0.029	-10000	0	-0.85	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
HDAC10	0.013	0.05	-10000	0	-0.85	3	3
HDAC5	0.013	0.05	-10000	0	-0.85	3	3
GNB1/GNG2	-0.024	0.12	-10000	0	-0.65	33	33
Histones	0.037	0.093	-10000	0	-1.5	2	2
ADRBK1	0.014	0.041	-10000	0	-0.85	2	2
HDAC4	0.015	0.029	-10000	0	-0.85	1	1
XPO1	0.016	0	-10000	0	-10000	0	0
HDAC5/ANKRA2	-0.002	0.038	-10000	0	-0.65	3	3
HDAC4/Ubc9	-0.001	0.022	-10000	0	-0.65	1	1
HDAC7	0.014	0.041	-10000	0	-0.85	2	2
HDAC5/14-3-3 E	-0.002	0.038	-10000	0	-0.65	3	3
TUBA1B	0.016	0	-10000	0	-10000	0	0
HDAC6	0.016	0	-10000	0	-10000	0	0
HDAC5/RFXANK	-0.004	0.062	-10000	0	-0.87	4	4
CAMK4	-0.05	0.23	-10000	0	-0.84	69	69
Tubulin/HDAC6	-0.007	0.055	-10000	0	-0.42	15	15
SUMO1	0.016	0	-10000	0	-10000	0	0
EntrezGene:9972	0	0	-10000	0	-10000	0	0
YWHAB	0.016	0	-10000	0	-10000	0	0
GATA1	-0.01	0.12	-10000	0	-0.65	31	31
EntrezGene:8021	0	0	-10000	0	-10000	0	0
YWHAE	0.016	0	-10000	0	-10000	0	0
NR3C1	0.012	0.055	-10000	0	-0.8	4	4
SUMO1/HDAC4	0.037	0.023	-10000	0	-0.47	1	1
SRF	0.016	0	-10000	0	-10000	0	0
HDAC4/YWHAB	-0.001	0.022	-10000	0	-0.65	1	1
Tubulin	-0.008	0.065	-10000	0	-0.5	15	15
HDAC4/14-3-3 E	-0.001	0.022	-10000	0	-0.65	1	1
GNB1	0.016	0	-10000	0	-10000	0	0
RANGAP1	0.013	0.047	-10000	0	-0.78	3	3
BCL6/BCoR	-0.004	0.055	-10000	0	-0.78	4	4
HDAC4/HDAC3/SMRT (N-CoR2)	-0.002	0.033	-10000	0	-0.56	3	3
HDAC4/SRF	-0.044	0.15	-10000	0	-0.56	66	66
HDAC4/ER alpha	-0.042	0.16	-10000	0	-0.63	59	59
EntrezGene:23225	0	0	-10000	0	-10000	0	0
positive regulation of chromatin silencing	0.037	0.09	-10000	0	-1.4	2	2
cell motility	-0.007	0.055	-10000	0	-0.42	15	15
EntrezGene:23636	0	0	-10000	0	-10000	0	0
UBE2I	0.016	0	-10000	0	-10000	0	0
HDAC7/HDAC3	-0.001	0.031	-10000	0	-0.65	2	2
BCL6	0.012	0.058	-10000	0	-0.85	4	4
HDAC4/CaMK II delta B	0.015	0.029	-10000	0	-0.85	1	1
Hsp90/HDAC6	0	0	-10000	0	-10000	0	0
ESR1	-0.038	0.21	-10000	0	-0.82	58	58
HDAC6/HDAC11	-0.003	0.041	-10000	0	-0.55	5	5
Ran/GTP/Exportin 1	-0.001	0.012	-10000	0	-10000	0	0
NPC	0	0	-10000	0	-10000	0	0
MEF2C	-0.024	0.18	-10000	0	-0.84	41	41
RAN	0.016	0	-10000	0	-10000	0	0
HDAC4/MEF2C	-0.023	0.1	-10000	0	-0.48	43	43
GNG2	-0.016	0.16	-10000	0	-0.85	33	33
NCOR2	0.014	0.041	-10000	0	-0.85	2	2
TUBB2A	0.004	0.09	-10000	0	-0.68	15	15
HDAC11	0.012	0.056	-10000	0	-0.73	5	5
HSP90AA1	0.016	0	-10000	0	-10000	0	0
RANBP2	0.016	0	-10000	0	-10000	0	0
ANKRA2	0.016	0	-10000	0	-10000	0	0
RFXANK	0.013	0.047	-10000	0	-0.78	3	3
nuclear import	0.002	0.03	0.45	4	-10000	0	4

