PARADIGM pathway analysis of mRNASeq expression data - Brain Lower Grade Glioma (Primary solid tumor)

Pathway.Name	Avg.Num.Perturbations
IL23-mediated signaling events	93
Ephrin A reverse signaling	84
TCGA08_retinoblastoma	66
FOXM1 transcription factor network	65
IL12-mediated signaling events	63
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	59
Aurora B signaling	58
Effects of Botulinum toxin	56
TCR signaling in naïve CD8+ T cells	51
E-cadherin signaling events	49

Pathway.Name	Significance.Ratio	Avg.Num.Perturbations	Total.Perturbations	Num.Entities	Min.Mean.Truth	Max.Mean.Truth	Min.Mean.Within	Max.Mean.Within	Min.Mean.Any	Max.Mean.Within.1
IL23-mediated signaling events	0.2548	93	5599	60	-0.71	0.014	1000	-1000	-0.14	-1000
Ephrin A reverse signaling	0.2301	84	589	7	-0.13	0	1000	-1000	-0.025	-1000
TCGA08_retinoblastoma	0.1808	66	529	8	-0.1	0.073	1000	-1000	-0.02	-1000
FOXM1 transcription factor network	0.1781	65	3336	51	-0.4	0.025	1000	-1000	-0.17	-1000
IL12-mediated signaling events	0.1726	63	5543	87	-0.56	0.13	1000	-1000	-0.11	-1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	0.1616	59	4033	68	-0.48	0.23	1000	-1000	-0.11	-1000
Aurora B signaling	0.1589	58	3922	67	-0.32	0.014	1000	-1000	-0.063	-1000
Effects of Botulinum toxin	0.1534	56	1480	26	-0.21	0.014	1000	-1000	-0.055	-1000
TCR signaling in naïve CD8+ T cells	0.1397	51	4782	93	-0.22	0.074	1000	-1000	-0.074	-1000
E-cadherin signaling events	0.1342	49	249	5	-0.13	0.014	1000	-1000	-0.042	-1000
Signaling events mediated by the Hedgehog family	0.1315	48	2516	52	-0.17	0.15	1000	-1000	-0.06	-1000
IL4-mediated signaling events	0.1315	48	4422	91	-0.6	0.43	1000	-1000	-0.13	-1000
Syndecan-1-mediated signaling events	0.1288	47	1621	34	-0.22	0.014	1000	-1000	-0.057	-1000
Thromboxane A2 receptor signaling	0.1205	44	4723	105	-0.23	0.064	1000	-1000	-0.053	-1000
Syndecan-4-mediated signaling events	0.1205	44	2988	67	-0.19	0.037	1000	-1000	-0.076	-1000
amb2 Integrin signaling	0.1041	38	3197	82	-0.22	0.014	1000	-1000	-0.07	-1000
Reelin signaling pathway	0.1041	38	2166	56	-0.29	0.014	1000	-1000	-0.07	-1000
a4b1 and a4b7 Integrin signaling	0.1014	37	189	5	-0.08	-0.041	1000	-1000	-0.036	-1000
Signaling events regulated by Ret tyrosine kinase	0.1014	37	3096	82	-0.18	0.014	1000	-1000	-0.08	-1000
Glypican 2 network	0.1014	37	151	4	-0.056	-0.014	1000	-1000	-0.033	-1000
Signaling mediated by p38-alpha and p38-beta	0.0986	36	1622	44	-0.15	0.014	1000	-1000	-0.058	-1000
Visual signal transduction: Cones	0.0959	35	1362	38	-0.16	0.016	1000	-1000	-0.056	-1000
Aurora C signaling	0.0959	35	247	7	-0.15	0	1000	-1000	-0.036	-1000
Endothelins	0.0959	35	3432	96	-0.18	0.016	1000	-1000	-0.072	-1000
Caspase cascade in apoptosis	0.0904	33	2475	74	-0.18	0.046	1000	-1000	-0.044	-1000
FOXA2 and FOXA3 transcription factor networks	0.0904	33	1549	46	-0.27	0.017	1000	-1000	-0.052	-1000
EGFR-dependent Endothelin signaling events	0.0877	32	674	21	-0.11	0.014	1000	-1000	-0.06	-1000
Visual signal transduction: Rods	0.0877	32	1693	52	-0.2	0.014	1000	-1000	-0.074	-1000
Calcium signaling in the CD4+ TCR pathway	0.0849	31	972	31	-0.19	0.014	1000	-1000	-0.081	-1000
Ras signaling in the CD4+ TCR pathway	0.0849	31	527	17	-0.13	0.023	1000	-1000	-0.033	-1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)	0.0822	30	2594	85	-0.14	0.014	1000	-1000	-0.068	-1000
p75(NTR)-mediated signaling	0.0822	30	3833	125	-0.16	0.014	1000	-1000	-0.082	-1000
Glypican 1 network	0.0822	30	1470	48	-0.16	0.029	1000	-1000	-0.046	-1000
PDGFR-alpha signaling pathway	0.0822	30	1329	44	-0.16	0.027	1000	-1000	-0.066	-1000
Glucocorticoid receptor regulatory network	0.0795	29	3350	114	-0.43	0.24	1000	-1000	-0.065	-1000
Osteopontin-mediated events	0.0767	28	1090	38	-0.13	0.015	1000	-1000	-0.089	-1000
Arf6 signaling events	0.0767	28	1760	62	-0.2	0.014	1000	-1000	-0.057	-1000
BCR signaling pathway	0.0767	28	2811	99	-0.18	0.029	1000	-1000	-0.076	-1000
HIF-1-alpha transcription factor network	0.0740	27	2092	76	-0.18	0.087	1000	-1000	-0.11	-1000
TCGA08_p53	0.0740	27	194	7	-0.076	0.049	1000	-1000	-0.013	-1000
LPA receptor mediated events	0.0740	27	2766	102	-0.18	0.019	1000	-1000	-0.075	-1000
PLK1 signaling events	0.0712	26	2246	85	-0.17	0.038	1000	-1000	-0.045	-1000
IL1-mediated signaling events	0.0712	26	1647	62	-0.19	0.065	1000	-1000	-0.091	-1000
Nephrin/Neph1 signaling in the kidney podocyte	0.0685	25	854	34	-0.067	0.014	1000	-1000	-0.054	-1000
Retinoic acid receptors-mediated signaling	0.0658	24	1411	58	-0.2	0.016	1000	-1000	-0.063	-1000
BMP receptor signaling	0.0630	23	1882	81	-0.18	0.049	1000	-1000	-0.079	-1000
Nongenotropic Androgen signaling	0.0630	23	1230	52	-0.099	0.03	1000	-1000	-0.057	-1000
PLK2 and PLK4 events	0.0603	22	68	3	-0.016	-0.005	1000	-1000	-0.014	-1000
Paxillin-independent events mediated by a4b1 and a4b7	0.0603	22	836	37	-0.14	0.014	1000	-1000	-0.051	-1000
RXR and RAR heterodimerization with other nuclear receptor	0.0603	22	1151	52	-0.18	0.027	1000	-1000	-0.059	-1000
Angiopoietin receptor Tie2-mediated signaling	0.0603	22	2017	88	-0.17	0.018	1000	-1000	-0.11	-1000
Syndecan-2-mediated signaling events	0.0575	21	1450	69	-0.16	0.034	1000	-1000	-0.046	-1000
Fc-epsilon receptor I signaling in mast cells	0.0575	21	2112	97	-0.19	0.04	1000	-1000	-0.074	-1000
Wnt signaling	0.0575	21	153	7	-0.041	-0.012	1000	-1000	-0.022	-1000
IL6-mediated signaling events	0.0575	21	1622	75	-0.16	0.063	1000	-1000	-0.095	-1000
Rapid glucocorticoid signaling	0.0575	21	425	20	-0.18	0.014	1000	-1000	-0.038	-1000
LPA4-mediated signaling events	0.0548	20	240	12	-0.056	0.014	1000	-1000	-0.021	-1000
Coregulation of Androgen receptor activity	0.0548	20	1551	76	-0.14	0.028	1000	-1000	-0.046	-1000
Ephrin B reverse signaling	0.0548	20	969	48	-0.12	0.089	1000	-1000	-0.06	-1000
IL2 signaling events mediated by STAT5	0.0548	20	459	22	-0.099	0.017	1000	-1000	-0.044	-1000
Neurotrophic factor-mediated Trk receptor signaling	0.0548	20	2514	120	-0.2	0.13	1000	-1000	-0.068	-1000
ErbB2/ErbB3 signaling events	0.0521	19	1283	65	-0.16	0.023	1000	-1000	-0.063	-1000
JNK signaling in the CD4+ TCR pathway	0.0521	19	323	17	-0.081	0.014	1000	-1000	-0.057	-1000
S1P5 pathway	0.0521	19	323	17	-0.12	0.053	1000	-1000	-0.048	-1000
FAS signaling pathway (CD95)	0.0521	19	906	47	-0.15	0.016	1000	-1000	-0.039	-1000
Regulation of nuclear SMAD2/3 signaling	0.0493	18	2530	136	-0.23	0.22	1000	-1000	-0.066	-1000
Lissencephaly gene (LIS1) in neuronal migration and development	0.0493	18	1000	54	-0.16	0.029	1000	-1000	-0.084	-1000
Presenilin action in Notch and Wnt signaling	0.0493	18	1148	61	-0.27	0.032	1000	-1000	-0.072	-1000
IL27-mediated signaling events	0.0493	18	960	51	-0.17	0.017	1000	-1000	-0.08	-1000
E-cadherin signaling in the nascent adherens junction	0.0493	18	1422	76	-0.13	0.014	1000	-1000	-0.083	-1000
Cellular roles of Anthrax toxin	0.0466	17	679	39	-0.16	0.019	1000	-1000	-0.027	-1000
Syndecan-3-mediated signaling events	0.0466	17	600	35	-0.16	0.014	1000	-1000	-0.058	-1000
Noncanonical Wnt signaling pathway	0.0438	16	433	26	-0.12	0.014	1000	-1000	-0.054	-1000
Signaling events mediated by PTP1B	0.0438	16	1233	76	-0.15	0.021	1000	-1000	-0.077	-1000
Signaling events mediated by HDAC Class III	0.0438	16	652	40	-0.12	0.096	1000	-1000	-0.037	-1000
IL2 signaling events mediated by PI3K	0.0438	16	968	58	-0.097	0.032	1000	-1000	-0.076	-1000
Canonical Wnt signaling pathway	0.0438	16	865	51	-0.27	0.097	1000	-1000	-0.052	-1000
ErbB4 signaling events	0.0384	14	992	69	-0.15	0.041	1000	-1000	-0.081	-1000
Ceramide signaling pathway	0.0384	14	1082	76	-0.15	0.023	1000	-1000	-0.059	-1000
TRAIL signaling pathway	0.0384	14	674	48	-0.053	0.027	1000	-1000	-0.06	-1000
S1P1 pathway	0.0384	14	515	36	-0.1	0.014	1000	-1000	-0.052	-1000
TCGA08_rtk_signaling	0.0384	14	381	26	-0.14	0.029	1000	-1000	-0.017	-1000
Stabilization and expansion of the E-cadherin adherens junction	0.0384	14	1109	74	-0.16	0.068	1000	-1000	-0.087	-1000
Signaling events mediated by Stem cell factor receptor (c-Kit)	0.0384	14	1116	78	-0.062	0.039	1000	-1000	-0.064	-1000
Paxillin-dependent events mediated by a4b1	0.0356	13	489	36	-0.14	0.03	1000	-1000	-0.065	-1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha	0.0356	13	616	45	-0.15	0.029	1000	-1000	-0.078	-1000
Sphingosine 1-phosphate (S1P) pathway	0.0329	12	355	28	-0.12	0.025	1000	-1000	-0.037	-1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes	0.0329	12	1051	83	-0.2	0.054	1000	-1000	-0.065	-1000
Integrins in angiogenesis	0.0329	12	1031	84	-0.095	0.014	1000	-1000	-0.088	-1000
EPHB forward signaling	0.0329	12	1096	85	-0.12	0.036	1000	-1000	-0.081	-1000
Aurora A signaling	0.0301	11	703	60	-0.13	0.032	1000	-1000	-0.06	-1000
Regulation of Telomerase	0.0301	11	1134	102	-0.13	0.046	1000	-1000	-0.1	-1000
E-cadherin signaling in keratinocytes	0.0301	11	483	43	-0.13	0.029	1000	-1000	-0.066	-1000
S1P4 pathway	0.0301	11	297	25	-0.12	0.028	1000	-1000	-0.046	-1000
BARD1 signaling events	0.0274	10	619	57	-0.052	0.03	1000	-1000	-0.055	-1000
Insulin-mediated glucose transport	0.0274	10	325	32	-0.11	0.034	1000	-1000	-0.059	-1000
Signaling mediated by p38-gamma and p38-delta	0.0274	10	161	15	-0.014	0.028	1000	-1000	-0.02	-1000
Regulation of p38-alpha and p38-beta	0.0274	10	560	54	-0.11	0.014	1000	-1000	-0.056	-1000
Plasma membrane estrogen receptor signaling	0.0274	10	929	86	-0.054	0.03	1000	-1000	-0.079	-1000
Regulation of Androgen receptor activity	0.0274	10	762	70	-0.13	0.03	1000	-1000	-0.062	-1000
Nectin adhesion pathway	0.0247	9	580	63	-0.13	0.045	1000	-1000	-0.066	-1000
ceramide signaling pathway	0.0247	9	454	49	-0.15	0.021	1000	-1000	-0.036	-1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha	0.0247	9	319	33	-0.1	0.041	1000	-1000	-0.054	-1000
Class I PI3K signaling events	0.0219	8	592	73	-0.095	0.029	1000	-1000	-0.062	-1000
p38 MAPK signaling pathway	0.0219	8	389	44	-0.074	0.019	1000	-1000	-0.065	-1000
Canonical NF-kappaB pathway	0.0192	7	274	39	-0.15	0.086	1000	-1000	-0.075	-1000
Circadian rhythm pathway	0.0192	7	157	22	-0.028	0.034	1000	-1000	-0.031	-1000
Atypical NF-kappaB pathway	0.0192	7	234	31	-0.088	0.028	1000	-1000	-0.037	-1000
S1P3 pathway	0.0192	7	303	42	-0.043	0.028	1000	-1000	-0.039	-1000
Signaling events mediated by PRL	0.0192	7	247	34	-0.059	0.021	1000	-1000	-0.034	-1000
EPO signaling pathway	0.0164	6	382	55	-0.11	0.055	1000	-1000	-0.081	-1000
IFN-gamma pathway	0.0164	6	473	68	-0.24	0.061	1000	-1000	-0.086	-1000
Signaling events mediated by VEGFR1 and VEGFR2	0.0164	6	785	125	-0.075	0.076	1000	-1000	-0.085	-1000
VEGFR1 specific signals	0.0164	6	345	56	-0.088	0.041	1000	-1000	-0.063	-1000
Class IB PI3K non-lipid kinase events	0.0164	6	18	3	-0.004	0.004	1000	-1000	-0.013	-1000
Hedgehog signaling events mediated by Gli proteins	0.0137	5	335	65	-0.045	0.064	1000	-1000	-0.061	-1000
HIF-2-alpha transcription factor network	0.0137	5	221	43	-0.11	0.11	1000	-1000	-0.08	-1000
Signaling events mediated by HDAC Class I	0.0137	5	614	104	-0.15	0.059	1000	-1000	-0.059	-1000
Insulin Pathway	0.0137	5	392	74	-0.17	0.038	1000	-1000	-0.084	-1000
Signaling events mediated by HDAC Class II	0.0110	4	351	75	-0.17	0.041	1000	-1000	-0.058	-1000
FoxO family signaling	0.0110	4	269	64	-0.11	0.13	1000	-1000	-0.054	-1000
PDGFR-beta signaling pathway	0.0110	4	473	97	-0.055	0.063	1000	-1000	-0.078	-1000
Class I PI3K signaling events mediated by Akt	0.0082	3	269	68	-0.11	0.054	1000	-1000	-0.051	-1000
Arf6 trafficking events	0.0082	3	258	71	-0.12	0.047	1000	-1000	-0.07	-1000
IGF1 pathway	0.0082	3	173	57	-0.049	0.054	1000	-1000	-0.086	-1000
Arf6 downstream pathway	0.0055	2	121	43	-0.026	0.027	1000	-1000	-0.038	-1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling	0.0027	1	37	23	-0.017	0.05	1000	-1000	-0.057	-1000
Alternative NF-kappaB pathway	0.0027	1	24	13	-0.006	0.014	1000	-1000	-0.063	-1000
mTOR signaling pathway	0.0000	0	49	53	-0.007	0.036	1000	-1000	-0.059	-1000
Sumoylation by RanBP2 regulates transcriptional repression	0.0000	0	14	27	-0.005	0.036	1000	-1000	-0.055	-1000
Arf1 pathway	0.0000	0	19	54	-0.006	0.036	1000	-1000	-0.038	-1000
Total	NA	2858	158786	7203	-20	5.6	131000	-131000	-8.1	-131000

