Lung Squamous Cell Carcinoma: PARADIGM pathway analysis of mRNA expression and copy number data<BR>(primary solid tumor cohort)

Pathway.Name	Avg.Num.Perturbations
TCGA08_retinoblastoma	27
HIF-1-alpha transcription factor network	24
IL23-mediated signaling events	22
IL4-mediated signaling events	20
Signaling mediated by p38-alpha and p38-beta	20
Osteopontin-mediated events	19
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	19
Noncanonical Wnt signaling pathway	18
Fc-epsilon receptor I signaling in mast cells	18
Glucocorticoid receptor regulatory network	18

Pathway.Name	Avg.Num.Perturbations	Total.Perturbations	Num.Entities	Min.Mean.Truth	Max.Mean.Truth	Min.Mean.Within	Max.Mean.Within	Min.Mean.Any	Max.Mean.Within.1
TCGA08_retinoblastoma	27	218	8	-0.068	0.088	1000	-1000	-0.003	-1000
HIF-1-alpha transcription factor network	24	1858	76	-0.27	0.035	1000	-1000	-0.035	-1000
IL23-mediated signaling events	22	1351	60	-0.51	0.034	1000	-1000	-0.057	-1000
IL4-mediated signaling events	20	1834	91	-0.56	0.52	1000	-1000	-0.087	-1000
Signaling mediated by p38-alpha and p38-beta	20	922	44	-0.17	0.034	1000	-1000	-0.014	-1000
Osteopontin-mediated events	19	741	38	-0.2	0.034	1000	-1000	-0.032	-1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	19	1345	68	-0.39	0.19	1000	-1000	-0.066	-1000
Noncanonical Wnt signaling pathway	18	478	26	-0.13	0.034	1000	-1000	-0.034	-1000
Fc-epsilon receptor I signaling in mast cells	18	1814	97	-0.12	0.045	1000	-1000	-0.045	-1000
Glucocorticoid receptor regulatory network	18	2140	114	-0.46	0.29	1000	-1000	-0.05	-1000
Endothelins	18	1798	96	-0.24	0.033	1000	-1000	-0.047	-1000
Wnt signaling	18	128	7	-0.13	0.028	1000	-1000	-0.013	-1000
Syndecan-1-mediated signaling events	16	550	34	-0.14	0.037	1000	-1000	-0.033	-1000
Thromboxane A2 receptor signaling	16	1680	105	-0.16	0.054	1000	-1000	-0.036	-1000
EPHB forward signaling	16	1366	85	-0.11	0.078	1000	-1000	-0.066	-1000
Signaling events mediated by the Hedgehog family	15	816	52	-0.25	0.049	1000	-1000	-0.034	-1000
Ephrin B reverse signaling	15	754	48	-0.11	0.043	1000	-1000	-0.031	-1000
BCR signaling pathway	15	1522	99	-0.21	0.05	1000	-1000	-0.054	-1000
FOXM1 transcription factor network	15	780	51	-0.25	0.043	1000	-1000	-0.069	-1000
Nectin adhesion pathway	14	906	63	-0.094	0.055	1000	-1000	-0.036	-1000
IGF1 pathway	14	838	57	-0.072	0.062	1000	-1000	-0.034	-1000
Signaling events mediated by Stem cell factor receptor (c-Kit)	14	1166	78	-0.17	0.073	1000	-1000	-0.04	-1000
TCR signaling in naïve CD8+ T cells	13	1225	93	-0.11	0.048	1000	-1000	-0.046	-1000
EGFR-dependent Endothelin signaling events	13	281	21	-0.075	0.048	1000	-1000	-0.041	-1000
IL12-mediated signaling events	12	1046	87	-0.21	0.037	1000	-1000	-0.047	-1000
IL1-mediated signaling events	12	790	62	-0.15	0.05	1000	-1000	-0.029	-1000
Calcium signaling in the CD4+ TCR pathway	12	386	31	-0.2	0.038	1000	-1000	-0.049	-1000
Glypican 1 network	11	571	48	-0.05	0.034	1000	-1000	-0.024	-1000
IFN-gamma pathway	11	751	68	-0.1	0.046	1000	-1000	-0.046	-1000
LPA receptor mediated events	11	1173	102	-0.2	0.034	1000	-1000	-0.086	-1000
Arf6 signaling events	10	631	62	-0.071	0.071	1000	-1000	-0.013	-1000
BMP receptor signaling	10	882	81	-0.16	0.058	1000	-1000	-0.036	-1000
S1P1 pathway	10	360	36	-0.19	0.033	1000	-1000	-0.03	-1000
FAS signaling pathway (CD95)	10	476	47	-0.15	0.079	1000	-1000	-0.029	-1000
Stabilization and expansion of the E-cadherin adherens junction	10	759	74	-0.098	0.052	1000	-1000	-0.056	-1000
Syndecan-4-mediated signaling events	10	679	67	-0.07	0.035	1000	-1000	-0.031	-1000
Caspase cascade in apoptosis	9	692	74	-0.061	0.047	1000	-1000	-0.029	-1000
Syndecan-2-mediated signaling events	9	662	69	-0.12	0.037	1000	-1000	-0.042	-1000
amb2 Integrin signaling	9	805	82	-0.11	0.038	1000	-1000	-0.03	-1000
HIF-2-alpha transcription factor network	9	402	43	-0.064	0.051	1000	-1000	-0.027	-1000
TCGA08_p53	9	66	7	-0.037	0.034	1000	-1000	-0.005	-1000
IL27-mediated signaling events	9	490	51	-0.19	0.12	1000	-1000	-0.04	-1000
E-cadherin signaling in keratinocytes	9	429	43	-0.031	0.048	1000	-1000	-0.021	-1000
mTOR signaling pathway	8	475	53	-0.031	0.087	1000	-1000	-0.033	-1000
TRAIL signaling pathway	8	394	48	-0.04	0.036	1000	-1000	-0.023	-1000
IL6-mediated signaling events	8	615	75	-0.075	0.053	1000	-1000	-0.04	-1000
VEGFR1 specific signals	8	456	56	-0.046	0.037	1000	-1000	-0.033	-1000
E-cadherin signaling events	8	40	5	-0.002	0.03	1000	-1000	0.018	-1000
PLK2 and PLK4 events	7	22	3	-0.014	0.032	1000	-1000	-0.003	-1000
Signaling events mediated by PTP1B	7	580	76	-0.088	0.067	1000	-1000	-0.026	-1000
Arf6 downstream pathway	7	330	43	-0.051	0.048	1000	-1000	-0.021	-1000
PDGFR-alpha signaling pathway	7	318	44	-0.12	0.05	1000	-1000	-0.027	-1000
Syndecan-3-mediated signaling events	7	264	35	-0.12	0.068	1000	-1000	-0.017	-1000
Integrins in angiogenesis	7	621	84	-0.1	0.064	1000	-1000	-0.042	-1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha	7	322	45	-0.074	0.038	1000	-1000	-0.042	-1000
Canonical Wnt signaling pathway	7	370	51	-0.12	0.066	1000	-1000	-0.036	-1000
Signaling events mediated by VEGFR1 and VEGFR2	7	912	125	-0.027	0.054	1000	-1000	-0.029	-1000
Regulation of nuclear SMAD2/3 signaling	6	820	136	-0.41	0.095	1000	-1000	-0.043	-1000
Coregulation of Androgen receptor activity	6	459	76	-0.2	0.056	1000	-1000	-0.026	-1000
Hedgehog signaling events mediated by Gli proteins	6	416	65	-0.16	0.078	1000	-1000	-0.034	-1000
Presenilin action in Notch and Wnt signaling	6	378	61	-0.12	0.067	1000	-1000	-0.04	-1000
FOXA2 and FOXA3 transcription factor networks	6	306	46	-0.1	0.052	1000	-1000	-0.062	-1000
Reelin signaling pathway	6	378	56	-0.072	0.081	1000	-1000	-0.034	-1000
Nongenotropic Androgen signaling	6	318	52	-0.08	0.054	1000	-1000	-0.028	-1000
E-cadherin signaling in the nascent adherens junction	6	477	76	-0.064	0.057	1000	-1000	-0.048	-1000
Plasma membrane estrogen receptor signaling	6	586	86	-0.068	0.048	1000	-1000	-0.053	-1000
Sphingosine 1-phosphate (S1P) pathway	5	158	28	-0.036	0.045	1000	-1000	-0.014	-1000
Visual signal transduction: Cones	5	203	38	-0.019	0.045	1000	-1000	-0.003	-1000
Cellular roles of Anthrax toxin	5	205	39	-0.058	0.033	1000	-1000	-0.02	-1000
p75(NTR)-mediated signaling	5	652	125	-0.13	0.076	1000	-1000	-0.04	-1000
Ceramide signaling pathway	5	403	76	-0.048	0.061	1000	-1000	-0.024	-1000
Signaling mediated by p38-gamma and p38-delta	5	85	15	-0.032	0.033	1000	-1000	-0.028	-1000
IL2 signaling events mediated by PI3K	5	310	58	-0.085	0.041	1000	-1000	-0.041	-1000
Glypican 2 network	5	21	4	0	0.003	1000	-1000	0	-1000
Neurotrophic factor-mediated Trk receptor signaling	5	613	120	-0.14	0.092	1000	-1000	-0.041	-1000
Visual signal transduction: Rods	5	265	52	-0.071	0.052	1000	-1000	-0.037	-1000
Regulation of Androgen receptor activity	5	351	70	-0.21	0.054	1000	-1000	-0.042	-1000
ErbB2/ErbB3 signaling events	4	283	65	-0.033	0.048	1000	-1000	-0.044	-1000
Lissencephaly gene (LIS1) in neuronal migration and development	4	225	54	-0.058	0.048	1000	-1000	-0.047	-1000
JNK signaling in the CD4+ TCR pathway	4	73	17	-0.022	0.046	1000	-1000	-0.026	-1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)	4	378	85	-0.097	0.079	1000	-1000	-0.036	-1000
Signaling events mediated by HDAC Class III	4	178	40	-0.062	0.063	1000	-1000	-0.026	-1000
ceramide signaling pathway	4	201	49	-0.026	0.045	1000	-1000	-0.024	-1000
RXR and RAR heterodimerization with other nuclear receptor	4	231	52	-0.025	0.083	1000	-1000	-0.021	-1000
FoxO family signaling	4	292	64	-0.12	0.062	1000	-1000	-0.038	-1000
Retinoic acid receptors-mediated signaling	4	251	58	-0.054	0.063	1000	-1000	-0.05	-1000
TCGA08_rtk_signaling	4	123	26	-0.073	0.083	1000	-1000	-0.008	-1000
IL2 signaling events mediated by STAT5	4	109	22	-0.068	0.034	1000	-1000	-0.035	-1000
Class I PI3K signaling events	4	331	73	-0.029	0.058	1000	-1000	-0.035	-1000
S1P3 pathway	4	195	42	-0.043	0.045	1000	-1000	-0.037	-1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha	4	132	33	-0.065	0.076	1000	-1000	-0.033	-1000
PDGFR-beta signaling pathway	4	422	97	-0.06	0.083	1000	-1000	-0.032	-1000
S1P4 pathway	4	105	25	-0.013	0.045	1000	-1000	-0.022	-1000
Ras signaling in the CD4+ TCR pathway	4	81	17	-0.012	0.035	1000	-1000	-0.025	-1000
Aurora B signaling	4	323	67	-0.099	0.055	1000	-1000	-0.026	-1000
ErbB4 signaling events	3	274	69	-0.085	0.047	1000	-1000	-0.037	-1000
a4b1 and a4b7 Integrin signaling	3	18	5	0.014	0.034	1000	-1000	0.012	-1000
PLK1 signaling events	3	322	85	-0.02	0.097	1000	-1000	-0.036	-1000
Class I PI3K signaling events mediated by Akt	3	216	68	-0.046	0.059	1000	-1000	-0.025	-1000
Paxillin-independent events mediated by a4b1 and a4b7	3	137	37	-0.036	0.061	1000	-1000	-0.032	-1000
S1P5 pathway	3	66	17	-0.007	0.033	1000	-1000	-0.012	-1000
Paxillin-dependent events mediated by a4b1	3	132	36	-0.048	0.061	1000	-1000	-0.025	-1000
Atypical NF-kappaB pathway	3	120	31	-0.004	0.034	1000	-1000	-0.016	-1000
Regulation of p38-alpha and p38-beta	3	163	54	-0.037	0.076	1000	-1000	-0.04	-1000
Regulation of Telomerase	3	352	102	-0.094	0.082	1000	-1000	-0.055	-1000
Insulin Pathway	3	274	74	-0.047	0.088	1000	-1000	-0.034	-1000
Angiopoietin receptor Tie2-mediated signaling	3	348	88	-0.047	0.039	1000	-1000	-0.064	-1000
LPA4-mediated signaling events	2	30	12	-0.014	0.051	1000	-1000	-0.026	-1000
EPO signaling pathway	2	152	55	-0.007	0.069	1000	-1000	-0.03	-1000
Insulin-mediated glucose transport	2	84	32	-0.027	0.061	1000	-1000	-0.012	-1000
Signaling events regulated by Ret tyrosine kinase	2	185	82	-0.03	0.057	1000	-1000	-0.056	-1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes	2	180	83	-0.027	0.061	1000	-1000	-0.023	-1000
Arf6 trafficking events	2	188	71	-0.035	0.056	1000	-1000	-0.025	-1000
p38 MAPK signaling pathway	2	97	44	-0.019	0.061	1000	-1000	-0.018	-1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling	1	32	23	0.007	0.06	1000	-1000	-0.025	-1000
Nephrin/Neph1 signaling in the kidney podocyte	1	41	34	-0.041	0.066	1000	-1000	-0.033	-1000
Canonical NF-kappaB pathway	1	64	39	-0.017	0.069	1000	-1000	-0.029	-1000
Signaling events mediated by HDAC Class II	1	77	75	-0.039	0.063	1000	-1000	-0.014	-1000
BARD1 signaling events	1	76	57	-0.049	0.075	1000	-1000	-0.036	-1000
Circadian rhythm pathway	1	36	22	-0.01	0.049	1000	-1000	-0.039	-1000
Ephrin A reverse signaling	1	12	7	0	0.033	1000	-1000	0	-1000
Aurora A signaling	1	117	60	-0.002	0.063	1000	-1000	-0.018	-1000
Signaling events mediated by HDAC Class I	1	186	104	-0.063	0.079	1000	-1000	-0.026	-1000
Sumoylation by RanBP2 regulates transcriptional repression	1	29	27	0	0.065	1000	-1000	-0.024	-1000
Rapid glucocorticoid signaling	1	20	20	0	0.044	1000	-1000	-0.002	-1000
Signaling events mediated by PRL	1	56	34	-0.028	0.049	1000	-1000	-0.033	-1000
Class IB PI3K non-lipid kinase events	1	3	3	-0.028	0.028	1000	-1000	-0.019	-1000
Alternative NF-kappaB pathway	1	21	13	0	0.074	1000	-1000	0	-1000
Aurora C signaling	0	4	7	0	0.055	1000	-1000	-0.013	-1000
Effects of Botulinum toxin	0	22	26	-0.005	0.056	1000	-1000	-0.002	-1000
Arf1 pathway	0	32	54	-0.002	0.045	1000	-1000	-0.017	-1000
Total	957	59783	7203	-12	7.9	131000	-131000	-4.1	-131000

TCGA08_retinoblastoma

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2B	0.008	0.05	-10000	0	-0.47	1	1
CDKN2C	0.029	0.027	-10000	0	-10000	0	0
CDKN2A	-0.038	0.15	-10000	0	-0.49	15	15
CCND2	0.045	0.1	0.23	31	-0.12	3	34
RB1	-0.068	0.13	0.56	1	-0.25	41	42
CDK4	0.063	0.12	0.26	37	-10000	0	37
CDK6	0.053	0.13	0.27	33	-0.41	2	35
G1/S progression	0.088	0.14	0.26	52	-0.41	2	54

HIF-1-alpha transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PKM2	-0.21	0.51	-9999	-1	34	34
HDAC7	-0.001	0.007	-9999	-10000	0	0
HIF1A/ARNT/Cbp/p300/Src-1	-0.16	0.46	-9999	-0.91	28	28
SMAD4	0.026	0.062	-9999	-0.51	2	2
ID2	-0.22	0.52	-9999	-1	34	34
AP1	-0.032	0.16	-9999	-0.43	18	18
ABCG2	-0.23	0.5	-9999	-1	35	35
HIF1A	-0.027	0.13	-9999	-0.38	7	7
TFF3	-0.26	0.53	-9999	-0.99	41	41
GATA2	0.017	0.05	-9999	-0.51	1	1
AKT1	-0.028	0.12	-9999	-0.34	7	7
response to hypoxia	-0.034	0.085	-9999	-0.18	19	19
MCL1	-0.21	0.5	-9999	-1	34	34
NDRG1	-0.25	0.53	-9999	-1	39	39
SERPINE1	-0.23	0.52	-9999	-1	36	36
FECH	-0.22	0.51	-9999	-0.99	36	36
FURIN	-0.22	0.51	-9999	-0.98	36	36
NCOA2	0.027	0.062	-9999	-0.51	2	2
EP300	-0.038	0.16	-9999	-0.37	17	17
HMOX1	-0.23	0.51	-9999	-1	34	34
BHLHE40	-0.23	0.49	-9999	-0.99	35	35
BHLHE41	-0.23	0.49	-9999	-0.99	35	35
HIF1A/ARNT/SMAD3/SMAD4/SP1	0.012	0.18	-9999	-0.43	11	11
ENG	-0.018	0.15	-9999	-0.41	10	10
JUN	-0.003	0.12	-9999	-0.51	7	7
RORA	-0.26	0.53	-9999	-1	39	39
ABCB1	-0.045	0.19	-9999	-1.2	3	3
TFRC	-0.26	0.48	-9999	-1	35	35
CXCR4	-0.24	0.54	-9999	-1	40	40
TF	-0.23	0.49	-9999	-0.99	34	34
CITED2	-0.22	0.51	-9999	-1	34	34
HIF1A/ARNT	-0.25	0.67	-9999	-1.3	32	32
LDHA	-0.062	0.32	-9999	-1.1	11	11
ETS1	-0.22	0.51	-9999	-1	35	35
PGK1	-0.22	0.51	-9999	-1	34	34
NOS2	-0.23	0.49	-9999	-0.99	35	35
ITGB2	-0.23	0.53	-9999	-1	35	35
ALDOA	-0.22	0.51	-9999	-1	34	34
Cbp/p300/CITED2	-0.23	0.53	-9999	-1.1	32	32
FOS	-0.036	0.16	-9999	-0.51	14	14
HK2	-0.22	0.52	-9999	-1	34	34
SP1	0.033	0.063	-9999	-0.51	2	2
GCK	-0.034	0.21	-9999	-0.94	3	3
HK1	-0.22	0.51	-9999	-1	33	33
NPM1	-0.22	0.5	-9999	-1	34	34
EGLN1	-0.21	0.51	-9999	-0.99	35	35
CREB1	0.032	0.051	-9999	-0.51	1	1
PGM1	-0.22	0.5	-9999	-1	34	34
SMAD3	0.009	0.11	-9999	-0.51	7	7
EDN1	-0.18	0.46	-9999	-1.2	24	24
IGFBP1	-0.22	0.51	-9999	-1	33	33
VEGFA	-0.15	0.39	-9999	-0.78	29	29
HIF1A/JAB1	-0.001	0.1	-9999	-0.47	3	3
CP	-0.27	0.49	-9999	-0.96	40	40
CXCL12	-0.24	0.54	-9999	-1.1	36	36
COPS5	0.034	0.008	-9999	-10000	0	0
SMAD3/SMAD4	0.023	0.1	-9999	-0.37	9	9
BNIP3	-0.24	0.52	-9999	-0.99	37	37
EGLN3	-0.26	0.54	-9999	-1	39	39
CA9	-0.26	0.52	-9999	-1	39	39
TERT	-0.2	0.5	-9999	-0.99	33	33
ENO1	-0.22	0.51	-9999	-1	34	34
PFKL	-0.22	0.51	-9999	-1	34	34
NCOA1	0.033	0.007	-9999	-10000	0	0
ADM	-0.25	0.52	-9999	-1	37	37
ARNT	-0.013	0.094	-9999	-0.37	1	1
HNF4A	0.035	0.017	-9999	-10000	0	0
ADFP	-0.23	0.49	-9999	-0.99	35	35
SLC2A1	-0.18	0.41	-9999	-0.82	31	31
LEP	-0.22	0.5	-9999	-1	34	34
HIF1A/ARNT/Cbp/p300	-0.17	0.48	-9999	-0.91	31	31
EPO	-0.083	0.32	-9999	-0.88	9	9
CREBBP	-0.018	0.12	-9999	-0.37	5	5
HIF1A/ARNT/Cbp/p300/HDAC7	-0.17	0.48	-9999	-0.94	29	29
PFKFB3	-0.22	0.51	-9999	-1	34	34
NT5E	-0.23	0.51	-9999	-1	34	34

IL23-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCL2	-0.39	0.52	-10000	0	-1.3	30	30
IL23A	-0.47	0.58	-10000	0	-1.2	49	49
NF kappa B1 p50/RelA/I kappa B alpha	-0.37	0.51	-10000	0	-1.1	37	37
positive regulation of T cell mediated cytotoxicity	-0.42	0.58	-10000	0	-1.3	35	35
ITGA3	-0.41	0.52	-10000	0	-1.2	36	36
IL17F	-0.19	0.33	-10000	0	-0.7	32	32
IL12B	-0.015	0.088	-10000	0	-0.54	3	3
STAT1 (dimer)	-0.41	0.55	-10000	0	-1.3	34	34
CD4	-0.35	0.48	-10000	0	-1.2	28	28
IL23	-0.45	0.55	-10000	0	-1.2	46	46
IL23R	-0.047	0.18	-10000	0	-1.1	4	4
IL1B	-0.48	0.61	-10000	0	-1.4	40	40
T-helper cell lineage commitment	0	0	-10000	0	-10000	0	0
IL24	-0.36	0.47	-10000	0	-1.2	28	28
TYK2	-0.006	0.042	-10000	0	-10000	0	0
STAT4	0.013	0.097	-10000	0	-0.51	5	5
STAT3	0.034	0.006	-10000	0	-10000	0	0
IL18RAP	-0.052	0.18	-10000	0	-0.52	20	20
IL12RB1	-0.005	0.04	-10000	0	-10000	0	0
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
IL12Rbeta1/TYK2	-0.002	0.053	-10000	0	-10000	0	0
IL23R/JAK2	-0.044	0.18	-10000	0	-0.95	4	4
positive regulation of chronic inflammatory response	-0.42	0.58	-10000	0	-1.3	35	35
natural killer cell activation	0.005	0.009	0.083	1	-10000	0	1
JAK2	-0.003	0.048	-10000	0	-10000	0	0
PIK3R1	0.007	0.099	-10000	0	-0.51	5	5
NFKB1	0.031	0.008	-10000	0	-10000	0	0
RELA	0.032	0.004	-10000	0	-10000	0	0
positive regulation of dendritic cell antigen processing and presentation	-0.43	0.52	-10000	0	-1.1	48	48
ALOX12B	-0.36	0.47	-10000	0	-1.2	29	29
CXCL1	-0.51	0.61	-10000	0	-1.3	48	48
T cell proliferation	-0.42	0.58	-10000	0	-1.3	35	35
NFKBIA	0.026	0.046	-10000	0	-0.52	1	1
IL17A	-0.16	0.26	-10000	0	-0.56	24	24
PI3K	-0.35	0.5	-10000	0	-1.2	32	32
IFNG	-0.04	0.06	0.15	1	-0.13	38	39
STAT3 (dimer)	-0.32	0.47	-10000	0	-1.1	32	32
IL18R1	-0.002	0.12	-10000	0	-0.51	7	7
IL23/IL23R/JAK2/TYK2/SOCS3	-0.22	0.33	-10000	0	-0.76	25	25
IL18/IL18R	-0.062	0.2	-10000	0	-0.4	33	33
macrophage activation	-0.021	0.022	-10000	0	-0.049	40	40
TNF	-0.41	0.52	-10000	0	-1.2	36	36
STAT3/STAT4	-0.38	0.53	-10000	0	-1.2	34	34
STAT4 (dimer)	-0.4	0.55	-10000	0	-1.3	34	34
IL18	-0.023	0.15	-10000	0	-0.51	13	13
IL19	-0.37	0.48	-10000	0	-1.1	32	32
STAT5A (dimer)	-0.4	0.55	-10000	0	-1.3	35	35
STAT1	0.011	0.1	-10000	0	-0.51	6	6
SOCS3	0.021	0.077	-10000	0	-0.51	3	3
CXCL9	-0.49	0.61	-10000	0	-1.3	52	52
MPO	-0.36	0.48	-10000	0	-1.1	31	31
positive regulation of humoral immune response	-0.42	0.58	-10000	0	-1.3	35	35
IL23/IL23R/JAK2/TYK2	-0.45	0.65	-10000	0	-1.4	35	35
IL6	-0.42	0.55	-10000	0	-1.2	37	37
STAT5A	0.033	0.011	-10000	0	-10000	0	0
IL2	0.02	0.028	-10000	0	-10000	0	0
positive regulation of tyrosine phosphorylation of STAT protein	0.005	0.009	0.083	1	-10000	0	1
CD3E	-0.36	0.47	-10000	0	-1.2	29	29
keratinocyte proliferation	-0.42	0.58	-10000	0	-1.3	35	35
NOS2	-0.36	0.48	-10000	0	-1.1	36	36

IL4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.43	0.61	-10000	0	-1.3	39	39
STAT6 (cleaved dimer)	-0.46	0.63	-10000	0	-1.4	43	43
IGHG1	-0.12	0.22	-10000	0	-0.58	7	7
IGHG3	-0.43	0.58	-10000	0	-1.3	42	42
AKT1	-0.2	0.33	-10000	0	-0.87	18	18
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1	-0.14	0.3	-10000	0	-0.95	11	11
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1	-0.21	0.36	-10000	0	-1	14	14
THY1	-0.45	0.62	-10000	0	-1.4	41	41
MYB	-0.026	0.15	-10000	0	-0.51	12	12
HMGA1	0.03	0.044	-10000	0	-0.51	1	1
IL4/IL4R/JAK1/IL2R gamma/JAK3	-0.24	0.37	-10000	0	-0.88	21	21
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP	-0.2	0.35	-10000	0	-1.1	11	11
SP1	0.015	0.073	-10000	0	-0.51	2	2
INPP5D	0	0	-10000	0	-10000	0	0
SOCS5	0.03	0.033	-10000	0	-10000	0	0
STAT6 (dimer)/ETS1	-0.45	0.63	-10000	0	-1.3	42	42
SOCS1	-0.27	0.37	-10000	0	-0.8	35	35
SOCS3	-0.2	0.33	-10000	0	-0.97	11	11
FCER2	-0.38	0.51	-10000	0	-1.1	37	37
PARP14	0.027	0.021	-10000	0	-10000	0	0
CCL17	-0.5	0.66	-10000	0	-1.4	44	44
GRB2	0.034	0.005	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP	-0.14	0.26	-10000	0	-0.72	12	12
T cell proliferation	-0.46	0.64	-10000	0	-1.4	41	41
IL4R/JAK1	-0.46	0.62	-10000	0	-1.4	42	42
EGR2	-0.52	0.68	-10000	0	-1.4	46	46
JAK2	-0.014	0.054	-10000	0	-10000	0	0
JAK3	0.037	0.013	-10000	0	-10000	0	0
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
JAK1	0.014	0.051	-10000	0	-0.5	1	1
COL1A2	-0.22	0.48	-10000	0	-1.6	15	15
CCL26	-0.54	0.68	-10000	0	-1.4	53	53
IL4R	-0.48	0.67	-10000	0	-1.5	42	42
PTPN6	0.031	0.05	-10000	0	-0.49	1	1
IL13RA2	-0.56	0.73	-10000	0	-1.5	49	49
IL13RA1	-0.02	0.083	-10000	0	-0.55	2	2
IRF4	-0.066	0.24	-10000	0	-1.1	5	5
ARG1	-0.14	0.32	-10000	0	-1.1	11	11
CBL	-0.22	0.34	-10000	0	-0.85	19	19
GTF3A	0.012	0.053	-10000	0	-10000	0	0
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
IL13RA1/JAK2	-0.019	0.091	-10000	0	-0.42	2	2
IRF4/BCL6	-0.055	0.2	-10000	0	-1.1	3	3
CD40LG	0.033	0.049	-10000	0	-0.51	1	1
MAPK14	-0.22	0.36	-10000	0	-0.89	19	19
mitosis	-0.19	0.31	-10000	0	-0.8	18	18
STAT6	-0.56	0.84	-10000	0	-1.7	41	41
SPI1	0.005	0.096	-10000	0	-0.4	6	6
RPS6KB1	-0.19	0.29	-10000	0	-0.76	18	18
STAT6 (dimer)	-0.56	0.85	-10000	0	-1.8	41	41
STAT6 (dimer)/PARP14	-0.48	0.69	-10000	0	-1.5	38	38
mast cell activation	0.008	0.015	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2	-0.22	0.37	-10000	0	-0.94	20	20
FRAP1	-0.2	0.33	-10000	0	-0.87	18	18
LTA	-0.44	0.61	-10000	0	-1.3	41	41
FES	0.021	0.076	-10000	0	-0.51	3	3
T-helper 1 cell differentiation	0.52	0.74	1.6	42	-10000	0	42
CCL11	-0.56	0.7	-10000	0	-1.5	50	50
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES	-0.18	0.34	-10000	0	-1	13	13
IL2RG	0.025	0.066	-10000	0	-0.5	2	2
IL10	-0.44	0.61	-10000	0	-1.3	40	40
IRS1	0.006	0.11	-10000	0	-0.51	7	7
IRS2	-0.004	0.13	-10000	0	-0.51	10	10
IL4	-0.095	0.24	-10000	0	-1.1	6	6
IL5	-0.44	0.61	-10000	0	-1.4	35	35
IL4/IL4R/JAK1/IL13RA1/JAK2	-0.36	0.52	-10000	0	-1.1	36	36
COL1A1	-0.33	0.61	-10000	0	-1.6	28	28
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1	-0.47	0.65	-10000	0	-1.5	36	36
IL2R gamma/JAK3	0.041	0.055	-10000	0	-0.37	2	2
TFF3	-0.53	0.68	-10000	0	-1.4	46	46
ALOX15	-0.46	0.62	-10000	0	-1.3	42	42
MYBL1	0.032	0.012	-10000	0	-10000	0	0
T-helper 2 cell differentiation	-0.5	0.56	-10000	0	-1.2	47	47
SHC1	0.032	0.008	-10000	0	-10000	0	0
CEBPB	0.018	0.059	-10000	0	-0.29	3	3
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2	-0.2	0.35	-10000	0	-0.99	15	15
mol:PI-3-4-5-P3	-0.2	0.33	-10000	0	-0.87	18	18
PI3K	-0.22	0.36	-10000	0	-0.95	18	18
DOK2	-0.025	0.16	-10000	0	-0.51	15	15
ETS1	0.026	0.066	-10000	0	-0.48	2	2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2	-0.13	0.23	-10000	0	-0.67	10	10
ITGB3	-0.45	0.62	-10000	0	-1.3	40	40
PIGR	-0.55	0.7	-10000	0	-1.5	46	46
IGHE	0.031	0.068	0.2	4	-0.26	1	5
MAPKKK cascade	-0.12	0.23	-10000	0	-0.65	10	10
BCL6	-0.003	0.1	-10000	0	-0.51	6	6
OPRM1	-0.45	0.62	-10000	0	-1.4	40	40
RETNLB	-0.42	0.62	-10000	0	-1.4	35	35
SELP	-0.52	0.72	-10000	0	-1.5	46	46
AICDA	-0.43	0.6	-10000	0	-1.4	37	37

Signaling mediated by p38-alpha and p38-beta

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
PTGS2	-0.17	0.41	-9999	-1.1	24	24
MKNK1	0.034	0.005	-9999	-10000	0	0
MAPK14	-0.04	0.14	-9999	-0.34	24	24
ATF2/c-Jun	-0.055	0.19	-9999	-0.63	11	11
MAPK11	-0.04	0.14	-9999	-0.34	23	23
MITF	-0.056	0.17	-9999	-0.44	23	23
MAPKAPK5	-0.048	0.15	-9999	-0.39	24	24
KRT8	-0.057	0.16	-9999	-0.39	27	27
MAPKAPK3	0.03	0.014	-9999	-10000	0	0
MAPKAPK2	0.034	0.005	-9999	-10000	0	0
p38alpha-beta/CK2	-0.063	0.21	-9999	-0.51	24	24
CEBPB	-0.049	0.16	-9999	-0.41	23	23
SLC9A1	-0.05	0.15	-9999	-0.39	24	24
mol:GDP	0	0	-9999	-10000	0	0
ATF2	-0.051	0.16	-9999	-0.39	25	25
p38alpha-beta/MNK1	-0.036	0.18	-9999	-0.42	24	24
JUN	-0.055	0.19	-9999	-0.62	11	11
PPARGC1A	-0.069	0.18	-9999	-0.41	29	29
USF1	-0.06	0.18	-9999	-0.43	25	25
RAB5/GDP/GDI1	-0.034	0.13	-9999	-0.31	23	23
NOS2	-0.055	0.15	-9999	-0.39	24	24
DDIT3	-0.057	0.16	-9999	-0.38	28	28
RAB5A	0.028	0.044	-9999	-0.51	1	1
HSPB1	-0.056	0.14	-9999	-0.34	27	27
p38alpha-beta/HBP1	-0.038	0.18	-9999	-0.41	24	24
CREB1	-0.06	0.18	-9999	-0.44	25	25
RAB5/GDP	0.02	0.034	-9999	-0.37	1	1
EIF4E	-0.051	0.15	-9999	-0.38	23	23
RPS6KA4	-0.051	0.16	-9999	-0.39	25	25
PLA2G4A	-0.098	0.2	-9999	-0.44	34	34
GDI1	-0.051	0.16	-9999	-0.41	24	24
TP53	-0.083	0.19	-9999	-0.52	24	24
RPS6KA5	-0.06	0.18	-9999	-0.42	26	26
ESR1	-0.067	0.17	-9999	-0.41	28	28
HBP1	0.026	0.062	-9999	-0.51	2	2
MEF2C	-0.069	0.19	-9999	-0.44	27	27
MEF2A	-0.049	0.15	-9999	-0.39	24	24
EIF4EBP1	-0.063	0.18	-9999	-0.44	25	25
KRT19	-0.1	0.21	-9999	-0.41	43	43
ELK4	-0.06	0.17	-9999	-0.41	27	27
ATF6	-0.045	0.15	-9999	-0.38	23	23
ATF1	-0.056	0.17	-9999	-0.42	25	25
p38alpha-beta/MAPKAPK2	-0.032	0.17	-9999	-0.4	24	24
p38alpha-beta/MAPKAPK3	-0.038	0.18	-9999	-0.42	24	24

Osteopontin-mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IKK alpha homodimer	-0.067	0.16	-9999	-0.33	34	34
NF kappa B1 p50/RelA/I kappa B alpha	-0.058	0.18	-9999	-0.49	13	13
alphaV/beta3 Integrin/Osteopontin/Src	-0.074	0.18	-9999	-0.4	34	34
AP1	-0.12	0.23	-9999	-0.54	27	27
ILK	-0.072	0.15	-9999	-0.33	35	35
bone resorption	-0.072	0.15	-9999	-0.4	15	15
PTK2B	0.029	0.017	-9999	-10000	0	0
PYK2/p130Cas	-0.046	0.17	-9999	-0.31	38	38
ITGAV	0.009	0.1	-9999	-0.52	5	5
mol:GTP	0	0	-9999	-10000	0	0
CD44/Rho Family GTPase/ROCK2	0.034	0.075	-9999	-0.37	5	5
alphaV/beta3 Integrin/Osteopontin	-0.056	0.18	-9999	-0.35	35	35
MAP3K1	-0.082	0.16	-9999	-0.33	38	38
JUN	0.003	0.11	-9999	-0.51	7	7
MAPK3	-0.091	0.16	-9999	-0.34	36	36
MAPK1	-0.085	0.16	-9999	-0.36	31	31
Rac1/GDP	0.025	0.005	-9999	-10000	0	0
NFKB1	0.033	0.008	-9999	-10000	0	0
MAPK8	-0.084	0.15	-9999	-0.32	36	36
ITGB3	0.021	0.053	-9999	-0.51	1	1
NFKBIA	-0.093	0.17	-9999	-0.45	20	20
FOS	-0.029	0.16	-9999	-0.51	14	14
CD44	0.016	0.096	-9999	-0.51	5	5
CHUK	0.03	0.044	-9999	-0.51	1	1
PLAU	-0.2	0.4	-9999	-1.1	22	22
NF kappa B1 p50/RelA	-0.054	0.21	-9999	-0.44	23	23
BCAR1	0.033	0.008	-9999	-10000	0	0
RELA	0.034	0	-9999	-10000	0	0
alphaV beta3 Integrin	0.02	0.093	-9999	-0.39	6	6
mol:GDP	0	0	-9999	-10000	0	0
SYK	-0.083	0.16	-9999	-0.34	39	39
VAV3	-0.14	0.18	-9999	-0.33	63	63
MAP3K14	-0.08	0.16	-9999	-0.34	36	36
ROCK2	0.033	0.007	-9999	-10000	0	0
SPP1	-0.1	0.22	-9999	-0.51	33	33
RAC1	0.033	0.006	-9999	-10000	0	0
Rac1/GTP	-0.13	0.17	-9999	-0.31	62	62
MMP2	-0.14	0.22	-9999	-0.57	27	27

Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FOXP3	0.029	0.052	-10000	0	-0.37	2	2
NFATC2	-0.098	0.27	-10000	0	-0.68	19	19
NFATC3	-0.036	0.1	-10000	0	-0.27	12	12
CD40LG	-0.33	0.42	-10000	0	-0.91	44	44
ITCH	-0.023	0.1	-10000	0	-0.24	9	9
CBLB	-0.018	0.094	-10000	0	-0.24	19	19
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment	-0.24	0.41	-10000	0	-1	25	25
JUNB	0.01	0.098	-10000	0	-0.51	5	5
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.029	0.13	-10000	0	-0.28	31	31
T cell anergy	-0.06	0.17	0.27	1	-0.38	29	30
TLE4	-0.084	0.24	-10000	0	-0.74	13	13
Jun/NFAT1-c-4/p21SNFT	-0.26	0.44	-10000	0	-0.98	34	34
AP-1/NFAT1-c-4	-0.38	0.55	-10000	0	-1.1	43	43
IKZF1	-0.082	0.24	-10000	0	-0.76	13	13
T-helper 2 cell differentiation	-0.098	0.25	-10000	0	-0.71	14	14
AP-1/NFAT1	-0.12	0.24	-10000	0	-0.54	27	27
CALM1	-0.009	0.084	-10000	0	-10000	0	0
EGR2	-0.27	0.55	-10000	0	-1.4	26	26
EGR3	-0.24	0.47	-10000	0	-1.1	28	28
NFAT1/FOXP3	-0.055	0.22	-10000	0	-0.56	16	16
EGR1	-0.021	0.15	-10000	0	-0.51	13	13
JUN	-0.023	0.12	-10000	0	-0.53	7	7
EGR4	0.001	0.001	-10000	0	-10000	0	0
mol:Ca2+	-0.029	0.071	-10000	0	-0.16	32	32
GBP3	-0.15	0.32	-10000	0	-0.78	28	28
FOSL1	0.027	0.027	-10000	0	-10000	0	0
NFAT1-c-4/MAF/IRF4	-0.22	0.45	-10000	0	-0.97	34	34
DGKA	-0.097	0.27	-10000	0	-0.78	15	15
CREM	0.032	0.007	-10000	0	-10000	0	0
NFAT1-c-4/PPARG	-0.25	0.45	-10000	0	-1	33	33
CTLA4	-0.063	0.19	-10000	0	-0.62	11	11
NFAT1-c-4 (dimer)/EGR1	-0.24	0.46	-10000	0	-1	34	34
NFAT1-c-4 (dimer)/EGR4	-0.22	0.44	-10000	0	-0.97	33	33
FOS	-0.055	0.16	-10000	0	-0.52	14	14
IFNG	-0.38	0.6	-10000	0	-1.4	37	37
T cell activation	-0.15	0.25	-10000	0	-0.83	8	8
MAF	-0.028	0.16	-10000	0	-0.51	16	16
T-helper 2 cell lineage commitment	0	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	0.19	0.39	0.84	31	-10000	0	31
TNF	-0.22	0.39	-10000	0	-0.9	32	32
FASLG	-0.38	0.66	-10000	0	-1.4	39	39
TBX21	-0.077	0.2	-10000	0	-0.54	22	22
BATF3	0	0	-10000	0	-10000	0	0
PRKCQ	-0.001	0.11	-10000	0	-0.52	6	6
PTPN1	-0.067	0.2	-10000	0	-0.56	14	14
NFAT1-c-4/ICER1	-0.22	0.44	-10000	0	-0.97	33	33
GATA3	0.029	0.027	-10000	0	-10000	0	0
T-helper 1 cell differentiation	-0.37	0.57	-10000	0	-1.3	37	37
IL2RA	-0.23	0.4	-10000	0	-0.95	28	28
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
CASP3	-0.061	0.2	-10000	0	-0.61	11	11
E2F1	0.037	0.011	-10000	0	-10000	0	0
PPARG	-0.025	0.16	-10000	0	-0.51	15	15
SLC3A2	-0.075	0.22	-10000	0	-0.65	12	12
IRF4	0.026	0.048	-10000	0	-0.51	1	1
PTGS2	-0.37	0.44	-10000	0	-0.93	49	49
CSF2	-0.35	0.44	-10000	0	-0.93	46	46
JunB/Fra1/NFAT1-c-4	-0.21	0.44	-10000	0	-0.94	34	34
IL4	-0.1	0.26	-10000	0	-0.74	14	14
IL5	-0.33	0.42	-10000	0	-0.91	43	43
IL2	-0.15	0.26	-10000	0	-0.84	8	8
IL3	-0.052	0.18	-10000	0	-0.76	7	7
RNF128	-0.11	0.25	-10000	0	-0.59	32	32
NFATC1	-0.19	0.39	-10000	0	-0.84	31	31
CDK4	0.12	0.21	0.62	11	-10000	0	11
PTPRK	-0.085	0.24	-10000	0	-0.72	14	14
IL8	-0.39	0.44	-10000	0	-0.93	50	50
POU2F1	0.038	0.011	-10000	0	-10000	0	0

Noncanonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC2	0.033	0.006	-9999	-10000	0	0
GNB1/GNG2	-0.1	0.2	-9999	-0.41	31	31
mol:DAG	-0.11	0.17	-9999	-0.4	25	25
PLCG1	-0.11	0.17	-9999	-0.42	25	25
YES1	-0.12	0.19	-9999	-0.41	35	35
FZD3	-0.006	0.13	-9999	-0.51	9	9
FZD6	0.013	0.096	-9999	-0.51	5	5
G protein	-0.1	0.19	-9999	-0.42	26	26
MAP3K7	-0.098	0.14	-9999	-0.37	21	21
mol:Ca2+	-0.11	0.16	-9999	-0.39	25	25
mol:IP3	-0.11	0.17	-9999	-0.4	25	25
NLK	-0.003	0.12	-9999	-0.82	3	3
GNB1	0.033	0.007	-9999	-10000	0	0
CAMK2A	-0.1	0.15	-9999	-0.39	22	22
MAP3K7IP1	0	0	-9999	-10000	0	0
Noncanonical Wnts/FZD	-0.13	0.2	-9999	-0.36	55	55
CSNK1A1	0.029	0.044	-9999	-0.51	1	1
GNAS	-0.13	0.18	-9999	-0.39	39	39
GO:0007205	-0.11	0.16	-9999	-0.41	23	23
WNT6	0.028	0.024	-9999	-10000	0	0
WNT4	-0.069	0.2	-9999	-0.51	27	27
NFAT1/CK1 alpha	-0.089	0.2	-9999	-0.45	23	23
GNG2	0.034	0.005	-9999	-10000	0	0
WNT5A	-0.084	0.2	-9999	-0.51	28	28
WNT11	0.004	0.092	-9999	-0.51	4	4
CDC42	-0.11	0.19	-9999	-0.44	26	26

Fc-epsilon receptor I signaling in mast cells

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
PPAP2A	0.015	0.088	-10000	0	-0.51	4	4
LAT2	-0.071	0.18	-10000	0	-0.42	26	26
AP1	-0.07	0.26	0.31	1	-0.58	24	25
mol:PIP3	-0.088	0.23	0.28	5	-0.5	29	34
IKBKB	-0.029	0.14	0.2	10	-0.28	21	31
AKT1	-0.013	0.2	0.43	7	-0.41	16	23
IKBKG	-0.039	0.13	0.2	7	-0.28	22	29
MS4A2	-0.055	0.19	-10000	0	-0.51	23	23
mol:Sphingosine-1-phosphate	0	0	-10000	0	-10000	0	0
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
MAP3K1	0.009	0.23	0.26	37	-0.44	20	57
mol:Ca2+	-0.061	0.18	0.24	6	-0.37	28	34
LYN	0.026	0.048	-10000	0	-0.52	1	1
CBLB	-0.064	0.17	0.21	1	-0.4	25	26
SHC1	0.032	0.008	-10000	0	-10000	0	0
RasGAP/p62DOK	0.045	0.057	-10000	0	-0.29	3	3
positive regulation of cell migration	0	0	-10000	0	-10000	0	0
INPP5D	0	0	-10000	0	-10000	0	0
PLD2	-0.087	0.18	0.35	4	-0.34	41	45
PTPN13	-0.072	0.22	-10000	0	-0.57	18	18
PTPN11	0.02	0.052	-10000	0	-0.52	1	1
GO:0007205	0	0	-10000	0	-10000	0	0
regulation of mast cell degranulation	0.006	0.18	0.37	8	-0.36	14	22
SYK	0.01	0.11	-10000	0	-0.52	6	6
GRB2	0.033	0.006	-10000	0	-10000	0	0
LAT/PLCgamma1/GRB2/SLP76/GADs	-0.1	0.23	-10000	0	-0.48	33	33
LAT	-0.07	0.18	-10000	0	-0.41	26	26
PAK2	0.011	0.25	0.27	38	-0.5	19	57
NFATC2	-0.021	0.056	-10000	0	-10000	0	0
HRAS	-0.069	0.23	0.26	4	-0.53	25	29
GAB2	0.032	0.014	-10000	0	-10000	0	0
PLA2G1B	-0.039	0.25	-10000	0	-0.89	12	12
Fc epsilon R1	-0.077	0.21	-10000	0	-0.4	41	41
Antigen/IgE/Fc epsilon R1	-0.068	0.19	-10000	0	-0.37	41	41
mol:GDP	-0.077	0.25	0.28	2	-0.59	23	25
JUN	0.004	0.11	-10000	0	-0.51	7	7
mol:Ca++	0	0	-10000	0	-10000	0	0
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
FOS	-0.029	0.16	-10000	0	-0.51	14	14
Antigen/IgE/Fc epsilon R1/LYN/SYK	-0.066	0.19	-10000	0	-0.42	26	26
CHUK	-0.044	0.13	0.21	6	-0.29	22	28
KLRG1	-0.069	0.17	-10000	0	-0.38	28	28
VAV1	-0.077	0.18	-10000	0	-0.41	29	29
calcium-dependent protein kinase C activity	0	0	-10000	0	-10000	0	0
CBL	-0.068	0.18	-10000	0	-0.41	26	26
negative regulation of mast cell degranulation	-0.066	0.16	-10000	0	-0.36	26	26
BTK	-0.091	0.28	-10000	0	-0.64	25	25
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK	-0.12	0.24	-10000	0	-0.4	47	47
GAB2/PI3K/SHP2	-0.076	0.14	-10000	0	-0.38	22	22
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP	-0.089	0.21	-10000	0	-0.5	24	24
RAF1	-0.037	0.27	-10000	0	-0.97	12	12
Fc epsilon R1/FcgammaRIIB/SHIP	-0.084	0.23	-10000	0	-0.39	47	47
FCER1G	0.025	0.064	-10000	0	-0.51	2	2
FCER1A	-0.094	0.22	-10000	0	-0.52	31	31
Antigen/IgE/Fc epsilon R1/Fyn	-0.056	0.19	-10000	0	-0.35	42	42
MAPK3	-0.033	0.25	-10000	0	-0.88	12	12
MAPK1	-0.038	0.26	-10000	0	-0.92	12	12
NFKB1	0.033	0.008	-10000	0	-10000	0	0
MAPK8	-0.016	0.22	-10000	0	-0.86	7	7
DUSP1	0.019	0.066	-10000	0	-0.51	2	2
NF-kappa-B/RelA	-0.011	0.089	0.16	3	-0.18	19	22
actin cytoskeleton reorganization	-0.051	0.21	-10000	0	-0.57	14	14
mol:Glucocorticoid Dexamethasone	0	0	-10000	0	-10000	0	0
PI3K	-0.075	0.19	-10000	0	-0.48	24	24
FER	-0.073	0.18	-10000	0	-0.4	27	27
RELA	0.034	0	-10000	0	-10000	0	0
ITK	-0.029	0.1	-10000	0	-0.33	11	11
SOS1	0.033	0.006	-10000	0	-10000	0	0
PLCG1	-0.077	0.25	0.29	2	-0.56	25	27
cytokine secretion	-0.017	0.056	-10000	0	-10000	0	0
SPHK1	-0.086	0.2	-10000	0	-0.42	32	32
PTK2	-0.055	0.22	-10000	0	-0.6	14	14
NTAL/PLCgamma1/GRB2/SLP76/GADs	-0.1	0.24	-10000	0	-0.51	32	32
EDG1	0	0	-10000	0	-10000	0	0
mol:DAG	-0.09	0.23	0.28	5	-0.5	29	34
MAP2K2	-0.039	0.25	-10000	0	-0.9	12	12
MAP2K1	-0.04	0.25	-10000	0	-0.9	12	12
MAP2K7	0.03	0.019	-10000	0	-10000	0	0
KLRG1/SHP2	-0.052	0.17	0.2	3	-0.42	20	23
MAP2K4	-0.032	0.28	-10000	0	-0.92	13	13
Fc epsilon R1/FcgammaRIIB	-0.088	0.24	-10000	0	-0.41	47	47
mol:Choline	-0.086	0.17	0.34	4	-0.34	41	45
SHC/Grb2/SOS1	-0.031	0.19	-10000	0	-0.42	21	21
FYN	0.026	0.062	-10000	0	-0.51	2	2
DOK1	0.033	0.006	-10000	0	-10000	0	0
PXN	-0.051	0.2	-10000	0	-0.55	14	14
HCLS1	-0.079	0.2	0.21	1	-0.43	29	30
PRKCB	-0.062	0.17	0.24	6	-0.36	30	36
FCGR2B	-0.024	0.16	-10000	0	-0.51	16	16
IGHE	-0.002	0.009	-10000	0	-10000	0	0
KLRG1/SHIP	-0.068	0.16	-10000	0	-0.37	26	26
LCP2	-0.011	0.15	-10000	0	-0.51	12	12
PLA2G4A	-0.1	0.2	-10000	0	-0.39	40	40
RASA1	0.028	0.044	-10000	0	-0.51	1	1
mol:Phosphatidic acid	-0.086	0.17	0.34	4	-0.34	41	45
IKK complex	-0.017	0.11	0.2	9	-0.22	19	28
WIPF1	0.011	0.1	-10000	0	-0.51	6	6

Glucocorticoid receptor regulatory network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PCK2	0.1	0.11	0.38	8	-10000	0	8
SMARCC2	0.034	0.004	-10000	0	-10000	0	0
SMARCC1	0.024	0.062	-10000	0	-0.51	2	2
TBX21	-0.19	0.3	0.38	1	-0.74	30	31
SUMO2	0.032	0.019	-10000	0	-10000	0	0
STAT1 (dimer)	0.004	0.13	-10000	0	-0.46	10	10
FKBP4	0.028	0.044	-10000	0	-0.51	1	1
FKBP5	0.024	0.064	-10000	0	-0.51	2	2
GR alpha/HSP90/FKBP51/HSP90	0.14	0.12	0.32	31	-10000	0	31
PRL	-0.077	0.13	-10000	0	-10000	0	0
cortisol/GR alpha (dimer)/TIF2	0.23	0.26	0.6	40	-10000	0	40
RELA	-0.068	0.11	-10000	0	-0.22	27	27
FGG	0.17	0.24	0.5	36	-0.57	3	39
GR beta/TIF2	0.13	0.14	0.34	30	-10000	0	30
IFNG	-0.46	0.52	-10000	0	-1.1	53	53
apoptosis	0.044	0.21	0.51	12	-0.54	5	17
CREB1	0.036	0.046	-10000	0	-0.5	1	1
histone acetylation	-0.064	0.17	0.3	3	-0.4	21	24
BGLAP	-0.11	0.16	-10000	0	-0.55	7	7
GR/PKAc	0.15	0.12	0.34	25	-10000	0	25
NF kappa B1 p50/RelA	-0.13	0.18	-10000	0	-0.35	51	51
SMARCD1	0.034	0.004	-10000	0	-10000	0	0
MDM2	0.1	0.11	0.24	49	-0.14	1	50
GATA3	0.037	0.029	-10000	0	-10000	0	0
AKT1	0.019	0.062	-10000	0	-0.51	2	2
CSF2	-0.18	0.38	-10000	0	-1.2	16	16
GSK3B	0.027	0.021	-10000	0	-10000	0	0
NR1I3	0.062	0.21	0.54	9	-0.64	3	12
CSN2	0.17	0.18	0.42	40	-10000	0	40
BRG1/BAF155/BAF170/BAF60A	0.072	0.052	-10000	0	-0.29	2	2
NFATC1	0.012	0.12	-10000	0	-0.5	8	8
POU2F1	0.037	0.016	-10000	0	-10000	0	0
CDKN1A	-0.026	0.22	-10000	0	-1.5	3	3
response to stress	0	0	-10000	0	-10000	0	0
response to UV	0.001	0.011	-10000	0	-10000	0	0
SFN	-0.027	0.17	-10000	0	-0.51	17	17
GR alpha/HSP90/FKBP51/HSP90/14-3-3	0.11	0.14	0.33	18	-0.32	3	21
prolactin receptor activity	0	0	-10000	0	-10000	0	0
EGR1	0.001	0.3	0.5	9	-0.78	16	25
JUN	-0.2	0.25	0.37	1	-0.51	46	47
IL4	-0.13	0.22	-10000	0	-0.65	15	15
CDK5R1	0.032	0.017	-10000	0	-10000	0	0
PRKACA	0.033	0.007	-10000	0	-10000	0	0
cortisol/GR alpha (monomer)/AP-1	-0.13	0.23	0.22	12	-0.47	38	50
GR alpha/HSP90/FKBP51/HSP90/PP5C	0.14	0.12	0.34	20	-10000	0	20
cortisol/GR alpha (monomer)	0.29	0.33	0.7	50	-10000	0	50
NCOA2	0.025	0.062	-10000	0	-0.51	2	2
response to hypoxia	0	0	-10000	0	-10000	0	0
FOS	-0.095	0.17	-10000	0	-0.47	19	19
AP-1/NFAT1-c-4	-0.33	0.39	-10000	0	-0.76	56	56
AFP	-0.15	0.22	-10000	0	-0.8	5	5
SUV420H1	0.034	0.005	-10000	0	-10000	0	0
IRF1	0.12	0.23	0.44	23	-0.85	4	27
TP53	0.024	0.11	-10000	0	-0.5	6	6
PPP5C	0.03	0.044	-10000	0	-0.51	1	1
KRT17	-0.44	0.56	-10000	0	-1.2	49	49
KRT14	-0.38	0.56	-10000	0	-1.4	35	35
TBP	0.041	0.012	-10000	0	-10000	0	0
CREBBP	0.098	0.11	0.31	29	-10000	0	29
HDAC1	0.028	0.011	-10000	0	-10000	0	0
HDAC2	0.042	0.026	-10000	0	-10000	0	0
AP-1	-0.34	0.39	-10000	0	-0.76	56	56
MAPK14	0.034	0.015	-10000	0	-10000	0	0
MAPK10	0.001	0.092	-10000	0	-0.5	4	4
MAPK11	0.031	0.02	-10000	0	-10000	0	0
KRT5	-0.42	0.55	-10000	0	-1.2	42	42
interleukin-1 receptor activity	0.008	0.025	-10000	0	-10000	0	0
NCOA1	0.035	0.01	-10000	0	-10000	0	0
STAT1	0.004	0.13	-10000	0	-0.46	10	10
CGA	-0.11	0.17	-10000	0	-0.53	12	12
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2	0.14	0.23	0.47	37	-0.29	1	38
MAPK3	0.033	0.018	-10000	0	-10000	0	0
MAPK1	0.029	0.046	-10000	0	-0.51	1	1
ICAM1	-0.26	0.36	-10000	0	-0.81	33	33
NFKB1	-0.067	0.11	-10000	0	-0.21	33	33
MAPK8	-0.15	0.22	0.43	1	-0.45	40	41
MAPK9	0.032	0.015	-10000	0	-10000	0	0
cortisol/GR alpha (dimer)	0.042	0.21	0.51	12	-0.56	5	17
BAX	-0.009	0.091	-10000	0	-10000	0	0
POMC	-0.25	0.49	-10000	0	-1.7	15	15
EP300	0.067	0.15	0.29	26	-0.45	7	33
cortisol/GR alpha (dimer)/p53	0.23	0.26	0.59	40	-10000	0	40
proteasomal ubiquitin-dependent protein catabolic process	0.071	0.1	0.23	33	-10000	0	33
SGK1	0.1	0.15	0.35	31	-0.28	3	34
IL13	-0.22	0.27	-10000	0	-0.72	22	22
IL6	-0.3	0.42	-10000	0	-0.94	35	35
PRKACG	0.033	0.007	-10000	0	-10000	0	0
IL5	-0.2	0.22	-10000	0	-0.72	10	10
IL2	-0.3	0.36	-10000	0	-0.91	28	28
CDK5	0.035	0.007	-10000	0	-10000	0	0
PRKACB	0.029	0.045	-10000	0	-0.51	1	1
HSP90AA1	0.033	0.008	-10000	0	-10000	0	0
IL8	-0.42	0.5	-10000	0	-1.1	52	52
CDK5R1/CDK5	0.049	0.021	-10000	0	-10000	0	0
NF kappa B1 p50/RelA/PKAc	-0.062	0.17	-10000	0	-0.36	15	15
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90	0.23	0.26	0.57	46	-10000	0	46
SMARCA4	0.032	0.011	-10000	0	-10000	0	0
chromatin remodeling	0.16	0.17	0.38	39	-10000	0	39
NF kappa B1 p50/RelA/Cbp	-0.041	0.2	0.38	5	-0.38	21	26
JUN (dimer)	-0.19	0.25	0.37	1	-0.51	46	47
YWHAH	0.026	0.062	-10000	0	-0.51	2	2
VIPR1	-0.12	0.2	-10000	0	-0.66	13	13
NR3C1	0.19	0.22	0.48	44	-10000	0	44
NR4A1	-0.009	0.14	-10000	0	-0.44	14	14
TIF2/SUV420H1	0.043	0.039	-10000	0	-0.37	1	1
MAPKKK cascade	0.044	0.21	0.51	12	-0.54	5	17
cortisol/GR alpha (dimer)/Src-1	0.25	0.27	0.59	48	-10000	0	48
PBX1	0.015	0.11	-10000	0	-0.5	6	6
POU1F1	0.034	0.018	-10000	0	-10000	0	0
SELE	-0.39	0.48	-10000	0	-1	47	47
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A	0.16	0.17	0.38	39	-10000	0	39
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90	0.23	0.26	0.57	46	-10000	0	46
mol:cortisol	0.17	0.21	0.41	55	-10000	0	55
MMP1	-0.38	0.57	-10000	0	-1.3	39	39

Endothelins

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
AKT1	-0.012	0.2	0.27	19	-0.38	25	44
PTK2B	0.028	0.017	-10000	0	-10000	0	0
mol:Ca2+	-0.08	0.28	-10000	0	-0.88	12	12
EDN1	-0.02	0.21	0.24	15	-0.45	24	39
EDN3	0.014	0.069	-10000	0	-0.51	2	2
EDN2	-0.14	0.23	-10000	0	-0.51	43	43
HRAS/GDP	-0.053	0.2	-10000	0	-0.47	20	20
ETA receptor/Endothelin-1/Gq/GTP/PLC beta	-0.039	0.18	-10000	0	-0.41	18	18
ADCY4	-0.022	0.17	0.35	1	-0.37	22	23
ADCY5	-0.024	0.15	0.27	1	-0.36	19	20
ADCY6	-0.016	0.17	0.31	2	-0.36	19	21
ADCY7	-0.02	0.17	0.31	2	-0.37	20	22
ADCY1	-0.017	0.17	0.31	2	-0.36	20	22
ADCY2	-0.024	0.16	0.31	2	-0.37	17	19
ADCY3	-0.022	0.17	0.31	2	-0.35	22	24
ADCY8	-0.024	0.16	0.35	1	-0.36	19	20
ADCY9	-0.02	0.17	0.31	2	-0.36	20	22
arachidonic acid secretion	-0.11	0.24	-10000	0	-0.5	32	32
ETB receptor/Endothelin-1/Gq/GTP	-0.056	0.17	-10000	0	-0.34	29	29
GNAO1	0.032	0.011	-10000	0	-10000	0	0
HRAS	0.029	0.045	-10000	0	-0.51	1	1
ETA receptor/Endothelin-1/G12/GTP	0.03	0.21	0.38	17	-0.38	20	37
ETA receptor/Endothelin-1/Gs/GTP	0.014	0.2	0.34	16	-0.34	26	42
mol:GTP	-0.001	0.006	-10000	0	-10000	0	0
COL3A1	-0.04	0.26	0.28	16	-0.54	25	41
EDNRB	0.002	0.096	-10000	0	-0.4	6	6
response to oxidative stress	0	0	-10000	0	-10000	0	0
CYSLTR2	-0.007	0.19	0.28	16	-0.42	18	34
CYSLTR1	-0.012	0.2	0.28	16	-0.42	20	36
SLC9A1	0.002	0.12	0.2	12	-0.29	10	22
mol:GDP	-0.065	0.21	-10000	0	-0.48	21	21
SLC9A3	-0.1	0.32	-10000	0	-0.7	29	29
RAF1	-0.076	0.2	-10000	0	-0.45	25	25
JUN	-0.091	0.31	-10000	0	-0.82	18	18
JAK2	-0.014	0.19	0.27	15	-0.37	24	39
mol:IP3	-0.048	0.17	-10000	0	-0.42	18	18
ETA receptor/Endothelin-1	0.019	0.25	0.44	18	-0.43	25	43
PLCB1	0.014	0.096	-10000	0	-0.51	5	5
PLCB2	0.032	0.01	-10000	0	-10000	0	0
ETA receptor/Endothelin-3	0.029	0.12	-10000	0	-0.38	7	7
FOS	-0.12	0.31	-10000	0	-0.84	20	20
Gai/GDP	-0.064	0.26	-10000	0	-0.73	16	16
CRK	0.032	0.008	-10000	0	-10000	0	0
mol:Ca ++	-0.062	0.24	-10000	0	-0.55	23	23
BCAR1	0.033	0.008	-10000	0	-10000	0	0
PRKCB1	-0.048	0.17	-10000	0	-0.39	20	20
GNAQ	-0.001	0.006	-10000	0	-10000	0	0
GNAZ	0.005	0.11	-10000	0	-0.51	7	7
GNAL	0.009	0.098	-10000	0	-0.51	5	5
Gs family/GDP	-0.062	0.19	-10000	0	-0.45	20	20
ETA receptor/Endothelin-1/Gq/GTP	-0.043	0.2	0.21	9	-0.39	24	33
MAPK14	-0.052	0.15	-10000	0	-0.41	15	15
TRPC6	-0.088	0.3	-10000	0	-1	11	11
GNAI2	0.029	0.018	-10000	0	-10000	0	0
GNAI3	0.033	0.007	-10000	0	-10000	0	0
GNAI1	0.001	0.13	-10000	0	-0.51	9	9
ETB receptor/Endothelin-1/Gq/GTP/PLC beta	-0.052	0.16	-10000	0	-0.37	21	21
ETB receptor/Endothelin-2	-0.11	0.19	-10000	0	-0.38	46	46
ETB receptor/Endothelin-3	0.011	0.09	-10000	0	-0.37	6	6
ETB receptor/Endothelin-1	-0.015	0.18	-10000	0	-0.38	25	25
MAPK3	-0.11	0.28	-10000	0	-0.75	20	20
MAPK1	-0.11	0.29	-10000	0	-0.79	20	20
Rac1/GDP	-0.051	0.2	-10000	0	-0.45	20	20
cAMP biosynthetic process	0.005	0.16	0.27	8	-0.44	10	18
MAPK8	-0.08	0.3	-10000	0	-0.74	18	18
SRC	0.032	0.012	-10000	0	-10000	0	0
ETB receptor/Endothelin-1/Gi/GTP	-0.042	0.16	0.17	1	-0.36	20	21
p130Cas/CRK/Src/PYK2	-0.074	0.22	-10000	0	-0.52	21	21
mol:K +	0	0	-10000	0	-10000	0	0
G12/GDP	-0.05	0.2	-10000	0	-0.45	20	20
COL1A2	-0.056	0.29	-10000	0	-0.62	24	24
EntrezGene:2778	0	0	-10000	0	-10000	0	0
ETA receptor/Endothelin-2	-0.096	0.2	-10000	0	-0.38	46	46
mol:DAG	-0.048	0.17	-10000	0	-0.42	18	18
MAP2K2	-0.091	0.23	-10000	0	-0.58	21	21
MAP2K1	-0.092	0.23	-10000	0	-0.57	22	22
EDNRA	0.028	0.14	0.24	18	-0.47	7	25
positive regulation of muscle contraction	-0.011	0.18	0.24	17	-0.38	18	35
Gq family/GDP	-0.059	0.2	-10000	0	-0.49	18	18
HRAS/GTP	-0.063	0.19	-10000	0	-0.44	21	21
PRKCH	-0.059	0.19	-10000	0	-0.45	20	20
RAC1	0.033	0.006	-10000	0	-10000	0	0
PRKCA	-0.051	0.17	-10000	0	-0.44	15	15
PRKCB	-0.049	0.17	-10000	0	-0.39	20	20
PRKCE	-0.038	0.16	0.25	4	-0.4	16	20
PRKCD	-0.054	0.16	-10000	0	-0.41	17	17
PRKCG	-0.049	0.16	-10000	0	-0.43	15	15
regulation of vascular smooth muscle contraction	-0.14	0.36	-10000	0	-1	20	20
PRKCQ	-0.065	0.18	-10000	0	-0.43	21	21
PLA2G4A	-0.12	0.26	-10000	0	-0.55	32	32
GNA14	0.011	0.08	-10000	0	-0.51	3	3
GNA15	-0.011	0.14	-10000	0	-0.51	11	11
GNA12	0.033	0.008	-10000	0	-10000	0	0
GNA11	0.023	0.063	-10000	0	-0.51	2	2
Rac1/GTP	0.03	0.21	0.38	17	-0.35	24	41
MMP1	-0.24	0.4	0.54	1	-0.91	39	40

Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Noncanonical Wnts/FZD	-0.13	0.2	-9999	-0.36	55	55
FZD6	0.013	0.096	-9999	-0.51	5	5
WNT6	0.028	0.024	-9999	-10000	0	0
WNT4	-0.069	0.2	-9999	-0.51	27	27
FZD3	-0.006	0.13	-9999	-0.51	9	9
WNT5A	-0.084	0.2	-9999	-0.51	28	28
WNT11	0.004	0.092	-9999	-0.51	4	4