×

Retinoic acid receptors-mediated signaling

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
HDAC1	0.016	0	-10000	0	-10000	0	0
HDAC3	0.016	0	-10000	0	-10000	0	0
VDR	-0.028	0.17	-10000	0	-0.66	58	58
Cbp/p300/PCAF	-0.002	0.041	-10000	0	-0.82	2	2
EP300	0.014	0.041	-10000	0	-0.85	2	2
RARs/AIB1/Cbp/p300/PCAF/9cRA	0.047	0.048	-10000	0	-0.52	2	2
KAT2B	0.015	0.029	-10000	0	-0.85	1	1
MAPK14	0.016	0	-10000	0	-10000	0	0
AKT1	0.025	0.06	0.25	9	-0.36	9	18
RAR alpha/9cRA/Cyclin H	-0.014	0.053	-10000	0	-0.47	5	5
mol:9cRA	0	0	-10000	0	-10000	0	0
RARs/Src-1/Cbp/p300/PCAF/9cRA	0.044	0.05	-10000	0	-0.51	2	2
CDC2	0.001	0.001	-10000	0	-10000	0	0
response to UV	0.002	0.002	-10000	0	-10000	0	0
RAR alpha/Jnk1	-0.009	0.094	-10000	0	-0.68	13	13
NCOR2	0.014	0.041	-10000	0	-0.85	2	2
VDR/VDR/Vit D3	-0.033	0.12	-10000	0	-0.5	58	58
RXRs/RARs/NRIP1/9cRA	0.045	0.097	-10000	0	-0.58	6	6
NCOA2	-0.039	0.21	-10000	0	-0.85	57	57
NCOA3	0.016	0	-10000	0	-10000	0	0
NCOA1	0.016	0	-10000	0	-10000	0	0
VDR/VDR/DNA	-0.028	0.17	-10000	0	-0.66	58	58
RARG	0.015	0.047	-10000	0	-0.78	3	3
RAR gamma1/9cRA	-0.002	0.03	-10000	0	-0.52	3	3
MAPK3	0.016	0.029	-10000	0	-0.86	1	1
MAPK1	0.015	0.029	-10000	0	-0.85	1	1
MAPK8	0.007	0.096	-10000	0	-0.85	11	11
mol:Vit D3	0	0	-10000	0	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.042	0.1	-10000	0	-0.44	22	22
RARA	0.014	0.076	-10000	0	-0.38	15	15
negative regulation of phosphoinositide 3-kinase cascade	0	0	-10000	0	-10000	0	0
RARs/TIF2/Cbp/p300/PCAF/9cRA	0.023	0.11	-10000	0	-0.44	22	22
PRKCA	0.019	0.032	-10000	0	-0.65	2	2
RXRs/RARs/NRIP1/9cRA/HDAC1	0.038	0.095	-10000	0	-0.5	11	11
RXRG	-0.003	0.096	-10000	0	-0.28	96	96
RXRA	0.024	0.074	-10000	0	-0.45	8	8
RXRB	0.009	0.085	-10000	0	-0.52	2	2
VDR/Vit D3/DNA	-0.033	0.12	-10000	0	-0.5	58	58
RBP1	-0.005	0.13	-10000	0	-0.74	25	25
CRBP1/9-cic-RA	-0.016	0.096	-10000	0	-0.57	25	25
RARB	0.012	0.077	-10000	0	-0.85	7	7
PRKCG	-0.038	0.18	-10000	0	-0.65	68	68
MNAT1	0.016	0	-10000	0	-10000	0	0
RAR alpha/RXRs	0.04	0.094	-10000	0	-0.44	7	7
RXRs/RARs/SMRT(N-CoR2)/9cRA	0.045	0.089	-10000	0	-0.51	5	5
proteasomal ubiquitin-dependent protein catabolic process	0.044	0.064	-10000	0	-0.38	7	7
RXRs/RARs/NRIP1/9cRA/HDAC3	0.038	0.095	-10000	0	-0.5	11	11
positive regulation of DNA binding	-0.014	0.05	-10000	0	-0.44	5	5
NRIP1	0.035	0.12	-10000	0	-1.3	5	5
RXRs/RARs	0.031	0.089	-10000	0	-0.43	11	11
RXRs/RXRs/DNA/9cRA	-0.024	0.073	-10000	0	-0.48	6	6
PRKACA	0.016	0	-10000	0	-10000	0	0
CDK7	0.016	0	-10000	0	-10000	0	0
TFIIH	0	0	-10000	0	-10000	0	0
RAR alpha/9cRA	-0.009	0.037	-10000	0	-10000	0	0
CCNH	0.016	0	-10000	0	-10000	0	0
CREBBP	0.016	0	-10000	0	-10000	0	0
RAR gamma2/9cRA	-0.001	0.023	-10000	0	-10000	0	0

×

Circadian rhythm pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
chromatin modification	-0.007	0.031	-10000	0	-0.58	1	1
CLOCK	-0.012	0.16	-10000	0	-0.84	33	33
TIMELESS/CRY2	0.041	0.047	-10000	0	-10000	0	0
DEC1/BMAL1	-0.003	0.038	-10000	0	-0.57	4	4
ATR	0.015	0.029	-10000	0	-0.85	1	1
NR1D1	0.036	0.088	-10000	0	-1.5	2	2
ARNTL	0.018	0.041	-10000	0	-0.85	2	2
TIMELESS	0.039	0.05	-10000	0	-0.51	1	1
NPAS2	-0.05	0.24	-10000	0	-0.84	73	73
CRY2	0.015	0.022	-10000	0	-0.65	1	1
mol:CO	-0.017	0.009	0.12	4	-10000	0	4
CHEK1	0.016	0	-10000	0	-10000	0	0
mol:HEME	0.017	0.009	-10000	0	-0.12	4	4
PER1	0.012	0.055	-10000	0	-0.8	4	4
BMAL/CLOCK/NPAS2	-0.019	0.2	-10000	0	-0.56	105	105
BMAL1/CLOCK	0.029	0.12	-10000	0	-1	4	4
S phase of mitotic cell cycle	-0.007	0.031	-10000	0	-0.58	1	1
TIMELESS/CHEK1/ATR	-0.007	0.032	-10000	0	-0.59	1	1
mol:NADPH	0.017	0.009	-10000	0	-0.12	4	4
PER1/TIMELESS	0.039	0.059	-10000	0	-0.84	1	1
PER1-2 / CRY1-2	0	0	-10000	0	-10000	0	0
DEC1	0.002	0.032	-10000	0	-0.65	2	2