IL23-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCL2	-0.62	0.56	-10000	0	-1.2	158	158
IL23A	-0.62	0.56	-10000	0	-1.2	144	144
NF kappa B1 p50/RelA/I kappa B alpha	-0.59	0.51	-10000	0	-1.1	152	152
positive regulation of T cell mediated cytotoxicity	-0.65	0.62	-10000	0	-1.3	154	154
ITGA3	-0.56	0.52	-10000	0	-1.1	142	142
IL17F	-0.36	0.33	-10000	0	-0.73	111	111
IL12B	-0.023	0.062	-10000	0	-0.53	4	4
STAT1 (dimer)	-0.62	0.59	-10000	0	-1.2	155	155
CD4	-0.55	0.51	-10000	0	-1.1	143	143
IL23	-0.6	0.53	-10000	0	-1.2	144	144
IL23R	-0.084	0.084	-10000	0	-0.5	1	1
IL1B	-0.66	0.61	-10000	0	-1.3	151	151
T-helper cell lineage commitment	0	0	-10000	0	-10000	0	0
IL24	-0.55	0.5	-10000	0	-1.1	142	142
TYK2	-0.001	0.018	-10000	0	-10000	0	0
STAT4	-0.17	0.26	-10000	0	-0.54	124	124
STAT3	0.014	0	-10000	0	-10000	0	0
IL18RAP	-0.09	0.22	-10000	0	-0.54	69	69
IL12RB1	-0.05	0.16	-10000	0	-0.58	31	31
PIK3CA	0.012	0.032	-10000	0	-0.6	1	1
IL12Rbeta1/TYK2	-0.04	0.12	-10000	0	-0.43	31	31
IL23R/JAK2	-0.096	0.1	-10000	0	-0.49	1	1
positive regulation of chronic inflammatory response	-0.65	0.62	-10000	0	-1.3	154	154
natural killer cell activation	0.008	0.007	0.046	1	-10000	0	1
JAK2	0.008	0.018	-10000	0	-10000	0	0
PIK3R1	0.014	0	-10000	0	-10000	0	0
NFKB1	0.01	0.026	-10000	0	-0.49	1	1
RELA	0.011	0.003	-10000	0	-10000	0	0
positive regulation of dendritic cell antigen processing and presentation	-0.57	0.49	-10000	0	-1.1	144	144
ALOX12B	-0.62	0.56	-10000	0	-1.2	151	151
CXCL1	-0.61	0.55	-10000	0	-1.2	152	152
T cell proliferation	-0.65	0.62	-10000	0	-1.3	154	154
NFKBIA	0.011	0.003	-10000	0	-10000	0	0
IL17A	-0.27	0.26	-10000	0	-0.57	98	98
PI3K	-0.61	0.52	-10000	0	-1.1	154	154
IFNG	-0.024	0.032	-10000	0	-0.1	13	13
STAT3 (dimer)	-0.57	0.48	-10000	0	-1.1	150	150
IL18R1	-0.049	0.18	-10000	0	-0.54	42	42
IL23/IL23R/JAK2/TYK2/SOCS3	-0.33	0.3	-10000	0	-0.66	112	112
IL18/IL18R	-0.1	0.21	-10000	0	-0.39	112	112
macrophage activation	-0.028	0.017	-10000	0	-0.044	136	136
TNF	-0.65	0.6	-10000	0	-1.2	156	156
STAT3/STAT4	-0.67	0.53	-10000	0	-1.1	179	179
STAT4 (dimer)	-0.69	0.6	-10000	0	-1.2	173	173
IL18	-0.031	0.15	-10000	0	-0.53	31	31
IL19	-0.55	0.5	-10000	0	-1.1	142	142
STAT5A (dimer)	-0.62	0.59	-10000	0	-1.2	151	151
STAT1	-0.001	0.085	-10000	0	-0.48	11	11
SOCS3	-0.11	0.23	-10000	0	-0.52	85	85
CXCL9	-0.65	0.57	-10000	0	-1.2	160	160
MPO	-0.64	0.57	-10000	0	-1.2	163	163
positive regulation of humoral immune response	-0.65	0.62	-10000	0	-1.3	154	154
IL23/IL23R/JAK2/TYK2	-0.71	0.75	-10000	0	-1.4	154	154
IL6	-0.62	0.56	-10000	0	-1.2	157	157
STAT5A	0.001	0.09	-10000	0	-0.6	8	8
IL2	0.006	0.006	-10000	0	-10000	0	0
positive regulation of tyrosine phosphorylation of STAT protein	0.008	0.007	0.046	1	-10000	0	1
CD3E	-0.63	0.56	-10000	0	-1.2	158	158
keratinocyte proliferation	-0.65	0.62	-10000	0	-1.3	154	154
NOS2	-0.57	0.53	-10000	0	-1.2	130	130

×

Ephrin A reverse signaling

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
MAPKKK cascade	-0.13	0.22	-9999	-0.44	110	110
EFNA5	-0.081	0.21	-9999	-0.55	62	62
FYN	-0.1	0.21	-9999	-0.4	110	110
neuron projection morphogenesis	-0.13	0.22	-9999	-0.44	110	110
cell-cell signaling	0	0	-9999	-10000	0	0
Ephrin A5/EPHA5	-0.13	0.22	-9999	-0.44	110	110
EPHA5	-0.12	0.24	-9999	-0.55	87	87

×

TCGA08_retinoblastoma

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
CDKN2B	-0.056	0.18	-10000	0	-0.55	45	45
CDKN2C	-0.016	0.13	-10000	0	-0.44	29	29
CDKN2A	-0.1	0.23	-10000	0	-0.55	74	74
CCND2	0.061	0.13	0.29	72	-0.14	2	74
RB1	-0.065	0.14	-10000	0	-0.31	72	72
CDK4	0.073	0.15	0.32	77	-10000	0	77
CDK6	0.064	0.15	0.32	72	-0.17	12	84
G1/S progression	0.053	0.15	0.31	74	-10000	0	74

×

FOXM1 transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC3	-0.2	0.63	-9999	-1.2	82	82
PLK1	0	0.19	-9999	-0.56	25	25
BIRC5	-0.22	0.55	-9999	-1.5	54	54
HSPA1B	-0.22	0.65	-9999	-1.2	90	90
MAP2K1	0.023	0.053	-9999	-0.53	1	1
BRCA2	-0.22	0.67	-9999	-1.2	94	94
FOXM1	-0.35	0.92	-9999	-1.8	88	88
XRCC1	-0.2	0.63	-9999	-1.2	82	82
FOXM1B/p19	-0.37	0.55	-9999	-1.3	91	91
Cyclin D1/CDK4	-0.19	0.59	-9999	-1.1	89	89
CDC2	-0.22	0.67	-9999	-1.3	88	88
TGFA	-0.18	0.58	-9999	-1	91	91
SKP2	-0.2	0.64	-9999	-1.2	90	90
CCNE1	0.012	0.039	-9999	-0.5	2	2
CKS1B	-0.2	0.63	-9999	-1.2	83	83
RB1	-0.17	0.29	-9999	-0.83	42	42
FOXM1C/SP1	-0.27	0.75	-9999	-1.5	89	89
AURKB	-0.26	0.58	-9999	-1.2	91	91
CENPF	-0.23	0.69	-9999	-1.3	86	86
CDK4	0.004	0.084	-9999	-0.48	10	10
MYC	-0.16	0.57	-9999	-1	86	86
CHEK2	0.01	0.1	-9999	-0.55	10	10
ONECUT1	-0.21	0.62	-9999	-1.2	90	90
CDKN2A	-0.11	0.24	-9999	-0.57	74	74
LAMA4	-0.2	0.63	-9999	-1.2	82	82
FOXM1B/HNF6	-0.29	0.76	-9999	-1.5	90	90
FOS	-0.28	0.68	-9999	-1.2	113	113
SP1	0.015	0.004	-9999	-10000	0	0
CDC25B	-0.2	0.63	-9999	-1.2	83	83
response to radiation	0.008	0.041	-9999	-10000	0	0
CENPB	-0.2	0.63	-9999	-1.2	82	82
CENPA	-0.24	0.69	-9999	-1.3	89	89
NEK2	-0.25	0.7	-9999	-1.3	96	96
HIST1H2BA	-0.2	0.63	-9999	-1.2	84	84
CCNA2	-0.05	0.18	-9999	-0.55	43	43
EP300	0.007	0.064	-9999	-0.6	4	4
CCNB1/CDK1	-0.27	0.76	-9999	-1.5	86	86
CCNB2	-0.26	0.72	-9999	-1.4	93	93
CCNB1	-0.22	0.68	-9999	-1.3	84	84
ETV5	-0.22	0.64	-9999	-1.2	90	90
ESR1	-0.22	0.65	-9999	-1.2	93	93
CCND1	-0.2	0.6	-9999	-1.1	91	91
GSK3A	0.025	0.036	-9999	-10000	0	0
Cyclin A-E1/CDK1-2	-0.012	0.16	-9999	-0.4	46	46
CDK2	0.002	0.089	-9999	-0.55	9	9
G2/M transition of mitotic cell cycle	0.008	0.049	-9999	-10000	0	0
FOXM1B/Cbp/p300	-0.4	0.57	-9999	-1.3	90	90
GAS1	-0.2	0.64	-9999	-1.2	85	85
MMP2	-0.21	0.65	-9999	-1.2	85	85
RB1/FOXM1C	-0.21	0.63	-9999	-1.2	90	90
CREBBP	0.014	0	-9999	-10000	0	0

×

IL12-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1	-0.13	0.17	-10000	0	-0.4	68	68
TBX21	-0.48	0.49	-10000	0	-1	130	130
B2M	0.01	0.046	-10000	0	-0.49	3	3
TYK2	0.001	0.018	-10000	0	-10000	0	0
IL12RB1	-0.048	0.16	-10000	0	-0.58	31	31
GADD45B	-0.36	0.39	-10000	0	-0.83	110	110
IL12RB2	-0.14	0.24	-10000	0	-0.54	98	98
GADD45G	-0.38	0.42	-10000	0	-0.89	107	107
natural killer cell activation	-0.016	0.022	-10000	0	-10000	0	0
RELB	0.01	0.049	-10000	0	-0.52	3	3
RELA	0.014	0	-10000	0	-10000	0	0
IL18	-0.035	0.16	-10000	0	-0.54	31	31
IL2RA	-0.069	0.19	-10000	0	-0.51	55	55
IFNG	-0.002	0.051	-10000	0	-0.48	4	4
STAT3 (dimer)	-0.37	0.36	-10000	0	-0.74	143	143
HLA-DRB5	-0.13	0.24	-10000	0	-0.54	95	95
FASLG	-0.46	0.46	-10000	0	-0.98	130	130
NF kappa B2 p52/RelB	-0.46	0.43	-10000	0	-0.92	145	145
CD4	0.002	0.073	-10000	0	-0.52	7	7
SOCS1	-0.034	0.15	-10000	0	-0.51	34	34
EntrezGene:6955	-0.002	0.01	-10000	0	-10000	0	0
CD3D	-0.12	0.23	-10000	0	-0.53	87	87
CD3E	-0.14	0.25	-10000	0	-0.54	98	98
CD3G	-0.026	0.13	-10000	0	-0.49	25	25
IL12Rbeta2/JAK2	-0.11	0.18	-10000	0	-0.4	98	98
CCL3	-0.56	0.57	-10000	0	-1.1	151	151
CCL4	-0.56	0.58	-10000	0	-1.2	146	146
HLA-A	0.007	0.058	-10000	0	-0.48	5	5
IL18/IL18R	-0.1	0.23	-10000	0	-0.42	107	107
NOS2	-0.42	0.44	-10000	0	-0.98	108	108
IL12/IL12R/TYK2/JAK2/SPHK2	-0.11	0.16	-10000	0	-0.39	53	53
IL1R1	-0.46	0.47	-10000	0	-1	119	119
IL4	0.018	0.023	-10000	0	-10000	0	0
JAK2	0.001	0.018	-10000	0	-10000	0	0
EntrezGene:6957	-0.002	0.01	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.13	0.26	-10000	0	-0.61	65	65
RAB7A	-0.3	0.32	-10000	0	-0.74	77	77
lysosomal transport	-0.28	0.3	-10000	0	-0.7	77	77
FOS	-0.35	0.45	-10000	0	-1.1	80	80
STAT4 (dimer)	-0.44	0.41	-10000	0	-0.86	143	143
STAT5A (dimer)	-0.47	0.43	-10000	0	-0.92	149	149
GZMA	-0.54	0.54	-10000	0	-1.1	145	145
GZMB	-0.51	0.52	-10000	0	-1.1	132	132
HLX	-0.004	0.097	-10000	0	-0.51	13	13
LCK	-0.52	0.53	-10000	0	-1	158	158
TCR/CD3/MHC II/CD4	-0.17	0.26	-10000	0	-0.51	109	109
IL2/IL2R	-0.12	0.2	-10000	0	-0.46	79	79
MAPK14	-0.37	0.4	-10000	0	-0.83	116	116
CCR5	-0.42	0.45	-10000	0	-0.95	113	113
IL1B	-0.2	0.28	-10000	0	-0.57	128	128
STAT6	-0.11	0.11	-10000	0	-0.26	19	19
STAT4	-0.17	0.26	-10000	0	-0.54	124	124
STAT3	0.014	0	-10000	0	-10000	0	0
STAT1	-0.001	0.085	-10000	0	-0.48	11	11
NFKB1	0.013	0.026	-10000	0	-0.48	1	1
NFKB2	0.008	0.055	-10000	0	-0.51	4	4
IL12B	-0.015	0.058	-10000	0	-0.52	4	4
CD8A	-0.079	0.21	-10000	0	-0.55	61	61
CD8B	-0.032	0.16	-10000	0	-0.56	29	29
T-helper 1 cell differentiation	0	0	-10000	0	-10000	0	0
natural killer cell mediated cytotoxicity	0.13	0.17	0.39	68	-10000	0	68
IL2RB	-0.099	0.22	-10000	0	-0.53	76	76
proteasomal ubiquitin-dependent protein catabolic process	-0.4	0.36	-10000	0	-0.77	143	143
IL2RG	-0.036	0.16	-10000	0	-0.51	35	35
IL12	-0.034	0.12	-10000	0	-0.45	24	24
STAT5A	0.001	0.09	-10000	0	-0.6	8	8
CD247	-0.021	0.13	-10000	0	-0.52	23	23
IL2	0	0.002	-10000	0	-10000	0	0
SPHK2	0.014	0	-10000	0	-10000	0	0
FRAP1	0	0	-10000	0	-10000	0	0
IL12A	-0.032	0.14	-10000	0	-0.61	20	20
IL12/IL12R/TYK2/JAK2	-0.53	0.57	-10000	0	-1.1	149	149
MAP2K3	-0.37	0.4	-10000	0	-0.82	122	122
RIPK2	0.014	0	-10000	0	-10000	0	0
MAP2K6	-0.37	0.4	-10000	0	-0.82	122	122
regulation of dendritic cell antigen processing and presentation	0	0	-10000	0	-10000	0	0
HLA-DRA	-0.099	0.22	-10000	0	-0.54	74	74
IL18RAP	-0.095	0.22	-10000	0	-0.55	69	69
IL12Rbeta1/TYK2	-0.037	0.12	-10000	0	-0.43	31	31
EOMES	-0.016	0.19	-10000	0	-1.3	5	5
STAT1 (dimer)	-0.36	0.35	-10000	0	-0.76	129	129
T cell proliferation	-0.32	0.29	-10000	0	-0.62	134	134
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
IL18R1	-0.054	0.18	-10000	0	-0.55	42	42
CD8-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.37	0.29	-10000	0	-0.69	138	138
ATF2	-0.34	0.36	-10000	0	-0.8	103	103