Syndecan-1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.033	0.006	-10000	0	-10000	0	0
CCL5	-0.022	0.16	-10000	0	-0.51	15	15
SDCBP	0.029	0.044	-10000	0	-0.51	1	1
FGFR/FGF2/Syndecan-1	-0.13	0.25	0.22	1	-0.61	26	27
mol:PI-4-5-P2	0	0	-10000	0	-10000	0	0
RP11-540L11.1	0	0	-10000	0	-10000	0	0
Syndecan-1/Laminin-5	-0.12	0.26	-10000	0	-0.6	27	27
Syndecan-1/Syntenin	-0.11	0.25	-10000	0	-0.63	23	23
MAPK3	-0.11	0.23	-10000	0	-0.54	26	26
HGF/MET	0.037	0.061	-10000	0	-0.37	3	3
TGFB1/TGF beta receptor Type II	0.033	0.006	-10000	0	-10000	0	0
BSG	0.033	0.007	-10000	0	-10000	0	0
keratinocyte migration	-0.12	0.26	-10000	0	-0.59	27	27
Syndecan-1/RANTES	-0.14	0.29	-10000	0	-0.62	31	31
Syndecan-1/CD147	-0.1	0.25	-10000	0	-0.57	26	26
Syndecan-1/Syntenin/PIP2	-0.11	0.24	-10000	0	-0.61	23	23
LAMA5	0.012	0.1	-10000	0	-0.51	6	6
positive regulation of cell-cell adhesion	-0.11	0.24	-10000	0	-0.59	23	23
MMP7	-0.044	0.19	-10000	0	-0.51	22	22
HGF	0.03	0.019	-10000	0	-10000	0	0
Syndecan-1/CASK	-0.13	0.24	-10000	0	-0.58	26	26
Syndecan-1/HGF/MET	-0.1	0.26	-10000	0	-0.59	25	25
regulation of cell adhesion	-0.11	0.22	-10000	0	-0.54	24	24
HPSE	0.005	0.11	-10000	0	-0.51	7	7
positive regulation of cell migration	-0.13	0.25	0.22	1	-0.61	26	27
SDC1	-0.13	0.26	-10000	0	-0.61	26	26
Syndecan-1/Collagen	-0.13	0.25	0.22	1	-0.61	26	27
PPIB	0.03	0.045	-10000	0	-0.51	1	1
MET	0.021	0.076	-10000	0	-0.51	3	3
PRKACA	0.033	0.007	-10000	0	-10000	0	0
MMP9	-0.013	0.15	-10000	0	-0.51	13	13
MAPK1	-0.11	0.23	-10000	0	-0.54	25	25
homophilic cell adhesion	-0.13	0.25	0.22	1	-0.6	26	27
MMP1	-0.12	0.23	-10000	0	-0.51	39	39

Thromboxane A2 receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGM2	-0.001	0.12	-10000	0	-0.51	8	8
GNB1/GNG2	-0.064	0.081	-10000	0	-0.19	41	41
AKT1	-0.04	0.12	0.24	1	-0.26	10	11
EGF	-0.031	0.15	-10000	0	-0.51	13	13
mol:TXA2	0	0.001	-10000	0	-10000	0	0
FGR	0.012	0.058	0.24	2	-10000	0	2
mol:Ca2+	-0.068	0.16	-10000	0	-0.3	44	44
LYN	0.011	0.06	0.24	2	-10000	0	2
RhoA/GTP	-0.028	0.071	-10000	0	-0.13	28	28
mol:PGI2	0	0	-10000	0	-10000	0	0
SYK	-0.088	0.18	-10000	0	-0.35	44	44
GNG2	0.034	0.005	-10000	0	-10000	0	0
ARRB2	0.032	0.008	-10000	0	-10000	0	0
TP alpha/Gq family/GDP/G beta5/gamma2	-0.031	0.17	-10000	0	-0.45	18	18
G beta5/gamma2	-0.073	0.12	-10000	0	-0.25	39	39
PRKCH	-0.089	0.19	-10000	0	-0.37	44	44
DNM1	0.028	0.046	-10000	0	-0.51	1	1
TXA2/TP beta/beta Arrestin3	0.011	0.11	-10000	0	-0.55	5	5
mol:GTP	0	0.001	-10000	0	-10000	0	0
PTGDR	0.028	0.024	-10000	0	-10000	0	0
G12 family/GTP	-0.077	0.16	-10000	0	-0.31	42	42
ADRBK1	0.034	0.005	-10000	0	-10000	0	0
ADRBK2	0.024	0.063	-10000	0	-0.51	2	2
RhoA/GTP/ROCK1	0.041	0.015	-10000	0	-10000	0	0
mol:GDP	0.03	0.12	0.46	5	-10000	0	5
mol:NADP	0.03	0.022	-10000	0	-10000	0	0
RAB11A	0.034	0.004	-10000	0	-10000	0	0
PRKG1	0.03	0.019	-10000	0	-10000	0	0
mol:IP3	-0.09	0.2	-10000	0	-0.38	44	44
cell morphogenesis	0.04	0.015	-10000	0	-10000	0	0
PLCB2	-0.13	0.27	-10000	0	-0.52	44	44
mol:cGMP	0	0.001	-10000	0	-10000	0	0
BLK	0.008	0.064	0.24	2	-0.24	2	4
mol:PDG2	0	0	-10000	0	-10000	0	0
HCK	0	0.077	0.24	2	-0.25	6	8
RHOA	0.031	0.011	-10000	0	-10000	0	0
PTGIR	0.026	0.062	-10000	0	-0.51	2	2
PRKCB1	-0.092	0.2	-10000	0	-0.38	45	45
GNAQ	0	0	-10000	0	-10000	0	0
mol:L-citrulline	0.03	0.022	-10000	0	-10000	0	0
TXA2/TXA2-R family	-0.13	0.27	-10000	0	-0.53	44	44
LCK	0	0.075	0.24	2	-0.24	2	4
TXA2/TP beta/beta Arrestin3/RAB11/GDP	0.039	0.044	-10000	0	-10000	0	0
TXA2-R family/G12 family/GDP/G beta/gamma	0.016	0.096	-10000	0	-0.38	8	8
TXA2/TP beta/beta Arrestin2/RAB11/GDP	0.038	0.045	-10000	0	-10000	0	0
MAPK14	-0.055	0.12	-10000	0	-0.24	42	42
TGM2/GTP	-0.11	0.23	-10000	0	-0.44	43	43
MAPK11	-0.054	0.12	-10000	0	-0.24	41	41
ARHGEF1	-0.041	0.097	-10000	0	-0.18	40	40
GNAI2	0.029	0.018	-10000	0	-10000	0	0
JNK cascade	-0.092	0.2	-10000	0	-0.39	44	44
RAB11/GDP	0.034	0.004	-10000	0	-10000	0	0
ICAM1	-0.069	0.16	-10000	0	-0.3	43	43
cAMP biosynthetic process	-0.085	0.19	-10000	0	-0.35	45	45
Gq family/GTP/EBP50	-0.042	0.13	-10000	0	-0.29	29	29
actin cytoskeleton reorganization	0.04	0.015	-10000	0	-10000	0	0
SRC	0.012	0.058	0.24	2	-10000	0	2
GNB5	0.02	0.086	-10000	0	-0.51	4	4
GNB1	0.033	0.007	-10000	0	-10000	0	0
EGF/EGFR	-0.015	0.11	0.22	4	-0.33	8	12
VCAM1	-0.073	0.17	-10000	0	-0.31	44	44
TP beta/Gq family/GDP/G beta5/gamma2	-0.031	0.17	-10000	0	-0.45	18	18
platelet activation	-0.071	0.16	-10000	0	-0.3	42	42
PGI2/IP	0.019	0.045	-10000	0	-0.37	2	2
PRKACA	0.016	0.033	-10000	0	-0.25	2	2
Gq family/GDP/G beta5/gamma2	-0.02	0.14	-10000	0	-0.39	16	16
TXA2/TP beta/beta Arrestin2	0.016	0.065	-10000	0	-0.43	2	2
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TBXA2R	0.007	0.031	-10000	0	-0.24	2	2
mol:DAG	-0.1	0.22	-10000	0	-0.43	45	45
EGFR	-0.031	0.17	-10000	0	-0.51	17	17
TXA2/TP alpha	-0.12	0.25	-10000	0	-0.48	45	45
Gq family/GTP	-0.023	0.09	-10000	0	-0.25	19	19
YES1	0.011	0.058	0.24	2	-0.24	1	3
GNAI2/GTP	0.019	0.045	-10000	0	-0.23	1	1
PGD2/DP	0.021	0.016	-10000	0	-10000	0	0
SLC9A3R1	-0.033	0.17	-10000	0	-0.51	18	18
FYN	0.011	0.068	0.24	2	-0.32	2	4
mol:NO	0.03	0.022	-10000	0	-10000	0	0
GNA15	-0.007	0.14	-10000	0	-0.51	11	11
PGK/cGMP	0.038	0.023	-10000	0	-10000	0	0
RhoA/GDP	0.031	0.011	-10000	0	-10000	0	0
TP alpha/TGM2/GDP/G beta/gamma	0.037	0.09	-10000	0	-0.34	4	4
NOS3	0.03	0.022	-10000	0	-10000	0	0
RAC1	0.033	0.006	-10000	0	-10000	0	0
PRKCA	-0.084	0.19	-10000	0	-0.36	44	44
PRKCB	-0.087	0.19	-10000	0	-0.36	45	45
PRKCE	-0.077	0.18	-10000	0	-0.36	37	37
PRKCD	-0.1	0.2	-10000	0	-0.39	44	44
PRKCG	-0.095	0.21	-10000	0	-0.39	45	45
muscle contraction	-0.12	0.25	-10000	0	-0.49	44	44
PRKCZ	-0.081	0.18	-10000	0	-0.34	44	44
ARR3	0.033	0.006	-10000	0	-10000	0	0
TXA2/TP beta	0.034	0.054	-10000	0	-0.24	2	2
PRKCQ	-0.096	0.19	-10000	0	-0.38	44	44
MAPKKK cascade	-0.11	0.24	-10000	0	-0.45	46	46
SELE	-0.093	0.2	-10000	0	-0.38	44	44
TP beta/GNAI2/GDP/G beta/gamma	0.054	0.049	-10000	0	-10000	0	0
ROCK1	0.034	0.005	-10000	0	-10000	0	0
GNA14	0.016	0.079	-10000	0	-0.51	3	3
chemotaxis	-0.16	0.31	-10000	0	-0.62	43	43
GNA12	0.033	0.008	-10000	0	-10000	0	0
GNA13	0.03	0.045	-10000	0	-0.51	1	1
GNA11	0.026	0.062	-10000	0	-0.51	2	2
Rac1/GTP	0.024	0.005	-10000	0	-10000	0	0

EPHB forward signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Ephrin A5/EPHB2	0.007	0.1	-10000	0	-0.31	13	13
cell-cell adhesion	0.078	0.12	0.3	30	-10000	0	30
Ephrin B/EPHB2/RasGAP	-0.012	0.17	-10000	0	-0.31	33	33
ITSN1	0.034	0.003	-10000	0	-10000	0	0
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
SHC1	0.032	0.008	-10000	0	-10000	0	0
Ephrin B1/EPHB3	-0.039	0.14	-10000	0	-0.36	22	22
Ephrin B1/EPHB1	-0.023	0.13	-10000	0	-0.35	18	18
HRAS/GDP	-0.11	0.16	-10000	0	-0.4	23	23
Ephrin B/EPHB1/GRB7	-0.005	0.15	-10000	0	-0.33	21	21
Endophilin/SYNJ1	-0.055	0.13	-10000	0	-0.29	33	33
KRAS	0.017	0.086	-10000	0	-0.51	4	4
Ephrin B/EPHB1/Src	-0.004	0.14	-10000	0	-0.32	20	20
endothelial cell migration	-0.005	0.1	-10000	0	-0.36	9	9
GRB2	0.034	0.005	-10000	0	-10000	0	0
GRB7	0.033	0.007	-10000	0	-10000	0	0
PAK1	-0.046	0.14	-10000	0	-0.32	24	24
HRAS	0.029	0.045	-10000	0	-0.51	1	1
RRAS	-0.061	0.14	-10000	0	-0.29	36	36
DNM1	0.028	0.046	-10000	0	-0.51	1	1
cell-cell signaling	0	0	-10000	0	-10000	0	0
CRK	-0.02	0.14	-10000	0	-0.31	21	21
lamellipodium assembly	-0.078	0.12	-10000	0	-0.3	30	30
Ephrin B/EPHB1/Src/p52 SHC/GRB2	-0.022	0.11	-10000	0	-0.38	7	7
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
EPHB2	-0.02	0.15	-10000	0	-0.51	13	13
EPHB3	-0.026	0.14	-10000	0	-0.51	12	12
EPHB1	-0.008	0.1	-10000	0	-0.51	5	5
EPHB4	0.013	0.097	-10000	0	-0.51	5	5
mol:GDP	-0.1	0.16	-10000	0	-0.41	22	22
Ephrin B/EPHB2	-0.019	0.16	-10000	0	-0.31	32	32
Ephrin B/EPHB3	-0.034	0.14	-10000	0	-0.34	24	24
JNK cascade	-0.005	0.2	0.36	22	-0.31	29	51
Ephrin B/EPHB1	-0.013	0.14	-10000	0	-0.33	21	21
RAP1/GDP	-0.09	0.16	-10000	0	-0.39	19	19
EFNB2	0.004	0.11	-10000	0	-0.51	7	7
EFNB3	0.032	0.009	-10000	0	-10000	0	0
EFNB1	-0.027	0.17	-10000	0	-0.51	17	17
Ephrin B2/EPHB1-2	-0.016	0.12	-10000	0	-0.3	19	19
RAP1B	0.033	0.007	-10000	0	-10000	0	0
RAP1A	0.026	0.062	-10000	0	-0.51	2	2
CDC42/GTP	-0.049	0.16	-10000	0	-0.35	28	28
Rap1/GTP	-0.055	0.13	-10000	0	-0.35	14	14
axon guidance	0.006	0.1	-10000	0	-0.31	13	13
MAPK3	-0.024	0.094	-10000	0	-0.37	6	6
MAPK1	-0.02	0.1	0.2	4	-0.37	7	11
Rac1/GDP	-0.098	0.16	-10000	0	-0.38	21	21
actin cytoskeleton reorganization	-0.098	0.12	-10000	0	-0.36	18	18
CDC42/GDP	-0.097	0.16	-10000	0	-0.39	21	21
PI3K	-0.003	0.11	-10000	0	-0.36	9	9
EFNA5	0.032	0.012	-10000	0	-10000	0	0
Ephrin B2/EPHB4	0.013	0.1	-10000	0	-0.38	9	9
Ephrin B/EPHB2/Intersectin/N-WASP	-0.053	0.15	-10000	0	-0.31	34	34
CDC42	0.034	0.005	-10000	0	-10000	0	0
RAS family/GTP	-0.062	0.14	-10000	0	-0.43	10	10
PTK2	0.048	0.17	0.62	11	-0.49	1	12
MAP4K4	-0.006	0.2	0.36	22	-0.32	29	51
SRC	0.032	0.012	-10000	0	-10000	0	0
KALRN	0.027	0.019	-10000	0	-10000	0	0
Intersectin/N-WASP	0.039	0.067	-10000	0	-0.37	4	4
neuron projection morphogenesis	-0.03	0.17	0.34	13	-0.42	9	22
MAP2K1	-0.023	0.1	-10000	0	-0.36	7	7
WASL	0.02	0.086	-10000	0	-0.51	4	4
Ephrin B1/EPHB1-2/NCK1	-0.029	0.16	-10000	0	-0.33	28	28
cell migration	-0.029	0.13	0.3	1	-0.38	10	11
NRAS	0.026	0.047	-10000	0	-0.51	1	1
SYNJ1	-0.056	0.13	-10000	0	-0.3	33	33
PXN	0.034	0.004	-10000	0	-10000	0	0
TF	-0.066	0.11	-10000	0	-0.28	28	28
HRAS/GTP	-0.042	0.15	-10000	0	-0.3	31	31
Ephrin B1/EPHB1-2	-0.037	0.15	-10000	0	-0.33	28	28
cell adhesion mediated by integrin	0.02	0.13	0.33	17	-0.19	1	18
RAC1	0.033	0.006	-10000	0	-10000	0	0
mol:GTP	-0.036	0.15	-10000	0	-0.3	32	32
RAC1-CDC42/GTP	-0.065	0.13	-10000	0	-0.43	10	10
RASA1	0.028	0.044	-10000	0	-0.51	1	1
RAC1-CDC42/GDP	-0.088	0.16	-10000	0	-0.39	18	18
ruffle organization	-0.055	0.16	0.36	4	-0.46	9	13
NCK1	0.021	0.062	-10000	0	-0.51	2	2
receptor internalization	-0.074	0.12	-10000	0	-0.3	30	30
Ephrin B/EPHB2/KALRN	-0.01	0.16	-10000	0	-0.31	28	28
ROCK1	0.044	0.18	0.19	71	-0.33	22	93
RAS family/GDP	-0.11	0.12	-10000	0	-0.38	17	17
Rac1/GTP	-0.063	0.14	-10000	0	-0.33	28	28
Ephrin B/EPHB1/Src/Paxillin	-0.031	0.12	-10000	0	-0.3	20	20

Signaling events mediated by the Hedgehog family

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB2	-0.14	0.28	-10000	0	-0.57	42	42
IHH	-0.014	0.09	-10000	0	-0.54	1	1
SHH Np/Cholesterol/GAS1	-0.042	0.14	-10000	0	-0.32	28	28
LRPAP1	0.031	0.011	-10000	0	-10000	0	0
dorsoventral neural tube patterning	0.042	0.14	0.32	28	-10000	0	28
SMO/beta Arrestin2	-0.12	0.24	-10000	0	-0.6	19	19
SMO	-0.13	0.24	-10000	0	-0.6	21	21
AKT1	-0.073	0.22	-10000	0	-0.72	12	12
ARRB2	0.032	0.008	-10000	0	-10000	0	0
BOC	0.023	0.026	-10000	0	-10000	0	0
ADRBK1	0.034	0.005	-10000	0	-10000	0	0
heart looping	-0.13	0.24	-10000	0	-0.59	21	21
STIL	-0.077	0.16	-10000	0	-0.46	11	11
DHH N/PTCH2	0.049	0.011	-10000	0	-10000	0	0
DHH N/PTCH1	-0.05	0.16	-10000	0	-0.3	41	41
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
DHH	0.034	0.004	-10000	0	-10000	0	0
PTHLH	-0.25	0.45	-10000	0	-0.96	43	43
determination of left/right symmetry	-0.13	0.24	-10000	0	-0.59	21	21
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
skeletal system development	-0.25	0.44	-10000	0	-0.94	43	43
IHH N/Hhip	-0.054	0.16	-10000	0	-0.42	21	21
DHH N/Hhip	-0.023	0.14	-10000	0	-0.37	19	19
mol:Cholesterol	0	0	-10000	0	-10000	0	0
heart development	-0.13	0.24	-10000	0	-0.59	21	21
pancreas development	-0.057	0.18	-10000	0	-0.51	20	20
HHAT	-0.005	0.14	-10000	0	-0.51	11	11
PI3K	0.004	0.076	-10000	0	-0.3	7	7
EntrezGene:84976	0	0	-10000	0	-10000	0	0
GAS1	-0.051	0.18	-10000	0	-0.51	21	21
somite specification	-0.13	0.24	-10000	0	-0.59	21	21
SHH Np/Cholesterol/PTCH1	-0.069	0.16	-10000	0	-0.46	11	11
SHH Np/Cholesterol/PTCH2	0.008	0.086	-10000	0	-0.29	12	12
SHH Np/Cholesterol/Megalin	0.002	0.091	-10000	0	-0.29	13	13
SHH	-0.013	0.1	-10000	0	-0.37	12	12
catabolic process	-0.069	0.17	-10000	0	-0.34	42	42
SMO/Vitamin D3	-0.1	0.2	-10000	0	-0.53	18	18
SHH Np/Cholesterol/Hhip	-0.044	0.13	-10000	0	-0.3	29	29
LRP2	0.022	0.052	-10000	0	-0.51	1	1
receptor-mediated endocytosis	-0.1	0.2	-10000	0	-0.52	17	17
SHH Np/Cholesterol/BOC	0	0.086	-10000	0	-0.29	12	12
SHH Np/Cholesterol/CDO	0.006	0.087	-10000	0	-0.29	12	12
mesenchymal cell differentiation	0.043	0.13	0.3	29	-10000	0	29
mol:Vitamin D3	-0.069	0.16	-10000	0	-0.46	11	11
IHH N/PTCH2	0.016	0.062	-10000	0	-0.32	1	1
CDON	0.03	0.02	-10000	0	-10000	0	0
IHH N/PTCH1	-0.062	0.18	-10000	0	-0.34	42	42
Megalin/LRPAP1	0.034	0.045	-10000	0	-0.37	1	1
PTCH2	0.033	0.006	-10000	0	-10000	0	0
SHH Np/Cholesterol	-0.004	0.082	-10000	0	-0.28	12	12
PTCH1	-0.069	0.17	-10000	0	-0.34	42	42
HHIP	-0.057	0.18	-10000	0	-0.51	20	20

Ephrin B reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EFNB2	0.004	0.11	-10000	0	-0.51	7	7
EPHB2	-0.019	0.15	-10000	0	-0.51	13	13
EFNB1	-0.028	0.12	-10000	0	-0.37	17	17
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	-0.021	0.14	-10000	0	-0.3	26	26
Ephrin B2/EPHB1-2	-0.015	0.12	-10000	0	-0.3	19	19
neuron projection morphogenesis	-0.03	0.13	-10000	0	-0.28	27	27
Ephrin B1/EPHB1-2/Tiam1	-0.03	0.15	-10000	0	-0.3	29	29
DNM1	0.029	0.046	-10000	0	-0.51	1	1
cell-cell signaling	0	0.004	-10000	0	-10000	0	0
MAP2K4	-0.076	0.21	-10000	0	-0.59	21	21
YES1	-0.1	0.3	-10000	0	-0.83	22	22
Ephrin B1/EPHB1-2/NCK2	-0.031	0.14	-10000	0	-0.31	29	29
PI3K	-0.064	0.22	-10000	0	-0.62	19	19
mol:GDP	-0.03	0.14	-10000	0	-0.3	29	29
ITGA2B	0.034	0.005	-10000	0	-10000	0	0
endothelial cell proliferation	0.013	0.1	-10000	0	-0.38	9	9
FYN	-0.1	0.3	-10000	0	-0.82	22	22
MAP3K7	-0.082	0.22	-10000	0	-0.61	22	22
FGR	-0.096	0.29	-10000	0	-0.8	22	22
TIAM1	0.034	0.005	-10000	0	-10000	0	0
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
RGS3	0.033	0.006	-10000	0	-10000	0	0
cell adhesion	-0.067	0.21	-10000	0	-0.6	18	18
LYN	-0.1	0.3	-10000	0	-0.81	22	22
Ephrin B1/EPHB1-2/Src Family Kinases	-0.1	0.27	-10000	0	-0.76	22	22
Ephrin B1/EPHB1-2	-0.088	0.24	-10000	0	-0.65	22	22
SRC	-0.096	0.29	-10000	0	-0.8	22	22
ITGB3	0.026	0.048	-10000	0	-0.51	1	1
EPHB1	-0.007	0.1	-10000	0	-0.51	5	5
EPHB4	0.013	0.097	-10000	0	-0.51	5	5
RAC1	0.033	0.006	-10000	0	-10000	0	0
Ephrin B2/EPHB4	0.013	0.1	-10000	0	-0.38	9	9
alphaIIb/beta3 Integrin	0.043	0.04	-10000	0	-0.37	1	1
BLK	-0.11	0.3	-10000	0	-0.82	22	22
HCK	-0.1	0.3	-10000	0	-0.82	22	22
regulation of stress fiber formation	0.032	0.14	0.3	29	-10000	0	29
MAPK8	-0.072	0.2	-10000	0	-0.57	20	20
Ephrin B1/EPHB1-2/RGS3	-0.03	0.15	-10000	0	-0.31	29	29
endothelial cell migration	-0.086	0.22	-10000	0	-0.56	23	23
NCK2	0.034	0.005	-10000	0	-10000	0	0
PTPN13	-0.026	0.18	-10000	0	-0.63	13	13
regulation of focal adhesion formation	0.032	0.14	0.3	29	-10000	0	29
chemotaxis	0.031	0.14	0.3	29	-10000	0	29
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
Rac1/GTP	-0.025	0.14	-10000	0	-0.29	26	26
angiogenesis	-0.087	0.23	-10000	0	-0.65	22	22
LCK	-0.11	0.3	-10000	0	-0.82	22	22

BCR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
JUN	-0.098	0.21	-10000	0	-0.49	27	27
IKBKB	-0.001	0.12	-10000	0	-0.31	12	12
AKT1	0	0.15	0.25	17	-0.26	20	37
IKBKG	-0.007	0.12	-10000	0	-0.3	13	13
CALM1	-0.07	0.25	0.32	1	-0.65	20	21
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
MAP3K1	-0.13	0.29	-10000	0	-0.7	26	26
MAP3K7	0.033	0.009	-10000	0	-10000	0	0
mol:Ca2+	-0.077	0.27	0.34	1	-0.7	20	21
DOK1	0.033	0.006	-10000	0	-10000	0	0
AP-1	-0.053	0.12	0.19	1	-0.28	24	25
LYN	0.029	0.044	-10000	0	-0.51	1	1
BLNK	0.015	0.096	-10000	0	-0.51	5	5
SHC1	0.032	0.008	-10000	0	-10000	0	0
BCR complex	-0.048	0.2	-10000	0	-0.48	25	25
CD22	-0.11	0.31	-10000	0	-0.84	20	20
CAMK2G	-0.062	0.23	0.31	2	-0.6	20	22
CSNK2A1	0.032	0.008	-10000	0	-10000	0	0
INPP5D	0	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1	-0.045	0.17	-10000	0	-0.38	26	26
GO:0007205	-0.08	0.28	0.34	1	-0.73	20	21
SYK	0.012	0.1	-10000	0	-0.51	6	6
ELK1	-0.074	0.26	0.32	1	-0.67	20	21
NFATC1	-0.13	0.28	-10000	0	-0.63	29	29
B-cell antigen/BCR complex	-0.048	0.2	-10000	0	-0.48	25	25
PAG1/CSK	0.029	0.082	-10000	0	-0.37	6	6
NFKBIB	0.018	0.055	0.13	1	-0.12	8	9
HRAS	-0.067	0.23	0.27	1	-0.6	20	21
NFKBIA	0.018	0.055	0.13	1	-0.12	9	10
NF-kappa-B/RelA/I kappa B beta	0.025	0.048	0.13	1	-10000	0	1
RasGAP/Csk	-0.032	0.22	-10000	0	-0.43	30	30
mol:GDP	-0.074	0.26	0.33	1	-0.68	20	21
PTEN	0.027	0.045	-10000	0	-0.51	1	1
CD79B	-0.05	0.19	-10000	0	-0.51	22	22
NF-kappa-B/RelA/I kappa B alpha	0.025	0.048	0.13	1	-10000	0	1
GRB2	0.034	0.005	-10000	0	-10000	0	0
PI3K/BCAP/CD19	-0.12	0.26	-10000	0	-0.63	27	27
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
mol:IP3	-0.082	0.28	0.34	1	-0.74	20	21
CSK	0.034	0.004	-10000	0	-10000	0	0
FOS	-0.091	0.24	0.31	1	-0.62	21	22
CHUK	-0.014	0.13	-10000	0	-0.33	15	15
IBTK	0.03	0.044	-10000	0	-0.51	1	1
CARD11/BCL10/MALT1/TAK1	-0.037	0.22	0.3	1	-0.57	18	19
PTPN6	-0.11	0.28	-10000	0	-0.8	19	19
RELA	0.034	0	-10000	0	-10000	0	0
BCL2A1	0.01	0.045	-10000	0	-0.11	4	4
VAV2	-0.17	0.37	-10000	0	-0.82	31	31
ubiquitin-dependent protein catabolic process	0.021	0.054	0.13	1	-0.12	8	9
BTK	-0.096	0.36	-10000	0	-1.2	14	14
CD19	-0.16	0.36	-10000	0	-0.87	26	26
MAP4K1	0.03	0.011	-10000	0	-10000	0	0
CD72	-0.035	0.17	-10000	0	-0.51	18	18
PAG1	0.009	0.1	-10000	0	-0.51	6	6
MAPK14	-0.1	0.23	-10000	0	-0.56	26	26
SH3BP5	0.027	0.046	-10000	0	-0.51	1	1
PIK3AP1	-0.095	0.3	-10000	0	-0.74	22	22
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72	-0.12	0.37	-10000	0	-0.9	23	23
RAF1	-0.064	0.21	0.26	1	-0.55	20	21
RasGAP/p62DOK/SHIP	-0.037	0.2	-10000	0	-0.41	30	30
CD79A	-0.021	0.15	-10000	0	-0.51	13	13
re-entry into mitotic cell cycle	-0.053	0.12	0.2	1	-0.28	25	26
RASA1	0.028	0.044	-10000	0	-0.51	1	1
MAPK3	-0.054	0.17	0.23	1	-0.47	18	19
MAPK1	-0.045	0.17	0.33	2	-0.46	17	19
CD72/SHP1	-0.089	0.31	0.35	3	-0.71	25	28
NFKB1	0.033	0.008	-10000	0	-10000	0	0
MAPK8	-0.1	0.23	-10000	0	-0.57	25	25
actin cytoskeleton organization	-0.13	0.29	0.35	1	-0.65	31	32
NF-kappa-B/RelA	0.05	0.094	0.24	1	-0.23	2	3
Calcineurin	-0.033	0.22	0.31	1	-0.58	18	19
PI3K	-0.11	0.21	-10000	0	-0.56	23	23
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2	-0.088	0.3	0.37	1	-0.76	21	22
SOS1	0.033	0.006	-10000	0	-10000	0	0
Bam32/HPK1	-0.16	0.38	-10000	0	-0.87	31	31
DAPP1	-0.21	0.44	-10000	0	-1	32	32
cytokine secretion	-0.11	0.25	-10000	0	-0.57	29	29
mol:DAG	-0.082	0.28	0.34	1	-0.74	20	21
PLCG2	0.014	0.096	-10000	0	-0.51	5	5
MAP2K1	-0.059	0.19	0.25	1	-0.53	18	19
B-cell antigen/BCR complex/FcgammaRIIB	-0.057	0.24	-10000	0	-0.5	29	29
mol:PI-3-4-5-P3	-0.039	0.16	0.24	10	-0.36	20	30
ETS1	-0.058	0.2	0.29	2	-0.55	19	21
B-cell antigen/BCR complex/LYN/SYK/BLNK	-0.021	0.21	-10000	0	-0.41	29	29
B-cell antigen/BCR complex/LYN	-0.12	0.33	-10000	0	-0.86	22	22
MALT1	0.031	0.012	-10000	0	-10000	0	0
TRAF6	0.023	0.075	-10000	0	-0.51	3	3
RAC1	-0.15	0.32	-10000	0	-0.72	31	31
B-cell antigen/BCR complex/LYN/SYK	-0.063	0.31	0.39	1	-0.73	22	23
CARD11	-0.073	0.26	0.32	1	-0.67	20	21
FCGR2B	-0.024	0.16	-10000	0	-0.51	16	16
PPP3CA	0.033	0.008	-10000	0	-10000	0	0
BCL10	0.029	0.045	-10000	0	-0.51	1	1
IKK complex	0.017	0.063	0.14	8	-0.12	6	14
PTPRC	-0.023	0.16	-10000	0	-0.51	15	15
PDPK1	-0.011	0.13	0.22	16	-0.25	16	32
PPP3CB	0.032	0.008	-10000	0	-10000	0	0
PPP3CC	0.026	0.045	-10000	0	-0.51	1	1
POU2F2	0.021	0.033	-10000	0	-10000	0	0

FOXM1 transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC3	-0.13	0.49	-9999	-1.2	18	18
PLK1	0.043	0.12	-9999	-1.3	1	1
BIRC5	-0.045	0.38	-9999	-1.5	10	10
HSPA1B	-0.13	0.5	-9999	-1.1	22	22
MAP2K1	0.02	0.058	-9999	-10000	0	0
BRCA2	-0.16	0.53	-9999	-1.2	22	22
FOXM1	-0.24	0.83	-9999	-1.9	21	21
XRCC1	-0.12	0.5	-9999	-1.2	18	18
FOXM1B/p19	-0.25	0.51	-9999	-1.3	23	23
Cyclin D1/CDK4	-0.15	0.5	-9999	-1.1	23	23
CDC2	-0.14	0.52	-9999	-1.2	22	22
TGFA	-0.16	0.48	-9999	-1	25	25
SKP2	-0.12	0.54	-9999	-1.2	20	20
CCNE1	0.02	0.065	-9999	-0.51	2	2
CKS1B	-0.12	0.5	-9999	-1.2	18	18
RB1	-0.08	0.33	-9999	-0.97	12	12
FOXM1C/SP1	-0.16	0.6	-9999	-1.4	21	21
AURKB	-0.021	0.28	-9999	-1	10	10
CENPF	-0.16	0.53	-9999	-1.2	23	23
CDK4	0.022	0.034	-9999	-10000	0	0
MYC	-0.13	0.44	-9999	-1	20	20
CHEK2	0.016	0.074	-9999	-0.56	1	1
ONECUT1	-0.16	0.5	-9999	-1.1	21	21
CDKN2A	-0.043	0.16	-9999	-0.5	15	15
LAMA4	-0.14	0.51	-9999	-1.2	18	18
FOXM1B/HNF6	-0.22	0.63	-9999	-1.5	21	21
FOS	-0.21	0.57	-9999	-1.2	30	30
SP1	0.027	0.062	-9999	-0.51	2	2
CDC25B	-0.13	0.5	-9999	-1.2	18	18
response to radiation	0.004	0.033	-9999	-10000	0	0
CENPB	-0.13	0.51	-9999	-1.2	19	19
CENPA	-0.14	0.52	-9999	-1.2	19	19
NEK2	-0.17	0.55	-9999	-1.2	24	24
HIST1H2BA	-0.14	0.51	-9999	-1.2	19	19
CCNA2	0.02	0.079	-9999	-0.52	3	3
EP300	0.005	0.12	-9999	-0.51	8	8
CCNB1/CDK1	-0.17	0.59	-9999	-1.5	18	18
CCNB2	-0.13	0.5	-9999	-1.2	17	17
CCNB1	-0.14	0.53	-9999	-1.3	18	18
ETV5	-0.096	0.6	-9999	-1.2	24	24
ESR1	-0.16	0.53	-9999	-1.2	21	21
CCND1	-0.17	0.5	-9999	-1.1	23	23
GSK3A	0.021	0.052	-9999	-10000	0	0
Cyclin A-E1/CDK1-2	0.034	0.11	-9999	-0.47	4	4
CDK2	0.028	0.048	-9999	-0.52	1	1
G2/M transition of mitotic cell cycle	0.004	0.039	-9999	-10000	0	0
FOXM1B/Cbp/p300	-0.16	0.55	-9999	-1.3	20	20
GAS1	-0.22	0.61	-9999	-1.3	33	33
MMP2	-0.2	0.58	-9999	-1.3	28	28
RB1/FOXM1C	-0.17	0.51	-9999	-1.1	24	24
CREBBP	0.033	0.007	-9999	-10000	0	0

Nectin adhesion pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.032	0.012	-10000	0	-10000	0	0
alphaV beta3 Integrin	0.028	0.084	-10000	0	-0.37	6	6
PTK2	-0.08	0.2	-10000	0	-0.43	32	32
positive regulation of JNK cascade	-0.04	0.15	-10000	0	-0.32	26	26
CDC42/GDP	-0.048	0.21	-10000	0	-0.44	28	28
Rac1/GDP	-0.047	0.2	-10000	0	-0.43	29	29
RAP1B	0.033	0.007	-10000	0	-10000	0	0
RAP1A	0.026	0.062	-10000	0	-0.51	2	2
CTNNB1	0.03	0.016	-10000	0	-10000	0	0
CDC42/GTP	-0.041	0.19	-10000	0	-0.4	26	26
nectin-3/I-afadin	-0.047	0.16	-10000	0	-0.37	29	29
RAPGEF1	-0.066	0.21	-10000	0	-0.47	28	28
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	-0.081	0.23	-10000	0	-0.52	29	29
PDGFB-D/PDGFRB	0.032	0.012	-10000	0	-10000	0	0
TLN1	-0.029	0.074	-10000	0	-0.4	2	2
Rap1/GTP	-0.049	0.15	-10000	0	-0.34	28	28
IQGAP1	0.034	0.005	-10000	0	-10000	0	0
Rap1/GTP/I-afadin	0.055	0.044	-10000	0	-0.29	2	2
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin	-0.047	0.16	-10000	0	-0.37	29	29
PVR	0.025	0.062	-10000	0	-0.51	2	2
Necl-5(dimer)	0.025	0.062	-10000	0	-0.51	2	2
mol:GDP	-0.077	0.24	-10000	0	-0.52	30	30
MLLT4	0.033	0.006	-10000	0	-10000	0	0
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
PI3K	-0.014	0.12	-10000	0	-0.31	15	15
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin	0.016	0.11	-10000	0	-0.37	12	12
positive regulation of lamellipodium assembly	-0.05	0.16	-10000	0	-0.34	28	28
PVRL1	-0.008	0.14	-10000	0	-0.51	12	12
PVRL3	-0.082	0.21	-10000	0	-0.51	29	29
PVRL2	0.033	0.008	-10000	0	-10000	0	0
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
CDH1	0.007	0.11	-10000	0	-0.51	7	7
CLDN1	-0.085	0.2	-10000	0	-0.51	28	28
JAM-A/CLDN1	-0.078	0.18	-10000	0	-0.38	34	34
SRC	-0.094	0.25	-10000	0	-0.58	29	29
ITGB3	0.026	0.048	-10000	0	-0.51	1	1
nectin-1(dimer)/I-afadin/I-afadin	0.016	0.11	-10000	0	-0.37	12	12
FARP2	-0.067	0.24	-10000	0	-0.53	24	24
RAC1	0.033	0.006	-10000	0	-10000	0	0
CTNNA1	0.032	0.008	-10000	0	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer)	-0.03	0.15	-10000	0	-0.33	29	29
nectin-1/I-afadin	0.016	0.11	-10000	0	-0.37	12	12
nectin-2/I-afadin	0.047	0.018	-10000	0	-10000	0	0
RAC1/GTP/IQGAP1/filamentous actin	0.044	0.01	-10000	0	-10000	0	0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin	-0.053	0.17	-10000	0	-0.34	38	38
CDC42/GTP/IQGAP1/filamentous actin	0.044	0.01	-10000	0	-10000	0	0
F11R	0.015	0.096	-10000	0	-0.51	5	5
positive regulation of filopodium formation	-0.04	0.15	-10000	0	-0.32	26	26
alphaV/beta3 Integrin/Talin	0.015	0.13	0.32	3	-0.38	6	9
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.047	0.018	-10000	0	-10000	0	0
nectin-2(dimer)/I-afadin/I-afadin	0.047	0.018	-10000	0	-10000	0	0
PIP5K1C	-0.033	0.09	-10000	0	-0.2	28	28
VAV2	-0.094	0.27	-10000	0	-0.56	30	30
RAP1/GDP	-0.044	0.19	-10000	0	-0.41	28	28
ITGAV	0.014	0.097	-10000	0	-0.51	5	5
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin	-0.026	0.14	-10000	0	-0.32	28	28
nectin-3(dimer)/I-afadin/I-afadin	-0.047	0.16	-10000	0	-0.37	29	29
Rac1/GTP	-0.058	0.2	-10000	0	-0.42	28	28
PTPRM	-0.03	0.096	-10000	0	-0.22	27	27
E-cadherin/beta catenin/alpha catenin	0.042	0.12	-10000	0	-0.28	16	16
adherens junction assembly	0	0	-10000	0	-10000	0	0
CDC42	0.034	0.005	-10000	0	-10000	0	0

IGF1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NCK2	0.034	0.005	-10000	0	-10000	0	0
PTK2	0.028	0.044	-10000	0	-0.51	1	1
CRKL	-0.053	0.13	-10000	0	-0.3	27	27
GRB2/SOS1/SHC	0.062	0.022	-10000	0	-10000	0	0
HRAS	0.029	0.045	-10000	0	-0.51	1	1
IRS1/Crk	-0.047	0.13	-10000	0	-0.3	28	28
IGF-1R heterotetramer/IGF1/PTP1B	-0.024	0.15	-10000	0	-0.32	28	28
AKT1	0.008	0.17	0.23	4	-0.37	16	20
BAD	0.006	0.16	0.2	6	-0.41	11	17
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	-0.054	0.13	-10000	0	-0.3	28	28
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.043	0.14	-10000	0	-0.3	29	29
RAF1	0.013	0.18	0.29	1	-0.44	12	13
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos	-0.011	0.15	-10000	0	-0.29	27	27
YWHAZ	0.025	0.062	-10000	0	-0.51	2	2
IGF-1R heterotetramer/IGF1/IRS1	-0.044	0.15	-10000	0	-0.3	33	33
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
RPS6KB1	0.014	0.16	0.24	5	-0.43	9	14
GNB2L1	0.032	0.009	-10000	0	-10000	0	0
positive regulation of MAPKKK cascade	0.011	0.15	0.3	2	-0.37	11	13
PXN	0.034	0.004	-10000	0	-10000	0	0
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
cell adhesion	0	0	-10000	0	-10000	0	0
GRB2/SOS1	0.048	0.012	-10000	0	-10000	0	0
HRAS/GTP	-0.03	0.12	-10000	0	-0.28	25	25
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc	0.013	0.14	-10000	0	-0.27	25	25
IGF-1R heterotetramer	-0.024	0.15	-10000	0	-0.54	11	11
IGF-1R heterotetramer/IGF1/IRS/Nck	-0.027	0.15	-10000	0	-0.3	28	28
Crk/p130 Cas/Paxillin	-0.015	0.14	-10000	0	-0.28	27	27
IGF1R	-0.024	0.15	-10000	0	-0.54	11	11
IGF1	-0.06	0.19	-10000	0	-0.53	20	20
IRS2/Crk	-0.062	0.15	-10000	0	-0.32	33	33
PI3K	-0.035	0.13	-10000	0	-0.39	14	14
apoptosis	-0.016	0.16	0.37	11	-0.24	5	16
HRAS/GDP	0.021	0.034	-10000	0	-0.37	1	1
PRKCD	-0.056	0.15	-10000	0	-0.39	21	21
RAF1/14-3-3 E	0.018	0.17	0.29	1	-0.38	13	14
BAD/14-3-3	0.015	0.16	0.25	5	-0.39	11	16
PRKCZ	0.013	0.16	0.24	5	-0.35	15	20
Crk/p130 Cas/Paxillin/FAK1	0.012	0.14	-10000	0	-0.44	7	7
PTPN1	0.033	0.007	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1	-0.058	0.16	-10000	0	-0.37	29	29
BCAR1	0.033	0.008	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/SHC/GRB10	-0.022	0.16	-10000	0	-0.32	30	30
mol:GDP	0	0	-10000	0	-10000	0	0
SOS1	0.033	0.006	-10000	0	-10000	0	0
IRS1/NCK2	-0.041	0.14	-10000	0	-0.3	28	28
GRB10	-0.001	0.13	-10000	0	-0.51	9	9
PTPN11	-0.057	0.13	-10000	0	-0.3	29	29
IRS1	-0.058	0.14	-10000	0	-0.3	33	33
IRS2	-0.072	0.16	-10000	0	-0.34	33	33
IGF-1R heterotetramer/IGF1	-0.053	0.18	-10000	0	-0.42	28	28
GRB2	0.034	0.005	-10000	0	-10000	0	0
PDPK1	0.021	0.17	0.25	5	-0.37	15	20
YWHAE	0.032	0.008	-10000	0	-10000	0	0
PRKD1	-0.067	0.18	-10000	0	-0.45	22	22
SHC1	0.032	0.008	-10000	0	-10000	0	0

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

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
MAP4K1	-0.055	0.16	-10000	0	-0.4	20	20
CRKL	-0.067	0.16	0.24	1	-0.4	23	24
HRAS	-0.046	0.16	-10000	0	-0.4	17	17
mol:PIP3	-0.035	0.17	-10000	0	-0.44	14	14
SPRED1	0.025	0.063	-10000	0	-0.51	2	2
SPRED2	0.028	0.045	-10000	0	-0.51	1	1
GAB1	-0.074	0.17	-10000	0	-0.42	25	25
FOXO3	-0.065	0.17	-10000	0	-0.42	19	19
AKT1	-0.068	0.18	-10000	0	-0.44	22	22
BAD	-0.065	0.17	-10000	0	-0.42	20	20
megakaryocyte differentiation	-0.08	0.17	-10000	0	-0.41	24	24
GSK3B	-0.036	0.18	0.37	1	-0.41	19	20
RAF1	-0.032	0.14	0.26	2	-0.33	15	17
SHC1	0.032	0.008	-10000	0	-10000	0	0
STAT3	-0.074	0.17	-10000	0	-0.42	24	24
STAT1	-0.17	0.39	-10000	0	-1	23	23
HRAS/SPRED1	-0.03	0.14	-10000	0	-0.34	16	16
cell proliferation	-0.069	0.17	0.28	1	-0.42	23	24
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
TEC	0.03	0.015	-10000	0	-10000	0	0
RPS6KB1	-0.065	0.18	-10000	0	-0.42	23	23
HRAS/SPRED2	-0.026	0.14	-10000	0	-0.33	15	15
LYN/TEC/p62DOK	-0.037	0.18	-10000	0	-0.43	19	19
MAPK3	-0.021	0.1	0.23	2	-0.29	5	7
STAP1	-0.092	0.19	-10000	0	-0.47	26	26
GRAP2	0.032	0.008	-10000	0	-10000	0	0
JAK2	-0.14	0.32	-10000	0	-0.83	22	22
STAT1 (dimer)	-0.17	0.38	-10000	0	-0.97	23	23
mol:Gleevec	0.002	0.007	-10000	0	-10000	0	0
GRB2/SOCS1/VAV1	-0.055	0.2	-10000	0	-0.45	24	24
actin filament polymerization	-0.071	0.17	-10000	0	-0.41	24	24
LYN	0.029	0.044	-10000	0	-0.51	1	1
STAP1/STAT5A (dimer)	-0.12	0.26	-10000	0	-0.64	24	24
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
CBL/CRKL/GRB2	-0.047	0.17	-10000	0	-0.4	19	19
PI3K	-0.055	0.16	-10000	0	-0.45	13	13
PTEN	0.027	0.044	-10000	0	-0.51	1	1
SCF/KIT/EPO/EPOR	-0.16	0.45	-10000	0	-1.3	18	18
MAPK8	-0.07	0.17	0.28	1	-0.43	23	24
STAT3 (dimer)	-0.073	0.17	-10000	0	-0.42	24	24
positive regulation of transcription	-0.016	0.09	0.22	2	-0.23	5	7
mol:GDP	-0.048	0.16	-10000	0	-0.42	17	17
PIK3C2B	-0.07	0.18	-10000	0	-0.45	22	22
CBL/CRKL	-0.057	0.16	-10000	0	-0.39	21	21
FER	-0.074	0.17	-10000	0	-0.43	24	24
SH2B3	-0.076	0.17	-10000	0	-0.43	24	24
PDPK1	-0.03	0.16	-10000	0	-0.41	14	14
SNAI2	-0.11	0.19	-10000	0	-0.41	34	34
positive regulation of cell proliferation	-0.13	0.28	-10000	0	-0.71	23	23
KITLG	-0.023	0.16	-10000	0	-0.52	13	13
cell motility	-0.13	0.28	-10000	0	-0.71	23	23
PTPN6	0.031	0.045	-10000	0	-0.5	1	1
EPOR	-0.036	0.19	-10000	0	-0.73	6	6
STAT5A (dimer)	-0.1	0.24	-10000	0	-0.6	23	23
SOCS1	0.028	0.046	-10000	0	-0.51	1	1
cell migration	0.073	0.17	0.42	24	-10000	0	24
SOS1	0.033	0.006	-10000	0	-10000	0	0
EPO	0.021	0.028	-10000	0	-10000	0	0
VAV1	0.008	0.11	-10000	0	-0.51	7	7
GRB10	-0.085	0.19	0.28	1	-0.44	26	27
PTPN11	0.033	0.044	-10000	0	-0.5	1	1
SCF/KIT	-0.074	0.18	-10000	0	-0.44	24	24
GO:0007205	0.003	0.009	-10000	0	-10000	0	0
MAP2K1	-0.026	0.11	0.24	2	-0.3	7	9
CBL	0.034	0.005	-10000	0	-10000	0	0
KIT	-0.17	0.46	-10000	0	-1.3	21	21
MAP2K2	-0.025	0.11	0.24	2	-0.3	7	9
SHC/Grb2/SOS1	-0.039	0.18	-10000	0	-0.42	21	21
STAT5A	-0.1	0.24	-10000	0	-0.61	23	23
GRB2	0.034	0.005	-10000	0	-10000	0	0
response to radiation	-0.1	0.19	-10000	0	-0.4	35	35
SHC/GRAP2	0.046	0.016	-10000	0	-10000	0	0
PTPRO	-0.081	0.17	-10000	0	-0.42	24	24
SH2B2	-0.072	0.17	-10000	0	-0.42	24	24
DOK1	0.033	0.006	-10000	0	-10000	0	0
MATK	-0.073	0.17	-10000	0	-0.43	23	23
CREBBP	0.012	0.063	-10000	0	-0.18	2	2
BCL2	-0.11	0.37	-10000	0	-1.2	13	13

TCR signaling in naïve CD8+ T cells

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GRB2/SOS1/SHC	-0.02	0.22	0.3	5	-0.54	19	24
FYN	-0.058	0.29	0.3	7	-0.72	20	27
LAT/GRAP2/SLP76	-0.041	0.24	0.33	2	-0.62	19	21
IKBKB	0.031	0.011	-10000	0	-10000	0	0
AKT1	-0.037	0.2	0.27	5	-0.46	22	27
B2M	0.01	0.11	-10000	0	-0.52	6	6
IKBKG	-0.004	0.064	0.14	4	-0.14	15	19
MAP3K8	-0.011	0.14	-10000	0	-0.51	12	12
mol:Ca2+	-0.017	0.016	-10000	0	-0.075	1	1
integrin-mediated signaling pathway	0.035	0.051	-10000	0	-0.31	3	3
LAT/GRAP2/SLP76/VAV1/PI3K Class IA	-0.067	0.28	0.32	4	-0.66	24	28
TRPV6	0.001	0.099	1.2	1	-10000	0	1
CD28	-0.004	0.14	-10000	0	-0.51	10	10
SHC1	-0.059	0.27	0.3	6	-0.68	20	26
receptor internalization	-0.096	0.32	0.23	1	-0.76	24	25
PRF1	-0.11	0.37	-10000	0	-1.1	16	16
KRAS	0.017	0.086	-10000	0	-0.51	4	4
GRB2	0.034	0.005	-10000	0	-10000	0	0
COT/AKT1	-0.028	0.18	0.24	6	-0.39	26	32
LAT	-0.069	0.27	0.33	2	-0.68	21	23
EntrezGene:6955	0	0.005	-10000	0	-10000	0	0
CD3D	-0.008	0.14	-10000	0	-0.52	11	11
CD3E	0.031	0.014	-10000	0	-10000	0	0
CD3G	-0.058	0.2	-10000	0	-0.51	25	25
RASGRP2	0.004	0.026	-10000	0	-0.2	1	1
RASGRP1	-0.032	0.18	0.32	3	-0.43	21	24
HLA-A	0.019	0.078	-10000	0	-0.52	3	3
RASSF5	0.029	0.045	-10000	0	-0.51	1	1
RAP1A/GTP/RAPL	0.036	0.051	-10000	0	-0.31	3	3
mol:GTP	0	0	-10000	0	-10000	0	0
mol:GDP	0.017	0.067	0.16	9	-0.12	10	19
PDK1/CARD11/BCL10/MALT1/TRAF6	-0.034	0.086	-10000	0	-0.23	19	19
PRKCA	-0.017	0.12	0.2	4	-0.29	18	22
GRAP2	0.032	0.008	-10000	0	-10000	0	0
mol:IP3	-0.05	0.17	-10000	0	-0.44	21	21
EntrezGene:6957	0	0.006	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.073	0.26	-10000	0	-0.65	20	20
ORAI1	-0.008	0.092	-10000	0	-1	1	1
CSK	-0.067	0.27	0.27	1	-0.67	21	22
B7 family/CD28	-0.082	0.31	-10000	0	-0.75	23	23
CHUK	0.03	0.044	-10000	0	-0.51	1	1
TCR/CD3/MHC I/CD8/LCK/ZAP-70	-0.092	0.31	0.26	1	-0.75	23	24
PTPN6	-0.07	0.28	0.24	1	-0.67	22	23
VAV1	-0.077	0.28	0.33	2	-0.7	22	24
Monovalent TCR/CD3	-0.077	0.24	-10000	0	-0.54	27	27
CBL	0.034	0.005	-10000	0	-10000	0	0
LCK	-0.063	0.3	0.3	6	-0.74	20	26
PAG1	-0.071	0.27	0.29	2	-0.69	21	23
RAP1A	0.026	0.062	-10000	0	-0.51	2	2
TCR/CD3/MHC I/CD8/LCK	-0.096	0.32	0.23	1	-0.76	23	24
CD80	0.024	0.023	-10000	0	-10000	0	0
CD86	-0.008	0.13	-10000	0	-0.51	10	10
PDK1/CARD11/BCL10/MALT1	-0.028	0.1	-10000	0	-0.28	17	17
HRAS	0.029	0.045	-10000	0	-0.51	1	1
GO:0035030	-0.084	0.24	-10000	0	-0.6	23	23
CD8A	0	0.006	-10000	0	-10000	0	0
CD8B	0.021	0.052	-10000	0	-0.52	1	1
PTPRC	-0.023	0.16	-10000	0	-0.51	15	15
PDK1/PKC theta	-0.055	0.23	0.36	2	-0.55	22	24
CSK/PAG1	-0.06	0.26	0.31	4	-0.68	19	23
SOS1	0.033	0.006	-10000	0	-10000	0	0
peptide-MHC class I	0.021	0.12	-10000	0	-0.48	7	7
GRAP2/SLP76	-0.049	0.29	0.35	2	-0.72	20	22
STIM1	-0.007	0.043	-10000	0	-0.5	1	1
RAS family/GTP	0.01	0.096	0.22	5	-0.18	15	20
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin	-0.11	0.35	0.23	1	-0.83	24	25
mol:DAG	-0.059	0.14	-10000	0	-0.39	22	22
RAP1A/GDP	0.01	0.035	0.1	4	-0.1	3	7
PLCG1	0.033	0.006	-10000	0	-10000	0	0
CD247	-0.037	0.18	-10000	0	-0.51	18	18
cytotoxic T cell degranulation	-0.1	0.34	-10000	0	-1	16	16
RAP1A/GTP	0.001	0.015	-10000	0	-0.085	3	3
mol:PI-3-4-5-P3	-0.047	0.23	0.29	5	-0.52	24	29
LAT/GRAP2/SLP76/VAV1/PLCgamma1	-0.055	0.23	-10000	0	-0.58	21	21
NRAS	0.026	0.047	-10000	0	-0.51	1	1
ZAP70	0.031	0.016	-10000	0	-10000	0	0
GRB2/SOS1	0.048	0.012	-10000	0	-10000	0	0
LAT/GRAP2/SLP76/VAV1	-0.056	0.23	-10000	0	-0.58	21	21
MALT1	0.031	0.012	-10000	0	-10000	0	0
TRAF6	0.023	0.075	-10000	0	-0.51	3	3
CD8 heterodimer	0.015	0.039	-10000	0	-0.38	1	1
CARD11	0.022	0.033	-10000	0	-10000	0	0
PRKCB	-0.044	0.098	-10000	0	-0.27	22	22
PRKCE	-0.022	0.11	-10000	0	-0.28	16	16
PRKCQ	-0.066	0.26	0.37	2	-0.62	24	26
LCP2	-0.011	0.14	-10000	0	-0.51	12	12
BCL10	0.029	0.045	-10000	0	-0.51	1	1
regulation of survival gene product expression	-0.027	0.17	0.24	6	-0.39	21	27
IKK complex	0.013	0.065	0.18	8	-0.12	2	10
RAS family/GDP	-0.004	0.016	-10000	0	-0.059	5	5
MAP3K14	-0.023	0.14	0.21	6	-0.3	25	31
PDPK1	-0.033	0.18	0.26	5	-0.43	22	27
TCR/CD3/MHC I/CD8/Fyn	-0.08	0.3	0.26	1	-0.71	22	23

EGFR-dependent Endothelin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HRAS	0.029	0.045	-9999	-0.51	1	1
EGFR	-0.031	0.17	-9999	-0.51	17	17
EGF/EGFR	-0.075	0.18	-9999	-0.34	41	41
EGF/EGFR dimer/SHC/GRB2/SOS1	-0.002	0.15	-9999	-0.32	22	22
mol:GTP	0	0	-9999	-10000	0	0
EDNRA	0.004	0.11	-9999	-0.51	6	6
response to oxidative stress	0	0	-9999	-10000	0	0
EGF	-0.031	0.15	-9999	-0.51	13	13
EGF/EGFR dimer/SHC	-0.026	0.15	-9999	-0.36	23	23
mol:GDP	-0.006	0.14	-9999	-0.31	22	22
mol:Ca2+	0	0	-9999	-10000	0	0
EDN1	-0.043	0.18	-9999	-0.51	19	19
GRB2/SOS1	0.048	0.012	-9999	-10000	0	0
HRAS/GTP	-0.019	0.13	-9999	-0.3	23	23
SHC1	0.032	0.008	-9999	-10000	0	0
HRAS/GDP	-0.007	0.14	-9999	-0.31	23	23
FRAP1	-0.059	0.1	-9999	-0.3	22	22
EGF/EGFR dimer	-0.049	0.17	-9999	-0.41	26	26
SOS1	0.033	0.006	-9999	-10000	0	0
GRB2	0.034	0.005	-9999	-10000	0	0
ETA receptor/Endothelin-1	-0.033	0.16	-9999	-0.4	23	23

IL12-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1	-0.007	0.16	-10000	0	-0.42	14	14
TBX21	-0.21	0.56	-10000	0	-1.4	25	25
B2M	0.011	0.1	-10000	0	-0.51	6	6
TYK2	0.024	0.037	-10000	0	-10000	0	0
IL12RB1	0.024	0.035	-10000	0	-10000	0	0
GADD45B	-0.12	0.42	-10000	0	-1	22	22
IL12RB2	-0.053	0.18	-10000	0	-0.52	19	19
GADD45G	-0.12	0.42	-10000	0	-1.1	20	20
natural killer cell activation	0.002	0.019	-10000	0	-10000	0	0
RELB	0.021	0.076	-10000	0	-0.51	3	3
RELA	0.034	0	-10000	0	-10000	0	0
IL18	-0.013	0.15	-10000	0	-0.51	13	13
IL2RA	-0.007	0.14	-10000	0	-0.51	11	11
IFNG	-0.098	0.21	-10000	0	-0.51	32	32
STAT3 (dimer)	-0.097	0.36	-10000	0	-0.86	23	23
HLA-DRB5	-0.005	0.13	-10000	0	-0.51	9	9
FASLG	-0.17	0.53	-10000	0	-1.4	20	20
NF kappa B2 p52/RelB	-0.13	0.46	-10000	0	-1.1	23	23
CD4	0.025	0.022	-10000	0	-10000	0	0
SOCS1	0.028	0.046	-10000	0	-0.51	1	1
EntrezGene:6955	-0.002	0.01	-10000	0	-10000	0	0
CD3D	-0.013	0.14	-10000	0	-0.51	11	11
CD3E	0.028	0.022	-10000	0	-10000	0	0
CD3G	-0.063	0.2	-10000	0	-0.51	25	25
IL12Rbeta2/JAK2	-0.026	0.15	-10000	0	-0.4	18	18
CCL3	-0.14	0.45	-10000	0	-1.2	19	19
CCL4	-0.14	0.46	-10000	0	-1.2	19	19
HLA-A	0.021	0.077	-10000	0	-0.52	3	3
IL18/IL18R	-0.026	0.21	-10000	0	-0.39	33	33
NOS2	-0.13	0.44	-10000	0	-1	25	25
IL12/IL12R/TYK2/JAK2/SPHK2	-0.007	0.16	-10000	0	-0.41	14	14
IL1R1	-0.16	0.49	-10000	0	-1.3	22	22
IL4	0.021	0.032	-10000	0	-10000	0	0
JAK2	0.022	0.035	-10000	0	-10000	0	0
EntrezGene:6957	-0.002	0.01	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.1	0.34	-10000	0	-0.98	16	16
RAB7A	-0.062	0.35	-10000	0	-0.84	20	20
lysosomal transport	-0.054	0.33	-10000	0	-0.79	20	20
FOS	-0.21	0.5	-10000	0	-1.2	30	30
STAT4 (dimer)	-0.11	0.42	-10000	0	-1	23	23
STAT5A (dimer)	-0.18	0.46	-10000	0	-1.1	25	25
GZMA	-0.14	0.43	-10000	0	-1.1	22	22
GZMB	-0.14	0.47	-10000	0	-1.3	19	19
HLX	0.033	0.01	-10000	0	-10000	0	0
LCK	-0.17	0.52	-10000	0	-1.2	24	24
TCR/CD3/MHC II/CD4	-0.1	0.32	-10000	0	-0.79	21	21
IL2/IL2R	0.029	0.13	-10000	0	-0.35	13	13
MAPK14	-0.12	0.44	-10000	0	-1	24	24
CCR5	-0.17	0.5	-10000	0	-1.2	24	24
IL1B	-0.079	0.21	-10000	0	-0.52	28	28
STAT6	-0.02	0.17	-10000	0	-0.44	10	10
STAT4	0.013	0.097	-10000	0	-0.51	5	5
STAT3	0.033	0.006	-10000	0	-10000	0	0
STAT1	0.011	0.1	-10000	0	-0.51	6	6
NFKB1	0.033	0.008	-10000	0	-10000	0	0
NFKB2	0.033	0.011	-10000	0	-10000	0	0
IL12B	0.014	0.082	-10000	0	-0.51	3	3
CD8A	0	0.007	-10000	0	-10000	0	0
CD8B	0.022	0.052	-10000	0	-0.51	1	1
T-helper 1 cell differentiation	0	0	-10000	0	-10000	0	0
natural killer cell mediated cytotoxicity	0.006	0.16	0.42	14	-10000	0	14
IL2RB	0.016	0.087	-10000	0	-0.51	4	4
proteasomal ubiquitin-dependent protein catabolic process	-0.091	0.37	-10000	0	-0.89	23	23
IL2RG	0.021	0.065	-10000	0	-0.51	2	2
IL12	0.011	0.077	-10000	0	-0.32	5	5
STAT5A	0.033	0.011	-10000	0	-10000	0	0
CD247	-0.041	0.17	-10000	0	-0.51	18	18
IL2	0.033	0.008	-10000	0	-10000	0	0
SPHK2	0.033	0.01	-10000	0	-10000	0	0
FRAP1	0	0	-10000	0	-10000	0	0
IL12A	0.008	0.068	-10000	0	-0.52	2	2
IL12/IL12R/TYK2/JAK2	-0.19	0.61	-10000	0	-1.4	23	23
MAP2K3	-0.13	0.44	-10000	0	-1	24	24
RIPK2	0.027	0.046	-10000	0	-0.51	1	1
MAP2K6	-0.13	0.44	-10000	0	-1	23	23
regulation of dendritic cell antigen processing and presentation	0	0	-10000	0	-10000	0	0
HLA-DRA	-0.008	0.13	-10000	0	-0.51	10	10
IL18RAP	-0.042	0.18	-10000	0	-0.52	20	20
IL12Rbeta1/TYK2	0.037	0.048	-10000	0	-10000	0	0
EOMES	-0.081	0.3	-10000	0	-1.1	11	11
STAT1 (dimer)	-0.16	0.39	-10000	0	-0.98	24	24
T cell proliferation	-0.057	0.29	-10000	0	-0.7	21	21
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
IL18R1	0.007	0.12	-10000	0	-0.51	7	7
CD8-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.084	0.33	-10000	0	-0.73	26	26
ATF2	-0.1	0.39	-10000	0	-0.89	24	24

IL1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
UBC13/UEV1A	0.025	0	-10000	0	-10000	0	0
PRKCZ	0	0	-10000	0	-10000	0	0
MAP3K7IP2	0	0	-10000	0	-10000	0	0
ERC1	0.027	0.045	-10000	0	-0.51	1	1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4	-0.087	0.21	-10000	0	-0.49	26	26
IRAK/TOLLIP	0.038	0.009	-10000	0	-10000	0	0
IKBKB	0.031	0.011	-10000	0	-10000	0	0
IKBKG	0.033	0.006	-10000	0	-10000	0	0
IL1 alpha/IL1R2	-0.14	0.22	-10000	0	-0.44	51	51
IL1A	-0.15	0.24	-10000	0	-0.51	45	45
IL1B	-0.073	0.18	-10000	0	-0.42	30	30
IRAK/TRAF6/p62/Atypical PKCs	0.014	0.069	-10000	0	-0.26	7	7
IL1R2	-0.042	0.17	-10000	0	-0.51	18	18
IL1R1	-0.003	0.13	-10000	0	-0.51	10	10
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.038	0.18	0.26	3	-0.5	15	18
TOLLIP	0.033	0.007	-10000	0	-10000	0	0
TICAM2	0	0	-10000	0	-10000	0	0
MAP3K3	0.033	0.01	-10000	0	-10000	0	0
TAK1/TAB1/TAB2	0.023	0.005	-10000	0	-10000	0	0
IKK complex/ELKS	0.043	0.075	-10000	0	-0.35	1	1
JUN	-0.034	0.075	0.16	2	-0.25	14	16
MAP3K7	0.034	0.009	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/PI3K	-0.063	0.21	-10000	0	-0.5	23	23
IL1 alpha/IL1R1/IL1RAP/MYD88	-0.1	0.2	-10000	0	-0.46	31	31
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4	-0.095	0.2	-10000	0	-0.44	32	32
IL1 beta fragment/IL1R1/IL1RAP	-0.078	0.21	-10000	0	-0.49	25	25
NFKB1	0.033	0.008	-10000	0	-10000	0	0
MAPK8	-0.021	0.056	0.17	2	-0.24	8	10
IRAK1	0.018	0.003	-10000	0	-10000	0	0
IL1RN/IL1R1	-0.046	0.18	-10000	0	-0.42	28	28
IRAK4	0.023	0.075	-10000	0	-0.51	3	3
PRKCI	-0.004	0.1	-10000	0	-0.51	6	6
TRAF6	0.023	0.075	-10000	0	-0.51	3	3
PI3K	0.004	0.076	-10000	0	-0.3	7	7
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.079	0.24	-10000	0	-0.51	27	27
CHUK	0.03	0.044	-10000	0	-0.51	1	1
IL1 beta fragment/IL1R1/IL1RAP/MYD88s	-0.078	0.21	-10000	0	-0.49	25	25
IL1 beta/IL1R2	-0.086	0.21	-10000	0	-0.41	39	39
IRAK/TRAF6/TAK1/TAB1/TAB2	0.041	0.044	-10000	0	-0.25	3	3
NF kappa B1 p50/RelA	-0.06	0.19	-10000	0	-0.47	22	22
IRAK3	-0.026	0.16	-10000	0	-0.51	15	15
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4	-0.07	0.21	-10000	0	-0.47	26	26
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.11	0.22	-10000	0	-0.46	35	35
IL1 alpha/IL1R1/IL1RAP	-0.11	0.22	-10000	0	-0.5	31	31
RELA	0.034	0	-10000	0	-10000	0	0
MAP3K7IP1	0	0	-10000	0	-10000	0	0
SQSTM1	0.029	0.019	-10000	0	-10000	0	0
MYD88	0.031	0.01	-10000	0	-10000	0	0
IRAK/TRAF6/MEKK3	0.05	0.048	-10000	0	-0.27	3	3
IL1RAP	-0.05	0.17	-10000	0	-0.51	18	18
UBE2N	0.034	0	-10000	0	-10000	0	0
IRAK/TRAF6	-0.072	0.18	-10000	0	-0.48	20	20
CASP1	0.006	0.12	-10000	0	-0.51	8	8
IL1RN/IL1R2	-0.071	0.2	-10000	0	-0.44	32	32
IL1 beta fragment/IL1R1/IL1RAP/MYD88	-0.069	0.21	-10000	0	-0.48	24	24
TMEM189-UBE2V1	0	0	-10000	0	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.088	0.22	-10000	0	-0.52	27	27
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
IL1RN	-0.057	0.19	-10000	0	-0.51	23	23
TRAF6/TAK1/TAB1/TAB2	0.043	0.044	-10000	0	-0.26	3	3
MAP2K6	0.003	0.063	0.18	2	-0.25	8	10