×

Class I PI3K signaling events mediated by Akt

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
BCL2L1	0.029	0	-10000	0	-10000	0	0
BAD/BCL-XL/YWHAZ	-0.002	0.032	-10000	0	-0.51	3	3
CDKN1B	0.047	0.022	-10000	0	-0.52	1	1
CDKN1A	0.043	0.047	-10000	0	-0.47	7	7
FRAP1	0	0	-10000	0	-10000	0	0
PRKDC	0.016	0	-10000	0	-10000	0	0
FOXO3	0.047	0.022	-10000	0	-0.52	1	1
AKT1	-0.001	0.02	-10000	0	-0.56	1	1
BAD	0.012	0.055	-10000	0	-0.8	4	4
AKT3	0.017	0.051	-10000	0	-0.46	10	10
mol:GTP	0	0	-10000	0	-10000	0	0
FOXO4	0.047	0.022	-10000	0	-0.52	1	1
AKT1/ASK1	-0.002	0.028	-10000	0	-0.46	3	3
BAD/YWHAZ	-0.002	0.035	-10000	0	-0.52	4	4
RICTOR	0.015	0.029	-10000	0	-0.85	1	1
RAF1	0.016	0	-10000	0	-10000	0	0
JNK cascade	0.002	0.027	0.45	3	-10000	0	3
TSC1	0.047	0.022	-10000	0	-0.52	1	1
YWHAZ	0.016	0	-10000	0	-10000	0	0
AKT1/RAF1	0.046	0.022	-10000	0	-0.52	1	1
EP300	0.014	0.041	-10000	0	-0.85	2	2
mol:GDP	0.038	0.022	-10000	0	-0.55	1	1
mol:PI-3-4-5-P3	0	0	-10000	0	-10000	0	0
TSC2	0.045	0.043	-10000	0	-0.63	3	3
YWHAQ	0.016	0	-10000	0	-10000	0	0
TBC1D4	0.027	0.04	-10000	0	-0.39	8	8
MAP3K5	0.014	0.041	-10000	0	-0.85	2	2
MAPKAP1	0.016	0	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.008	0.072	0.34	1	-10000	0	1
YWHAH	0.016	0	-10000	0	-10000	0	0
AKT1S1	0.046	0.036	-10000	0	-0.98	1	1
CASP9	0.047	0.022	-10000	0	-0.52	1	1
YWHAB	0.016	0	-10000	0	-10000	0	0
p27Kip1/KPNA1	0.054	0.021	-10000	0	-0.48	1	1
GBL	0	0	-10000	0	-10000	0	0
PDK1/Src/Hsp90	-0.002	0.03	-10000	0	-0.51	3	3
YWHAE	0.016	0	-10000	0	-10000	0	0
SRC	0.015	0.022	-10000	0	-0.65	1	1
AKT2/p21CIP1	-0.004	0.044	-10000	0	-0.46	7	7
KIAA1303	0	0	-10000	0	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL	0.023	0.006	-10000	0	-10000	0	0
CHUK	0.046	0.027	-10000	0	-0.49	2	2
BAD/BCL-XL	0.06	0.043	-10000	0	-0.67	2	2
mTORC2	-0.001	0.018	-10000	0	-0.53	1	1
AKT2	0.02	0.028	-10000	0	-0.46	3	3
FOXO1-3a-4/14-3-3 family	0.021	0.084	-10000	0	-0.57	1	1
PDPK1	0.014	0.041	-10000	0	-0.85	2	2
MDM2	0.047	0.022	-10000	0	-0.52	1	1
MAPKKK cascade	-0.045	0.021	0.51	1	-10000	0	1
MDM2/Cbp/p300	0.06	0.035	-10000	0	-0.54	3	3
TSC1/TSC2	0.053	0.042	-10000	0	-0.6	3	3
proteasomal ubiquitin-dependent protein catabolic process	-0.002	0.03	-10000	0	-0.51	3	3
glucose import	-0.015	0.15	-10000	0	-0.41	108	108
mTOR/RHEB/GDP/Raptor/GBL/PRAS40	0.04	0.018	-10000	0	-0.44	1	1
response to stress	0	0	-10000	0	-10000	0	0
SLC2A4	-0.015	0.15	-10000	0	-0.41	106	106
GSK3A	0.047	0.022	-10000	0	-0.52	1	1
FOXO1	0.044	0.036	-10000	0	-0.52	1	1
GSK3B	0.047	0.022	-10000	0	-0.52	1	1
SFN	-0.23	0.35	-10000	0	-0.72	299	299
G1/S transition of mitotic cell cycle	0.055	0.021	-10000	0	-0.5	1	1
p27Kip1/14-3-3 family	-0.01	0.1	-10000	0	-10000	0	0
PRKACA	0.016	0	-10000	0	-10000	0	0
KPNA1	0.016	0	-10000	0	-10000	0	0
HSP90AA1	0.016	0	-10000	0	-10000	0	0
YWHAG	0.016	0	-10000	0	-10000	0	0
RHEB	0.016	0	-10000	0	-10000	0	0
CREBBP	0.016	0	-10000	0	-10000	0	0