×

Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FOXP3	-0.015	0.11	-10000	0	-0.58	10	10
NFATC2	-0.14	0.31	-10000	0	-0.68	72	72
NFATC3	-0.047	0.11	-10000	0	-0.31	7	7
CD40LG	-0.38	0.49	-10000	0	-1	116	116
ITCH	-0.035	0.13	-10000	0	-0.54	2	2
CBLB	-0.037	0.13	-10000	0	-0.64	3	3
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment	-0.35	0.41	-10000	0	-0.94	89	89
JUNB	-0.036	0.16	-10000	0	-0.51	35	35
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.088	0.13	-10000	0	-0.64	2	2
T cell anergy	-0.11	0.21	-10000	0	-0.47	61	61
TLE4	-0.089	0.26	-10000	0	-0.66	44	44
Jun/NFAT1-c-4/p21SNFT	-0.36	0.46	-10000	0	-0.99	100	100
AP-1/NFAT1-c-4	-0.46	0.59	-10000	0	-1.2	118	118
IKZF1	-0.1	0.28	-10000	0	-0.73	44	44
T-helper 2 cell differentiation	-0.19	0.3	-10000	0	-0.75	53	53
AP-1/NFAT1	-0.17	0.26	-10000	0	-0.57	84	84
CALM1	-0.028	0.088	-10000	0	-0.76	1	1
EGR2	-0.3	0.54	-10000	0	-1	100	100
EGR3	-0.34	0.59	-10000	0	-1.2	92	92
NFAT1/FOXP3	-0.13	0.26	-10000	0	-0.64	58	58
EGR1	-0.11	0.23	-10000	0	-0.53	79	79
JUN	-0.004	0.078	-10000	0	-0.51	8	8
EGR4	-0.21	0.28	-10000	0	-0.55	144	144
mol:Ca2+	-0.044	0.086	-10000	0	-0.3	1	1
GBP3	-0.17	0.36	-10000	0	-0.75	85	85
FOSL1	-0.096	0.22	-10000	0	-0.53	74	74
NFAT1-c-4/MAF/IRF4	-0.33	0.45	-10000	0	-0.97	96	96
DGKA	-0.082	0.23	-10000	0	-0.6	43	43
CREM	0.011	0.041	-10000	0	-0.54	2	2
NFAT1-c-4/PPARG	-0.34	0.46	-10000	0	-0.96	103	103
CTLA4	-0.13	0.31	-10000	0	-0.72	61	61
NFAT1-c-4 (dimer)/EGR1	-0.38	0.53	-10000	0	-1	117	117
NFAT1-c-4 (dimer)/EGR4	-0.44	0.49	-10000	0	-1	120	120
FOS	-0.096	0.22	-10000	0	-0.56	66	66
IFNG	-0.18	0.24	-10000	0	-0.75	35	35
T cell activation	-0.17	0.28	-10000	0	-0.69	53	53
MAF	0.011	0.046	-10000	0	-0.6	2	2
T-helper 2 cell lineage commitment	0	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	0.23	0.41	0.87	76	-10000	0	76
TNF	-0.48	0.51	-10000	0	-1	154	154
FASLG	-0.35	0.56	-10000	0	-1.2	84	84
TBX21	-0.04	0.17	-10000	0	-0.53	37	37
BATF3	-0.037	0.16	-10000	0	-0.54	34	34
PRKCQ	-0.007	0.11	-10000	0	-0.58	13	13
PTPN1	-0.082	0.23	-10000	0	-0.62	40	40
NFAT1-c-4/ICER1	-0.32	0.45	-10000	0	-0.96	100	100
GATA3	-0.1	0.22	-10000	0	-0.53	77	77
T-helper 1 cell differentiation	-0.16	0.25	-10000	0	-0.73	35	35
IL2RA	-0.32	0.35	-10000	0	-0.8	94	94
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
CASP3	-0.083	0.23	-10000	0	-0.64	37	37
E2F1	-0.004	0.1	-10000	0	-0.49	16	16
PPARG	-0.013	0.12	-10000	0	-0.57	17	17
SLC3A2	-0.082	0.23	-10000	0	-0.64	36	36
IRF4	-0.048	0.18	-10000	0	-0.54	41	41
PTGS2	-0.41	0.53	-10000	0	-1.1	118	118
CSF2	-0.37	0.48	-10000	0	-1	110	110
JunB/Fra1/NFAT1-c-4	-0.38	0.46	-10000	0	-0.97	111	111
IL4	-0.19	0.31	-10000	0	-0.8	51	51
IL5	-0.37	0.48	-10000	0	-1	110	110
IL2	-0.17	0.29	-10000	0	-0.71	51	51
IL3	-0.066	0.076	-10000	0	-0.95	1	1
RNF128	-0.16	0.3	-10000	0	-0.57	124	124
NFATC1	-0.23	0.42	-10000	0	-0.88	76	76
CDK4	0.14	0.24	0.59	37	-0.49	1	38
PTPRK	-0.086	0.24	-10000	0	-0.63	44	44
IL8	-0.44	0.53	-10000	0	-1.1	127	127
POU2F1	0.013	0.032	-10000	0	-0.6	1	1

×

Aurora B signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Condensin I complex	-0.12	0.26	-9999	-0.59	71	71
STMN1	-0.098	0.2	-9999	-0.4	106	106
Aurora B/RasGAP/Survivin	-0.17	0.28	-9999	-0.55	119	119
Chromosomal passenger complex/Cul3 protein complex	-0.086	0.19	-9999	-0.39	87	87
BIRC5	-0.14	0.26	-9999	-0.57	95	95
DES	-0.32	0.46	-9999	-0.95	112	112
Aurora C/Aurora B/INCENP	-0.097	0.17	-9999	-0.33	118	118
Aurora B/TACC1	-0.091	0.16	-9999	-0.34	105	105
Aurora B/PP2A	-0.11	0.19	-9999	-0.4	105	105
mol:GTP	0	0	-9999	-10000	0	0
CBX5	-0.027	0.075	-9999	-0.17	66	66
mitotic metaphase/anaphase transition	0.001	0.006	-9999	-10000	0	0
NDC80	-0.19	0.32	-9999	-0.61	124	124
Cul3 protein complex	-0.007	0.05	-9999	-0.36	7	7
KIF2C	-0.12	0.27	-9999	-0.43	114	114
PEBP1	0.008	0.034	-9999	-0.62	1	1
KIF20A	-0.17	0.27	-9999	-0.56	116	116
mol:GDP	0	0	-9999	-10000	0	0
Aurora B/RasGAP	-0.11	0.19	-9999	-0.4	105	105
SEPT1	0.009	0.052	-9999	-0.48	4	4
SMC2	0.014	0	-9999	-10000	0	0
SMC4	-0.009	0.1	-9999	-0.48	17	17
NSUN2/NPM1/Nucleolin	-0.16	0.33	-9999	-0.84	66	66
PSMA3	0.014	0	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	-0.001	0.004	-9999	-10000	0	0
H3F3B	-0.072	0.15	-9999	-0.3	104	104
AURKB	-0.15	0.27	-9999	-0.57	105	105
AURKC	-0.019	0.13	-9999	-0.52	23	23
CDCA8	-0.047	0.17	-9999	-0.52	39	39
cytokinesis	-0.26	0.41	-9999	-0.82	114	114
Aurora B/Septin1	-0.24	0.38	-9999	-0.77	113	113
AURKA	-0.011	0.11	-9999	-0.49	18	18
INCENP	0.009	0.009	-9999	-10000	0	0
KLHL13	0.011	0.046	-9999	-0.6	2	2
BUB1	-0.11	0.24	-9999	-0.56	81	81
hSgo1/Aurora B/Survivin	-0.22	0.35	-9999	-0.65	130	130
EVI5	0.013	0.003	-9999	-10000	0	0
RhoA/GTP	-0.23	0.36	-9999	-0.73	110	110
SGOL1	-0.11	0.24	-9999	-0.55	83	83
CENPA	-0.16	0.31	-9999	-0.56	115	115
NCAPG	-0.12	0.24	-9999	-0.55	89	89
Aurora B/HC8 Proteasome	-0.11	0.19	-9999	-0.4	105	105
NCAPD2	0.01	0.045	-9999	-0.48	3	3
Aurora B/PP1-gamma	-0.11	0.19	-9999	-0.4	105	105
RHOA	0.014	0	-9999	-10000	0	0
NCAPH	-0.061	0.19	-9999	-0.55	49	49
NPM1	-0.13	0.24	-9999	-0.62	66	66
RASA1	0.014	0	-9999	-10000	0	0
KLHL9	0.006	0.072	-9999	-0.6	5	5
mitotic prometaphase	-0.006	0.01	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	-0.11	0.19	-9999	-0.4	105	105
PPP1CC	0.014	0	-9999	-10000	0	0
Centraspindlin	-0.26	0.4	-9999	-0.78	118	118
RhoA/GDP	0	0	-9999	-10000	0	0
NSUN2	-0.13	0.24	-9999	-0.62	66	66
MYLK	-0.08	0.16	-9999	-0.3	112	112
KIF23	-0.11	0.23	-9999	-0.55	79	79
VIM	-0.16	0.24	-9999	-0.44	143	143
RACGAP1	0.004	0.056	-9999	-0.52	4	4
mitosis	0	0	-9999	-10000	0	0
NCL	-0.13	0.24	-9999	-0.62	66	66
Chromosomal passenger complex	-0.2	0.38	-9999	-0.68	118	118
Chromosomal passenger complex/EVI5	-0.17	0.3	-9999	-0.58	114	114
TACC1	0.014	0	-9999	-10000	0	0
PPP2R5D	0.014	0	-9999	-10000	0	0
CUL3	0.014	0	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0

×

Effects of Botulinum toxin

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
STX1A	-0.06	0.15	-9999	-0.36	71	71
UniProt:P19321	0	0	-9999	-10000	0	0
RIMS1/UNC13B	-0.092	0.17	-9999	-0.4	84	84
STXBP1	-0.015	0.12	-9999	-0.49	21	21
ACh/CHRNA1	-0.13	0.17	-9999	-0.37	112	112
RAB3GAP2/RIMS1/UNC13B	-0.076	0.14	-9999	-0.33	84	84
mol:Ca2+	0	0	-9999	-10000	0	0
UniProt:P30996	0	0	-9999	-10000	0	0
UniProt:Q60393	0	0	-9999	-10000	0	0
CST086	0	0	-9999	-10000	0	0
RIMS1	-0.12	0.24	-9999	-0.55	84	84
mol:ACh	-0.04	0.069	-9999	-0.14	120	120
RAB3GAP2	0.014	0	-9999	-10000	0	0
STX1A/SNAP25/VAMP2	-0.14	0.21	-9999	-0.45	95	95
UniProt:P10844	0	0	-9999	-10000	0	0
muscle contraction	-0.13	0.17	-9999	-0.37	112	112
UNC13B	0.012	0.032	-9999	-0.6	1	1
CHRNA1	-0.15	0.25	-9999	-0.53	111	111
UniProt:P10845	0	0	-9999	-10000	0	0
ACh/Synaptotagmin 1	-0.16	0.21	-9999	-0.41	148	148
SNAP25	-0.075	0.13	-9999	-0.24	121	121
VAMP2	0.007	0	-9999	-10000	0	0
SYT1	-0.21	0.27	-9999	-0.53	148	148
UniProt:Q00496	0	0	-9999	-10000	0	0
STXIA/STXBP1	-0.057	0.16	-9999	-0.37	73	73
STX1A/SNAP25 fragment 1/VAMP2	-0.14	0.21	-9999	-0.45	95	95

×

TCR signaling in naïve CD8+ T 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
GRB2/SOS1/SHC	-0.14	0.19	-10000	0	-0.46	79	79
FYN	-0.15	0.28	-10000	0	-0.55	97	97
LAT/GRAP2/SLP76	-0.17	0.23	-10000	0	-0.51	94	94
IKBKB	0.014	0	-10000	0	-10000	0	0
AKT1	-0.11	0.19	-10000	0	-0.4	87	87
B2M	0.008	0.046	-10000	0	-0.49	3	3
IKBKG	-0.035	0.047	-10000	0	-0.15	19	19
MAP3K8	0	0.083	-10000	0	-0.49	10	10
mol:Ca2+	-0.028	0.043	-10000	0	-0.11	74	74
integrin-mediated signaling pathway	-0.01	0.056	-10000	0	-0.32	11	11
LAT/GRAP2/SLP76/VAV1/PI3K Class IA	-0.16	0.27	-10000	0	-0.57	91	91
TRPV6	-0.12	0.24	-10000	0	-0.56	82	82
CD28	-0.078	0.21	-10000	0	-0.54	60	60
SHC1	-0.15	0.27	-10000	0	-0.55	92	92
receptor internalization	-0.13	0.24	-10000	0	-0.52	83	83
PRF1	-0.18	0.37	-10000	0	-0.94	54	54
KRAS	0.013	0.026	-10000	0	-0.48	1	1
GRB2	0.014	0	-10000	0	-10000	0	0
COT/AKT1	-0.082	0.16	-10000	0	-0.34	72	72
LAT	-0.17	0.27	-10000	0	-0.55	98	98
EntrezGene:6955	-0.002	0.006	-10000	0	-10000	0	0
CD3D	-0.12	0.23	-10000	0	-0.53	87	87
CD3E	-0.14	0.25	-10000	0	-0.55	98	98
CD3G	-0.026	0.13	-10000	0	-0.49	25	25
RASGRP2	-0.007	0.025	-10000	0	-0.18	2	2
RASGRP1	-0.12	0.2	-10000	0	-0.4	91	91
HLA-A	0.005	0.059	-10000	0	-0.49	5	5
RASSF5	-0.002	0.095	-10000	0	-0.54	11	11
RAP1A/GTP/RAPL	-0.01	0.056	-10000	0	-0.32	11	11
mol:GTP	0	0	-10000	0	-10000	0	0
mol:GDP	-0.016	0.063	-10000	0	-0.11	40	40
PDK1/CARD11/BCL10/MALT1/TRAF6	-0.065	0.082	-10000	0	-0.22	50	50
PRKCA	-0.08	0.11	-10000	0	-0.26	72	72
GRAP2	-0.049	0.17	-10000	0	-0.52	43	43
mol:IP3	-0.1	0.2	0.21	45	-0.4	83	128
EntrezGene:6957	-0.002	0.007	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.12	0.22	-10000	0	-0.48	80	80
ORAI1	0.074	0.12	0.31	81	-10000	0	81
CSK	-0.15	0.27	-10000	0	-0.56	93	93
B7 family/CD28	-0.22	0.28	-10000	0	-0.62	96	96
CHUK	0.014	0	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8/LCK/ZAP-70	-0.18	0.31	-10000	0	-0.61	99	99
PTPN6	-0.16	0.28	-10000	0	-0.56	98	98
VAV1	-0.16	0.29	-10000	0	-0.58	94	94
Monovalent TCR/CD3	-0.11	0.2	-10000	0	-0.37	122	122
CBL	0.014	0	-10000	0	-10000	0	0
LCK	-0.17	0.3	-10000	0	-0.58	108	108
PAG1	-0.16	0.27	-10000	0	-0.56	92	92
RAP1A	0.014	0	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8/LCK	-0.17	0.3	-10000	0	-0.61	96	96
CD80	-0.053	0.18	-10000	0	-0.52	44	44
CD86	-0.026	0.14	-10000	0	-0.55	25	25
PDK1/CARD11/BCL10/MALT1	-0.079	0.1	-10000	0	-0.26	58	58
HRAS	0.013	0.026	-10000	0	-0.48	1	1
GO:0035030	-0.16	0.25	-10000	0	-0.52	92	92
CD8A	-0.081	0.21	-10000	0	-0.55	61	61
CD8B	-0.034	0.16	-10000	0	-0.57	29	29
PTPRC	-0.045	0.17	-10000	0	-0.54	38	38
PDK1/PKC theta	-0.13	0.24	-10000	0	-0.49	84	84
CSK/PAG1	-0.15	0.27	-10000	0	-0.56	85	85
SOS1	0.014	0	-10000	0	-10000	0	0
peptide-MHC class I	0.006	0.058	-10000	0	-0.39	7	7
GRAP2/SLP76	-0.18	0.27	-10000	0	-0.57	96	96
STIM1	0.04	0.063	0.22	1	-10000	0	1
RAS family/GTP	-0.023	0.085	-10000	0	-0.17	34	34
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin	-0.14	0.26	-10000	0	-0.55	83	83
mol:DAG	-0.11	0.16	-10000	0	-0.36	86	86
RAP1A/GDP	-0.005	0.028	-10000	0	-10000	0	0
PLCG1	0.014	0	-10000	0	-10000	0	0
CD247	-0.021	0.13	-10000	0	-0.52	23	23
cytotoxic T cell degranulation	-0.16	0.34	-10000	0	-0.89	54	54
RAP1A/GTP	-0.004	0.007	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	-0.13	0.23	-10000	0	-0.47	90	90
LAT/GRAP2/SLP76/VAV1/PLCgamma1	-0.14	0.25	0.23	39	-0.52	84	123
NRAS	0.014	0	-10000	0	-10000	0	0
ZAP70	-0.059	0.19	-10000	0	-0.53	49	49
GRB2/SOS1	0	0	-10000	0	-10000	0	0
LAT/GRAP2/SLP76/VAV1	-0.17	0.23	-10000	0	-0.51	92	92
MALT1	0.014	0	-10000	0	-10000	0	0
TRAF6	0.012	0.032	-10000	0	-0.6	1	1
CD8 heterodimer	-0.082	0.2	-10000	0	-0.47	75	75
CARD11	-0.008	0.11	-10000	0	-0.58	14	14
PRKCB	-0.1	0.12	-10000	0	-0.27	92	92
PRKCE	-0.083	0.11	-10000	0	-0.26	74	74
PRKCQ	-0.16	0.26	-10000	0	-0.55	89	89
LCP2	-0.004	0.094	-10000	0	-0.49	13	13
BCL10	0.014	0	-10000	0	-10000	0	0
regulation of survival gene product expression	-0.09	0.17	-10000	0	-0.34	87	87
IKK complex	-0.011	0.062	-10000	0	-0.11	22	22
RAS family/GDP	-0.007	0.01	-10000	0	-10000	0	0
MAP3K14	-0.055	0.13	-10000	0	-0.27	53	53
PDPK1	-0.1	0.18	-10000	0	-0.39	79	79
TCR/CD3/MHC I/CD8/Fyn	-0.18	0.32	-10000	0	-0.62	99	99

×

E-cadherin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin	-0.09	0.15	-9999	-0.38	51	51
E-cadherin/beta catenin	-0.1	0.17	-9999	-0.38	95	95
CTNNB1	0.014	0	-9999	-10000	0	0
JUP	0.001	0.086	-9999	-0.57	8	8
CDH1	-0.13	0.25	-9999	-0.54	95	95