Calcium signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC1	-0.023	0.085	-10000	0	-0.35	8	8
NFATC2	-0.005	0.039	-10000	0	-10000	0	0
NFATC3	-0.005	0.037	-10000	0	-10000	0	0
CD40LG	-0.14	0.26	0.34	1	-0.56	34	35
PTGS2	-0.18	0.3	0.34	1	-0.63	39	40
JUNB	0.01	0.098	-10000	0	-0.51	5	5
CaM/Ca2+/Calcineurin A alpha-beta B1	0.004	0.031	-10000	0	-10000	0	0
CaM/Ca2+	0.005	0.031	-10000	0	-10000	0	0
CALM1	0.021	0.026	-10000	0	-10000	0	0
JUN	-0.007	0.12	-10000	0	-0.52	7	7
mol:Ca2+	-0.007	0.012	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0.017	0.014	-10000	0	-10000	0	0
FOSL1	0.027	0.027	-10000	0	-10000	0	0
CREM	0.033	0.007	-10000	0	-10000	0	0
Jun/NFAT1-c-4/p21SNFT	-0.067	0.16	-10000	0	-0.36	24	24
FOS	-0.04	0.16	-10000	0	-0.49	15	15
IFNG	-0.2	0.31	-10000	0	-0.62	44	44
AP-1/NFAT1-c-4	-0.16	0.34	-10000	0	-0.69	33	33
FASLG	-0.16	0.3	0.34	1	-0.63	34	35
NFAT1-c-4/ICER1	-0.029	0.11	-10000	0	-0.33	8	8
IL2RA	-0.16	0.29	0.34	1	-0.6	35	36
FKBP12/FK506	0.024	0.005	-10000	0	-10000	0	0
CSF2	-0.16	0.29	0.34	1	-0.6	36	37
JunB/Fra1/NFAT1-c-4	-0.022	0.13	-10000	0	-0.38	8	8
IL4	-0.14	0.26	0.34	1	-0.56	33	34
IL2	-0.024	0.23	-10000	0	-0.98	8	8
IL3	-0.01	0.18	-10000	0	-0.72	9	9
FKBP1A	0.033	0.007	-10000	0	-10000	0	0
BATF3	0	0	-10000	0	-10000	0	0
mol:FK506	0	0	-10000	0	-10000	0	0
POU2F1	0.038	0.011	-10000	0	-10000	0	0

Glypican 1 network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer	-0.002	0.13	-10000	0	-0.35	15	15
fibroblast growth factor receptor signaling pathway	-0.002	0.12	-10000	0	-0.34	15	15
LAMA1	0.024	0.03	-10000	0	-10000	0	0
PRNP	0.018	0.087	-10000	0	-0.51	4	4
GPC1/SLIT2	-0.05	0.18	-10000	0	-0.39	30	30
SMAD2	-0.018	0.095	-10000	0	-0.29	16	16
GPC1/PrPc/Cu2+	-0.005	0.12	-10000	0	-0.33	18	18
GPC1/Laminin alpha1	-0.006	0.12	-10000	0	-0.37	15	15
TDGF1	0.03	0.016	-10000	0	-10000	0	0
CRIPTO/GPC1	0	0.12	-10000	0	-0.37	15	15
APP/GPC1	-0.016	0.15	-10000	0	-0.38	20	20
mol:NO	0	0	-10000	0	-10000	0	0
YES1	-0.021	0.1	-10000	0	-0.32	16	16
FLT1	0.005	0.12	-10000	0	-0.51	8	8
GPC1/TGFB/TGFBR1/TGFBR2	0.016	0.12	-10000	0	-0.32	16	16
SERPINC1	0.03	0.017	-10000	0	-10000	0	0
FYN	-0.022	0.11	-10000	0	-0.32	17	17
FGR	-0.018	0.099	-10000	0	-0.32	15	15
positive regulation of MAPKKK cascade	-0.043	0.17	-10000	0	-0.37	23	23
SLIT2	-0.036	0.17	-10000	0	-0.51	18	18
GPC1/NRG	-0.026	0.17	-10000	0	-0.46	18	18
NRG1	-0.006	0.13	-10000	0	-0.51	9	9
GPC1/VEGF165 homodimer/VEGFR1 homodimer	0	0.14	-10000	0	-0.33	23	23
LYN	-0.016	0.096	-10000	0	-0.31	14	14
mol:Spermine	-0.031	0.11	-10000	0	-0.37	15	15
cell growth	-0.002	0.12	-10000	0	-0.34	15	15
BMP signaling pathway	0.025	0.16	0.51	15	-10000	0	15
SRC	-0.019	0.099	-10000	0	-0.32	15	15
TGFBR1	0.034	0.005	-10000	0	-10000	0	0
mol:Cu2+	0	0	-10000	0	-10000	0	0
PLA2G2A	0.001	0.12	-10000	0	-0.51	7	7
GPC1	-0.025	0.16	-10000	0	-0.51	15	15
TGFBR1 (dimer)	0.034	0.005	-10000	0	-10000	0	0
VEGFA	0.027	0.061	-10000	0	-0.51	2	2
BLK	-0.028	0.1	-10000	0	-0.32	17	17
HCK	-0.034	0.12	-10000	0	-0.32	22	22
FGF2	0.014	0.088	-10000	0	-0.51	4	4
FGFR1	0.018	0.063	-10000	0	-0.51	2	2
VEGFR1 homodimer	0.005	0.12	-10000	0	-0.51	8	8
TGFBR2	0.026	0.047	-10000	0	-0.51	1	1
cell death	-0.016	0.15	-10000	0	-0.38	20	20
ATIII/GPC1	0.001	0.12	-10000	0	-0.37	14	14
PLA2G2A/GPC1	-0.021	0.16	-10000	0	-0.4	20	20
LCK	-0.039	0.12	-10000	0	-0.32	25	25
neuron differentiation	-0.026	0.17	-10000	0	-0.46	18	18
PrPc/Cu2+	0.014	0.063	-10000	0	-0.37	4	4
APP	0.011	0.1	-10000	0	-0.51	6	6
TGFBR2 (dimer)	0.026	0.047	-10000	0	-0.51	1	1

IFN-gamma pathway

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
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2	-0.033	0.15	-10000	0	-0.28	35	35
positive regulation of NF-kappaB transcription factor activity	0	0.001	-10000	0	-10000	0	0
CRKL	0.031	0.012	-10000	0	-10000	0	0
STAT1 (dimer)/Cbp/p300	-0.04	0.18	-10000	0	-0.45	15	15
IFN-gammaR/JAK1/JAK1/JAK2/JAK2	0.009	0.1	-10000	0	-0.34	8	8
antigen processing and presentation of peptide antigen via MHC class I	-0.026	0.092	-10000	0	-0.3	10	10
CaM/Ca2+	-0.028	0.14	-10000	0	-0.27	33	33
RAP1A	0.026	0.062	-10000	0	-0.51	2	2
STAT1 (dimer)/SHP2	-0.053	0.16	0.28	1	-0.32	32	33
AKT1	0.013	0.15	0.33	3	-0.32	9	12
MAP2K1	-0.063	0.13	0.28	1	-0.32	14	15
MAP3K11	-0.055	0.13	0.29	1	-0.27	34	35
IFNGR1	-0.006	0.12	-10000	0	-0.51	7	7
mol:GTP	0	0	-10000	0	-10000	0	0
CaM/Ca2+/CAMKII	-0.009	0.12	-10000	0	-0.49	5	5
Rap1/GTP	-0.043	0.1	-10000	0	-0.32	6	6
CRKL/C3G	0.046	0.016	-10000	0	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP	-0.027	0.15	-10000	0	-0.28	35	35
CEBPB	-0.048	0.18	-10000	0	-0.51	11	11
STAT3	0.033	0.006	-10000	0	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1	-0.03	0.2	-10000	0	-0.74	6	6
STAT1	-0.063	0.15	0.29	1	-0.32	32	33
CALM1	0.033	0.007	-10000	0	-10000	0	0
IFN-gamma (dimer)	-0.1	0.21	-10000	0	-0.51	32	32
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
STAT1 (dimer)/PIAS1	-0.049	0.16	0.29	1	-0.31	32	33
CEBPB/PTGES2/Cbp/p300	-0.019	0.14	-10000	0	-0.38	11	11
mol:Ca2+	-0.035	0.14	-10000	0	-0.27	35	35
MAPK3	-0.048	0.15	-10000	0	-0.64	3	3
STAT1 (dimer)	-0.001	0.15	-10000	0	-0.45	9	9
MAPK1	-0.068	0.2	-10000	0	-0.71	8	8
JAK2	0.013	0.034	-10000	0	-10000	0	0
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
JAK1	0.014	0.055	-10000	0	-0.54	1	1
CAMK2D	0.025	0.062	-10000	0	-0.51	2	2
DAPK1	-0.03	0.14	-10000	0	-0.53	6	6
SMAD7	0.014	0.073	0.23	1	-0.24	3	4
CBL/CRKL/C3G	-0.025	0.12	-10000	0	-0.35	5	5
PI3K	-0.028	0.11	-10000	0	-0.28	16	16
IFNG	-0.1	0.22	-10000	0	-0.51	32	32
apoptosis	-0.016	0.12	-10000	0	-0.45	4	4
CAMK2G	0.033	0.007	-10000	0	-10000	0	0
STAT3 (dimer)	0.033	0.006	-10000	0	-10000	0	0
CAMK2A	0.033	0.008	-10000	0	-10000	0	0
CAMK2B	0.022	0.052	-10000	0	-0.51	1	1
FRAP1	0.005	0.14	0.32	3	-0.32	7	10
PRKCD	0.018	0.14	0.34	3	-0.32	7	10
RAP1B	0.033	0.007	-10000	0	-10000	0	0
negative regulation of cell growth	-0.026	0.092	-10000	0	-0.3	10	10
PTPN2	0.034	0.005	-10000	0	-10000	0	0
EP300	0.005	0.12	-10000	0	-0.51	8	8
IRF1	-0.063	0.15	0.41	1	-0.49	11	12
STAT1 (dimer)/PIASy	-0.053	0.15	0.29	1	-0.32	30	31
SOCS1	0.002	0.19	-10000	0	-1.2	4	4
mol:GDP	-0.026	0.12	-10000	0	-0.34	5	5
CASP1	0.009	0.092	0.23	1	-0.28	9	10
PTGES2	0.034	0.004	-10000	0	-10000	0	0
IRF9	-0.002	0.07	0.24	1	-0.35	1	2
mol:PI-3-4-5-P3	-0.032	0.1	-10000	0	-0.28	16	16
RAP1/GDP	-0.017	0.12	-10000	0	-0.37	4	4
CBL	-0.055	0.13	0.29	1	-0.27	34	35
MAP3K1	-0.06	0.14	0.29	1	-0.28	37	38
PIAS1	0.034	0.004	-10000	0	-10000	0	0
PIAS4	0.033	0.007	-10000	0	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class II	-0.026	0.092	-10000	0	-0.3	10	10
PTPN11	-0.054	0.13	0.31	1	-0.28	35	36
CREBBP	0.033	0.007	-10000	0	-10000	0	0
RAPGEF1	0.034	0.004	-10000	0	-10000	0	0

LPA receptor mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	0.014	0.086	-10000	0	-0.23	16	16
NF kappa B1 p50/RelA/I kappa B alpha	0.002	0.087	-10000	0	-0.3	5	5
AP1	-0.053	0.12	-10000	0	-0.26	33	33
mol:PIP3	-0.052	0.12	-10000	0	-0.27	27	27
AKT1	-0.011	0.13	0.28	3	-0.37	8	11
PTK2B	-0.041	0.1	-10000	0	-0.22	33	33
RHOA	-0.032	0.1	-10000	0	-0.32	13	13
PIK3CB	0.015	0.076	-10000	0	-0.51	3	3
mol:Ca2+	-0.025	0.072	-10000	0	-0.27	9	9
MAGI3	0.024	0.063	-10000	0	-0.51	2	2
RELA	0.034	0	-10000	0	-10000	0	0
apoptosis	-0.011	0.074	-10000	0	-0.22	16	16
HRAS/GDP	0.021	0.034	-10000	0	-0.24	2	2
positive regulation of microtubule depolymerization	-0.013	0.11	0.18	17	-0.24	11	28
NF kappa B1 p50/RelA	-0.04	0.092	-10000	0	-0.29	13	13
endothelial cell migration	-0.051	0.19	-10000	0	-0.58	17	17
ADCY4	-0.027	0.1	-10000	0	-0.29	15	15
ADCY5	-0.022	0.088	-10000	0	-0.27	11	11
ADCY6	-0.022	0.094	-10000	0	-0.27	12	12
ADCY7	-0.025	0.1	-10000	0	-0.3	13	13
ADCY1	-0.02	0.092	-10000	0	-0.26	12	12
ADCY2	-0.031	0.095	-10000	0	-0.3	11	11
ADCY3	-0.027	0.099	-10000	0	-0.28	14	14
ADCY8	-0.03	0.093	-10000	0	-0.27	13	13
ADCY9	-0.02	0.091	-10000	0	-0.26	12	12
GSK3B	-0.011	0.11	0.19	17	-0.25	11	28
arachidonic acid secretion	-0.032	0.1	-10000	0	-0.28	16	16
GNG2	0.033	0.006	-10000	0	-10000	0	0
TRIP6	0.003	0.078	-10000	0	-0.37	6	6
GNAO1	-0.011	0.083	-10000	0	-0.25	16	16
HRAS	0.029	0.045	-10000	0	-0.51	1	1
NFKBIA	-0.024	0.081	-10000	0	-0.29	8	8
GAB1	0.024	0.063	-10000	0	-0.51	2	2
mol:GTP	0	0	-10000	0	-10000	0	0
lamellipodium assembly	0.034	0.15	-10000	0	-0.86	4	4
JUN	0.004	0.11	-10000	0	-0.51	7	7
LPA/LPA2/NHERF2	0.004	0.052	-10000	0	-0.31	2	2
TIAM1	0.012	0.17	-10000	0	-1	4	4
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
mol:IP3	-0.025	0.073	-10000	0	-0.28	9	9
PLCB3	-0.001	0.06	-10000	0	-0.3	4	4
FOS	-0.029	0.16	-10000	0	-0.51	14	14
positive regulation of mitosis	-0.032	0.1	-10000	0	-0.28	16	16
LPA/LPA1-2-3	-0.022	0.07	-10000	0	-0.22	17	17
mol:Ca ++	0	0	-10000	0	-10000	0	0
JNK cascade	0	0.001	-10000	0	-10000	0	0
BCAR1	0.033	0.008	-10000	0	-10000	0	0
stress fiber formation	-0.015	0.082	-10000	0	-0.27	7	7
GNAZ	-0.023	0.1	-10000	0	-0.28	20	20
EGFR/PI3K-beta/Gab1	-0.048	0.12	-10000	0	-0.28	27	27
positive regulation of dendritic cell cytokine production	-0.022	0.07	-10000	0	-0.22	17	17
LPA/LPA2/MAGI-3	0.003	0.051	-10000	0	-0.31	2	2
ARHGEF1	-0.006	0.082	0.19	2	-0.22	17	19
GNAI2	-0.013	0.082	-10000	0	-0.25	16	16
GNAI3	-0.012	0.083	-10000	0	-0.24	17	17
GNAI1	-0.028	0.11	-10000	0	-0.29	23	23
LPA/LPA3	-0.011	0.035	-10000	0	-0.11	17	17
LPA/LPA2	-0.011	0.035	-10000	0	-0.11	17	17
LPA/LPA1	-0.027	0.093	-10000	0	-0.29	17	17
HB-EGF/EGFR	-0.067	0.18	-10000	0	-0.4	33	33
HBEGF	-0.05	0.14	-10000	0	-0.37	25	25
mol:DAG	-0.025	0.073	-10000	0	-0.28	9	9
cAMP biosynthetic process	-0.026	0.11	0.2	3	-0.29	15	18
NFKB1	0.033	0.008	-10000	0	-10000	0	0
SRC	0.032	0.012	-10000	0	-10000	0	0
GNB1	0.033	0.007	-10000	0	-10000	0	0
LYN	-0.023	0.079	-10000	0	-0.29	7	7
GNAQ	-0.009	0.028	-10000	0	-0.086	17	17
LPAR2	-0.001	0.001	-10000	0	-10000	0	0
LPAR3	0	0.001	-10000	0	-10000	0	0
LPAR1	-0.017	0.054	-10000	0	-0.17	17	17
IL8	-0.2	0.23	-10000	0	-0.48	56	56
PTK2	-0.006	0.073	-10000	0	-0.21	17	17
Rac1/GDP	0.025	0.005	-10000	0	-10000	0	0
CASP3	-0.012	0.075	-10000	0	-0.23	16	16
EGFR	-0.031	0.17	-10000	0	-0.51	17	17
PLCG1	-0.011	0.056	-10000	0	-0.16	15	15
PLD2	-0.009	0.079	-10000	0	-0.21	19	19
G12/G13	0.012	0.09	-10000	0	-0.23	17	17
PI3K-beta	-0.037	0.11	-10000	0	-0.35	9	9
cell migration	0.015	0.064	-10000	0	-0.26	4	4
SLC9A3R2	0.023	0.064	-10000	0	-0.51	2	2
PXN	-0.016	0.084	-10000	0	-0.28	7	7
HRAS/GTP	-0.033	0.1	-10000	0	-0.28	16	16
RAC1	0.033	0.006	-10000	0	-10000	0	0
MMP9	-0.014	0.15	-10000	0	-0.51	13	13
PRKCE	0.031	0.01	-10000	0	-10000	0	0
PRKCD	-0.027	0.071	-10000	0	-0.32	6	6
Gi(beta/gamma)	-0.026	0.11	-10000	0	-0.28	16	16
mol:LPA	-0.017	0.054	-10000	0	-0.17	17	17
TRIP6/p130 Cas/FAK1/Paxillin	0.007	0.095	-10000	0	-0.32	5	5
MAPKKK cascade	-0.032	0.1	-10000	0	-0.28	16	16
contractile ring contraction involved in cytokinesis	-0.034	0.1	-10000	0	-0.32	13	13
mol:GDP	0	0	-10000	0	-10000	0	0
GNA14	-0.005	0.052	-10000	0	-0.31	3	3
GNA15	-0.02	0.085	-10000	0	-0.3	12	12
GNA12	0.033	0.008	-10000	0	-10000	0	0
GNA13	0.03	0.045	-10000	0	-0.51	1	1
MAPT	-0.014	0.11	0.18	17	-0.24	11	28
GNA11	-0.001	0.047	-10000	0	-0.32	2	2
Rac1/GTP	0.034	0.16	-10000	0	-0.91	4	4
MMP2	-0.051	0.19	-10000	0	-0.59	17	17

Arf6 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CENTA1/KIF3B	0.02	0.009	-10000	0	-10000	0	0
ARNO/beta Arrestin1-2	-0.006	0.091	-10000	0	-0.22	20	20
EGFR	-0.031	0.17	-10000	0	-0.51	17	17
EPHA2	-0.01	0.14	-10000	0	-0.51	11	11
USP6	0.032	0.008	-10000	0	-10000	0	0
IQSEC1	0.032	0.01	-10000	0	-10000	0	0
EGFR/EGFR/EGF/EGF	-0.049	0.17	-10000	0	-0.41	26	26
ARRB2	0.008	0.048	-10000	0	-0.32	3	3
mol:GTP	0.003	0.026	0.11	1	-0.17	2	3
ARRB1	0.029	0.022	-10000	0	-10000	0	0
FBXO8	0.031	0.013	-10000	0	-10000	0	0
TSHR	0.026	0.062	-10000	0	-0.51	2	2
EGF	-0.031	0.15	-10000	0	-0.51	13	13
somatostatin receptor activity	0	0	0.001	3	-0.001	12	15
ARAP2	0	0	0	9	0	13	22
mol:GDP	-0.008	0.097	0.19	1	-0.27	11	12
mol:PI-3-4-5-P3	0	0	0	7	-0.001	13	20
ITGA2B	0.034	0.005	-10000	0	-10000	0	0
ARF6	0.026	0.062	-10000	0	-0.51	2	2
Ephrin A1/EPHA2/NCK1/GIT1	0.027	0.12	-10000	0	-0.36	11	11
ADAP1	0	0	0	4	0	10	14
KIF13B	0.03	0.014	-10000	0	-10000	0	0
HGF/MET	0.037	0.061	-10000	0	-0.37	3	3
PXN	0.034	0.004	-10000	0	-10000	0	0
ARF6/GTP	-0.006	0.1	0.18	6	-0.25	13	19
EGFR/EGFR/EGF/EGF/ARFGEP100	-0.028	0.16	-10000	0	-0.35	26	26
ADRB2	-0.043	0.18	-10000	0	-0.51	19	19
receptor agonist activity	0	0	0	9	0	9	18
actin filament binding	0	0	0	2	0	11	13
SRC	0.032	0.012	-10000	0	-10000	0	0
ITGB3	0.026	0.048	-10000	0	-0.51	1	1
GNAQ	0	0	0.001	8	-0.001	10	18
EFA6/PI-4-5-P2	0	0	0.001	6	-0.001	10	16
ARF6/GDP	0.009	0.11	0.19	3	-0.37	7	10
ARF6/GDP/GULP/ACAP1	-0.037	0.15	0.2	1	-0.29	30	31
alphaIIb/beta3 Integrin/paxillin/GIT1	0.071	0.06	-10000	0	-0.29	3	3
ACAP1	0	0	0	3	-10000	0	3
ACAP2	0	0	0	9	0	12	21
LHCGR/beta Arrestin2	0.015	0.069	-10000	0	-0.44	3	3
EFNA1	0.021	0.076	-10000	0	-0.51	3	3
HGF	0.03	0.019	-10000	0	-10000	0	0
CYTH3	0	0	0.001	10	-0.001	9	19
CYTH2	-0.001	0.001	-10000	0	-0.004	13	13
NCK1	0.021	0.062	-10000	0	-0.51	2	2
fibronectin binding	0	0	0	6	0	13	19
endosomal lumen acidification	0	0	0	11	0	6	17
microtubule-based process	0	0	-10000	0	-10000	0	0
GULP1	-0.071	0.2	-10000	0	-0.51	26	26
GNAQ/ARNO	0	0.003	0.008	8	-0.006	10	18
mol:Phosphatidic acid	0	0	0	9	0	12	21
PIP3-E	0	0	0	4	0	18	22
MET	0.021	0.076	-10000	0	-0.51	3	3
GNA14	0.016	0.079	-10000	0	-0.51	3	3
GNA15	-0.007	0.14	-10000	0	-0.51	11	11
GIT1	0.026	0.062	-10000	0	-0.51	2	2
mol:PI-4-5-P2	0	0	0.001	8	-0.001	11	19
GNA11	0.026	0.062	-10000	0	-0.51	2	2
LHCGR	0.018	0.076	-10000	0	-0.51	3	3
AGTR1	0.008	0.077	-10000	0	-0.51	3	3
desensitization of G-protein coupled receptor protein signaling pathway	0.015	0.069	-10000	0	-0.44	3	3
IPCEF1/ARNO	-0.028	0.12	-10000	0	-0.27	26	26
alphaIIb/beta3 Integrin	0.043	0.04	-10000	0	-0.37	1	1

BMP receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS	-0.063	0.21	-9999	-0.36	45	45
SMAD6-7/SMURF1	0.05	0.065	-9999	-0.32	4	4
NOG	0.033	0.013	-9999	-10000	0	0
SMAD9	-0.032	0.18	-9999	-0.63	10	10
SMAD4	0.026	0.062	-9999	-0.51	2	2
SMAD5	-0.05	0.15	-9999	-0.47	11	11
BMP7/USAG1	-0.16	0.24	-9999	-0.46	55	55
SMAD5/SKI	-0.039	0.16	-9999	-0.45	11	11
SMAD1	0.003	0.11	-9999	-0.44	7	7
BMP2	-0.057	0.19	-9999	-0.51	23	23
SMAD1/SMAD1/SMAD4	0.011	0.12	-9999	-0.44	5	5
BMPR1A	0.022	0.075	-9999	-0.51	3	3
BMPR1B	0.027	0.024	-9999	-10000	0	0
BMPR1A-1B/BAMBI	0.023	0.11	-9999	-0.34	11	11
AHSG	0.017	0.019	-9999	-10000	0	0
CER1	0.031	0.01	-9999	-10000	0	0
BMP2-4/CER1	-0.014	0.14	-9999	-0.33	23	23
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA	-0.063	0.17	-9999	-0.45	16	16
BMP2-4 (homodimer)	-0.033	0.16	-9999	-0.39	24	24
RGMB	0.032	0.008	-9999	-10000	0	0
BMP6/BMPR2/BMPR1A-1B	0.038	0.1	-9999	-0.32	9	9
RGMA	-0.061	0.2	-9999	-0.51	25	25
SMURF1	0.022	0.075	-9999	-0.51	3	3
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP	-0.056	0.16	-9999	-0.43	16	16
BMP2-4/USAG1	-0.13	0.21	-9999	-0.38	56	56
SMAD6/SMURF1/SMAD5	-0.044	0.16	-9999	-0.44	11	11
SOSTDC1	-0.15	0.24	-9999	-0.51	46	46
BMP7/BMPR2/BMPR1A-1B	-0.016	0.16	-9999	-0.3	33	33
SKI	0.033	0.007	-9999	-10000	0	0
BMP6 (homodimer)	0.006	0.099	-9999	-0.51	5	5
HFE2	0.026	0.062	-9999	-0.51	2	2
ZFYVE16	0.032	0.009	-9999	-10000	0	0
MAP3K7	0.034	0.009	-9999	-10000	0	0
BMP2-4/CHRD	-0.022	0.11	-9999	-0.33	14	14
SMAD5/SMAD5/SMAD4	-0.042	0.16	-9999	-0.46	12	12
MAPK1	0.028	0.044	-9999	-0.51	1	1
TAK1/TAB family	-0.041	0.15	-9999	-0.37	17	17
BMP7 (homodimer)	-0.075	0.21	-9999	-0.51	29	29
NUP214	0.034	0.004	-9999	-10000	0	0
BMP6/FETUA	0.009	0.07	-9999	-0.37	4	4
SMAD1/SKI	0.015	0.12	-9999	-0.43	8	8
SMAD6	0.033	0.01	-9999	-10000	0	0
CTDSP2	0.034	0.005	-9999	-10000	0	0
BMP2-4/FETUA	-0.02	0.11	-9999	-0.33	14	14
MAP3K7IP1	0	0	-9999	-10000	0	0
GREM1	-0.032	0.17	-9999	-0.51	17	17
BMPR2 (homodimer)	0.025	0.062	-9999	-0.51	2	2
GADD34/PP1CA	0.058	0.041	-9999	-0.32	1	1
BMPR1A-1B (homodimer)	0.034	0.062	-9999	-0.36	3	3
CHRDL1	0.027	0.048	-9999	-0.51	1	1
ENDOFIN/SMAD1	0.016	0.12	-9999	-0.43	8	8
SMAD6-7/SMURF1/SMAD1	0.03	0.13	-9999	-0.47	4	4
SMAD6/SMURF1	0.022	0.075	-9999	-0.51	3	3
BAMBI	-0.006	0.13	-9999	-0.51	9	9
SMURF2	0.026	0.062	-9999	-0.51	2	2
BMP2-4/CHRDL1	-0.013	0.15	-9999	-0.34	22	22
BMP2-4/GREM1	-0.051	0.18	-9999	-0.38	33	33
SMAD7	0.028	0.045	-9999	-0.51	1	1
SMAD8A/SMAD8A/SMAD4	-0.028	0.18	-9999	-0.56	12	12
SMAD1/SMAD6	0.007	0.12	-9999	-0.43	8	8
TAK1/SMAD6	0.04	0.059	-9999	-0.37	3	3
BMP7	-0.076	0.21	-9999	-0.51	29	29
BMP6	0.006	0.099	-9999	-0.51	5	5
MAP3K7IP2	0	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1	-0.06	0.16	-9999	-0.4	19	19
PPM1A	0.034	0.005	-9999	-10000	0	0
SMAD1/SMURF2	0.012	0.13	-9999	-0.47	8	8
SMAD7/SMURF1	0.034	0.068	-9999	-0.37	4	4
CTDSPL	0.027	0.045	-9999	-0.51	1	1
PPP1CA	0.034	0.005	-9999	-10000	0	0
XIAP	0	0	-9999	-10000	0	0
CTDSP1	0.033	0.006	-9999	-10000	0	0
PPP1R15A	0.029	0.045	-9999	-0.51	1	1
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS	-0.11	0.23	-9999	-0.52	29	29
CHRD	0.016	0.019	-9999	-10000	0	0
BMPR2	0.025	0.062	-9999	-0.51	2	2
BMP2-4/BMPR2/BMPR1A-1B/RGM	-0.07	0.18	-9999	-0.48	17	17
BMP4	0.019	0.066	-9999	-0.51	2	2
FST	-0.065	0.2	-9999	-0.51	26	26
BMP2-4/NOG	-0.012	0.14	-9999	-0.33	23	23
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1	-0.01	0.16	-9999	-0.3	32	32

S1P1 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
VEGFR2 homodimer/VEGFA homodimer	0.031	0.064	-9999	-0.33	4	4
PDGFRB	0.031	0.012	-9999	-10000	0	0
SPHK1	-0.057	0.23	-9999	-0.89	10	10
mol:S1P	-0.074	0.22	-9999	-0.75	12	12
S1P1/S1P/Gi	-0.098	0.21	-9999	-0.47	27	27
GNAO1	0.024	0.022	-9999	-10000	0	0
PDGFB-D/PDGFRB/PLCgamma1	-0.08	0.2	-9999	-0.45	23	23
PLCG1	-0.097	0.2	-9999	-0.45	26	26
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.031	0.012	-9999	-10000	0	0
GNAI2	0.021	0.025	-9999	-10000	0	0
GNAI3	0.025	0.02	-9999	-10000	0	0
GNAI1	-0.007	0.13	-9999	-0.51	9	9
mol:GDP	0	0	-9999	-10000	0	0
EDG1	-0.011	0.049	-9999	-0.29	4	4
S1P1/S1P	-0.072	0.17	-9999	-0.53	15	15
negative regulation of cAMP metabolic process	-0.094	0.2	-9999	-0.45	27	27
MAPK3	-0.13	0.26	-9999	-0.64	27	27
calcium-dependent phospholipase C activity	-0.002	0.004	-9999	-10000	0	0
Rac1/GDP	0.025	0.005	-9999	-10000	0	0
RhoA/GDP	0.023	0.008	-9999	-10000	0	0
KDR	0.02	0.064	-9999	-0.52	2	2
PLCB2	-0.054	0.16	-9999	-0.48	14	14
RAC1	0.033	0.006	-9999	-10000	0	0
RhoA/GTP	-0.057	0.15	-9999	-0.44	15	15
receptor internalization	-0.067	0.16	-9999	-0.49	15	15
PTGS2	-0.19	0.4	-9999	-1	26	26
Rac1/GTP	-0.058	0.15	-9999	-0.44	15	15
RHOA	0.031	0.011	-9999	-10000	0	0
VEGFA	0.024	0.064	-9999	-0.52	2	2
negative regulation of T cell proliferation	-0.094	0.2	-9999	-0.45	27	27
GO:0007205	0	0	-9999	-10000	0	0
GNAZ	-0.002	0.11	-9999	-0.51	7	7
MAPK1	-0.12	0.25	-9999	-0.62	26	26
S1P1/S1P/PDGFB-D/PDGFRB	-0.062	0.18	-9999	-0.51	15	15
ABCC1	-0.024	0.15	-9999	-0.51	12	12

FAS signaling pathway (CD95)

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPTAN1	-0.008	0.066	0.21	5	-10000	0	5
RFC1	-0.003	0.074	0.21	7	-0.47	1	8
PRKDC	0.002	0.09	0.22	13	-0.47	1	14
RIPK1	0.035	0.007	-10000	0	-10000	0	0
CASP7	-0.035	0.18	-10000	0	-0.72	8	8
FASLG/FAS/FADD/FAF1	-0.027	0.12	0.22	6	-0.32	19	25
MAP2K4	-0.043	0.22	0.26	2	-0.56	15	17
mol:ceramide	-0.061	0.19	-10000	0	-0.51	17	17
GSN	-0.023	0.097	0.21	5	-0.32	9	14
FASLG/FAS/FADD/FAF1/Caspase 8	-0.04	0.16	0.26	1	-0.43	17	18
FAS	-0.023	0.15	-10000	0	-0.51	13	13
BID	-0.028	0.05	-10000	0	-0.33	4	4
MAP3K1	-0.001	0.2	0.27	4	-0.64	9	13
MAP3K7	0.033	0.01	-10000	0	-10000	0	0
RB1	-0.009	0.073	0.21	6	-0.28	2	8
CFLAR	0.017	0.095	-10000	0	-0.5	5	5
HGF/MET	0.017	0.12	-10000	0	-0.34	15	15
ARHGDIB	-0.008	0.11	0.24	12	-0.32	6	18
FADD	0.026	0.019	-10000	0	-10000	0	0
actin filament polymerization	0.023	0.096	0.32	9	-0.2	5	14
NFKB1	-0.035	0.15	-10000	0	-0.67	6	6
MAPK8	-0.06	0.24	0.27	1	-0.53	23	24
DFFA	-0.008	0.07	0.21	6	-10000	0	6
DNA fragmentation during apoptosis	-0.008	0.069	0.21	6	-10000	0	6
FAS/FADD/MET	0.013	0.11	-10000	0	-0.34	11	11
CFLAR/RIP1	0.038	0.068	-10000	0	-0.31	5	5
FAIM3	0.034	0.01	-10000	0	-10000	0	0
FAF1	0.027	0.019	-10000	0	-10000	0	0
PARP1	-0.009	0.071	0.21	6	-10000	0	6
DFFB	-0.008	0.07	0.21	6	-10000	0	6
CHUK	-0.04	0.15	-10000	0	-0.58	8	8
FASLG	-0.035	0.16	-10000	0	-0.51	15	15
FAS/FADD	-0.001	0.11	-10000	0	-0.37	11	11
HGF	0.03	0.019	-10000	0	-10000	0	0
LMNA	-0.003	0.069	0.23	1	-0.26	2	3
CASP6	-0.005	0.06	0.21	5	-10000	0	5
CASP10	0.016	0.077	-10000	0	-0.51	3	3
CASP3	-0.007	0.08	0.26	5	-0.22	13	18
PTPN13	-0.016	0.15	-10000	0	-0.51	13	13
CASP8	-0.029	0.042	-10000	0	-0.38	2	2
IL6	-0.15	0.42	-10000	0	-1.2	19	19
MET	0.021	0.076	-10000	0	-0.51	3	3
ICAD/CAD	-0.008	0.07	0.41	1	-10000	0	1
FASLG/FAS/FADD/FAF1/Caspase 10	-0.061	0.2	-10000	0	-0.52	17	17
activation of caspase activity by cytochrome c	-0.028	0.05	-10000	0	-0.33	4	4
PAK2	0.079	0.13	0.23	60	-0.3	1	61
BCL2	-0.005	0.12	-10000	0	-0.51	7	7

Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization	-0.014	0.11	-10000	0	-0.3	17	17
epithelial cell differentiation	0.036	0.094	-10000	0	-0.27	12	12
CYFIP2	0.026	0.047	-10000	0	-0.51	1	1
ENAH	-0.015	0.11	0.28	3	-0.33	6	9
EGFR	-0.031	0.17	-10000	0	-0.51	17	17
EPHA2	-0.01	0.14	-10000	0	-0.51	11	11
MYO6	-0.011	0.092	-10000	0	-0.28	14	14
CTNNB1	0.03	0.016	-10000	0	-10000	0	0
ABI1/Sra1/Nap1	0.052	0.052	-10000	0	-0.32	2	2
AQP5	-0.063	0.17	-10000	0	-0.48	20	20
CTNND1	0.017	0.096	-10000	0	-0.51	5	5
mol:PI-4-5-P2	-0.007	0.08	-10000	0	-0.26	13	13
regulation of calcium-dependent cell-cell adhesion	-0.026	0.1	-10000	0	-0.28	19	19
EGF	-0.031	0.15	-10000	0	-0.51	13	13
NCKAP1	0.027	0.047	-10000	0	-0.51	1	1
AQP3	-0.098	0.19	-10000	0	-0.47	29	29
cortical microtubule organization	0.036	0.094	-10000	0	-0.27	12	12
GO:0000145	-0.028	0.071	-10000	0	-0.24	13	13
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.041	0.097	-10000	0	-0.27	12	12
MLLT4	0.033	0.006	-10000	0	-10000	0	0
ARF6/GDP	-0.056	0.11	-10000	0	-0.32	18	18
ARF6	0.026	0.062	-10000	0	-0.51	2	2
Ephrin A1/EPHA2/NCK1/GIT1	0.027	0.12	-10000	0	-0.36	11	11
mol:Ca2+	0	0	-10000	0	-10000	0	0
VASP	-0.019	0.07	-10000	0	-0.26	9	9
PVRL2	0.033	0.008	-10000	0	-10000	0	0
ZYX	-0.011	0.083	-10000	0	-0.26	14	14
ARF6/GTP	0.027	0.13	-10000	0	-0.35	12	12
CDH1	0.007	0.11	-10000	0	-0.51	7	7
EGFR/EGFR/EGF/EGF	-0.041	0.15	-10000	0	-0.31	32	32
RhoA/GDP	0.037	0.091	-10000	0	-0.26	12	12
actin cytoskeleton organization	-0.036	0.095	-10000	0	-0.31	13	13
IGF-1R heterotetramer	-0.006	0.14	-10000	0	-0.51	11	11
GIT1	0.026	0.062	-10000	0	-0.51	2	2
IGF1R	-0.006	0.14	-10000	0	-0.51	11	11
IGF1	-0.048	0.18	-10000	0	-0.51	20	20
DIAPH1	0.005	0.19	-10000	0	-0.62	7	7
Wnt receptor signaling pathway	-0.036	0.094	0.27	12	-10000	0	12
RHOA	0.031	0.011	-10000	0	-10000	0	0
RhoA/GTP	-0.053	0.1	-10000	0	-0.32	17	17
CTNNA1	0.032	0.008	-10000	0	-10000	0	0
VCL	-0.036	0.098	-10000	0	-0.32	13	13
EFNA1	0.021	0.076	-10000	0	-0.51	3	3
LPP	-0.024	0.063	-10000	0	-0.26	9	9
Ephrin A1/EPHA2	0.002	0.13	-10000	0	-0.31	20	20
SEC6/SEC8	-0.004	0.063	-10000	0	-0.25	8	8
MGAT3	-0.027	0.1	-10000	0	-0.29	19	19
HGF/MET	0.023	0.093	-10000	0	-0.26	13	13
HGF	0.03	0.019	-10000	0	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN	-0.014	0.11	-10000	0	-0.3	17	17
actin cable formation	0.035	0.13	0.34	7	-0.28	6	13
KIAA1543	-0.026	0.07	-10000	0	-0.25	12	12
KIFC3	-0.004	0.076	-10000	0	-0.26	11	11
NCK1	0.021	0.062	-10000	0	-0.51	2	2
EXOC3	0.027	0.014	-10000	0	-10000	0	0
ACTN1	-0.006	0.08	-10000	0	-0.26	12	12
NCK1/GIT1	0.03	0.062	-10000	0	-0.37	3	3
mol:GDP	0.036	0.094	-10000	0	-0.27	12	12
EXOC4	0.034	0.004	-10000	0	-10000	0	0
STX4	-0.002	0.074	-10000	0	-0.26	10	10
PIP5K1C	-0.007	0.081	-10000	0	-0.26	13	13
LIMA1	0.005	0.12	-10000	0	-0.51	8	8
ABI1	0.033	0.007	-10000	0	-10000	0	0
ROCK1	-0.011	0.13	0.29	6	-0.39	6	12
adherens junction assembly	-0.02	0.11	-10000	0	-0.46	4	4
IGF-1R heterotetramer/IGF1	-0.038	0.15	-10000	0	-0.29	36	36
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0.047	0.018	-10000	0	-10000	0	0
MET	0.021	0.076	-10000	0	-0.51	3	3
PLEKHA7	-0.005	0.079	-10000	0	-0.26	12	12
mol:GTP	0.025	0.12	-10000	0	-0.36	11	11
establishment of epithelial cell apical/basal polarity	0.013	0.11	0.36	5	-0.29	1	6
cortical actin cytoskeleton stabilization	-0.014	0.11	-10000	0	-0.3	17	17
regulation of cell-cell adhesion	-0.036	0.095	-10000	0	-0.31	13	13
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton	-0.014	0.11	-10000	0	-0.3	17	17

Syndecan-4-mediated signaling events

Figure S36. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S36. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.038	0.17	-10000	0	-0.53	12	12
Syndecan-4/Syndesmos	-0.026	0.17	-10000	0	-0.47	15	15
positive regulation of JNK cascade	-0.066	0.23	-10000	0	-0.53	26	26
Syndecan-4/ADAM12	-0.05	0.2	-10000	0	-0.51	20	20
CCL5	-0.022	0.16	-10000	0	-0.51	15	15
Rac1/GDP	0.025	0.005	-10000	0	-10000	0	0
DNM2	0.033	0.007	-10000	0	-10000	0	0
ITGA5	0.025	0.063	-10000	0	-0.51	2	2
SDCBP	0.029	0.044	-10000	0	-0.51	1	1
PLG	0.032	0.019	-10000	0	-10000	0	0
ADAM12	-0.012	0.14	-10000	0	-0.51	12	12
mol:GTP	0	0	-10000	0	-10000	0	0
NUDT16L1	0.032	0.011	-10000	0	-10000	0	0
mol:PI-4-5-P2	0	0	-10000	0	-10000	0	0
Syndecan-4/PKC alpha	-0.034	0.018	-10000	0	-10000	0	0
Syndecan-4/Laminin alpha1	-0.031	0.17	-10000	0	-0.48	14	14
Syndecan-4/CXCL12/CXCR4	-0.07	0.25	-10000	0	-0.56	26	26
Syndecan-4/Laminin alpha3	-0.054	0.18	-10000	0	-0.5	14	14
MDK	0.005	0.11	-10000	0	-0.51	7	7
Syndecan-4/FZD7	-0.06	0.19	-10000	0	-0.49	18	18
Syndecan-4/Midkine	-0.044	0.18	-10000	0	-0.46	17	17
FZD7	-0.04	0.18	-10000	0	-0.51	19	19
Syndecan-4/FGFR1/FGF	-0.037	0.18	-10000	0	-0.48	13	13
THBS1	0.025	0.063	-10000	0	-0.51	2	2
integrin-mediated signaling pathway	-0.048	0.18	-10000	0	-0.45	19	19
positive regulation of MAPKKK cascade	-0.066	0.23	-10000	0	-0.53	26	26
Syndecan-4/TACI	-0.029	0.18	-10000	0	-0.47	16	16
CXCR4	-0.034	0.17	-10000	0	-0.51	18	18
cell adhesion	-0.012	0.1	0.2	1	-0.33	12	13
Syndecan-4/Dynamin	-0.028	0.18	-10000	0	-0.47	16	16
Syndecan-4/TSP1	-0.032	0.18	-10000	0	-0.46	17	17
Syndecan-4/GIPC	-0.031	0.18	-10000	0	-0.45	18	18
Syndecan-4/RANTES	-0.052	0.22	-10000	0	-0.55	20	20
ITGB1	0.025	0.062	-10000	0	-0.51	2	2
LAMA1	0.024	0.03	-10000	0	-10000	0	0
LAMA3	-0.024	0.16	-10000	0	-0.51	15	15
RAC1	0.033	0.006	-10000	0	-10000	0	0
PRKCA	0.013	0.13	0.84	3	-0.48	1	4
Syndecan-4/alpha-Actinin	-0.029	0.18	-10000	0	-0.46	17	17
TFPI	0.002	0.11	-10000	0	-0.51	7	7
F2	0.027	0.024	-10000	0	-10000	0	0
alpha5/beta1 Integrin	0.035	0.069	-10000	0	-0.37	4	4
positive regulation of cell adhesion	-0.058	0.17	-10000	0	-0.5	13	13
ACTN1	0.032	0.014	-10000	0	-10000	0	0
TNC	-0.019	0.14	-10000	0	-0.51	11	11
Syndecan-4/CXCL12	-0.054	0.21	-10000	0	-0.5	22	22
FGF6	0.01	0.1	-10000	0	-0.51	6	6
RHOA	0.031	0.011	-10000	0	-10000	0	0
CXCL12	-0.024	0.16	-10000	0	-0.51	14	14
TNFRSF13B	0.027	0.046	-10000	0	-0.51	1	1
FGF2	0.014	0.088	-10000	0	-0.51	4	4
FGFR1	0.018	0.063	-10000	0	-0.51	2	2
Syndecan-4/PI-4-5-P2	-0.046	0.16	-10000	0	-0.45	18	18
mol:GDP	0	0	-10000	0	-10000	0	0
FN1	-0.01	0.13	-10000	0	-0.5	10	10
cell migration	-0.015	0.013	-10000	0	-10000	0	0
PRKCD	0.029	0.018	-10000	0	-10000	0	0
vasculogenesis	-0.03	0.17	-10000	0	-0.44	18	18
SDC4	-0.041	0.17	-10000	0	-0.47	18	18
Syndecan-4/Tenascin C	-0.051	0.19	-10000	0	-0.47	19	19
Syndecan-4/PI-4-5-P2/PKC alpha	-0.027	0.014	-10000	0	-10000	0	0
Syndecan-4/Syntenin	-0.03	0.18	-10000	0	-0.47	17	17
MMP9	-0.013	0.15	-10000	0	-0.5	13	13
Rac1/GTP	-0.012	0.1	0.21	1	-0.34	12	13
cytoskeleton organization	-0.025	0.17	-10000	0	-0.46	15	15
GIPC1	0.029	0.044	-10000	0	-0.51	1	1
Syndecan-4/TFPI	-0.043	0.19	-10000	0	-0.47	19	19

Caspase cascade in apoptosis

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TOP1	-0.013	0.17	0.29	1	-0.47	14	15
ACTA1	-0.036	0.16	0.27	3	-0.49	14	17
NUMA1	-0.024	0.2	0.29	1	-0.51	17	18
SPTAN1	-0.032	0.16	0.27	3	-0.51	12	15
LIMK1	-0.037	0.18	0.35	4	-0.53	13	17
BIRC3	-0.026	0.16	-10000	0	-0.51	14	14
BIRC2	0.033	0.01	-10000	0	-10000	0	0
BAX	0.034	0.005	-10000	0	-10000	0	0
CASP10	-0.042	0.11	-10000	0	-0.43	11	11
CRMA	0	0	-10000	0	-10000	0	0
XIAP	0	0	-10000	0	-0.001	5	5
PTK2	-0.016	0.16	0.29	1	-0.47	14	15
DIABLO	0.034	0.003	-10000	0	-10000	0	0
apoptotic nuclear changes	-0.032	0.16	0.27	3	-0.5	12	15
response to UV	0	0	-10000	0	-10000	0	0
CRADD	0.027	0.061	-10000	0	-0.51	2	2
GSN	-0.047	0.18	0.27	3	-0.46	18	21
MADD	0.033	0.007	-10000	0	-10000	0	0
TFAP2A	-0.008	0.15	-10000	0	-0.55	9	9
BID	-0.02	0.091	-10000	0	-0.3	13	13
MAP3K1	-0.04	0.18	-10000	0	-0.55	15	15
TRADD	0.029	0.044	-10000	0	-0.51	1	1
mol:Ca2+	0	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0.047	0.035	-10000	0	-0.37	1	1
mol:Activated DNA	0	0	-10000	0	-10000	0	0
ARHGDIB	-0.036	0.2	0.27	3	-0.61	13	16
CASP9	0.033	0.006	-10000	0	-10000	0	0
DNA repair	-0.014	0.062	0.2	2	-0.2	7	9
neuron apoptosis	-0.022	0.2	-10000	0	-0.78	9	9
mol:NAD	0	0	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	-0.03	0.2	0.28	2	-0.51	17	19
APAF1	0.031	0.044	-10000	0	-0.51	1	1
CASP6	-0.028	0.24	-10000	0	-0.96	8	8
TRAF2	0.033	0.01	-10000	0	-10000	0	0
ICAD/CAD	-0.031	0.16	0.28	4	-0.49	12	16
CASP7	0.023	0.087	0.28	11	-0.22	2	13
KRT18	-0.015	0.15	-10000	0	-0.64	7	7
apoptosis	-0.036	0.18	0.29	2	-0.54	13	15
DFFA	-0.031	0.16	0.27	3	-0.51	12	15
DFFB	-0.031	0.16	0.28	3	-0.51	12	15
PARP1	0.014	0.062	0.2	7	-0.2	2	9
actin filament polymerization	0.031	0.18	0.5	12	-0.37	6	18
TNF	0.026	0.048	-10000	0	-0.51	1	1
CYCS	-0.002	0.075	-10000	0	-0.25	8	8
SATB1	-0.036	0.22	-10000	0	-0.89	8	8
SLK	-0.032	0.16	0.27	3	-0.51	12	15
p15 BID/BAX	0	0.099	0.2	1	-0.32	10	11
CASP2	-0.003	0.091	-10000	0	-0.33	7	7
JNK cascade	0.04	0.18	0.54	15	-10000	0	15
CASP3	-0.031	0.17	0.3	3	-0.53	12	15
LMNB2	-0.008	0.18	0.26	1	-0.66	7	8
RIPK1	0.033	0.006	-10000	0	-10000	0	0
CASP4	0.027	0.062	-10000	0	-0.51	2	2
Mammalian IAPs/DIABLO	0.022	0.1	-10000	0	-0.29	14	14
negative regulation of DNA binding	-0.007	0.15	-10000	0	-0.55	9	9
stress fiber formation	-0.031	0.16	0.27	3	-0.5	12	15
GZMB	-0.022	0.13	-10000	0	-0.5	10	10
CASP1	-0.005	0.11	-10000	0	-0.43	8	8
LMNB1	-0.033	0.22	0.26	1	-0.57	15	16
APP	-0.022	0.2	-10000	0	-0.79	9	9
TNFRSF1A	0.021	0.075	-10000	0	-0.51	3	3
response to stress	0	0	0.001	3	-0.001	4	7
CASP8	0.004	0.043	-10000	0	-0.37	2	2
VIM	-0.033	0.18	0.3	2	-0.5	16	18
LMNA	0.005	0.12	0.26	1	-0.41	8	9
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD	0.001	0.097	-10000	0	-0.34	7	7
LRDD	0	0	-10000	0	-10000	0	0
SREBF1	-0.032	0.16	0.27	3	-0.51	12	15
APAF-1/Caspase 9	0.019	0.12	-10000	0	-0.61	5	5
nuclear fragmentation during apoptosis	-0.023	0.19	0.29	1	-0.5	17	18
CFL2	-0.033	0.18	0.38	6	-0.52	12	18
GAS2	-0.061	0.17	0.28	2	-0.4	22	24
positive regulation of apoptosis	-0.013	0.19	0.27	1	-0.52	12	13
PRF1	-0.002	0.12	-10000	0	-0.51	8	8

Syndecan-2-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Syndecan-2/Fibronectin	-0.008	0.12	-10000	0	-0.35	14	14
EPHB2	-0.02	0.15	-10000	0	-0.51	13	13
Syndecan-2/TACI	0.013	0.073	-10000	0	-0.31	7	7
LAMA1	0.024	0.03	-10000	0	-10000	0	0
Syndecan-2/alpha2 ITGB1	-0.024	0.16	-10000	0	-0.33	29	29
HRAS	0.029	0.045	-10000	0	-0.51	1	1
Syndecan-2/CASK	-0.003	0.061	-10000	0	-0.3	6	6
ITGA5	0.025	0.063	-10000	0	-0.51	2	2
BAX	-0.003	0.054	-10000	0	-10000	0	0
EPB41	0.034	0.005	-10000	0	-10000	0	0
positive regulation of cell-cell adhesion	0.014	0.066	-10000	0	-0.28	7	7
LAMA3	-0.024	0.16	-10000	0	-0.51	15	15
EZR	0	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0	0	-10000	0	-10000	0	0
CAV2	-0.048	0.19	-10000	0	-0.51	23	23
Syndecan-2/MMP2	-0.022	0.13	-10000	0	-0.35	19	19
RP11-540L11.1	0	0	-10000	0	-10000	0	0
alpha2 ITGB1	-0.014	0.15	-10000	0	-0.38	20	20
dendrite morphogenesis	-0.013	0.12	-10000	0	-0.34	16	16
Syndecan-2/GM-CSF	-0.017	0.12	-10000	0	-0.34	15	15
determination of left/right symmetry	-0.002	0.073	-10000	0	-0.36	6	6
Syndecan-2/PKC delta	0.016	0.068	-10000	0	-0.31	6	6
GNB2L1	0.032	0.009	-10000	0	-10000	0	0
MAPK3	-0.016	0.11	0.2	7	-0.32	15	22
MAPK1	-0.02	0.12	0.2	6	-0.33	15	21
Syndecan-2/RACK1	0.029	0.069	-10000	0	-0.26	7	7
NF1	0.03	0.044	-10000	0	-0.51	1	1
FGFR/FGF/Syndecan-2	-0.002	0.073	-10000	0	-0.36	6	6
ITGA2	-0.038	0.18	-10000	0	-0.51	19	19
MAPK8	0	0.062	-10000	0	-0.3	6	6
Syndecan-2/alpha2/beta1 Integrin	-0.005	0.13	-10000	0	-0.29	22	22
Syndecan-2/Kininogen	0.009	0.045	-10000	0	-0.31	2	2
ITGB1	0.025	0.062	-10000	0	-0.51	2	2
SRC	0.013	0.068	-10000	0	-0.26	6	6
Syndecan-2/CASK/Protein 4.1	0.016	0.061	-10000	0	-0.28	6	6
extracellular matrix organization	0.017	0.068	-10000	0	-0.3	6	6
actin cytoskeleton reorganization	-0.008	0.12	-10000	0	-0.35	14	14
Syndecan-2/Caveolin-2/Ras	-0.013	0.13	-10000	0	-0.3	25	25
Syndecan-2/Laminin alpha3	-0.008	0.1	-10000	0	-0.31	16	16
Syndecan-2/RasGAP	0.037	0.076	-10000	0	-0.25	8	8
alpha5/beta1 Integrin	0.035	0.069	-10000	0	-0.37	4	4
PRKCD	0.03	0.013	-10000	0	-10000	0	0
Syndecan-2 dimer	-0.013	0.12	-10000	0	-0.34	16	16
GO:0007205	0.003	0.001	-10000	0	-10000	0	0
DNA mediated transformation	0	0	-10000	0	-10000	0	0
Syndecan-2/RasGAP/Src	0.023	0.065	-10000	0	-0.25	7	7
RHOA	0.031	0.011	-10000	0	-10000	0	0
SDCBP	0.029	0.044	-10000	0	-0.51	1	1
TNFRSF13B	0.027	0.046	-10000	0	-0.51	1	1
RASA1	0.028	0.044	-10000	0	-0.51	1	1
alpha2/beta1 Integrin	-0.014	0.15	-10000	0	-0.38	20	20
Syndecan-2/Synbindin	0.017	0.068	-10000	0	-0.31	6	6
TGFB1	0.033	0.006	-10000	0	-10000	0	0
CASP3	0.011	0.069	0.2	6	-0.28	6	12
FN1	-0.009	0.13	-10000	0	-0.51	10	10
Syndecan-2/IL8	-0.072	0.16	-10000	0	-0.33	39	39
SDC2	-0.002	0.073	-10000	0	-0.36	6	6
KNG1	0.017	0.019	-10000	0	-10000	0	0
Syndecan-2/Neurofibromin	0.015	0.073	-10000	0	-0.31	7	7
TRAPPC4	0.034	0.005	-10000	0	-10000	0	0
CSF2	-0.024	0.14	-10000	0	-0.51	11	11
Syndecan-2/TGFB1	0.017	0.068	-10000	0	-0.31	6	6
Syndecan-2/Syntenin/PI-4-5-P2	0.014	0.066	-10000	0	-0.28	7	7
Syndecan-2/Ezrin	0.015	0.061	-10000	0	-0.28	6	6
PRKACA	0.014	0.073	0.2	8	-0.28	6	14
angiogenesis	-0.072	0.16	-10000	0	-0.33	39	39
MMP2	-0.03	0.16	-10000	0	-0.51	16	16
IL8	-0.12	0.23	-10000	0	-0.51	38	38
calcineurin-NFAT signaling pathway	0.013	0.073	-10000	0	-0.31	7	7

amb2 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2	-0.02	0.19	-9999	-0.44	21	21
alphaM/beta2 Integrin/GPIbA	0.013	0.13	-9999	-0.38	12	12
alphaM/beta2 Integrin/proMMP-9	-0.01	0.17	-9999	-0.41	21	21
PLAUR	-0.003	0.13	-9999	-0.51	10	10
HMGB1	0.026	0.025	-9999	-10000	0	0
alphaM/beta2 Integrin/Talin	0.019	0.12	-9999	-0.4	10	10
AGER	-0.008	0.1	-9999	-0.52	5	5
RAP1A	0.026	0.062	-9999	-0.51	2	2
SELPLG	0.019	0.087	-9999	-0.51	4	4
mol:LDL	0	0	-9999	-10000	0	0
alphaM/beta2 Integrin/RAGE/HMGB1	-0.011	0.16	-9999	-0.37	18	18
mol:GTP	0	0	-9999	-10000	0	0
MMP9	-0.013	0.15	-9999	-0.51	13	13
CYR61	-0.01	0.13	-9999	-0.51	10	10
TLN1	0.031	0.01	-9999	-10000	0	0
Rap1/GTP	0.014	0.14	-9999	-0.45	10	10
RHOA	0.031	0.011	-9999	-10000	0	0
P-selectin oligomer	-0.057	0.2	-9999	-0.51	24	24
MYH2	-0.006	0.14	-9999	-0.48	8	8
MST1R	-0.007	0.13	-9999	-0.51	9	9
leukocyte activation during inflammatory response	0.025	0.11	-9999	-0.35	10	10
APOB	0.028	0.045	-9999	-0.51	1	1
mol:GDP	0	0	-9999	-10000	0	0
complement component iC3b receptor activity	0	0	-9999	-10000	0	0
MMP2	-0.03	0.16	-9999	-0.51	16	16
JAM3	0.019	0.066	-9999	-0.51	2	2
GP1BA	0.026	0.026	-9999	-10000	0	0
alphaM/beta2 Integrin/CTGF	0.011	0.15	-9999	-0.41	14	14
alphaM/beta2 Integrin	-0.008	0.15	-9999	-0.49	10	10
JAM3 homodimer	0.019	0.066	-9999	-0.51	2	2
ICAM2	0.027	0.048	-9999	-0.51	1	1
ICAM1	0.001	0.12	-9999	-0.51	7	7
phagocytosis triggered by activation of immune response cell surface activating receptor	-0.008	0.15	-9999	-0.46	11	11
cell adhesion	0.012	0.13	-9999	-0.38	12	12
NFKB1	-0.061	0.18	-9999	-0.45	19	19
THY1	0.02	0.077	-9999	-0.51	3	3
RhoA/GDP	0.023	0.008	-9999	-10000	0	0
Lipoprotein(a)	0.038	0.034	-9999	-0.31	1	1
alphaM/beta2 Integrin/LRP/tPA	-0.007	0.16	-9999	-0.36	20	20
IL6	-0.11	0.27	-9999	-0.74	20	20
ITGB2	-0.011	0.14	-9999	-0.52	10	10
elevation of cytosolic calcium ion concentration	-0.035	0.21	-9999	-0.44	27	27
alphaM/beta2 Integrin/JAM2/JAM3	0.011	0.16	-9999	-0.41	16	16
JAM2	0.01	0.11	-9999	-0.51	6	6
alphaM/beta2 Integrin/ICAM1	-0.004	0.18	-9999	-0.38	22	22
alphaM/beta2 Integrin/uPA/Plg	-0.013	0.17	-9999	-0.36	24	24
RhoA/GTP	-0.035	0.13	-9999	-0.48	9	9
positive regulation of phagocytosis	-0.008	0.18	-9999	-0.53	13	13
Ron/MSP	0.015	0.1	-9999	-0.37	9	9
alphaM/beta2 Integrin/uPAR/uPA	-0.034	0.22	-9999	-0.44	27	27
alphaM/beta2 Integrin/uPAR	0	0.18	-9999	-0.51	14	14
PLAU	-0.039	0.17	-9999	-0.51	18	18
PLAT	-0.025	0.14	-9999	-0.51	12	12
actin filament polymerization	-0.004	0.13	-9999	-0.45	8	8
MST1	0.03	0.013	-9999	-10000	0	0
alphaM/beta2 Integrin/lipoprotein(a)	0.031	0.12	-9999	-0.35	10	10
TNF	-0.068	0.17	-9999	-0.46	16	16
RAP1B	0.033	0.007	-9999	-10000	0	0
alphaM/beta2 Integrin/uPA	-0.031	0.18	-9999	-0.4	25	25
fibrinolysis	-0.014	0.17	-9999	-0.36	24	24
HCK	0.006	0.11	-9999	-0.51	7	7
dendritic cell antigen processing and presentation	-0.008	0.15	-9999	-0.46	11	11
VTN	0.032	0.014	-9999	-10000	0	0
alphaM/beta2 Integrin/CYR61	-0.005	0.17	-9999	-0.45	16	16
LPA	0.032	0.014	-9999	-10000	0	0
LRP1	0.034	0.004	-9999	-10000	0	0
cell migration	-0.048	0.2	-9999	-0.43	27	27
FN1	-0.009	0.13	-9999	-0.51	10	10
alphaM/beta2 Integrin/Thy1	0.01	0.14	-9999	-0.39	14	14
MPO	0.029	0.046	-9999	-0.51	1	1
KNG1	0.017	0.019	-9999	-10000	0	0
RAP1/GDP	0.038	0.042	-9999	-0.31	2	2
ROCK1	-0.004	0.14	-9999	-0.48	8	8
ELA2	0	0	-9999	-10000	0	0
PLG	0.033	0.011	-9999	-10000	0	0
CTGF	0.019	0.087	-9999	-0.51	4	4
alphaM/beta2 Integrin/Hck	0.004	0.16	-9999	-0.49	13	13
ITGAM	0.01	0.092	-9999	-0.52	4	4
alphaM/beta2 Integrin/P-Selectin/PSGL1	-0.027	0.21	-9999	-0.43	26	26
HP	0.008	0.099	-9999	-0.51	5	5
leukocyte adhesion	-0.034	0.18	-9999	-0.47	17	17
SELP	-0.057	0.2	-9999	-0.51	24	24

HIF-2-alpha transcription factor network

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
MMP14	-0.002	0.25	-10000	0	-1.1	7	7
oxygen homeostasis	0.002	0.012	-10000	0	-10000	0	0
TCEB2	0.033	0.006	-10000	0	-10000	0	0
TCEB1	0.032	0.008	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C/HIF2A	-0.003	0.19	-10000	0	-0.44	15	15
EPO	-0.001	0.24	-10000	0	-0.59	10	10
FIH (dimer)	0.031	0.025	-10000	0	-10000	0	0
APEX1	0.027	0.031	-10000	0	-10000	0	0
SERPINE1	-0.036	0.3	0.47	1	-0.64	21	22
FLT1	-0.05	0.32	-10000	0	-0.97	15	15
ADORA2A	-0.018	0.26	0.47	1	-0.66	11	12
germ cell development	-0.007	0.26	0.47	1	-0.64	11	12
SLC11A2	-0.008	0.27	0.47	1	-0.65	13	14
BHLHE40	-0.026	0.26	-10000	0	-0.58	18	18
HIF1AN	0.031	0.025	-10000	0	-10000	0	0
HIF2A/ARNT/SIRT1	0.01	0.21	-10000	0	-0.47	15	15
ETS1	0.029	0.074	-10000	0	-0.34	4	4
CITED2	0.031	0.098	-10000	0	-0.84	1	1
KDR	-0.021	0.25	-10000	0	-0.88	10	10
PGK1	-0.011	0.28	0.47	1	-0.67	14	15
SIRT1	0.033	0.007	-10000	0	-10000	0	0
response to hypoxia	0	0	-10000	0	-10000	0	0
HIF2A/ARNT	0.001	0.32	-10000	0	-0.69	17	17
EPAS1	-0.031	0.18	-10000	0	-0.42	21	21
SP1	0.032	0.064	-10000	0	-0.51	2	2
ABCG2	-0.026	0.27	-10000	0	-0.66	14	14
EFNA1	-0.02	0.28	-10000	0	-0.7	13	13
FXN	-0.015	0.26	0.42	2	-0.63	13	15
POU5F1	-0.01	0.27	0.47	1	-0.67	11	12
neuron apoptosis	-0.002	0.32	0.67	17	-10000	0	17
EP300	0.005	0.12	-10000	0	-0.51	8	8
EGLN3	-0.064	0.2	-10000	0	-0.52	24	24
EGLN2	0.025	0.05	-10000	0	-0.52	1	1
EGLN1	0.023	0.067	-10000	0	-0.51	2	2
VHL/Elongin B/Elongin C	0.051	0.06	-10000	0	-0.32	3	3
VHL	0.019	0.076	-10000	0	-0.51	3	3
ARNT	0.027	0.03	-10000	0	-10000	0	0
SLC2A1	-0.051	0.3	0.38	1	-0.63	23	24
TWIST1	-0.054	0.3	0.42	2	-0.68	21	23
ELK1	0.04	0.008	-10000	0	-10000	0	0
HIF2A/ARNT/Cbp/p300	-0.003	0.23	-10000	0	-0.48	17	17
VEGFA	-0.01	0.28	0.47	1	-0.64	15	16
CREBBP	0.033	0.007	-10000	0	-10000	0	0

TCGA08_p53

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2A	-0.037	0.11	-10000	0	-0.37	15	15
TP53	-0.019	0.073	0.19	1	-0.32	6	7
Senescence	-0.027	0.08	0.19	1	-0.26	12	13
Apoptosis	-0.027	0.08	0.19	1	-0.26	12	13
Activated_Oncogenes	0	0	-10000	0	-10000	0	0
MDM2	0.026	0.095	0.26	17	-0.37	1	18
MDM4	0.034	0.005	-10000	0	-10000	0	0