×

Signaling events mediated by HDAC Class I

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NF kappa B/RelA	-0.042	0.13	-9999	-0.52	48	48
Ran/GTP/Exportin 1/HDAC1	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.021	0.12	-9999	-0.43	48	48
SUMO1	0.016	0	-9999	-10000	0	0
ZFPM1	0.004	0.094	-9999	-0.74	14	14
NPC/RanGAP1/SUMO1/Ubc9	0.027	0.016	-9999	-10000	0	0
FKBP3	0.016	0	-9999	-10000	0	0
Histones	-0.017	0.052	-9999	-10000	0	0
YY1/LSF	0.037	0.037	-9999	-0.69	2	2
SMG5	0.016	0	-9999	-10000	0	0
RAN	0.016	0	-9999	-10000	0	0
I kappa B alpha/HDAC3	0.009	0.11	-9999	-0.37	47	47
I kappa B alpha/HDAC1	0.016	0.076	-9999	-10000	0	0
SAP18	0.016	0	-9999	-10000	0	0
RELA	0.018	0.095	-9999	-0.32	47	47
HDAC1/Smad7	-0.001	0.019	-9999	-0.56	1	1
RANGAP1	0.013	0.047	-9999	-0.78	3	3
HDAC3/TR2	0.016	0.076	-9999	-10000	0	0
NuRD/MBD3 Complex	0.058	0.028	-9999	-0.41	1	1
NF kappa B1 p50/RelA	0.023	0.09	-9999	-0.75	1	1
EntrezGene:23225	0	0	-9999	-10000	0	0
GATA2	-0.07	0.24	-9999	-0.73	103	103
GATA1	-0.01	0.12	-9999	-0.65	31	31
Mad/Max	-0.001	0.023	-9999	-0.48	2	2
NuRD/MBD3 Complex/GATA1/Fog1	0.061	0.058	-9999	-0.5	5	5
RBBP7	0.016	0	-9999	-10000	0	0
NPC	0	0	-9999	-10000	0	0
RBBP4	0.015	0.029	-9999	-0.85	1	1
MAX	0.016	0	-9999	-10000	0	0
EntrezGene:9972	0	0	-9999	-10000	0	0
FBXW11	0.016	0	-9999	-10000	0	0
NFKBIA	0.009	0.084	-9999	-10000	0	0
KAT2B	0.015	0.029	-9999	-0.85	1	1
mol:GTP	0	0	-9999	-10000	0	0
SIN3/HDAC complex	0.044	0.06	-9999	-10000	0	0
SIN3 complex	-0.019	0.097	-9999	-0.51	33	33
SMURF1	0.016	0	-9999	-10000	0	0
CHD3	0.013	0.05	-9999	-0.85	3	3
SAP30	-0.014	0.16	-9999	-0.85	31	31
EntrezGene:23636	0	0	-9999	-10000	0	0
NCOR1	0.015	0.029	-9999	-0.85	1	1
YY1/HDAC3	0.032	0.076	-9999	-0.75	1	1
YY1/HDAC2	0.038	0.032	-9999	-0.84	1	1
YY1/HDAC1	0.038	0.032	-9999	-0.84	1	1
NuRD/MBD2 Complex (MeCP1)	0.06	0.018	-9999	-10000	0	0
PPARG	-0.039	0.12	-9999	-0.46	52	52
HDAC8/hEST1B	0	0	-9999	-10000	0	0
UBE2I	0.016	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.016	0	-9999	-10000	0	0
TNFRSF1A	0.016	0	-9999	-10000	0	0
HDAC3/SMRT (N-CoR2)	0.015	0.081	-9999	-0.64	2	2
MBD3L2	0	0.002	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	-0.001	0.019	-9999	-0.56	1	1
CREBBP	0.016	0	-9999	-10000	0	0
NuRD/MBD3/MBD3L2 Complex	0.062	0.031	-9999	-0.46	1	1
HDAC1	0.016	0	-9999	-10000	0	0
HDAC3	0.009	0.084	-9999	-10000	0	0
HDAC2	0.016	0	-9999	-10000	0	0
YY1	0.037	0.035	-9999	-0.65	2	2
HDAC8	0.016	0	-9999	-10000	0	0
SMAD7	0.015	0.029	-9999	-0.85	1	1
NCOR2	0.014	0.041	-9999	-0.85	2	2
MXD1	0.015	0.032	-9999	-0.65	2	2
STAT3	0.032	0.023	-9999	-0.45	2	2
NFKB1	0.015	0.029	-9999	-0.85	1	1
EntrezGene:8021	0	0	-9999	-10000	0	0
RANBP2	0.016	0	-9999	-10000	0	0
YY1/LSF/HDAC1	-0.002	0.032	-9999	-0.64	2	2
YY1/SAP30/HDAC1	-0.019	0.095	-9999	-0.51	32	32
EP300	0.014	0.041	-9999	-0.85	2	2
STAT3 (dimer non-phopshorylated)	0.032	0.023	-9999	-0.45	2	2
proteasomal ubiquitin-dependent protein catabolic process	0.009	0.084	-9999	-10000	0	0
histone deacetylation	0.06	0.017	-9999	-10000	0	0
STAT3 (dimer non-phopshorylated)/HDAC3	0.028	0.073	-9999	-10000	0	0
nuclear export	0	0	-9999	-10000	0	0
PRKACA	0.016	0	-9999	-10000	0	0
GATAD2B	0.016	0	-9999	-10000	0	0
GATAD2A	0.016	0	-9999	-10000	0	0
GATA2/HDAC3	-0.036	0.17	-9999	-0.46	103	103
GATA1/HDAC1	-0.017	0.087	-9999	-0.48	31	31
GATA1/HDAC3	-0.004	0.1	-9999	-0.53	1	1
CHD4	0.016	0	-9999	-10000	0	0
TNF-alpha/TNFR1A	-0.058	0.17	-9999	-0.57	90	90
SIN3/HDAC complex/Mad/Max	0.051	0.051	-9999	-10000	0	0
NuRD Complex	0.069	0.029	-9999	-10000	0	0
positive regulation of chromatin silencing	-0.017	0.051	-9999	-10000	0	0
SIN3B	0.014	0.041	-9999	-0.85	2	2
MTA2	0.016	0	-9999	-10000	0	0
SIN3A	0.016	0	-9999	-10000	0	0
XPO1	0.016	0	-9999	-10000	0	0
SUMO1/HDAC1	0.037	0.015	-9999	-10000	0	0
HDAC complex	-0.001	0.017	-9999	-0.51	1	1
GATA1/Fog1	-0.025	0.11	-9999	-0.5	45	45
FKBP25/HDAC1/HDAC2	0	0	-9999	-10000	0	0
TNF	-0.062	0.23	-9999	-0.75	90	90
negative regulation of cell growth	0.051	0.05	-9999	-10000	0	0
NuRD/MBD2/PRMT5 Complex	0.06	0.018	-9999	-10000	0	0
Ran/GTP/Exportin 1	-0.001	0.012	-9999	-10000	0	0
NF kappa B/RelA/I kappa B alpha	-0.035	0.11	-9999	-0.45	47	47
SIN3/HDAC complex/NCoR1	0.048	0.051	-9999	-10000	0	0
TFCP2	0.015	0.029	-9999	-0.85	1	1
NR2C1	0.016	0	-9999	-10000	0	0
MBD3	0.011	0.062	-9999	-0.81	5	5
MBD2	0.016	0	-9999	-10000	0	0