×

Signaling events mediated by the Hedgehog family

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
TGFB2	-0.095	0.29	-10000	0	-0.72	44	44
IHH	-0.01	0.074	-10000	0	-0.47	4	4
SHH Np/Cholesterol/GAS1	-0.084	0.15	-10000	0	-0.32	96	96
LRPAP1	0.014	0	-10000	0	-10000	0	0
dorsoventral neural tube patterning	0.084	0.15	0.32	96	-10000	0	96
SMO/beta Arrestin2	-0.035	0.18	-10000	0	-0.7	14	14
SMO	-0.044	0.19	-10000	0	-0.63	21	21
AKT1	0.004	0.087	-10000	0	-0.32	6	6
ARRB2	0.014	0	-10000	0	-10000	0	0
BOC	0.008	0.058	-10000	0	-0.54	4	4
ADRBK1	0.014	0	-10000	0	-10000	0	0
heart looping	-0.043	0.19	-10000	0	-0.6	22	22
STIL	-0.084	0.22	-10000	0	-0.55	47	47
DHH N/PTCH2	-0.056	0.14	-10000	0	-0.4	51	51
DHH N/PTCH1	-0.064	0.2	-10000	0	-0.56	27	27
PIK3CA	0.012	0.032	-10000	0	-0.6	1	1
DHH	-0.042	0.17	-10000	0	-0.54	37	37
PTHLH	-0.11	0.34	-10000	0	-0.93	43	43
determination of left/right symmetry	-0.043	0.19	-10000	0	-0.6	22	22
PIK3R1	0.014	0	-10000	0	-10000	0	0
skeletal system development	-0.1	0.34	-10000	0	-0.92	43	43
IHH N/Hhip	-0.11	0.21	-10000	0	-0.44	102	102
DHH N/Hhip	-0.14	0.2	-10000	0	-0.41	127	127
mol:Cholesterol	0	0	-10000	0	-10000	0	0
heart development	-0.043	0.19	-10000	0	-0.6	22	22
pancreas development	-0.14	0.25	-10000	0	-0.55	99	99
HHAT	-0.007	0.11	-10000	0	-0.57	13	13
PI3K	-0.001	0.023	-10000	0	-0.44	1	1
EntrezGene:84976	0	0	-10000	0	-10000	0	0
GAS1	-0.016	0.12	-10000	0	-0.49	22	22
somite specification	-0.043	0.19	-10000	0	-0.6	22	22
SHH Np/Cholesterol/PTCH1	-0.087	0.22	-10000	0	-0.55	47	47
SHH Np/Cholesterol/PTCH2	-0.082	0.15	-10000	0	-0.32	93	93
SHH Np/Cholesterol/Megalin	-0.17	0.2	-10000	0	-0.36	171	171
SHH	-0.073	0.19	-10000	0	-0.42	80	80
catabolic process	-0.044	0.19	-10000	0	-0.55	23	23
SMO/Vitamin D3	-0.079	0.22	-10000	0	-0.6	37	37
SHH Np/Cholesterol/Hhip	-0.15	0.2	-10000	0	-0.36	151	151
LRP2	-0.17	0.27	-10000	0	-0.55	121	121
receptor-mediated endocytosis	-0.17	0.22	-10000	0	-0.59	60	60
SHH Np/Cholesterol/BOC	-0.072	0.14	-10000	0	-0.36	54	54
SHH Np/Cholesterol/CDO	-0.086	0.16	-10000	0	-0.33	95	95
mesenchymal cell differentiation	0.15	0.2	0.36	151	-10000	0	151
mol:Vitamin D3	-0.085	0.22	-10000	0	-0.55	47	47
IHH N/PTCH2	-0.009	0.11	-10000	0	-0.44	19	19
CDON	-0.018	0.13	-10000	0	-0.57	20	20
IHH N/PTCH1	-0.044	0.19	-10000	0	-0.56	23	23
Megalin/LRPAP1	-0.13	0.19	-10000	0	-0.39	121	121
PTCH2	-0.01	0.12	-10000	0	-0.58	15	15
SHH Np/Cholesterol	-0.071	0.14	-10000	0	-0.33	80	80
PTCH1	-0.044	0.19	-10000	0	-0.56	23	23
HHIP	-0.14	0.25	-10000	0	-0.55	99	99

×

IL4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.39	0.44	-10000	0	-1.1	64	64
STAT6 (cleaved dimer)	-0.47	0.44	-10000	0	-1	118	118
IGHG1	-0.16	0.22	-10000	0	-0.78	17	17
IGHG3	-0.38	0.42	-10000	0	-0.96	91	91
AKT1	-0.24	0.3	-10000	0	-0.76	52	52
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1	-0.22	0.3	-10000	0	-0.78	54	54
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1	-0.23	0.27	-10000	0	-0.7	44	44
THY1	-0.4	0.47	-10000	0	-1.1	70	70
MYB	-0.06	0.19	-10000	0	-0.54	48	48
HMGA1	0.011	0.041	-10000	0	-0.54	2	2
IL4/IL4R/JAK1/IL2R gamma/JAK3	-0.32	0.35	-10000	0	-0.77	99	99
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP	-0.23	0.27	-10000	0	-0.69	48	48
SP1	0.02	0.013	-10000	0	-10000	0	0
INPP5D	0.008	0.055	-10000	0	-0.51	4	4
SOCS5	0.027	0.017	-10000	0	-10000	0	0
STAT6 (dimer)/ETS1	-0.45	0.46	-10000	0	-1	113	113
SOCS1	-0.3	0.33	-10000	0	-0.77	76	76
SOCS3	-0.36	0.42	-10000	0	-0.97	90	90
FCER2	-0.44	0.47	-10000	0	-1.1	84	84
PARP14	-0.002	0.086	-10000	0	-0.54	9	9
CCL17	-0.4	0.45	-10000	0	-1.1	79	79
GRB2	0.014	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP	-0.19	0.23	-10000	0	-0.6	47	47
T cell proliferation	-0.4	0.46	-10000	0	-1.1	79	79
IL4R/JAK1	-0.4	0.43	-10000	0	-1.1	68	68
EGR2	-0.5	0.54	-10000	0	-1.2	101	101
JAK2	-0.003	0.027	-10000	0	-10000	0	0
JAK3	-0.06	0.19	-10000	0	-0.53	49	49
PIK3R1	0.014	0	-10000	0	-10000	0	0
JAK1	0.005	0.012	-10000	0	-10000	0	0
COL1A2	-0.16	0.25	-10000	0	-0.75	32	32
CCL26	-0.4	0.45	-10000	0	-1.1	62	62
IL4R	-0.42	0.46	-10000	0	-1.1	67	67
PTPN6	0.006	0.097	-10000	0	-0.52	12	12
IL13RA2	-0.6	0.59	-10000	0	-1.3	138	138
IL13RA1	-0.012	0.078	-10000	0	-0.63	5	5
IRF4	-0.18	0.35	-10000	0	-1.1	36	36
ARG1	-0.13	0.24	-10000	0	-0.86	22	22
CBL	-0.3	0.33	-10000	0	-0.74	91	91
GTF3A	0.011	0.03	-10000	0	-10000	0	0
PIK3CA	0.012	0.032	-10000	0	-0.6	1	1
IL13RA1/JAK2	-0.012	0.066	-10000	0	-0.46	5	5
IRF4/BCL6	-0.16	0.32	-10000	0	-1	34	34
CD40LG	-0.039	0.15	-10000	0	-0.49	36	36
MAPK14	-0.32	0.36	-10000	0	-0.8	95	95
mitosis	-0.23	0.28	-10000	0	-0.71	52	52
STAT6	-0.44	0.51	-10000	0	-1.2	86	86
SPI1	-0.006	0.11	-10000	0	-0.52	15	15
RPS6KB1	-0.21	0.27	-10000	0	-0.69	49	49
STAT6 (dimer)	-0.44	0.51	-10000	0	-1.2	86	86
STAT6 (dimer)/PARP14	-0.43	0.47	-10000	0	-1.1	90	90
mast cell activation	0.011	0.012	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2	-0.27	0.32	-10000	0	-0.8	66	66
FRAP1	-0.24	0.3	-10000	0	-0.76	52	52
LTA	-0.42	0.48	-10000	0	-1.1	78	78
FES	0.007	0.061	-10000	0	-0.5	5	5
T-helper 1 cell differentiation	0.43	0.49	1.1	86	-10000	0	86
CCL11	-0.38	0.42	-10000	0	-1.1	62	62
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES	-0.25	0.31	-10000	0	-0.8	55	55
IL2RG	-0.037	0.16	-10000	0	-0.51	35	35
IL10	-0.49	0.56	-10000	0	-1.3	89	89
IRS1	0.014	0	-10000	0	-10000	0	0
IRS2	0.012	0.032	-10000	0	-0.6	1	1
IL4	-0.096	0.11	-10000	0	-10000	0	0
IL5	-0.39	0.44	-10000	0	-1.1	72	72
IL4/IL4R/JAK1/IL13RA1/JAK2	-0.32	0.35	-10000	0	-0.83	72	72
COL1A1	-0.34	0.5	-10000	0	-1.1	83	83
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1	-0.39	0.44	-10000	0	-1.1	60	60
IL2R gamma/JAK3	-0.071	0.18	-10000	0	-0.43	72	72
TFF3	-0.41	0.45	-10000	0	-1.1	69	69
ALOX15	-0.4	0.44	-10000	0	-1.1	70	70
MYBL1	0.011	0.037	-10000	0	-0.48	2	2
T-helper 2 cell differentiation	-0.35	0.38	-10000	0	-0.88	84	84
SHC1	0.009	0.052	-10000	0	-0.48	4	4
CEBPB	-0.006	0.12	-10000	0	-0.57	14	14
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2	-0.22	0.26	-10000	0	-0.69	44	44
mol:PI-3-4-5-P3	-0.24	0.3	-10000	0	-0.76	52	52
PI3K	-0.25	0.32	-10000	0	-0.82	52	52
DOK2	-0.071	0.2	-10000	0	-0.53	57	57
ETS1	0.02	0.054	-10000	0	-0.48	4	4
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2	-0.17	0.22	-10000	0	-0.58	44	44
ITGB3	-0.43	0.49	-10000	0	-1.2	82	82
PIGR	-0.49	0.56	-10000	0	-1.3	94	94
IGHE	0.019	0.066	-10000	0	-0.26	11	11
MAPKKK cascade	-0.17	0.22	-10000	0	-0.57	44	44
BCL6	0.016	0.006	-10000	0	-10000	0	0
OPRM1	-0.41	0.45	-10000	0	-1.1	74	74
RETNLB	-0.4	0.44	-10000	0	-1.1	71	71
SELP	-0.4	0.45	-10000	0	-1.1	74	74
AICDA	-0.38	0.42	-10000	0	-1	68	68

×

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.004	0.078	-9999	-0.6	6	6
CCL5	-0.091	0.22	-9999	-0.53	70	70
SDCBP	0.014	0	-9999	-10000	0	0
FGFR/FGF2/Syndecan-1	-0.13	0.18	-9999	-0.47	55	55
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
Syndecan-1/Laminin-5	-0.12	0.18	-9999	-0.44	57	57
Syndecan-1/Syntenin	-0.12	0.18	-9999	-0.44	55	55
MAPK3	-0.094	0.16	-9999	-0.46	30	30
HGF/MET	-0.16	0.22	-9999	-0.42	139	139
TGFB1/TGF beta receptor Type II	0.004	0.078	-9999	-0.6	6	6
BSG	0.014	0	-9999	-10000	0	0
keratinocyte migration	-0.12	0.18	-9999	-0.43	57	57
Syndecan-1/RANTES	-0.17	0.22	-9999	-0.48	91	91
Syndecan-1/CD147	-0.11	0.17	-9999	-0.49	31	31
Syndecan-1/Syntenin/PIP2	-0.12	0.16	-9999	-0.42	55	55
LAMA5	0.011	0.041	-9999	-0.54	2	2
positive regulation of cell-cell adhesion	-0.13	0.15	-9999	-0.42	55	55
MMP7	-0.15	0.25	-9999	-0.54	105	105
HGF	-0.069	0.19	-9999	-0.5	59	59
Syndecan-1/CASK	-0.13	0.17	-9999	-0.45	55	55
Syndecan-1/HGF/MET	-0.22	0.24	-9999	-0.51	117	117
regulation of cell adhesion	-0.084	0.16	-9999	-0.44	30	30
HPSE	-0.057	0.19	-9999	-0.56	45	45
positive regulation of cell migration	-0.13	0.18	-9999	-0.47	55	55
SDC1	-0.14	0.18	-9999	-0.47	55	55
Syndecan-1/Collagen	-0.13	0.18	-9999	-0.47	55	55
PPIB	0.014	0	-9999	-10000	0	0
MET	-0.14	0.25	-9999	-0.54	101	101
PRKACA	0.014	0	-9999	-10000	0	0
MMP9	-0.15	0.25	-9999	-0.52	111	111
MAPK1	-0.094	0.16	-9999	-0.46	30	30
homophilic cell adhesion	-0.13	0.18	-9999	-0.46	55	55
MMP1	-0.045	0.15	-9999	-0.48	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	0.01	0.037	-10000	0	-0.48	2	2
GNB1/GNG2	-0.083	0.081	-10000	0	-0.18	119	119
AKT1	-0.066	0.11	-10000	0	-0.21	77	77
EGF	-0.044	0.17	-10000	0	-0.56	37	37
mol:TXA2	-0.001	0.001	-10000	0	-10000	0	0
FGR	0.015	0.072	-10000	0	-0.32	3	3
mol:Ca2+	-0.11	0.16	-10000	0	-0.3	121	121
LYN	0.013	0.078	-10000	0	-0.31	7	7
RhoA/GTP	-0.054	0.053	-10000	0	-0.14	22	22
mol:PGI2	0	0	-10000	0	-10000	0	0
SYK	-0.13	0.18	-10000	0	-0.35	119	119
GNG2	0.009	0.056	-10000	0	-0.6	3	3
ARRB2	0.014	0	-10000	0	-10000	0	0
TP alpha/Gq family/GDP/G beta5/gamma2	0.011	0.095	-10000	0	-0.38	17	17
G beta5/gamma2	-0.1	0.1	-10000	0	-0.24	116	116
PRKCH	-0.12	0.18	-10000	0	-0.34	113	113
DNM1	-0.12	0.24	-10000	0	-0.52	92	92
TXA2/TP beta/beta Arrestin3	-0.048	0.077	-10000	0	-0.25	26	26
mol:GTP	-0.001	0.001	-10000	0	-10000	0	0
PTGDR	-0.045	0.16	-10000	0	-0.49	42	42
G12 family/GTP	-0.13	0.13	-10000	0	-0.3	118	118
ADRBK1	0.014	0	-10000	0	-10000	0	0
ADRBK2	0.008	0.061	-10000	0	-0.57	4	4
RhoA/GTP/ROCK1	0	0	-10000	0	-10000	0	0
mol:GDP	0.064	0.11	0.3	25	-10000	0	25
mol:NADP	0.003	0.075	-10000	0	-0.53	7	7
RAB11A	0.014	0	-10000	0	-10000	0	0
PRKG1	-0.048	0.18	-10000	0	-0.58	38	38
mol:IP3	-0.14	0.19	-10000	0	-0.37	121	121
cell morphogenesis	0	0	-10000	0	-10000	0	0
PLCB2	-0.19	0.25	-10000	0	-0.5	120	120
mol:cGMP	-0.001	0.001	-10000	0	-10000	0	0
BLK	-0.036	0.11	-10000	0	-0.34	15	15
mol:PDG2	0	0	-10000	0	-10000	0	0
HCK	0.005	0.093	-10000	0	-0.34	10	10
RHOA	0.014	0	-10000	0	-10000	0	0
PTGIR	-0.017	0.12	-10000	0	-0.52	21	21
PRKCB1	-0.14	0.19	-10000	0	-0.36	121	121
GNAQ	0.014	0	-10000	0	-10000	0	0
mol:L-citrulline	0.003	0.075	-10000	0	-0.53	7	7
TXA2/TXA2-R family	-0.2	0.26	-10000	0	-0.52	122	122
LCK	-0.029	0.12	-10000	0	-0.34	19	19
TXA2/TP beta/beta Arrestin3/RAB11/GDP	-0.026	0.068	-10000	0	-0.35	5	5
TXA2-R family/G12 family/GDP/G beta/gamma	0.023	0.05	-10000	0	-0.75	1	1
TXA2/TP beta/beta Arrestin2/RAB11/GDP	-0.024	0.064	-10000	0	-0.35	4	4
MAPK14	-0.078	0.13	-10000	0	-0.23	117	117
TGM2/GTP	-0.16	0.21	-10000	0	-0.42	122	122
MAPK11	-0.08	0.13	-10000	0	-0.23	118	118
ARHGEF1	-0.059	0.096	-10000	0	-0.18	72	72
GNAI2	0.014	0	-10000	0	-10000	0	0
JNK cascade	-0.14	0.2	-10000	0	-0.38	124	124
RAB11/GDP	0.015	0.001	-10000	0	-10000	0	0
ICAM1	-0.11	0.16	-10000	0	-0.29	123	123
cAMP biosynthetic process	-0.14	0.18	-10000	0	-0.35	122	122
Gq family/GTP/EBP50	0.01	0.079	-10000	0	-0.29	18	18
actin cytoskeleton reorganization	0	0	-10000	0	-10000	0	0
SRC	0.016	0.07	-10000	0	-0.32	3	3
GNB5	0.014	0	-10000	0	-10000	0	0
GNB1	0.014	0	-10000	0	-10000	0	0
EGF/EGFR	-0.022	0.11	-10000	0	-0.3	19	19
VCAM1	-0.14	0.19	-10000	0	-0.37	121	121
TP beta/Gq family/GDP/G beta5/gamma2	0.011	0.095	-10000	0	-0.38	17	17
platelet activation	-0.1	0.16	-10000	0	-0.3	118	118
PGI2/IP	-0.018	0.089	-10000	0	-0.37	21	21
PRKACA	-0.013	0.082	-10000	0	-0.3	14	14
Gq family/GDP/G beta5/gamma2	0.01	0.09	-10000	0	-0.35	17	17
TXA2/TP beta/beta Arrestin2	-0.075	0.15	-10000	0	-0.53	32	32
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TBXA2R	-0.007	0.087	-10000	0	-0.3	17	17
mol:DAG	-0.15	0.21	-10000	0	-0.41	118	118
EGFR	-0.082	0.21	-10000	0	-0.55	62	62
TXA2/TP alpha	-0.18	0.24	-10000	0	-0.48	122	122
Gq family/GTP	-0.012	0.063	-10000	0	-0.23	23	23
YES1	0.015	0.073	-10000	0	-0.32	3	3
GNAI2/GTP	-0.025	0.063	-10000	0	-0.35	4	4
PGD2/DP	-0.038	0.12	-10000	0	-0.35	42	42
SLC9A3R1	0.011	0.046	-10000	0	-0.6	2	2
FYN	0.016	0.07	-10000	0	-0.32	3	3
mol:NO	0.003	0.075	-10000	0	-0.53	7	7
GNA15	-0.006	0.11	-10000	0	-0.56	13	13
PGK/cGMP	-0.044	0.12	-10000	0	-0.35	45	45
RhoA/GDP	0.015	0.001	-10000	0	-10000	0	0
TP alpha/TGM2/GDP/G beta/gamma	-0.024	0.073	-10000	0	-0.43	4	4
NOS3	0.003	0.075	-10000	0	-0.53	7	7
RAC1	0.014	0	-10000	0	-10000	0	0
PRKCA	-0.12	0.18	-10000	0	-0.34	117	117
PRKCB	-0.15	0.2	-10000	0	-0.38	126	126
PRKCE	-0.12	0.18	-10000	0	-0.35	117	117
PRKCD	-0.14	0.2	-10000	0	-0.39	118	118
PRKCG	-0.18	0.22	-10000	0	-0.42	144	144
muscle contraction	-0.18	0.24	-10000	0	-0.49	122	122
PRKCZ	-0.13	0.18	-10000	0	-0.35	124	124
ARR3	0.001	0.026	-10000	0	-0.48	1	1
TXA2/TP beta	-0.028	0.072	-10000	0	-0.37	5	5
PRKCQ	-0.13	0.18	-10000	0	-0.35	121	121
MAPKKK cascade	-0.17	0.23	-10000	0	-0.45	121	121
SELE	-0.13	0.18	-10000	0	-0.34	138	138
TP beta/GNAI2/GDP/G beta/gamma	-0.023	0.069	-10000	0	-0.38	4	4
ROCK1	0.014	0	-10000	0	-10000	0	0
GNA14	-0.006	0.11	-10000	0	-0.56	13	13
chemotaxis	-0.23	0.3	-10000	0	-0.61	120	120
GNA12	0.012	0.032	-10000	0	-0.6	1	1
GNA13	0.014	0	-10000	0	-10000	0	0
GNA11	0.002	0.085	-10000	0	-0.6	7	7
Rac1/GTP	0.003	0.005	-10000	0	-10000	0	0