IL27-mediated signaling events

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
TGFB1	0.041	0.008	-10000	0	-10000	0	0
CD4-positive alpha-beta T cell lineage commitment	0	0.001	-10000	0	-10000	0	0
cytokine production during immune response	0.12	0.22	0.64	14	-10000	0	14
IL27/IL27R/JAK1	-0.11	0.27	-10000	0	-1.3	5	5
TBX21	-0.18	0.26	-10000	0	-0.7	24	24
IL12B	0.009	0.077	-10000	0	-0.51	3	3
IL12A	-0.004	0.043	-10000	0	-0.37	2	2
IL6ST	0.007	0.067	-10000	0	-0.52	2	2
IL27RA/JAK1	-0.053	0.24	-10000	0	-1.4	5	5
IL27	-0.069	0.19	-10000	0	-0.52	22	22
TYK2	0.012	0.034	-10000	0	-10000	0	0
T-helper cell lineage commitment	0.009	0.12	-10000	0	-10000	0	0
T-helper 2 cell differentiation	0.12	0.22	0.64	14	-10000	0	14
T cell proliferation during immune response	0.12	0.22	0.64	14	-10000	0	14
MAPKKK cascade	-0.12	0.22	-10000	0	-0.64	14	14
STAT3	0.033	0.006	-10000	0	-10000	0	0
STAT2	0.034	0.004	-10000	0	-10000	0	0
STAT1	0.01	0.11	-10000	0	-0.52	6	6
IL12RB1	0.031	0.008	-10000	0	-10000	0	0
positive regulation of tyrosine phosphorylation of STAT protein	0	0	-10000	0	-10000	0	0
IL12RB2	-0.19	0.26	-10000	0	-0.63	31	31
IL27/IL27R/JAK2/TYK2	-0.13	0.22	-10000	0	-0.67	13	13
positive regulation of T cell mediated cytotoxicity	-0.12	0.22	-10000	0	-0.64	14	14
STAT1 (dimer)	-0.19	0.36	-10000	0	-0.99	18	18
JAK2	0.013	0.03	-10000	0	-10000	0	0
JAK1	0.029	0.044	-10000	0	-0.51	1	1
STAT2 (dimer)	-0.12	0.21	-10000	0	-0.64	13	13
T cell proliferation	-0.15	0.23	-10000	0	-0.69	14	14
IL12/IL12R/TYK2/JAK2	-0.11	0.3	-10000	0	-0.89	17	17
IL17A	0.009	0.12	-10000	0	-10000	0	0
mast cell activation	0.12	0.22	0.64	14	-10000	0	14
IFNG	-0.035	0.058	-10000	0	-0.13	38	38
T cell differentiation	-0.01	0.011	-10000	0	-0.026	38	38
STAT3 (dimer)	-0.11	0.22	-10000	0	-0.64	13	13
STAT5A (dimer)	-0.11	0.22	-10000	0	-0.64	13	13
STAT4 (dimer)	-0.12	0.22	-10000	0	-0.65	15	15
STAT4	0.013	0.097	-10000	0	-0.51	5	5
T cell activation	-0.003	0.024	0.12	5	-10000	0	5
IL27R/JAK2/TYK2	-0.064	0.25	-10000	0	-1.3	5	5
GATA3	0.019	0.048	-10000	0	-10000	0	0
IL18	-0.028	0.1	-10000	0	-0.37	13	13
positive regulation of mast cell cytokine production	-0.11	0.21	-10000	0	-0.63	13	13
IL27/EBI3	-0.044	0.14	-10000	0	-0.38	22	22
IL27RA	-0.066	0.25	-10000	0	-1.4	5	5
IL6	-0.038	0.16	-10000	0	-0.5	16	16
STAT5A	0.033	0.011	-10000	0	-10000	0	0
monocyte differentiation	-0.002	0.004	-10000	0	-10000	0	0
IL2	0.02	0.089	-10000	0	-10000	0	0
IL1B	-0.067	0.14	-10000	0	-0.37	28	28
EBI3	0.015	0.031	-10000	0	-10000	0	0
TNF	0.001	0.033	-10000	0	-0.37	1	1

E-cadherin signaling in keratinocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
keratinocyte differentiation	0.022	0.14	0.22	2	-0.41	10	12
adherens junction organization	-0.007	0.14	-10000	0	-0.36	16	16
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.024	0.16	0.27	2	-0.39	11	13
FMN1	-0.001	0.13	-10000	0	-0.33	15	15
mol:IP3	-0.016	0.092	-10000	0	-0.33	9	9
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.002	0.14	-10000	0	-0.35	15	15
CTNNB1	0.032	0.017	-10000	0	-10000	0	0
AKT1	-0.025	0.11	-10000	0	-0.39	10	10
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin	-0.015	0.18	-10000	0	-0.54	11	11
CTNND1	0.02	0.098	-10000	0	-0.52	5	5
mol:PI-4-5-P2	-0.003	0.13	-10000	0	-0.33	15	15
VASP	-0.005	0.14	-10000	0	-0.35	16	16
ZYX	-0.007	0.14	-10000	0	-0.35	16	16
JUB	-0.001	0.13	-10000	0	-0.33	15	15
EGFR(dimer)	-0.016	0.17	-10000	0	-0.4	18	18
E-cadherin/beta catenin-gamma catenin	0.015	0.12	-10000	0	-0.31	16	16
mol:PI-3-4-5-P3	-0.013	0.11	-10000	0	-0.36	10	10
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
PI3K	-0.013	0.11	-10000	0	-0.36	10	10
FYN	0.022	0.12	0.22	1	-0.32	7	8
mol:Ca2+	-0.015	0.09	-10000	0	-0.32	9	9
JUP	0	0.13	-10000	0	-0.5	10	10
PIK3R1	0.009	0.099	-10000	0	-0.51	5	5
mol:DAG	-0.016	0.092	-10000	0	-0.33	9	9
CDH1	0.009	0.11	-10000	0	-0.51	7	7
RhoA/GDP	0.027	0.16	0.26	3	-0.4	10	13
establishment of polarity of embryonic epithelium	-0.005	0.14	-10000	0	-0.34	16	16
SRC	0.032	0.012	-10000	0	-10000	0	0
RAC1	0.033	0.006	-10000	0	-10000	0	0
RHOA	0.031	0.011	-10000	0	-10000	0	0
EGFR	-0.031	0.17	-10000	0	-0.51	17	17
CASR	0.022	0.12	0.22	1	-0.31	9	10
RhoA/GTP	0.048	0.12	0.23	1	-0.3	9	10
AKT2	-0.022	0.097	-10000	0	-0.34	10	10
actin cable formation	-0.004	0.14	0.26	2	-0.34	16	18
apoptosis	-0.022	0.14	0.4	10	-0.23	2	12
CTNNA1	0.036	0.01	-10000	0	-10000	0	0
mol:GDP	0.009	0.16	0.24	1	-0.4	12	13
PIP5K1A	-0.004	0.13	-10000	0	-0.34	15	15
PLCG1	-0.018	0.092	-10000	0	-0.34	9	9
Rac1/GTP	-0.007	0.16	-10000	0	-0.41	14	14
homophilic cell adhesion	0.003	0.005	-10000	0	-10000	0	0

mTOR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GBL	0	0	-10000	0	-10000	0	0
MKNK1	0.034	0.005	-10000	0	-10000	0	0
mol:PIP3	-0.018	0.082	0.4	1	-0.28	11	12
FRAP1	0.05	0.074	0.23	1	-0.45	1	2
AKT1	0.054	0.13	0.24	12	-0.26	11	23
INSR	0.029	0.044	-10000	0	-0.51	1	1
Insulin Receptor/Insulin	0.04	0.031	-10000	0	-0.31	1	1
mol:GTP	0.08	0.13	0.29	11	-0.28	5	16
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit	-0.002	0.038	-10000	0	-0.21	2	2
TSC2	0.029	0.045	-10000	0	-0.51	1	1
RHEB/GDP	-0.004	0.069	-10000	0	-0.28	4	4
TSC1	0.031	0.044	-10000	0	-0.51	1	1
Insulin Receptor/IRS1	0.009	0.087	-10000	0	-0.29	11	11
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA	0.004	0.05	-10000	0	-0.23	2	2
mol:GDP	0	0	-10000	0	-10000	0	0
EIF3A	0.033	0.011	-10000	0	-10000	0	0
RPS6KB1	0.075	0.1	0.25	15	-10000	0	15
MAP3K5	-0.003	0.057	0.18	1	-0.29	5	6
PIK3R1	0.007	0.099	-10000	0	-0.51	5	5
apoptosis	-0.003	0.057	0.18	1	-0.29	5	6
mol:LY294002	0	0	0.001	1	-0.001	10	11
EIF4B	0.072	0.094	0.24	15	-10000	0	15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.083	0.092	0.25	12	-10000	0	12
eIF4E/eIF4G1/eIF4A1	0.002	0.045	-10000	0	-0.28	1	1
KIAA1303	0	0	-10000	0	-10000	0	0
PI3K	-0.008	0.087	-10000	0	-0.29	12	12
mTOR/RHEB/GTP/Raptor/GBL	0.057	0.085	0.21	16	-0.21	2	18
FKBP1A	0.034	0.007	-10000	0	-10000	0	0
RHEB/GTP	0.074	0.11	0.26	9	-0.28	4	13
mol:Amino Acids	0	0	0.001	1	-0.001	10	11
FKBP12/Rapamycin	0.027	0.007	-10000	0	-10000	0	0
PDPK1	0.031	0.12	0.16	52	-0.26	11	63
EIF4E	0.033	0.008	-10000	0	-10000	0	0
ASK1/PP5C	0.052	0.14	-10000	0	-0.57	6	6
mTOR/RHEB/GTP/Raptor/GBL/eIF4E	0.007	0.055	-10000	0	-10000	0	0
TSC1/TSC2	0.087	0.14	0.31	11	-0.3	5	16
tumor necrosis factor receptor activity	0	0	0.001	10	-0.001	1	11
RPS6	0.031	0.013	-10000	0	-10000	0	0
PPP5C	0.03	0.044	-10000	0	-0.51	1	1
EIF4G1	0.006	0.074	-10000	0	-0.51	3	3
IRS1	-0.009	0.084	-10000	0	-0.31	10	10
INS	0.033	0.006	-10000	0	-10000	0	0
PTEN	0.026	0.044	-10000	0	-0.51	1	1
PDK2	0.03	0.12	0.16	51	-0.26	11	62
EIF4EBP1	-0.031	0.22	-10000	0	-1.1	6	6
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
PPP2R5D	0.048	0.076	0.24	3	-0.41	1	4
peptide biosynthetic process	0.017	0.028	0.19	1	-0.28	1	2
RHEB	0.034	0.006	-10000	0	-10000	0	0
EIF4A1	0.032	0.009	-10000	0	-10000	0	0
mol:Rapamycin	0.001	0.002	0.003	77	-0.003	2	79
EEF2	0.017	0.029	0.19	1	-0.29	1	2
eIF4E/4E-BP1	-0.014	0.2	-10000	0	-0.99	6	6

TRAIL signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TNFSF10	-0.04	0.16	-10000	0	-0.51	16	16
positive regulation of NF-kappaB transcription factor activity	-0.023	0.12	-10000	0	-0.36	16	16
MAP2K4	0.02	0.1	-10000	0	-0.33	5	5
IKBKB	0.031	0.011	-10000	0	-10000	0	0
TNFRSF10B	0.019	0.075	-10000	0	-0.51	3	3
TNFRSF10A	0.021	0.063	-10000	0	-0.51	2	2
SMPD1	-0.018	0.075	-10000	0	-0.22	17	17
IKBKG	0.033	0.006	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
TNFRSF10D	0.024	0.047	-10000	0	-0.51	1	1
TRAIL/TRAILR2	-0.027	0.14	-10000	0	-0.4	17	17
TRAIL/TRAILR3	-0.028	0.12	-10000	0	-0.36	17	17
TRAIL/TRAILR1	-0.025	0.13	-10000	0	-0.39	16	16
TRAIL/TRAILR4	-0.023	0.12	-10000	0	-0.36	16	16
TRAIL/TRAILR1/DAP3/GTP	-0.01	0.11	-10000	0	-0.31	16	16
IKK complex	0.036	0.082	-10000	0	-0.45	1	1
RIPK1	0.033	0.006	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
DAP3/GTP	0.024	0.006	-10000	0	-10000	0	0
MAPK3	-0.032	0.12	-10000	0	-0.37	16	16
MAP3K1	-0.021	0.12	-10000	0	-0.44	7	7
TRAILR4 (trimer)	0.024	0.047	-10000	0	-0.51	1	1
TRADD	0.029	0.044	-10000	0	-0.51	1	1
TRAILR1 (trimer)	0.021	0.063	-10000	0	-0.51	2	2
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2	-0.021	0.1	-10000	0	-0.32	14	14
CFLAR	0.015	0.096	-10000	0	-0.51	5	5
MAPK1	-0.032	0.12	-10000	0	-0.39	15	15
TRAIL/TRAILR1/FADD/TRADD/RIP	0	0.11	-10000	0	-0.3	13	13
mol:ceramide	-0.018	0.075	-10000	0	-0.22	17	17
FADD	0.031	0.011	-10000	0	-10000	0	0
MAPK8	0.023	0.12	0.27	1	-0.37	5	6
TRAF2	0.033	0.01	-10000	0	-10000	0	0
TRAILR3 (trimer)	0.013	0.078	-10000	0	-0.51	3	3
CHUK	0.03	0.044	-10000	0	-0.51	1	1
TRAIL/TRAILR1/FADD	-0.014	0.11	-10000	0	-0.34	15	15
DAP3	0.032	0.008	-10000	0	-10000	0	0
CASP10	0.034	0.18	0.36	3	-0.45	11	14
JNK cascade	-0.023	0.12	-10000	0	-0.36	16	16
TRAIL (trimer)	-0.04	0.16	-10000	0	-0.51	16	16
TNFRSF10C	0.013	0.078	-10000	0	-0.51	3	3
TRAIL/TRAILR1/DAP3/GTP/FADD	-0.006	0.1	-10000	0	-0.29	15	15
TRAIL/TRAILR2/FADD	-0.016	0.12	-10000	0	-0.35	16	16
cell death	-0.018	0.075	-10000	0	-0.22	17	17
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2	-0.022	0.11	-10000	0	-0.32	15	15
TRAILR2 (trimer)	0.019	0.075	-10000	0	-0.51	3	3
CASP8	-0.007	0.14	-10000	0	-0.68	5	5
negative regulation of caspase activity	0	0	-10000	0	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP	-0.001	0.11	-10000	0	-0.3	15	15

IL6-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.023	0.24	-10000	0	-0.7	7	7
CRP	-0.028	0.24	-10000	0	-0.72	6	6
cell cycle arrest	-0.051	0.27	-10000	0	-0.7	13	13
TIMP1	-0.047	0.27	-10000	0	-0.88	8	8
IL6ST	0.023	0.065	-10000	0	-0.5	2	2
Rac1/GDP	-0.025	0.18	0.34	1	-0.45	12	13
AP1	0.03	0.14	-10000	0	-0.46	3	3
GAB2	0.033	0.015	-10000	0	-10000	0	0
TNFSF11	-0.075	0.32	-10000	0	-0.96	12	12
HSP90B1	0.035	0.12	-10000	0	-0.96	2	2
GAB1	0.025	0.063	-10000	0	-0.5	2	2
MAPK14	-0.034	0.16	0.29	1	-0.87	3	4
AKT1	0.043	0.096	0.29	2	-0.45	3	5
FOXO1	0.037	0.1	-10000	0	-0.41	4	4
MAP2K6	-0.032	0.16	0.28	2	-0.4	12	14
mol:GTP	0	0.002	-10000	0	-10000	0	0
MAP2K4	-0.03	0.18	0.34	1	-0.48	13	14
MITF	-0.022	0.15	0.29	2	-0.38	13	15
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TYK2	0.032	0.014	-10000	0	-10000	0	0
A2M	-0.03	0.25	-10000	0	-1.4	5	5
CEBPB	0.037	0.045	-10000	0	-0.51	1	1
GRB2/SOS1/GAB family/SHP2	0.027	0.099	-10000	0	-0.45	1	1
STAT3	-0.055	0.28	-10000	0	-0.75	13	13
STAT1	-0.026	0.22	-10000	0	-0.95	8	8
CEBPD	-0.045	0.28	-10000	0	-0.83	10	10
PIK3CA	0.01	0.062	-10000	0	-0.51	2	2
PI3K	0.005	0.076	-10000	0	-0.33	6	6
JUN	0.004	0.11	-10000	0	-0.51	7	7
PIAS3/MITF	-0.013	0.15	-10000	0	-0.42	9	9
MAPK11	-0.032	0.17	0.29	1	-0.87	3	4
STAT3 (dimer)/FOXO1	-0.015	0.26	-10000	0	-0.62	12	12
GRB2/SOS1/GAB family	0.01	0.18	-10000	0	-0.58	7	7
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK	-0.045	0.18	-10000	0	-0.42	17	17
GRB2	0.035	0.006	-10000	0	-10000	0	0
JAK2	0.029	0.017	-10000	0	-10000	0	0
LBP	-0.003	0.2	-10000	0	-0.61	5	5
PIK3R1	0.007	0.099	-10000	0	-0.51	5	5
JAK1	0.031	0.046	-10000	0	-0.52	1	1
MYC	-0.042	0.3	-10000	0	-0.88	11	11
FGG	-0.067	0.28	-10000	0	-0.82	11	11
macrophage differentiation	-0.051	0.27	-10000	0	-0.7	13	13
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4	-0.013	0.16	-10000	0	-0.31	26	26
JUNB	-0.053	0.27	-10000	0	-0.81	11	11
FOS	-0.029	0.16	-10000	0	-0.51	14	14
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4	-0.025	0.16	0.3	3	-0.38	15	18
STAT1/PIAS1	-0.012	0.18	0.34	2	-0.44	14	16
GRB2/SOS1/GAB family/SHP2/PI3K	0.046	0.077	-10000	0	-0.37	2	2
STAT3 (dimer)	-0.056	0.28	-10000	0	-0.74	13	13
PRKCD	-0.026	0.21	0.35	3	-0.54	13	16
IL6R	0.018	0.089	-10000	0	-0.52	4	4
SOCS3	-0.039	0.2	-10000	0	-1.2	3	3
gp130 (dimer)/JAK1/JAK1/LMO4	0.027	0.12	-10000	0	-0.31	14	14
Rac1/GTP	-0.027	0.18	0.33	1	-0.49	11	12
HCK	0.007	0.11	-10000	0	-0.51	7	7
MAPKKK cascade	0.048	0.098	-10000	0	-0.44	2	2
bone resorption	-0.068	0.3	-10000	0	-0.85	13	13
IRF1	-0.064	0.3	-10000	0	-0.88	12	12
mol:GDP	-0.035	0.17	0.3	2	-0.42	15	17
SOS1	0.035	0.007	-10000	0	-10000	0	0
VAV1	-0.035	0.18	0.3	2	-0.42	15	17
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3	-0.034	0.19	-10000	0	-0.74	5	5
PTPN11	0.021	0.081	-10000	0	-0.92	1	1
IL6/IL6RA	-0.024	0.14	-10000	0	-0.38	19	19
gp130 (dimer)/TYK2/TYK2/LMO4	0.028	0.11	-10000	0	-0.31	13	13
gp130 (dimer)/JAK2/JAK2/LMO4	0.022	0.11	-10000	0	-0.31	13	13
IL6	-0.046	0.16	-10000	0	-0.51	16	16
PIAS3	0.034	0.005	-10000	0	-10000	0	0
PTPRE	-0.001	0.11	-10000	0	-0.51	6	6
PIAS1	0.034	0.004	-10000	0	-10000	0	0
RAC1	0.034	0.006	-10000	0	-10000	0	0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4	-0.031	0.14	0.27	3	-0.28	26	29
LMO4	-0.011	0.14	-10000	0	-0.5	11	11
STAT3 (dimer)/PIAS3	-0.043	0.27	-10000	0	-0.69	13	13
MCL1	0.053	0.099	-10000	0	-10000	0	0

VEGFR1 specific signals

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer	-0.003	0.17	-10000	0	-0.63	10	10
VEGFR1 homodimer/NRP1	-0.025	0.16	-10000	0	-0.62	10	10
mol:DAG	-0.024	0.15	-10000	0	-0.54	11	11
VEGFR1 homodimer/NRP1/VEGFR 121	-0.006	0.16	-10000	0	-0.56	11	11
CaM/Ca2+	-0.006	0.15	-10000	0	-0.51	11	11
HIF1A	0.011	0.12	-10000	0	-0.42	10	10
GAB1	0.024	0.063	-10000	0	-0.51	2	2
AKT1	0.021	0.18	0.33	1	-0.52	11	12
PLCG1	-0.025	0.15	-10000	0	-0.54	11	11
NOS3	0.012	0.15	0.26	1	-0.5	10	11
CBL	0.034	0.005	-10000	0	-10000	0	0
mol:NO	0.018	0.15	0.41	2	-0.48	10	12
FLT1	-0.021	0.18	-10000	0	-0.75	9	9
PGF	0.022	0.052	-10000	0	-0.51	1	1
VEGFR1 homodimer/NRP2/VEGFR121	0.006	0.18	-10000	0	-0.56	12	12
CALM1	0.033	0.007	-10000	0	-10000	0	0
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
eNOS/Hsp90	0.024	0.15	-10000	0	-0.46	11	11
endothelial cell proliferation	-0.019	0.15	-10000	0	-0.55	10	10
mol:Ca2+	-0.024	0.15	-10000	0	-0.53	11	11
MAPK3	-0.044	0.13	0.35	1	-0.53	9	10
MAPK1	-0.043	0.13	0.35	1	-0.45	12	13
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
PLGF homodimer	0.022	0.052	-10000	0	-0.51	1	1
PRKACA	0.033	0.007	-10000	0	-10000	0	0
RP11-342D11.1	0	0	-10000	0	-10000	0	0
CAV1	-0.027	0.16	-10000	0	-0.51	15	15
VEGFA homodimer	0.027	0.061	-10000	0	-0.51	2	2
VEGFR1 homodimer/VEGFA homodimer	-0.006	0.18	-10000	0	-0.6	11	11
platelet activating factor biosynthetic process	-0.032	0.14	0.34	1	-0.53	8	9
PI3K	-0.017	0.15	-10000	0	-0.45	13	13
PRKCA	-0.046	0.14	0.19	1	-0.48	12	13
PRKCB	-0.041	0.14	0.19	1	-0.5	11	12
VEGFR1 homodimer/PLGF homodimer	-0.011	0.17	-10000	0	-0.6	11	11
VEGFA	0.027	0.061	-10000	0	-0.51	2	2
VEGFB	0.034	0	-10000	0	-10000	0	0
mol:IP3	-0.024	0.15	-10000	0	-0.54	11	11
RASA1	-0.02	0.16	-10000	0	-0.55	11	11
NRP2	0.025	0.063	-10000	0	-0.51	2	2
VEGFR1 homodimer	-0.021	0.18	-10000	0	-0.74	9	9
VEGFB homodimer	0.034	0	-10000	0	-10000	0	0
NCK1	0.021	0.062	-10000	0	-0.51	2	2
eNOS/Caveolin-1	0.001	0.18	0.47	1	-0.48	14	15
PTPN11	0.031	0.044	-10000	0	-0.51	1	1
mol:PI-3-4-5-P3	-0.017	0.14	-10000	0	-0.44	13	13
mol:L-citrulline	0.018	0.15	0.41	2	-0.48	10	12
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP	0.034	0.17	-10000	0	-0.54	11	11
VEGFR1 homodimer/VEGFA homodimer/NCK1	0.006	0.15	-10000	0	-0.48	12	12
CD2AP	0.034	0.005	-10000	0	-10000	0	0
PI3K/GAB1	-0.014	0.15	-10000	0	-0.46	13	13
PDPK1	0.037	0.17	0.35	1	-0.44	12	13
VEGFR1 homodimer/VEGFA homodimer/SHP2	0.011	0.17	-10000	0	-0.54	12	12
mol:NADP	0.018	0.15	0.41	2	-0.48	10	12
HSP90AA1	0.033	0.008	-10000	0	-10000	0	0
ubiquitin-dependent protein catabolic process	0.032	0.17	-10000	0	-0.53	11	11
VEGFR1 homodimer/NRP2	-0.01	0.17	-10000	0	-0.57	12	12

E-cadherin signaling events

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
E-cadherin/beta catenin-gamma catenin	0.015	0.12	-9999	-0.33	16	16
E-cadherin/beta catenin	0.023	0.089	-9999	-0.37	7	7
CTNNB1	0.03	0.016	-9999	-10000	0	0
JUP	-0.002	0.13	-9999	-0.51	10	10
CDH1	0.007	0.11	-9999	-0.51	7	7

PLK2 and PLK4 events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLK2	-0.01	0.14	-9999	-0.51	11	11
PLK4	0.032	0.012	-9999	-10000	0	0
regulation of centriole replication	-0.014	0.1	-9999	-0.37	11	11

Signaling events mediated by PTP1B

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
PDGFRB	0.032	0.012	-10000	0	-10000	0	0
Jak2/Leptin Receptor	-0.027	0.16	-10000	0	-0.47	14	14
PTP1B/AKT1	-0.051	0.15	-10000	0	-0.37	17	17
FYN	0.026	0.062	-10000	0	-0.51	2	2
p210 bcr-abl/PTP1B	-0.067	0.14	0.19	1	-0.35	20	21
EGFR	-0.037	0.17	-10000	0	-0.52	17	17
EGF/EGFR	-0.088	0.19	-10000	0	-0.41	32	32
CSF1	0.032	0.014	-10000	0	-10000	0	0
AKT1	0.025	0.064	-10000	0	-0.52	2	2
INSR	0.029	0.044	-10000	0	-0.51	1	1
PTP1B/N-cadherin	-0.056	0.15	-10000	0	-0.36	20	20
Insulin Receptor/Insulin	-0.025	0.15	-10000	0	-0.43	9	9
HCK	0.006	0.11	-10000	0	-0.51	7	7
CRK	0.032	0.008	-10000	0	-10000	0	0
TYK2	-0.065	0.14	0.2	2	-0.35	18	20
EGF	-0.036	0.15	-10000	0	-0.52	13	13
YES1	0.028	0.044	-10000	0	-0.51	1	1
CAV1	-0.086	0.18	0.22	1	-0.42	25	26
TXN	0.025	0.048	-10000	0	-0.52	1	1
PTP1B/IRS1/GRB2	-0.052	0.16	-10000	0	-0.37	18	18
cell migration	0.067	0.14	0.35	20	-0.19	1	21
STAT3	0.033	0.006	-10000	0	-10000	0	0
PRLR	0.023	0.05	-10000	0	-0.5	1	1
ITGA2B	0.033	0.005	-10000	0	-10000	0	0
CSF1R	0.033	0.008	-10000	0	-10000	0	0
Prolactin Receptor/Prolactin	0.039	0.047	-10000	0	-0.37	1	1
FGR	0.033	0.01	-10000	0	-10000	0	0
PTP1B/p130 Cas	-0.051	0.14	-10000	0	-0.34	19	19
Crk/p130 Cas	-0.037	0.15	-10000	0	-0.37	14	14
DOK1	-0.054	0.14	-10000	0	-0.37	15	15
JAK2	-0.039	0.16	-10000	0	-0.51	13	13
Jak2/Leptin Receptor/Leptin	-0.027	0.17	-10000	0	-0.44	12	12
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
PTPN1	-0.068	0.14	0.19	1	-0.35	20	21
LYN	0.029	0.044	-10000	0	-0.51	1	1
CDH2	0.008	0.081	-10000	0	-0.51	3	3
SRC	0	0.098	-10000	0	-0.73	2	2
ITGB3	0.025	0.049	-10000	0	-0.51	1	1
CAT1/PTP1B	-0.057	0.19	0.23	1	-0.51	14	15
CAPN1	0.014	0.098	-10000	0	-0.52	5	5
CSK	0.034	0.004	-10000	0	-10000	0	0
PI3K	-0.026	0.14	-10000	0	-0.49	8	8
mol:H2O2	-0.001	0.004	-10000	0	-10000	0	0
STAT3 (dimer)	-0.024	0.16	-10000	0	-0.45	10	10
negative regulation of transcription	-0.038	0.16	-10000	0	-0.5	13	13
FCGR2A	-0.011	0.14	-10000	0	-0.51	12	12
FER	0.023	0.049	-10000	0	-0.52	1	1
alphaIIb/beta3 Integrin	0.041	0.04	-10000	0	-0.38	1	1
BLK	0.013	0.068	-10000	0	-0.51	2	2
Insulin Receptor/Insulin/Shc	0.059	0.038	-10000	0	-0.32	1	1
RHOA	0.029	0.01	-10000	0	-10000	0	0
LEPR	0.023	0.064	-10000	0	-0.51	2	2
BCAR1	0.033	0.008	-10000	0	-10000	0	0
p210 bcr-abl/Grb2	0.034	0.005	-10000	0	-10000	0	0
mol:NADPH	-0.002	0.003	-10000	0	-10000	0	0
TRPV6	-0.015	0.18	-10000	0	-0.53	10	10
PRL	0.034	0.018	-10000	0	-10000	0	0
SOCS3	0.004	0.2	-10000	0	-1.4	3	3
SPRY2	-0.014	0.14	-10000	0	-0.51	10	10
Insulin Receptor/Insulin/IRS1	0.039	0.088	-10000	0	-0.32	8	8
CSF1/CSF1R	-0.04	0.15	-10000	0	-0.35	17	17
Ras protein signal transduction	0.028	0.11	0.66	4	-10000	0	4
IRS1	0.006	0.11	-10000	0	-0.51	7	7
INS	0.033	0.006	-10000	0	-10000	0	0
LEP	0.017	0.056	-10000	0	-0.51	1	1
STAT5B	-0.051	0.15	-10000	0	-0.38	17	17
STAT5A	-0.051	0.15	-10000	0	-0.38	17	17
GRB2	0.034	0.005	-10000	0	-10000	0	0
PDGFB-D/PDGFRB	-0.052	0.14	-10000	0	-0.34	19	19
CSN2	0.049	0.069	-10000	0	-10000	0	0
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
LAT	-0.043	0.19	-10000	0	-0.62	13	13
YBX1	0.036	0.045	-10000	0	-0.5	1	1
LCK	-0.004	0.13	-10000	0	-0.51	10	10
SHC1	0.032	0.008	-10000	0	-10000	0	0
NOX4	-0.049	0.19	-10000	0	-0.51	21	21

Arf6 downstream pathway

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
PLAUR	-0.051	0.3	-10000	0	-1.1	11	11
regulation of axonogenesis	0.017	0.1	0.53	4	-10000	0	4
myoblast fusion	-0.009	0.14	0.46	11	-10000	0	11
mol:GTP	0.004	0.091	-10000	0	-0.28	12	12
regulation of calcium-dependent cell-cell adhesion	-0.047	0.098	0.27	11	-10000	0	11
ARF1/GTP	0.026	0.079	-10000	0	-0.36	3	3
mol:GM1	-0.003	0.069	-10000	0	-0.23	10	10
mol:Choline	-0.023	0.11	-10000	0	-0.42	9	9
lamellipodium assembly	-0.018	0.16	-10000	0	-0.52	12	12
MAPK3	0.002	0.11	-10000	0	-0.37	11	11
ARF6/GTP/NME1/Tiam1	0.048	0.099	-10000	0	-0.27	11	11
ARF1	0.034	0.005	-10000	0	-10000	0	0
ARF6/GDP	0.009	0.14	-10000	0	-0.47	11	11
ARF1/GDP	0.013	0.14	-10000	0	-0.41	13	13
ARF6	0.024	0.094	-10000	0	-0.69	2	2
RAB11A	0.034	0.004	-10000	0	-10000	0	0
TIAM1	0.031	0.019	-10000	0	-10000	0	0
fibronectin binding	0	0	-10000	0	-10000	0	0
MAPK1	0	0.12	-10000	0	-0.4	11	11
actin filament bundle formation	-0.01	0.14	0.4	13	-10000	0	13
KALRN	-0.009	0.11	-10000	0	-0.38	10	10
RAB11FIP3/RAB11A	0.047	0.016	-10000	0	-10000	0	0
RhoA/GDP	0.01	0.14	-10000	0	-0.41	13	13
NME1	0.031	0.019	-10000	0	-10000	0	0
Rac1/GDP	0.013	0.14	-10000	0	-0.41	13	13
substrate adhesion-dependent cell spreading	0.004	0.091	-10000	0	-0.28	12	12
cortical actin cytoskeleton organization	-0.019	0.16	-10000	0	-0.52	12	12
RAC1	0.033	0.006	-10000	0	-10000	0	0
liver development	0.004	0.091	-10000	0	-0.28	12	12
ARF6/GTP	0.004	0.091	-10000	0	-0.28	12	12
RhoA/GTP	0.023	0.078	-10000	0	-0.23	9	9
mol:GDP	-0.022	0.14	-10000	0	-0.44	13	13
ARF6/GTP/RAB11FIP3/RAB11A	0.045	0.075	-10000	0	-0.39	2	2
RHOA	0.031	0.011	-10000	0	-10000	0	0
PLD1	-0.021	0.12	-10000	0	-0.43	9	9
RAB11FIP3	0.031	0.014	-10000	0	-10000	0	0
tube morphogenesis	-0.018	0.16	-10000	0	-0.52	12	12
ruffle organization	-0.017	0.1	-10000	0	-0.53	4	4
regulation of epithelial cell migration	0.004	0.091	-10000	0	-0.28	12	12
PLD2	0.004	0.081	-10000	0	-0.35	5	5
PIP5K1A	-0.017	0.1	-10000	0	-0.54	4	4
mol:Phosphatidic acid	-0.023	0.11	-10000	0	-0.42	9	9
Rac1/GTP	-0.019	0.16	-10000	0	-0.53	12	12

PDGFR-alpha signaling pathway

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
PDGFRA	-0.009	0.13	-9999	-0.51	9	9
PDGF/PDGFRA/CRKL	0.012	0.097	-9999	-0.36	9	9
positive regulation of JUN kinase activity	0.048	0.084	-9999	-0.28	8	8
CRKL	0.031	0.012	-9999	-10000	0	0
PDGF/PDGFRA/Caveolin-3	0.013	0.096	-9999	-0.36	9	9
AP1	-0.11	0.29	-9999	-0.88	17	17
mol:IP3	-0.014	0.084	-9999	-0.38	7	7
PLCG1	-0.014	0.084	-9999	-0.38	7	7
PDGF/PDGFRA/alphaV Integrin	-0.001	0.12	-9999	-0.39	13	13
RAPGEF1	0.034	0.004	-9999	-10000	0	0
CRK	0.032	0.008	-9999	-10000	0	0
mol:Ca2+	-0.014	0.084	-9999	-0.38	7	7
CAV3	0.032	0.009	-9999	-10000	0	0
CAV1	-0.027	0.16	-9999	-0.51	15	15
SHC/Grb2/SOS1	0.05	0.085	-9999	-0.28	8	8
PDGF/PDGFRA/Shf	0.003	0.12	-9999	-0.39	12	12
FOS	-0.12	0.28	-9999	-0.86	17	17
JUN	-0.043	0.078	-9999	-0.41	6	6
oligodendrocyte development	-0.001	0.12	-9999	-0.39	13	13
GRB2	0.034	0.005	-9999	-10000	0	0
PIK3R1	0.006	0.099	-9999	-0.51	5	5
mol:DAG	-0.014	0.084	-9999	-0.38	7	7
PDGF/PDGFRA	-0.009	0.13	-9999	-0.51	9	9
actin cytoskeleton reorganization	0.006	0.1	-9999	-0.34	11	11
SRF	0.017	0.013	-9999	-10000	0	0
SHC1	0.032	0.008	-9999	-10000	0	0
PI3K	-0.002	0.088	-9999	-0.31	9	9
PDGF/PDGFRA/Crk/C3G	0.037	0.088	-9999	-0.3	9	9
JAK1	-0.014	0.089	-9999	-0.36	9	9
ELK1/SRF	-0.004	0.077	-9999	-0.29	6	6
SHB	0.019	0.076	-9999	-0.51	3	3
SHF	0.018	0.087	-9999	-0.51	4	4
CSNK2A1	0.035	0.022	-9999	-10000	0	0
GO:0007205	-0.021	0.085	-9999	-0.4	7	7
SOS1	0.033	0.006	-9999	-10000	0	0
Ras protein signal transduction	0.048	0.084	-9999	-0.28	8	8
PDGF/PDGFRA/SHB	0.007	0.1	-9999	-0.34	11	11
PDGF/PDGFRA/Caveolin-1	-0.026	0.16	-9999	-0.42	19	19
ITGAV	0.014	0.097	-9999	-0.51	5	5
ELK1	-0.03	0.076	-9999	-0.35	7	7
PIK3CA	0.009	0.062	-9999	-0.51	2	2
PDGF/PDGFRA/Crk	0.014	0.096	-9999	-0.36	9	9
JAK-STAT cascade	-0.014	0.089	-9999	-0.36	9	9
cell proliferation	0.003	0.12	-9999	-0.39	12	12

Syndecan-3-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	0.031	0.011	-9999	-10000	0	0
Syndecan-3/Src/Cortactin	-0.037	0.15	-9999	-0.48	5	5
Syndecan-3/Neurocan	0.028	0.093	-9999	-0.5	4	4
POMC	-0.021	0.16	-9999	-0.51	14	14
EGFR	-0.031	0.17	-9999	-0.51	17	17
Syndecan-3/EGFR	-0.001	0.12	-9999	-0.51	3	3
AGRP	0.028	0.023	-9999	-10000	0	0
NCSTN	0.032	0.008	-9999	-10000	0	0
PSENEN	0.031	0.011	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
APH1B	0.03	0.044	-9999	-0.51	1	1
APH1A	0.015	0.096	-9999	-0.51	5	5
NCAN	0.033	0.007	-9999	-10000	0	0
long-term memory	0.038	0.095	-9999	-0.48	4	4
Syndecan-3/IL8	-0.052	0.15	-9999	-0.28	37	37
PSEN1	0.03	0.044	-9999	-0.51	1	1
Src/Cortactin	0.042	0.02	-9999	-10000	0	0
FYN	0.026	0.062	-9999	-0.51	2	2
limb bud formation	-0.001	0.087	-9999	-0.52	4	4
MC4R	0.025	0.062	-9999	-0.51	2	2
SRC	0.032	0.012	-9999	-10000	0	0
PTN	-0.12	0.23	-9999	-0.51	39	39
FGFR/FGF/Syndecan-3	-0.001	0.088	-9999	-0.52	4	4
neuron projection morphogenesis	-0.034	0.15	-9999	-0.47	5	5
Syndecan-3/AgRP	0.026	0.094	-9999	-0.5	4	4
Syndecan-3/AgRP/MC4R	0.035	0.1	-9999	-0.49	4	4
Fyn/Cortactin	0.041	0.04	-9999	-0.37	1	1
SDC3	-0.001	0.089	-9999	-0.53	4	4
GO:0007205	0	0	-9999	-10000	0	0
positive regulation of leukocyte migration	-0.051	0.15	-9999	-0.28	37	37
IL8	-0.12	0.23	-9999	-0.51	38	38
Syndecan-3/Fyn/Cortactin	0.04	0.098	-9999	-0.49	4	4
Syndecan-3/CASK	-0.002	0.084	-9999	-0.5	4	4
alpha-MSH/MC4R	-0.001	0.13	-9999	-0.37	16	16
Gamma Secretase	0.068	0.086	-9999	-0.33	5	5

Integrins in angiogenesis

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
VEGFR2 homodimer/VEGFA homodimer	0.035	0.062	-10000	0	-0.31	4	4
alphaV beta3 Integrin	0.03	0.1	-10000	0	-0.32	10	10
PTK2	-0.001	0.15	0.29	2	-0.5	8	10
IGF1R	-0.006	0.14	-10000	0	-0.51	11	11
PI4KB	0.032	0.008	-10000	0	-10000	0	0
MFGE8	0.03	0.045	-10000	0	-0.51	1	1
SRC	0.032	0.012	-10000	0	-10000	0	0
CDKN1B	0.015	0.04	-10000	0	-10000	0	0
VEGFA	0.027	0.061	-10000	0	-0.51	2	2
ILK	0.018	0.04	-10000	0	-10000	0	0
ROCK1	0.034	0.005	-10000	0	-10000	0	0
AKT1	0.008	0.059	-10000	0	-0.38	2	2
PTK2B	0.007	0.094	-10000	0	-0.34	7	7
alphaV/beta3 Integrin/JAM-A	0.029	0.11	-10000	0	-0.3	13	13
CBL	0.034	0.005	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
alphaV beta3 Integrin/ANGPTL3	0.042	0.08	-10000	0	-0.31	6	6
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.027	0.17	-10000	0	-0.32	34	34
VEGF/Rho/ROCK/alphaV/beta3 Integrin	0.012	0.097	-10000	0	-0.36	6	6
alphaV/beta3 Integrin/Syndecan-1	0.015	0.13	-10000	0	-0.35	15	15
PI4KA	0.032	0.009	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.067	0.2	-10000	0	-0.37	38	38
PI4 Kinase	0.045	0.016	-10000	0	-10000	0	0
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
alphaV/beta3 Integrin/Osteopontin	-0.052	0.16	-10000	0	-0.34	35	35
RPS6KB1	-0.1	0.16	-10000	0	-0.49	16	16
TLN1	0.031	0.01	-10000	0	-10000	0	0
MAPK3	-0.059	0.19	-10000	0	-0.65	12	12
GPR124	0.027	0.018	-10000	0	-10000	0	0
MAPK1	-0.062	0.2	-10000	0	-0.66	12	12
PXN	0.034	0.004	-10000	0	-10000	0	0
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
alphaV/beta3 Integrin/Tumstatin	0.044	0.084	-10000	0	-0.32	7	7
cell adhesion	0.017	0.09	-10000	0	-0.29	10	10
ANGPTL3	0.028	0.046	-10000	0	-0.51	1	1
VEGFR2 homodimer/VEGFA homodimer/Src	0.048	0.06	-10000	0	-0.32	3	3
IGF-1R heterotetramer	-0.006	0.14	-10000	0	-0.51	11	11
Rac1/GDP	0.025	0.005	-10000	0	-10000	0	0
TGFBR2	0.026	0.047	-10000	0	-0.51	1	1
ITGB3	0.026	0.048	-10000	0	-0.51	1	1
IGF1	-0.048	0.18	-10000	0	-0.51	20	20
RAC1	0.033	0.006	-10000	0	-10000	0	0
regulation of cell-matrix adhesion	0.035	0.074	-10000	0	-0.31	5	5
apoptosis	0.014	0.096	-10000	0	-0.51	5	5
CD47	0.014	0.087	-10000	0	-0.51	4	4
alphaV/beta3 Integrin/CD47	0.027	0.093	-10000	0	-0.32	9	9
VCL	0.026	0.062	-10000	0	-0.51	2	2
alphaV/beta3 Integrin/Del1	-0.011	0.14	-10000	0	-0.37	18	18
CSF1	0.032	0.014	-10000	0	-10000	0	0
PIK3C2A	0.011	0.068	-10000	0	-0.47	2	2
PI4 Kinase/Pyk2	0.008	0.092	-10000	0	-0.31	9	9
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.048	0.1	-10000	0	-0.36	7	7
FAK1/Vinculin	0.015	0.13	0.27	3	-0.41	8	11
alphaV beta3/Integrin/ppsTEM5	0.035	0.075	-10000	0	-0.31	5	5
RHOA	0.031	0.011	-10000	0	-10000	0	0
VTN	0.032	0.014	-10000	0	-10000	0	0
BCAR1	0.033	0.008	-10000	0	-10000	0	0
FGF2	0.014	0.088	-10000	0	-0.51	4	4
F11R	-0.005	0.081	-10000	0	-0.37	7	7
alphaV/beta3 Integrin/Lactadherin	0.043	0.084	-10000	0	-0.32	7	7
alphaV/beta3 Integrin/TGFBR2	0.039	0.09	-10000	0	-0.36	6	6
alphaV/beta3 Integrin/c-FMS/Cbl/Cas	0.064	0.072	-10000	0	-0.28	5	5
HSP90AA1	0.033	0.008	-10000	0	-10000	0	0
alphaV/beta3 Integrin/Talin	0.039	0.072	-10000	0	-0.28	6	6
mol:GDP	0	0	-10000	0	-10000	0	0
FN1	-0.009	0.13	-10000	0	-0.51	10	10
alphaV/beta3 Integrin/Pyk2	0.033	0.098	-10000	0	-0.34	7	7
SDC1	-0.007	0.14	-10000	0	-0.51	11	11
VAV3	-0.053	0.13	-10000	0	-0.29	33	33
PTPN11	0.031	0.044	-10000	0	-0.51	1	1
IRS1	0.006	0.11	-10000	0	-0.51	7	7
FAK1/Paxillin	0.019	0.13	0.27	3	-0.41	7	10
cell migration	0.012	0.12	0.25	4	-0.38	7	11
ITGAV	0.014	0.097	-10000	0	-0.51	5	5
PI3K	-0.005	0.1	-10000	0	-0.3	12	12
SPP1	-0.1	0.22	-10000	0	-0.51	33	33
KDR	0.023	0.062	-10000	0	-0.51	2	2
mol:PI-4-5-P2	0	0	-10000	0	-10000	0	0
alphaV/beta3 Integrin/Caspase 8	0.014	0.097	-10000	0	-0.51	5	5
COL4A3	0.03	0.045	-10000	0	-0.51	1	1
angiogenesis	-0.054	0.2	-10000	0	-0.66	12	12
Rac1/GTP	-0.04	0.13	-10000	0	-0.27	33	33
EDIL3	-0.039	0.16	-10000	0	-0.51	15	15
cell proliferation	0.039	0.089	-10000	0	-0.36	6	6

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

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
BAG4	0.028	0.014	-10000	0	-10000	0	0
Caspase 8 (4 units)	-0.005	0.16	-10000	0	-0.48	10	10
NEF	-0.011	0.046	-10000	0	-0.27	3	3
NFKBIA	0.013	0.065	-10000	0	-0.6	1	1
BIRC3	-0.03	0.17	-10000	0	-0.52	15	15
CYCS	-0.03	0.13	-10000	0	-0.42	10	10
RIPK1	0.033	0.006	-10000	0	-10000	0	0
CD247	-0.053	0.21	-10000	0	-0.59	19	19
MAP2K7	-0.02	0.19	-10000	0	-0.68	8	8
protein ubiquitination	0.014	0.093	0.23	1	-0.36	4	5
CRADD	0.027	0.061	-10000	0	-0.51	2	2
DAXX	0.034	0.005	-10000	0	-10000	0	0
FAS	-0.018	0.15	-10000	0	-0.51	13	13
BID	-0.03	0.14	0.19	5	-0.37	16	21
NF-kappa-B/RelA/I kappa B alpha	0.028	0.11	-10000	0	-0.31	12	12
TRADD	0.029	0.044	-10000	0	-0.51	1	1
MAP3K5	0.022	0.075	-10000	0	-0.51	3	3
CFLAR	0.015	0.096	-10000	0	-0.51	5	5
FADD	0.031	0.011	-10000	0	-10000	0	0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin	0.028	0.11	-10000	0	-0.31	12	12
MAPK8	-0.017	0.18	-10000	0	-0.63	8	8
APAF1	0.031	0.044	-10000	0	-0.51	1	1
TRAF1	0.024	0.064	-10000	0	-0.51	2	2
TRAF2	0.033	0.01	-10000	0	-10000	0	0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG	-0.027	0.15	0.2	5	-0.36	18	23
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD	0.019	0.11	-10000	0	-0.37	6	6
CHUK	0.015	0.098	-10000	0	-0.39	4	4
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8	0.036	0.12	-10000	0	-0.28	15	15
TCRz/NEF	-0.048	0.19	-10000	0	-0.54	19	19
TNF	0.026	0.048	-10000	0	-0.51	1	1
FASLG	-0.074	0.24	-10000	0	-0.65	20	20
NFKB1	0.017	0.042	-10000	0	-0.16	1	1
TNFR1A/BAG4/TNF-alpha	0.038	0.058	-10000	0	-0.32	2	2
CASP6	-0.019	0.21	-10000	0	-0.66	11	11
CASP7	-0.043	0.21	-10000	0	-0.59	16	16
RELA	0.017	0.046	-10000	0	-0.16	2	2
CASP2	0.034	0.004	-10000	0	-10000	0	0
CASP3	-0.052	0.22	-10000	0	-0.59	17	17
TNFRSF1A	0.021	0.075	-10000	0	-0.51	3	3
TNFR1A/BAG4	0.03	0.054	-10000	0	-0.37	2	2
CASP8	0.026	0.062	-10000	0	-0.51	2	2
CASP9	0.033	0.006	-10000	0	-10000	0	0
MAP3K14	0.017	0.11	0.25	1	-0.43	4	5
APAF-1/Caspase 9	-0.037	0.16	-10000	0	-0.47	13	13
BCL2	-0.029	0.17	-10000	0	-0.57	9	9

Canonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.042	0.041	0.41	1	-10000	0	1
AES	0.039	0.035	0.38	1	-10000	0	1
FBXW11	0.032	0.008	-10000	0	-10000	0	0
mol:GTP	0	0.002	-10000	0	-10000	0	0
LRP6/FZD1	0.038	0.051	-10000	0	-0.37	2	2
SMAD4	0.026	0.062	-10000	0	-0.51	2	2
DKK2	0.011	0.089	-10000	0	-0.51	4	4
TLE1	0.027	0.079	0.28	1	-0.5	3	4
MACF1	0.022	0.075	-10000	0	-0.51	3	3
CTNNB1	0.018	0.13	0.35	3	-0.37	6	9
WIF1	-0.06	0.18	-10000	0	-0.51	21	21
beta catenin/RanBP3	0.031	0.17	0.43	16	-0.37	3	19
KREMEN2	-0.097	0.21	-10000	0	-0.51	30	30
DKK1	-0.093	0.2	-10000	0	-0.51	29	29
beta catenin/beta TrCP1	0.035	0.13	0.35	3	-0.35	5	8
FZD1	0.028	0.045	-10000	0	-0.51	1	1
AXIN2	-0.047	0.27	0.68	2	-1.4	5	7
AXIN1	0.033	0.011	-10000	0	-10000	0	0
RAN	0.035	0.003	-10000	0	-10000	0	0
Axin1/APC/GSK3/beta catenin	0.019	0.12	-10000	0	-0.58	5	5
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4	0.014	0.15	0.28	1	-0.46	9	10
Axin1/APC/GSK3	0.027	0.062	0.25	1	-0.28	2	3
Axin1/APC/GSK3/beta catenin/Macf1	0.033	0.11	-10000	0	-0.38	4	4
HNF1A	0.036	0.041	0.25	2	-10000	0	2
CTBP1	0.037	0.034	0.25	2	-10000	0	2
MYC	0.003	0.35	0.6	14	-1.4	6	20
RANBP3	0.033	0.007	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	-0.054	0.15	-10000	0	-0.32	35	35
NKD1	0.027	0.025	-10000	0	-10000	0	0
TCF4	0.007	0.12	-10000	0	-0.46	9	9
TCF3	0.035	0.044	0.29	1	-0.39	1	2
WNT1/LRP6/FZD1/Axin1	0.066	0.055	-10000	0	-0.3	2	2
Ran/GTP	0.026	0.004	-10000	0	-10000	0	0
CtBP/CBP/TCF/TLE1/AES	0.026	0.19	0.5	13	-0.43	3	16
LEF1	0.023	0.094	0.38	1	-0.5	4	5
DVL1	0.032	0.079	0.25	1	-0.45	2	3
CSNK2A1	0.033	0.008	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES	-0.007	0.2	0.3	1	-0.57	11	12
DKK1/LRP6/Kremen 2	-0.12	0.19	-10000	0	-0.35	54	54
LRP6	0.028	0.045	-10000	0	-0.51	1	1
CSNK1A1	0.037	0.06	0.42	1	-0.5	1	2
NLK	0.032	0.01	-10000	0	-10000	0	0
CCND1	-0.067	0.46	0.59	6	-1.5	12	18
WNT1	0.034	0.005	-10000	0	-10000	0	0
GSK3A	0.034	0.007	-10000	0	-10000	0	0
GSK3B	0.029	0.013	-10000	0	-10000	0	0
FRAT1	0.032	0.011	-10000	0	-10000	0	0
PPP2R5D	0.034	0.058	-10000	0	-0.36	1	1
APC	0.032	0.072	-10000	0	-0.28	2	2
WNT1/LRP6/FZD1	0.047	0.085	0.24	17	-0.27	2	19
CREBBP	0.04	0.032	0.25	2	-10000	0	2

Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaV beta3 Integrin	0.028	0.084	-10000	0	-0.37	6	6
AKT1	0.02	0.2	0.35	4	-0.56	11	15
PTK2B	-0.001	0.15	0.36	2	-0.48	8	10
VEGFR2 homodimer/Frs2	0.002	0.12	-10000	0	-0.41	9	9
CAV1	-0.027	0.16	-10000	0	-0.51	15	15
CALM1	0.033	0.007	-10000	0	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2	0.012	0.12	-10000	0	-0.41	9	9
endothelial cell proliferation	0.04	0.17	0.32	9	-0.45	10	19
mol:Ca2+	0.007	0.14	0.37	2	-0.35	14	16
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac	0.046	0.13	-10000	0	-0.4	9	9
RP11-342D11.1	-0.008	0.13	-10000	0	-0.34	15	15
CDH5	0.026	0.062	-10000	0	-0.51	2	2
VEGFA homodimer	0.054	0.09	-10000	0	-0.33	6	6
SHC1	0.032	0.008	-10000	0	-10000	0	0
SHC2	0.027	0.027	-10000	0	-10000	0	0
HRAS/GDP	0.01	0.11	-10000	0	-0.39	5	5
SH2D2A	0.017	0.087	-10000	0	-0.51	4	4
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS	0.023	0.15	-10000	0	-0.49	8	8
VEGFR2 homodimer/VEGFA homodimer/TsAd	0.006	0.13	-10000	0	-0.38	11	11
VEGFR1 homodimer	0.005	0.12	-10000	0	-0.51	8	8
SHC/GRB2/SOS1	0.052	0.14	-10000	0	-0.45	4	4
GRB10	-0.008	0.19	0.37	2	-0.55	13	15
PTPN11	0.031	0.044	-10000	0	-0.51	1	1
GRB2	0.034	0.005	-10000	0	-10000	0	0
PAK1	0.028	0.046	-10000	0	-0.51	1	1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin	0.049	0.15	-10000	0	-0.44	8	8
HRAS	0.029	0.045	-10000	0	-0.51	1	1
VEGF/Rho/ROCK1/Integrin Complex	0.002	0.14	-10000	0	-0.48	8	8
HIF1A	0.022	0.075	-10000	0	-0.51	3	3
FRS2	0.033	0.007	-10000	0	-10000	0	0
oxygen and reactive oxygen species metabolic process	0.044	0.13	-10000	0	-0.39	9	9
mol:GTP	0	0	-10000	0	-10000	0	0
FLT4	0.032	0.009	-10000	0	-10000	0	0
Nck/Pak	0.031	0.061	-10000	0	-0.37	3	3
VEGFR2 homodimer/VEGFA homodimer/Fyn	0.01	0.14	-10000	0	-0.42	10	10
mol:GDP	0.022	0.12	-10000	0	-0.44	4	4
mol:NADP	0.03	0.14	0.33	3	-0.45	7	10
eNOS/Hsp90	0.038	0.14	0.33	3	-0.42	7	10
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
mol:IP3	0.007	0.15	0.37	2	-0.36	14	16
HIF1A/ARNT	0.039	0.053	-10000	0	-0.29	3	3
SHB	0.019	0.076	-10000	0	-0.51	3	3
VEGFA	0.022	0.066	-10000	0	-0.5	2	2
VEGFC	0.005	0.11	-10000	0	-0.51	6	6
FAK1/Vinculin	0.018	0.18	0.33	2	-0.61	8	10
mol:Ca ++	0	0	-10000	0	-10000	0	0
RHOA	0.031	0.011	-10000	0	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	0.031	0.16	-10000	0	-0.44	11	11
PTPN6	0.028	0.044	-10000	0	-0.51	1	1
EPAS1	0	0.14	-10000	0	-0.51	9	9
mol:L-citrulline	0.03	0.14	0.33	3	-0.45	7	10
ITGAV	0.014	0.097	-10000	0	-0.51	5	5
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2	0.047	0.14	-10000	0	-0.4	9	9
VEGFR2 homodimer/VEGFA homodimer	0.007	0.14	-10000	0	-0.37	16	16
VEGFR2/3 heterodimer	0.002	0.12	-10000	0	-0.41	9	9
VEGFB	0.034	0	-10000	0	-10000	0	0
MAPK11	-0.005	0.14	0.31	9	-0.45	7	16
VEGFR2 homodimer	-0.009	0.12	-10000	0	-0.51	7	7
FLT1	0.005	0.12	-10000	0	-0.51	8	8
NEDD4	0.022	0.066	-10000	0	-0.5	2	2
MAPK3	-0.001	0.14	0.34	5	-0.49	5	10
MAPK1	-0.002	0.14	0.3	9	-0.53	4	13
VEGFA145/NRP2	0.033	0.079	-10000	0	-0.47	3	3
VEGFR1/2 heterodimer	-0.01	0.15	-10000	0	-0.45	12	12
KDR	-0.009	0.12	-10000	0	-0.51	7	7
VEGFA165/NRP1/VEGFR2 homodimer	0.026	0.15	-10000	0	-0.36	14	14
SRC	0.032	0.012	-10000	0	-10000	0	0
platelet activating factor biosynthetic process	0.005	0.15	0.34	5	-0.48	5	10
PI3K	-0.024	0.15	-10000	0	-0.53	8	8
VEGFR2 homodimer/VEGFA homodimer/NCK1	0.008	0.12	-10000	0	-0.4	8	8
FES	0.003	0.15	0.37	2	-0.36	15	17
GAB1	-0.009	0.17	-10000	0	-0.46	13	13
VEGFR2 homodimer/VEGFA homodimer/Src	0.011	0.12	-10000	0	-0.41	9	9
CTNNB1	0.03	0.016	-10000	0	-10000	0	0
SOS1	0.033	0.006	-10000	0	-10000	0	0
ARNT	0.032	0.008	-10000	0	-10000	0	0
eNOS/Caveolin-1	0.015	0.16	0.35	1	-0.42	10	11
VEGFR2 homodimer/VEGFA homodimer/Yes	0.01	0.12	-10000	0	-0.38	10	10
PI3K/GAB1	0.011	0.18	-10000	0	-0.47	12	12
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak	0.042	0.12	-10000	0	-0.42	5	5
PRKACA	0.033	0.007	-10000	0	-10000	0	0
VEGFR2/3 heterodimer/VEGFC homodimer	0.002	0.13	-10000	0	-0.37	13	13
HSP90AA1	0.033	0.008	-10000	0	-10000	0	0
CDC42	0.008	0.15	0.37	2	-0.39	11	13
actin cytoskeleton reorganization	0.006	0.13	-10000	0	-0.38	11	11
PTK2	-0.003	0.18	0.33	2	-0.64	8	10
EDG1	-0.008	0.13	-10000	0	-0.34	15	15
mol:DAG	0.007	0.15	0.37	2	-0.36	14	16
CaM/Ca2+	0.02	0.14	0.34	2	-0.37	10	12
MAP2K3	-0.014	0.094	-10000	0	-0.39	5	5
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4	-0.006	0.18	-10000	0	-0.56	13	13
PLCG1	0.007	0.15	0.37	2	-0.36	14	16
VEGFR2 homodimer/VEGFA homodimer/Src/Shb	0.037	0.13	-10000	0	-0.36	10	10
IQGAP1	0.034	0.005	-10000	0	-10000	0	0
YES1	0.028	0.044	-10000	0	-0.51	1	1
VEGFR2 homodimer/VEGFA homodimer/SHP2	0.013	0.13	-10000	0	-0.4	10	10
VEGFR2 homodimer/VEGFA homodimer/SHP1	0.008	0.13	-10000	0	-0.44	9	9
cell migration	0.025	0.17	0.31	4	-0.56	8	12
mol:PI-3-4-5-P3	-0.022	0.14	-10000	0	-0.49	8	8
FYN	0.026	0.062	-10000	0	-0.51	2	2
VEGFB/NRP1	0.009	0.13	-10000	0	-0.34	14	14
mol:NO	0.03	0.14	0.33	3	-0.45	7	10
PXN	0.034	0.004	-10000	0	-10000	0	0
HRAS/GTP	-0.007	0.1	-10000	0	-0.39	5	5
VEGFR2 homodimer/VEGFA homodimer/GRB10	-0.018	0.18	-10000	0	-0.56	13	13
VHL	0.019	0.076	-10000	0	-0.51	3	3
ITGB3	0.026	0.048	-10000	0	-0.51	1	1
NOS3	0.028	0.16	0.33	3	-0.51	7	10
VEGFR2 homodimer/VEGFA homodimer/Sck	0.01	0.12	-10000	0	-0.41	9	9
RAC1	0.033	0.006	-10000	0	-10000	0	0
PRKCA	-0.004	0.14	0.36	2	-0.54	5	7
PRKCB	-0.005	0.14	0.36	2	-0.34	13	15
VCL	0.026	0.062	-10000	0	-0.51	2	2
VEGFA165/NRP1	0.011	0.14	-10000	0	-0.34	16	16
VEGFR1/2 heterodimer/VEGFA homodimer	-0.001	0.16	-10000	0	-0.43	13	13
VEGFA165/NRP2	0.033	0.079	-10000	0	-0.47	3	3
MAPKKK cascade	-0.013	0.15	-10000	0	-0.49	11	11
NRP2	0.025	0.063	-10000	0	-0.51	2	2
VEGFC homodimer	0.005	0.11	-10000	0	-0.51	6	6
NCK1	0.021	0.062	-10000	0	-0.51	2	2
ROCK1	0.034	0.005	-10000	0	-10000	0	0
FAK1/Paxillin	0.024	0.18	0.33	2	-0.6	8	10
MAP3K13	-0.011	0.1	-10000	0	-0.35	9	9
PDPK1	-0.023	0.13	0.28	1	-0.47	8	9