×

Canonical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FBXW11	0.02	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.095	0.053	-9999	-10000	0	0
ERC1	0.016	0	-9999	-10000	0	0
RIP2/NOD2	-0.041	0.15	-9999	-0.6	61	61
NFKBIA	0.059	0.018	-9999	-10000	0	0
BIRC2	0.016	0	-9999	-10000	0	0
IKBKB	0.016	0	-9999	-10000	0	0
RIPK2	0.015	0.022	-9999	-0.65	1	1
IKBKG	-0.017	0.063	-9999	-0.47	3	3
IKK complex/A20	-0.047	0.13	-9999	-0.67	15	15
NEMO/A20/RIP2	0.015	0.022	-9999	-0.65	1	1
XPO1	0.016	0	-9999	-10000	0	0
NEMO/ATM	0.044	0.077	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
RAN	0.016	0	-9999	-10000	0	0
Exportin 1/RanGTP	0	0	-9999	-10000	0	0
IKK complex/ELKS	-0.013	0.05	-9999	-10000	0	0
BCL10/MALT1/TRAF6	-0.001	0.019	-9999	-0.56	1	1
NOD2	-0.038	0.2	-9999	-0.79	60	60
NFKB1	0.019	0.029	-9999	-0.84	1	1
RELA	0.02	0	-9999	-10000	0	0
MALT1	0.015	0.029	-9999	-0.85	1	1
cIAP1/UbcH5C	0	0	-9999	-10000	0	0
ATM	0.014	0.041	-9999	-0.85	2	2
TNF/TNFR1A	-0.058	0.17	-9999	-0.57	90	90
TRAF6	0.016	0	-9999	-10000	0	0
PRKCA	0.015	0.032	-9999	-0.65	2	2
CHUK	0.015	0.029	-9999	-0.85	1	1
UBE2D3	0.016	0	-9999	-10000	0	0
TNF	-0.062	0.23	-9999	-0.75	90	90
NF kappa B1 p50/RelA	-0.001	0.018	-9999	-0.55	1	1
BCL10	0.016	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.059	0.018	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.02	0	-9999	-10000	0	0
TNFRSF1A	0.016	0	-9999	-10000	0	0
IKK complex	-0.015	0.056	-9999	-10000	0	0
CYLD	0.016	0	-9999	-10000	0	0
IKK complex/PKC alpha	-0.014	0.053	-9999	-10000	0	0

×

Arf6 downstream pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLAUR	0.024	0.18	-10000	0	-0.81	31	31
regulation of axonogenesis	-0.03	0.045	0.35	7	-10000	0	7
myoblast fusion	-0.01	0.077	0.35	31	-10000	0	31
mol:GTP	-0.007	0.038	-10000	0	-0.26	10	10
regulation of calcium-dependent cell-cell adhesion	-0.028	0.08	0.52	14	-10000	0	14
ARF1/GTP	-0.005	0.026	-10000	0	-10000	0	0
mol:GM1	0.008	0.031	-10000	0	-0.26	2	2
mol:Choline	0.028	0.059	-10000	0	-0.57	7	7
lamellipodium assembly	-0.012	0.071	-10000	0	-0.5	11	11
MAPK3	0.026	0.062	-10000	0	-0.39	11	11
ARF6/GTP/NME1/Tiam1	0.029	0.081	-10000	0	-0.52	14	14
ARF1	0.016	0	-10000	0	-10000	0	0
ARF6/GDP	0.01	0.078	-10000	0	-0.35	31	31
ARF1/GDP	0.022	0.073	-10000	0	-0.49	10	10
ARF6	0.011	0.021	-10000	0	-10000	0	0
RAB11A	0.016	0	-10000	0	-10000	0	0
TIAM1	0.006	0.098	-10000	0	-0.83	12	12
fibronectin binding	0	0	-10000	0	-10000	0	0
MAPK1	0.026	0.062	-10000	0	-0.38	12	12
actin filament bundle formation	0.012	0.066	0.49	10	-10000	0	10
KALRN	-0.014	0.08	-10000	0	-0.46	21	21
RAB11FIP3/RAB11A	-0.001	0.031	-10000	0	-0.65	2	2
RhoA/GDP	-0.012	0.066	-10000	0	-0.5	10	10
NME1	0.016	0.032	-10000	0	-0.65	2	2
Rac1/GDP	-0.012	0.066	-10000	0	-0.5	10	10
substrate adhesion-dependent cell spreading	-0.007	0.038	-10000	0	-0.26	10	10
cortical actin cytoskeleton organization	-0.012	0.071	-10000	0	-0.5	11	11
RAC1	0.016	0	-10000	0	-10000	0	0
liver development	-0.007	0.038	-10000	0	-0.26	10	10
ARF6/GTP	-0.007	0.038	-10000	0	-0.26	10	10
RhoA/GTP	-0.005	0.026	-10000	0	-10000	0	0
mol:GDP	-0.012	0.075	-10000	0	-0.52	11	11
ARF6/GTP/RAB11FIP3/RAB11A	-0.005	0.035	-10000	0	-0.61	2	2
RHOA	0.016	0	-10000	0	-10000	0	0
PLD1	0.022	0.031	-10000	0	-10000	0	0
RAB11FIP3	0.014	0.041	-10000	0	-0.85	2	2
tube morphogenesis	-0.012	0.071	-10000	0	-0.5	11	11
ruffle organization	0.03	0.045	-10000	0	-0.35	7	7
regulation of epithelial cell migration	-0.007	0.038	-10000	0	-0.26	10	10
PLD2	0.017	0.066	-10000	0	-0.64	7	7
PIP5K1A	0.03	0.045	-10000	0	-0.35	7	7
mol:Phosphatidic acid	0.028	0.059	-10000	0	-0.57	7	7
Rac1/GTP	-0.012	0.072	-10000	0	-0.5	11	11