×

Syndecan-4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.001	0.053	-9999	-10000	0	0
Syndecan-4/Syndesmos	-0.14	0.24	-9999	-0.55	76	76
positive regulation of JNK cascade	-0.15	0.22	-9999	-0.51	81	81
Syndecan-4/ADAM12	-0.18	0.26	-9999	-0.52	114	114
CCL5	-0.091	0.22	-9999	-0.53	70	70
Rac1/GDP	0	0	-9999	-10000	0	0
DNM2	0.014	0	-9999	-10000	0	0
ITGA5	-0.011	0.11	-9999	-0.49	18	18
SDCBP	0.014	0	-9999	-10000	0	0
PLG	0.003	0.025	-9999	-0.44	1	1
ADAM12	-0.074	0.2	-9999	-0.5	62	62
mol:GTP	0	0	-9999	-10000	0	0
NUDT16L1	0.014	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
Syndecan-4/PKC alpha	-0.03	0.041	-9999	-0.18	1	1
Syndecan-4/Laminin alpha1	-0.17	0.27	-9999	-0.57	90	90
Syndecan-4/CXCL12/CXCR4	-0.14	0.25	-9999	-0.54	81	81
Syndecan-4/Laminin alpha3	-0.16	0.26	-9999	-0.57	85	85
MDK	-0.039	0.16	-9999	-0.53	36	36
Syndecan-4/FZD7	-0.16	0.28	-9999	-0.6	86	86
Syndecan-4/Midkine	-0.16	0.26	-9999	-0.55	93	93
FZD7	-0.045	0.18	-9999	-0.59	36	36
Syndecan-4/FGFR1/FGF	-0.15	0.21	-9999	-0.5	79	79
THBS1	-0.085	0.21	-9999	-0.51	69	69
integrin-mediated signaling pathway	-0.16	0.26	-9999	-0.55	95	95
positive regulation of MAPKKK cascade	-0.15	0.22	-9999	-0.51	81	81
Syndecan-4/TACI	-0.15	0.24	-9999	-0.55	80	80
CXCR4	-0.011	0.12	-9999	-0.55	16	16
cell adhesion	0.021	0.053	-9999	-0.26	9	9
Syndecan-4/Dynamin	-0.14	0.24	-9999	-0.55	76	76
Syndecan-4/TSP1	-0.18	0.26	-9999	-0.53	108	108
Syndecan-4/GIPC	-0.14	0.24	-9999	-0.55	76	76
Syndecan-4/RANTES	-0.19	0.26	-9999	-0.55	99	99
ITGB1	0.011	0.037	-9999	-0.48	2	2
LAMA1	-0.054	0.19	-9999	-0.58	42	42
LAMA3	-0.031	0.16	-9999	-0.56	29	29
RAC1	0.014	0	-9999	-10000	0	0
PRKCA	0.037	0.055	-9999	-0.54	1	1
Syndecan-4/alpha-Actinin	-0.15	0.25	-9999	-0.54	91	91
TFPI	-0.086	0.21	-9999	-0.53	68	68
F2	-0.005	0.052	-9999	-0.48	4	4
alpha5/beta1 Integrin	-0.019	0.082	-9999	-0.36	19	19
positive regulation of cell adhesion	-0.18	0.28	-9999	-0.58	95	95
ACTN1	-0.017	0.12	-9999	-0.49	23	23
TNC	-0.056	0.18	-9999	-0.54	46	46
Syndecan-4/CXCL12	-0.14	0.24	-9999	-0.54	81	81
FGF6	0.001	0.003	-9999	-10000	0	0
RHOA	0.014	0	-9999	-10000	0	0
CXCL12	0.004	0.073	-9999	-0.52	7	7
TNFRSF13B	-0.006	0.076	-9999	-0.48	9	9
FGF2	0.009	0.052	-9999	-0.56	3	3
FGFR1	0.012	0.032	-9999	-0.6	1	1
Syndecan-4/PI-4-5-P2	-0.14	0.24	-9999	-0.55	76	76
mol:GDP	0	0	-9999	-10000	0	0
FN1	0.002	0.088	-9999	-0.47	12	12
cell migration	-0.006	0.018	-9999	-10000	0	0
PRKCD	-0.01	0.13	-9999	-0.58	17	17
vasculogenesis	-0.18	0.25	-9999	-0.51	109	109
SDC4	-0.15	0.25	-9999	-0.58	76	76
Syndecan-4/Tenascin C	-0.17	0.27	-9999	-0.57	95	95
Syndecan-4/PI-4-5-P2/PKC alpha	-0.024	0.033	-9999	-10000	0	0
Syndecan-4/Syntenin	-0.14	0.24	-9999	-0.55	76	76
MMP9	-0.15	0.25	-9999	-0.53	111	111
Rac1/GTP	0.021	0.054	-9999	-0.26	9	9
cytoskeleton organization	-0.13	0.23	-9999	-0.52	76	76
GIPC1	0.014	0	-9999	-10000	0	0
Syndecan-4/TFPI	-0.18	0.26	-9999	-0.56	92	92

×

amb2 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2	-0.086	0.18	-9999	-0.45	63	63
alphaM/beta2 Integrin/GPIbA	-0.077	0.17	-9999	-0.46	54	54
alphaM/beta2 Integrin/proMMP-9	-0.16	0.22	-9999	-0.41	136	136
PLAUR	-0.023	0.13	-9999	-0.49	27	27
HMGB1	-0.001	0.022	-9999	-10000	0	0
alphaM/beta2 Integrin/Talin	-0.066	0.16	-9999	-0.48	42	42
AGER	-0.021	0.11	-9999	-0.61	12	12
RAP1A	0.014	0	-9999	-10000	0	0
SELPLG	-0.022	0.14	-9999	-0.59	22	22
mol:LDL	0	0	-9999	-10000	0	0
alphaM/beta2 Integrin/RAGE/HMGB1	-0.13	0.18	-9999	-0.47	60	60
mol:GTP	0	0	-9999	-10000	0	0
MMP9	-0.15	0.25	-9999	-0.52	111	111
CYR61	-0.1	0.23	-9999	-0.55	75	75
TLN1	0.014	0	-9999	-10000	0	0
Rap1/GTP	-0.089	0.13	-9999	-0.43	31	31
RHOA	0.014	0	-9999	-10000	0	0
P-selectin oligomer	-0.025	0.13	-9999	-0.48	26	26
MYH2	-0.086	0.15	-9999	-0.4	41	41
MST1R	0.001	0.086	-9999	-0.57	8	8
leukocyte activation during inflammatory response	-0.11	0.19	-9999	-0.4	86	86
APOB	-0.073	0.2	-9999	-0.55	56	56
mol:GDP	0	0	-9999	-10000	0	0
complement component iC3b receptor activity	0	0	-9999	-10000	0	0
MMP2	-0.022	0.14	-9999	-0.53	24	24
JAM3	0.014	0	-9999	-10000	0	0
GP1BA	-0.006	0.11	-9999	-0.58	12	12
alphaM/beta2 Integrin/CTGF	-0.09	0.19	-9999	-0.45	64	64
alphaM/beta2 Integrin	-0.097	0.17	-9999	-0.43	46	46
JAM3 homodimer	0.014	0	-9999	-10000	0	0
ICAM2	0.012	0.032	-9999	-0.6	1	1
ICAM1	-0.027	0.14	-9999	-0.5	29	29
phagocytosis triggered by activation of immune response cell surface activating receptor	-0.096	0.16	-9999	-0.43	46	46
cell adhesion	-0.077	0.17	-9999	-0.46	54	54
NFKB1	-0.16	0.27	-9999	-0.64	58	58
THY1	-0.003	0.1	-9999	-0.57	11	11
RhoA/GDP	0	0	-9999	-10000	0	0
Lipoprotein(a)	-0.071	0.14	-9999	-0.33	80	80
alphaM/beta2 Integrin/LRP/tPA	-0.083	0.17	-9999	-0.46	48	48
IL6	-0.21	0.34	-9999	-0.79	68	68
ITGB2	-0.048	0.16	-9999	-0.57	30	30
elevation of cytosolic calcium ion concentration	-0.11	0.21	-9999	-0.47	75	75
alphaM/beta2 Integrin/JAM2/JAM3	-0.054	0.15	-9999	-0.44	41	41
JAM2	0.012	0.032	-9999	-0.6	1	1
alphaM/beta2 Integrin/ICAM1	-0.096	0.18	-9999	-0.51	39	39
alphaM/beta2 Integrin/uPA/Plg	-0.098	0.19	-9999	-0.45	63	63
RhoA/GTP	-0.088	0.16	-9999	-0.41	43	43
positive regulation of phagocytosis	-0.1	0.19	-9999	-0.52	45	45
Ron/MSP	-0.041	0.12	-9999	-0.4	38	38
alphaM/beta2 Integrin/uPAR/uPA	-0.11	0.21	-9999	-0.52	61	61
alphaM/beta2 Integrin/uPAR	-0.087	0.19	-9999	-0.48	59	59
PLAU	-0.06	0.18	-9999	-0.51	52	52
PLAT	-0.044	0.16	-9999	-0.48	43	43
actin filament polymerization	-0.083	0.15	-9999	-0.38	41	41
MST1	-0.032	0.16	-9999	-0.55	30	30
alphaM/beta2 Integrin/lipoprotein(a)	-0.11	0.19	-9999	-0.4	86	86
TNF	-0.22	0.36	-9999	-0.78	85	85
RAP1B	0.013	0.026	-9999	-0.48	1	1
alphaM/beta2 Integrin/uPA	-0.11	0.2	-9999	-0.44	82	82
fibrinolysis	-0.098	0.18	-9999	-0.45	63	63
HCK	-0.013	0.12	-9999	-0.53	18	18
dendritic cell antigen processing and presentation	-0.096	0.16	-9999	-0.43	46	46
VTN	-0.011	0.12	-9999	-0.55	16	16
alphaM/beta2 Integrin/CYR61	-0.13	0.22	-9999	-0.44	104	104
LPA	-0.025	0.13	-9999	-0.48	26	26
LRP1	0.014	0	-9999	-10000	0	0
cell migration	-0.16	0.22	-9999	-0.44	112	112
FN1	-0.002	0.088	-9999	-0.48	12	12
alphaM/beta2 Integrin/Thy1	-0.076	0.17	-9999	-0.48	51	51
MPO	-0.13	0.24	-9999	-0.54	92	92
KNG1	-0.018	0.1	-9999	-0.48	17	17
RAP1/GDP	-0.001	0.015	-9999	-0.28	1	1
ROCK1	-0.076	0.15	-9999	-0.4	37	37
ELA2	0	0	-9999	-10000	0	0
PLG	0.001	0.026	-9999	-0.48	1	1
CTGF	-0.029	0.15	-9999	-0.53	29	29
alphaM/beta2 Integrin/Hck	-0.08	0.21	-9999	-0.58	43	43
ITGAM	-0.046	0.16	-9999	-0.6	27	27
alphaM/beta2 Integrin/P-Selectin/PSGL1	-0.092	0.21	-9999	-0.5	58	58
HP	-0.1	0.22	-9999	-0.53	77	77
leukocyte adhesion	-0.11	0.17	-9999	-0.56	35	35
SELP	-0.025	0.13	-9999	-0.48	26	26

×

Reelin signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDK5R1/CDK5	-0.025	0.1	-9999	-0.43	21	21
VLDLR	-0.002	0.099	-9999	-0.59	10	10
CRKL	0.014	0	-9999	-10000	0	0
LRPAP1	0.014	0	-9999	-10000	0	0
FYN	0.014	0	-9999	-10000	0	0
ITGA3	-0.008	0.1	-9999	-0.5	16	16
RELN/VLDLR/Fyn	-0.094	0.15	-9999	-0.33	103	103
MAPK8IP1/MKK7/MAP3K11/JNK1	-0.011	0.055	-9999	-10000	0	0
AKT1	-0.069	0.16	-9999	-0.49	21	21
MAP2K7	0.014	0	-9999	-10000	0	0
RAPGEF1	0.014	0	-9999	-10000	0	0
DAB1	-0.091	0.23	-9999	-0.58	65	65
RELN/LRP8/DAB1	-0.13	0.18	-9999	-0.39	96	96
LRPAP1/LRP8	-0.001	0.023	-9999	-0.44	1	1
RELN/LRP8/DAB1/Fyn	-0.12	0.17	-9999	-0.36	95	95
DAB1/alpha3/beta1 Integrin	-0.12	0.17	-9999	-0.53	36	36
long-term memory	-0.29	0.29	-9999	-0.65	118	118
DAB1/LIS1	-0.12	0.17	-9999	-0.54	27	27
DAB1/CRLK/C3G	-0.11	0.16	-9999	-0.52	27	27
PIK3CA	0.012	0.032	-9999	-0.6	1	1
DAB1/NCK2	-0.12	0.17	-9999	-0.54	27	27
ARHGEF2	0.012	0.032	-9999	-0.6	1	1
mol:Src family inhibitors PP1 and PP2	0	0	-9999	-10000	0	0
GRIN2A	-0.17	0.26	-9999	-0.55	118	118
CDK5R1	-0.021	0.14	-9999	-0.6	21	21
RELN	-0.13	0.25	-9999	-0.54	96	96
PIK3R1	0.014	0	-9999	-10000	0	0
RELN/LRP8/Fyn	-0.085	0.15	-9999	-0.32	96	96
GRIN2A/RELN/LRP8/DAB1/Fyn	-0.21	0.24	-9999	-0.46	146	146
MAPK8	-0.003	0.1	-9999	-0.6	10	10
RELN/VLDLR/DAB1	-0.14	0.19	-9999	-0.36	145	145
ITGB1	0.011	0.037	-9999	-0.48	2	2
MAP1B	-0.1	0.2	-9999	-0.37	101	101
RELN/LRP8	-0.085	0.15	-9999	-0.37	50	50
GRIN2B/RELN/LRP8/DAB1/Fyn	-0.22	0.24	-9999	-0.45	147	147
PI3K	-0.001	0.023	-9999	-0.44	1	1
mol:PP2	0	0	-9999	-10000	0	0
alpha3/beta1 Integrin	-0.017	0.078	-9999	-0.36	17	17
RAP1A	-0.068	0.17	-9999	-0.48	27	27
PAFAH1B1	0.014	0	-9999	-10000	0	0
MAPK8IP1	0.011	0.046	-9999	-0.6	2	2
CRLK/C3G	0	0	-9999	-10000	0	0
GRIN2B	-0.18	0.27	-9999	-0.54	131	131
NCK2	0.014	0	-9999	-10000	0	0
neuron differentiation	-0.041	0.14	-9999	-0.44	21	21
neuron adhesion	-0.061	0.18	-9999	-0.48	30	30
LRP8	0.012	0.032	-9999	-0.6	1	1
GSK3B	-0.057	0.15	-9999	-0.47	20	20
RELN/VLDLR/DAB1/Fyn	-0.13	0.18	-9999	-0.38	101	101
MAP3K11	0.014	0	-9999	-10000	0	0
RELN/VLDLR/DAB1/P13K	-0.082	0.16	-9999	-0.31	102	102
CDK5	0.014	0	-9999	-10000	0	0
MAPT	0.008	0.088	-9999	-0.55	8	8
neuron migration	-0.066	0.19	-9999	-0.52	28	28
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1	-0.041	0.14	-9999	-0.45	21	21
RELN/VLDLR	-0.084	0.14	-9999	-0.34	59	59