Regulation of nuclear SMAD2/3 signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EP300	0.002	0.12	-10000	0	-0.51	8	8
HSPA8	0.03	0.044	-10000	0	-0.51	1	1
SMAD3/SMAD4/ER alpha	0.013	0.15	-10000	0	-0.39	11	11
AKT1	-0.002	0.078	-10000	0	-0.5	2	2
GSC	-0.016	0.18	-10000	0	-1.4	2	2
NKX2-5	-0.016	0.13	-10000	0	-0.48	10	10
muscle cell differentiation	0.032	0.17	0.42	18	-10000	0	18
SMAD2-3/SMAD4/SP1	0	0.18	-10000	0	-0.48	9	9
SMAD4	0	0.095	-10000	0	-0.63	2	2
CBFB	0.032	0.008	-10000	0	-10000	0	0
SAP18	0.033	0.007	-10000	0	-10000	0	0
Cbp/p300/MSG1	0.039	0.093	-10000	0	-0.32	8	8
SMAD3/SMAD4/VDR	0.025	0.16	-10000	0	-0.39	11	11
MYC	0.021	0.094	-10000	0	-0.47	5	5
CDKN2B	-0.41	0.7	-10000	0	-1.6	35	35
AP1	-0.029	0.19	-10000	0	-0.44	18	18
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1	0.04	0.1	-10000	0	-0.42	4	4
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1	-0.075	0.17	-10000	0	-0.36	35	35
SP3	0.034	0.014	-10000	0	-10000	0	0
CREB1	0.03	0.044	-10000	0	-0.51	1	1
FOXH1	0.022	0.032	-10000	0	-10000	0	0
SMAD3/SMAD4/GR	0.022	0.12	-10000	0	-0.36	7	7
GATA3	0.031	0.027	-10000	0	-10000	0	0
SKI/SIN3/HDAC complex/NCoR1	0.017	0.082	-10000	0	-0.37	5	5
MEF2C/TIF2	-0.024	0.16	0.33	2	-0.57	7	9
endothelial cell migration	0.095	0.4	1.4	13	-10000	0	13
MAX	0.036	0.015	-10000	0	-10000	0	0
RBBP7	0.032	0.011	-10000	0	-10000	0	0
RBBP4	0.03	0.044	-10000	0	-0.51	1	1
RUNX2	0.027	0.061	-10000	0	-0.51	2	2
RUNX3	-0.003	0.13	-10000	0	-0.51	10	10
RUNX1	0.022	0.075	-10000	0	-0.51	3	3
CTBP1	0.03	0.011	-10000	0	-10000	0	0
NR3C1	0.034	0.018	-10000	0	-10000	0	0
VDR	-0.001	0.13	-10000	0	-0.51	9	9
CDKN1A	-0.038	0.22	-10000	0	-1.2	4	4
KAT2B	0	0.005	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1	0.014	0.093	-10000	0	-0.29	4	4
DCP1A	0.031	0.01	-10000	0	-10000	0	0
SKI	0.033	0.007	-10000	0	-10000	0	0
SERPINE1	-0.098	0.4	-10000	0	-1.4	13	13
SMAD3/SMAD4/ATF2	0.019	0.12	-10000	0	-0.35	8	8
SMAD3/SMAD4/ATF3	0.001	0.14	-10000	0	-0.36	13	13
SAP30	0.031	0.01	-10000	0	-10000	0	0
Cbp/p300/PIAS3	0.043	0.091	-10000	0	-0.32	7	7
JUN	-0.041	0.18	-10000	0	-0.48	15	15
SMAD3/SMAD4/IRF7	0.022	0.13	-10000	0	-0.33	11	11
TFE3	0.026	0.038	-10000	0	-0.17	1	1
COL1A2	-0.068	0.28	-10000	0	-0.92	14	14
mesenchymal cell differentiation	-0.015	0.13	0.38	9	-10000	0	9
DLX1	0.027	0.027	-10000	0	-10000	0	0
TCF3	0.03	0.044	-10000	0	-0.51	1	1
FOS	-0.035	0.16	-10000	0	-0.53	14	14
SMAD3/SMAD4/Max	0.025	0.12	-10000	0	-0.36	7	7
Cbp/p300/SNIP1	0.04	0.089	-10000	0	-0.32	8	8
ZBTB17	0.034	0.014	-10000	0	-10000	0	0
LAMC1	-0.019	0.14	-10000	0	-0.6	6	6
TGIF2/HDAC complex/SMAD3/SMAD4	0.017	0.12	-10000	0	-0.38	8	8
IRF7	0.03	0.047	-10000	0	-0.5	1	1
ESR1	0.007	0.11	-10000	0	-0.47	7	7
HNF4A	0.033	0.011	-10000	0	-10000	0	0
MEF2C	-0.029	0.16	0.33	2	-0.55	8	10
SMAD2-3/SMAD4	0.004	0.13	-10000	0	-0.32	9	9
Cbp/p300/Src-1	0.041	0.091	-10000	0	-0.32	8	8
IGHV3OR16-13	-0.008	0.095	-10000	0	-0.52	4	4
TGIF2/HDAC complex	0.028	0.045	-10000	0	-0.51	1	1
CREBBP	0.03	0.019	-10000	0	-10000	0	0
SKIL	-0.001	0.094	-10000	0	-0.51	5	5
HDAC1	0.033	0.01	-10000	0	-10000	0	0
HDAC2	0.033	0.009	-10000	0	-10000	0	0
SNIP1	0.033	0.007	-10000	0	-10000	0	0
GCN5L2	0.001	0.008	-10000	0	-10000	0	0
SMAD3/SMAD4/TFE3	0.023	0.14	-10000	0	-0.35	12	12
MSG1/HSC70	0.044	0.038	-10000	0	-0.37	1	1
SMAD2	0.003	0.065	-10000	0	-0.34	2	2
SMAD3	-0.011	0.12	-10000	0	-0.5	7	7
SMAD3/E2F4-5/DP1/p107/SMAD4	0.001	0.086	-10000	0	-0.26	9	9
SMAD2/SMAD2/SMAD4	-0.014	0.071	-10000	0	-0.32	4	4
NCOR1	0.032	0.008	-10000	0	-10000	0	0
NCOA2	0.025	0.062	-10000	0	-0.51	2	2
NCOA1	0.033	0.007	-10000	0	-10000	0	0
MYOD/E2A	0.026	0.094	-10000	0	-0.37	8	8
SMAD2-3/SMAD4/SP1/MIZ-1	0.005	0.18	-10000	0	-0.48	9	9
IFNB1	-0.009	0.1	-10000	0	-0.41	6	6
SMAD3/SMAD4/MEF2C	-0.026	0.17	-10000	0	-0.55	8	8
CITED1	0.031	0.016	-10000	0	-10000	0	0
SMAD2-3/SMAD4/ARC105	0.017	0.12	-10000	0	-0.33	5	5
RBL1	0.032	0.008	-10000	0	-10000	0	0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB	-0.12	0.25	-10000	0	-0.54	36	36
RUNX1-3/PEBPB2	0.033	0.11	-10000	0	-0.37	10	10
SMAD7	-0.045	0.2	-10000	0	-0.63	10	10
MYC/MIZ-1	0.04	0.077	-10000	0	-0.33	5	5
SMAD3/SMAD4	-0.03	0.19	0.31	1	-0.5	16	17
IL10	-0.003	0.088	-10000	0	-0.36	3	3
PIASy/HDAC complex	0.031	0.015	-10000	0	-10000	0	0
PIAS3	0.032	0.013	-10000	0	-10000	0	0
CDK2	0.028	0.048	-10000	0	-0.52	1	1
IL5	-0.004	0.093	-10000	0	-0.42	3	3
CDK4	0.031	0.019	-10000	0	-10000	0	0
PIAS4	0.031	0.015	-10000	0	-10000	0	0
ATF3	0.006	0.11	-10000	0	-0.51	6	6
SMAD3/SMAD4/SP1	-0.002	0.17	-10000	0	-0.43	12	12
FOXG1	0.021	0.033	-10000	0	-10000	0	0
FOXO3	-0.018	0.072	-10000	0	-0.37	3	3
FOXO1	-0.025	0.092	-10000	0	-0.37	7	7
FOXO4	-0.015	0.067	-10000	0	-0.37	2	2
heart looping	-0.029	0.16	0.33	2	-0.54	8	10
CEBPB	0.012	0.055	-10000	0	-0.51	1	1
SMAD3/SMAD4/DLX1	0.016	0.12	-10000	0	-0.36	8	8
MYOD1	0.008	0.11	-10000	0	-0.51	7	7
SMAD3/SMAD4/HNF4	0.02	0.12	-10000	0	-0.35	8	8
SMAD3/SMAD4/GATA3	0.028	0.12	-10000	0	-0.36	7	7
SnoN/SIN3/HDAC complex/NCoR1	-0.001	0.094	-10000	0	-0.51	5	5
SMAD3/SMAD4/RUNX1-3/PEBPB2	0.026	0.16	-10000	0	-0.41	12	12
SMAD3/SMAD4/SP1-3	0.018	0.17	-10000	0	-0.54	7	7
MED15	0.031	0.012	-10000	0	-10000	0	0
SP1	0.004	0.09	-10000	0	-0.28	8	8
SIN3B	0.033	0.006	-10000	0	-10000	0	0
SIN3A	0.034	0.003	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5	-0.002	0.14	-10000	0	-0.34	14	14
ITGB5	-0.027	0.16	-10000	0	-0.65	6	6
TGIF/SIN3/HDAC complex/CtBP	0.023	0.066	-10000	0	-0.41	2	2
SMAD3/SMAD4/AR	0.006	0.13	-10000	0	-0.36	11	11
AR	0.013	0.08	-10000	0	-0.51	3	3
negative regulation of cell growth	-0.012	0.11	-10000	0	-0.34	8	8
SMAD3/SMAD4/MYOD	0.002	0.14	-10000	0	-0.36	14	14
E2F5	0.015	0.088	-10000	0	-0.51	4	4
E2F4	0.032	0.008	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF	0.035	0.12	-10000	0	-0.32	9	9
SMAD2-3/SMAD4/FOXO1-3a-4	-0.076	0.19	-10000	0	-0.4	33	33
TFDP1	0.033	0.008	-10000	0	-10000	0	0
SMAD3/SMAD4/AP1	-0.015	0.2	-10000	0	-0.46	17	17
SMAD3/SMAD4/RUNX2	0.015	0.13	-10000	0	-0.38	9	9
TGIF2	0.028	0.045	-10000	0	-0.51	1	1
TGIF1	0.029	0.044	-10000	0	-0.51	1	1
ATF2	0.034	0.005	-10000	0	-10000	0	0

Coregulation of Androgen receptor activity

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NRIP1	0.005	0.12	-9999	-0.51	8	8
SVIL	0.005	0.12	-9999	-0.51	8	8
ZNF318	0.03	0.01	-9999	-10000	0	0
JMJD2C	0.007	0.001	-9999	-10000	0	0
T-DHT/AR/Ubc9	-0.01	0.087	-9999	-0.27	6	6
CARM1	0.033	0.007	-9999	-10000	0	0
PRDX1	0.015	0.079	-9999	-0.51	3	3
PELP1	0.032	0.008	-9999	-10000	0	0
CTNNB1	0.031	0.016	-9999	-10000	0	0
AKT1	0.024	0.062	-9999	-0.51	2	2
PTK2B	0.029	0.017	-9999	-10000	0	0
MED1	0.022	0.075	-9999	-0.51	3	3
MAK	0.027	0.018	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
HIP1	0.034	0.011	-9999	-10000	0	0
GSN	0.005	0.12	-9999	-0.51	8	8
NCOA2	0.025	0.062	-9999	-0.51	2	2
NCOA6	0.027	0.062	-9999	-0.51	2	2
DNA-PK	0.056	0.037	-9999	-0.32	1	1
NCOA4	0.033	0.007	-9999	-10000	0	0
PIAS3	0.035	0.006	-9999	-10000	0	0
cell proliferation	-0.005	0.055	-9999	-0.53	1	1
XRCC5	0.033	0.005	-9999	-10000	0	0
UBE3A	0.036	0.005	-9999	-10000	0	0
T-DHT/AR/SNURF	-0.026	0.076	-9999	-0.2	12	12
FHL2	-0.15	0.36	-9999	-0.97	24	24
RANBP9	0.035	0.007	-9999	-10000	0	0
JMJD1A	-0.025	0.057	-9999	-0.13	32	32
CDK6	0.011	0.1	-9999	-0.51	6	6
TGFB1I1	0.031	0.045	-9999	-0.51	1	1
T-DHT/AR/CyclinD1	-0.035	0.12	-9999	-0.36	15	15
XRCC6	0.032	0.007	-9999	-10000	0	0
T-DHT/AR	-0.039	0.13	-9999	-0.2	48	48
CTDSP1	0.034	0.006	-9999	-10000	0	0
CTDSP2	0.032	0.004	-9999	-10000	0	0
BRCA1	0.031	0.044	-9999	-0.51	1	1
TCF4	0	0.13	-9999	-0.51	9	9
CDKN2A	-0.042	0.16	-9999	-0.51	15	15
SRF	0.004	0.071	-9999	-0.16	18	18
NKX3-1	-0.058	0.099	-9999	-0.23	35	35
KLK3	0.021	0.055	-9999	-10000	0	0
TMF1	0.027	0.045	-9999	-0.51	1	1
HNRNPA1	0.033	0.005	-9999	-10000	0	0
AOF2	0.002	0	-9999	-10000	0	0
APPL1	0.008	0.044	-9999	-0.37	2	2
T-DHT/AR/Caspase 8	-0.016	0.094	-9999	-0.29	8	8
AR	-0.02	0.095	-9999	-0.46	4	4
UBA3	0	0	-9999	-10000	0	0
PATZ1	0.028	0.044	-9999	-0.51	1	1
PAWR	0.02	0.086	-9999	-0.51	4	4
PRKDC	0.028	0.044	-9999	-0.51	1	1
PA2G4	0.033	0.004	-9999	-10000	0	0
UBE2I	0.033	0.006	-9999	-10000	0	0
T-DHT/AR/Cyclin D3/CDK11 p58	-0.01	0.08	-9999	-0.22	8	8
RPS6KA3	0.03	0.045	-9999	-0.51	1	1
T-DHT/AR/ARA70	-0.01	0.087	-9999	-0.24	8	8
LATS2	0.025	0.062	-9999	-0.51	2	2
T-DHT/AR/PRX1	-0.019	0.093	-9999	-0.31	8	8
Cyclin D3/CDK11 p58	0.024	0.008	-9999	-10000	0	0
VAV3	-0.093	0.22	-9999	-0.51	33	33
KLK2	-0.009	0.054	-9999	-0.34	1	1
CASP8	0.025	0.062	-9999	-0.51	2	2
T-DHT/AR/TIF2/CARM1	0.001	0.095	-9999	-0.35	5	5
TMPRSS2	-0.2	0.39	-9999	-0.92	33	33
CCND1	-0.013	0.14	-9999	-0.51	12	12
PIAS1	0.036	0.004	-9999	-10000	0	0
mol:T-DHT	-0.021	0.033	-9999	-0.066	51	51
CDC2L1	0	0	-9999	-10000	0	0
PIAS4	0.036	0.007	-9999	-10000	0	0
T-DHT/AR/CDK6	-0.022	0.1	-9999	-0.3	12	12
CMTM2	0.026	0.027	-9999	-10000	0	0
SNURF	0	0	-9999	-10000	0	0
ZMIZ1	0	0.052	-9999	-10000	0	0
CCND3	0.033	0.013	-9999	-10000	0	0
TGIF1	0.028	0.044	-9999	-0.51	1	1
FKBP4	0.029	0.045	-9999	-0.51	1	1

Hedgehog signaling events mediated by Gli proteins

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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.033	0.01	-10000	0	-10000	0	0
HDAC2	0.034	0.009	-10000	0	-10000	0	0
GNB1/GNG2	0.004	0.14	-10000	0	-0.32	23	23
forebrain development	-0.08	0.23	-10000	0	-0.65	15	15
GNAO1	0.032	0.011	-10000	0	-10000	0	0
SMO/beta Arrestin2	-0.023	0.15	-10000	0	-0.37	24	24
SMO	-0.054	0.2	-10000	0	-0.51	24	24
ARRB2	0.032	0.01	-10000	0	-10000	0	0
GLI3/SPOP	0.007	0.16	0.28	1	-0.48	7	8
mol:GTP	0	0.002	-10000	0	-10000	0	0
GSK3B	0.028	0.013	-10000	0	-10000	0	0
GNAI2	0.028	0.018	-10000	0	-10000	0	0
SIN3/HDAC complex	0.078	0.029	-10000	0	-10000	0	0
GNAI1	0.001	0.13	-10000	0	-0.51	9	9
XPO1	0.027	0.019	-10000	0	-10000	0	0
GLI1/Su(fu)	-0.09	0.23	-10000	0	-0.62	16	16
SAP30	0.032	0.01	-10000	0	-10000	0	0
mol:GDP	-0.054	0.2	-10000	0	-0.51	24	24
MIM/GLI2A	-0.024	0.14	-10000	0	-0.48	11	11
IFT88	0.029	0.044	-10000	0	-0.51	1	1
GNAI3	0.033	0.007	-10000	0	-10000	0	0
GLI2	-0.013	0.12	-10000	0	-0.44	6	6
GLI3	-0.006	0.16	0.27	2	-0.48	8	10
CSNK1D	0.033	0.006	-10000	0	-10000	0	0
CSNK1E	0.029	0.044	-10000	0	-0.51	1	1
SAP18	0.033	0.007	-10000	0	-10000	0	0
embryonic digit morphogenesis	0.029	0.044	-10000	0	-0.51	1	1
GNG2	0.034	0.005	-10000	0	-10000	0	0
Gi family/GTP	-0.047	0.16	-10000	0	-0.35	27	27
SIN3B	0.033	0.006	-10000	0	-10000	0	0
SIN3A	0.034	0.003	-10000	0	-10000	0	0
GLI3/Su(fu)	-0.005	0.15	-10000	0	-0.48	8	8
GLI2/Su(fu)	-0.028	0.15	-10000	0	-0.5	6	6
FOXA2	-0.16	0.39	-10000	0	-0.97	27	27
neural tube patterning	-0.08	0.23	-10000	0	-0.65	15	15
SPOP	0.034	0.003	-10000	0	-10000	0	0
Su(fu)/PIAS1	-0.004	0.1	-10000	0	-0.66	1	1
GNB1	0.033	0.007	-10000	0	-10000	0	0
CSNK1G2	0.033	0.007	-10000	0	-10000	0	0
CSNK1G3	0.032	0.008	-10000	0	-10000	0	0
MTSS1	-0.024	0.14	-10000	0	-0.48	11	11
embryonic limb morphogenesis	-0.08	0.23	-10000	0	-0.65	15	15
SUFU	-0.011	0.095	-10000	0	-0.71	1	1
LGALS3	0.022	0.075	-10000	0	-0.51	3	3
catabolic process	-0.014	0.19	-10000	0	-0.55	10	10
GLI3A/CBP	-0.005	0.11	-10000	0	-0.37	12	12
KIF3A	0.025	0.062	-10000	0	-0.51	2	2
GLI1	-0.083	0.23	-10000	0	-0.67	15	15
RAB23	0.029	0.045	-10000	0	-0.51	1	1
CSNK1A1	0.029	0.044	-10000	0	-0.51	1	1
IFT172	0.031	0.017	-10000	0	-10000	0	0
RBBP7	0.032	0.011	-10000	0	-10000	0	0
Su(fu)/Galectin3	-0.008	0.11	-10000	0	-0.42	5	5
GNAZ	0.004	0.11	-10000	0	-0.51	7	7
RBBP4	0.03	0.044	-10000	0	-0.51	1	1
CSNK1G1	0.034	0.004	-10000	0	-10000	0	0
PIAS1	0.034	0.004	-10000	0	-10000	0	0
PRKACA	0.033	0.007	-10000	0	-10000	0	0
GLI2/SPOP	0.002	0.12	-10000	0	-0.42	6	6
STK36	0.027	0.046	-10000	0	-0.51	1	1
Gi family/GNB1/GNG2/GDP	-0.037	0.15	-10000	0	-0.43	14	14
PTCH1	-0.077	0.22	-10000	0	-0.7	12	12
MIM/GLI1	-0.1	0.27	-10000	0	-0.62	26	26
CREBBP	-0.005	0.11	-10000	0	-0.37	12	12
Su(fu)/SIN3/HDAC complex	0.013	0.081	-10000	0	-0.4	4	4

Presenilin action in Notch and Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved)	0.031	0.11	-10000	0	-0.45	6	6
HDAC1	0.035	0.017	-10000	0	-10000	0	0
AES	0.034	0.008	-10000	0	-10000	0	0
FBXW11	0.032	0.008	-10000	0	-10000	0	0
DTX1	0.03	0.044	-10000	0	-0.51	1	1
LRP6/FZD1	0.038	0.051	-10000	0	-0.37	2	2
TLE1	0.022	0.075	-10000	0	-0.5	3	3
AP1	-0.024	0.1	-10000	0	-0.28	19	19
NCSTN	0.032	0.008	-10000	0	-10000	0	0
ADAM10	0.033	0.01	-10000	0	-10000	0	0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4	-0.011	0.17	-10000	0	-0.7	6	6
NICD/RBPSUH	0.033	0.11	-10000	0	-0.49	4	4
WIF1	-0.06	0.18	-10000	0	-0.51	21	21
NOTCH1	0.012	0.093	-10000	0	-0.47	5	5
PSENEN	0.031	0.011	-10000	0	-10000	0	0
KREMEN2	-0.098	0.21	-10000	0	-0.51	30	30
DKK1	-0.093	0.2	-10000	0	-0.51	29	29
beta catenin/beta TrCP1	0.013	0.086	-10000	0	-0.29	5	5
APH1B	0.03	0.044	-10000	0	-0.51	1	1
APH1A	0.015	0.096	-10000	0	-0.51	5	5
AXIN1	0.005	0.092	-10000	0	-0.53	3	3
CtBP/CBP/TCF1/TLE1/AES	0.018	0.071	0.27	2	-0.29	2	4
PSEN1	0.03	0.044	-10000	0	-0.51	1	1
FOS	-0.029	0.16	-10000	0	-0.51	14	14
JUN	0.004	0.11	-10000	0	-0.51	7	7
MAP3K7	0.034	0.011	-10000	0	-10000	0	0
CTNNB1	-0.003	0.084	-10000	0	-0.3	6	6
MAPK3	0.034	0.003	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	-0.055	0.15	-10000	0	-0.32	35	35
HNF1A	0.03	0.024	-10000	0	-10000	0	0
CTBP1	0.031	0.012	-10000	0	-10000	0	0
MYC	-0.034	0.29	-10000	0	-1.5	6	6
NKD1	0.028	0.025	-10000	0	-10000	0	0
FZD1	0.028	0.045	-10000	0	-0.51	1	1
NOTCH1 precursor/Deltex homolog 1	0.034	0.11	-10000	0	-0.46	6	6
apoptosis	-0.024	0.1	-10000	0	-0.28	19	19
Delta 1/NOTCHprecursor	0.03	0.11	-10000	0	-0.45	6	6
DLL1	0.021	0.076	-10000	0	-0.51	3	3
PPARD	0.025	0.03	-10000	0	-10000	0	0
Gamma Secretase	0.067	0.086	-10000	0	-0.32	5	5
APC	-0.005	0.12	-10000	0	-0.5	6	6
DVL1	0.009	0.075	-10000	0	-0.37	4	4
CSNK2A1	0.032	0.008	-10000	0	-10000	0	0
MAP3K7IP1	0	0.006	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	-0.12	0.19	-10000	0	-0.35	54	54
LRP6	0.028	0.045	-10000	0	-0.51	1	1
CSNK1A1	0.029	0.044	-10000	0	-0.51	1	1
NLK	0.019	0.015	-10000	0	-10000	0	0
CCND1	-0.097	0.4	-10000	0	-1.4	12	12
WNT1	0.034	0.005	-10000	0	-10000	0	0
Axin1/APC/beta catenin	0.008	0.13	-10000	0	-0.42	8	8
DKK2	0.011	0.089	-10000	0	-0.51	4	4
NOTCH1 precursor/DVL1	0.014	0.13	-10000	0	-0.48	6	6
GSK3B	0.028	0.013	-10000	0	-10000	0	0
FRAT1	0.033	0.011	-10000	0	-10000	0	0
NOTCH/Deltex homolog 1	0.035	0.11	-10000	0	-0.46	6	6
PPP2R5D	0.017	0.049	-10000	0	-0.34	2	2
MAPK1	0.028	0.044	-10000	0	-0.51	1	1
WNT1/LRP6/FZD1	0.003	0.13	-10000	0	-0.29	20	20
RBPJ	0.032	0.009	-10000	0	-10000	0	0
CREBBP	0.032	0.012	-10000	0	-10000	0	0

FOXA2 and FOXA3 transcription factor networks

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
ACADVL	-0.005	0.26	-10000	0	-0.78	8	8
PCK1	0.014	0.18	-10000	0	-0.73	1	1
HNF4A	0.012	0.26	-10000	0	-0.82	5	5
KCNJ11	-0.006	0.3	-10000	0	-0.86	9	9
AKT1	0.023	0.17	-10000	0	-0.6	2	2
response to starvation	0.005	0.004	-10000	0	-10000	0	0
DLK1	-0.005	0.3	0.68	3	-0.84	8	11
NKX2-1	-0.1	0.49	-10000	0	-1.3	20	20
ACADM	-0.005	0.27	-10000	0	-0.81	8	8
TAT	0.017	0.18	-10000	0	-0.73	1	1
CEBPB	0.033	0.045	-10000	0	-0.5	1	1
CEBPA	0.021	0.088	-10000	0	-0.51	4	4
TTR	-0.036	0.26	-10000	0	-0.74	9	9
PKLR	0.009	0.26	-10000	0	-0.78	7	7
APOA1	0.003	0.31	-10000	0	-0.93	7	7
CPT1C	-0.065	0.35	0.6	1	-0.84	20	21
ALAS1	0.018	0.16	-10000	0	-0.53	1	1
TFRC	-0.079	0.46	-10000	0	-1.3	16	16
FOXF1	0.052	0.099	0.31	16	-0.36	1	17
NF1	0.037	0.044	-10000	0	-0.5	1	1
HNF1A (dimer)	0.04	0.042	-10000	0	-0.21	1	1
CPT1A	-0.004	0.26	-10000	0	-0.79	8	8
HMGCS1	0	0.31	0.6	2	-0.86	11	13
NR3C1	0.041	0.021	-10000	0	-10000	0	0
CPT1B	-0.01	0.27	-10000	0	-0.81	9	9
chromatin remodeling	0	0	-10000	0	-10000	0	0
SP1	0.029	0.067	-10000	0	-0.41	3	3
GCK	-0.006	0.27	0.6	1	-0.85	7	8
CREB1	0.036	0.047	-10000	0	-0.5	1	1
IGFBP1	0.022	0.14	-10000	0	-10000	0	0
PDX1	0.013	0.24	-10000	0	-1.2	3	3
UCP2	-0.028	0.31	-10000	0	-0.93	11	11
ALDOB	-0.002	0.28	-10000	0	-0.83	8	8
AFP	-0.037	0.15	-10000	0	-0.53	5	5
BDH1	0.046	0.35	0.59	1	-0.9	10	11
HADH	-0.009	0.29	-10000	0	-0.87	8	8
F2	0	0.3	-10000	0	-0.93	7	7
HNF1A	0.04	0.042	-10000	0	-0.21	1	1
G6PC	0.027	0.1	-10000	0	-0.64	1	1
SLC2A2	0.03	0.22	-10000	0	-1	2	2
INS	0	0.024	-10000	0	-10000	0	0
FOXA1	-0.041	0.2	0.29	5	-0.46	26	31
FOXA3	0.013	0.12	-10000	0	-0.43	6	6
FOXA2	0.01	0.34	-10000	0	-0.94	8	8
ABCC8	-0.011	0.3	-10000	0	-0.87	9	9
ALB	-0.037	0.15	-10000	0	-0.64	3	3

Reelin signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDK5R1/CDK5	0.047	0.017	-10000	0	-10000	0	0
VLDLR	-0.009	0.13	-10000	0	-0.51	9	9
CRKL	0.031	0.012	-10000	0	-10000	0	0
LRPAP1	0.031	0.011	-10000	0	-10000	0	0
FYN	0.026	0.062	-10000	0	-0.51	2	2
ITGA3	-0.004	0.12	-10000	0	-0.51	7	7
RELN/VLDLR/Fyn	0.016	0.1	-10000	0	-0.32	11	11
MAPK8IP1/MKK7/MAP3K11/JNK1	0.081	0.051	-10000	0	-0.25	1	1
AKT1	-0.024	0.11	-10000	0	-0.39	9	9
MAP2K7	0.03	0.019	-10000	0	-10000	0	0
RAPGEF1	0.034	0.004	-10000	0	-10000	0	0
DAB1	0.033	0.01	-10000	0	-10000	0	0
RELN/LRP8/DAB1	0.028	0.097	-10000	0	-0.29	12	12
LRPAP1/LRP8	0.009	0.11	-10000	0	-0.37	12	12
RELN/LRP8/DAB1/Fyn	0.037	0.11	-10000	0	-0.3	13	13
DAB1/alpha3/beta1 Integrin	-0.025	0.14	-10000	0	-0.31	23	23
long-term memory	0.044	0.12	-10000	0	-0.31	13	13
DAB1/LIS1	0.012	0.13	-10000	0	-0.3	19	19
DAB1/CRLK/C3G	0	0.12	-10000	0	-0.29	19	19
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
DAB1/NCK2	0.014	0.13	-10000	0	-0.3	18	18
ARHGEF2	0.029	0.044	-10000	0	-0.51	1	1
mol:Src family inhibitors PP1 and PP2	0	0	-10000	0	-10000	0	0
GRIN2A	0.033	0.006	-10000	0	-10000	0	0
CDK5R1	0.032	0.016	-10000	0	-10000	0	0
RELN	0.03	0.017	-10000	0	-10000	0	0
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
RELN/LRP8/Fyn	0.024	0.12	-10000	0	-0.34	13	13
GRIN2A/RELN/LRP8/DAB1/Fyn	0.05	0.12	-10000	0	-0.3	13	13
MAPK8	0.033	0.007	-10000	0	-10000	0	0
RELN/VLDLR/DAB1	0.021	0.089	-10000	0	-0.29	9	9
ITGB1	0.025	0.062	-10000	0	-0.51	2	2
MAP1B	-0.072	0.17	-10000	0	-0.33	38	38
RELN/LRP8	0.023	0.1	-10000	0	-0.32	12	12
GRIN2B/RELN/LRP8/DAB1/Fyn	0.043	0.12	-10000	0	-0.32	13	13
PI3K	0.004	0.076	-10000	0	-0.3	7	7
mol:PP2	0	0	-10000	0	-10000	0	0
alpha3/beta1 Integrin	0.011	0.1	-10000	0	-0.37	9	9
RAP1A	-0.029	0.13	0.34	3	-0.44	4	7
PAFAH1B1	0.032	0.008	-10000	0	-10000	0	0
MAPK8IP1	0.032	0.014	-10000	0	-10000	0	0
CRLK/C3G	0.046	0.016	-10000	0	-10000	0	0
GRIN2B	0.024	0.062	-10000	0	-0.51	2	2
NCK2	0.034	0.005	-10000	0	-10000	0	0
neuron differentiation	0.014	0.081	-10000	0	-0.33	3	3
neuron adhesion	-0.047	0.14	0.32	4	-0.46	6	10
LRP8	-0.013	0.15	-10000	0	-0.51	12	12
GSK3B	-0.003	0.12	-10000	0	-0.5	5	5
RELN/VLDLR/DAB1/Fyn	0.027	0.098	-10000	0	-0.28	11	11
MAP3K11	0.034	0	-10000	0	-10000	0	0
RELN/VLDLR/DAB1/P13K	-0.018	0.1	-10000	0	-0.36	9	9
CDK5	0.034	0.004	-10000	0	-10000	0	0
MAPT	0	0.013	-10000	0	-10000	0	0
neuron migration	0	0.13	-10000	0	-0.44	5	5
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1	0.014	0.081	-10000	0	-0.33	3	3
RELN/VLDLR	0.003	0.14	-10000	0	-0.32	19	19

Nongenotropic Androgen signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.006	0.03	-10000	0	-0.37	1	1
GNB1/GNG2	0.044	0.057	-10000	0	-0.29	3	3
regulation of S phase of mitotic cell cycle	-0.002	0.053	-10000	0	-0.24	5	5
GNAO1	0.032	0.011	-10000	0	-10000	0	0
HRAS	0.029	0.045	-10000	0	-0.52	1	1
SHBG/T-DHT	0.022	0.006	-10000	0	-10000	0	0
PELP1	0.032	0.008	-10000	0	-10000	0	0
AKT1	0.004	0.043	-10000	0	-0.37	2	2
MAP2K1	-0.02	0.073	0.18	1	-0.28	4	5
T-DHT/AR	0.01	0.057	-10000	0	-0.37	3	3
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
mol:GTP	-0.001	0.002	-10000	0	-0.006	17	17
GNAI2	0.029	0.018	-10000	0	-10000	0	0
GNAI3	0.033	0.007	-10000	0	-10000	0	0
GNAI1	0.001	0.13	-10000	0	-0.51	9	9
mol:GDP	-0.016	0.061	-10000	0	-0.27	6	6
cell proliferation	-0.047	0.15	-10000	0	-0.42	18	18
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
FOS	-0.08	0.26	-10000	0	-0.8	16	16
mol:Ca2+	-0.006	0.024	-10000	0	-0.067	16	16
MAPK3	-0.035	0.11	-10000	0	-0.3	16	16
MAPK1	-0.024	0.13	-10000	0	-0.52	6	6
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
mol:IP3	0	0.001	-10000	0	-0.004	16	16
cAMP biosynthetic process	-0.001	0.016	-10000	0	-10000	0	0
GNG2	0.034	0.005	-10000	0	-10000	0	0
potassium channel inhibitor activity	0	0.001	-10000	0	-0.004	16	16
HRAS/GTP	0.029	0.069	-10000	0	-0.28	4	4
actin cytoskeleton reorganization	0.009	0.057	-10000	0	-0.26	5	5
SRC	0.031	0.012	-10000	0	-10000	0	0
voltage-gated calcium channel activity	0	0.001	-10000	0	-0.004	16	16
PI3K	0.005	0.065	-10000	0	-0.31	5	5
apoptosis	0.042	0.16	0.43	18	-10000	0	18
T-DHT/AR/PELP1	0.028	0.055	-10000	0	-0.32	3	3
HRAS/GDP	0.031	0.09	-10000	0	-0.29	5	5
CREB1	-0.046	0.17	-10000	0	-0.46	18	18
RAC1-CDC42/GTP	0.014	0.062	-10000	0	-0.26	5	5
AR	0.013	0.08	-10000	0	-0.51	3	3
GNB1	0.033	0.007	-10000	0	-10000	0	0
RAF1	0	0.072	-10000	0	-0.28	4	4
RAC1-CDC42/GDP	0.054	0.091	-10000	0	-0.31	3	3
T-DHT/AR/PELP1/Src	0.04	0.058	-10000	0	-0.29	3	3
MAP2K2	-0.018	0.072	0.18	1	-0.28	4	5
T-DHT/AR/PELP1/Src/PI3K	-0.002	0.053	-10000	0	-0.24	5	5
GNAZ	0.005	0.11	-10000	0	-0.51	7	7
SHBG	0.032	0.009	-10000	0	-10000	0	0
Gi family/GNB1/GNG2/GDP	-0.012	0.16	-10000	0	-0.53	9	9
mol:T-DHT	0	0.001	-10000	0	-0.002	12	12
RAC1	0.033	0.006	-10000	0	-10000	0	0
GNRH1	-0.013	0.083	-10000	0	-0.37	8	8
Gi family/GTP	-0.013	0.095	-10000	0	-0.25	17	17
CDC42	0.034	0.005	-10000	0	-10000	0	0

E-cadherin signaling in the nascent adherens junction

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	-0.028	0.14	-10000	0	-0.39	15	15
KLHL20	-0.007	0.11	0.26	1	-0.3	10	11
CYFIP2	0.026	0.047	-10000	0	-0.51	1	1
Rac1/GDP	-0.001	0.1	0.25	1	-0.28	7	8
ENAH	-0.028	0.14	-10000	0	-0.39	17	17
AP1M1	0.033	0.007	-10000	0	-10000	0	0
RAP1B	0.033	0.007	-10000	0	-10000	0	0
RAP1A	0.026	0.062	-10000	0	-0.51	2	2
CTNNB1	0.03	0.016	-10000	0	-10000	0	0
CDC42/GTP	0.01	0.078	-10000	0	-10000	0	0
ABI1/Sra1/Nap1	-0.032	0.059	-10000	0	-0.2	10	10
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin	0.056	0.084	-10000	0	-0.29	7	7
RAPGEF1	-0.02	0.13	-10000	0	-0.36	14	14
CTNND1	0.017	0.096	-10000	0	-0.51	5	5
regulation of calcium-dependent cell-cell adhesion	-0.023	0.15	-10000	0	-0.38	20	20
CRK	-0.017	0.14	-10000	0	-0.38	15	15
E-cadherin/gamma catenin/alpha catenin	0.019	0.12	-10000	0	-0.33	16	16
alphaE/beta7 Integrin	0.047	0.013	-10000	0	-10000	0	0
IQGAP1	0.034	0.005	-10000	0	-10000	0	0
NCKAP1	0.027	0.047	-10000	0	-0.51	1	1
Rap1/GTP/I-afadin	0.055	0.044	-10000	0	-0.29	2	2
DLG1	-0.019	0.11	-10000	0	-0.37	11	11
ChemicalAbstracts:7440-70-2	0	0	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	-0.01	0.044	-10000	0	-0.25	2	2
MLLT4	0.033	0.006	-10000	0	-10000	0	0
ARF6/GTP/NME1/Tiam1	0.057	0.045	-10000	0	-0.29	2	2
PI3K	-0.011	0.057	-10000	0	-0.33	2	2
ARF6	0.026	0.062	-10000	0	-0.51	2	2
mol:Ca2+	0	0	-10000	0	-10000	0	0
E-cadherin/gamma catenin	0	0.14	-10000	0	-0.39	16	16
TIAM1	0.034	0.005	-10000	0	-10000	0	0
E-cadherin(dimer)/Ca2+	0.041	0.097	-10000	0	-0.27	12	12
AKT1	0.006	0.057	0.15	2	-0.21	4	6
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
CDH1	0.007	0.11	-10000	0	-0.51	7	7
RhoA/GDP	0.004	0.1	0.25	1	-0.28	6	7
actin cytoskeleton organization	-0.002	0.082	0.22	1	-0.21	10	11
CDC42/GDP	0.002	0.11	0.25	1	-0.28	7	8
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin	-0.015	0.1	-10000	0	-0.27	20	20
ITGB7	0.034	0.005	-10000	0	-10000	0	0
RAC1	0.033	0.006	-10000	0	-10000	0	0
E-cadherin/beta catenin/alpha catenin/p120 catenin	0.045	0.1	-10000	0	-0.29	12	12
E-cadherin/Ca2+/beta catenin/alpha catenin	0.036	0.071	-10000	0	-0.27	7	7
mol:GDP	-0.016	0.11	0.25	1	-0.32	7	8
CDC42/GTP/IQGAP1	0.044	0.01	-10000	0	-10000	0	0
JUP	-0.002	0.13	-10000	0	-0.51	10	10
p120 catenin/RhoA/GDP	0.007	0.11	0.26	1	-0.28	7	8
RAC1/GTP/IQGAP1	0.044	0.01	-10000	0	-10000	0	0
PIP5K1C/AP1M1	0.044	0.037	-10000	0	-0.37	1	1
RHOA	0.031	0.011	-10000	0	-10000	0	0
CDC42	0.034	0.005	-10000	0	-10000	0	0
CTNNA1	0.032	0.008	-10000	0	-10000	0	0
positive regulation of S phase of mitotic cell cycle	-0.007	0.077	0.16	1	-0.23	12	13
NME1	0.034	0.003	-10000	0	-10000	0	0
clathrin coat assembly	0	0	-10000	0	-10000	0	0
TJP1	-0.03	0.14	-10000	0	-0.4	16	16
regulation of cell-cell adhesion	-0.002	0.062	-10000	0	-10000	0	0
WASF2	-0.004	0.047	-10000	0	-0.14	6	6
Rap1/GTP	0.009	0.087	-10000	0	-10000	0	0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin	0.046	0.12	-10000	0	-0.29	16	16
CCND1	-0.011	0.095	0.19	1	-0.29	12	13
VAV2	-0.043	0.23	-10000	0	-0.65	13	13
RAP1/GDP	0.013	0.096	0.27	1	-10000	0	1
adherens junction assembly	-0.029	0.14	-10000	0	-0.39	16	16
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
ABI1	0.033	0.007	-10000	0	-10000	0	0
PIP5K1C	0.028	0.046	-10000	0	-0.51	1	1
regulation of heterotypic cell-cell adhesion	0.025	0.11	-10000	0	-0.28	16	16
E-cadherin/beta catenin	-0.004	0.083	-10000	0	-0.35	8	8
mol:GTP	0	0	-10000	0	-10000	0	0
SRC	-0.031	0.14	-10000	0	-0.4	16	16
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
Rac1/GTP	-0.064	0.16	-10000	0	-0.5	12	12
E-cadherin/beta catenin/alpha catenin	0.041	0.083	-10000	0	-0.32	7	7
ITGAE	0.032	0.008	-10000	0	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.024	0.15	-10000	0	-0.39	20	20

Plasma membrane estrogen receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	0.048	0.08	-10000	0	-0.27	7	7
ER alpha/Gai/GDP/Gbeta gamma	-0.038	0.18	-10000	0	-0.48	14	14
AKT1	-0.041	0.22	-10000	0	-0.82	10	10
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
E2/ER alpha (dimer)/PELP1/Src/PI3K	-0.04	0.22	-10000	0	-0.83	10	10
mol:Ca2+	-0.029	0.11	-10000	0	-0.38	7	7
IGF1R	-0.006	0.14	-10000	0	-0.51	11	11
E2/ER alpha (dimer)/Striatin	0.014	0.086	-10000	0	-0.31	9	9
SHC1	0.032	0.008	-10000	0	-10000	0	0
apoptosis	0.039	0.21	0.77	10	-10000	0	10
RhoA/GTP	-0.006	0.082	-10000	0	-0.25	14	14
E2/ER alpha (dimer)/PELP1/Src/p130 Cas	-0.004	0.17	-10000	0	-0.48	10	10
regulation of stress fiber formation	0.025	0.099	0.35	3	-0.28	1	4
E2/ERA-ERB (dimer)	0.02	0.077	-10000	0	-0.31	7	7
KRAS	0.017	0.086	-10000	0	-0.51	4	4
G13/GTP	0.018	0.075	-10000	0	-0.28	8	8
pseudopodium formation	-0.025	0.099	0.28	1	-0.35	3	4
E2/ER alpha (dimer)/PELP1	0.019	0.077	-10000	0	-0.31	7	7
GRB2	0.034	0.005	-10000	0	-10000	0	0
GNG2	0.034	0.005	-10000	0	-10000	0	0
GNAO1	0.032	0.011	-10000	0	-10000	0	0
HRAS	0.029	0.045	-10000	0	-0.51	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
mol:NO	-0.024	0.16	-10000	0	-0.52	11	11
E2/ER beta (dimer)	0.024	0.007	-10000	0	-10000	0	0
mol:GDP	-0.011	0.098	-10000	0	-0.4	7	7
mol:NADP	-0.024	0.16	-10000	0	-0.52	11	11
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
mol:IP3	-0.035	0.11	-10000	0	-0.38	8	8
IGF-1R heterotetramer	-0.006	0.14	-10000	0	-0.51	11	11
PLCB1	-0.03	0.11	-10000	0	-0.34	12	12
PLCB2	-0.023	0.11	-10000	0	-0.4	8	8
IGF1	-0.048	0.18	-10000	0	-0.51	20	20
mol:L-citrulline	-0.024	0.16	-10000	0	-0.52	11	11
RHOA	0.031	0.011	-10000	0	-10000	0	0
Gai/GDP	-0.051	0.23	-10000	0	-0.65	16	16
JNK cascade	0.024	0.007	-10000	0	-10000	0	0
BCAR1	0.033	0.008	-10000	0	-10000	0	0
ESR2	0.033	0.011	-10000	0	-10000	0	0
GNAQ	0	0	-10000	0	-10000	0	0
ESR1	0	0.12	-10000	0	-0.51	7	7
Gq family/GDP/Gbeta gamma	-0.04	0.2	-10000	0	-0.55	17	17
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1	0.031	0.062	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC	-0.005	0.16	-10000	0	-0.46	11	11
GNAZ	0.005	0.11	-10000	0	-0.51	7	7
E2/ER alpha (dimer)	0.001	0.083	-10000	0	-0.37	7	7
STRN	0.021	0.076	-10000	0	-0.51	3	3
GNAL	0.009	0.098	-10000	0	-0.51	5	5
PELP1	0.032	0.008	-10000	0	-10000	0	0
MAPK11	0.017	0.007	-10000	0	-10000	0	0
GNAI2	0.029	0.018	-10000	0	-10000	0	0
GNAI3	0.033	0.007	-10000	0	-10000	0	0
GNAI1	0.001	0.13	-10000	0	-0.51	9	9
HBEGF	-0.06	0.2	0.32	4	-0.52	17	21
cAMP biosynthetic process	0.005	0.081	-10000	0	-0.26	12	12
SRC	-0.03	0.18	0.28	2	-0.52	10	12
PI3K	0.004	0.076	-10000	0	-0.3	7	7
GNB1	0.033	0.007	-10000	0	-10000	0	0
G13/GDP/Gbeta gamma	0.021	0.1	-10000	0	-0.35	8	8
SOS1	0.033	0.006	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1	-0.068	0.15	-10000	0	-0.4	17	17
Gs family/GTP	0.012	0.085	-10000	0	-0.26	12	12
EntrezGene:2778	0	0	-10000	0	-10000	0	0
RAS family/GTP	0.038	0.073	-10000	0	-0.29	6	6
vasodilation	-0.022	0.16	-10000	0	-0.5	11	11
mol:DAG	-0.035	0.11	-10000	0	-0.38	8	8
Gs family/GDP/Gbeta gamma	-0.01	0.1	-10000	0	-0.34	9	9
MSN	-0.028	0.1	0.29	1	-0.38	3	4
Gq family/GTP	-0.021	0.12	-10000	0	-0.34	15	15
mol:PI-3-4-5-P3	-0.037	0.21	-10000	0	-0.79	10	10
NRAS	0.026	0.047	-10000	0	-0.51	1	1
mol:E2	0	0	-10000	0	-10000	0	0
cell adhesion	0.022	0.16	0.5	11	-10000	0	11
GRB2/SOS1	0.048	0.012	-10000	0	-10000	0	0
RhoA/GDP	0.003	0.1	-10000	0	-0.38	7	7
NOS3	-0.026	0.17	-10000	0	-0.55	11	11
GNA11	0.026	0.062	-10000	0	-0.51	2	2
MAPKKK cascade	-0.005	0.18	0.37	1	-0.58	10	11
E2/ER alpha (dimer)/PELP1/Src	-0.011	0.17	-10000	0	-0.48	12	12
ruffle organization	-0.025	0.099	0.28	1	-0.35	3	4
ROCK2	-0.014	0.092	0.3	1	-10000	0	1
GNA14	0.016	0.079	-10000	0	-0.51	3	3
GNA15	-0.007	0.14	-10000	0	-0.51	11	11
GNA13	0.03	0.045	-10000	0	-0.51	1	1
MMP9	-0.04	0.2	0.34	6	-0.53	13	19
MMP2	-0.046	0.18	0.32	3	-0.52	12	15

Sphingosine 1-phosphate (S1P) pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.033	0.01	-10000	0	-10000	0	0
SPHK1	-0.005	0.13	-10000	0	-0.51	10	10
GNAI2	0.029	0.018	-10000	0	-10000	0	0
mol:S1P	-0.028	0.13	-10000	0	-0.37	16	16
GNAO1	0.032	0.011	-10000	0	-10000	0	0
mol:Sphinganine-1-P	-0.009	0.091	-10000	0	-0.37	9	9
growth factor activity	0	0	-10000	0	-10000	0	0
S1P/S1P2/G12/G13	0.007	0.12	-10000	0	-0.28	17	17
GNAI3	0.033	0.007	-10000	0	-10000	0	0
G12/G13	0.045	0.037	-10000	0	-0.37	1	1
S1PR3	0	0	-10000	0	-10000	0	0
S1PR2	0	0	-10000	0	-10000	0	0
EDG1	0	0	-10000	0	-10000	0	0
S1P1/S1P	-0.031	0.12	-10000	0	-0.32	16	16
S1PR5	0	0	-10000	0	-10000	0	0
S1PR4	0	0	-10000	0	-10000	0	0
GNAI1	0.001	0.13	-10000	0	-0.51	9	9
S1P/S1P5/G12	-0.013	0.12	-10000	0	-0.3	16	16
S1P/S1P3/Gq	-0.036	0.16	-10000	0	-0.43	16	16
S1P/S1P4/Gi	-0.022	0.13	0.21	1	-0.39	11	12
GNAQ	0	0	-10000	0	-10000	0	0
GNAZ	0.005	0.11	-10000	0	-0.51	7	7
GNA14	0.016	0.079	-10000	0	-0.51	3	3
GNA15	-0.007	0.14	-10000	0	-0.51	11	11
GNA12	0.033	0.008	-10000	0	-10000	0	0
GNA13	0.03	0.045	-10000	0	-0.51	1	1
GNA11	0.026	0.062	-10000	0	-0.51	2	2
ABCC1	-0.023	0.15	-10000	0	-0.51	12	12

Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin	0.041	0.062	-10000	0	-0.27	5	5
RGS9BP	-0.002	0.12	-10000	0	-0.51	7	7
mol:GTP	0	0	-10000	0	-10000	0	0
GRK1	0	0	-10000	0	-10000	0	0
mol:Na +	-0.004	0.1	-10000	0	-0.32	14	14
mol:ADP	0.004	0.031	-10000	0	-0.37	1	1
GNAT2	0.028	0.045	-10000	0	-0.51	1	1
RGS9-1/Gbeta5/R9AP	0.013	0.12	-10000	0	-0.32	15	15
mol:GDP	0	0	-10000	0	-10000	0	0
PDE6H/GNAT2/GTP	0.039	0.033	-10000	0	-0.31	1	1
GRK7	0.021	0.047	-10000	0	-0.51	1	1
CNGB3	-0.019	0.14	-10000	0	-0.51	11	11
Cone Metarhodopsin II/X-Arrestin	0.025	0.005	-10000	0	-10000	0	0
mol:Ca2+	-0.007	0.1	-10000	0	-0.29	14	14
Cone PDE6	0.027	0.12	-10000	0	-0.28	17	17
Cone Metarhodopsin II	0.014	0.026	-10000	0	-0.28	1	1
Na + (4 Units)	0.009	0.1	-10000	0	-0.29	14	14
GNAT2/GDP	0.021	0.11	-10000	0	-0.28	16	16
GNB5	0.02	0.086	-10000	0	-0.51	4	4
mol:GMP (4 units)	0.021	0.06	0.19	9	-0.29	3	12
Cone Transducin	0.045	0.066	-10000	0	-0.29	5	5
SLC24A2	0.031	0.013	-10000	0	-10000	0	0
GNB3/GNGT2	0.035	0.068	-10000	0	-0.37	4	4
GNB3	0.032	0.01	-10000	0	-10000	0	0
GNAT2/GTP	0.021	0.032	-10000	0	-0.37	1	1
CNGA3	0.018	0.077	-10000	0	-0.51	3	3
ARR3	0.033	0.006	-10000	0	-10000	0	0
absorption of light	0	0	-10000	0	-10000	0	0
cGMP/Cone CNG Channel	-0.003	0.1	-10000	0	-0.32	14	14
mol:Pi	0.013	0.12	-10000	0	-0.32	15	15
Cone CNG Channel	0.015	0.11	-10000	0	-0.27	17	17
mol:all-trans-retinal	0	0	-10000	0	-10000	0	0
mol:K +	0.031	0.013	-10000	0	-10000	0	0
RGS9	0.015	0.089	-10000	0	-0.51	4	4
PDE6C	0.026	0.062	-10000	0	-0.51	2	2
GNGT2	0.019	0.087	-10000	0	-0.51	4	4
mol:cGMP (4 units)	0	0	-10000	0	-10000	0	0
PDE6H	0.032	0.008	-10000	0	-10000	0	0

Cellular roles of Anthrax toxin

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
ANTXR1	0.011	0.097	-10000	0	-0.51	5	5
ANTXR2	0.024	0.063	-10000	0	-0.51	2	2
negative regulation of myeloid dendritic cell antigen processing and presentation	-0.004	0.014	-10000	0	-0.069	7	7
monocyte activation	-0.019	0.13	-10000	0	-0.41	14	14
MAP2K2	-0.001	0.11	-10000	0	-0.58	5	5
MAP2K1	-0.007	0.013	-10000	0	-10000	0	0
MAP2K7	-0.006	0.012	-10000	0	-10000	0	0
MAP2K6	-0.015	0.048	-10000	0	-0.27	5	5
CYAA	-0.018	0.055	-10000	0	-0.27	7	7
MAP2K4	-0.008	0.029	-10000	0	-0.33	1	1
IL1B	-0.058	0.11	-10000	0	-0.28	28	28
Channel	0.021	0.07	-10000	0	-0.28	7	7
NLRP1	-0.012	0.037	-10000	0	-0.21	4	4
CALM1	0.033	0.007	-10000	0	-10000	0	0
negative regulation of phagocytosis	0.003	0.058	-10000	0	-0.39	3	3
mol:Ca2+	0	0	-10000	0	-10000	0	0
regulation of endothelial cell proliferation	0.004	0.014	0.069	7	-10000	0	7
MAPK3	-0.007	0.013	-10000	0	-10000	0	0
MAPK1	-0.006	0.032	0.13	2	-0.33	1	3
PGR	-0.009	0.034	0.13	1	-0.27	2	3
PA/Cellular Receptors	0.021	0.076	-10000	0	-0.31	7	7
apoptosis	-0.004	0.014	-10000	0	-0.069	7	7
LOC728358	0	0	-10000	0	-10000	0	0
Lethal toxin (unfolded)	0.021	0.066	-10000	0	-0.27	7	7
macrophage activation	-0.008	0.03	0.12	2	-0.32	1	3
TNF	0.026	0.048	-10000	0	-0.51	1	1
VCAM1	-0.021	0.13	-10000	0	-0.41	14	14
platelet activation	0.003	0.058	-10000	0	-0.39	3	3
MAPKKK cascade	0.004	0.032	0.17	2	-0.13	1	3
IL18	-0.031	0.088	-10000	0	-0.3	14	14
negative regulation of macrophage activation	-0.004	0.014	-10000	0	-0.069	7	7
LEF	-0.004	0.014	-10000	0	-0.069	7	7
CASP1	-0.009	0.038	-10000	0	-0.11	14	14
mol:cAMP	0.003	0.058	-10000	0	-0.39	3	3
necrosis	-0.004	0.014	-10000	0	-0.069	7	7
intracellular pH reduction	0	0	-10000	0	-10000	0	0
PAGA	0	0	-10000	0	-10000	0	0
Edema toxin (unfolded)	0.021	0.066	-10000	0	-0.27	7	7
mol:Epigallocatechin-3-gallate (EGCG)	0	0	-10000	0	-10000	0	0

p75(NTR)-mediated signaling

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
Sortilin/TRAF6	0.033	0.075	-10000	0	-0.37	5	5
Necdin/E2F1	-0.002	0.12	-10000	0	-0.37	15	15
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E	0.037	0.092	-10000	0	-0.27	10	10
NGF (dimer)/p75(NTR)/BEX1	0.02	0.048	-10000	0	-0.31	1	1
NT-4/5 (dimer)/p75(NTR)	0.018	0.022	-10000	0	-10000	0	0
IKBKB	0.031	0.011	-10000	0	-10000	0	0
AKT1	0.076	0.12	0.37	1	-0.31	6	7
IKBKG	0.033	0.006	-10000	0	-10000	0	0
BDNF	-0.023	0.15	-10000	0	-0.51	12	12
MGDIs/NGR/p75(NTR)/LINGO1	0.023	0.096	-10000	0	-0.32	9	9
FURIN	0.015	0.097	-10000	0	-0.51	5	5
proBDNF (dimer)/p75(NTR)/Sortilin	0.007	0.11	-10000	0	-0.32	14	14
LINGO1	0.026	0.03	-10000	0	-10000	0	0
Sortilin/TRAF6/NRIF	0.017	0.08	-10000	0	-0.28	9	9
proBDNF (dimer)	-0.023	0.15	-10000	0	-0.51	12	12
NTRK1	0.032	0.011	-10000	0	-10000	0	0
RTN4R	0	0.13	-10000	0	-0.51	9	9
neuron apoptosis	-0.035	0.14	-10000	0	-0.55	7	7
IRAK1	0.034	0.005	-10000	0	-10000	0	0
SHC1	0.011	0.018	-10000	0	-10000	0	0
ARHGDIA	0.033	0.006	-10000	0	-10000	0	0
RhoA/GTP	0.023	0.008	-10000	0	-10000	0	0
Gamma Secretase	0.068	0.086	-10000	0	-0.33	5	5
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1	0.037	0.076	-10000	0	-0.35	4	4
MAGEH1	0.02	0.077	-10000	0	-0.51	3	3
proNGF (dimer)/p75(NTR)/Sortilin/Necdin	0.003	0.12	-10000	0	-0.3	18	18
Mammalian IAPs/DIABLO	0.022	0.1	-10000	0	-0.29	14	14
proNGF (dimer)	0	0	-10000	0	-10000	0	0
MAGED1	0.018	0.087	-10000	0	-0.51	4	4
APP	0.011	0.1	-10000	0	-0.51	6	6
NT-4/5 (dimer)	0	0	-10000	0	-10000	0	0
ZNF274	0.029	0.044	-10000	0	-0.51	1	1
RhoA/GDP/RHOGDI	0.033	0.028	-10000	0	-10000	0	0
NGF	0	0	-10000	0	-10000	0	0
cell cycle arrest	-0.013	0.034	-10000	0	-0.26	2	2
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK	0.015	0.047	-10000	0	-0.25	4	4
NT-4/5 (dimer)/p75(NTR)/TRAF6	0.029	0.057	-10000	0	-0.32	3	3
NCSTN	0.032	0.008	-10000	0	-10000	0	0
mol:GTP	0.032	0.04	-10000	0	-0.31	1	1
PSENEN	0.031	0.011	-10000	0	-10000	0	0
mol:ceramide	0.008	0.038	-10000	0	-0.28	2	2
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs	-0.003	0.047	-10000	0	-0.2	7	7
p75(NTR)/beta APP	0.019	0.088	-10000	0	-0.38	6	6
BEX1	0.011	0.059	-10000	0	-0.51	1	1
mol:GDP	-0.007	0.01	-10000	0	-10000	0	0
NGF (dimer)	0.003	0.13	-10000	0	-0.3	24	24
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI	0.036	0.097	-10000	0	-0.29	9	9
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
RAC1/GTP	0.031	0.023	-10000	0	-10000	0	0
MYD88	0.031	0.01	-10000	0	-10000	0	0
CHUK	0.03	0.044	-10000	0	-0.51	1	1
NGF (dimer)/p75(NTR)/PKA	0.032	0.04	-10000	0	-0.31	1	1
RHOB	0.018	0.077	-10000	0	-0.51	3	3
RHOA	0.031	0.011	-10000	0	-10000	0	0
MAGE-G1/E2F1	0.047	0.018	-10000	0	-10000	0	0
NT3 (dimer)	-0.006	0.12	-10000	0	-0.51	7	7
TP53	-0.049	0.1	-10000	0	-0.28	18	18
PRDM4	0.009	0.041	-10000	0	-0.29	2	2
BDNF (dimer)	-0.12	0.2	-10000	0	-0.34	61	61
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
SORT1	0.025	0.062	-10000	0	-0.51	2	2
activation of caspase activity	0.032	0.089	-10000	0	-0.27	10	10
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6	0.039	0.07	-10000	0	-0.29	5	5
RHOC	0.033	0.007	-10000	0	-10000	0	0
XIAP	0	0	-10000	0	-10000	0	0
MAPK10	-0.037	0.1	0.3	1	-0.33	8	9
DIABLO	0.034	0.003	-10000	0	-10000	0	0
SMPD2	0.008	0.039	-10000	0	-0.29	2	2
APH1B	0.03	0.044	-10000	0	-0.51	1	1
APH1A	0.015	0.096	-10000	0	-0.51	5	5
proNGF (dimer)/p75(NTR)/Sortilin	0.03	0.049	-10000	0	-0.31	2	2
PSEN1	0.03	0.044	-10000	0	-0.51	1	1
APAF-1/Pro-Caspase 9	0.046	0.035	-10000	0	-0.37	1	1
NT3 (dimer)/p75(NTR)	0.007	0.092	-10000	0	-0.37	7	7
MAPK8	-0.026	0.1	0.3	1	-0.32	7	8
MAPK9	-0.03	0.099	0.3	1	-0.34	6	7
APAF1	0.031	0.044	-10000	0	-0.51	1	1
NTF3	-0.006	0.12	-10000	0	-0.51	7	7
NTF4	0	0	-10000	0	-10000	0	0
NDN	-0.033	0.17	-10000	0	-0.51	17	17
RAC1/GDP	0.025	0.005	-10000	0	-10000	0	0
RhoA-B-C/GDP	0.039	0.065	-10000	0	-0.25	4	4
p75 CTF/Sortilin/TRAF6/NRIF	0.058	0.083	-10000	0	-0.29	7	7
RhoA-B-C/GTP	0.032	0.04	-10000	0	-0.31	1	1
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	0.02	0.12	-10000	0	-0.28	18	18
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6	0.014	0.12	-10000	0	-0.3	17	17
PRKACB	0.029	0.045	-10000	0	-0.51	1	1
proBDNF (dimer)/p75 ECD	0	0.12	-10000	0	-0.37	13	13
ChemicalAbstracts:86-01-1	0	0	-10000	0	-10000	0	0
BIRC3	-0.026	0.16	-10000	0	-0.51	14	14
BIRC2	0.033	0.01	-10000	0	-10000	0	0
neuron projection morphogenesis	-0.03	0.066	-10000	0	-0.26	4	4
BAD	-0.035	0.1	0.3	1	-0.33	7	8
RIPK2	0.027	0.046	-10000	0	-0.51	1	1
NGFR	0.023	0.034	-10000	0	-10000	0	0
CYCS	0	0.065	-10000	0	-0.32	5	5
ADAM17	0.028	0.046	-10000	0	-0.51	1	1
NGF (dimer)/p75(NTR)/TRAF6/RIP2	0.04	0.065	-10000	0	-0.3	4	4
BCL2L11	-0.035	0.1	0.3	1	-0.33	7	8
BDNF (dimer)/p75(NTR)	-0.005	0.12	-10000	0	-0.38	12	12
PI3K	0.004	0.065	-10000	0	-0.29	5	5
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1	0.046	0.053	-10000	0	-0.29	2	2
NDNL2	0.034	0.004	-10000	0	-10000	0	0
YWHAE	0.032	0.008	-10000	0	-10000	0	0
PRKCI	-0.004	0.1	-10000	0	-0.51	6	6
NGF (dimer)/p75(NTR)	0.018	0.022	-10000	0	-10000	0	0
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE	0.037	0.08	-10000	0	-0.34	5	5
TRAF6	0.023	0.075	-10000	0	-0.51	3	3
RAC1	0.033	0.006	-10000	0	-10000	0	0
PRKCZ	0	0	-10000	0	-10000	0	0
PLG	0.033	0.011	-10000	0	-10000	0	0
oligodendrocyte cell fate commitment	0	0	-10000	0	-10000	0	0
CASP6	-0.015	0.088	-10000	0	-0.28	14	14
SQSTM1	0.029	0.019	-10000	0	-10000	0	0
NGFRAP1	0.004	0.12	-10000	0	-0.51	8	8
CASP3	-0.036	0.099	0.3	1	-0.32	7	8
E2F1	0.032	0.008	-10000	0	-10000	0	0
CASP9	0.033	0.006	-10000	0	-10000	0	0
IKK complex	0.059	0.071	-10000	0	-10000	0	0
NGF (dimer)/TRKA	0.024	0.008	-10000	0	-10000	0	0
MMP7	-0.044	0.19	-10000	0	-0.51	22	22
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	0.048	0.077	-10000	0	-0.28	6	6
MMP3	-0.13	0.22	-10000	0	-0.51	39	39
APAF-1/Caspase 9	-0.024	0.087	-10000	0	-0.43	2	2

Ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	-0.005	0.076	-10000	0	-0.37	6	6
MAP4K4	-0.007	0.11	-10000	0	-0.37	6	6
BAG4	0.028	0.014	-10000	0	-10000	0	0
PKC zeta/ceramide	-0.008	0.075	0.14	2	-0.31	5	7
NFKBIA	0.028	0.045	-10000	0	-0.51	1	1
BIRC3	-0.026	0.16	-10000	0	-0.51	14	14
BAX	0.006	0.058	-10000	0	-0.32	4	4
RIPK1	0.033	0.006	-10000	0	-10000	0	0
AKT1	0.006	0.11	0.61	4	-0.48	2	6
BAD	-0.01	0.075	-10000	0	-0.31	5	5
SMPD1	0.01	0.069	0.23	2	-0.26	4	6
RB1	-0.012	0.072	0.17	1	-0.27	7	8
FADD/Caspase 8	0.018	0.13	0.28	4	-0.36	8	12
MAP2K4	-0.017	0.083	0.2	1	-0.32	6	7
NSMAF	0.029	0.044	-10000	0	-0.51	1	1
response to UV	0	0	-10000	0	-10000	0	0
RAF1	-0.009	0.078	0.18	3	-0.35	4	7
EGF	-0.031	0.15	-10000	0	-0.51	13	13
mol:ceramide	-0.007	0.08	0.15	4	-0.33	5	9
MADD	0.033	0.007	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
mol:Free Fatty acid	-0.006	0.076	-10000	0	-0.37	6	6
ASAH1	0.023	0.062	-10000	0	-0.51	2	2
negative regulation of cell cycle	-0.012	0.071	0.17	1	-0.27	7	8
cell proliferation	-0.016	0.11	-10000	0	-0.28	17	17
BID	-0.031	0.21	-10000	0	-0.65	14	14
MAP3K1	-0.016	0.085	0.17	1	-0.29	9	10
EIF2A	0.049	0.12	0.3	11	-0.29	5	16
TRADD	0.029	0.044	-10000	0	-0.51	1	1
CRADD	0.027	0.061	-10000	0	-0.51	2	2
MAPK3	-0.005	0.073	-10000	0	-0.37	3	3
response to heat	0	0	-10000	0	-10000	0	0
MAPK1	-0.009	0.076	-10000	0	-0.37	3	3
Cathepsin D/ceramide	0.013	0.079	-10000	0	-0.31	5	5
FADD	0	0.1	0.22	3	-0.37	6	9
KSR1	-0.008	0.082	0.18	4	-0.3	6	10
MAPK8	-0.011	0.074	-10000	0	-0.38	3	3
PRKRA	-0.002	0.079	0.19	4	-0.39	3	7
PDGFA	-0.001	0.12	-10000	0	-0.51	7	7
TRAF2	0.033	0.01	-10000	0	-10000	0	0
IGF1	-0.048	0.18	-10000	0	-0.51	20	20
mol:GD3	0	0	-10000	0	-10000	0	0
ganglioside biosynthetic process	-0.007	0.079	0.15	4	-0.32	5	9
CTSD	0.033	0.007	-10000	0	-10000	0	0
regulation of nitric oxide biosynthetic process	0.048	0.011	-10000	0	-10000	0	0
response to radiation	0	0	-10000	0	-10000	0	0
ERK1/PKC delta	-0.017	0.12	-10000	0	-0.29	17	17
PRKCD	0.03	0.013	-10000	0	-10000	0	0
PRKCZ	0	0	-10000	0	-10000	0	0
mol:GW4869	0	0	-10000	0	-10000	0	0
mol:sphingosine	-0.006	0.076	-10000	0	-0.37	6	6
RelA/NF kappa B1	0.048	0.011	-10000	0	-10000	0	0
mol:glutathione	0	0	-10000	0	-10000	0	0
PAWR	0.02	0.086	-10000	0	-0.51	4	4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD	0.001	0.11	-10000	0	-0.35	8	8
TNFR1A/BAG4/TNF-alpha	0.038	0.058	-10000	0	-0.32	2	2
mol:Sphingosine-1-phosphate	-0.005	0.076	-10000	0	-0.37	6	6
MAP2K1	-0.011	0.074	-10000	0	-0.38	3	3
mol:C11AG	0	0	-10000	0	-10000	0	0
RELA	0.034	0	-10000	0	-10000	0	0
CYCS	0.013	0.061	0.17	6	-0.25	3	9
TNFRSF1A	0.021	0.075	-10000	0	-0.51	3	3
NFKB1	0.033	0.008	-10000	0	-10000	0	0
TNFR1A/BAG4	0.03	0.054	-10000	0	-0.37	2	2
EIF2AK2	-0.006	0.089	0.2	7	-0.32	6	13
TNF-alpha/TNFR1A/FAN	0.046	0.063	-10000	0	-0.32	3	3
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
CASP8	0.006	0.12	-10000	0	-0.42	8	8
MAP2K2	-0.011	0.076	-10000	0	-0.38	3	3
SMPD3	0.012	0.078	0.22	2	-0.27	6	8
TNF	0.026	0.048	-10000	0	-0.51	1	1
PKC zeta/PAR4	0.015	0.062	-10000	0	-0.37	4	4
mol:PHOSPHOCHOLINE	0.034	0.076	0.2	18	-0.36	1	19
NF kappa B1/RelA/I kappa B alpha	0.061	0.066	-10000	0	-0.27	5	5
AIFM1	0.011	0.061	0.17	6	-0.3	2	8
BCL2	-0.005	0.12	-10000	0	-0.51	7	7

Signaling mediated by p38-gamma and p38-delta

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
EEF2K	-0.017	0.049	-10000	0	-0.32	4	4
SNTA1	0.028	0.045	-10000	0	-0.51	1	1
response to hypoxia	0	0	-10000	0	-10000	0	0
STMN1	-0.02	0.055	-10000	0	-0.32	5	5
MAPK12	-0.017	0.098	0.21	4	-0.32	12	16
CCND1	-0.032	0.14	-10000	0	-0.48	12	12
p38 gamma/SNTA1	0.003	0.099	-10000	0	-0.31	11	11
MAP2K3	0.032	0.009	-10000	0	-10000	0	0
PKN1	0.033	0.007	-10000	0	-10000	0	0
G2/M transition checkpoint	-0.016	0.099	0.21	5	-0.32	12	17
MAP2K6	-0.001	0.069	0.24	2	-0.29	7	9
MAPT	0.001	0.056	0.18	1	-0.22	4	5
MAPK13	0.008	0.054	-10000	0	-0.37	3	3
hyperosmotic response	0	0	-10000	0	-10000	0	0
ZAK	0.013	0.039	-10000	0	-0.32	2	2