×

Arf6 trafficking events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SLC2A4	-0.068	0.24	-10000	0	-0.71	102	102
CLTC	0.04	0.016	-10000	0	-10000	0	0
calcium ion-dependent exocytosis	0.033	0.02	-10000	0	-10000	0	0
Dynamin 2/GTP	-0.001	0.017	-10000	0	-0.36	2	2
EXOC4	0.016	0	-10000	0	-10000	0	0
CD59	0.036	0.016	-10000	0	-10000	0	0
CPE	-0.055	0.19	-10000	0	-0.52	129	129
CTNNB1	0.016	0	-10000	0	-10000	0	0
membrane fusion	0.032	0.021	-10000	0	-10000	0	0
CTNND1	0.04	0.018	-10000	0	-10000	0	0
DNM2	0.016	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.04	0.023	-10000	0	-0.37	2	2
TSHR	-0.071	0.21	-10000	0	-0.52	152	152
INS	0.014	0.014	-10000	0	-10000	0	0
BIN1	-0.022	0.16	-10000	0	-0.68	48	48
mol:Choline	0.032	0.021	-10000	0	-10000	0	0
growth hormone secretagogue receptor activity	0	0	-10000	0	-10000	0	0
mol:GDP	0.023	0.021	-10000	0	-0.41	2	2
membrane depolarization	0	0	-10000	0	-10000	0	0
ARF6	0.016	0	-10000	0	-10000	0	0
mol:Ca2+	-0.001	0.017	-10000	0	-0.36	2	2
JUP	0.034	0.031	-10000	0	-0.39	1	1
ASAP2/amphiphysin II	-0.023	0.096	-10000	0	-0.52	12	12
ARF6/GTP	0	0	-10000	0	-10000	0	0
CDH1	0.012	0.078	-10000	0	-10000	0	0
clathrin-independent pinocytosis	0	0	-10000	0	-10000	0	0
MAPK8IP3	0.003	0.1	-10000	0	-0.79	14	14
positive regulation of endocytosis	0	0	-10000	0	-10000	0	0
EXOC2	0.016	0	-10000	0	-10000	0	0
substrate adhesion-dependent cell spreading	0.054	0.026	-10000	0	-0.73	1	1
insulin receptor binding	0	0	-10000	0	-10000	0	0
SPAG9	0.016	0	-10000	0	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	0.014	0.046	-10000	0	-10000	0	0
positive regulation of phagocytosis	0.024	0	-10000	0	-10000	0	0
ARF6/GTP/JIP3	-0.008	0.066	-10000	0	-0.53	14	14
ACAP1	0.023	0.041	-10000	0	-0.33	5	5
mol:GTP	0	0	-10000	0	-10000	0	0
CHRM2	0.029	0.015	-10000	0	-10000	0	0
clathrin heavy chain/ACAP1	0.044	0.023	-10000	0	-10000	0	0
JIP4/KLC1	0	0	-10000	0	-10000	0	0
EXOC1	0.016	0	-10000	0	-10000	0	0
exocyst	0.054	0.027	-10000	0	-0.75	1	1
RALA/GTP	0	0	-10000	0	-10000	0	0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex	0	0	-10000	0	-10000	0	0
receptor recycling	0	0	-10000	0	-10000	0	0
CTNNA1	0.04	0.018	-10000	0	-10000	0	0
NME1	0.023	0.021	-10000	0	-0.41	2	2
clathrin coat assembly	0.04	0.016	-10000	0	-10000	0	0
IL2RA	-0.004	0.097	-10000	0	-10000	0	0
VAMP3	0.024	0	-10000	0	-10000	0	0
GLUT4/clathrin heavy chain/ACAP1	-0.04	0.11	-10000	0	-0.43	39	39
EXOC6	0.016	0	-10000	0	-10000	0	0
PLD1	0	0	-10000	0	-10000	0	0
PLD2	-0.003	0.031	-10000	0	-0.35	7	7
EXOC5	0.016	0	-10000	0	-10000	0	0
PIP5K1C	0.04	0.023	-10000	0	-0.37	2	2
SDC1	0.029	0.044	-10000	0	-0.39	1	1
ARF6/GDP	0.022	0.02	-10000	0	-0.41	2	2
EXOC7	0.015	0.029	-10000	0	-0.85	1	1
E-cadherin/beta catenin	-0.015	0.047	-10000	0	-10000	0	0
mol:Phosphatidic acid	0.032	0.021	-10000	0	-10000	0	0
endocytosis	0.023	0.095	0.52	12	-10000	0	12
SCAMP2	0.016	0	-10000	0	-10000	0	0
ADRB2	0.026	0.091	-10000	0	-0.45	11	11
EXOC3	0.015	0.029	-10000	0	-0.85	1	1
ASAP2	0.012	0.058	-10000	0	-0.85	4	4
Dynamin 2/GDP	0.031	0.019	-10000	0	-0.36	2	2
KLC1	0.016	0	-10000	0	-10000	0	0
AVPR2	-0.014	0.15	-10000	0	-0.46	50	50
RALA	0.016	0	-10000	0	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.012	0.04	-10000	0	-10000	0	0

×

Alternative 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
IKK alpha homodimer	-0.021	0.12	-9999	-0.65	29	29
FBXW11	0.016	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.016	0	-9999	-10000	0	0
CHUK	0.015	0.029	-9999	-0.85	1	1
NF kappa B2 p100/RelB	-0.016	0.088	-9999	-0.49	28	28
NFKB1	0.015	0.029	-9999	-0.85	1	1
MAP3K14	-0.011	0.15	-9999	-0.84	28	28
NF kappa B1 p50/RelB	-0.001	0.031	-9999	-0.65	2	2
RELB	0.015	0.029	-9999	-0.85	1	1
NFKB2	0.016	0	-9999	-10000	0	0
NF kappa B2 p52/RelB	-0.001	0.019	-9999	-0.57	1	1
regulation of B cell activation	-0.001	0.019	-9999	-0.57	1	1