×

a4b1 and a4b7 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ITGB1	0.011	0.037	-9999	-0.48	2	2
ITGB7	-0.041	0.17	-9999	-0.54	36	36
ITGA4	-0.048	0.18	-9999	-0.53	42	42
alpha4/beta7 Integrin	-0.08	0.17	-9999	-0.44	67	67
alpha4/beta1 Integrin	-0.045	0.13	-9999	-0.39	42	42

×

Signaling events regulated by Ret tyrosine kinase

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
PTK2	-0.038	0.05	-9999	-10000	0	0
Crk/p130 Cas/Paxillin	-0.09	0.14	-9999	-0.43	35	35
JUN	-0.08	0.2	-9999	-0.53	41	41
HRAS	0.013	0.026	-9999	-0.48	1	1
RET51/GFRalpha1/GDNF/GRB10	-0.16	0.22	-9999	-0.45	96	96
RAP1A	0.014	0	-9999	-10000	0	0
FRS2	0.011	0.041	-9999	-0.54	2	2
RAP1A/GDP	0	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/DOK1	-0.16	0.22	-9999	-0.46	95	95
EntrezGene:5979	0	0	-9999	-10000	0	0
PTPN11	0.014	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.014	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/Enigma	-0.092	0.17	-9999	-0.37	92	92
RHOA	0.014	0	-9999	-10000	0	0
RAP1A/GTP	-0.15	0.2	-9999	-0.62	40	40
GRB7	-0.036	0.14	-9999	-0.48	34	34
RET51/GFRalpha1/GDNF	-0.16	0.22	-9999	-0.45	95	95
MAPKKK cascade	-0.12	0.18	-9999	-0.56	37	37
BCAR1	0.012	0.032	-9999	-0.6	1	1
RET9/GFRalpha1/GDNF/IRS1	-0.088	0.17	-9999	-0.41	63	63
lamellipodium assembly	-0.084	0.13	-9999	-0.39	36	36
RET51/GFRalpha1/GDNF/SHC	-0.16	0.22	-9999	-0.46	95	95
PIK3CA	0.012	0.032	-9999	-0.6	1	1
RET9/GFRalpha1/GDNF/SHC	-0.09	0.18	-9999	-0.37	89	89
RET9/GFRalpha1/GDNF/Shank3	-0.092	0.17	-9999	-0.36	93	93
MAPK3	-0.11	0.21	-9999	-0.58	40	40
DOK1	0.012	0.032	-9999	-0.6	1	1
DOK6	-0.047	0.18	-9999	-0.58	38	38
PXN	0.014	0	-9999	-10000	0	0
neurite development	-0.1	0.22	-9999	-0.54	51	51
DOK5	0.004	0.078	-9999	-0.6	6	6
GFRA1	-0.069	0.2	-9999	-0.56	53	53
MAPK8	-0.087	0.2	-9999	-0.54	41	41
HRAS/GTP	-0.14	0.21	-9999	-0.43	95	95
tube development	-0.085	0.16	-9999	-0.38	64	64
MAPK1	-0.11	0.21	-9999	-0.58	40	40
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.04	0.15	-9999	-0.33	63	63
Rac1/GDP	0	0	-9999	-10000	0	0
SRC	0.014	0	-9999	-10000	0	0
PDLIM7	0.005	0.068	-9999	-0.48	7	7
RET51/GFRalpha1/GDNF/Dok6	-0.17	0.26	-9999	-0.67	55	55
SHC1	0.009	0.052	-9999	-0.48	4	4
RET51/GFRalpha1/GDNF/Dok4	-0.17	0.23	-9999	-0.47	101	101
RET51/GFRalpha1/GDNF/Dok5	-0.16	0.22	-9999	-0.46	100	100
PRKCA	0.012	0.032	-9999	-0.6	1	1
HRAS/GDP	-0.001	0.018	-9999	-0.34	1	1
CREB1	-0.067	0.18	-9999	-0.4	64	64
PIK3R1	0.014	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.042	0.15	-9999	-0.34	63	63
RET51/GFRalpha1/GDNF/Grb7	-0.18	0.24	-9999	-0.49	97	97
mol:GDP	0	0	-9999	-10000	0	0
RET	-0.12	0.24	-9999	-0.55	89	89
DOK4	-0.006	0.11	-9999	-0.6	12	12
JNK cascade	-0.078	0.2	-9999	-0.51	41	41
RET9/GFRalpha1/GDNF/FRS2	-0.089	0.17	-9999	-0.37	89	89
SHANK3	0.006	0.066	-9999	-0.5	6	6
RASA1	0.014	0	-9999	-10000	0	0
NCK1	0.012	0.032	-9999	-0.6	1	1
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.04	0.15	-9999	-0.33	63	63
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.092	0.2	-9999	-0.58	34	34
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK	-0.092	0.2	-9999	-0.51	45	45
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.095	0.21	-9999	-0.54	44	44
PI3K	-0.088	0.23	-9999	-0.63	36	36
SOS1	0.014	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/Shank3/Grb2	-0.085	0.16	-9999	-0.38	64	64
GRB10	0.012	0.032	-9999	-0.6	1	1
activation of MAPKK activity	-0.086	0.2	-9999	-0.48	56	56
RET51/GFRalpha1/GDNF/FRS2	-0.16	0.22	-9999	-0.46	95	95
GAB1	0.011	0.041	-9999	-0.54	2	2
IRS1	0.014	0	-9999	-10000	0	0
IRS2	0.012	0.032	-9999	-0.6	1	1
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.096	0.21	-9999	-0.63	34	34
RET51/GFRalpha1/GDNF/PKC alpha	-0.16	0.22	-9999	-0.46	95	95
GRB2	0.014	0	-9999	-10000	0	0
PRKACA	0.014	0	-9999	-10000	0	0
GDNF	-0.068	0.2	-9999	-0.58	50	50
RAC1	0.014	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/IRS1	-0.16	0.22	-9999	-0.45	95	95
Rac1/GTP	-0.099	0.15	-9999	-0.47	36	36
RET9/GFRalpha1/GDNF	-0.098	0.19	-9999	-0.41	88	88
GFRalpha1/GDNF	-0.11	0.22	-9999	-0.47	88	88

×

Glypican 2 network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MDK	-0.039	0.16	-9999	-0.53	36	36
GPC2	-0.014	0.13	-9999	-0.58	17	17
GPC2/Midkine	-0.056	0.15	-9999	-0.42	49	49
neuron projection morphogenesis	-0.056	0.15	-9999	-0.41	49	49

×

Signaling mediated by p38-alpha and p38-beta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTGS2	-0.15	0.38	-9999	-1.1	46	46
MKNK1	0.007	0.064	-9999	-0.6	4	4
MAPK14	-0.038	0.12	-9999	-0.35	7	7
ATF2/c-Jun	-0.027	0.15	-9999	-0.61	13	13
MAPK11	-0.043	0.14	-9999	-0.51	9	9
MITF	-0.039	0.16	-9999	-0.35	61	61
MAPKAPK5	-0.036	0.15	-9999	-0.35	57	57
KRT8	-0.1	0.22	-9999	-0.42	88	88
MAPKAPK3	0.011	0.046	-9999	-0.6	2	2
MAPKAPK2	0.014	0	-9999	-10000	0	0
p38alpha-beta/CK2	-0.058	0.19	-9999	-0.44	59	59
CEBPB	-0.051	0.19	-9999	-0.41	59	59
SLC9A1	-0.036	0.16	-9999	-0.35	57	57
mol:GDP	0	0	-9999	-10000	0	0
ATF2	-0.043	0.18	-9999	-0.77	8	8
p38alpha-beta/MNK1	-0.037	0.16	-9999	-0.56	12	12
JUN	-0.027	0.15	-9999	-0.6	13	13
PPARGC1A	-0.057	0.19	-9999	-0.4	66	66
USF1	-0.036	0.15	-9999	-0.35	57	57
RAB5/GDP/GDI1	-0.05	0.095	-9999	-0.44	5	5
NOS2	-0.078	0.27	-9999	-1.1	18	18
DDIT3	-0.039	0.16	-9999	-0.35	57	57
RAB5A	0.014	0	-9999	-10000	0	0
HSPB1	-0.036	0.15	-9999	-0.45	17	17
p38alpha-beta/HBP1	-0.033	0.16	-9999	-0.34	57	57
CREB1	-0.037	0.16	-9999	-0.37	58	58
RAB5/GDP	0	0	-9999	-10000	0	0
EIF4E	-0.026	0.14	-9999	-0.58	8	8
RPS6KA4	-0.036	0.15	-9999	-0.35	57	57
PLA2G4A	-0.043	0.18	-9999	-0.61	17	17
GDI1	-0.036	0.15	-9999	-0.35	57	57
TP53	-0.058	0.2	-9999	-0.44	66	66
RPS6KA5	-0.044	0.17	-9999	-0.36	63	63
ESR1	-0.054	0.18	-9999	-0.39	64	64
HBP1	0.014	0	-9999	-10000	0	0
MEF2C	-0.044	0.16	-9999	-0.36	64	64
MEF2A	-0.037	0.16	-9999	-0.36	57	57
EIF4EBP1	-0.041	0.17	-9999	-0.38	58	58
KRT19	-0.096	0.22	-9999	-0.41	91	91
ELK4	-0.037	0.16	-9999	-0.36	57	57
ATF6	-0.036	0.15	-9999	-0.35	57	57
ATF1	-0.037	0.16	-9999	-0.37	58	58
p38alpha-beta/MAPKAPK2	-0.033	0.16	-9999	-0.53	8	8
p38alpha-beta/MAPKAPK3	-0.035	0.16	-9999	-0.53	10	10

×

Visual signal transduction: Cones

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin	-0.04	0.1	-9999	-0.29	50	50
RGS9BP	-0.001	0.094	-9999	-0.59	9	9
mol:GTP	0	0	-9999	-10000	0	0
GRK1	0.011	0.032	-9999	-0.6	1	1
mol:Na +	-0.1	0.15	-9999	-0.32	118	118
mol:ADP	0.016	0.044	-9999	-0.36	5	5
GNAT2	0.009	0.037	-9999	-0.48	2	2
RGS9-1/Gbeta5/R9AP	-0.039	0.12	-9999	-0.39	37	37
mol:GDP	0	0	-9999	-10000	0	0
PDE6H/GNAT2/GTP	-0.012	0.061	-9999	-0.3	15	15
GRK7	0.006	0.052	-9999	-0.48	4	4
CNGB3	-0.014	0.1	-9999	-0.48	17	17
Cone Metarhodopsin II/X-Arrestin	-0.001	0.018	-9999	-0.34	1	1
mol:Ca2+	-0.15	0.2	-9999	-0.34	171	171
Cone PDE6	-0.043	0.11	-9999	-0.35	32	32
Cone Metarhodopsin II	-0.004	0.032	-9999	-0.27	5	5
Na + (4 Units)	-0.16	0.19	-9999	-0.34	171	171
GNAT2/GDP	-0.034	0.11	-9999	-0.35	32	32
GNB5	0.014	0	-9999	-10000	0	0
mol:GMP (4 units)	0.004	0.061	-9999	-0.26	17	17
Cone Transducin	-0.042	0.11	-9999	-0.31	50	50
SLC24A2	-0.12	0.24	-9999	-0.55	85	85
GNB3/GNGT2	-0.054	0.14	-9999	-0.4	49	49
GNB3	-0.035	0.16	-9999	-0.56	31	31
GNAT2/GTP	-0.002	0.025	-9999	-0.34	2	2
CNGA3	-0.14	0.25	-9999	-0.53	103	103
ARR3	0.001	0.026	-9999	-0.48	1	1
absorption of light	0	0	-9999	-10000	0	0
cGMP/Cone CNG Channel	-0.1	0.16	-9999	-0.32	118	118
mol:Pi	-0.039	0.12	-9999	-0.39	37	37
Cone CNG Channel	-0.091	0.14	-9999	-0.34	48	48
mol:all-trans-retinal	0	0	-9999	-10000	0	0
mol:K +	-0.12	0.24	-9999	-0.55	85	85
RGS9	-0.038	0.17	-9999	-0.58	32	32
PDE6C	0.003	0.037	-9999	-0.48	2	2
GNGT2	-0.014	0.12	-9999	-0.55	18	18
mol:cGMP (4 units)	0	0	-9999	-10000	0	0
PDE6H	-0.01	0.094	-9999	-0.48	14	14

×

Aurora C signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
INCENP	0.014	0	-9999	-10000	0	0
Aurora C/Aurora B/INCENP	-0.1	0.16	-9999	-0.32	119	119
metaphase	0	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
H3F3B	-0.03	0.044	-9999	-10000	0	0
AURKB	-0.15	0.26	-9999	-0.56	105	105
AURKC	-0.019	0.13	-9999	-0.52	23	23