IL2 signaling events mediated by PI3K

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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.031	0.11	-10000	0	-0.48	1	1
UGCG	-0.001	0.15	-10000	0	-0.81	5	5
AKT1/mTOR/p70S6K/Hsp90/TERT	0.015	0.18	0.27	2	-0.51	10	12
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucosylceramide	0.001	0.15	-10000	0	-0.79	5	5
mol:DAG	-0.026	0.2	-10000	0	-0.91	7	7
CaM/Ca2+/Calcineurin A alpha-beta B1	0.001	0.2	-10000	0	-0.54	13	13
FRAP1	-0.011	0.23	-10000	0	-0.64	13	13
FOXO3	0.001	0.21	0.31	1	-0.63	10	11
AKT1	-0.001	0.23	-10000	0	-0.67	11	11
GAB2	0.032	0.014	-10000	0	-10000	0	0
SMPD1	0.006	0.13	-10000	0	-0.76	4	4
SGMS1	-0.008	0.16	-10000	0	-0.72	7	7
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	-0.01	0.059	-10000	0	-0.32	5	5
CALM1	0.033	0.007	-10000	0	-10000	0	0
cell proliferation	0.006	0.19	0.27	1	-0.61	8	9
EIF3A	0.033	0.011	-10000	0	-10000	0	0
PI3K	0.006	0.077	-10000	0	-0.38	5	5
RPS6KB1	0.009	0.067	-10000	0	-10000	0	0
mol:sphingomyelin	-0.026	0.2	-10000	0	-0.91	7	7
natural killer cell activation	0	0.002	-10000	0	-0.014	1	1
JAK3	0.035	0.008	-10000	0	-10000	0	0
PIK3R1	0.008	0.099	-10000	0	-0.51	5	5
JAK1	0.032	0.044	-10000	0	-0.51	1	1
NFKB1	0.033	0.008	-10000	0	-10000	0	0
MYC	0.012	0.25	0.43	1	-0.98	7	8
MYB	-0.085	0.35	-10000	0	-1.3	12	12
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.013	0.16	-10000	0	-0.46	11	11
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.041	0.075	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	0.015	0.16	0.25	1	-0.44	11	12
Rac1/GDP	0	0.058	-10000	0	-0.29	5	5
T cell proliferation	0.014	0.15	0.24	1	-0.42	11	12
SHC1	0.032	0.008	-10000	0	-10000	0	0
RAC1	0.033	0.006	-10000	0	-10000	0	0
positive regulation of cyclin-dependent protein kinase activity	-0.004	0.02	-10000	0	-0.066	12	12
PRKCZ	0.014	0.15	0.25	1	-0.43	11	12
NF kappa B1 p50/RelA	0.015	0.21	-10000	0	-0.54	13	13
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K	0.029	0.11	-10000	0	-0.38	5	5
HSP90AA1	0.033	0.008	-10000	0	-10000	0	0
RELA	0.034	0	-10000	0	-10000	0	0
IL2RA	-0.007	0.14	-10000	0	-0.51	11	11
IL2RB	0.018	0.088	-10000	0	-0.51	4	4
TERT	0.022	0.047	-10000	0	-0.51	1	1
E2F1	-0.01	0.12	-10000	0	-0.42	12	12
SOS1	0.033	0.008	-10000	0	-10000	0	0
RPS6	0.031	0.013	-10000	0	-10000	0	0
mol:cAMP	0.002	0.01	0.032	12	-10000	0	12
PTPN11	0.03	0.044	-10000	0	-0.51	1	1
IL2RG	0.023	0.066	-10000	0	-0.51	2	2
actin cytoskeleton organization	0.014	0.15	0.24	1	-0.42	11	12
GRB2	0.033	0.007	-10000	0	-10000	0	0
IL2	0.034	0.009	-10000	0	-10000	0	0
PIK3CA	0.01	0.062	-10000	0	-0.51	2	2
Rac1/GTP	0.012	0.065	-10000	0	-0.28	5	5
LCK	-0.003	0.13	-10000	0	-0.51	10	10
BCL2	-0.03	0.26	-10000	0	-0.75	14	14

Glypican 2 network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MDK	0.005	0.11	-9999	-0.51	7	7
GPC2	0	0	-9999	-10000	0	0
GPC2/Midkine	0.003	0.083	-9999	-0.37	7	7
neuron projection morphogenesis	0.003	0.083	-9999	-0.37	7	7

Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.031	0.012	-10000	0	-10000	0	0
RAS family/GTP/Tiam1	-0.004	0.08	-10000	0	-0.3	6	6
NT3 (dimer)/TRKC	0.014	0.09	-10000	0	-0.37	7	7
NT3 (dimer)/TRKB	-0.087	0.17	-10000	0	-0.34	45	45
SHC/Grb2/SOS1/GAB1/PI3K	0.001	0.066	-10000	0	-0.27	6	6
RAPGEF1	0.034	0.004	-10000	0	-10000	0	0
BDNF	-0.023	0.15	-10000	0	-0.51	12	12
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
DYNLT1	0.034	0.005	-10000	0	-10000	0	0
NTRK1	0.032	0.011	-10000	0	-10000	0	0
NTRK2	-0.14	0.24	-10000	0	-0.51	45	45
NTRK3	0.033	0.013	-10000	0	-10000	0	0
NT-4/5 (dimer)/TRKB	-0.078	0.16	-10000	0	-0.32	45	45
neuron apoptosis	0.027	0.15	0.34	10	-0.25	1	11
SHC 2-3/Grb2	-0.029	0.16	-10000	0	-0.36	10	10
SHC1	0.032	0.008	-10000	0	-10000	0	0
SHC2	-0.025	0.14	0.24	1	-0.41	8	9
SHC3	-0.039	0.14	0.24	1	-0.38	13	14
STAT3 (dimer)	-0.001	0.11	-10000	0	-0.36	12	12
NT3 (dimer)/TRKA	0.021	0.087	-10000	0	-0.32	7	7
RIN/GDP	0.054	0.079	0.27	4	-10000	0	4
GIPC1	0.029	0.044	-10000	0	-0.51	1	1
KRAS	0.017	0.086	-10000	0	-0.51	4	4
DNAJA3	0.032	0.061	0.24	2	-10000	0	2
RIN/GTP	0.021	0.032	-10000	0	-0.37	1	1
CCND1	-0.042	0.21	-10000	0	-0.77	12	12
MAGED1	0.018	0.087	-10000	0	-0.51	4	4
PTPN11	0.031	0.044	-10000	0	-0.51	1	1
RICS	0	0	-10000	0	-10000	0	0
NT-4/5 (dimer)	0	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1	0.062	0.022	-10000	0	-10000	0	0
GRB2	0.034	0.005	-10000	0	-10000	0	0
NGF (dimer)/TRKA/MATK	0.039	0.034	-10000	0	-0.31	1	1
TRKA/NEDD4-2	0.042	0.038	-10000	0	-0.37	1	1
ELMO1	0.029	0.045	-10000	0	-0.51	1	1
RhoG/GTP/ELMO1/DOCK1	0.04	0.032	-10000	0	-0.31	1	1
NGF	0	0	-10000	0	-10000	0	0
HRAS	0.029	0.045	-10000	0	-0.51	1	1
DOCK1	0.033	0.007	-10000	0	-10000	0	0
GAB2	0.032	0.014	-10000	0	-10000	0	0
RIT2	0.029	0.044	-10000	0	-0.51	1	1
RIT1	0.019	0.077	-10000	0	-0.51	3	3
FRS2	0.033	0.007	-10000	0	-10000	0	0
DNM1	0.028	0.046	-10000	0	-0.51	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.032	0.008	-10000	0	-10000	0	0
SH2B1 (homopentamer)	0	0	-10000	0	-10000	0	0
RhoG/GTP	0.042	0.064	0.25	2	-10000	0	2
mol:GDP	0.057	0.096	0.32	4	-10000	0	4
NGF (dimer)	0	0	-10000	0	-10000	0	0
RhoG/GDP	0.021	0.032	-10000	0	-0.37	1	1
RIT1/GDP	0.045	0.078	0.26	1	-0.29	1	2
TIAM1	0.034	0.005	-10000	0	-10000	0	0
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
BDNF (dimer)/TRKB	-0.091	0.2	-10000	0	-0.36	49	49
KIDINS220/CRKL/C3G	0.046	0.016	-10000	0	-10000	0	0
SHC/RasGAP	0.041	0.038	-10000	0	-0.37	1	1
FRS2 family/SHP2	0.066	0.02	-10000	0	-10000	0	0
SHC/GRB2/SOS1/GAB1	0.068	0.055	-10000	0	-0.29	2	2
RIT1/GTP	0.015	0.055	-10000	0	-0.37	3	3
NT3 (dimer)	-0.006	0.12	-10000	0	-0.51	7	7
RAP1/GDP	0.037	0.056	0.18	1	-10000	0	1
KIDINS220/CRKL	0.031	0.012	-10000	0	-10000	0	0
BDNF (dimer)	-0.023	0.15	-10000	0	-0.51	12	12
ubiquitin-dependent protein catabolic process	0.038	0.032	-10000	0	-0.31	1	1
Schwann cell development	-0.02	0.025	-10000	0	-10000	0	0
EHD4	0.033	0.01	-10000	0	-10000	0	0
FRS2 family/GRB2/SOS1	0.08	0.026	-10000	0	-10000	0	0
FRS2 family/SHP2/CRK family/C3G/GAB2	0.028	0.049	-10000	0	-10000	0	0
RAP1B	0.033	0.007	-10000	0	-10000	0	0
RAP1A	0.026	0.062	-10000	0	-0.51	2	2
CDC42/GTP	-0.075	0.17	-10000	0	-0.3	49	49
ABL1	0.034	0.004	-10000	0	-10000	0	0
SH2B family/GRB2/SOS1	0.048	0.012	-10000	0	-10000	0	0
Rap1/GTP	-0.027	0.11	-10000	0	-0.54	2	2
STAT3	0	0.11	-10000	0	-0.36	12	12
axon guidance	-0.089	0.15	-10000	0	-0.29	49	49
MAPK3	0.022	0.043	0.19	6	-0.29	1	7
MAPK1	0.016	0.046	0.19	4	-0.29	2	6
CDC42/GDP	0.057	0.078	0.27	4	-10000	0	4
NTF3	-0.006	0.12	-10000	0	-0.51	7	7
NTF4	0	0	-10000	0	-10000	0	0
NGF (dimer)/TRKA/FAIM	0.033	0.035	-10000	0	-0.31	1	1
PI3K	0.004	0.076	-10000	0	-0.3	7	7
FRS3	0.034	0.003	-10000	0	-10000	0	0
FAIM	0.024	0.045	-10000	0	-0.51	1	1
GAB1	0.024	0.063	-10000	0	-0.51	2	2
RASGRF1	0.022	0.067	0.24	2	-10000	0	2
SOS1	0.033	0.006	-10000	0	-10000	0	0
MCF2L	-0.005	0.071	-10000	0	-0.31	7	7
RGS19	0.03	0.044	-10000	0	-0.51	1	1
CDC42	0.034	0.005	-10000	0	-10000	0	0
RAS family/GTP	0.061	0.098	0.39	1	-10000	0	1
Rac1/GDP	0.055	0.074	0.28	3	-10000	0	3
NGF (dimer)/TRKA/GRIT	0.022	0.007	-10000	0	-10000	0	0
neuron projection morphogenesis	0.02	0.18	-10000	0	-0.83	5	5
NGF (dimer)/TRKA/NEDD4-2	0.039	0.033	-10000	0	-0.31	1	1
MAP2K1	0.031	0.066	0.28	1	-0.27	2	3
NGFR	0.023	0.034	-10000	0	-10000	0	0
NGF (dimer)/TRKA/GIPC/GAIP	0.024	0.041	-10000	0	-0.25	3	3
RAS family/GTP/PI3K	-0.009	0.07	-10000	0	-0.26	9	9
FRS2 family/SHP2/GRB2/SOS1	0.092	0.034	-10000	0	-10000	0	0
NRAS	0.026	0.047	-10000	0	-0.51	1	1
GRB2/SOS1	0.048	0.012	-10000	0	-10000	0	0
PRKCI	-0.004	0.1	-10000	0	-0.51	6	6
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
RAC1	0.033	0.006	-10000	0	-10000	0	0
PRKCZ	0	0	-10000	0	-10000	0	0
MAPKKK cascade	0.005	0.052	-10000	0	-0.39	1	1
RASA1	0.028	0.044	-10000	0	-0.51	1	1
TRKA/c-Abl	0.047	0.014	-10000	0	-10000	0	0
SQSTM1	0.029	0.019	-10000	0	-10000	0	0
BDNF (dimer)/TRKB/GIPC	-0.075	0.19	-10000	0	-0.34	48	48
NGF (dimer)/TRKA/p62/Atypical PKCs	0.014	0.065	-10000	0	-0.27	6	6
MATK	0.028	0.046	-10000	0	-0.51	1	1
NEDD4L	0.028	0.045	-10000	0	-0.51	1	1
RAS family/GDP	-0.01	0.036	-10000	0	-10000	0	0
NGF (dimer)/TRKA	0	0.044	0.27	2	-10000	0	2
Rac1/GTP	-0.012	0.049	-10000	0	-0.24	2	2
FRS2 family/SHP2/CRK family	0.085	0.041	-10000	0	-10000	0	0

Visual signal transduction: Rods

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:K +	0.034	0.004	-10000	0	-10000	0	0
GNAT1/GTP	0.019	0.033	-10000	0	-0.37	1	1
Metarhodopsin II/Arrestin	0.035	0.034	-10000	0	-0.31	1	1
PDE6G/GNAT1/GTP	0.038	0.023	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
absorption of light	0	0	-10000	0	-10000	0	0
GNAT1	0.026	0.046	-10000	0	-0.51	1	1
GRK1	0	0	-10000	0	-10000	0	0
CNG Channel	0.021	0.085	-10000	0	-0.26	7	7
mol:Na +	0.025	0.09	-10000	0	-0.41	3	3
mol:ADP	0	0	-10000	0	-10000	0	0
RGS9-1/Gbeta5/R9AP	0.013	0.12	-10000	0	-0.32	15	15
mol:GDP	0	0	-10000	0	-10000	0	0
cGMP/CNG Channel	0.037	0.099	-10000	0	-0.43	3	3
CNGB1	0.033	0.007	-10000	0	-10000	0	0
RDH5	0.033	0.013	-10000	0	-10000	0	0
SAG	0.029	0.045	-10000	0	-0.51	1	1
mol:Ca2+	0.011	0.12	0.33	4	-0.67	1	5
Na + (4 Units)	0.019	0.083	-10000	0	-0.39	3	3
RGS9	0.015	0.089	-10000	0	-0.51	4	4
GNB1/GNGT1	-0.035	0.16	-10000	0	-0.37	27	27
GNAT1/GDP	0.019	0.11	-10000	0	-0.28	16	16
GUCY2D	0.028	0.044	-10000	0	-0.51	1	1
GNGT1	-0.071	0.2	-10000	0	-0.51	27	27
GUCY2F	0.025	0.063	-10000	0	-0.51	2	2
GNB5	0.02	0.086	-10000	0	-0.51	4	4
mol:GMP (4 units)	0.007	0.07	-10000	0	-0.27	8	8
mol:11-cis-retinal	0.033	0.013	-10000	0	-10000	0	0
mol:cGMP	0.04	0.083	-10000	0	-0.34	5	5
GNB1	0.033	0.007	-10000	0	-10000	0	0
Rhodopsin	0.042	0.021	-10000	0	-10000	0	0
SLC24A1	0.034	0.004	-10000	0	-10000	0	0
CNGA1	0.017	0.067	-10000	0	-0.51	2	2
Metarhodopsin II	0.019	0.008	-10000	0	-10000	0	0
mol:Ca ++	0	0	-10000	0	-10000	0	0
GC1/GCAP Family	0.049	0.081	-10000	0	-0.3	6	6
RGS9BP	-0.002	0.12	-10000	0	-0.51	7	7
Metarhodopsin II/Transducin	-0.032	0.11	-10000	0	-0.27	23	23
GCAP Family/Ca ++	0.04	0.068	-10000	0	-0.29	5	5
PDE6A/B	0.014	0.096	-10000	0	-0.37	8	8
mol:Pi	0.013	0.12	-10000	0	-0.32	15	15
mol:all-trans-retinal	0	0	-10000	0	-10000	0	0
Transducin	-0.015	0.14	-10000	0	-0.3	27	27
PDE6B	0.003	0.11	-10000	0	-0.51	6	6
PDE6A	0.024	0.063	-10000	0	-0.51	2	2
PDE6G	0.032	0.014	-10000	0	-10000	0	0
RHO	0.029	0.012	-10000	0	-10000	0	0
PDE6	0.01	0.13	-10000	0	-0.29	20	20
GUCA1A	0.023	0.075	-10000	0	-0.51	3	3
GC2/GCAP Family	0.052	0.078	-10000	0	-0.3	5	5
GUCA1C	0.019	0.064	-10000	0	-0.51	2	2
GUCA1B	0.033	0.01	-10000	0	-10000	0	0

Regulation of Androgen receptor activity

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
HDAC1	0.017	0.006	-10000	0	-10000	0	0
SMARCC1	-0.005	0.16	-10000	0	-1.1	3	3
REL	0.004	0.11	-10000	0	-0.51	7	7
HDAC7	-0.033	0.12	0.22	3	-0.32	8	11
JUN	0.004	0.11	-10000	0	-0.51	7	7
EP300	0.005	0.12	-10000	0	-0.51	8	8
KAT2B	0	0	-10000	0	-10000	0	0
KAT5	0	0	-10000	0	-10000	0	0
MAPK14	-0.007	0.072	-10000	0	-0.37	5	5
FOXO1	0.015	0.096	-10000	0	-0.51	5	5
T-DHT/AR	-0.007	0.14	-10000	0	-0.33	8	8
MAP2K6	0.004	0.098	-10000	0	-0.51	5	5
BRM/BAF57	0.041	0.032	-10000	0	-10000	0	0
MAP2K4	0.018	0.049	-10000	0	-0.5	1	1
SMARCA2	0.028	0.02	-10000	0	-10000	0	0
PDE9A	-0.055	0.25	-10000	0	-1	9	9
NCOA2	0.026	0.062	-10000	0	-0.51	2	2
CEBPA	0.016	0.087	-10000	0	-0.51	4	4
EHMT2	0.033	0.01	-10000	0	-10000	0	0
cell proliferation	0.001	0.15	0.41	4	-0.37	6	10
NR0B1	-0.19	0.23	-10000	0	-0.51	51	51
EGR1	-0.021	0.15	-10000	0	-0.51	13	13
RXRs/9cRA	0.054	0.048	-10000	0	-0.3	2	2
AR/RACK1/Src	0.01	0.096	0.3	3	-0.28	4	7
AR/GR	0.015	0.084	-10000	0	-0.36	3	3
GNB2L1	0.032	0.009	-10000	0	-10000	0	0
PKN1	0.033	0.007	-10000	0	-10000	0	0
RCHY1	0.024	0.062	-10000	0	-0.51	2	2
epidermal growth factor receptor activity	0	0	-10000	0	-10000	0	0
MAPK8	0.002	0.039	-10000	0	-0.36	1	1
T-DHT/AR/TIF2/CARM1	0.018	0.1	-10000	0	-0.33	6	6
SRC	-0.02	0.078	0.19	8	-0.28	6	14
NR3C1	0.032	0.012	-10000	0	-10000	0	0
KLK3	-0.011	0.12	-10000	0	-10000	0	0
APPBP2	0.021	0.027	-10000	0	-10000	0	0
TRIM24	0.023	0.076	-10000	0	-0.51	3	3
T-DHT/AR/TIP60	-0.028	0.067	-10000	0	-0.27	7	7
TMPRSS2	-0.21	0.45	-10000	0	-1	33	33
RXRG	0.031	0.015	-10000	0	-10000	0	0
mol:9cRA	0	0	-10000	0	-10000	0	0
RXRA	0.025	0.063	-10000	0	-0.51	2	2
RXRB	0.034	0.006	-10000	0	-10000	0	0
CARM1	0.033	0.007	-10000	0	-10000	0	0
NR2C2	0.028	0.044	-10000	0	-0.51	1	1
KLK2	0.015	0.089	0.32	1	-0.4	1	2
AR	0.002	0.08	-10000	0	-0.34	4	4
SENP1	0.034	0.004	-10000	0	-10000	0	0
HSP90AA1	0.033	0.008	-10000	0	-10000	0	0
MDM2	0.028	0.044	-10000	0	-0.51	1	1
SRY	-0.001	0	-10000	0	-10000	0	0
GATA2	0.026	0.045	-10000	0	-0.51	1	1
MYST2	0	0	-10000	0	-10000	0	0
HOXB13	-0.095	0.22	-10000	0	-0.51	34	34
T-DHT/AR/RACK1/Src	0.007	0.098	0.31	3	-0.29	4	7
positive regulation of transcription	0.026	0.045	-10000	0	-0.51	1	1
DNAJA1	0.02	0.027	-10000	0	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.014	0.049	-10000	0	-0.32	3	3
NCOA1	0.04	0.032	-10000	0	-0.18	2	2
SPDEF	0.028	0.029	-10000	0	-10000	0	0
T-DHT/AR/TIF2	0	0.095	0.22	1	-0.35	5	6
T-DHT/AR/Hsp90	-0.004	0.086	0.24	1	-0.29	5	6
GSK3B	0.028	0.013	-10000	0	-10000	0	0
NR2C1	0.034	0.003	-10000	0	-10000	0	0
mol:T-DHT	-0.029	0.066	0.23	1	-0.29	6	7
SIRT1	0.033	0.007	-10000	0	-10000	0	0
ZMIZ2	0.032	0.006	-10000	0	-10000	0	0
POU2F1	0.002	0.065	-10000	0	-0.18	3	3
T-DHT/AR/DAX-1	-0.11	0.14	-10000	0	-0.29	44	44
CREBBP	0.033	0.007	-10000	0	-10000	0	0
SMARCE1	0.034	0.006	-10000	0	-10000	0	0

ErbB2/ErbB3 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
USP8	-0.008	0.026	-10000	0	-0.32	1	1
RAS family/GTP	0.018	0.1	-10000	0	-0.3	2	2
NFATC4	-0.023	0.075	-10000	0	-0.28	3	3
ERBB2IP	0.032	0.01	-10000	0	-10000	0	0
HSP90 (dimer)	0.033	0.008	-10000	0	-10000	0	0
mammary gland morphogenesis	0.001	0.097	-10000	0	-0.29	10	10
JUN	0.019	0.071	-10000	0	-10000	0	0
HRAS	0.029	0.045	-10000	0	-0.51	1	1
DOCK7	-0.029	0.087	-10000	0	-0.29	9	9
ErbB2/ErbB3/neuregulin 1 beta/SHC	0.027	0.1	-10000	0	-0.32	10	10
AKT1	0.001	0.043	-10000	0	-0.36	2	2
BAD	-0.01	0.035	-10000	0	-0.31	2	2
MAPK10	-0.023	0.058	0.2	1	-0.2	3	4
mol:GTP	0	0.001	-10000	0	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta	0.002	0.1	-10000	0	-0.31	10	10
RAF1	0.006	0.1	-10000	0	-0.3	3	3
ErbB2/ErbB3/neuregulin 2	0.027	0.054	-10000	0	-0.31	3	3
STAT3	0.007	0.17	-10000	0	-0.91	5	5
cell migration	-0.014	0.057	0.22	1	-0.21	1	2
mol:PI-3-4-5-P3	-0.001	0.002	-10000	0	-10000	0	0
cell proliferation	-0.031	0.22	-10000	0	-0.6	12	12
FOS	-0.033	0.19	-10000	0	-0.45	21	21
NRAS	0.026	0.047	-10000	0	-0.51	1	1
mol:Ca2+	0.001	0.097	-10000	0	-0.29	10	10
MAPK3	-0.015	0.17	-10000	0	-0.54	7	7
MAPK1	-0.027	0.19	-10000	0	-0.58	10	10
JAK2	-0.029	0.086	-10000	0	-0.3	9	9
NF2	0.004	0.082	-10000	0	-0.65	2	2
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1	0.006	0.075	-10000	0	-0.27	8	8
NRG1	-0.006	0.13	-10000	0	-0.51	9	9
GRB2/SOS1	0.048	0.012	-10000	0	-10000	0	0
MAPK8	-0.006	0.098	-10000	0	-0.29	9	9
MAPK9	-0.015	0.06	0.25	2	-0.23	1	3
ERBB2	-0.028	0.043	-10000	0	-0.39	2	2
ERBB3	0.029	0.045	-10000	0	-0.51	1	1
SHC1	0.032	0.008	-10000	0	-10000	0	0
RAC1	0.033	0.006	-10000	0	-10000	0	0
apoptosis	0.005	0.044	0.35	2	-0.2	1	3
STAT3 (dimer)	0.009	0.17	-10000	0	-0.89	5	5
RNF41	-0.011	0.024	-10000	0	-0.29	1	1
FRAP1	-0.007	0.035	-10000	0	-0.31	2	2
RAC1-CDC42/GTP	-0.017	0.062	-10000	0	-0.22	9	9
ErbB2/ErbB2/HSP90 (dimer)	0.004	0.045	-10000	0	-0.33	2	2
CHRNA1	-0.003	0.15	-10000	0	-0.41	9	9
myelination	-0.012	0.09	0.33	2	-0.27	3	5
PPP3CB	-0.026	0.083	-10000	0	-0.27	9	9
KRAS	0.017	0.086	-10000	0	-0.51	4	4
RAC1-CDC42/GDP	0.034	0.086	-10000	0	-0.24	8	8
NRG2	0.03	0.019	-10000	0	-10000	0	0
mol:GDP	0.006	0.074	-10000	0	-0.27	8	8
SOS1	0.033	0.006	-10000	0	-10000	0	0
MAP2K2	-0.001	0.1	-10000	0	-0.33	3	3
SRC	0.032	0.012	-10000	0	-10000	0	0
mol:cAMP	-0.001	0.001	-10000	0	-10000	0	0
PTPN11	-0.029	0.09	-10000	0	-0.29	9	9
MAP2K1	-0.024	0.18	-10000	0	-0.55	8	8
heart morphogenesis	0.001	0.097	-10000	0	-0.29	10	10
RAS family/GDP	0.026	0.11	-10000	0	-0.3	2	2
GRB2	0.033	0.006	-10000	0	-10000	0	0
PRKACA	0.003	0.093	-10000	0	-0.65	3	3
CHRNE	0.012	0.018	-10000	0	-10000	0	0
HSP90AA1	0.033	0.008	-10000	0	-10000	0	0
activation of caspase activity	-0.001	0.043	0.36	2	-10000	0	2
nervous system development	0.001	0.097	-10000	0	-0.29	10	10
CDC42	0.034	0.005	-10000	0	-10000	0	0

Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1	0.033	0.007	-9999	-10000	0	0
VLDLR	-0.009	0.13	-9999	-0.51	9	9
LRPAP1	0.031	0.011	-9999	-10000	0	0
NUDC	0.034	0.005	-9999	-10000	0	0
RELN/LRP8	0.023	0.1	-9999	-0.32	12	12
CaM/Ca2+	0.024	0.005	-9999	-10000	0	0
KATNA1	0.033	0.006	-9999	-10000	0	0
GO:0030286	0	0	-9999	-10000	0	0
ABL1	0.001	0.095	-9999	-0.29	12	12
IQGAP1/CaM	0.048	0.012	-9999	-10000	0	0
DAB1	0.033	0.01	-9999	-10000	0	0
IQGAP1	0.034	0.005	-9999	-10000	0	0
PLA2G7	-0.05	0.19	-9999	-0.51	22	22
CALM1	0.033	0.007	-9999	-10000	0	0
DYNLT1	0.034	0.005	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
LRPAP1/LRP8	0.009	0.11	-9999	-0.37	12	12
UniProt:Q4QZ09	0	0	-9999	-10000	0	0
CLIP1	0.027	0.061	-9999	-0.51	2	2
CDK5R1	0.032	0.016	-9999	-10000	0	0
LIS1/Poliovirus Protein 3A	0.011	0.004	-9999	-10000	0	0
CDK5R2	0.033	0.006	-9999	-10000	0	0
mol:PP1	0	0	-9999	-10000	0	0
RELN/VLDLR/DAB1	0.021	0.097	-9999	-0.32	9	9
YWHAE	0.032	0.008	-9999	-10000	0	0
NDEL1/14-3-3 E	0.017	0.088	-9999	-10000	0	0
MAP1B	-0.058	0.12	-9999	-0.28	33	33
RAC1	0.016	0.007	-9999	-10000	0	0
p35/CDK5	0.009	0.09	-9999	-0.27	12	12
RELN	0.03	0.017	-9999	-10000	0	0
PAFAH/LIS1	-0.019	0.12	-9999	-0.32	21	21
LIS1/CLIP170	0.029	0.042	-9999	-0.32	2	2
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain	0.023	0.073	-9999	-10000	0	0
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3	-0.004	0.097	-9999	-0.29	9	9
GO:0005869	0	0	-9999	-10000	0	0
NDEL1	0.001	0.083	-9999	-10000	0	0
LIS1/IQGAP1	0.033	0.013	-9999	-10000	0	0
RHOA	0.016	0.007	-9999	-10000	0	0
PAFAH1B1	0.015	0.006	-9999	-10000	0	0
PAFAH1B3	0.033	0.007	-9999	-10000	0	0
PAFAH1B2	0.03	0.045	-9999	-0.51	1	1
MAP1B/LIS1/Dynein heavy chain	-0.023	0.092	-9999	-0.3	2	2
NDEL1/Katanin 60/Dynein heavy chain	0.027	0.088	-9999	-10000	0	0
LRP8	-0.013	0.15	-9999	-0.51	12	12
NDEL1/Katanin 60	0.012	0.09	-9999	-10000	0	0
P39/CDK5	0.01	0.09	-9999	-0.27	12	12
LIS1/NudC/Dynein intermediate chain/microtubule organizing center	0.033	0.013	-9999	-10000	0	0
CDK5	-0.022	0.087	-9999	-0.28	12	12
PPP2R5D	0.03	0.044	-9999	-0.51	1	1
LIS1/CLIP170/Dynein Complex/Dynactin Complex	0.025	0.036	-9999	-0.27	2	2
CSNK2A1	0.032	0.008	-9999	-10000	0	0
RELN/VLDLR/DAB1/LIS1	0.03	0.093	-9999	-0.28	9	9
RELN/VLDLR	0.003	0.14	-9999	-0.32	19	19
CDC42	0.016	0.007	-9999	-10000	0	0

JNK signaling in the CD4+ TCR 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
LAT/GRAP2/SLP76/HPK1	0.037	0.1	-10000	0	-0.29	11	11
MAP4K1	0.03	0.011	-10000	0	-10000	0	0
MAP3K8	-0.011	0.14	-10000	0	-0.51	12	12
PRKCB	0	0	-10000	0	-10000	0	0
DBNL	0.03	0.044	-10000	0	-0.51	1	1
CRKL	0.031	0.012	-10000	0	-10000	0	0
MAP3K1	0.003	0.079	-10000	0	-0.4	1	1
JUN	-0.022	0.14	-10000	0	-0.61	6	6
MAP3K7	0.004	0.08	-10000	0	-0.33	2	2
GRAP2	0.032	0.008	-10000	0	-10000	0	0
CRK	0.032	0.008	-10000	0	-10000	0	0
MAP2K4	-0.006	0.11	0.24	3	-0.38	7	10
LAT	0.031	0.018	-10000	0	-10000	0	0
LCP2	-0.011	0.14	-10000	0	-0.51	12	12
MAPK8	-0.006	0.14	-10000	0	-0.75	5	5
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family	0.01	0.086	-10000	0	-0.34	2	2
LAT/GRAP2/SLP76/HPK1/HIP-55	0.046	0.1	-10000	0	-0.28	11	11

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

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
MET/RANBP9	0.038	0.06	-10000	0	-0.37	3	3
CRKL	-0.002	0.15	0.36	1	-0.45	12	13
mol:PIP3	0.014	0.05	0.46	1	-10000	0	1
AKT1	0.008	0.067	0.33	2	-10000	0	2
PTK2B	0.029	0.017	-10000	0	-10000	0	0
RAPGEF1	-0.003	0.14	0.34	1	-0.45	10	11
RANBP10	0.029	0.044	-10000	0	-0.51	1	1
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
HGF/MET/SHIP2	0.048	0.067	-10000	0	-0.32	4	4
MAP3K5	0.003	0.15	0.34	1	-0.45	10	11
HGF/MET/CIN85/CBL/ENDOPHILINS	0.056	0.08	-10000	0	-0.29	6	6
AP1	-0.022	0.14	-10000	0	-0.37	18	18
mol:SU11274	0	0	-10000	0	-10000	0	0
SHC1	0.032	0.008	-10000	0	-10000	0	0
apoptosis	-0.097	0.3	-10000	0	-0.78	23	23
STAT3 (dimer)	0.013	0.063	-10000	0	-0.28	1	1
GAB1/CRKL/SHP2/PI3K	-0.006	0.13	-10000	0	-0.48	6	6
INPP5D	0	0	-10000	0	-10000	0	0
CBL/CRK	0.011	0.14	-10000	0	-0.45	10	10
PTPN11	0.031	0.044	-10000	0	-0.51	1	1
GO:0007205	0	0	-10000	0	-10000	0	0
PLCG1	0.033	0.006	-10000	0	-10000	0	0
PTEN	0.027	0.045	-10000	0	-0.51	1	1
ELK1	-0.001	0.086	0.3	8	-10000	0	8
mol:SU5416	0	0	-10000	0	-10000	0	0
SHP2/GRB2/SOS1GAB1	0.01	0.056	-10000	0	-0.25	3	3
PAK1	0.008	0.077	0.3	2	-0.53	1	3
HGF/MET/RANBP10	0.05	0.066	-10000	0	-0.32	4	4
HRAS	0.012	0.1	-10000	0	-0.55	4	4
DOCK1	0	0.14	0.3	2	-0.44	11	13
GAB1	-0.008	0.14	-10000	0	-0.47	12	12
CRK	-0.009	0.14	-10000	0	-0.45	12	12
mol:PHA665752	0	0	-10000	0	-10000	0	0
mol:GDP	0.02	0.093	-10000	0	-0.53	3	3
JUN	0.004	0.11	-10000	0	-0.51	7	7
EntrezGene:200958	0	0	-10000	0	-10000	0	0
HGF/MET	0.007	0.046	-10000	0	-0.26	4	4
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
cell morphogenesis	0.079	0.15	0.36	11	-0.35	3	14
GRB2/SHC	0.044	0.053	-10000	0	-0.23	3	3
FOS	-0.029	0.16	-10000	0	-0.51	14	14
GLMN	0.004	0.001	-10000	0	-10000	0	0
cell motility	-0.001	0.085	0.3	8	-10000	0	8
HGF/MET/MUC20	0.034	0.052	-10000	0	-0.31	3	3
cell migration	0.043	0.052	-10000	0	-0.23	3	3
GRB2	0.034	0.005	-10000	0	-10000	0	0
CBL	0.034	0.005	-10000	0	-10000	0	0
MET/RANBP10	0.035	0.07	-10000	0	-0.38	4	4
HGF/MET/Paxillin/FAK1/FAK12/RasGAP	0.018	0.05	-10000	0	-0.23	5	5
MET/MUC20	0.016	0.055	-10000	0	-0.37	3	3
RAP1B	0.002	0.14	0.37	2	-0.43	10	12
RAP1A	-0.008	0.13	0.33	1	-0.42	10	11
HGF/MET/RANBP9	0.053	0.059	-10000	0	-0.32	3	3
RAF1	0.015	0.1	-10000	0	-0.52	4	4
STAT3	0.013	0.064	-10000	0	-0.29	1	1
cell proliferation	0.024	0.091	0.28	4	-0.39	2	6
RPS6KB1	0.015	0.02	-10000	0	-10000	0	0
MAPK3	-0.015	0.086	0.55	2	-10000	0	2
MAPK1	0.01	0.16	0.73	6	-10000	0	6
RANBP9	0.033	0.007	-10000	0	-10000	0	0
MAPK8	0.02	0.14	0.36	1	-0.52	5	6
SRC	0.009	0.059	-10000	0	-10000	0	0
PI3K	0.003	0.07	-10000	0	-0.25	8	8
MET/Glomulin	0.017	0.053	-10000	0	-0.32	3	3
SOS1	0.033	0.006	-10000	0	-10000	0	0
MAP2K1	0.015	0.094	-10000	0	-0.49	4	4
MET	0.021	0.076	-10000	0	-0.51	3	3
MAP4K1	0.007	0.15	0.36	1	-0.46	10	11
PTK2	0.028	0.044	-10000	0	-0.51	1	1
MAP2K2	0.015	0.096	-10000	0	-0.49	4	4
BAD	0.006	0.062	0.32	1	-10000	0	1
MAP2K4	0.001	0.13	0.33	1	-0.4	10	11
SHP2/GRB2/SOS1/GAB1	0.024	0.13	-10000	0	-0.41	10	10
INPPL1	0.027	0.046	-10000	0	-0.51	1	1
PXN	0.034	0.004	-10000	0	-10000	0	0
SH3KBP1	0.018	0.077	-10000	0	-0.51	3	3
HGS	0.003	0.038	-10000	0	-0.24	3	3
PLCgamma1/PKC	0.025	0.005	-10000	0	-10000	0	0
HGF	0.03	0.019	-10000	0	-10000	0	0
RASA1	0.028	0.044	-10000	0	-0.51	1	1
NCK1	0.021	0.062	-10000	0	-0.51	2	2
PTPRJ	0.03	0.044	-10000	0	-0.51	1	1
NCK/PLCgamma1	0.032	0.066	-10000	0	-0.24	6	6
PDPK1	0.01	0.051	0.32	2	-10000	0	2
HGF/MET/SHIP	0.034	0.052	-10000	0	-0.31	3	3

Signaling events mediated by HDAC Class III

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EP300	0.005	0.12	-10000	0	-0.51	8	8
HDAC4	0.033	0.01	-10000	0	-10000	0	0
induction of apoptosis	0	0	-10000	0	-10000	0	0
regulation of S phase of mitotic cell cycle	0.003	0.019	-10000	0	-0.13	3	3
CDKN1A	-0.017	0.11	0.37	1	-0.74	3	4
KAT2B	0	0	-10000	0	-10000	0	0
BAX	0.034	0.005	-10000	0	-10000	0	0
FOXO3	0.013	0.092	0.4	8	-0.23	1	9
FOXO1	0.015	0.096	-10000	0	-0.51	5	5
FOXO4	0.003	0.065	-10000	0	-0.27	8	8
response to UV	0	0	-10000	0	-10000	0	0
XRCC6	0.033	0.007	-10000	0	-10000	0	0
TAT	0.032	0.011	-10000	0	-10000	0	0
mol:Lysophosphatidic acid	0	0	-10000	0	-10000	0	0
MYOD1	-0.009	0.079	-10000	0	-0.37	7	7
PPARGC1A	0.007	0.098	-10000	0	-0.51	5	5
FHL2	-0.057	0.19	-10000	0	-0.51	23	23
response to nutrient levels	0	0	-10000	0	-10000	0	0
KU70/SIRT1	0.047	0.022	-10000	0	-10000	0	0
HIST2H4A	-0.003	0.019	0.13	3	-10000	0	3
SIRT1/FOXO3a	0.031	0.073	0.31	7	-0.18	4	11
SIRT1	0.033	0.027	0.22	3	-10000	0	3
response to hypoxia	0	0	-10000	0	-10000	0	0
SIRT1/MEF2D/HDAC4	0.061	0.028	-10000	0	-10000	0	0
SIRT1/Histone H1b	0.016	0.076	-10000	0	-0.24	10	10
apoptosis	-0.062	0.025	-10000	0	-10000	0	0
SIRT1/PGC1A	0.023	0.069	-10000	0	-0.32	5	5
p53/SIRT1	0.03	0.082	0.41	3	-0.38	3	6
SIRT1/FOXO4	0.019	0.069	-10000	0	-0.23	8	8
FOXO1/FHL2/SIRT1	-0.01	0.14	-10000	0	-0.33	24	24
HIST1H1E	-0.005	0.077	-10000	0	-0.28	11	11
SIRT1/p300	0.026	0.088	-10000	0	-0.36	7	7
muscle cell differentiation	-0.006	0.068	0.31	6	-10000	0	6
TP53	0.017	0.082	0.22	3	-0.51	3	6
KU70/SIRT1/BAX	0.063	0.026	-10000	0	-10000	0	0
CREBBP	0.033	0.007	-10000	0	-10000	0	0
MEF2D	0.033	0.007	-10000	0	-10000	0	0
HIV-1 Tat/SIRT1	0.046	0.021	-10000	0	-10000	0	0
ACSS2	0.015	0.015	-10000	0	-10000	0	0
SIRT1/PCAF/MYOD	0.006	0.068	-10000	0	-0.32	6	6

ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K4	-0.012	0.14	0.23	1	-0.5	7	8
BAG4	0.028	0.014	-10000	0	-10000	0	0
BAD	0.001	0.046	-10000	0	-0.15	5	5
NFKBIA	0.028	0.045	-10000	0	-0.51	1	1
BIRC3	-0.026	0.16	-10000	0	-0.51	14	14
BAX	0.002	0.044	-10000	0	-0.16	3	3
EnzymeConsortium:3.1.4.12	0.002	0.033	0.087	1	-0.1	7	8
IKBKB	0.003	0.14	0.28	1	-0.47	7	8
MAP2K2	0.001	0.051	0.19	3	-0.21	1	4
MAP2K1	0	0.05	0.19	2	-0.21	1	3
SMPD1	0.002	0.04	-10000	0	-0.17	3	3
GO:0005551	0	0	-10000	0	-10000	0	0
FADD/Caspase 8	0.017	0.15	0.27	3	-0.46	8	11
MAP2K4	-0.005	0.054	-10000	0	-0.21	5	5
protein ubiquitination	-0.003	0.14	-10000	0	-0.48	7	7
EnzymeConsortium:2.7.1.37	-0.002	0.053	0.19	2	-0.22	1	3
response to UV	0	0.001	0.002	2	-10000	0	2
RAF1	0.001	0.052	0.18	3	-0.19	2	5
CRADD	0.027	0.062	-10000	0	-0.51	2	2
mol:ceramide	0.003	0.048	0.12	1	-0.15	7	8
I-kappa-B-alpha/RELA/p50/ubiquitin	0.041	0.031	-10000	0	-0.31	1	1
MADD	0.033	0.007	-10000	0	-10000	0	0
MAP3K1	-0.004	0.057	-10000	0	-0.2	6	6
TRADD	0.029	0.044	-10000	0	-0.51	1	1
RELA/p50	0.034	0	-10000	0	-10000	0	0
MAPK3	0.004	0.052	0.19	2	-0.2	1	3
MAPK1	0.001	0.055	0.2	1	-0.22	3	4
p50/RELA/I-kappa-B-alpha	0.045	0.037	-10000	0	-0.37	1	1
FADD	0.007	0.14	0.27	2	-0.5	7	9
KSR1	0.002	0.056	0.19	3	-0.17	5	8
MAPK8	-0.005	0.054	0.17	1	-0.2	3	4
TRAF2	0.033	0.01	-10000	0	-10000	0	0
response to radiation	0	0	-10000	0	-10000	0	0
CHUK	-0.01	0.13	-10000	0	-0.47	7	7
TNF R/SODD	0.03	0.054	-10000	0	-0.37	2	2
TNF	0.026	0.049	-10000	0	-0.51	1	1
CYCS	0.01	0.05	0.16	3	-0.16	3	6
IKBKG	-0.006	0.13	-10000	0	-0.47	7	7
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD	-0.006	0.14	-10000	0	-0.49	8	8
RELA	0.034	0	-10000	0	-10000	0	0
RIPK1	0.033	0.006	-10000	0	-10000	0	0
AIFM1	0.008	0.049	0.15	2	-0.16	3	5
TNF/TNF R/SODD	0.038	0.058	-10000	0	-0.32	2	2
TNFRSF1A	0.021	0.075	-10000	0	-0.51	3	3
response to heat	0	0	-10000	0	-10000	0	0
CASP8	0.019	0.12	-10000	0	-0.57	5	5
NSMAF	-0.002	0.14	0.25	2	-0.48	7	9
response to hydrogen peroxide	0	0.001	0.002	2	-10000	0	2
BCL2	-0.005	0.12	-10000	0	-0.51	7	7

RXR and RAR heterodimerization with other nuclear receptor

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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.012	0.045	-10000	0	-10000	0	0
VDR	-0.001	0.13	-10000	0	-0.51	9	9
FAM120B	0.033	0.007	-10000	0	-10000	0	0
RXRs/LXRs/DNA/9cRA	0.026	0.087	-10000	0	-0.3	6	6
RXRs/LXRs/DNA/Oxysterols	0.025	0.12	-10000	0	-0.42	7	7
MED1	0.023	0.075	-10000	0	-0.51	3	3
mol:9cRA	0.002	0.013	-10000	0	-10000	0	0
RARs/THRs/DNA/Src-1	-0.013	0.1	-10000	0	-0.38	3	3
RXRs/NUR77	0.074	0.068	-10000	0	-0.33	2	2
RXRs/PPAR	0.005	0.094	-10000	0	-0.26	15	15
NCOR2	0.027	0.061	-10000	0	-0.51	2	2
VDR/VDR/Vit D3	0	0.092	-10000	0	-0.37	9	9
RARs/VDR/DNA/Vit D3	0.012	0.14	-10000	0	-0.33	20	20
RARA	0.034	0.005	-10000	0	-10000	0	0
NCOA1	0.033	0.007	-10000	0	-10000	0	0
VDR/VDR/DNA	-0.001	0.13	-10000	0	-0.51	9	9
RARs/RARs/DNA/9cRA	0.017	0.1	-10000	0	-0.29	14	14
RARG	0.027	0.062	-10000	0	-0.51	2	2
RPS6KB1	0.018	0.058	0.51	2	-10000	0	2
RARs/THRs/DNA/SMRT	-0.014	0.11	-10000	0	-0.38	3	3
THRA	0.024	0.063	-10000	0	-0.51	2	2
mol:Bile acids	0	0	-10000	0	-10000	0	0
VDR/Vit D3/DNA	0	0.092	-10000	0	-0.37	9	9
RXRs/PPAR/9cRA/PGJ2/DNA	0.058	0.07	-10000	0	-0.35	2	2
NR1H4	0.026	0.048	-10000	0	-0.51	1	1
RXRs/LXRs/DNA	0.083	0.1	-10000	0	-0.3	5	5
NR1H2	0.034	0.021	-10000	0	-10000	0	0
NR1H3	0.021	0.079	-10000	0	-0.5	3	3
RXRs/VDR/DNA/Vit D3	0.051	0.1	-10000	0	-0.32	8	8
NR4A1	0.032	0.016	-10000	0	-10000	0	0
mol:ATRA	0	0	-10000	0	-10000	0	0
RXRs/FXR/9cRA/MED1	0.018	0.075	-10000	0	-0.28	7	7
RXRG	0.032	0.024	-10000	0	-10000	0	0
RXR alpha/CCPG	0.041	0.054	-10000	0	-0.38	2	2
RXRA	0.025	0.067	-10000	0	-0.52	2	2
RXRB	0.034	0.022	-10000	0	-10000	0	0
THRB	0.031	0.013	-10000	0	-10000	0	0
PPARG	-0.025	0.16	-10000	0	-0.51	15	15
PPARD	0.034	0.003	-10000	0	-10000	0	0
TNF	0.015	0.14	-10000	0	-0.69	3	3
mol:Oxysterols	0.002	0.012	-10000	0	-10000	0	0
cholesterol transport	0.025	0.12	-10000	0	-0.41	7	7
PPARA	0.032	0.008	-10000	0	-10000	0	0
mol:Vit D3	0	0	-10000	0	-10000	0	0
RARB	-0.025	0.16	-10000	0	-0.51	14	14
RXRs/NUR77/BCL2	0.005	0.068	-10000	0	-0.24	8	8
SREBF1	0.017	0.13	-10000	0	-0.75	2	2
RXRs/RXRs/DNA/9cRA	0.058	0.07	-10000	0	-0.35	2	2
ABCA1	-0.008	0.23	-10000	0	-1	7	7
RARs/THRs	0.039	0.12	-10000	0	-0.29	16	16
RXRs/FXR	0.07	0.075	-10000	0	-0.33	3	3
BCL2	-0.005	0.12	-10000	0	-0.51	7	7

FoxO family signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G6PC	0.002	0.087	-10000	0	-10000	0	0
PLK1	0.005	0.2	-10000	0	-0.74	5	5
CDKN1B	0.062	0.16	-10000	0	-0.38	6	6
FOXO3	0.006	0.22	-10000	0	-0.71	8	8
KAT2B	0.003	0.018	-10000	0	-0.052	6	6
FOXO1/SIRT1	0.022	0.092	-10000	0	-0.4	3	3
CAT	-0.016	0.28	-10000	0	-1.1	7	7
CTNNB1	0.03	0.016	-10000	0	-10000	0	0
AKT1	0.024	0.073	-10000	0	-0.54	2	2
FOXO1	0.004	0.095	-10000	0	-0.4	4	4
MAPK10	-0.002	0.093	0.19	5	-0.28	13	18
mol:GTP	0.001	0.002	-10000	0	-10000	0	0
FOXO4	0.019	0.15	0.29	1	-0.51	7	8
response to oxidative stress	0.006	0.019	-10000	0	-0.056	5	5
FOXO3A/SIRT1	0.034	0.2	-10000	0	-0.74	5	5
XPO1	0.031	0.011	-10000	0	-10000	0	0
EP300	0.007	0.12	-10000	0	-0.51	8	8
BCL2L11	0.035	0.036	-10000	0	-10000	0	0
FOXO1/SKP2	0.004	0.1	-10000	0	-0.42	3	3
mol:GDP	0.006	0.019	-10000	0	-0.056	5	5
RAN	0.035	0.003	-10000	0	-10000	0	0
GADD45A	0.024	0.23	-10000	0	-0.76	10	10
YWHAQ	0.033	0.007	-10000	0	-10000	0	0
FOXO1/14-3-3 family	0.016	0.16	-10000	0	-0.62	7	7
MST1	0.027	0.034	-10000	0	-10000	0	0
CSNK1D	0.033	0.006	-10000	0	-10000	0	0
CSNK1E	0.029	0.044	-10000	0	-0.51	1	1
FOXO4/14-3-3 family	-0.01	0.2	-10000	0	-0.65	9	9
YWHAB	0.033	0.006	-10000	0	-10000	0	0
MAPK8	0.011	0.084	0.2	5	-0.27	10	15
MAPK9	0.012	0.086	0.2	7	-0.27	10	17
YWHAG	0.034	0.005	-10000	0	-10000	0	0
YWHAE	0.032	0.008	-10000	0	-10000	0	0
YWHAZ	0.025	0.062	-10000	0	-0.51	2	2
SIRT1	0.034	0.021	-10000	0	-10000	0	0
SOD2	0.015	0.24	-10000	0	-0.83	9	9
RBL2	0.017	0.22	-10000	0	-0.83	6	6
RAL/GDP	0.026	0.094	-10000	0	-0.32	10	10
CHUK	0.026	0.054	-10000	0	-0.5	1	1
Ran/GTP	0.027	0.009	-10000	0	-10000	0	0
CSNK1G2	0.033	0.007	-10000	0	-10000	0	0
RAL/GTP	0.03	0.089	-10000	0	-0.29	10	10
CSNK1G1	0.034	0.004	-10000	0	-10000	0	0
FASLG	-0.12	0.46	-10000	0	-1.5	16	16
SKP2	0.006	0.1	-10000	0	-0.51	6	6
USP7	0.034	0.006	-10000	0	-10000	0	0
IKBKB	0.026	0.033	-10000	0	-10000	0	0
CCNB1	-0.003	0.24	-10000	0	-0.9	6	6
FOXO1-3a-4/beta catenin	0.041	0.17	-10000	0	-0.42	9	9
proteasomal ubiquitin-dependent protein catabolic process	0.004	0.1	-10000	0	-0.42	3	3
CSNK1A1	0.029	0.044	-10000	0	-0.51	1	1
SGK1	0.003	0.018	-10000	0	-0.052	6	6
CSNK1G3	0.032	0.008	-10000	0	-10000	0	0
Ran/GTP/Exportin 1	0.043	0.019	-10000	0	-10000	0	0
ZFAND5	0.021	0.14	-10000	0	-0.62	3	3
SFN	-0.027	0.17	-10000	0	-0.51	17	17
CDK2	0.033	0.044	-10000	0	-0.5	1	1
FOXO3A/14-3-3	-0.002	0.19	-10000	0	-0.69	8	8
CREBBP	0.036	0.007	-10000	0	-10000	0	0
FBXO32	-0.014	0.34	-10000	0	-1.4	7	7
BCL6	-0.022	0.29	-10000	0	-1.2	7	7
RALB	0.002	0.13	-10000	0	-0.51	9	9
RALA	0.03	0.044	-10000	0	-0.51	1	1
YWHAH	0.026	0.062	-10000	0	-0.51	2	2

Retinoic acid receptors-mediated 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
HDAC1	0.033	0.01	-10000	0	-10000	0	0
HDAC3	0.033	0.008	-10000	0	-10000	0	0
VDR	-0.001	0.13	-10000	0	-0.51	9	9
Cbp/p300/PCAF	0.025	0.08	-10000	0	-0.31	8	8
EP300	0.005	0.12	-10000	0	-0.51	8	8
RARs/AIB1/Cbp/p300/PCAF/9cRA	-0.008	0.1	-10000	0	-0.41	6	6
KAT2B	0	0	-10000	0	-10000	0	0
MAPK14	0.034	0.009	-10000	0	-10000	0	0
AKT1	-0.008	0.12	0.21	12	-0.32	10	22
RAR alpha/9cRA/Cyclin H	0.043	0.091	-10000	0	-0.48	2	2
mol:9cRA	0	0	-10000	0	-10000	0	0
RARs/Src-1/Cbp/p300/PCAF/9cRA	-0.013	0.1	-10000	0	-0.31	9	9
CDC2	0	0.004	-10000	0	-10000	0	0
response to UV	0	0.006	-10000	0	-10000	0	0
RAR alpha/Jnk1	0.028	0.035	-10000	0	-10000	0	0
NCOR2	0.027	0.061	-10000	0	-0.51	2	2
VDR/VDR/Vit D3	0	0.092	-10000	0	-0.37	9	9
RXRs/RARs/NRIP1/9cRA	-0.015	0.19	-10000	0	-0.64	9	9
NCOA2	0.025	0.062	-10000	0	-0.51	2	2
NCOA3	0.026	0.062	-10000	0	-0.51	2	2
NCOA1	0.033	0.007	-10000	0	-10000	0	0
VDR/VDR/DNA	-0.001	0.13	-10000	0	-0.51	9	9
RARG	0.026	0.062	-10000	0	-0.51	2	2
RAR gamma1/9cRA	0.039	0.042	-10000	0	-0.31	2	2
MAPK3	0.032	0.013	-10000	0	-10000	0	0
MAPK1	0.028	0.044	-10000	0	-0.51	1	1
MAPK8	0.031	0.015	-10000	0	-10000	0	0
mol:Vit D3	0	0	-10000	0	-10000	0	0
RXRs/VDR/DNA/Vit D3	0.017	0.14	-10000	0	-0.62	4	4
RARA	0.02	0.029	-10000	0	-0.23	1	1
negative regulation of phosphoinositide 3-kinase cascade	0	0	-10000	0	-10000	0	0
RARs/TIF2/Cbp/p300/PCAF/9cRA	-0.017	0.11	-10000	0	-0.37	9	9
PRKCA	0.027	0.049	-10000	0	-0.51	1	1
RXRs/RARs/NRIP1/9cRA/HDAC1	-0.023	0.19	-10000	0	-0.68	9	9
RXRG	0.02	0.037	-10000	0	-0.31	1	1
RXRA	0.01	0.076	-10000	0	-0.43	3	3
RXRB	0.022	0.035	-10000	0	-0.31	1	1
VDR/Vit D3/DNA	0	0.092	-10000	0	-0.37	9	9
RBP1	-0.054	0.19	-10000	0	-0.51	22	22
CRBP1/9-cic-RA	-0.038	0.14	-10000	0	-0.37	22	22
RARB	-0.026	0.16	-10000	0	-0.51	14	14
PRKCG	0.031	0.022	-10000	0	-10000	0	0
MNAT1	0.034	0.005	-10000	0	-10000	0	0
RAR alpha/RXRs	-0.01	0.16	-10000	0	-0.63	5	5
RXRs/RARs/SMRT(N-CoR2)/9cRA	0	0.13	-10000	0	-0.55	4	4
proteasomal ubiquitin-dependent protein catabolic process	-0.009	0.1	-10000	0	-0.3	10	10
RXRs/RARs/NRIP1/9cRA/HDAC3	-0.024	0.19	-10000	0	-0.68	9	9
positive regulation of DNA binding	0.033	0.083	-10000	0	-0.44	2	2
NRIP1	-0.052	0.31	-10000	0	-1.3	8	8
RXRs/RARs	-0.02	0.18	-10000	0	-0.55	10	10
RXRs/RXRs/DNA/9cRA	0.007	0.11	-10000	0	-0.52	4	4
PRKACA	0.033	0.007	-10000	0	-10000	0	0
CDK7	0.032	0.01	-10000	0	-10000	0	0
TFIIH	0.062	0.022	-10000	0	-10000	0	0
RAR alpha/9cRA	0.063	0.048	-10000	0	-10000	0	0
CCNH	0.031	0.013	-10000	0	-10000	0	0
CREBBP	0.033	0.007	-10000	0	-10000	0	0
RAR gamma2/9cRA	0.057	0.038	-10000	0	-0.26	1	1

TCGA08_rtk_signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.001	0.13	-10000	0	-0.51	9	9
HRAS	0.029	0.045	-10000	0	-0.51	1	1
EGFR	-0.031	0.17	-10000	0	-0.51	17	17
AKT	0.048	0.11	0.28	3	-0.41	4	7
FOXO3	0.03	0.044	-10000	0	-0.51	1	1
AKT1	0.025	0.062	-10000	0	-0.51	2	2
FOXO1	0.015	0.096	-10000	0	-0.51	5	5
AKT3	0.022	0.065	-10000	0	-0.51	2	2
FOXO4	0.033	0.006	-10000	0	-10000	0	0
MET	0.021	0.076	-10000	0	-0.51	3	3
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
PIK3CB	0.015	0.076	-10000	0	-0.51	3	3
NRAS	0.026	0.047	-10000	0	-0.51	1	1
PIK3CG	0.022	0.076	-10000	0	-0.51	3	3
PIK3R3	0.018	0.077	-10000	0	-0.51	3	3
PIK3R2	0.033	0.007	-10000	0	-10000	0	0
NF1	0.03	0.044	-10000	0	-0.51	1	1
RAS	-0.008	0.092	-10000	0	-0.29	8	8
ERBB2	0.025	0.063	-10000	0	-0.51	2	2
proliferation/survival/translation	-0.073	0.1	0.35	4	-0.24	15	19
PI3K	0.025	0.11	0.23	6	-0.3	8	14
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
KRAS	0.017	0.086	-10000	0	-0.51	4	4
FOXO	0.083	0.074	0.23	10	-10000	0	10
AKT2	0.031	0.01	-10000	0	-10000	0	0
PTEN	0.027	0.045	-10000	0	-0.51	1	1

IL2 signaling events mediated by STAT5

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GAB2	0.032	0.014	-10000	0	-10000	0	0
ELF1	0.012	0.1	-10000	0	-0.35	11	11
CCNA2	0.022	0.075	-10000	0	-0.51	3	3
PIK3CA	0.01	0.062	-10000	0	-0.51	2	2
JAK3	0.034	0.007	-10000	0	-10000	0	0
PIK3R1	0.007	0.099	-10000	0	-0.51	5	5
JAK1	0.031	0.044	-10000	0	-0.51	1	1
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.028	0.13	-10000	0	-0.43	6	6
SHC1	0.033	0.008	-10000	0	-10000	0	0
SP1	-0.009	0.12	-10000	0	-0.37	14	14
IL2RA	-0.034	0.21	-10000	0	-0.78	11	11
IL2RB	0.017	0.087	-10000	0	-0.51	4	4
SOS1	0.034	0.006	-10000	0	-10000	0	0
IL2RG	0.022	0.065	-10000	0	-0.51	2	2
G1/S transition of mitotic cell cycle	-0.068	0.28	-10000	0	-0.81	16	16
PTPN11	0.031	0.044	-10000	0	-0.51	1	1
CCND2	-0.057	0.22	-10000	0	-0.72	14	14
LCK	-0.004	0.13	-10000	0	-0.51	10	10
GRB2	0.034	0.006	-10000	0	-10000	0	0
IL2	0.033	0.008	-10000	0	-10000	0	0
CDK6	0.011	0.1	-10000	0	-0.51	6	6
CCND3	0.027	0.12	0.4	1	-0.45	2	3

Class I PI3K signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ARF5/GTP	-0.018	0.07	-10000	0	-0.25	7	7
DAPP1	-0.022	0.17	-10000	0	-0.49	11	11
Src family/SYK family/BLNK-LAT/BTK-ITK	-0.023	0.22	-10000	0	-0.6	14	14
mol:DAG	0.005	0.096	0.18	8	-0.27	7	15
HRAS	0.029	0.047	-10000	0	-0.51	1	1
RAP1A	0.026	0.062	-10000	0	-0.5	2	2
ARF5/GDP	0.016	0.091	-10000	0	-0.36	2	2
PLCG2	0.014	0.096	-10000	0	-0.51	5	5
PLCG1	0.033	0.006	-10000	0	-10000	0	0
ARF5	0.027	0.061	-10000	0	-0.51	2	2
mol:GTP	-0.016	0.067	-10000	0	-0.26	6	6
ARF1/GTP	-0.008	0.063	-10000	0	-0.24	6	6
RHOA	0.031	0.011	-10000	0	-10000	0	0
YES1	0.028	0.044	-10000	0	-0.51	1	1
RAP1A/GTP	-0.009	0.074	0.16	15	-0.26	6	21
ADAP1	-0.015	0.064	-10000	0	-0.25	6	6
ARAP3	-0.015	0.066	-10000	0	-0.26	6	6
INPPL1	0.027	0.046	-10000	0	-0.51	1	1
PREX1	-0.002	0.13	-10000	0	-0.51	9	9
ARHGEF6	0.023	0.075	-10000	0	-0.51	3	3
ARHGEF7	0.033	0.011	-10000	0	-10000	0	0
ARF1	0.034	0.005	-10000	0	-10000	0	0
NRAS	0.026	0.047	-10000	0	-0.49	1	1
FYN	0.026	0.062	-10000	0	-0.51	2	2
ARF6	0.026	0.062	-10000	0	-0.51	2	2
FGR	0.033	0.01	-10000	0	-10000	0	0
mol:Ca2+	0.005	0.055	0.14	5	-0.16	3	8
mol:IP4	0	0	-10000	0	-10000	0	0
TIAM1	0.034	0.005	-10000	0	-10000	0	0
ZAP70	0.031	0.016	-10000	0	-10000	0	0
mol:IP3	0.003	0.073	0.17	5	-0.2	6	11
LYN	0.029	0.044	-10000	0	-0.51	1	1
ARF1/GDP	0.02	0.087	-10000	0	-0.36	2	2
RhoA/GDP	0.024	0.085	-10000	0	-0.24	5	5
PDK1/Src/Hsp90	0.058	0.039	-10000	0	-0.32	1	1
BLNK	0.015	0.096	-10000	0	-0.51	5	5
actin cytoskeleton reorganization	-0.003	0.11	-10000	0	-0.47	3	3
SRC	0.032	0.012	-10000	0	-10000	0	0
PLEKHA2	-0.01	0.035	-10000	0	-0.31	2	2
RAC1	0.033	0.006	-10000	0	-10000	0	0
PTEN	0.025	0.045	-10000	0	-0.48	1	1
HSP90AA1	0.033	0.008	-10000	0	-10000	0	0
ARF6/GTP	-0.018	0.075	-10000	0	-0.26	8	8
RhoA/GTP	-0.008	0.076	0.29	1	-0.25	6	7
Src family/SYK family/BLNK-LAT	-0.013	0.18	-10000	0	-0.59	9	9
BLK	0.013	0.068	-10000	0	-0.51	2	2
PDPK1	0.03	0.044	-10000	0	-0.51	1	1
CYTH1	-0.015	0.064	-10000	0	-0.25	6	6
HCK	0.006	0.11	-10000	0	-0.51	7	7
CYTH3	-0.015	0.064	-10000	0	-0.25	6	6
CYTH2	-0.015	0.064	-10000	0	-0.25	6	6
KRAS	0.017	0.087	-10000	0	-0.51	4	4
GO:0030676	0	0	-10000	0	-10000	0	0
FOXO3	0.008	0.057	-10000	0	-0.43	1	1
SGK1	0.011	0.057	-10000	0	-0.46	1	1
INPP5D	0	0	-10000	0	-10000	0	0
mol:GDP	0.004	0.084	-10000	0	-0.32	3	3
SOS1	0.033	0.006	-10000	0	-10000	0	0
SYK	0.012	0.1	-10000	0	-0.51	6	6
ARF6/GDP	0.005	0.085	-10000	0	-0.27	3	3
mol:PI-3-4-5-P3	-0.018	0.064	-10000	0	-0.26	6	6
ARAP3/RAP1A/GTP	-0.01	0.075	0.16	15	-0.26	6	21
VAV1	0.008	0.11	-10000	0	-0.51	7	7
mol:PI-3-4-P2	0.005	0.031	-10000	0	-0.37	1	1
RAS family/GTP/PI3K Class I	0.038	0.081	-10000	0	-0.26	6	6
PLEKHA1	-0.016	0.049	-10000	0	-0.31	4	4
Rac1/GDP	0.019	0.088	-10000	0	-0.36	2	2
LAT	0.031	0.018	-10000	0	-10000	0	0
Rac1/GTP	0.002	0.11	-10000	0	-0.38	7	7
ITK	-0.019	0.067	-10000	0	-0.25	7	7
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma	-0.001	0.13	0.21	7	-0.39	7	14
LCK	-0.004	0.13	-10000	0	-0.51	10	10
BTK	-0.029	0.088	-10000	0	-0.27	14	14

S1P3 pathway

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
PDGFRB	0.032	0.012	-9999	-10000	0	0
mol:S1P	0	0.004	-9999	-0.034	2	2
S1P1/S1P/Gi	-0.015	0.11	-9999	-0.29	17	17
GNAO1	0.032	0.015	-9999	-10000	0	0
S1P/S1P3/G12/G13	0.039	0.031	-9999	-0.28	1	1
AKT1	-0.006	0.15	-9999	-0.53	10	10
AKT3	-0.012	0.17	-9999	-1	3	3
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.032	0.012	-9999	-10000	0	0
GNAI2	0.028	0.02	-9999	-10000	0	0
GNAI3	0.033	0.011	-9999	-10000	0	0
GNAI1	0	0.13	-9999	-0.51	9	9
mol:GDP	0	0	-9999	-10000	0	0
S1PR3	0.001	0.005	-9999	-0.039	2	2
S1PR2	0	0	-9999	-10000	0	0
EDG1	0	0	-9999	-10000	0	0
mol:Ca2+	-0.005	0.1	-9999	-0.32	8	8
MAPK3	-0.01	0.096	-9999	-0.33	6	6
MAPK1	-0.008	0.084	-9999	-0.31	5	5
JAK2	-0.033	0.14	-9999	-0.42	12	12
CXCR4	-0.043	0.14	-9999	-0.34	20	20
FLT1	0.005	0.12	-9999	-0.51	8	8
RhoA/GDP	0.023	0.008	-9999	-10000	0	0
Rac1/GDP	0.025	0.005	-9999	-10000	0	0
SRC	-0.012	0.097	-9999	-0.34	6	6
S1P/S1P3/Gi	-0.006	0.1	-9999	-0.32	8	8
RAC1	0.033	0.006	-9999	-10000	0	0
RhoA/GTP	0.009	0.1	-9999	-0.4	3	3
VEGFA	0.027	0.063	-9999	-0.51	2	2
S1P/S1P2/Gi	-0.006	0.099	-9999	-0.25	18	18
VEGFR1 homodimer/VEGFA homodimer	0.025	0.11	-9999	-0.41	8	8
RHOA	0.031	0.011	-9999	-10000	0	0
S1P/S1P3/Gq	-0.016	0.1	-9999	-0.29	16	16
GNAQ	0	0	-9999	-10000	0	0
GNAZ	0.005	0.11	-9999	-0.51	7	7
G12/G13	0.045	0.037	-9999	-0.37	1	1
GNA14	0.016	0.079	-9999	-0.51	3	3
GNA15	-0.007	0.14	-9999	-0.51	11	11
GNA12	0.033	0.008	-9999	-10000	0	0
GNA13	0.03	0.045	-9999	-0.51	1	1
GNA11	0.026	0.062	-9999	-0.51	2	2
Rac1/GTP	0.004	0.1	-9999	-0.32	6	6

Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HIF3A	0.031	0.017	-9999	-10000	0	0
oxygen homeostasis	0	0	-9999	-10000	0	0
TCEB2	0.033	0.006	-9999	-10000	0	0
TCEB1	0.032	0.008	-9999	-10000	0	0
HIF1A/p53	0.002	0.096	-9999	-0.36	6	6
HIF1A	-0.006	0.079	-9999	-0.38	4	4
COPS5	0.032	0.008	-9999	-10000	0	0
VHL/Elongin B/Elongin C/RBX1/CUL2	0.076	0.066	-9999	-0.28	3	3
FIH (dimer)	0.033	0.006	-9999	-10000	0	0
CDKN2A	-0.042	0.16	-9999	-0.51	15	15
ARNT/IPAS	0.044	0.02	-9999	-10000	0	0
HIF1AN	0.033	0.006	-9999	-10000	0	0
GNB2L1	0.032	0.009	-9999	-10000	0	0
HIF1A/ARNT	0.01	0.086	-9999	-0.43	3	3
CUL2	0.032	0.011	-9999	-10000	0	0
OS9	0.033	0.01	-9999	-10000	0	0
RACK1/Elongin B/Elongin C	0.06	0.024	-9999	-10000	0	0
response to hypoxia	0	0	-9999	-10000	0	0
HIF1A/Hsp90	0.007	0.088	-9999	-0.39	4	4
PHD1-3/OS9	-0.003	0.14	-9999	-0.3	24	24
HIF1A/RACK1/Elongin B/Elongin C	0.033	0.092	-9999	-0.37	4	4
VHL	0.019	0.076	-9999	-0.51	3	3
HSP90AA1	0.033	0.008	-9999	-10000	0	0
HIF1A/JAB1	0.01	0.087	-9999	-0.39	4	4
EGLN3	-0.065	0.19	-9999	-0.51	24	24
EGLN2	0.028	0.044	-9999	-0.51	1	1
EGLN1	0.025	0.063	-9999	-0.51	2	2
TP53	0.017	0.077	-9999	-0.51	3	3
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A	-0.011	0.19	-9999	-0.59	14	14
ARNT	0.032	0.008	-9999	-10000	0	0
ARD1A	0	0	-9999	-10000	0	0
RBX1	0.032	0.011	-9999	-10000	0	0
HIF1A/p19ARF	-0.032	0.11	-9999	-0.29	18	18

PDGFR-beta 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
S1P1/Sphingosine-1-phosphate	0.006	0.13	0.27	1	-0.39	10	11
PDGFB-D/PDGFRB/SLAP	0.021	0.095	-10000	0	-0.38	8	8
PDGFB-D/PDGFRB/APS/CBL	0.043	0.013	-10000	0	-10000	0	0
AKT1	0.037	0.15	0.28	3	-0.41	4	7
mol:PI-4-5-P2	0	0.001	-10000	0	-10000	0	0
mol:Sphingosine-1-phosphate	0.008	0.14	-10000	0	-0.4	11	11
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
FGR	-0.001	0.099	-10000	0	-0.45	5	5
mol:Ca2+	0.009	0.12	-10000	0	-0.45	5	5
MYC	0.01	0.2	0.37	1	-0.83	6	7
SHC1	0.032	0.008	-10000	0	-10000	0	0
HRAS/GDP	0.033	0.05	-10000	0	-0.26	2	2
LRP1/PDGFRB/PDGFB	0.06	0.027	-10000	0	-10000	0	0
GRB10	-0.001	0.13	-10000	0	-0.51	9	9
PTPN11	0.031	0.044	-10000	0	-0.51	1	1
GO:0007205	0.008	0.12	-10000	0	-0.46	5	5
PTEN	0.027	0.045	-10000	0	-0.51	1	1
GRB2	0.034	0.005	-10000	0	-10000	0	0
GRB7	0.033	0.007	-10000	0	-10000	0	0
PDGFB-D/PDGFRB/SHP2	0.045	0.037	-10000	0	-0.37	1	1
PDGFB-D/PDGFRB/GRB10	0.019	0.1	-10000	0	-0.37	9	9
cell cycle arrest	0.021	0.095	-10000	0	-0.37	8	8
HRAS	0.029	0.045	-10000	0	-0.51	1	1
HIF1A	0.028	0.14	0.27	3	-0.38	5	8
GAB1	0.003	0.14	-10000	0	-0.44	8	8
mol:GTP	0	0	-10000	0	-10000	0	0
DNM2	0.002	0.13	0.31	1	-0.42	8	9
PDGFB-D/PDGFRB	0.059	0.031	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
PDGFB-D/PDGFRB/LMW-PTP	0.047	0.016	-10000	0	-10000	0	0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB	0.001	0.14	-10000	0	-0.43	11	11
positive regulation of MAPKKK cascade	0.045	0.037	-10000	0	-0.37	1	1
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
mol:IP3	0.008	0.12	-10000	0	-0.46	5	5
E5	-0.001	0.002	-10000	0	-10000	0	0
CSK	0.034	0.004	-10000	0	-10000	0	0
PDGFB-D/PDGFRB/GRB7	0.047	0.016	-10000	0	-10000	0	0
SHB	0.019	0.076	-10000	0	-0.51	3	3
BLK	-0.06	0.18	-10000	0	-0.47	22	22
PTPN2	0.033	0.009	-10000	0	-10000	0	0
PDGFB-D/PDGFRB/SNX15	0.048	0.014	-10000	0	-10000	0	0
BCAR1	0.033	0.008	-10000	0	-10000	0	0
VAV2	-0.002	0.16	-10000	0	-0.52	8	8
CBL	0.034	0.005	-10000	0	-10000	0	0
PDGFB-D/PDGFRB/DEP1	0.044	0.038	-10000	0	-0.38	1	1
LCK	-0.038	0.18	-10000	0	-0.57	14	14
PDGFRB	0.031	0.015	-10000	0	-10000	0	0
ACP1	0.033	0.006	-10000	0	-10000	0	0
HCK	-0.018	0.16	-10000	0	-0.69	7	7
ABL1	0.003	0.12	0.23	3	-0.46	6	9
PDGFB-D/PDGFRB/CBL	0.004	0.15	-10000	0	-0.51	7	7
PTPN1	0.033	0.009	-10000	0	-10000	0	0
SNX15	0.034	0	-10000	0	-10000	0	0
STAT3	0.033	0.006	-10000	0	-10000	0	0
STAT1	0.011	0.1	-10000	0	-0.51	6	6
cell proliferation	0.014	0.18	0.36	1	-0.67	7	8
SLA	0.002	0.12	-10000	0	-0.51	8	8
actin cytoskeleton reorganization	0.058	0.094	0.34	4	-0.26	3	7
SRC	0.009	0.049	-10000	0	-0.33	1	1
PI3K	-0.034	0.096	-10000	0	-0.28	18	18
PDGFB-D/PDGFRB/GRB7/SHC	0.06	0.025	-10000	0	-10000	0	0
SH2B2	0	0	-10000	0	-10000	0	0
PLCgamma1/SPHK1	0.008	0.14	-10000	0	-0.41	11	11
LYN	0.005	0.074	-10000	0	-0.51	2	2
LRP1	0.034	0.004	-10000	0	-10000	0	0
SOS1	0.033	0.006	-10000	0	-10000	0	0
STAT5B	0.033	0.006	-10000	0	-10000	0	0
STAT5A	0.033	0.011	-10000	0	-10000	0	0
NCK1-2/p130 Cas	0.066	0.064	-10000	0	-0.27	2	2
SPHK1	-0.005	0.14	-10000	0	-0.51	10	10
EDG1	0	0.003	-10000	0	-10000	0	0
mol:DAG	0.008	0.12	-10000	0	-0.46	5	5
PLCG1	0.008	0.12	-10000	0	-0.47	5	5
NHERF/PDGFRB	0.01	0.13	-10000	0	-0.32	19	19
YES1	0.005	0.08	-10000	0	-0.54	2	2
cell migration	0.01	0.13	-10000	0	-0.32	19	19
SHC/Grb2/SOS1	0.083	0.046	-10000	0	-10000	0	0
SLC9A3R2	0.023	0.064	-10000	0	-0.51	2	2
SLC9A3R1	-0.033	0.17	-10000	0	-0.51	18	18
NHERF1-2/PDGFRB/PTEN	0.017	0.13	-10000	0	-0.3	20	20
FYN	-0.002	0.098	-10000	0	-0.53	4	4
DOK1	0.023	0.035	-10000	0	-10000	0	0
HRAS/GTP	0.021	0.034	-10000	0	-0.24	2	2
PDGFB	0.03	0.017	-10000	0	-10000	0	0
RAC1	-0.006	0.19	-10000	0	-0.64	9	9
PRKCD	0.024	0.041	0.19	2	-10000	0	2
FER	0.021	0.049	0.19	4	-0.3	1	5
MAPKKK cascade	0.01	0.069	0.35	2	-10000	0	2
RASA1	0.022	0.048	0.19	3	-0.29	1	4
NCK1	0.021	0.062	-10000	0	-0.51	2	2
NCK2	0.034	0.005	-10000	0	-10000	0	0
p62DOK/Csk	0.044	0.033	-10000	0	-10000	0	0
PDGFB-D/PDGFRB/SHB	0.034	0.061	-10000	0	-0.37	3	3
chemotaxis	0.004	0.12	0.23	3	-0.45	6	9
STAT1-3-5/STAT1-3-5	0.055	0.074	-10000	0	-0.27	5	5
Bovine Papilomavirus E5/PDGFRB	0.022	0.012	-10000	0	-10000	0	0
PTPRJ	0.03	0.044	-10000	0	-0.51	1	1

S1P4 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	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
GNAO1	0.032	0.011	-10000	0	-10000	0	0
CDC42/GTP	0.007	0.1	-10000	0	-0.31	7	7
PLCG1	-0.013	0.094	-10000	0	-0.31	8	8
mol:GTP	0	0	-10000	0	-10000	0	0
GNAI2	0.029	0.018	-10000	0	-10000	0	0
GNAI3	0.033	0.007	-10000	0	-10000	0	0
G12/G13	0.045	0.037	-10000	0	-0.37	1	1
cell migration	0.004	0.098	-10000	0	-0.3	7	7
S1PR5	0	0	-10000	0	-10000	0	0
S1PR4	0	0	-10000	0	-10000	0	0
MAPK3	-0.011	0.093	-10000	0	-0.32	7	7
MAPK1	-0.01	0.082	-10000	0	-0.23	15	15
S1P/S1P5/Gi	-0.007	0.099	-10000	0	-0.26	18	18
GNAI1	0.001	0.13	-10000	0	-0.51	9	9
CDC42/GDP	0.025	0.004	-10000	0	-10000	0	0
S1P/S1P5/G12	0.022	0.005	-10000	0	-10000	0	0
RHOA	0.02	0.039	0.19	5	-0.27	1	6
S1P/S1P4/Gi	-0.007	0.099	-10000	0	-0.26	18	18
mol:GDP	0	0	-10000	0	-10000	0	0
GNAZ	0.005	0.11	-10000	0	-0.51	7	7
S1P/S1P4/G12/G13	0.039	0.029	-10000	0	-0.28	1	1
GNA12	0.033	0.008	-10000	0	-10000	0	0
GNA13	0.03	0.045	-10000	0	-0.51	1	1
CDC42	0.034	0.005	-10000	0	-10000	0	0

Ras signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ERK1-2/ELK1	0	0.14	-9999	-0.44	6	6
MAP3K8	-0.012	0.14	-9999	-0.51	12	12
FOS	0.001	0.1	-9999	-0.41	4	4
PRKCA	0.025	0.048	-9999	-0.52	1	1
PTPN7	0.026	0.024	-9999	-10000	0	0
HRAS	0.029	0.045	-9999	-0.51	1	1
PRKCB	-0.001	0.005	-9999	-0.016	15	15
NRAS	0.026	0.047	-9999	-0.51	1	1
RAS family/GTP	0.035	0.073	-9999	-0.29	6	6
MAPK3	0.018	0.055	-9999	-0.37	1	1
MAP2K1	-0.006	0.083	-9999	-0.43	3	3
ELK1	0.027	0.021	-9999	-10000	0	0
BRAF	0	0.072	-9999	-0.41	4	4
mol:GTP	0	0.001	-9999	-0.004	17	17
MAPK1	0.005	0.11	-9999	-0.5	5	5
RAF1	0.005	0.05	-9999	-0.56	1	1
KRAS	0.017	0.086	-9999	-0.51	4	4

Aurora B signaling

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
Condensin I complex	-0.003	0.1	-9999	-0.38	6	6
STMN1	0.006	0.056	-9999	-0.38	3	3
Aurora B/RasGAP/Survivin	0.03	0.11	-9999	-0.35	11	11
Chromosomal passenger complex/Cul3 protein complex	-0.075	0.16	-9999	-0.27	41	41
BIRC5	-0.002	0.14	-9999	-0.52	10	10
DES	-0.035	0.23	-9999	-0.66	17	17
Aurora C/Aurora B/INCENP	0.054	0.046	-9999	-0.31	2	2
Aurora B/TACC1	0.031	0.037	-9999	-0.33	1	1
Aurora B/PP2A	0.041	0.051	-9999	-0.38	2	2
mol:GTP	0	0	-9999	-10000	0	0
CBX5	0.009	0.027	-9999	-0.22	2	2
mitotic metaphase/anaphase transition	0	0.004	-9999	-10000	0	0
NDC80	0.006	0.065	-9999	-0.53	2	2
Cul3 protein complex	-0.051	0.16	-9999	-0.32	37	37
KIF2C	-0.017	0.16	-9999	-0.6	8	8
PEBP1	0.023	0.077	-9999	-0.52	3	3
KIF20A	0.029	0.045	-9999	-0.52	1	1
mol:GDP	0	0	-9999	-10000	0	0
Aurora B/RasGAP	0.039	0.051	-9999	-0.38	2	2
SEPT1	0.029	0.045	-9999	-0.51	1	1
SMC2	0.019	0.087	-9999	-0.51	4	4
SMC4	0.018	0.046	-9999	-0.51	1	1
NSUN2/NPM1/Nucleolin	-0.007	0.17	-9999	-0.54	12	12
PSMA3	0.033	0.006	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	-0.001	0.003	-9999	-10000	0	0
H3F3B	0.015	0.029	-9999	-0.34	1	1
AURKB	0.028	0.047	-9999	-0.54	1	1
AURKC	0.033	0.006	-9999	-10000	0	0
CDCA8	0.026	0.065	-9999	-0.54	2	2
cytokinesis	-0.006	0.16	-9999	-0.82	4	4
Aurora B/Septin1	0.011	0.16	-9999	-0.74	4	4
AURKA	0.031	0.045	-9999	-0.52	1	1
INCENP	0.029	0.046	-9999	-0.52	1	1
KLHL13	-0.099	0.22	-9999	-0.51	35	35
BUB1	0.02	0.088	-9999	-0.52	4	4
hSgo1/Aurora B/Survivin	0.029	0.11	-9999	-0.37	10	10
EVI5	0.033	0.007	-9999	-10000	0	0
RhoA/GTP	0.024	0.16	-9999	-0.72	4	4
SGOL1	0.025	0.062	-9999	-0.51	2	2
CENPA	-0.005	0.15	-9999	-0.56	6	6
NCAPG	0	0	-9999	-10000	0	0
Aurora B/HC8 Proteasome	0.043	0.038	-9999	-0.39	1	1
NCAPD2	0.032	0.01	-9999	-10000	0	0
Aurora B/PP1-gamma	0.044	0.037	-9999	-0.39	1	1
RHOA	0.031	0.011	-9999	-10000	0	0
NCAPH	0.023	0.075	-9999	-0.51	3	3
NPM1	-0.025	0.15	-9999	-0.45	12	12
RASA1	0.028	0.044	-9999	-0.51	1	1
KLHL9	0.022	0.062	-9999	-0.51	2	2
mitotic prometaphase	-0.001	0.003	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.043	0.038	-9999	-0.39	1	1
PPP1CC	0.034	0.003	-9999	-10000	0	0
Centraspindlin	0.014	0.18	-9999	-0.82	4	4
RhoA/GDP	0.023	0.008	-9999	-10000	0	0
NSUN2	0.002	0.1	-9999	-0.31	12	12
MYLK	0.008	0.048	-9999	-0.33	3	3
KIF23	0.024	0.077	-9999	-0.52	3	3
VIM	-0.012	0.088	-9999	-0.38	8	8
RACGAP1	0.03	0.045	-9999	-0.52	1	1
mitosis	0	0	-9999	-10000	0	0
NCL	-0.004	0.09	-9999	-0.3	11	11
Chromosomal passenger complex	-0.013	0.15	-9999	-0.45	8	8
Chromosomal passenger complex/EVI5	0.055	0.13	-9999	-0.37	10	10
TACC1	0.028	0.014	-9999	-10000	0	0
PPP2R5D	0.03	0.044	-9999	-0.51	1	1
CUL3	0.034	0.005	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0

ErbB4 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF	-0.001	0.14	-10000	0	-0.61	4	4
epithelial cell differentiation	0.005	0.12	-10000	0	-0.71	2	2
ITCH	0.033	0.022	-10000	0	-10000	0	0
WWP1	0.008	0.17	-10000	0	-1.4	2	2
FYN	0.026	0.062	-10000	0	-0.51	2	2
EGFR	-0.031	0.17	-10000	0	-0.51	17	17
PRL	0.031	0.014	-10000	0	-10000	0	0
neuron projection morphogenesis	0.004	0.095	0.34	1	-0.48	2	3
PTPRZ1	-0.085	0.22	-10000	0	-0.51	33	33
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC	0.042	0.1	-10000	0	-0.42	2	2
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta	-0.004	0.1	-10000	0	-0.5	4	4
ADAM17	0.028	0.05	-10000	0	-0.34	2	2
ErbB4/ErbB4	0.016	0.099	-10000	0	-0.78	2	2
ErbB4/ErbB4/neuregulin 3/neuregulin 3	0.025	0.11	-10000	0	-0.59	3	3
NCOR1	0.032	0.008	-10000	0	-10000	0	0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn	0.004	0.12	-10000	0	-0.53	5	5
GRIN2B	-0.011	0.12	-10000	0	-0.56	4	4
ErbB4/ErbB2/betacellulin	0	0.12	-10000	0	-0.54	4	4
STAT1	0.011	0.1	-10000	0	-0.51	6	6
HBEGF	-0.023	0.16	-10000	0	-0.51	15	15
PRLR	0.02	0.05	-10000	0	-0.51	1	1
E4ICDs/ETO2	0.023	0.1	-10000	0	-0.59	3	3
axon guidance	0.02	0.12	0.36	1	-0.74	2	3
NEDD4	0.025	0.065	-10000	0	-0.51	2	2
Prolactin receptor/Prolactin receptor/Prolactin	0.032	0.044	-10000	0	-0.37	1	1
CBFA2T3	0.018	0.067	-10000	0	-0.51	2	2
ErbB4/ErbB2/HBEGF	-0.004	0.14	-10000	0	-0.55	5	5
MAPK3	0.013	0.094	0.34	1	-0.4	2	3
STAT1 (dimer)	0.02	0.12	-10000	0	-0.61	4	4
MAPK1	0.012	0.097	0.34	1	-0.49	2	3
JAK2	0.029	0.017	-10000	0	-10000	0	0
ErbB4/ErbB2/neuregulin 1 beta	-0.008	0.12	-10000	0	-0.6	4	4
NRG1	-0.015	0.096	-10000	0	-0.37	10	10
NRG3	0.022	0.075	-10000	0	-0.51	3	3
NRG2	0.03	0.019	-10000	0	-10000	0	0
NRG4	-0.027	0.15	-10000	0	-0.51	13	13
heart development	0.02	0.12	0.36	1	-0.74	2	3
neural crest cell migration	-0.008	0.12	-10000	0	-0.59	4	4
ERBB2	0.006	0.065	-10000	0	-0.51	2	2
WWOX/E4ICDs	0.03	0.097	-10000	0	-0.71	2	2
SHC1	0.032	0.008	-10000	0	-10000	0	0
ErbB4/EGFR/neuregulin 4	-0.023	0.16	-10000	0	-0.57	6	6
apoptosis	-0.012	0.1	0.56	3	-10000	0	3
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta	0.029	0.097	-10000	0	-0.71	2	2
ErbB4/ErbB2/epiregulin	0.007	0.11	-10000	0	-0.54	4	4
ErbB4/ErbB4/betacellulin/betacellulin	0.001	0.13	-10000	0	-0.71	2	2
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2	0.021	0.14	-10000	0	-0.63	3	3
MDM2	0.015	0.1	-10000	0	-0.71	2	2
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta	0.005	0.1	-10000	0	-0.45	4	4
STAT5A	0.016	0.12	0.33	1	-0.71	2	3
ErbB4/EGFR/neuregulin 1 beta	-0.026	0.16	-10000	0	-0.52	9	9
DLG4	0.031	0.012	-10000	0	-10000	0	0
GRB2/SHC	0.047	0.014	-10000	0	-10000	0	0
E4ICDs/TAB2/NCoR1	0.028	0.091	-10000	0	-0.67	2	2
STAT5A (dimer)	0.012	0.14	-10000	0	-0.79	2	2
MAP3K7IP2	0	0	-10000	0	-10000	0	0
STAT5B (dimer)	0.035	0.12	-10000	0	-0.71	2	2
LRIG1	-0.009	0.14	-10000	0	-0.51	11	11
EREG	-0.002	0.093	-10000	0	-0.51	4	4
BTC	-0.02	0.15	-10000	0	-0.51	13	13
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta	0.013	0.12	-10000	0	-0.75	2	2
ERBB4	0.016	0.1	-10000	0	-0.78	2	2
STAT5B	0.033	0.006	-10000	0	-10000	0	0
YAP1	0.005	0.11	-10000	0	-0.58	5	5
GRB2	0.034	0.005	-10000	0	-10000	0	0
ErbB4/ErbB2/neuregulin 4	-0.004	0.13	-10000	0	-0.6	4	4
glial cell differentiation	-0.028	0.089	0.66	2	-10000	0	2
WWOX	0.033	0.008	-10000	0	-10000	0	0
cell proliferation	-0.055	0.16	-10000	0	-0.55	9	9

a4b1 and a4b7 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ITGB1	0.025	0.062	-9999	-0.51	2	2
ITGB7	0.034	0.005	-9999	-10000	0	0
ITGA4	0.014	0.097	-9999	-0.51	5	5
alpha4/beta7 Integrin	0.033	0.076	-9999	-0.37	5	5
alpha4/beta1 Integrin	0.027	0.094	-9999	-0.42	6	6

PLK1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
regulation of centriole-centriole cohesion	0.007	0.046	0.15	14	-10000	0	14
BUB1B	-0.005	0.08	-10000	0	-0.34	7	7
PLK1	0.008	0.02	-10000	0	-0.14	1	1
PLK1S1	0.003	0.01	-10000	0	-0.053	1	1
KIF2A	0.004	0.017	-10000	0	-10000	0	0
regulation of mitotic centrosome separation	0.008	0.02	-10000	0	-0.14	1	1
GOLGA2	0.023	0.075	-10000	0	-0.51	3	3
Hec1/SPC24	0.021	0.045	-10000	0	-0.33	2	2
WEE1	0.007	0.089	-10000	0	-0.47	4	4
cytokinesis	0.005	0.083	-10000	0	-0.42	3	3
PP2A-alpha B56	0.045	0.16	-10000	0	-0.81	5	5
AURKA	0.011	0.027	-10000	0	-0.3	1	1
PICH/PLK1	0	0.096	-10000	0	-0.36	8	8
CENPE	-0.001	0.047	-10000	0	-0.32	3	3
RhoA/GTP	0.023	0.008	-10000	0	-10000	0	0
positive regulation of microtubule depolymerization	0.004	0.018	-10000	0	-10000	0	0
PPP2CA	0.032	0.008	-10000	0	-10000	0	0
FZR1	0.033	0.006	-10000	0	-10000	0	0
TPX2	0.01	0.046	-10000	0	-0.3	3	3
PAK1	0.027	0.047	-10000	0	-0.52	1	1
SPC24	0	0	-10000	0	-10000	0	0
FBXW11	0.032	0.008	-10000	0	-10000	0	0
CLSPN	0.008	0.041	-10000	0	-0.24	4	4
GORASP1	0.032	0.01	-10000	0	-10000	0	0
metaphase	0	0.001	0.012	1	-10000	0	1
mol:GTP	0	0	-10000	0	-10000	0	0
NLP	0.003	0.01	-10000	0	-0.053	1	1
G2 phase of mitotic cell cycle	-0.001	0.002	0.014	1	-0.012	1	2
STAG2	0.027	0.061	-10000	0	-0.51	2	2
GRASP65/GM130/RAB1/GTP	-0.02	0.15	-10000	0	-0.53	12	12
spindle elongation	0.008	0.02	-10000	0	-0.14	1	1
ODF2	0.034	0.004	-10000	0	-10000	0	0
BUB1	0.01	0.16	-10000	0	-0.88	5	5
TPT1	0.002	0.047	-10000	0	-0.19	8	8
CDC25C	-0.003	0.08	-10000	0	-0.3	10	10
CDC25B	0.029	0.045	-10000	0	-0.52	1	1
SGOL1	-0.007	0.046	-10000	0	-0.15	14	14
RHOA	0.031	0.011	-10000	0	-10000	0	0
CCNB1/CDK1	0.035	0.08	-10000	0	-0.39	4	4
CDC14B	0.008	0.002	-10000	0	-10000	0	0
CDC20	0.022	0.075	-10000	0	-0.51	3	3
PLK1/PBIP1	-0.002	0.058	-10000	0	-0.28	6	6
mitosis	-0.002	0.004	0.035	1	-10000	0	1
FBXO5	0.006	0.028	0.14	2	-10000	0	2
CDC2	0.001	0.004	-10000	0	-0.017	4	4
NDC80	0.026	0.062	-10000	0	-0.51	2	2
metaphase plate congression	0.009	0.041	-10000	0	-0.23	4	4
ERCC6L	0.001	0.11	-10000	0	-0.38	8	8
NLP/gamma Tubulin	0.004	0.018	-10000	0	-0.094	1	1
microtubule cytoskeleton organization	0.002	0.046	-10000	0	-0.19	8	8
G2/M transition DNA damage checkpoint	-0.001	0.002	0.013	1	-10000	0	1
PPP1R12A	0.031	0.044	-10000	0	-0.51	1	1
interphase	-0.001	0.002	0.013	1	-10000	0	1
PLK1/PRC1-2	0.04	0.065	-10000	0	-0.46	2	2
GRASP65/GM130/RAB1/GTP/PLK1	0.047	0.053	-10000	0	-0.26	3	3
RAB1A	0.032	0.01	-10000	0	-10000	0	0
prophase	0	0	-10000	0	-10000	0	0
Aurora A/BORA	0.006	0.018	-10000	0	-0.15	1	1
mitotic prometaphase	-0.001	0.003	0.018	4	-10000	0	4
proteasomal ubiquitin-dependent protein catabolic process	0.014	0.07	-10000	0	-0.49	2	2
microtubule-based process	0.026	0.039	-10000	0	-0.39	1	1
Golgi organization	0.008	0.02	-10000	0	-0.14	1	1
Cohesin/SA2	0.023	0.041	-10000	0	-0.23	3	3
PPP1CB/MYPT1	0.042	0.05	-10000	0	-0.37	2	2
KIF20A	0.029	0.044	-10000	0	-0.51	1	1
APC/C/CDC20	0.023	0.055	-10000	0	-0.34	3	3
PPP2R1A	0.033	0.007	-10000	0	-10000	0	0
chromosome segregation	-0.002	0.057	-10000	0	-0.28	6	6
PRC1	0.025	0.063	-10000	0	-0.51	2	2
ECT2	0.097	0.15	0.22	80	-0.29	10	90
C13orf34	0.006	0.018	-10000	0	-0.13	1	1
NUDC	0.009	0.041	-10000	0	-0.23	4	4
regulation of attachment of spindle microtubules to kinetochore	-0.005	0.079	-10000	0	-0.33	7	7
spindle assembly	0.006	0.016	-10000	0	-0.09	1	1
spindle stabilization	0.003	0.01	-10000	0	-0.053	1	1
APC/C/HCDH1	0.031	0.006	-10000	0	-10000	0	0
MKLP2/PLK1	0.026	0.039	-10000	0	-0.39	1	1
CCNB1	0.025	0.064	-10000	0	-0.52	2	2
PPP1CB	0.029	0.045	-10000	0	-0.51	1	1
BTRC	0.033	0.006	-10000	0	-10000	0	0
ROCK2	0.006	0.057	-10000	0	-0.27	3	3
TUBG1	0.006	0.036	-10000	0	-0.18	5	5
G2/M transition of mitotic cell cycle	0	0.07	-10000	0	-0.38	4	4
MLF1IP	-0.008	0.074	-10000	0	-0.37	6	6
INCENP	0.03	0.045	-10000	0	-0.51	1	1

Class I PI3K signaling events mediated by Akt

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.015	0.006	-10000	0	-10000	0	0
BAD/BCL-XL/YWHAZ	0.044	0.03	-10000	0	-10000	0	0
CDKN1B	0.024	0.095	-10000	0	-0.42	5	5
CDKN1A	0.018	0.092	-10000	0	-0.42	5	5
FRAP1	0	0	-10000	0	-10000	0	0
PRKDC	0.028	0.044	-10000	0	-0.51	1	1
FOXO3	0.019	0.089	-10000	0	-0.45	4	4
AKT1	0.016	0.09	-10000	0	-0.44	5	5
BAD	0.034	0	-10000	0	-10000	0	0
AKT3	0.009	0.048	-10000	0	-0.32	3	3
mol:GTP	0	0	-10000	0	-10000	0	0
FOXO4	0.017	0.088	-10000	0	-0.42	5	5
AKT1/ASK1	0.04	0.11	-10000	0	-0.5	5	5
BAD/YWHAZ	0.059	0.041	-10000	0	-0.32	1	1
RICTOR	0.027	0.014	-10000	0	-10000	0	0
RAF1	0.032	0.009	-10000	0	-10000	0	0
JNK cascade	-0.038	0.11	0.48	5	-10000	0	5
TSC1	0.016	0.09	-10000	0	-0.42	5	5
YWHAZ	0.025	0.062	-10000	0	-0.51	2	2
AKT1/RAF1	0.046	0.097	-10000	0	-0.41	5	5
EP300	0.005	0.12	-10000	0	-0.51	8	8
mol:GDP	0.016	0.089	-10000	0	-0.43	5	5
mol:PI-3-4-5-P3	0	0	-10000	0	-10000	0	0
TSC2	0.019	0.073	-10000	0	-0.37	4	4
YWHAQ	0.033	0.007	-10000	0	-10000	0	0
TBC1D4	0.003	0.042	-10000	0	-0.29	3	3
MAP3K5	0.022	0.075	-10000	0	-0.51	3	3
MAPKAP1	0.034	0.004	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.015	0.12	0.47	6	-0.2	1	7
YWHAH	0.026	0.062	-10000	0	-0.51	2	2
AKT1S1	0.015	0.09	-10000	0	-0.42	5	5
CASP9	0.019	0.085	-10000	0	-0.45	4	4
YWHAB	0.033	0.006	-10000	0	-10000	0	0
p27Kip1/KPNA1	0.037	0.1	0.26	1	-0.45	5	6
GBL	0	0	-10000	0	-10000	0	0
PDK1/Src/Hsp90	0.058	0.039	-10000	0	-0.32	1	1
YWHAE	0.032	0.008	-10000	0	-10000	0	0
SRC	0.032	0.012	-10000	0	-10000	0	0
AKT2/p21CIP1	0.014	0.086	-10000	0	-0.41	4	4
KIAA1303	0	0	-10000	0	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL	0.021	0.038	-10000	0	-0.3	1	1
CHUK	0.02	0.074	-10000	0	-0.37	4	4
BAD/BCL-XL	0.046	0.091	-10000	0	-0.42	4	4
mTORC2	0.034	0.018	-10000	0	-10000	0	0
AKT2	0.014	0.028	-10000	0	-0.32	1	1
FOXO1-3a-4/14-3-3 family	0.016	0.16	-10000	0	-0.66	6	6
PDPK1	0.03	0.044	-10000	0	-0.51	1	1
MDM2	0.018	0.091	-10000	0	-0.4	5	5
MAPKKK cascade	-0.046	0.095	0.4	5	-10000	0	5
MDM2/Cbp/p300	0.05	0.12	0.27	2	-0.42	6	8
TSC1/TSC2	0.008	0.086	-10000	0	-0.41	5	5
proteasomal ubiquitin-dependent protein catabolic process	0.047	0.12	0.26	2	-0.4	6	8
glucose import	-0.002	0.037	-10000	0	-0.27	3	3
mTOR/RHEB/GDP/Raptor/GBL/PRAS40	0.022	0.061	0.24	1	-0.26	4	5
response to stress	0	0	-10000	0	-10000	0	0
SLC2A4	-0.002	0.038	-10000	0	-0.27	3	3
GSK3A	0.02	0.086	0.27	1	-0.45	4	5
FOXO1	0.01	0.1	-10000	0	-0.47	5	5
GSK3B	0.033	0.11	0.27	2	-0.42	5	7
SFN	-0.027	0.17	-10000	0	-0.51	17	17
G1/S transition of mitotic cell cycle	0.049	0.12	0.28	11	-0.44	4	15
p27Kip1/14-3-3 family	0.015	0.13	-10000	0	-0.64	4	4
PRKACA	0.033	0.007	-10000	0	-10000	0	0
KPNA1	0.025	0.045	-10000	0	-0.51	1	1
HSP90AA1	0.033	0.008	-10000	0	-10000	0	0
YWHAG	0.034	0.005	-10000	0	-10000	0	0
RHEB	0.034	0.005	-10000	0	-10000	0	0
CREBBP	0.033	0.007	-10000	0	-10000	0	0

Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.005	0.098	-10000	0	-0.46	6	6
CRKL	0.031	0.012	-10000	0	-10000	0	0
Rac1/GDP	0.025	0.005	-10000	0	-10000	0	0
DOCK1	0.033	0.007	-10000	0	-10000	0	0
ITGA4	0.014	0.097	-10000	0	-0.51	5	5
alpha4/beta7 Integrin/MAdCAM1	0.061	0.072	-10000	0	-0.28	5	5
EPO	0.031	0.017	-10000	0	-10000	0	0
alpha4/beta7 Integrin	0.033	0.076	-10000	0	-0.37	5	5
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.032	0.008	-10000	0	-10000	0	0
alpha4/beta1 Integrin	0.027	0.094	-10000	0	-0.42	6	6
EPO/EPOR (dimer)	0.045	0.019	-10000	0	-10000	0	0
lamellipodium assembly	0.049	0.14	-10000	0	-0.48	7	7
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
PI3K	0.004	0.076	-10000	0	-0.3	7	7
ARF6	0.026	0.062	-10000	0	-0.51	2	2
JAK2	0.009	0.075	-10000	0	-0.32	6	6
PXN	0.034	0.004	-10000	0	-10000	0	0
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
MADCAM1	0.032	0.011	-10000	0	-10000	0	0
cell adhesion	0.058	0.071	-10000	0	-0.28	5	5
CRKL/CBL	0.046	0.016	-10000	0	-10000	0	0
ITGB1	0.025	0.062	-10000	0	-0.51	2	2
SRC	-0.013	0.11	-10000	0	-0.35	12	12
ITGB7	0.034	0.005	-10000	0	-10000	0	0
RAC1	0.033	0.006	-10000	0	-10000	0	0
alpha4/beta1 Integrin/VCAM1	0.017	0.13	-10000	0	-0.38	13	13
p130Cas/Crk/Dock1	0.017	0.11	-10000	0	-0.32	11	11
VCAM1	-0.005	0.13	-10000	0	-0.51	9	9
RHOA	0.031	0.011	-10000	0	-10000	0	0
alpha4/beta1 Integrin/Paxillin/GIT1	0.056	0.1	-10000	0	-0.36	7	7
BCAR1	-0.036	0.099	0.19	3	-0.33	12	15
EPOR	0.033	0.006	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
CBL	0.034	0.005	-10000	0	-10000	0	0
GIT1	0.026	0.062	-10000	0	-0.51	2	2
Rac1/GTP	0.049	0.15	-10000	0	-0.58	5	5

S1P5 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-10000	0	-10000	0	0
telencephalon oligodendrocyte cell migration	-0.005	0.097	0.3	7	-10000	0	7
GNAI2	0.029	0.018	-10000	0	-10000	0	0
S1P/S1P5/G12	0.022	0.005	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
GNAO1	0.032	0.011	-10000	0	-10000	0	0
RhoA/GTP	0.008	0.1	-10000	0	-0.3	7	7
negative regulation of cAMP metabolic process	-0.006	0.098	-10000	0	-0.26	18	18
GNAZ	0.005	0.11	-10000	0	-0.51	7	7
GNAI3	0.033	0.007	-10000	0	-10000	0	0
GNA12	0.033	0.008	-10000	0	-10000	0	0
S1PR5	0	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
S1P/S1P5/Gi	-0.007	0.099	-10000	0	-0.26	18	18
RhoA/GDP	0.023	0.008	-10000	0	-10000	0	0
RHOA	0.031	0.011	-10000	0	-10000	0	0
GNAI1	0.001	0.13	-10000	0	-0.51	9	9

Paxillin-dependent events mediated by a4b1

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.031	0.012	-10000	0	-10000	0	0
Rac1/GDP	0.033	0.016	-10000	0	-10000	0	0
DOCK1	0.033	0.007	-10000	0	-10000	0	0
ITGA4	0.014	0.097	-10000	0	-0.51	5	5
RAC1	0.033	0.006	-10000	0	-10000	0	0
alpha4/beta7 Integrin	0.033	0.076	-10000	0	-0.37	5	5
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.032	0.008	-10000	0	-10000	0	0
alpha4/beta1 Integrin	0.044	0.087	-10000	0	-0.36	6	6
alpha4/beta7 Integrin/Paxillin	0.04	0.064	-10000	0	-0.29	5	5
lamellipodium assembly	0.008	0.13	-10000	0	-0.38	13	13
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
PI3K	0.004	0.076	-10000	0	-0.3	7	7
ARF6	0.026	0.062	-10000	0	-0.51	2	2
TLN1	0.031	0.01	-10000	0	-10000	0	0
PXN	0.016	0.004	-10000	0	-10000	0	0
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
ARF6/GTP	0.043	0.096	-10000	0	-0.3	9	9
cell adhesion	0.053	0.076	-10000	0	-0.32	4	4
CRKL/CBL	0.046	0.016	-10000	0	-10000	0	0
alpha4/beta1 Integrin/Paxillin	0.035	0.079	-10000	0	-0.33	6	6
ITGB1	0.025	0.062	-10000	0	-0.51	2	2
ITGB7	0.034	0.005	-10000	0	-10000	0	0
ARF6/GDP	0.026	0.063	-10000	0	-0.5	2	2
alpha4/beta1 Integrin/Paxillin/VCAM1	0.029	0.12	-10000	0	-0.33	13	13
p130Cas/Crk/Dock1	0.061	0.024	-10000	0	-10000	0	0
VCAM1	-0.005	0.13	-10000	0	-0.51	9	9
alpha4/beta1 Integrin/Paxillin/Talin	0.055	0.077	-10000	0	-0.32	4	4
alpha4/beta1 Integrin/Paxillin/GIT1	0.05	0.096	-10000	0	-0.34	7	7
BCAR1	0.033	0.008	-10000	0	-10000	0	0
mol:GDP	-0.048	0.094	0.34	7	-10000	0	7
CBL	0.034	0.005	-10000	0	-10000	0	0
PRKACA	0.033	0.007	-10000	0	-10000	0	0
GIT1	0.026	0.062	-10000	0	-0.51	2	2
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton	0.055	0.077	-10000	0	-0.32	4	4
Rac1/GTP	0.006	0.14	-10000	0	-0.42	13	13

Atypical NF-kappaB pathway

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
BCL3/RelA	0.034	0.075	-9999	-0.37	5	5
FBXW11	0.032	0.008	-9999	-10000	0	0
NF kappa B1 p50/c-Rel	0.017	0.063	-9999	-0.31	5	5
NF kappa B1 p50/RelA/I kappa B alpha	0.019	0.093	-9999	-0.42	3	3
NFKBIA	0.002	0.091	-9999	-0.27	12	12
MAPK14	0.034	0.009	-9999	-10000	0	0
NF kappa B1 p105/p50	0.031	0.015	-9999	-10000	0	0
ARRB2	0.018	0.005	-9999	-10000	0	0
REL	0.005	0.11	-9999	-0.51	7	7
response to oxidative stress	0	0	-9999	-10000	0	0
BCL3/NF kappa B1 p50	0.023	0.057	-9999	-0.31	4	4
response to UV	0	0	-9999	-10000	0	0
NF kappa B1 p105/RelA	0.033	0.014	-9999	-10000	0	0
PIK3CA	0.009	0.062	-9999	-0.51	2	2
NF kappa B1 p50 dimer	0.024	0.009	-9999	-10000	0	0
PIK3R1	0.006	0.099	-9999	-0.51	5	5
NFKB1	0.015	0.006	-9999	-10000	0	0
RELA	0.034	0	-9999	-10000	0	0
positive regulation of anti-apoptosis	0.007	0.088	-9999	-0.24	14	14
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2	0.02	0.093	-9999	-0.42	3	3
SRC	0.032	0.012	-9999	-10000	0	0
PI3K	0.004	0.076	-9999	-0.3	7	7
NF kappa B1 p50/RelA	0.007	0.089	-9999	-0.24	14	14
IKBKB	0.031	0.011	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.032	0.008	-9999	-10000	0	0
SYK	0.012	0.1	-9999	-0.51	6	6
I kappa B alpha/PIK3R1	0.004	0.1	-9999	-0.3	10	10
cell death	0.019	0.09	-9999	-0.4	3	3
NF kappa B1 p105/c-Rel	0.017	0.063	-9999	-0.31	5	5
LCK	-0.004	0.13	-9999	-0.51	10	10
BCL3	0.015	0.096	-9999	-0.51	5	5

Regulation of p38-alpha and p38-beta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
RIP1/MEKK3	0.044	0.012	-10000	0	-10000	0	0
response to insulin stimulus	0	0	-10000	0	-10000	0	0
RIPK1	0.033	0.006	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
MAP2K6	0.015	0.096	-10000	0	-0.51	5	5
mol:GTP	0	0	-10000	0	-10000	0	0
MAP2K4	0.029	0.044	-10000	0	-0.51	1	1
RAC1-CDC42/GTP/PAK family	0.006	0.029	-10000	0	-0.2	2	2
response to UV	0	0	-10000	0	-10000	0	0
YES1	0.028	0.044	-10000	0	-0.51	1	1
interleukin-1 receptor activity	0	0	-10000	0	-10000	0	0
tumor necrosis factor receptor activity	0	0	-10000	0	-10000	0	0
MAP3K3	0.033	0.01	-10000	0	-10000	0	0
FYN	0.026	0.062	-10000	0	-0.51	2	2
MAP3K12	0.034	0.005	-10000	0	-10000	0	0
FGR	0.033	0.01	-10000	0	-10000	0	0
p38 alpha/TAB1	-0.037	0.1	-10000	0	-0.34	12	12
PRKG1	0.03	0.019	-10000	0	-10000	0	0
DUSP8	0.023	0.064	-10000	0	-0.51	2	2
PGK/cGMP/p38 alpha	0.015	0.12	-10000	0	-0.36	10	10
apoptosis	-0.035	0.098	-10000	0	-0.32	12	12
RAL/GTP	0.02	0.089	-10000	0	-0.31	10	10
LYN	0.029	0.044	-10000	0	-0.51	1	1
DUSP1	0.019	0.066	-10000	0	-0.51	2	2
PAK1	0.028	0.046	-10000	0	-0.51	1	1
SRC	0.032	0.012	-10000	0	-10000	0	0
RAC1/OSM/MEKK3/MKK3	0.076	0.034	-10000	0	-10000	0	0
TRAF6	0.023	0.075	-10000	0	-0.51	3	3
RAC1	0.033	0.006	-10000	0	-10000	0	0
epidermal growth factor receptor activity	0	0	-10000	0	-10000	0	0
mol:LPS	0	0	-10000	0	-10000	0	0
mol:cGMP	0	0	-10000	0	-10000	0	0
CCM2	0.033	0.006	-10000	0	-10000	0	0
RAC1-CDC42/GTP	0.044	0.011	-10000	0	-10000	0	0
MAPK11	0.015	0.14	0.25	2	-0.43	8	10
BLK	0.013	0.068	-10000	0	-0.51	2	2
HCK	0.006	0.11	-10000	0	-0.51	7	7
MAP2K3	0.032	0.009	-10000	0	-10000	0	0
DUSP16	0.024	0.063	-10000	0	-0.51	2	2
DUSP10	0.016	0.088	-10000	0	-0.51	4	4
TRAF6/MEKK3	0.036	0.046	-10000	0	-0.28	3	3
MAP3K7IP1	0	0	-10000	0	-10000	0	0
MAPK14	0.011	0.14	0.22	2	-0.4	10	12
positive regulation of innate immune response	0.017	0.16	0.25	3	-0.48	8	11
LCK	-0.004	0.13	-10000	0	-0.51	10	10
p38alpha-beta/MKP7	0.024	0.15	0.32	1	-0.47	8	9
p38alpha-beta/MKP5	0.023	0.16	0.32	1	-0.46	8	9
PGK/cGMP	0.023	0.012	-10000	0	-10000	0	0
PAK2	0.014	0.046	-10000	0	-0.51	1	1
p38alpha-beta/MKP1	0.023	0.15	0.32	1	-0.46	8	9
CDC42	0.034	0.005	-10000	0	-10000	0	0
RALB	0.001	0.13	-10000	0	-0.51	9	9
RALA	0.029	0.044	-10000	0	-0.51	1	1
PAK3	0.025	0.03	-10000	0	-10000	0	0

Regulation of Telomerase

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Telomerase catalytic core complex	-0.042	0.22	-9999	-0.92	5	5
RAD9A	0.034	0.005	-9999	-10000	0	0
AP1	-0.022	0.16	-9999	-0.42	18	18
IFNAR2	0.024	0.063	-9999	-0.51	2	2
AKT1	0.006	0.072	-9999	-0.32	5	5
ER alpha/Oestrogen	0	0.084	-9999	-0.37	7	7
NFX1/SIN3/HDAC complex	0.024	0.063	-9999	-0.32	3	3
EGF	-0.031	0.15	-9999	-0.51	13	13
SMG5	0.033	0.007	-9999	-10000	0	0
SMG6	0.032	0.008	-9999	-10000	0	0
SP3/HDAC2	0.046	0.025	-9999	-10000	0	0
TERT/c-Abl	-0.026	0.21	-9999	-0.84	5	5
SAP18	0.033	0.007	-9999	-10000	0	0
MRN complex	0.061	0.023	-9999	-10000	0	0
WT1	-0.016	0.14	-9999	-0.51	11	11
WRN	0.03	0.011	-9999	-10000	0	0
SP1	0.024	0.065	-9999	-0.52	2	2
SP3	0.034	0.005	-9999	-10000	0	0
TERF2IP	0.032	0.012	-9999	-10000	0	0
Telomerase/Nucleolin	-0.011	0.2	-9999	-0.76	5	5
Mad/Max	0.042	0.04	-9999	-0.37	1	1
TERT	-0.044	0.23	-9999	-0.97	5	5
CCND1	-0.075	0.34	-9999	-1.2	12	12
MAX	0.033	0.008	-9999	-10000	0	0
RBBP7	0.032	0.011	-9999	-10000	0	0
RBBP4	0.03	0.044	-9999	-0.51	1	1
TERF2	0.028	0.015	-9999	-10000	0	0
PTGES3	0.034	0.004	-9999	-10000	0	0
SIN3A	0.034	0.003	-9999	-10000	0	0
Telomerase/911	0.038	0.089	-9999	-0.42	3	3
CDKN1B	-0.062	0.14	-9999	-0.33	32	32
RAD1	0.025	0.045	-9999	-0.51	1	1
XRCC5	0.034	0.005	-9999	-10000	0	0
XRCC6	0.033	0.007	-9999	-10000	0	0
SAP30	0.032	0.01	-9999	-10000	0	0
TRF2/PARP2	0.044	0.019	-9999	-10000	0	0
UBE3A	0.034	0.005	-9999	-10000	0	0
JUN	0.004	0.11	-9999	-0.51	7	7
E6	0	0.003	-9999	-10000	0	0
HPV-16 E6/E6AP	0.023	0.012	-9999	-10000	0	0
FOS	-0.029	0.16	-9999	-0.51	14	14
IFN-gamma/IRF1	-0.063	0.18	-9999	-0.39	33	33
PARP2	0.033	0.008	-9999	-10000	0	0
BLM	0.023	0.075	-9999	-0.51	3	3
Telomerase	0.042	0.068	-9999	-0.28	1	1
IRF1	0.017	0.088	-9999	-0.5	4	4
ESR1	0	0.12	-9999	-0.51	7	7
KU/TER	0.048	0.013	-9999	-10000	0	0
ATM/TRF2	0.045	0.035	-9999	-0.34	1	1
ubiquitin-dependent protein catabolic process	0.028	0.065	-9999	-0.28	2	2
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex	0.028	0.066	-9999	-0.29	2	2
HDAC1	0.033	0.01	-9999	-10000	0	0
HDAC2	0.03	0.02	-9999	-10000	0	0
ATM	0.013	0.036	-9999	-0.4	1	1
SMAD3	-0.002	0.081	-9999	-0.37	7	7
ABL1	0.034	0.004	-9999	-10000	0	0
MXD1	0.027	0.047	-9999	-0.51	1	1
MRE11A	0.034	0.005	-9999	-10000	0	0
HUS1	0.029	0.044	-9999	-0.51	1	1
RPS6KB1	0.034	0.004	-9999	-10000	0	0
TERT/NF kappa B1/14-3-3	-0.008	0.22	-9999	-0.79	6	6
NR2F2	0.018	0.086	-9999	-0.5	4	4
MAPK3	0.013	0.014	-9999	-10000	0	0
MAPK1	0.01	0.034	-9999	-0.38	1	1
TGFB1/TGF beta receptor Type II	0.033	0.006	-9999	-10000	0	0
NFKB1	0.033	0.008	-9999	-10000	0	0
HNRNPC	0.033	0.007	-9999	-10000	0	0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis	0.013	0.036	-9999	-0.4	1	1
NBN	0.032	0.008	-9999	-10000	0	0
EGFR	-0.031	0.17	-9999	-0.51	17	17
mol:Oestrogen	0	0.002	-9999	-10000	0	0
EGF/EGFR	-0.049	0.17	-9999	-0.41	26	26
MYC	0.012	0.096	-9999	-0.51	5	5
IL2	0.03	0.019	-9999	-10000	0	0
KU	0.048	0.013	-9999	-10000	0	0
RAD50	0.032	0.008	-9999	-10000	0	0
HSP90AA1	0.033	0.008	-9999	-10000	0	0
TGFB1	0.033	0.006	-9999	-10000	0	0
TRF2/BLM	0.037	0.057	-9999	-0.35	3	3
FRAP1	0	0	-9999	-10000	0	0
KU/TERT	-0.017	0.21	-9999	-0.84	5	5
SP1/HDAC2	0.04	0.057	-9999	-0.38	2	2
PINX1	0.029	0.012	-9999	-10000	0	0
Telomerase/EST1A	-0.012	0.2	-9999	-0.76	5	5
Smad3/Myc	0.009	0.092	-9999	-0.34	9	9
911 complex	0.048	0.053	-9999	-0.32	2	2
IFNG	-0.094	0.21	-9999	-0.5	32	32
Telomerase/PinX1	-0.015	0.19	-9999	-0.75	5	5
Telomerase/AKT1/mTOR/p70S6K	0.013	0.11	-9999	-0.61	2	2
SIN3B	0.033	0.006	-9999	-10000	0	0
YWHAE	0.032	0.008	-9999	-10000	0	0
Telomerase/EST1B	-0.009	0.19	-9999	-0.76	5	5
response to DNA damage stimulus	0.006	0.016	-9999	-0.13	1	1
MRN complex/TRF2/Rap1	0.082	0.039	-9999	-10000	0	0
TRF2/WRN	0.04	0.025	-9999	-10000	0	0
Telomerase/hnRNP C1/C2	-0.012	0.2	-9999	-0.76	5	5
E2F1	0.03	0.016	-9999	-10000	0	0
ZNFX1	0.03	0.044	-9999	-0.51	1	1
PIF1	0.034	0.004	-9999	-10000	0	0
NCL	0.034	0.005	-9999	-10000	0	0
DKC1	0.033	0.006	-9999	-10000	0	0
telomeric DNA binding	0	0	-9999	-10000	0	0

Insulin Pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CBL/APS/CAP	0.035	0.074	-10000	0	-0.25	8	8
TC10/GTP	0.037	0.049	-10000	0	-0.26	3	3
Insulin Receptor/Insulin/IRS1/Shp2	0.058	0.094	-10000	0	-0.29	9	9
HRAS	0.029	0.045	-10000	0	-0.51	1	1
APS homodimer	0	0	-10000	0	-10000	0	0
GRB14	-0.047	0.18	-10000	0	-0.51	21	21
FOXO3	0.023	0.068	-10000	0	-0.66	1	1
AKT1	0.024	0.16	0.33	1	-0.45	5	6
INSR	0.032	0.045	-10000	0	-0.51	1	1
Insulin Receptor/Insulin	0.074	0.047	-10000	0	-0.25	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
GRB10	-0.001	0.13	-10000	0	-0.51	9	9
SORBS1	0.029	0.022	-10000	0	-10000	0	0
CRK	0.032	0.008	-10000	0	-10000	0	0
PTPN1	0.016	0.038	-10000	0	-0.24	1	1
CAV1	-0.027	0.12	-10000	0	-0.31	20	20
CBL/APS/CAP/Crk-II/C3G	0.071	0.031	-10000	0	-10000	0	0
Insulin Receptor/Insulin/IRS1/NCK2	0.058	0.09	-10000	0	-0.29	8	8
mol:GDP	0	0	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	-0.002	0.086	-10000	0	-0.26	13	13
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B	0.021	0.095	-10000	0	-0.45	2	2
RPS6KB1	0.02	0.15	0.31	1	-0.42	5	6
PARD6A	0.024	0.03	-10000	0	-10000	0	0
CBL	0.034	0.005	-10000	0	-10000	0	0
tumor necrosis factor-mediated signaling pathway	0	0	-10000	0	-10000	0	0
DOK1	0.029	0.019	-10000	0	-10000	0	0
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
Insulin Receptor/Insuli/IRS1/GRB2/Shc	0.03	0.15	-10000	0	-0.42	5	5
HRAS/GTP	0.005	0.06	-10000	0	-0.24	7	7
Insulin Receptor	0.032	0.045	-10000	0	-0.51	1	1
Insulin Receptor/Insuli/IRS1/GRB2/SHC	0.069	0.089	-10000	0	-0.28	7	7
PRKCI	-0.035	0.16	-10000	0	-0.57	11	11
Insulin Receptor/Insulin/GRB14/PDK1	-0.039	0.12	-10000	0	-0.31	18	18
SHC1	0.032	0.008	-10000	0	-10000	0	0
negative regulation of MAPKKK cascade	0.043	0.054	-10000	0	-10000	0	0
PI3K	0.002	0.092	-10000	0	-0.26	13	13
NCK2	0.034	0.005	-10000	0	-10000	0	0
RHOQ	0.02	0.075	-10000	0	-0.51	3	3
mol:H2O2	0.001	0.004	-10000	0	-10000	0	0
HRAS/GDP	0.021	0.034	-10000	0	-0.24	2	2
AKT2	0.018	0.16	0.33	1	-0.45	4	5
PRKCZ	-0.02	0.11	-10000	0	-0.59	5	5
SH2B2	0	0	-10000	0	-10000	0	0
SHC/SHIP	0.007	0.065	-10000	0	-0.26	8	8
F2RL2	0.007	0.072	-10000	0	-0.51	2	2
TRIP10	0.031	0.017	-10000	0	-10000	0	0
Insulin Receptor/Insulin/Shc	0.06	0.036	-10000	0	-0.27	1	1
TC10/GTP/CIP4/Exocyst	0.031	0.053	-10000	0	-0.31	3	3
Insulin Receptor/Insulin/SHC/GRB2/Sos1	0.088	0.049	-10000	0	-0.26	1	1
RAPGEF1	0.034	0.004	-10000	0	-10000	0	0
RASA1	0.028	0.044	-10000	0	-0.51	1	1
NCK1	0.021	0.062	-10000	0	-0.51	2	2
CBL/APS/CAP/Crk-II	0.057	0.026	-10000	0	-10000	0	0
TC10/GDP	0.015	0.054	-10000	0	-0.37	3	3
Insulin Receptor/Insulin/SHC/GRB10	0.055	0.092	-10000	0	-0.29	8	8
INPP5D	-0.019	0.059	-10000	0	-0.27	8	8
SOS1	0.033	0.006	-10000	0	-10000	0	0
SGK1	-0.006	0.01	-10000	0	-10000	0	0
mol:cAMP	0	0	-10000	0	-10000	0	0
PTPN11	0.031	0.044	-10000	0	-0.51	1	1
IRS1	0.006	0.11	-10000	0	-0.51	7	7
p62DOK/RasGAP	0.043	0.055	-10000	0	-10000	0	0
INS	0.036	0.01	-10000	0	-10000	0	0
mol:PI-3-4-P2	-0.019	0.059	-10000	0	-0.27	8	8
GRB2	0.034	0.005	-10000	0	-10000	0	0
EIF4EBP1	0.014	0.15	0.31	1	-0.42	6	7
PTPRA	0.035	0.01	-10000	0	-10000	0	0
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
TC10/GTP/CIP4	0.031	0.053	-10000	0	-0.31	3	3
PDPK1	0.03	0.044	-10000	0	-0.51	1	1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos	0.018	0.065	-10000	0	-0.26	2	2
Insulin Receptor/Insulin/IRS1	0.042	0.083	-10000	0	-0.29	8	8
Insulin Receptor/Insulin/IRS3	0.049	0.038	-10000	0	-0.37	1	1
Par3/Par6	0.029	0.077	-10000	0	-0.28	5	5

Angiopoietin receptor Tie2-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	0.006	0.17	-9999	-0.65	6	6
NCK1/PAK1/Dok-R	-0.04	0.089	-9999	-0.38	6	6
NCK1/Dok-R	-0.008	0.19	-9999	-0.81	6	6
PIK3CA	0.009	0.062	-9999	-0.51	2	2
mol:beta2-estradiol	-0.007	0.012	-9999	-10000	0	0
RELA	0.034	0	-9999	-10000	0	0
SHC1	0.033	0.008	-9999	-10000	0	0
Rac/GDP	0.025	0.005	-9999	-10000	0	0
F2	0.013	0.027	-9999	-10000	0	0
TNIP2	0.027	0.045	-9999	-0.51	1	1
NF kappa B/RelA	0.039	0.16	-9999	-0.7	6	6
FN1	-0.009	0.13	-9999	-0.51	10	10
PLD2	-0.004	0.17	-9999	-0.82	6	6
PTPN11	0.031	0.044	-9999	-0.51	1	1
GRB14	-0.047	0.18	-9999	-0.51	21	21
ELK1	0.007	0.17	-9999	-0.77	6	6
GRB7	0.033	0.007	-9999	-10000	0	0
PAK1	0.028	0.046	-9999	-0.51	1	1
Tie2/Ang1/alpha5/beta1 Integrin	0.016	0.19	-9999	-0.75	6	6
CDKN1A	0.014	0.18	-9999	-0.78	4	4
ITGA5	0.025	0.063	-9999	-0.51	2	2
mol:GTP	0	0	-9999	-10000	0	0
RasGAP/Dok-R	-0.001	0.19	-9999	-0.8	6	6
CRK	0.032	0.008	-9999	-10000	0	0
mol:NO	0.014	0.14	-9999	-0.52	6	6
PLG	0.001	0.16	-9999	-0.75	6	6
mol:GDP	0	0	-9999	-10000	0	0
chemokinesis	0.011	0.16	-9999	-0.64	6	6
GRB2	0.034	0.005	-9999	-10000	0	0
PIK3R1	0.007	0.099	-9999	-0.51	5	5
ANGPT2	0.014	0.16	-9999	-1.3	1	1
BMX	-0.004	0.16	-9999	-0.75	6	6
ANGPT1	0.016	0.053	-9999	-10000	0	0
tube development	0.015	0.15	-9999	-0.67	2	2
ANGPT4	0.023	0.075	-9999	-0.51	3	3
response to hypoxia	-0.002	0.017	-9999	-10000	0	0
Tie2/Ang1/GRB14	-0.019	0.18	-9999	-0.76	6	6
alpha5/beta1 Integrin	0.035	0.069	-9999	-0.37	4	4
FGF2	0.014	0.088	-9999	-0.51	4	4
STAT5A (dimer)	0.026	0.19	-9999	-0.73	3	3
mol:L-citrulline	0.014	0.14	-9999	-0.52	6	6
AGTR1	0.009	0.077	-9999	-0.51	3	3
MAPK14	0.015	0.17	-9999	-0.75	6	6
Tie2/SHP2	0.012	0.11	-9999	-0.51	1	1
TEK	0.021	0.084	-9999	-10000	0	0
RPS6KB1	0.01	0.16	-9999	-0.63	6	6
Angiotensin II/AT1	0.008	0.056	-9999	-0.36	3	3
Tie2/Ang1/GRB2	0.02	0.17	-9999	-0.76	6	6
MAPK3	-0.007	0.16	-9999	-0.78	6	6
MAPK1	-0.002	0.17	-9999	-0.78	6	6
Tie2/Ang1/GRB7	0.02	0.17	-9999	-0.76	6	6
NFKB1	0.033	0.008	-9999	-10000	0	0
MAPK8	0	0.16	-9999	-0.75	6	6
PI3K	-0.018	0.16	-9999	-0.71	6	6
FES	0.011	0.17	-9999	-0.74	6	6
Crk/Dok-R	0.001	0.19	-9999	-0.8	6	6
Tie2/Ang1/ABIN2	0.014	0.16	-9999	-0.76	6	6
blood circulation	0	0	-9999	-10000	0	0
negative regulation of caspase activity	0.012	0.16	-9999	-0.6	6	6
STAT5A	0.033	0.011	-9999	-10000	0	0
mol:ROS	0	0	-9999	-10000	0	0
PTK2	0.017	0.17	-9999	-0.66	5	5
Tie2/Ang2	0.006	0.18	-9999	-0.91	2	2
Tie2/Ang1	0.004	0.16	-9999	-0.79	6	6
FOXO1	0.012	0.17	-9999	-0.61	7	7
ELF1	0.038	0.023	-9999	-10000	0	0
ELF2	-0.009	0.21	-9999	-1.1	6	6
mol:Choline	-0.004	0.17	-9999	-0.8	6	6
cell migration	-0.025	0.058	-9999	-0.21	7	7
FYN	0.01	0.17	-9999	-0.76	2	2
DOK2	-0.025	0.16	-9999	-0.51	15	15
negative regulation of cell cycle	0.019	0.17	-9999	-0.69	4	4
ETS1	0.028	0.067	-9999	-0.51	2	2
PXN	0.02	0.16	-9999	-0.57	5	5
ITGB1	0.025	0.062	-9999	-0.51	2	2
NOS3	0.011	0.15	-9999	-0.58	6	6
RAC1	0.033	0.006	-9999	-10000	0	0
TNF	0.03	0.054	-9999	-0.51	1	1
MAPKKK cascade	-0.004	0.17	-9999	-0.8	6	6
RASA1	0.028	0.044	-9999	-0.51	1	1
Tie2/Ang1/Shc	0.019	0.16	-9999	-0.76	6	6
NCK1	0.021	0.062	-9999	-0.51	2	2
vasculogenesis	0.016	0.13	-9999	-0.47	6	6
mol:Phosphatidic acid	-0.004	0.17	-9999	-0.8	6	6
mol:Angiotensin II	0.002	0.002	-9999	-10000	0	0
mol:NADP	0.014	0.14	-9999	-0.52	6	6
Rac1/GTP	0.015	0.16	-9999	-0.6	6	6
MMP2	-0.023	0.17	-9999	-0.75	6	6

LPA4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ADCY4	-0.012	0.043	-10000	0	-0.32	3	3
ADCY5	-0.007	0.008	-10000	0	-10000	0	0
ADCY6	-0.006	0.002	-10000	0	-10000	0	0
ADCY7	-0.008	0.025	-10000	0	-0.32	1	1
ADCY1	-0.006	0.002	-10000	0	-10000	0	0
ADCY2	-0.011	0.036	-10000	0	-0.32	2	2
ADCY3	-0.011	0.035	-10000	0	-0.32	2	2
ADCY8	-0.014	0.028	-10000	0	-0.32	1	1
PRKCE	0.008	0.003	-10000	0	-10000	0	0
ADCY9	-0.008	0.025	-10000	0	-0.32	1	1
mol:DAG	0	0	-10000	0	-10000	0	0
cAMP biosynthetic process	0.051	0.11	0.28	19	-0.3	1	20

EPO signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.025	0.11	-10000	0	-0.55	1	1
CRKL	0.026	0.072	0.28	1	-0.31	1	2
mol:DAG	0.031	0.072	-10000	0	-0.43	1	1
HRAS	0.028	0.085	0.28	4	-10000	0	4
MAPK8	0.027	0.058	0.22	1	-0.32	1	2
RAP1A	0.025	0.08	0.28	1	-0.27	3	4
GAB1	0.026	0.076	0.28	1	-0.3	2	3
MAPK14	0.029	0.06	0.22	1	-0.32	1	2
EPO	0.032	0.022	-10000	0	-10000	0	0
PLCG1	0.031	0.073	-10000	0	-0.44	1	1
EPOR/TRPC2/IP3 Receptors	0.034	0.018	-10000	0	-10000	0	0
RAPGEF1	0.034	0.004	-10000	0	-10000	0	0
EPO/EPOR (dimer)/SOCS3	0.052	0.065	-10000	0	-0.33	3	3
GAB1/SHC/GRB2/SOS1	0.057	0.075	0.27	1	-0.27	2	3
EPO/EPOR (dimer)	0.047	0.03	-10000	0	-10000	0	0
IRS2	0.01	0.096	0.28	1	-0.27	9	10
STAT1	0.019	0.1	-10000	0	-0.34	5	5
STAT5B	0.033	0.082	-10000	0	-0.49	1	1
cell proliferation	0.005	0.061	0.19	7	-0.3	1	8
GAB1/SHIP/PIK3R1/SHP2/SHC	0.02	0.084	-10000	0	-0.36	3	3
TEC	0.026	0.071	0.28	1	-0.31	1	2
SOCS3	0.021	0.077	-10000	0	-0.51	3	3
STAT1 (dimer)	0.02	0.1	-10000	0	-0.34	5	5
JAK2	0.031	0.019	-10000	0	-10000	0	0
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
EPO/EPOR (dimer)/JAK2	0.069	0.083	-10000	0	-0.27	2	2
EPO/EPOR	0.047	0.03	-10000	0	-10000	0	0
LYN	0.028	0.047	-10000	0	-0.52	1	1
TEC/VAV2	0.019	0.1	0.27	1	-0.27	4	5
elevation of cytosolic calcium ion concentration	0.034	0.018	-10000	0	-10000	0	0
SHC1	0.032	0.008	-10000	0	-10000	0	0
EPO/EPOR (dimer)/LYN	0.058	0.053	-10000	0	-0.36	1	1
mol:IP3	0.031	0.072	-10000	0	-0.43	1	1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP	0.005	0.11	0.27	1	-0.33	6	7
SH2B3	0.033	0.047	-10000	0	-0.52	1	1
NFKB1	0.029	0.06	0.22	1	-0.32	1	2
EPO/EPOR (dimer)/JAK2/SOCS3	0.008	0.057	-10000	0	-0.32	3	3
PTPN6	0.018	0.062	-10000	0	-0.32	1	1
TEC/VAV2/GRB2	0.033	0.1	0.27	1	-0.28	2	3
EPOR	0.034	0.018	-10000	0	-10000	0	0
INPP5D	0	0	-10000	0	-10000	0	0
mol:GDP	0.056	0.076	0.27	1	-0.28	2	3
SOS1	0.033	0.006	-10000	0	-10000	0	0
PLCG2	0.014	0.096	-10000	0	-0.51	5	5
CRKL/CBL/C3G	0.055	0.076	0.27	1	-0.29	1	2
VAV2	0.009	0.098	0.28	1	-0.26	10	11
CBL	0.029	0.073	0.28	1	-0.31	1	2
SHC/Grb2/SOS1	0.033	0.055	-10000	0	-0.29	1	1
STAT5A	0.033	0.082	-10000	0	-0.49	1	1
GRB2	0.034	0.005	-10000	0	-10000	0	0
STAT5 (dimer)	0.044	0.11	-10000	0	-0.36	6	6
LYN/PLCgamma2	0.029	0.083	-10000	0	-0.37	6	6
PTPN11	0.031	0.044	-10000	0	-0.51	1	1
BTK	0.009	0.1	0.28	1	-0.27	10	11
BCL2	-0.007	0.22	-10000	0	-0.89	8	8