×

mTOR signaling pathway

Figure S128. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S128. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GBL	0	0	-10000	0	-10000	0	0
MKNK1	0.016	0	-10000	0	-10000	0	0
mol:PIP3	-0.014	0.073	-10000	0	-0.43	21	21
FRAP1	0.016	0.024	-10000	0	-10000	0	0
AKT1	0.022	0.076	-10000	0	-0.52	11	11
INSR	0.014	0.041	-10000	0	-0.85	2	2
Insulin Receptor/Insulin	-0.003	0.036	-10000	0	-0.48	5	5
mol:GTP	-0.011	0.06	-10000	0	-0.57	5	5
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit	-0.003	0.016	-10000	0	-10000	0	0
TSC2	0.013	0.05	-10000	0	-0.85	3	3
RHEB/GDP	-0.009	0.053	-10000	0	-0.51	5	5
TSC1	0.016	0	-10000	0	-10000	0	0
Insulin Receptor/IRS1	0.009	0.066	-10000	0	-0.46	13	13
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA	-0.003	0.02	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
EIF3A	0.016	0	-10000	0	-10000	0	0
RPS6KB1	0.028	0.043	-10000	0	-0.38	3	3
MAP3K5	0.013	0.023	-10000	0	-0.46	2	2
PIK3R1	0.011	0.066	-10000	0	-0.78	6	6
apoptosis	0.013	0.023	-10000	0	-0.46	2	2
mol:LY294002	0	0	0.001	1	-0.001	29	30
EIF4B	0.036	0.039	-10000	0	-0.34	2	2
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	-0.005	0.032	-10000	0	-0.4	2	2
eIF4E/eIF4G1/eIF4A1	-0.001	0.012	-10000	0	-10000	0	0
KIAA1303	0	0	-10000	0	-10000	0	0
PI3K	0.014	0.082	-10000	0	-0.45	22	22
mTOR/RHEB/GTP/Raptor/GBL	0.034	0.033	-10000	0	-0.27	3	3
FKBP1A	0.016	0.001	-10000	0	-10000	0	0
RHEB/GTP	-0.009	0.052	-10000	0	-0.5	5	5
mol:Amino Acids	0	0	0.001	1	-0.001	29	30
FKBP12/Rapamycin	0	0.001	-10000	0	-10000	0	0
PDPK1	-0.014	0.076	-10000	0	-0.56	10	10
EIF4E	0.016	0	-10000	0	-10000	0	0
ASK1/PP5C	0.024	0.037	-10000	0	-0.65	2	2
mTOR/RHEB/GTP/Raptor/GBL/eIF4E	0.022	0.001	-10000	0	-10000	0	0
TSC1/TSC2	-0.012	0.066	-10000	0	-0.63	5	5
tumor necrosis factor receptor activity	0	0	0.001	29	-0.001	1	30
RPS6	0.015	0.032	-10000	0	-0.65	2	2
PPP5C	0.016	0	-10000	0	-10000	0	0
EIF4G1	0.016	0	-10000	0	-10000	0	0
IRS1	0	0.064	-10000	0	-0.31	31	31
INS	-0.002	0.038	-10000	0	-0.65	3	3
PTEN	0.016	0	-10000	0	-10000	0	0
PDK2	-0.013	0.07	-10000	0	-0.51	11	11
EIF4EBP1	-0.014	0.18	-10000	0	-1.2	18	18
PIK3CA	0.01	0.071	-10000	0	-0.85	6	6
PPP2R5D	0.024	0.027	-10000	0	-10000	0	0
peptide biosynthetic process	0.018	0.043	-10000	0	-0.46	7	7
RHEB	0.016	0	-10000	0	-10000	0	0
EIF4A1	0.016	0	-10000	0	-10000	0	0
mol:Rapamycin	0	0	-10000	0	-0.003	11	11
EEF2	0.018	0.043	-10000	0	-0.46	7	7
eIF4E/4E-BP1	-0.004	0.17	-10000	0	-1.1	18	18

×

Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SMAD4	0.016	0	-9999	-10000	0	0
SMAD2	0.017	0.018	-9999	-0.32	2	2
SMAD3	0.052	0.021	-9999	-10000	0	0
SMAD3/SMAD4	0.058	0.024	-9999	-0.39	1	1
SMAD4/Ubc9/PIASy	-0.001	0.027	-9999	-0.56	2	2
SMAD2/SMAD2/SMAD4	-0.002	0.027	-9999	-10000	0	0
PPM1A	0.016	0	-9999	-10000	0	0
CALM1	0.016	0	-9999	-10000	0	0
SMAD2/SMAD4	0.025	0.017	-9999	-10000	0	0
MAP3K1	0.015	0.022	-9999	-0.65	1	1
TRAP-1/SMAD4	-0.018	0.11	-9999	-0.65	24	24
MAPK3	0.015	0.029	-9999	-0.85	1	1
MAPK1	0.015	0.029	-9999	-0.85	1	1
NUP214	0.016	0	-9999	-10000	0	0
CTDSP1	0.015	0.029	-9999	-0.85	1	1
CTDSP2	0.016	0	-9999	-10000	0	0
CTDSPL	0.015	0.022	-9999	-0.65	1	1
KPNB1	0.015	0.029	-9999	-0.85	1	1
TGFBRAP1	-0.007	0.14	-9999	-0.85	24	24
UBE2I	0.016	0	-9999	-10000	0	0
NUP153	0.015	0.029	-9999	-0.85	1	1
KPNA2	0.013	0.045	-9999	-0.65	4	4
PIAS4	0.014	0.041	-9999	-0.85	2	2