×

Endothelins

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	-0.094	0.22	-10000	0	-0.56	39	39
PTK2B	-0.01	0.11	-10000	0	-0.48	18	18
mol:Ca2+	-0.062	0.25	-10000	0	-0.83	22	22
EDN1	-0.085	0.19	-10000	0	-0.47	54	54
EDN3	-0.017	0.13	-10000	0	-0.59	19	19
EDN2	-0.009	0.08	-10000	0	-0.48	10	10
HRAS/GDP	-0.091	0.21	-10000	0	-0.5	49	49
ETA receptor/Endothelin-1/Gq/GTP/PLC beta	-0.048	0.16	-10000	0	-0.44	30	30
ADCY4	-0.11	0.23	-10000	0	-0.51	67	67
ADCY5	-0.11	0.24	-10000	0	-0.56	62	62
ADCY6	-0.1	0.22	-10000	0	-0.52	59	59
ADCY7	-0.1	0.22	-10000	0	-0.51	62	62
ADCY1	-0.16	0.26	-10000	0	-0.53	88	88
ADCY2	-0.11	0.24	-10000	0	-0.54	65	65
ADCY3	-0.1	0.22	-10000	0	-0.51	62	62
ADCY8	-0.14	0.26	-10000	0	-0.54	82	82
ADCY9	-0.1	0.23	-10000	0	-0.52	61	61
arachidonic acid secretion	-0.088	0.22	-10000	0	-0.52	48	48
ETB receptor/Endothelin-1/Gq/GTP	-0.043	0.16	-10000	0	-0.41	39	39
GNAO1	0.004	0.078	-10000	0	-0.6	6	6
HRAS	0.012	0.026	-10000	0	-0.48	1	1
ETA receptor/Endothelin-1/G12/GTP	-0.096	0.2	0.26	13	-0.54	38	51
ETA receptor/Endothelin-1/Gs/GTP	-0.12	0.23	0.24	13	-0.54	62	75
mol:GTP	0	0.005	-10000	0	-10000	0	0
COL3A1	-0.18	0.33	-10000	0	-0.63	107	107
EDNRB	-0.046	0.18	-10000	0	-0.6	35	35
response to oxidative stress	0	0	-10000	0	-10000	0	0
CYSLTR2	-0.12	0.27	-10000	0	-0.68	48	48
CYSLTR1	-0.11	0.25	-10000	0	-0.65	43	43
SLC9A1	-0.066	0.1	-10000	0	-0.32	24	24
mol:GDP	-0.1	0.23	-10000	0	-0.53	54	54
SLC9A3	-0.096	0.26	-10000	0	-0.65	54	54
RAF1	-0.1	0.22	-10000	0	-0.52	54	54
JUN	-0.043	0.2	-10000	0	-0.72	12	12
JAK2	-0.094	0.22	-10000	0	-0.56	39	39
mol:IP3	-0.056	0.18	-10000	0	-0.5	31	31
ETA receptor/Endothelin-1	-0.13	0.25	0.3	13	-0.58	53	66
PLCB1	-0.008	0.11	-10000	0	-0.6	12	12
PLCB2	-0.015	0.12	-10000	0	-0.58	17	17
ETA receptor/Endothelin-3	-0.07	0.15	-10000	0	-0.48	37	37
FOS	-0.13	0.32	-10000	0	-0.9	43	43
Gai/GDP	0	0.14	-10000	0	-1	6	6
CRK	0.014	0.001	-10000	0	-10000	0	0
mol:Ca ++	-0.11	0.26	-10000	0	-0.57	62	62
BCAR1	0.013	0.032	-10000	0	-0.6	1	1
PRKCB1	-0.055	0.17	-10000	0	-0.48	31	31
GNAQ	0.014	0.007	-10000	0	-10000	0	0
GNAZ	0.012	0.032	-10000	0	-0.6	1	1
GNAL	-0.05	0.19	-10000	0	-0.6	38	38
Gs family/GDP	-0.14	0.21	-10000	0	-0.5	72	72
ETA receptor/Endothelin-1/Gq/GTP	-0.045	0.15	-10000	0	-0.41	28	28
MAPK14	-0.036	0.16	-10000	0	-0.48	26	26
TRPC6	-0.067	0.26	-10000	0	-0.89	22	22
GNAI2	0.014	0	-10000	0	-10000	0	0
GNAI3	0.014	0	-10000	0	-10000	0	0
GNAI1	-0.004	0.1	-10000	0	-0.6	11	11
ETB receptor/Endothelin-1/Gq/GTP/PLC beta	-0.046	0.17	-10000	0	-0.43	40	40
ETB receptor/Endothelin-2	-0.041	0.14	-10000	0	-0.42	44	44
ETB receptor/Endothelin-3	-0.048	0.17	-10000	0	-0.48	48	48
ETB receptor/Endothelin-1	-0.1	0.2	-10000	0	-0.46	69	69
MAPK3	-0.12	0.29	-10000	0	-0.77	48	48
MAPK1	-0.12	0.29	-10000	0	-0.79	45	45
Rac1/GDP	-0.09	0.21	-10000	0	-0.52	43	43
cAMP biosynthetic process	-0.12	0.24	-10000	0	-0.54	67	67
MAPK8	-0.058	0.22	-10000	0	-0.65	28	28
SRC	0.014	0	-10000	0	-10000	0	0
ETB receptor/Endothelin-1/Gi/GTP	-0.025	0.13	-10000	0	-0.38	27	27
p130Cas/CRK/Src/PYK2	-0.097	0.23	-10000	0	-0.58	43	43
mol:K +	0	0	-10000	0	-10000	0	0
G12/GDP	-0.09	0.21	-10000	0	-0.51	48	48
COL1A2	-0.14	0.29	-10000	0	-0.72	55	55
EntrezGene:2778	0	0	-10000	0	-10000	0	0
ETA receptor/Endothelin-2	-0.061	0.13	-10000	0	-0.42	30	30
mol:DAG	-0.056	0.18	-10000	0	-0.5	31	31
MAP2K2	-0.11	0.25	-10000	0	-0.6	51	51
MAP2K1	-0.11	0.25	-10000	0	-0.61	50	50
EDNRA	-0.063	0.16	-10000	0	-0.49	31	31
positive regulation of muscle contraction	-0.072	0.19	-10000	0	-0.51	35	35
Gq family/GDP	-0.11	0.2	-10000	0	-0.58	39	39
HRAS/GTP	-0.098	0.22	-10000	0	-0.51	49	49
PRKCH	-0.046	0.17	-10000	0	-0.53	24	24
RAC1	0.014	0	-10000	0	-10000	0	0
PRKCA	-0.047	0.18	-10000	0	-0.53	25	25
PRKCB	-0.084	0.21	-10000	0	-0.5	47	47
PRKCE	-0.051	0.18	-10000	0	-0.52	29	29
PRKCD	-0.061	0.2	-10000	0	-0.6	30	30
PRKCG	-0.15	0.24	-10000	0	-0.48	84	84
regulation of vascular smooth muscle contraction	-0.15	0.37	-10000	0	-1.1	42	42
PRKCQ	-0.056	0.19	-10000	0	-0.52	34	34
PLA2G4A	-0.097	0.24	-10000	0	-0.58	48	48
GNA14	-0.007	0.11	-10000	0	-0.56	13	13
GNA15	-0.007	0.11	-10000	0	-0.57	13	13
GNA12	0.012	0.032	-10000	0	-0.6	1	1
GNA11	0.001	0.085	-10000	0	-0.6	7	7
Rac1/GTP	-0.095	0.2	0.26	12	-0.53	38	50
MMP1	0.016	0.15	-10000	0	-0.41	21	21

×

Caspase cascade in apoptosis

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
TOP1	-0.046	0.15	-10000	0	-0.34	60	60
ACTA1	-0.069	0.19	-10000	0	-0.41	68	68
NUMA1	-0.046	0.15	-10000	0	-0.33	63	63
SPTAN1	-0.058	0.18	0.25	2	-0.4	65	67
LIMK1	-0.058	0.18	0.25	2	-0.4	65	67
BIRC3	-0.035	0.16	-10000	0	-0.55	32	32
BIRC2	0.014	0	-10000	0	-10000	0	0
BAX	0.014	0	-10000	0	-10000	0	0
CASP10	-0.086	0.2	-10000	0	-0.44	73	73
CRMA	0	0	-10000	0	-10000	0	0
XIAP	0.014	0	-10000	0	-10000	0	0
PTK2	-0.046	0.15	0.21	1	-0.33	65	66
DIABLO	0.014	0	-10000	0	-10000	0	0
apoptotic nuclear changes	-0.057	0.18	0.25	2	-0.4	65	67
response to UV	0	0	-10000	0	-10000	0	0
CRADD	0.014	0	-10000	0	-10000	0	0
GSN	-0.064	0.19	-10000	0	-0.41	63	63
MADD	0.014	0	-10000	0	-10000	0	0
TFAP2A	-0.18	0.3	-10000	0	-0.65	94	94
BID	-0.043	0.12	-10000	0	-0.24	76	76
MAP3K1	-0.014	0.069	-10000	0	-0.22	4	4
TRADD	0.011	0.041	-10000	0	-0.54	2	2
mol:Ca2+	0	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0.008	0.011	-10000	0	-10000	0	0
mol:Activated DNA	0	0	-10000	0	-10000	0	0
ARHGDIB	-0.06	0.19	0.25	2	-0.41	66	68
CASP9	0.014	0	-10000	0	-10000	0	0
DNA repair	0.003	0.062	-10000	0	-0.2	13	13
neuron apoptosis	0.004	0.049	-10000	0	-0.43	1	1
mol:NAD	0	0	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	-0.05	0.18	-10000	0	-0.39	62	62
APAF1	0.014	0	-10000	0	-10000	0	0
CASP6	-0.028	0.12	-10000	0	-0.6	4	4
TRAF2	0.014	0	-10000	0	-10000	0	0
ICAD/CAD	-0.049	0.18	0.25	1	-0.39	62	63
CASP7	0.019	0.078	0.27	27	-0.21	1	28
KRT18	-0.071	0.19	-10000	0	-0.63	35	35
apoptosis	-0.069	0.18	-10000	0	-0.39	70	70
DFFA	-0.058	0.18	0.25	2	-0.41	62	64
DFFB	-0.058	0.18	0.25	2	-0.4	65	67
PARP1	-0.003	0.062	0.2	13	-10000	0	13
actin filament polymerization	0.046	0.17	0.37	62	-0.25	1	63
TNF	-0.15	0.25	-10000	0	-0.54	109	109
CYCS	-0.025	0.082	-10000	0	-0.21	27	27
SATB1	-0.023	0.12	-10000	0	-0.52	7	7
SLK	-0.059	0.18	0.25	2	-0.4	65	67
p15 BID/BAX	-0.031	0.1	-10000	0	-0.26	30	30
CASP2	-0.015	0.11	-10000	0	-0.34	12	12
JNK cascade	0.014	0.069	0.22	4	-10000	0	4
CASP3	-0.07	0.2	0.26	2	-0.43	68	70
LMNB2	-0.011	0.089	-10000	0	-0.36	7	7
RIPK1	0.014	0	-10000	0	-10000	0	0
CASP4	-0.019	0.12	-10000	0	-0.49	24	24
Mammalian IAPs/DIABLO	-0.025	0.082	-10000	0	-0.32	18	18
negative regulation of DNA binding	-0.18	0.29	-10000	0	-0.64	94	94
stress fiber formation	-0.058	0.18	0.25	2	-0.4	65	67
GZMB	-0.11	0.23	-10000	0	-0.47	101	101
CASP1	-0.007	0.089	-10000	0	-0.29	30	30
LMNB1	-0.019	0.1	-10000	0	-0.39	11	11
APP	0.004	0.049	-10000	0	-0.43	1	1
TNFRSF1A	0.005	0.068	-10000	0	-0.52	6	6
response to stress	0	0	-10000	0	-10000	0	0
CASP8	-0.003	0.073	-10000	0	-0.35	15	15
VIM	-0.075	0.18	-10000	0	-0.39	71	71
LMNA	-0.011	0.089	-10000	0	-0.35	7	7
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD	-0.025	0.11	-10000	0	-0.37	12	12
LRDD	0.008	0.061	-10000	0	-0.57	4	4
SREBF1	-0.068	0.19	0.24	1	-0.4	70	71
APAF-1/Caspase 9	-0.006	0.043	-10000	0	-10000	0	0
nuclear fragmentation during apoptosis	-0.045	0.15	-10000	0	-0.33	63	63
CFL2	-0.048	0.18	0.25	1	-0.38	62	63
GAS2	-0.067	0.19	0.25	2	-0.41	69	71
positive regulation of apoptosis	-0.012	0.093	-10000	0	-0.36	8	8
PRF1	-0.065	0.2	-10000	0	-0.54	52	52

×

FOXA2 and FOXA3 transcription factor networks

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
ACADVL	-0.17	0.39	-10000	0	-0.98	44	44
PCK1	-0.24	0.44	-10000	0	-1.1	61	61
HNF4A	-0.2	0.43	-10000	0	-1.1	42	42
KCNJ11	-0.24	0.51	-10000	0	-1.2	61	61
AKT1	-0.074	0.17	-10000	0	-0.42	20	20
response to starvation	-0.002	0.02	-10000	0	-10000	0	0
DLK1	-0.24	0.46	-10000	0	-1	66	66
NKX2-1	-0.067	0.21	-10000	0	-0.83	6	6
ACADM	-0.17	0.39	-10000	0	-0.97	46	46
TAT	-0.21	0.4	-10000	0	-0.97	56	56
CEBPB	-0.009	0.12	-10000	0	-0.58	14	14
CEBPA	-0.015	0.13	-10000	0	-0.56	19	19
TTR	-0.15	0.28	-10000	0	-0.77	35	35
PKLR	-0.19	0.4	-10000	0	-0.95	53	53
APOA1	-0.22	0.48	-10000	0	-1.3	43	43
CPT1C	-0.17	0.39	-10000	0	-0.99	44	44
ALAS1	-0.063	0.21	0.48	1	-0.64	8	9
TFRC	-0.17	0.32	-10000	0	-0.76	46	46
FOXF1	-0.005	0.09	-10000	0	-0.52	10	10
NF1	0.017	0.056	-10000	0	-0.6	3	3
HNF1A (dimer)	0.011	0.044	-10000	0	-0.66	1	1
CPT1A	-0.17	0.39	-10000	0	-0.98	46	46
HMGCS1	-0.17	0.39	-10000	0	-0.96	47	47
NR3C1	-0.024	0.077	-10000	0	-0.3	1	1
CPT1B	-0.19	0.41	-10000	0	-0.99	53	53
chromatin remodeling	0	0	-10000	0	-10000	0	0
SP1	0.011	0.023	-10000	0	-10000	0	0
GCK	-0.24	0.48	-10000	0	-1.1	70	70
CREB1	-0.004	0.056	-10000	0	-0.22	2	2
IGFBP1	-0.27	0.53	-10000	0	-1.3	68	68
PDX1	-0.073	0.21	-10000	0	-0.71	8	8
UCP2	-0.19	0.42	-10000	0	-1	54	54
ALDOB	-0.19	0.44	-10000	0	-1.1	50	50
AFP	-0.091	0.17	-10000	0	-0.54	26	26
BDH1	-0.21	0.45	-10000	0	-1.1	59	59
HADH	-0.17	0.41	-10000	0	-0.99	48	48
F2	-0.2	0.42	-10000	0	-1.1	37	37
HNF1A	0.011	0.044	-10000	0	-0.66	1	1
G6PC	-0.074	0.22	-10000	0	-0.8	19	19
SLC2A2	-0.088	0.23	-10000	0	-0.77	4	4
INS	0.016	0.094	0.24	9	-0.55	4	13
FOXA1	-0.051	0.16	-10000	0	-0.51	35	35
FOXA3	-0.13	0.24	-10000	0	-0.54	77	77
FOXA2	-0.21	0.47	-10000	0	-1.1	56	56
ABCC8	-0.26	0.53	-10000	0	-1.2	66	66
ALB	-0.12	0.28	-10000	0	-0.92	30	30

×

EGFR-dependent Endothelin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HRAS	0.013	0.026	-9999	-0.48	1	1
EGFR	-0.082	0.21	-9999	-0.55	62	62
EGF/EGFR	-0.11	0.16	-9999	-0.37	78	78
EGF/EGFR dimer/SHC/GRB2/SOS1	-0.075	0.14	-9999	-0.34	59	59
mol:GTP	0	0	-9999	-10000	0	0
EDNRA	-0.017	0.13	-9999	-0.53	21	21
response to oxidative stress	0	0	-9999	-10000	0	0
EGF	-0.044	0.17	-9999	-0.56	37	37
EGF/EGFR dimer/SHC	-0.091	0.17	-9999	-0.37	91	91
mol:GDP	-0.074	0.14	-9999	-0.34	59	59
mol:Ca2+	0	0	-9999	-10000	0	0
EDN1	-0.039	0.16	-9999	-0.53	36	36
GRB2/SOS1	0	0	-9999	-10000	0	0
HRAS/GTP	-0.067	0.13	-9999	-0.5	12	12
SHC1	0.009	0.052	-9999	-0.48	4	4
HRAS/GDP	-0.069	0.13	-9999	-0.51	12	12
FRAP1	-0.041	0.15	-9999	-0.33	59	59
EGF/EGFR dimer	-0.11	0.19	-9999	-0.43	89	89
SOS1	0.014	0	-9999	-10000	0	0
GRB2	0.014	0	-9999	-10000	0	0
ETA receptor/Endothelin-1	-0.058	0.14	-9999	-0.39	54	54

×

Visual signal transduction: Rods

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:K +	0.014	0	-9999	-10000	0	0
GNAT1/GTP	-0.022	0.086	-9999	-0.35	23	23
Metarhodopsin II/Arrestin	-0.034	0.1	-9999	-0.32	39	39
PDE6G/GNAT1/GTP	-0.052	0.12	-9999	-0.34	56	56
mol:GTP	0	0	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
GNAT1	-0.02	0.12	-9999	-0.49	23	23
GRK1	0.011	0.032	-9999	-0.6	1	1
CNG Channel	-0.2	0.2	-9999	-0.56	63	63
mol:Na +	-0.2	0.2	-9999	-0.5	75	75
mol:ADP	0.011	0.032	-9999	-0.6	1	1
RGS9-1/Gbeta5/R9AP	-0.039	0.12	-9999	-0.39	37	37
mol:GDP	0	0	-9999	-10000	0	0
cGMP/CNG Channel	-0.2	0.2	-9999	-0.52	75	75
CNGB1	-0.2	0.27	-9999	-0.53	143	143
RDH5	-0.017	0.12	-9999	-0.48	23	23
SAG	0.003	0.005	-9999	-10000	0	0
mol:Ca2+	-0.17	0.21	-9999	-0.48	75	75
Na + (4 Units)	-0.18	0.18	-9999	-0.47	75	75
RGS9	-0.038	0.17	-9999	-0.58	32	32
GNB1/GNGT1	-0.001	0.017	-9999	-0.33	1	1
GNAT1/GDP	-0.048	0.11	-9999	-0.34	34	34
GUCY2D	-0.002	0.072	-9999	-0.48	8	8
GNGT1	-0.001	0.025	-9999	-0.48	1	1
GUCY2F	0.004	0.051	-9999	-0.48	4	4
GNB5	0.014	0	-9999	-10000	0	0
mol:GMP (4 units)	-0.068	0.17	-9999	-0.36	61	61
mol:11-cis-retinal	-0.017	0.12	-9999	-0.48	23	23
mol:cGMP	-0.08	0.16	-9999	-0.39	45	45
GNB1	0.014	0	-9999	-10000	0	0
Rhodopsin	-0.06	0.14	-9999	-0.36	61	61
SLC24A1	0.014	0	-9999	-10000	0	0
CNGA1	-0.037	0.16	-9999	-0.56	32	32
Metarhodopsin II	-0.031	0.09	-9999	-0.29	40	40
mol:Ca ++	0	0	-9999	-10000	0	0
GC1/GCAP Family	-0.1	0.16	-9999	-0.39	66	66
RGS9BP	-0.001	0.094	-9999	-0.59	9	9
Metarhodopsin II/Transducin	-0.015	0.08	-9999	-0.3	15	15
GCAP Family/Ca ++	-0.1	0.16	-9999	-0.37	76	76
PDE6A/B	-0.07	0.16	-9999	-0.41	62	62
mol:Pi	-0.039	0.12	-9999	-0.39	37	37
mol:all-trans-retinal	0	0	-9999	-10000	0	0
Transducin	-0.017	0.068	-9999	-0.27	23	23
PDE6B	-0.031	0.15	-9999	-0.54	30	30
PDE6A	-0.043	0.17	-9999	-0.54	37	37
PDE6G	-0.042	0.17	-9999	-0.57	35	35
RHO	-0.046	0.17	-9999	-0.52	39	39
PDE6	-0.1	0.17	-9999	-0.6	22	22
GUCA1A	-0.15	0.25	-9999	-0.54	106	106
GC2/GCAP Family	-0.1	0.16	-9999	-0.38	64	64
GUCA1C	-0.012	0.087	-9999	-0.48	12	12
GUCA1B	-0.001	0.094	-9999	-0.59	9	9