Insulin-mediated glucose transport

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Insulin responsive Vesicles	0.059	0.11	0.25	1	-0.29	6	7
CaM/Ca2+	0.024	0.005	-10000	0	-10000	0	0
AKT1	0.025	0.062	-10000	0	-0.51	2	2
AKT2	0.031	0.01	-10000	0	-10000	0	0
STXBP4	0.034	0.004	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucose	0.039	0.11	0.2	7	-0.29	8	15
YWHAZ	0.025	0.062	-10000	0	-0.51	2	2
CALM1	0.033	0.007	-10000	0	-10000	0	0
YWHAQ	0.033	0.007	-10000	0	-10000	0	0
TBC1D4	0.005	0.062	-10000	0	-0.37	4	4
mol:Ca2+	0	0	-10000	0	-10000	0	0
YWHAH	0.026	0.062	-10000	0	-0.51	2	2
YWHAB	0.033	0.006	-10000	0	-10000	0	0
SNARE/Synip	0.061	0.025	-10000	0	-10000	0	0
YWHAG	0.034	0.005	-10000	0	-10000	0	0
ASIP	0	0	-10000	0	-10000	0	0
PRKCI	-0.004	0.1	-10000	0	-0.51	6	6
AS160/CaM/Ca2+	0.024	0.005	-10000	0	-10000	0	0
RHOQ	0.02	0.075	-10000	0	-0.51	3	3
GYS1	0.008	0.028	-10000	0	-0.27	1	1
PRKCZ	0	0	-10000	0	-10000	0	0
TRIP10	0.031	0.017	-10000	0	-10000	0	0
TC10/GTP/CIP4/Exocyst	0.031	0.053	-10000	0	-0.31	3	3
AS160/14-3-3	-0.008	0.13	-10000	0	-0.59	5	5
VAMP2	0.031	0.015	-10000	0	-10000	0	0
SLC2A4	0.039	0.12	0.21	6	-0.32	8	14
STX4	0.034	0.005	-10000	0	-10000	0	0
GSK3B	0.014	0.053	-10000	0	-0.33	3	3
SFN	-0.027	0.17	-10000	0	-0.51	17	17
LNPEP	0.031	0.012	-10000	0	-10000	0	0
YWHAE	0.032	0.008	-10000	0	-10000	0	0

Signaling events regulated by Ret tyrosine kinase

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.007	0.081	-10000	0	-0.44	2	2
Crk/p130 Cas/Paxillin	-0.024	0.07	-10000	0	-0.28	1	1
JUN	0.009	0.077	-10000	0	-0.29	2	2
HRAS	0.029	0.045	-10000	0	-0.51	1	1
RET51/GFRalpha1/GDNF/GRB10	0.035	0.089	-10000	0	-0.29	7	7
RAP1A	0.026	0.062	-10000	0	-0.51	2	2
FRS2	0.033	0.007	-10000	0	-10000	0	0
RAP1A/GDP	0.019	0.045	-10000	0	-0.37	2	2
RET51/GFRalpha1/GDNF/DOK1	0.054	0.056	-10000	0	-0.29	1	1
EntrezGene:5979	0	0	-10000	0	-10000	0	0
PTPN11	0.031	0.044	-10000	0	-0.51	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.032	0.008	-10000	0	-10000	0	0
RET9/GFRalpha1/GDNF/Enigma	0.047	0.04	-10000	0	-0.29	1	1
RHOA	0.031	0.011	-10000	0	-10000	0	0
RAP1A/GTP	0.042	0.073	-10000	0	-0.27	5	5
GRB7	0.033	0.007	-10000	0	-10000	0	0
RET51/GFRalpha1/GDNF	0.053	0.056	-10000	0	-0.29	1	1
MAPKKK cascade	0.022	0.052	-10000	0	-0.28	1	1
BCAR1	0.033	0.008	-10000	0	-10000	0	0
RET9/GFRalpha1/GDNF/IRS1	0.031	0.077	-10000	0	-0.29	7	7
lamellipodium assembly	0.003	0.085	-10000	0	-0.28	3	3
RET51/GFRalpha1/GDNF/SHC	0.052	0.056	-10000	0	-0.29	1	1
PIK3CA	0.009	0.062	-10000	0	-0.51	2	2
RET9/GFRalpha1/GDNF/SHC	0.046	0.041	-10000	0	-0.29	1	1
RET9/GFRalpha1/GDNF/Shank3	0.047	0.04	-10000	0	-0.29	1	1
MAPK3	0.017	0.099	0.35	3	-0.26	5	8
DOK1	0.033	0.006	-10000	0	-10000	0	0
DOK6	-0.03	0.15	-10000	0	-0.51	13	13
PXN	0.034	0.004	-10000	0	-10000	0	0
neurite development	0.012	0.1	0.29	6	-0.35	2	8
DOK5	0.01	0.11	-10000	0	-0.51	6	6
GFRA1	0.031	0.016	-10000	0	-10000	0	0
MAPK8	0.027	0.058	-10000	0	-0.26	2	2
HRAS/GTP	0.037	0.064	-10000	0	-0.3	1	1
tube development	0.045	0.043	0.22	2	-0.27	1	3
MAPK1	0.008	0.095	0.3	3	-0.26	6	9
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2	0.022	0.03	-10000	0	-0.24	1	1
Rac1/GDP	0.025	0.005	-10000	0	-10000	0	0
SRC	0.032	0.012	-10000	0	-10000	0	0
PDLIM7	0.032	0.008	-10000	0	-10000	0	0
RET51/GFRalpha1/GDNF/Dok6	0.016	0.11	-10000	0	-0.3	12	12
SHC1	0.032	0.008	-10000	0	-10000	0	0
RET51/GFRalpha1/GDNF/Dok4	0.05	0.069	-10000	0	-0.31	3	3
RET51/GFRalpha1/GDNF/Dok5	0.044	0.08	-10000	0	-0.3	5	5
PRKCA	0.03	0.045	-10000	0	-0.51	1	1
HRAS/GDP	0.021	0.034	-10000	0	-0.37	1	1
CREB1	0.022	0.035	-10000	0	-10000	0	0
PIK3R1	0.006	0.099	-10000	0	-0.51	5	5
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2	0.018	0.036	-10000	0	-0.27	1	1
RET51/GFRalpha1/GDNF/Grb7	0.054	0.056	-10000	0	-0.29	1	1
mol:GDP	0	0	-10000	0	-10000	0	0
RET	0.021	0.035	-10000	0	-10000	0	0
DOK4	0.026	0.062	-10000	0	-0.51	2	2
JNK cascade	0.009	0.076	-10000	0	-0.28	2	2
RET9/GFRalpha1/GDNF/FRS2	0.048	0.04	-10000	0	-0.29	1	1
SHANK3	0.032	0.008	-10000	0	-10000	0	0
RASA1	0.028	0.044	-10000	0	-0.51	1	1
NCK1	0.021	0.062	-10000	0	-0.51	2	2
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1	0.021	0.03	-10000	0	-0.24	1	1
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2	0.023	0.034	-10000	0	-0.23	1	1
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK	0.015	0.045	-10000	0	-0.26	3	3
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1	0.023	0.03	-10000	0	-0.23	1	1
PI3K	0.009	0.12	-10000	0	-0.41	3	3
SOS1	0.033	0.006	-10000	0	-10000	0	0
RET9/GFRalpha1/GDNF/Shank3/Grb2	0.057	0.046	-10000	0	-0.27	1	1
GRB10	-0.001	0.13	-10000	0	-0.51	9	9
activation of MAPKK activity	0.036	0.044	-10000	0	-0.31	1	1
RET51/GFRalpha1/GDNF/FRS2	0.054	0.056	-10000	0	-0.29	1	1
GAB1	0.024	0.063	-10000	0	-0.51	2	2
IRS1	0.006	0.11	-10000	0	-0.51	7	7
IRS2	-0.004	0.13	-10000	0	-0.51	10	10
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2	0.018	0.041	-10000	0	-0.27	1	1
RET51/GFRalpha1/GDNF/PKC alpha	0.052	0.063	-10000	0	-0.29	2	2
GRB2	0.034	0.005	-10000	0	-10000	0	0
PRKACA	0.033	0.007	-10000	0	-10000	0	0
GDNF	0.024	0.045	-10000	0	-0.51	1	1
RAC1	0.033	0.006	-10000	0	-10000	0	0
RET51/GFRalpha1/GDNF/IRS1	0.037	0.089	-10000	0	-0.29	7	7
Rac1/GTP	0.012	0.1	-10000	0	-0.36	2	2
RET9/GFRalpha1/GDNF	0.033	0.035	-10000	0	-0.31	1	1
GFRalpha1/GDNF	0.036	0.04	-10000	0	-0.37	1	1

Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.031	0.011	-10000	0	-10000	0	0
NFATC1	0.032	0.12	0.27	1	-0.49	3	4
NFATC2	0.014	0.077	0.19	2	-0.32	4	6
NFATC3	0.015	0.007	-10000	0	-10000	0	0
YWHAE	0.032	0.008	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/CABIN1	0.007	0.085	-10000	0	-0.34	4	4
Exportin 1/Ran/NUP214	0.061	0.024	-10000	0	-10000	0	0
mol:DAG	0	0	-10000	0	-10000	0	0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV	0.04	0.092	-10000	0	-0.32	3	3
BCL2/BAX	0.016	0.092	-10000	0	-0.37	7	7
CaM/Ca2+/Calcineurin A alpha-beta B1	0.025	0.005	-10000	0	-10000	0	0
CaM/Ca2+	0.025	0.005	-10000	0	-10000	0	0
BAX	0.034	0.005	-10000	0	-10000	0	0
MAPK14	0.034	0.009	-10000	0	-10000	0	0
BAD	0.034	0	-10000	0	-10000	0	0
CABIN1/MEF2D	0.021	0.089	-10000	0	-0.34	4	4
Calcineurin A alpha-beta B1/BCL2	-0.005	0.12	-10000	0	-0.51	7	7
FKBP8	0.033	0.007	-10000	0	-10000	0	0
activation-induced cell death of T cells	-0.021	0.088	0.33	4	-10000	0	4
KPNB1	0.023	0.075	-10000	0	-0.51	3	3
KPNA2	0.026	0.062	-10000	0	-0.51	2	2
XPO1	0.03	0.011	-10000	0	-10000	0	0
SFN	-0.027	0.17	-10000	0	-0.51	17	17
MAP3K8	-0.011	0.14	-10000	0	-0.51	12	12
NFAT4/CK1 alpha	0.026	0.055	-10000	0	-0.26	5	5
MEF2D/NFAT1/Cbp/p300	0.052	0.1	-10000	0	-0.31	3	3
CABIN1	0.007	0.086	-10000	0	-0.35	4	4
CALM1	0.033	0.007	-10000	0	-10000	0	0
RAN	0.034	0.003	-10000	0	-10000	0	0
MAP3K1	0.017	0.087	-10000	0	-0.51	4	4
CAMK4	0.028	0.045	-10000	0	-0.51	1	1
mol:Ca2+	0.001	0	-10000	0	-10000	0	0
MAPK3	0.034	0.003	-10000	0	-10000	0	0
YWHAH	0.026	0.062	-10000	0	-0.51	2	2
Calcineurin A alpha-beta B1/AKAP79/PKA	0.041	0.051	-10000	0	-0.37	2	2
YWHAB	0.033	0.006	-10000	0	-10000	0	0
MAPK8	0.033	0.007	-10000	0	-10000	0	0
MAPK9	0.032	0.009	-10000	0	-10000	0	0
YWHAG	0.034	0.005	-10000	0	-10000	0	0
FKBP1A	0.033	0.007	-10000	0	-10000	0	0
NFAT1-c-4/YWHAQ	0.042	0.12	0.28	2	-0.45	3	5
PRKCH	0.016	0.096	-10000	0	-0.51	5	5
CABIN1/Cbp/p300	0.026	0.094	-10000	0	-0.37	8	8
CASP3	0.031	0.011	-10000	0	-10000	0	0
PIM1	0.033	0.01	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0.023	0.005	-10000	0	-10000	0	0
apoptosis	0.016	0.029	-10000	0	-10000	0	0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1	0.007	0.12	-10000	0	-0.47	6	6
PRKCB	0	0	-10000	0	-10000	0	0
PRKCE	0.031	0.01	-10000	0	-10000	0	0
JNK2/NFAT4	0.035	0.017	-10000	0	-10000	0	0
BAD/BCL-XL	0.046	0.016	-10000	0	-10000	0	0
PRKCD	0.03	0.013	-10000	0	-10000	0	0
NUP214	0.034	0.004	-10000	0	-10000	0	0
PRKCZ	0	0	-10000	0	-10000	0	0
PRKCA	0.03	0.045	-10000	0	-0.51	1	1
PRKCG	0.033	0.006	-10000	0	-10000	0	0
PRKCQ	0.007	0.11	-10000	0	-0.51	6	6
FKBP38/BCL2	0.015	0.092	-10000	0	-0.37	7	7
EP300	0.005	0.12	-10000	0	-0.51	8	8
PRKCB1	0	0	-10000	0	-10000	0	0
CSNK2A1	0.032	0.008	-10000	0	-10000	0	0
NFATc/JNK1	0.046	0.12	0.28	1	-0.46	3	4
CaM/Ca2+/FKBP38	0.044	0.013	-10000	0	-10000	0	0
FKBP12/FK506	0.024	0.005	-10000	0	-10000	0	0
CSNK1A1	0.016	0.027	-10000	0	-0.31	1	1
CaM/Ca2+/CAMK IV	0.041	0.032	-10000	0	-0.31	1	1
NFATc/ERK1	0.049	0.12	0.28	1	-0.46	3	4
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV	0.036	0.093	-10000	0	-0.32	3	3
NR4A1	0.027	0.089	0.24	1	-0.3	2	3
GSK3B	0.029	0.013	-10000	0	-10000	0	0
positive T cell selection	0.015	0.007	-10000	0	-10000	0	0
NFAT1/CK1 alpha	0.014	0.066	0.17	1	-0.3	4	5
RCH1/ KPNB1	0.037	0.069	-10000	0	-0.37	4	4
YWHAQ	0.033	0.007	-10000	0	-10000	0	0
PRKACA	0.033	0.007	-10000	0	-10000	0	0
AKAP5	0.024	0.063	-10000	0	-0.51	2	2
MEF2D	0.033	0.007	-10000	0	-10000	0	0
mol:FK506	0	0	-10000	0	-10000	0	0
YWHAZ	0.025	0.062	-10000	0	-0.51	2	2
NFATc/p38 alpha	0.051	0.12	0.28	1	-0.47	3	4
CREBBP	0.034	0.007	-10000	0	-10000	0	0
BCL2	-0.005	0.12	-10000	0	-0.51	7	7

Arf6 trafficking events

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
SLC2A4	0.031	0.015	-10000	0	-10000	0	0
CLTC	0.022	0.11	-10000	0	-0.59	4	4
calcium ion-dependent exocytosis	-0.007	0.066	-10000	0	-0.33	4	4
Dynamin 2/GTP	0.027	0.038	-10000	0	-0.28	2	2
EXOC4	0.034	0.004	-10000	0	-10000	0	0
CD59	-0.011	0.095	-10000	0	-0.54	4	4
CPE	-0.01	0.083	-10000	0	-0.32	10	10
CTNNB1	0.03	0.016	-10000	0	-10000	0	0
membrane fusion	-0.006	0.062	-10000	0	-0.31	4	4
CTNND1	0.005	0.067	0.19	4	-0.27	7	11
DNM2	0.033	0.007	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.02	0.095	-10000	0	-0.52	3	3
TSHR	0.008	0.054	-10000	0	-0.31	4	4
INS	0.009	0.12	-10000	0	-0.6	5	5
BIN1	0.03	0.044	-10000	0	-0.51	1	1
mol:Choline	-0.006	0.062	-10000	0	-0.31	4	4
growth hormone secretagogue receptor activity	0	0	-10000	0	-10000	0	0
mol:GDP	0.012	0.039	-10000	0	-0.31	2	2
membrane depolarization	0	0	-10000	0	-10000	0	0
ARF6	0.026	0.062	-10000	0	-0.51	2	2
mol:Ca2+	0.027	0.038	-10000	0	-0.28	2	2
JUP	-0.017	0.11	-10000	0	-0.48	6	6
ASAP2/amphiphysin II	0.034	0.048	-10000	0	-0.28	3	3
ARF6/GTP	0.018	0.046	-10000	0	-0.37	2	2
CDH1	-0.012	0.089	-10000	0	-0.56	3	3
clathrin-independent pinocytosis	0.018	0.046	-10000	0	-0.37	2	2
MAPK8IP3	0.029	0.045	-10000	0	-0.51	1	1
positive regulation of endocytosis	0.018	0.046	-10000	0	-0.37	2	2
EXOC2	0.029	0.044	-10000	0	-0.51	1	1
substrate adhesion-dependent cell spreading	0.031	0.064	-10000	0	-0.24	3	3
insulin receptor binding	0	0	-10000	0	-10000	0	0
SPAG9	0.034	0.003	-10000	0	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.03	0.098	0.47	4	-10000	0	4
positive regulation of phagocytosis	0.012	0.039	-10000	0	-0.31	2	2
ARF6/GTP/JIP3	0.035	0.052	-10000	0	-0.31	3	3
ACAP1	-0.004	0.057	-10000	0	-0.34	3	3
mol:GTP	0	0	-10000	0	-10000	0	0
CHRM2	-0.035	0.14	-10000	0	-0.74	4	4
clathrin heavy chain/ACAP1	0.022	0.1	-10000	0	-0.52	4	4
JIP4/KLC1	0.056	0.045	-10000	0	-0.29	2	2
EXOC1	0.027	0.045	-10000	0	-0.51	1	1
exocyst	0.031	0.065	-10000	0	-0.24	3	3
RALA/GTP	0.022	0.032	-10000	0	-0.37	1	1
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex	0.039	0.043	-10000	0	-0.31	2	2
receptor recycling	0.018	0.046	-10000	0	-0.37	2	2
CTNNA1	0.013	0.043	0.19	4	-0.26	2	6
NME1	0.012	0.039	-10000	0	-0.31	2	2
clathrin coat assembly	0.023	0.11	-10000	0	-0.58	4	4
IL2RA	-0.019	0.12	-10000	0	-0.77	3	3
VAMP3	0.012	0.039	-10000	0	-0.31	2	2
GLUT4/clathrin heavy chain/ACAP1	0.033	0.1	-10000	0	-0.49	4	4
EXOC6	0.03	0.044	-10000	0	-0.51	1	1
PLD1	-0.013	0.083	-10000	0	-0.32	9	9
PLD2	0.009	0.049	-10000	0	-0.3	3	3
EXOC5	0.034	0.005	-10000	0	-10000	0	0
PIP5K1C	-0.009	0.086	-10000	0	-0.53	3	3
SDC1	-0.022	0.13	-10000	0	-0.58	6	6
ARF6/GDP	0.026	0.04	-10000	0	-0.31	2	2
EXOC7	0.034	0.005	-10000	0	-10000	0	0
E-cadherin/beta catenin	0.035	0.1	-10000	0	-0.49	4	4
mol:Phosphatidic acid	-0.006	0.062	-10000	0	-0.31	4	4
endocytosis	-0.033	0.047	0.28	3	-10000	0	3
SCAMP2	0.034	0.003	-10000	0	-10000	0	0
ADRB2	-0.013	0.14	-10000	0	-0.61	5	5
EXOC3	0.027	0.014	-10000	0	-10000	0	0
ASAP2	0	0	-10000	0	-10000	0	0
Dynamin 2/GDP	0.032	0.039	-10000	0	-0.28	2	2
KLC1	0.033	0.007	-10000	0	-10000	0	0
AVPR2	0.024	0.11	-10000	0	-0.55	4	4
RALA	0.029	0.044	-10000	0	-0.51	1	1
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0.019	0.11	-10000	0	-0.46	4	4

p38 MAPK signaling pathway

Figure S114. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S114. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TRAF6/ASK1	0.014	0.065	-9999	-0.32	5	5
TRAF2/ASK1	0.037	0.05	-9999	-0.31	3	3
ATM	0.03	0.044	-9999	-0.51	1	1
MAP2K3	-0.014	0.12	-9999	-0.39	9	9
response to stress	0	0	-9999	-10000	0	0
MAP2K6	-0.019	0.12	-9999	-0.46	6	6
hyperosmotic response	0	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
GADD45G	0.022	0.052	-9999	-0.51	1	1
TXN	0.005	0.029	-9999	-0.33	1	1
CALM1	0.033	0.007	-9999	-10000	0	0
GADD45A	0.016	0.088	-9999	-0.51	4	4
GADD45B	0.025	0.063	-9999	-0.51	2	2
MAP3K1	0.017	0.087	-9999	-0.51	4	4
MAP3K6	0.026	0.062	-9999	-0.51	2	2
MAP3K7	0.034	0.009	-9999	-10000	0	0
MAP3K4	0.03	0.044	-9999	-0.51	1	1
mol:Ca2+	0	0	-9999	-10000	0	0
ASK1/ASK2	0.034	0.076	-9999	-0.37	5	5
TAK1/TAB family	-0.008	0.031	-9999	-0.15	6	6
RAC1/OSM/MEKK3	0.061	0.021	-9999	-10000	0	0
TRAF2	0.033	0.01	-9999	-10000	0	0
RAC1/OSM/MEKK3/MKK3	0.012	0.11	-9999	-0.33	7	7
TRAF6	0.003	0.047	-9999	-0.33	3	3
RAC1	0.033	0.006	-9999	-10000	0	0
mol:LPS	0	0	-9999	-10000	0	0
CAMK2B	0.022	0.052	-9999	-0.51	1	1
CCM2	0.033	0.006	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB	0.035	0.037	-9999	-0.31	1	1
MAPK11	0.032	0.008	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB/ASK1	0.044	0.063	-9999	-0.29	4	4
OSM/MEKK3	0.048	0.018	-9999	-10000	0	0
TAOK1	0	0.076	-9999	-0.32	8	8
TAOK2	0.016	0.028	-9999	-0.32	1	1
TAOK3	0.01	0.054	-9999	-0.32	4	4
MAP3K7IP1	0	0	-9999	-10000	0	0
MAPK14	0.034	0.009	-9999	-10000	0	0
MAP3K7IP2	0	0	-9999	-10000	0	0
MAP3K5	0.022	0.075	-9999	-0.51	3	3
MAP3K10	0.022	0.063	-9999	-0.51	2	2
MAP3K3	0.033	0.01	-9999	-10000	0	0
TRX/ASK1	0.019	0.06	-9999	-0.29	5	5
GADD45/MTK1/MTK1	0.044	0.086	-9999	-0.28	8	8

Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SMAD4	0.026	0.062	-9999	-0.51	2	2
SMAD2	0.007	0.06	-9999	-0.23	4	4
SMAD3	0.017	0.068	-9999	-0.44	1	1
SMAD3/SMAD4	0.031	0.075	-9999	-0.38	2	2
SMAD4/Ubc9/PIASy	0.057	0.05	-9999	-0.32	2	2
SMAD2/SMAD2/SMAD4	0.06	0.081	-9999	-0.28	1	1
PPM1A	0.034	0.005	-9999	-10000	0	0
CALM1	0.033	0.007	-9999	-10000	0	0
SMAD2/SMAD4	0.02	0.071	-9999	-0.26	5	5
MAP3K1	0.017	0.087	-9999	-0.51	4	4
TRAP-1/SMAD4	0.038	0.06	-9999	-0.37	3	3
MAPK3	0.034	0.003	-9999	-10000	0	0
MAPK1	0.028	0.044	-9999	-0.51	1	1
NUP214	0.034	0.004	-9999	-10000	0	0
CTDSP1	0.033	0.006	-9999	-10000	0	0
CTDSP2	0.034	0.005	-9999	-10000	0	0
CTDSPL	0.027	0.045	-9999	-0.51	1	1
KPNB1	0.023	0.075	-9999	-0.51	3	3
TGFBRAP1	0.03	0.044	-9999	-0.51	1	1
UBE2I	0.033	0.006	-9999	-10000	0	0
NUP153	0.033	0.007	-9999	-10000	0	0
KPNA2	0.026	0.062	-9999	-0.51	2	2
PIAS4	0.033	0.007	-9999	-10000	0	0

Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity	-0.041	0.028	-10000	0	-10000	0	0
KIRREL	0.035	0.014	-10000	0	-10000	0	0
Nephrin/NEPH1Par3/Par6/Atypical PKCs	0.041	0.028	-10000	0	-10000	0	0
PLCG1	0.033	0.006	-10000	0	-10000	0	0
ARRB2	0.032	0.008	-10000	0	-10000	0	0
WASL	0.02	0.086	-10000	0	-0.51	4	4
Nephrin/NEPH1/podocin/CD2AP	0.066	0.042	-10000	0	-10000	0	0
ChemicalAbstracts:57-88-5	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP	0.011	0.075	-10000	0	-0.51	2	2
FYN	0.038	0.067	0.28	5	-0.22	2	7
mol:Ca2+	0.062	0.041	-10000	0	-10000	0	0
mol:DAG	0.063	0.042	-10000	0	-10000	0	0
NPHS2	0.035	0.015	-10000	0	-10000	0	0
mol:IP3	0.063	0.042	-10000	0	-10000	0	0
regulation of endocytosis	0.054	0.047	-10000	0	-0.2	2	2
Nephrin/NEPH1/podocin/Cholesterol	0.049	0.032	-10000	0	-10000	0	0
establishment of cell polarity	0.041	0.028	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2	0.062	0.065	-10000	0	-0.29	2	2
Nephrin/NEPH1/beta Arrestin2	0.057	0.048	-10000	0	-0.21	2	2
NPHS1	0.03	0.024	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin	0.05	0.044	-10000	0	-0.22	2	2
TJP1	0.027	0.061	-10000	0	-0.51	2	2
NCK1	0.021	0.062	-10000	0	-0.51	2	2
NCK2	0.034	0.005	-10000	0	-10000	0	0
heterophilic cell adhesion	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/PLCgamma1	0.065	0.042	-10000	0	-10000	0	0
CD2AP	0.034	0.005	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/GRB2	0.066	0.042	-10000	0	-10000	0	0
GRB2	0.034	0.005	-10000	0	-10000	0	0
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
TRPC6	0.015	0.084	0.29	3	-0.29	6	9
cytoskeleton organization	0.007	0.073	0.24	3	-0.46	2	5
Nephrin/NEPH1	0.035	0.022	-10000	0	-10000	0	0
Nephrin/NEPH1/ZO-1	0.051	0.054	-10000	0	-0.32	2	2

Canonical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FBXW11	0.033	0.015	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.055	0.097	-9999	-0.3	2	2
ERC1	0.027	0.045	-9999	-0.51	1	1
RIP2/NOD2	0.005	0.12	-9999	-0.4	12	12
NFKBIA	0.011	0.047	-9999	-0.56	1	1
BIRC2	0.033	0.01	-9999	-10000	0	0
IKBKB	0.031	0.011	-9999	-10000	0	0
RIPK2	0.027	0.046	-9999	-0.51	1	1
IKBKG	0.007	0.089	-9999	-0.4	2	2
IKK complex/A20	0.029	0.12	-9999	-0.43	3	3
NEMO/A20/RIP2	0.027	0.046	-9999	-0.51	1	1
XPO1	0.03	0.011	-9999	-10000	0	0
NEMO/ATM	0.02	0.11	-9999	-0.39	3	3
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
RAN	0.034	0.003	-9999	-10000	0	0
Exportin 1/RanGTP	0.041	0.016	-9999	-10000	0	0
IKK complex/ELKS	0.023	0.1	-9999	-0.38	2	2
BCL10/MALT1/TRAF6	0.051	0.066	-9999	-0.32	4	4
NOD2	-0.017	0.15	-9999	-0.51	13	13
NFKB1	0.034	0.015	-9999	-10000	0	0
RELA	0.036	0.013	-9999	-10000	0	0
MALT1	0.031	0.012	-9999	-10000	0	0
cIAP1/UbcH5C	0.046	0.016	-9999	-10000	0	0
ATM	0.03	0.044	-9999	-0.51	1	1
TNF/TNFR1A	0.033	0.064	-9999	-0.37	3	3
TRAF6	0.023	0.075	-9999	-0.51	3	3
PRKCA	0.03	0.045	-9999	-0.51	1	1
CHUK	0.03	0.044	-9999	-0.51	1	1
UBE2D3	0.033	0.008	-9999	-10000	0	0
TNF	0.026	0.048	-9999	-0.51	1	1
NF kappa B1 p50/RelA	0.069	0.039	-9999	-0.29	1	1
BCL10	0.029	0.045	-9999	-0.51	1	1
proteasomal ubiquitin-dependent protein catabolic process	0.011	0.047	-9999	-0.56	1	1
beta TrCP1/SCF ubiquitin ligase complex	0.033	0.015	-9999	-10000	0	0
TNFRSF1A	0.021	0.075	-9999	-0.51	3	3
IKK complex	0.03	0.11	-9999	-0.37	3	3
CYLD	0.033	0.007	-9999	-10000	0	0
IKK complex/PKC alpha	0.042	0.11	-9999	-10000	0	0

Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5	0.079	0.029	-9999	-10000	0	0
HDAC3	0.033	0.008	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	0.008	0.005	-9999	-10000	0	0
GATA1/HDAC4	0.048	0.013	-9999	-10000	0	0
GATA1/HDAC5	0.048	0.013	-9999	-10000	0	0
GATA2/HDAC5	0.039	0.039	-9999	-0.37	1	1
HDAC5/BCL6/BCoR	0.021	0.077	-9999	-0.32	6	6
HDAC9	0.027	0.046	-9999	-0.51	1	1
Glucocorticoid receptor/Hsp90/HDAC6	0.061	0.025	-9999	-10000	0	0
HDAC4/ANKRA2	0.045	0.017	-9999	-10000	0	0
HDAC5/YWHAB	0.048	0.014	-9999	-10000	0	0
NPC/RanGAP1/SUMO1/Ubc9	0.017	0.013	-9999	-10000	0	0
GATA2	0.026	0.045	-9999	-0.51	1	1
HDAC4/RFXANK	0.047	0.015	-9999	-10000	0	0
BCOR	0.033	0.006	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
HDAC10	0.032	0.012	-9999	-10000	0	0
HDAC5	0.033	0.01	-9999	-10000	0	0
GNB1/GNG2	0.048	0.013	-9999	-10000	0	0
Histones	0.021	0.062	-9999	-0.36	3	3
ADRBK1	0.034	0.005	-9999	-10000	0	0
HDAC4	0.033	0.01	-9999	-10000	0	0
XPO1	0.03	0.011	-9999	-10000	0	0
HDAC5/ANKRA2	0.046	0.017	-9999	-10000	0	0
HDAC4/Ubc9	0.047	0.014	-9999	-10000	0	0
HDAC7	0	0	-9999	-10000	0	0
HDAC5/14-3-3 E	0.046	0.016	-9999	-10000	0	0
TUBA1B	0.034	0.004	-9999	-10000	0	0
HDAC6	0.033	0.01	-9999	-10000	0	0
HDAC5/RFXANK	0.047	0.014	-9999	-10000	0	0
CAMK4	0.028	0.045	-9999	-0.51	1	1
Tubulin/HDAC6	0.052	0.065	-9999	-0.32	4	4
SUMO1	0.033	0.006	-9999	-10000	0	0
EntrezGene:9972	0	0	-9999	-10000	0	0
YWHAB	0.033	0.006	-9999	-10000	0	0
GATA1	0.034	0.005	-9999	-10000	0	0
EntrezGene:8021	0	0	-9999	-10000	0	0
YWHAE	0.032	0.008	-9999	-10000	0	0
NR3C1	0.032	0.012	-9999	-10000	0	0
SUMO1/HDAC4	0.049	0.034	-9999	-10000	0	0
SRF	0.034	0.004	-9999	-10000	0	0
HDAC4/YWHAB	0.048	0.014	-9999	-10000	0	0
Tubulin	0.035	0.069	-9999	-0.37	4	4
HDAC4/14-3-3 E	0.046	0.017	-9999	-10000	0	0
GNB1	0.033	0.007	-9999	-10000	0	0
RANGAP1	0.033	0.007	-9999	-10000	0	0
BCL6/BCoR	0.01	0.081	-9999	-0.37	6	6
HDAC4/HDAC3/SMRT (N-CoR2)	0.058	0.048	-9999	-0.32	2	2
HDAC4/SRF	0.06	0.038	-9999	-0.32	1	1
HDAC4/ER alpha	0.02	0.09	-9999	-0.37	7	7
EntrezGene:23225	0	0	-9999	-10000	0	0
positive regulation of chromatin silencing	0.021	0.062	-9999	-0.36	3	3
cell motility	0.052	0.065	-9999	-0.32	4	4
EntrezGene:23636	0	0	-9999	-10000	0	0
UBE2I	0.033	0.006	-9999	-10000	0	0
HDAC7/HDAC3	0.024	0.006	-9999	-10000	0	0
BCL6	-0.003	0.1	-9999	-0.51	6	6
HDAC4/CaMK II delta B	0.033	0.01	-9999	-10000	0	0
Hsp90/HDAC6	0.047	0.015	-9999	-10000	0	0
ESR1	0	0.12	-9999	-0.51	7	7
HDAC6/HDAC11	0.046	0.015	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.046	0.037	-9999	-10000	0	0
NPC	0.02	0.002	-9999	-10000	0	0
MEF2C	0.006	0.11	-9999	-0.51	6	6
RAN	0.034	0.003	-9999	-10000	0	0
HDAC4/MEF2C	0.063	0.091	-9999	-0.28	8	8
GNG2	0.034	0.005	-9999	-10000	0	0
NCOR2	0.027	0.061	-9999	-0.51	2	2
TUBB2A	0.016	0.088	-9999	-0.51	4	4
HDAC11	0.032	0.009	-9999	-10000	0	0
HSP90AA1	0.033	0.008	-9999	-10000	0	0
RANBP2	0.034	0.004	-9999	-10000	0	0
ANKRA2	0.032	0.009	-9999	-10000	0	0
RFXANK	0.033	0.007	-9999	-10000	0	0
nuclear import	-0.039	0.018	-9999	-10000	0	0

BARD1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BARD1/CSTF1	0.049	0.011	-10000	0	-10000	0	0
ATM	0.03	0.044	-10000	0	-0.51	1	1
UBE2D3	0.033	0.008	-10000	0	-10000	0	0
PRKDC	0.028	0.044	-10000	0	-0.51	1	1
ATR	0.025	0.015	-10000	0	-10000	0	0
UBE2L3	0.032	0.009	-10000	0	-10000	0	0
FANCD2	0.017	0.03	-10000	0	-0.32	1	1
protein ubiquitination	0.066	0.077	-10000	0	-0.33	4	4
XRCC5	0.034	0.005	-10000	0	-10000	0	0
XRCC6	0.033	0.007	-10000	0	-10000	0	0
M/R/N Complex	0.061	0.023	-10000	0	-10000	0	0
MRE11A	0.034	0.005	-10000	0	-10000	0	0
DNA-PK	0.059	0.038	-10000	0	-0.32	1	1
FA complex/FANCD2/Ubiquitin	0.02	0.11	-10000	0	-0.42	6	6
FANCF	0.019	0.086	-10000	0	-0.51	4	4
BRCA1	0.03	0.044	-10000	0	-0.51	1	1
CCNE1	0.022	0.063	-10000	0	-0.51	2	2
CDK2/Cyclin E1	0.037	0.069	-10000	0	-0.52	2	2
FANCG	0.031	0.01	-10000	0	-10000	0	0
BRCA1/BACH1/BARD1	0.046	0.035	-10000	0	-0.37	1	1
FANCE	0.016	0.096	-10000	0	-0.51	5	5
FANCC	0.034	0.004	-10000	0	-10000	0	0
NBN	0.032	0.008	-10000	0	-10000	0	0
FANCA	0.025	0.048	-10000	0	-0.51	1	1
DNA repair	0.024	0.095	0.27	1	-0.34	2	3
BRCA1/BARD1/ubiquitin	0.046	0.035	-10000	0	-0.37	1	1
BARD1/DNA-PK	0.075	0.042	-10000	0	-0.29	1	1
FANCL	0.031	0.01	-10000	0	-10000	0	0
mRNA polyadenylation	-0.049	0.011	-10000	0	-10000	0	0
BRCA1/BARD1/CTIP/M/R/N Complex	0.033	0.047	-10000	0	-0.38	1	1
BRCA1/BACH1/BARD1/TopBP1	0.05	0.051	-10000	0	-0.32	2	2
BRCA1/BARD1/P53	0.044	0.071	-10000	0	-0.28	4	4
BARD1/CSTF1/BRCA1	0.063	0.035	-10000	0	-0.32	1	1
BRCA1/BACH1	0.03	0.044	-10000	0	-0.51	1	1
BARD1	0.033	0.006	-10000	0	-10000	0	0
PCNA	0.033	0.007	-10000	0	-10000	0	0
BRCA1/BARD1/UbcH5C	0.061	0.037	-10000	0	-0.32	1	1
BRCA1/BARD1/UbcH7	0.06	0.038	-10000	0	-0.32	1	1
BRCA1/BARD1/RAD51/PCNA	0.072	0.053	-10000	0	-0.29	2	2
BARD1/DNA-PK/P53	0.071	0.068	-10000	0	-0.27	3	3
BRCA1/BARD1/Ubiquitin	0.046	0.035	-10000	0	-0.37	1	1
BRCA1/BARD1/CTIP	0.045	0.045	-10000	0	-0.29	2	2
FA complex	0.028	0.074	-10000	0	-0.24	6	6
BARD1/EWS	0.047	0.014	-10000	0	-10000	0	0
RBBP8	0.013	0.032	-10000	0	-0.37	1	1
TP53	0.017	0.077	-10000	0	-0.51	3	3
TOPBP1	0.025	0.045	-10000	0	-0.51	1	1
G1/S transition of mitotic cell cycle	-0.042	0.069	0.28	4	-10000	0	4
BRCA1/BARD1	0.073	0.08	-10000	0	-0.34	4	4
CSTF1	0.034	0.004	-10000	0	-10000	0	0
BARD1/EWS-Fli1	0.025	0.005	-10000	0	-10000	0	0
CDK2	0.03	0.044	-10000	0	-0.51	1	1
UniProt:Q9BZD1	0	0	-10000	0	-10000	0	0
RAD51	0.03	0.045	-10000	0	-0.51	1	1
RAD50	0.032	0.008	-10000	0	-10000	0	0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme	0.046	0.035	-10000	0	-0.37	1	1
EWSR1	0.033	0.008	-10000	0	-10000	0	0

Circadian rhythm pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
chromatin modification	0.029	0.12	-10000	0	-1.2	1	1
CLOCK	0.032	0.015	-10000	0	-10000	0	0
TIMELESS/CRY2	0.039	0.11	-10000	0	-1.3	1	1
DEC1/BMAL1	0.044	0.05	-10000	0	-0.37	2	2
ATR	0.025	0.015	-10000	0	-10000	0	0
NR1D1	0.01	0.11	-10000	0	-1.3	1	1
ARNTL	0.028	0.063	-10000	0	-0.5	2	2
TIMELESS	0.012	0.12	-10000	0	-1.3	1	1
NPAS2	0.012	0.11	-10000	0	-0.5	6	6
CRY2	0.033	0.007	-10000	0	-10000	0	0
mol:CO	-0.01	0.018	0.14	2	-10000	0	2
CHEK1	0.02	0.086	-10000	0	-0.51	4	4
mol:HEME	0.01	0.018	-10000	0	-0.14	2	2
PER1	0.032	0.009	-10000	0	-10000	0	0
BMAL/CLOCK/NPAS2	0.049	0.088	-10000	0	-0.31	7	7
BMAL1/CLOCK	0.021	0.12	-10000	0	-0.72	2	2
S phase of mitotic cell cycle	0.029	0.12	-10000	0	-1.2	1	1
TIMELESS/CHEK1/ATR	0.029	0.12	-10000	0	-1.2	1	1
mol:NADPH	0.01	0.018	-10000	0	-0.14	2	2
PER1/TIMELESS	0.038	0.11	-10000	0	-1.3	1	1
PER1-2 / CRY1-2	0	0	-10000	0	-10000	0	0
DEC1	0.033	0.01	-10000	0	-10000	0	0

Ephrin A reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAPKKK cascade	0.033	0.037	-10000	0	-0.31	1	1
EFNA5	0.032	0.012	-10000	0	-10000	0	0
FYN	0.013	0.055	0.19	5	-0.29	3	8
neuron projection morphogenesis	0.033	0.037	-10000	0	-0.31	1	1
cell-cell signaling	0	0	-10000	0	-10000	0	0
Ephrin A5/EPHA5	0.033	0.038	-10000	0	-0.31	1	1
EPHA5	0.022	0.051	-10000	0	-0.51	1	1

Aurora A signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Aurora A/GADD45A	0.036	0.068	-10000	0	-0.48	1	1
BIRC5	-0.002	0.13	-10000	0	-0.51	10	10
NFKBIA	0.017	0.062	0.26	6	-0.3	1	7
CPEB1	0.008	0.099	-10000	0	-0.51	5	5
AKT1	0.01	0.052	0.26	2	-0.39	1	3
NDEL1	0.032	0.009	-10000	0	-10000	0	0
Aurora A/BRCA1	0.026	0.038	-10000	0	-10000	0	0
NDEL1/TACC3	0.051	0.055	-10000	0	-0.42	1	1
GADD45A	0.016	0.088	-10000	0	-0.51	4	4
GSK3B	0.029	0.018	-10000	0	-10000	0	0
PAK1/Aurora A	0.041	0.049	-10000	0	-10000	0	0
MDM2	0.03	0.044	-10000	0	-0.51	1	1
JUB	0	0	-10000	0	-10000	0	0
TPX2	0.008	0.054	-10000	0	-0.37	3	3
TP53	0.004	0.075	-10000	0	-0.32	5	5
DLG7	0.012	0.026	-10000	0	-0.19	1	1
AURKAIP1	0.033	0.007	-10000	0	-10000	0	0
ARHGEF7	0.033	0.011	-10000	0	-10000	0	0
G2 phase of mitotic cell cycle	0	0	-10000	0	-10000	0	0
Aurora A/NDEL1/TACC3	0.054	0.057	-10000	0	-0.44	1	1
G2/M transition of mitotic cell cycle	0.026	0.038	-10000	0	-10000	0	0
AURKA	0.02	0.038	-10000	0	-0.23	1	1
AURKB	0	0.067	-10000	0	-0.18	12	12
CDC25B	0.015	0.041	-10000	0	-0.29	1	1
G2/M transition checkpoint	0.01	0.028	-10000	0	-10000	0	0
mRNA polyadenylation	0.014	0.069	-10000	0	-0.29	6	6
Aurora A/CPEB	0.015	0.069	-10000	0	-0.29	6	6
Aurora A/TACC1/TRAP/chTOG	0.061	0.07	-10000	0	-0.26	3	3
BRCA1	0.03	0.044	-10000	0	-0.51	1	1
centrosome duplication	0.041	0.049	-10000	0	-10000	0	0
regulation of centrosome cycle	0.049	0.054	-10000	0	-0.42	1	1
spindle assembly	0.06	0.069	-10000	0	-0.26	3	3
TDRD7	0.02	0.086	-10000	0	-0.51	4	4
Aurora A/RasGAP/Survivin	0.047	0.096	-10000	0	-0.3	7	7
CENPA	0.005	0.073	-10000	0	-0.32	6	6
Aurora A/PP2A	0.044	0.052	-10000	0	-0.3	1	1
meiosis	0	0	-10000	0	-10000	0	0
protein catabolic process	0.021	0.054	-10000	0	-0.3	1	1
negative regulation of DNA binding	0.004	0.075	-10000	0	-0.32	5	5
prophase	0	0	-10000	0	-10000	0	0
GIT1/beta-PIX	0.041	0.05	-10000	0	-0.37	2	2
RASA1	0.028	0.044	-10000	0	-0.51	1	1
Ajuba/Aurora A	0.01	0.028	-10000	0	-10000	0	0
mitotic prometaphase	0.001	0.019	-10000	0	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.02	0.038	-10000	0	-0.23	1	1
TACC1	0.028	0.014	-10000	0	-10000	0	0
TACC3	0.025	0.047	-10000	0	-0.51	1	1
Aurora A/Antizyme1	0.063	0.044	-10000	0	-10000	0	0
Aurora A/RasGAP	0.043	0.049	-10000	0	-0.3	1	1
OAZ1	0.033	0.006	-10000	0	-10000	0	0
RAN	0.034	0.003	-10000	0	-10000	0	0
mitosis	0	0	-10000	0	-10000	0	0
PRKACA	0.033	0.013	-10000	0	-10000	0	0
GIT1	0.026	0.062	-10000	0	-0.51	2	2
GIT1/beta-PIX/PAK1	0.053	0.059	-10000	0	-0.32	3	3
Importin alpha/Importin beta/TPX2	0.008	0.054	-10000	0	-0.37	3	3
PPP2R5D	0.03	0.044	-10000	0	-0.51	1	1
Aurora A/TPX2	0.023	0.058	-10000	0	-0.44	1	1
PAK1	0.028	0.046	-10000	0	-0.51	1	1
CKAP5	0.033	0.007	-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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NF kappa B/RelA	0.042	0.089	-10000	0	-0.32	3	3
Ran/GTP/Exportin 1/HDAC1	0.008	0.005	-10000	0	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.027	0.1	-10000	0	-0.33	5	5
SUMO1	0.033	0.006	-10000	0	-10000	0	0
ZFPM1	0.025	0.062	-10000	0	-0.51	2	2
NPC/RanGAP1/SUMO1/Ubc9	0.017	0.013	-10000	0	-10000	0	0
FKBP3	0.033	0.008	-10000	0	-10000	0	0
Histones	0.068	0.073	-10000	0	-10000	0	0
YY1/LSF	0.02	0.087	-10000	0	-0.28	10	10
SMG5	0.033	0.007	-10000	0	-10000	0	0
RAN	0.034	0.003	-10000	0	-10000	0	0
I kappa B alpha/HDAC3	0.017	0.059	-10000	0	-0.3	4	4
I kappa B alpha/HDAC1	0.03	0.074	-10000	0	-0.51	1	1
SAP18	0.033	0.007	-10000	0	-10000	0	0
RELA	0.019	0.08	0.29	1	-0.3	1	2
HDAC1/Smad7	0.05	0.065	-10000	0	-0.32	4	4
RANGAP1	0.033	0.007	-10000	0	-10000	0	0
HDAC3/TR2	0.035	0.064	-10000	0	-10000	0	0
NuRD/MBD3 Complex	0.041	0.036	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	0.025	0.092	0.25	1	-0.29	3	4
EntrezGene:23225	0	0	-10000	0	-10000	0	0
GATA2	0.026	0.045	-10000	0	-0.51	1	1
GATA1	0.034	0.005	-10000	0	-10000	0	0
Mad/Max	0.043	0.038	-10000	0	-0.37	1	1
NuRD/MBD3 Complex/GATA1/Fog1	0.037	0.066	-10000	0	-0.32	1	1
RBBP7	0.032	0.011	-10000	0	-10000	0	0
NPC	0.02	0.002	-10000	0	-10000	0	0
RBBP4	0.03	0.044	-10000	0	-0.51	1	1
MAX	0.033	0.006	-10000	0	-10000	0	0
EntrezGene:9972	0	0	-10000	0	-10000	0	0
FBXW11	0.032	0.008	-10000	0	-10000	0	0
NFKBIA	0.015	0.057	-10000	0	-0.55	1	1
KAT2B	0	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
SIN3/HDAC complex	0.022	0.055	-10000	0	-0.35	2	2
SIN3 complex	0.078	0.029	-10000	0	-10000	0	0
SMURF1	0.022	0.075	-10000	0	-0.51	3	3
CHD3	0.031	0.012	-10000	0	-10000	0	0
SAP30	0.032	0.01	-10000	0	-10000	0	0
EntrezGene:23636	0	0	-10000	0	-10000	0	0
NCOR1	0.032	0.008	-10000	0	-10000	0	0
YY1/HDAC3	0.012	0.081	-10000	0	-0.45	2	2
YY1/HDAC2	0.02	0.087	-10000	0	-0.28	10	10
YY1/HDAC1	0.021	0.087	-10000	0	-0.28	10	10
NuRD/MBD2 Complex (MeCP1)	0.036	0.049	-10000	0	-0.24	1	1
PPARG	-0.004	0.13	0.3	1	-0.34	16	17
HDAC8/hEST1B	0.064	0.02	-10000	0	-10000	0	0
UBE2I	0.033	0.006	-10000	0	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.032	0.008	-10000	0	-10000	0	0
TNFRSF1A	0.021	0.075	-10000	0	-0.51	3	3
HDAC3/SMRT (N-CoR2)	0.03	0.073	-10000	0	-0.27	2	2
MBD3L2	0.018	0.086	-10000	0	-0.51	4	4
ubiquitin-dependent protein catabolic process	0.049	0.065	-10000	0	-0.32	4	4
CREBBP	0.033	0.007	-10000	0	-10000	0	0
NuRD/MBD3/MBD3L2 Complex	0.034	0.074	-10000	0	-0.34	2	2
HDAC1	0.033	0.01	-10000	0	-10000	0	0
HDAC3	0.02	0.034	-10000	0	-10000	0	0
HDAC2	0.034	0.009	-10000	0	-10000	0	0
YY1	0	0.08	-10000	0	-0.32	8	8
HDAC8	0.034	0.005	-10000	0	-10000	0	0
SMAD7	0.028	0.045	-10000	0	-0.51	1	1
NCOR2	0.027	0.061	-10000	0	-0.51	2	2
MXD1	0.027	0.046	-10000	0	-0.51	1	1
STAT3	0.008	0.076	-10000	0	-0.32	8	8
NFKB1	0.033	0.008	-10000	0	-10000	0	0
EntrezGene:8021	0	0	-10000	0	-10000	0	0
RANBP2	0.034	0.004	-10000	0	-10000	0	0
YY1/LSF/HDAC1	0.038	0.087	-10000	0	-0.26	10	10
YY1/SAP30/HDAC1	0.036	0.086	-10000	0	-0.26	10	10
EP300	0.005	0.12	-10000	0	-0.51	8	8
STAT3 (dimer non-phopshorylated)	0.008	0.076	-10000	0	-0.32	8	8
proteasomal ubiquitin-dependent protein catabolic process	0.015	0.057	-10000	0	-0.55	1	1
histone deacetylation	0.036	0.049	-10000	0	-0.24	1	1
STAT3 (dimer non-phopshorylated)/HDAC3	0.021	0.072	-10000	0	-10000	0	0
nuclear export	-0.063	0.02	-10000	0	-10000	0	0
PRKACA	0.033	0.007	-10000	0	-10000	0	0
GATAD2B	0.032	0.008	-10000	0	-10000	0	0
GATAD2A	0.033	0.007	-10000	0	-10000	0	0
GATA2/HDAC3	0.024	0.072	-10000	0	-0.43	1	1
GATA1/HDAC1	0.048	0.013	-10000	0	-10000	0	0
GATA1/HDAC3	0.034	0.064	-10000	0	-10000	0	0
CHD4	0.032	0.01	-10000	0	-10000	0	0
TNF-alpha/TNFR1A	0.033	0.064	-10000	0	-0.37	3	3
SIN3/HDAC complex/Mad/Max	0.026	0.066	-10000	0	-0.34	3	3
NuRD Complex	0.038	0.064	-10000	0	-0.31	1	1
positive regulation of chromatin silencing	0.065	0.071	-10000	0	-10000	0	0
SIN3B	0.033	0.006	-10000	0	-10000	0	0
MTA2	0.034	0	-10000	0	-10000	0	0
SIN3A	0.034	0.003	-10000	0	-10000	0	0
XPO1	0.03	0.011	-10000	0	-10000	0	0
SUMO1/HDAC1	0.049	0.036	-10000	0	-10000	0	0
HDAC complex	0.079	0.04	-10000	0	-0.29	1	1
GATA1/Fog1	0.042	0.049	-10000	0	-0.37	2	2
FKBP25/HDAC1/HDAC2	0.063	0.025	-10000	0	-10000	0	0
TNF	0.026	0.048	-10000	0	-0.51	1	1
negative regulation of cell growth	0.026	0.066	-10000	0	-0.34	3	3
NuRD/MBD2/PRMT5 Complex	0.036	0.049	-10000	0	-0.24	1	1
Ran/GTP/Exportin 1	0.046	0.037	-10000	0	-10000	0	0
NF kappa B/RelA/I kappa B alpha	0.005	0.082	-10000	0	-0.33	6	6
SIN3/HDAC complex/NCoR1	0.013	0.082	-10000	0	-0.34	5	5
TFCP2	0.034	0.004	-10000	0	-10000	0	0
NR2C1	0.034	0.003	-10000	0	-10000	0	0
MBD3	0.033	0.006	-10000	0	-10000	0	0
MBD2	0.029	0.044	-10000	0	-0.51	1	1

Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.033	0.01	-10000	0	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	0.007	0.011	-10000	0	-10000	0	0
MDM2/SUMO1	0.046	0.041	-10000	0	-0.24	1	1
HDAC4	0.033	0.01	-10000	0	-10000	0	0
Ran/GTP/Exportin 1/HDAC1	0.007	0.011	-10000	0	-10000	0	0
SUMO1	0.033	0.006	-10000	0	-10000	0	0
NPC/RanGAP1/SUMO1	0.014	0.012	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
XPO1	0.009	0.018	-10000	0	-10000	0	0
EntrezGene:23636	0	0	-10000	0	-10000	0	0
RAN	0.034	0.003	-10000	0	-10000	0	0
EntrezGene:8021	0	0	-10000	0	-10000	0	0
RANBP2	0.034	0.004	-10000	0	-10000	0	0
SUMO1/HDAC4	0.049	0.034	-10000	0	-10000	0	0
SUMO1/HDAC1	0.049	0.036	-10000	0	-10000	0	0
RANGAP1	0.033	0.007	-10000	0	-10000	0	0
MDM2/SUMO1/SUMO1	0.065	0.068	-10000	0	-0.29	4	4
NPC/RanGAP1/SUMO1/RanBP2/Ubc9	0.017	0.013	-10000	0	-10000	0	0
Ran/GTP	0.036	0.031	-10000	0	-0.17	1	1
EntrezGene:23225	0	0	-10000	0	-10000	0	0
MDM2	0.03	0.044	-10000	0	-0.51	1	1
UBE2I	0.033	0.006	-10000	0	-10000	0	0
Ran/GTP/Exportin 1	0.052	0.063	0.2	18	-10000	0	18
NPC	0.02	0.002	-10000	0	-10000	0	0
PIAS2	0.017	0.087	-10000	0	-0.51	4	4
PIAS1	0.034	0.004	-10000	0	-10000	0	0
EntrezGene:9972	0	0	-10000	0	-10000	0	0

Rapid glucocorticoid signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma	0.039	0.063	-10000	0	-0.27	5	5
MAPK9	0.009	0.002	-10000	0	-10000	0	0
adrenocorticotropin secretion	0.008	0.007	-10000	0	-10000	0	0
GNB1/GNG2	0.044	0.011	-10000	0	-10000	0	0
GNB1	0.033	0.007	-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	0.009	0.004	-10000	0	-10000	0	0
Gs family/GTP	0.008	0.055	-10000	0	-0.28	5	5
EntrezGene:2778	0	0	-10000	0	-10000	0	0
vasopressin secretion	0	0	-10000	0	-10000	0	0
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
ChemicalAbstracts:86-01-1	0	0	-10000	0	-10000	0	0
glutamate secretion	0.004	0.013	0.075	5	-10000	0	5
GNAL	0.009	0.098	-10000	0	-0.51	5	5
GNG2	0.034	0.005	-10000	0	-10000	0	0
CRH	0.031	0.015	-10000	0	-10000	0	0
mol:cortisol	0	0	-10000	0	-10000	0	0
MAPK8	0.009	0.002	-10000	0	-10000	0	0
MAPK11	0.009	0.002	-10000	0	-10000	0	0

Signaling events mediated by PRL

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCNE1	0.022	0.063	-9999	-0.51	2	2
mol:Halofuginone	0.002	0.025	-9999	-0.22	2	2
ITGA1	0.023	0.063	-9999	-0.51	2	2
CDKN1A	0.009	0.083	-9999	-0.46	3	3
PRL-3/alpha Tubulin	0.044	0.019	-9999	-10000	0	0
mol:Ca2+	-0.024	0.017	-9999	-10000	0	0
AGT	0.026	0.028	-9999	-10000	0	0
CCNA2	-0.028	0.13	-9999	-0.77	3	3
TUBA1B	0.034	0.004	-9999	-10000	0	0
EGR1	-0.021	0.11	-9999	-0.36	15	15
CDK2/Cyclin E1	0.032	0.1	-9999	-0.48	3	3
MAPK3	0.015	0.009	-9999	-10000	0	0
PRL-2 /Rab GGTase beta	0.049	0.011	-9999	-10000	0	0
MAPK1	0.011	0.032	-9999	-0.37	1	1
PTP4A1	-0.027	0.13	-9999	-0.94	2	2
PTP4A3	0.03	0.016	-9999	-10000	0	0
PTP4A2	0.034	0.005	-9999	-10000	0	0
ITGB1	0.009	0.045	-9999	-0.37	2	2
SRC	0.032	0.012	-9999	-10000	0	0
RAC1	0.012	0.06	-9999	-0.38	1	1
Rab GGTase beta/Rab GGTase alpha	0.047	0.014	-9999	-10000	0	0
PRL-1/ATF-5	-0.004	0.14	-9999	-0.76	3	3
RABGGTA	0.033	0.006	-9999	-10000	0	0
BCAR1	-0.021	0.013	-9999	-10000	0	0
RHOC	0.008	0.067	-9999	-10000	0	0
RHOA	-0.001	0.087	-9999	-0.32	7	7
cell motility	0.018	0.079	-9999	-10000	0	0
PRL-1/alpha Tubulin	0.006	0.14	-9999	-0.89	2	2
PRL-3/alpha1 Integrin	0.035	0.052	-9999	-0.37	2	2
ROCK1	0.02	0.073	-9999	-10000	0	0
RABGGTB	0.033	0.007	-9999	-10000	0	0
CDK2	0.03	0.044	-9999	-0.51	1	1
mitosis	-0.027	0.12	-9999	-0.93	2	2
ATF5	0.014	0.079	-9999	-0.51	3	3

Class IB PI3K non-lipid kinase events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
cAMP biosynthetic process	-0.028	0.045	0.51	1	-10000	0	1
PI3K Class IB/PDE3B	0.028	0.046	-10000	0	-0.51	1	1
PDE3B	0.028	0.046	-10000	0	-0.51	1	1

Alternative NF-kappaB 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IKK alpha homodimer	0.043	0.049	-9999	-0.37	2	2
FBXW11	0.032	0.008	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.032	0.008	-9999	-10000	0	0
CHUK	0.03	0.044	-9999	-0.51	1	1
NF kappa B2 p100/RelB	0.074	0.075	-9999	-0.28	5	5
NFKB1	0.033	0.008	-9999	-10000	0	0
MAP3K14	0.03	0.044	-9999	-0.51	1	1
NF kappa B1 p50/RelB	0.038	0.06	-9999	-0.37	3	3
RELB	0.021	0.076	-9999	-0.51	3	3
NFKB2	0.033	0.011	-9999	-10000	0	0
NF kappa B2 p52/RelB	0.035	0.052	-9999	-0.31	3	3
regulation of B cell activation	0.034	0.052	-9999	-0.31	3	3

Aurora C 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
INCENP	0.03	0.044	-9999	-0.51	1	1
Aurora C/Aurora B/INCENP	0.055	0.044	-9999	-0.29	2	2
metaphase	0	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
H3F3B	0.015	0.012	-9999	-10000	0	0
AURKB	0.028	0.044	-9999	-0.51	1	1
AURKC	0.033	0.006	-9999	-10000	0	0

Effects of Botulinum toxin

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
STX1A	0.008	0.008	-10000	0	-10000	0	0
UniProt:P19321	0	0	-10000	0	-10000	0	0
RIMS1/UNC13B	0.041	0.025	-10000	0	-10000	0	0
STXBP1	0.033	0.01	-10000	0	-10000	0	0
ACh/CHRNA1	0.022	0.037	-10000	0	-0.33	1	1
RAB3GAP2/RIMS1/UNC13B	0.056	0.031	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
UniProt:P30996	0	0	-10000	0	-10000	0	0
UniProt:Q60393	0	0	-10000	0	-10000	0	0
CST086	0	0	-10000	0	-10000	0	0
RIMS1	0.031	0.018	-10000	0	-10000	0	0
mol:ACh	0.002	0.026	0.12	2	-0.084	1	3
RAB3GAP2	0.034	0.005	-10000	0	-10000	0	0
STX1A/SNAP25/VAMP2	0.042	0.048	-10000	0	-10000	0	0
UniProt:P10844	0	0	-10000	0	-10000	0	0
muscle contraction	0.022	0.037	-10000	0	-0.33	1	1
UNC13B	0.03	0.016	-10000	0	-10000	0	0
CHRNA1	0.029	0.045	-10000	0	-0.51	1	1
UniProt:P10845	0	0	-10000	0	-10000	0	0
ACh/Synaptotagmin 1	0.001	0.083	-10000	0	-0.33	8	8
SNAP25	0.004	0.011	-10000	0	-10000	0	0
VAMP2	0.005	0.005	-10000	0	-10000	0	0
SYT1	-0.005	0.12	-10000	0	-0.51	8	8
UniProt:Q00496	0	0	-10000	0	-10000	0	0
STXIA/STXBP1	0.029	0.014	-10000	0	-10000	0	0
STX1A/SNAP25 fragment 1/VAMP2	0.042	0.048	-10000	0	-10000	0	0

Arf1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
coatomer protein complex	0.01	0.017	-9999	-10000	0	0
EntrezGene:79658	0	0	-9999	-10000	0	0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A	0.018	0.029	-9999	-10000	0	0
AP2	0.018	0.051	-9999	-0.37	2	2
mol:DAG	0	0	-9999	-10000	0	0
Arfaptin 2/Rac/GTP	0.045	0.012	-9999	-10000	0	0
CLTB	0.031	0.015	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ER cargo protein	0.02	0.012	-9999	-10000	0	0
CD4	0.031	0.013	-9999	-10000	0	0
CLTA	0.032	0.01	-9999	-10000	0	0
mol:GTP	-0.002	0.003	-9999	-10000	0	0
ARFGAP1	0.009	0.001	-9999	-10000	0	0
mol:PI-4-5-P2	0.006	0.023	-9999	-0.18	2	2
ARF1/GTP	0.018	0.015	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein	0.012	0.007	-9999	-10000	0	0
mol:Choline	0.005	0.024	-9999	-0.19	2	2
mol:GDP	0	0	-9999	-10000	0	0
ARF1	0.034	0.006	-9999	-10000	0	0
DDEF1	0.004	0.024	-9999	-0.19	2	2
ARF1/GDP	0.006	0.017	-9999	-0.11	1	1
AP2M1	0.009	0.062	-9999	-0.51	2	2
EntrezGene:1313	0	0	-9999	-10000	0	0
actin filament polymerization	0.015	0.006	-9999	-10000	0	0
Rac/GTP	0.026	0.005	-9999	-10000	0	0
ARF1/GTP/GGA3/ARF-GAP1	0.045	0.028	-9999	-0.28	1	1
ARFIP2	0.029	0.015	-9999	-10000	0	0
COPA	0.032	0.008	-9999	-10000	0	0
RAC1	0.033	0.006	-9999	-10000	0	0
ARF1/GTP/coatomer protein complex	0.023	0.034	-9999	-0.18	1	1
ARF1/GTP/ARHGAP10	0.022	0.005	-9999	-10000	0	0
GGA3	0.03	0.044	-9999	-0.51	1	1
ARF1/GTP/Membrin	0.026	0.025	-9999	-0.23	1	1
AP2A1	0.033	0.01	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ARF-GAP1	0.01	0.039	-9999	-0.22	1	1
ARF1/GDP/Membrin	0.03	0.028	-9999	-0.26	1	1
Arfaptin 2/Rac/GDP	0.043	0.013	-9999	-10000	0	0
CYTH2	-0.002	0.003	-9999	-10000	0	0
ARF1/GTP/GGA3	0.042	0.031	-9999	-0.33	1	1
mol:ATP	0	0	-9999	-10000	0	0
Rac/GDP	0.025	0.005	-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	0.007	0.037	-9999	-0.23	1	1
PLD2	0.005	0.024	-9999	-0.19	2	2
ARF-GAP1/v-SNARE	0.009	0.001	-9999	-10000	0	0
PIP5K1A	0.006	0.023	-9999	-0.18	2	2
ARF1/GTP/Membrin/GBF1/p115	0.02	0.023	-9999	-10000	0	0
mol:Phosphatic acid	0	0	-9999	-10000	0	0
mol:Phosphatidic acid	0.005	0.024	-9999	-0.19	2	2
KDEL Receptor/Ligand/ARF-GAP1	0.009	0.001	-9999	-10000	0	0
GOSR2	0.013	0.029	-9999	-0.32	1	1
USO1	0.01	0.039	-9999	-0.32	2	2
GBF1	0.011	0.039	-9999	-0.32	2	2
ARF1/GTP/Arfaptin 2	0.043	0.014	-9999	-10000	0	0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex	0.024	0.052	-9999	-0.32	2	2

pid_entity	TCGA.66.2800	TCGA.66.2795	TCGA.66.2794	TCGA.66.2793
109_MAP3K5	-0.33	-0.35	0.073	-0.39
47_PPARGC1A	0.034	0	0.034	0.034
105_BMP4	0.034	0.034	0.034	0.034
105_BMP6	0.034	0.034	0.034	0.034
105_BMP7	0.034	0.034	0.034	-0.51
105_BMP2	0.034	0.034	0.034	0
131_RELN/VLDLR	0.089	0	0	0
30_TGFB1/TGF beta receptor Type II	0	0	0.034	0.035
84_STAT5B	-0.011	-0.07	-0.11	-0.99
84_STAT5A	-0.011	-0.07	-0.11	-0.99