×

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	-0.002	0.037	-9999	-0.57	3	3
EntrezGene:79658	0	0	-9999	-10000	0	0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A	0.024	0.026	-9999	-0.39	2	2
AP2	-0.001	0.022	-9999	-0.65	1	1
mol:DAG	0	0	-9999	-10000	0	0
Arfaptin 2/Rac/GTP	0	0.02	-9999	-0.6	1	1
CLTB	0.014	0.041	-9999	-0.85	2	2
coatomer protein complex/ARF1/GTP/ER cargo protein	0.032	0.02	-9999	-0.38	2	2
CD4	-0.008	0.14	-9999	-0.85	25	25
CLTA	0.016	0	-9999	-10000	0	0
mol:GTP	0.002	0.002	-9999	-10000	0	0
ARFGAP1	0.013	0.028	-9999	-0.58	2	2
mol:PI-4-5-P2	-0.003	0.029	-9999	-0.29	8	8
ARF1/GTP	-0.002	0.026	-9999	-0.46	2	2
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein	0.034	0.029	-9999	-0.54	2	2
mol:Choline	-0.003	0.029	-9999	-0.3	8	8
mol:GDP	0	0	-9999	-10000	0	0
ARF1	0.016	0.001	-9999	-10000	0	0
DDEF1	-0.003	0.029	-9999	-0.29	8	8
ARF1/GDP	-0.002	0.025	-9999	-0.48	2	2
AP2M1	0.016	0	-9999	-10000	0	0
EntrezGene:1313	0	0	-9999	-10000	0	0
actin filament polymerization	0	0.002	-9999	-10000	0	0
Rac/GTP	0	0.001	-9999	-10000	0	0
ARF1/GTP/GGA3/ARF-GAP1	-0.001	0.022	-9999	-0.44	2	2
ARFIP2	-0.001	0.028	-9999	-0.83	1	1
COPA	0.016	0	-9999	-10000	0	0
RAC1	0.016	0	-9999	-10000	0	0
ARF1/GTP/coatomer protein complex	0.031	0.019	-9999	-0.32	2	2
ARF1/GTP/ARHGAP10	0	0.002	-9999	-10000	0	0
GGA3	0.016	0	-9999	-10000	0	0
ARF1/GTP/Membrin	-0.001	0.011	-9999	-10000	0	0
AP2A1	0.015	0.029	-9999	-0.85	1	1
coatomer protein complex/ARF1/GTP/ARF-GAP1	0.033	0.034	-9999	-0.62	2	2
ARF1/GDP/Membrin	-0.001	0.01	-9999	-10000	0	0
Arfaptin 2/Rac/GDP	0	0.02	-9999	-0.58	1	1
CYTH2	0.014	0.041	-9999	-0.84	2	2
ARF1/GTP/GGA3	0	0.003	-9999	-10000	0	0
mol:ATP	0	0	-9999	-10000	0	0
Rac/GDP	0	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	0.036	0.057	-9999	-0.41	2	2
PLD2	-0.003	0.029	-9999	-0.3	8	8
ARF-GAP1/v-SNARE	0.013	0.028	-9999	-0.57	2	2
PIP5K1A	-0.003	0.029	-9999	-0.29	8	8
ARF1/GTP/Membrin/GBF1/p115	-0.002	0.021	-9999	-0.35	2	2
mol:Phosphatic acid	0	0	-9999	-10000	0	0
mol:Phosphatidic acid	-0.003	0.029	-9999	-0.3	8	8
KDEL Receptor/Ligand/ARF-GAP1	0.013	0.028	-9999	-0.57	2	2
GOSR2	-0.001	0.011	-9999	-10000	0	0
USO1	-0.002	0.031	-9999	-0.86	1	1
GBF1	-0.002	0.031	-9999	-0.86	1	1
ARF1/GTP/Arfaptin 2	-0.001	0.022	-9999	-0.64	1	1
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex	-0.016	0.095	-9999	-0.56	26	26

×

Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.016	0	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	-0.001	0.015	-9999	-0.4	1	1
MDM2/SUMO1	0.037	0.015	-9999	-10000	0	0
HDAC4	0.015	0.029	-9999	-0.85	1	1
Ran/GTP/Exportin 1/HDAC1	0	0.007	-9999	-10000	0	0
SUMO1	0.016	0	-9999	-10000	0	0
NPC/RanGAP1/SUMO1	0.021	0.02	-9999	-0.36	2	2
mol:GTP	0	0	-9999	-10000	0	0
XPO1	0.036	0.015	-9999	-10000	0	0
EntrezGene:23636	0	0	-9999	-10000	0	0
RAN	0.016	0	-9999	-10000	0	0
EntrezGene:8021	0	0	-9999	-10000	0	0
RANBP2	0.016	0	-9999	-10000	0	0
SUMO1/HDAC4	0.037	0.023	-9999	-0.47	1	1
SUMO1/HDAC1	0.037	0.015	-9999	-10000	0	0
RANGAP1	0.013	0.047	-9999	-0.78	3	3
MDM2/SUMO1/SUMO1	-0.001	0.017	-9999	-0.51	1	1
NPC/RanGAP1/SUMO1/RanBP2/Ubc9	0.027	0.016	-9999	-0.29	2	2
Ran/GTP	-0.001	0.013	-9999	-10000	0	0
EntrezGene:23225	0	0	-9999	-10000	0	0
MDM2	0.016	0	-9999	-10000	0	0
UBE2I	0.016	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	-0.001	0.012	-9999	-10000	0	0
NPC	0	0	-9999	-10000	0	0
PIAS2	0.015	0.029	-9999	-0.85	1	1
PIAS1	0.016	0	-9999	-10000	0	0
EntrezGene:9972	0	0	-9999	-10000	0	0

pid_entity	TCGA.Y8.A8S1	TCGA.Y8.A8S0	TCGA.Y8.A8RZ	TCGA.Y8.A8RY
109_MAP3K5	0.07	0.07	-0.21	0.07
47_PPARGC1A	0.016	0.016	0.016	0.016
105_BMP4	0.016	0.016	0.016	0.016
105_BMP6	0.016	0.016	0.016	0.016
105_BMP7	-0.65	-0.65	0.016	0.016
105_BMP2	0.016	0.016	0.016	0.016
131_RELN/VLDLR	0	-0.36	0	-0.36
30_TGFB1/TGF beta receptor Type II	0.016	0.016	0.016	0.016
84_STAT5B	0.06	-0.058	-0.23	0.057
84_STAT5A	0.06	-0.058	-0.23	0.057