×

Calcium signaling in the CD4+ TCR 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC1	-0.011	0.095	-9999	-0.38	21	21
NFATC2	-0.046	0.14	-9999	-0.36	57	57
NFATC3	0.011	0.032	-9999	-0.39	1	1
CD40LG	-0.15	0.29	-9999	-0.67	65	65
PTGS2	-0.19	0.33	-9999	-0.68	90	90
JUNB	-0.036	0.16	-9999	-0.51	35	35
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.006	0.025	-9999	-0.46	1	1
CaM/Ca2+	-0.005	0.025	-9999	-0.46	1	1
CALM1	0.01	0.033	-9999	-0.61	1	1
JUN	0.001	0.075	-9999	-0.5	8	8
mol:Ca2+	-0.005	0.011	-9999	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0.001	0.003	-9999	-10000	0	0
FOSL1	-0.096	0.22	-9999	-0.53	74	74
CREM	0.011	0.041	-9999	-0.54	2	2
Jun/NFAT1-c-4/p21SNFT	-0.12	0.18	-9999	-0.52	46	46
FOS	-0.09	0.22	-9999	-0.55	66	66
IFNG	-0.14	0.27	-9999	-0.62	56	56
AP-1/NFAT1-c-4	-0.17	0.32	-9999	-0.7	70	70
FASLG	-0.15	0.29	-9999	-0.65	62	62
NFAT1-c-4/ICER1	-0.061	0.16	-9999	-0.44	30	30
IL2RA	-0.17	0.3	-9999	-0.66	70	70
FKBP12/FK506	0	0	-9999	-10000	0	0
CSF2	-0.14	0.26	-9999	-0.61	56	56
JunB/Fra1/NFAT1-c-4	-0.14	0.2	-9999	-0.5	68	68
IL4	-0.14	0.26	-9999	-0.61	56	56
IL2	-0.008	0.015	-9999	-10000	0	0
IL3	-0.019	0.05	-9999	-0.88	1	1
FKBP1A	0.014	0	-9999	-10000	0	0
BATF3	-0.037	0.16	-9999	-0.54	34	34
mol:FK506	0	0	-9999	-10000	0	0
POU2F1	0.013	0.032	-9999	-0.6	1	1

×

Ras signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ERK1-2/ELK1	-0.095	0.22	-9999	-0.46	81	81
MAP3K8	-0.001	0.083	-9999	-0.49	10	10
FOS	-0.087	0.2	-9999	-0.5	58	58
PRKCA	0.011	0.033	-9999	-0.6	1	1
PTPN7	-0.13	0.24	-9999	-0.55	91	91
HRAS	0.013	0.026	-9999	-0.48	1	1
PRKCB	-0.064	0.19	-9999	-0.52	53	53
NRAS	0.014	0.001	-9999	-10000	0	0
RAS family/GTP	0.023	0.023	-9999	-0.24	2	2
MAPK3	-0.071	0.18	-9999	-0.46	53	53
MAP2K1	-0.015	0.13	-9999	-0.49	16	16
ELK1	0.013	0.006	-9999	-10000	0	0
BRAF	-0.055	0.14	-9999	-0.46	30	30
mol:GTP	-0.001	0.002	-9999	-0.005	62	62
MAPK1	-0.071	0.18	-9999	-0.46	53	53
RAF1	-0.037	0.1	-9999	-0.47	15	15
KRAS	0.013	0.026	-9999	-0.48	1	1

×

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MET/RANBP9	-0.1	0.17	-9999	-0.38	101	101
CRKL	-0.041	0.12	-9999	-0.48	6	6
mol:PIP3	-0.019	0.007	-9999	-10000	0	0
AKT1	0.002	0.018	-9999	-0.33	1	1
PTK2B	-0.01	0.11	-9999	-0.48	18	18
RAPGEF1	-0.031	0.12	-9999	-0.44	6	6
RANBP10	0.014	0	-9999	-10000	0	0
PIK3CA	0.012	0.032	-9999	-0.6	1	1
HGF/MET/SHIP2	-0.13	0.18	-9999	-0.35	139	139
MAP3K5	-0.035	0.14	-9999	-0.43	15	15
HGF/MET/CIN85/CBL/ENDOPHILINS	-0.12	0.16	-9999	-0.38	70	70
AP1	-0.083	0.16	-9999	-0.4	66	66
mol:SU11274	0	0	-9999	-10000	0	0
SHC1	0.009	0.052	-9999	-0.48	4	4
apoptosis	-0.09	0.23	-9999	-0.77	35	35
STAT3 (dimer)	-0.044	0.13	-9999	-0.4	9	9
GAB1/CRKL/SHP2/PI3K	-0.054	0.091	-9999	-0.52	3	3
INPP5D	0.008	0.055	-9999	-0.51	4	4
CBL/CRK	-0.031	0.12	-9999	-0.44	6	6
PTPN11	0.014	0	-9999	-10000	0	0
GO:0007205	0	0	-9999	-10000	0	0
PLCG1	0.014	0	-9999	-10000	0	0
PTEN	0.014	0	-9999	-10000	0	0
ELK1	-0.056	0.09	-9999	-0.2	101	101
mol:SU5416	0	0	-9999	-10000	0	0
SHP2/GRB2/SOS1GAB1	-0.044	0.067	-9999	-0.29	6	6
PAK1	-0.017	0.079	-9999	-0.31	4	4
HGF/MET/RANBP10	-0.13	0.18	-9999	-0.35	139	139
HRAS	-0.097	0.23	-9999	-0.63	47	47
DOCK1	-0.033	0.12	-9999	-0.44	6	6
GAB1	-0.051	0.13	-9999	-0.3	50	50
CRK	-0.041	0.12	-9999	-0.48	6	6
mol:PHA665752	0	0	-9999	-10000	0	0
mol:GDP	-0.12	0.21	-9999	-0.58	54	54
JUN	0.003	0.075	-9999	-0.5	8	8
EntrezGene:200958	0	0	-9999	-10000	0	0
HGF/MET	-0.069	0.12	-9999	-0.28	70	70
PIK3R1	0.014	0	-9999	-10000	0	0
cell morphogenesis	-0.014	0.13	-9999	-0.45	5	5
GRB2/SHC	-0.047	0.12	-9999	-0.27	50	50
FOS	-0.087	0.22	-9999	-0.55	66	66
GLMN	0	0	-9999	-10000	0	0
cell motility	-0.056	0.09	-9999	-0.2	101	101
HGF/MET/MUC20	-0.14	0.19	-9999	-0.36	139	139
cell migration	-0.046	0.11	-9999	-0.26	50	50
GRB2	0.014	0	-9999	-10000	0	0
CBL	0.014	0	-9999	-10000	0	0
MET/RANBP10	-0.1	0.17	-9999	-0.38	101	101
HGF/MET/Paxillin/FAK1/FAK12/RasGAP	-0.055	0.13	-9999	-0.34	22	22
MET/MUC20	-0.11	0.18	-9999	-0.39	101	101
RAP1B	-0.022	0.11	-9999	-0.44	5	5
RAP1A	-0.021	0.11	-9999	-0.44	5	5
HGF/MET/RANBP9	-0.13	0.18	-9999	-0.35	139	139
RAF1	-0.083	0.22	-9999	-0.58	47	47
STAT3	-0.044	0.13	-9999	-0.4	9	9
cell proliferation	-0.055	0.17	-9999	-0.39	60	60
RPS6KB1	-0.018	0.047	-9999	-10000	0	0
MAPK3	-0.056	0.082	-9999	-0.21	2	2
MAPK1	-0.056	0.082	-9999	-0.2	45	45
RANBP9	0.014	0	-9999	-10000	0	0
MAPK8	-0.021	0.14	-9999	-0.45	18	18
SRC	-0.043	0.13	-9999	-0.4	9	9
PI3K	-0.045	0.11	-9999	-0.36	6	6
MET/Glomulin	-0.085	0.16	-9999	-0.34	101	101
SOS1	0.014	0	-9999	-10000	0	0
MAP2K1	-0.069	0.2	-9999	-0.54	46	46
MET	-0.14	0.25	-9999	-0.54	101	101
MAP4K1	-0.043	0.14	-9999	-0.44	14	14
PTK2	0.014	0	-9999	-10000	0	0
MAP2K2	-0.069	0.2	-9999	-0.54	46	46
BAD	0.01	0.017	-9999	-0.31	1	1
MAP2K4	-0.025	0.13	-9999	-0.43	13	13
SHP2/GRB2/SOS1/GAB1	-0.083	0.13	-9999	-0.38	47	47
INPPL1	0.014	0	-9999	-10000	0	0
PXN	0.014	0	-9999	-10000	0	0
SH3KBP1	0.014	0	-9999	-10000	0	0
HGS	-0.055	0.11	-9999	-0.26	62	62
PLCgamma1/PKC	0	0	-9999	-10000	0	0
HGF	-0.069	0.19	-9999	-0.5	59	59
RASA1	0.014	0	-9999	-10000	0	0
NCK1	0.012	0.032	-9999	-0.6	1	1
PTPRJ	0.013	0.026	-9999	-0.48	1	1
NCK/PLCgamma1	-0.044	0.11	-9999	-0.41	6	6
PDPK1	-0.008	0.02	-9999	-0.37	1	1
HGF/MET/SHIP	-0.14	0.19	-9999	-0.36	140	140

×

p75(NTR)-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Sortilin/TRAF6	-0.002	0.032	-10000	0	-0.44	2	2
Necdin/E2F1	-0.047	0.14	-10000	0	-0.42	41	41
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E	-0.076	0.13	-10000	0	-0.32	58	58
NGF (dimer)/p75(NTR)/BEX1	-0.11	0.18	-10000	0	-0.37	109	109
NT-4/5 (dimer)/p75(NTR)	-0.065	0.15	-10000	0	-0.39	61	61
IKBKB	0.014	0	-10000	0	-10000	0	0
AKT1	-0.044	0.15	-10000	0	-0.32	58	58
IKBKG	0.014	0	-10000	0	-10000	0	0
BDNF	-0.087	0.21	-10000	0	-0.5	71	71
MGDIs/NGR/p75(NTR)/LINGO1	-0.087	0.18	-10000	0	-0.39	82	82
FURIN	0.014	0	-10000	0	-10000	0	0
proBDNF (dimer)/p75(NTR)/Sortilin	-0.1	0.17	-10000	0	-0.34	108	108
LINGO1	-0.02	0.14	-10000	0	-0.6	20	20
Sortilin/TRAF6/NRIF	-0.001	0.018	-10000	0	-10000	0	0
proBDNF (dimer)	-0.087	0.21	-10000	0	-0.5	71	71
NTRK1	-0.006	0.1	-10000	0	-0.52	14	14
RTN4R	-0.028	0.15	-10000	0	-0.56	27	27
neuron apoptosis	-0.063	0.17	-10000	0	-0.54	17	17
IRAK1	0.014	0	-10000	0	-10000	0	0
SHC1	-0.073	0.18	-10000	0	-0.35	100	100
ARHGDIA	0.014	0	-10000	0	-10000	0	0
RhoA/GTP	0	0	-10000	0	-10000	0	0
Gamma Secretase	0	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1	-0.089	0.15	-10000	0	-0.35	65	65
MAGEH1	0.002	0.085	-10000	0	-0.6	7	7
proNGF (dimer)/p75(NTR)/Sortilin/Necdin	-0.11	0.17	-10000	0	-0.39	78	78
Mammalian IAPs/DIABLO	-0.025	0.082	-10000	0	-0.32	18	18
proNGF (dimer)	-0.072	0.2	-10000	0	-0.55	55	55
MAGED1	0.014	0	-10000	0	-10000	0	0
APP	0.014	0	-10000	0	-10000	0	0
NT-4/5 (dimer)	-0.012	0.09	-10000	0	-0.48	13	13
ZNF274	0.014	0	-10000	0	-10000	0	0
RhoA/GDP/RHOGDI	-0.051	0.15	-10000	0	-0.33	57	57
NGF	-0.072	0.2	-10000	0	-0.55	55	55
cell cycle arrest	-0.072	0.14	-10000	0	-0.31	58	58
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK	-0.029	0.12	-10000	0	-0.4	9	9
NT-4/5 (dimer)/p75(NTR)/TRAF6	-0.055	0.12	-10000	0	-0.32	62	62
NCSTN	0.014	0	-10000	0	-10000	0	0
mol:GTP	-0.092	0.16	-10000	0	-0.34	98	98
PSENEN	0.014	0	-10000	0	-10000	0	0
mol:ceramide	-0.056	0.16	-10000	0	-0.35	58	58
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs	-0.017	0.11	-10000	0	-0.4	11	11
p75(NTR)/beta APP	-0.052	0.13	-10000	0	-0.38	50	50
BEX1	-0.015	0.13	-10000	0	-0.6	17	17
mol:GDP	-0.08	0.17	-10000	0	-0.35	98	98
NGF (dimer)	-0.13	0.17	-10000	0	-0.37	84	84
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI	-0.078	0.16	-10000	0	-0.41	51	51
PIK3R1	0.014	0	-10000	0	-10000	0	0
RAC1/GTP	-0.079	0.14	-10000	0	-0.34	59	59
MYD88	0.008	0.061	-10000	0	-0.57	4	4
CHUK	0.014	0	-10000	0	-10000	0	0
NGF (dimer)/p75(NTR)/PKA	-0.092	0.16	-10000	0	-0.34	98	98
RHOB	0.009	0.052	-10000	0	-0.48	4	4
RHOA	0.014	0	-10000	0	-10000	0	0
MAGE-G1/E2F1	-0.015	0.071	-10000	0	-0.35	16	16
NT3 (dimer)	-0.008	0.091	-10000	0	-0.48	13	13
TP53	-0.052	0.16	-10000	0	-0.51	20	20
PRDM4	-0.056	0.16	-10000	0	-0.35	58	58
BDNF (dimer)	-0.16	0.19	-10000	0	-0.43	83	83
PIK3CA	0.012	0.032	-10000	0	-0.6	1	1
SORT1	0.012	0.032	-10000	0	-0.6	1	1
activation of caspase activity	-0.075	0.13	-10000	0	-0.32	58	58
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.084	0.14	-10000	0	-0.36	59	59
RHOC	0.011	0.041	-10000	0	-0.54	2	2
XIAP	0.014	0	-10000	0	-10000	0	0
MAPK10	-0.045	0.16	-10000	0	-0.49	19	19
DIABLO	0.014	0	-10000	0	-10000	0	0
SMPD2	-0.056	0.16	-10000	0	-0.35	58	58
APH1B	0.014	0	-10000	0	-10000	0	0
APH1A	0.014	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin	-0.093	0.16	-10000	0	-0.34	99	99
PSEN1	0.014	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0	0	-10000	0	-10000	0	0
NT3 (dimer)/p75(NTR)	-0.064	0.15	-10000	0	-0.39	60	60
MAPK8	-0.048	0.16	-10000	0	-0.47	20	20
MAPK9	-0.042	0.16	-10000	0	-0.5	15	15
APAF1	0.014	0	-10000	0	-10000	0	0
NTF3	-0.008	0.091	-10000	0	-0.48	13	13
NTF4	-0.012	0.09	-10000	0	-0.48	13	13
NDN	-0.031	0.16	-10000	0	-0.6	27	27
RAC1/GDP	0	0	-10000	0	-10000	0	0
RhoA-B-C/GDP	-0.071	0.12	-10000	0	-0.48	8	8
p75 CTF/Sortilin/TRAF6/NRIF	-0.006	0.051	-10000	0	-0.38	6	6
RhoA-B-C/GTP	-0.092	0.16	-10000	0	-0.34	98	98
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.082	0.14	-10000	0	-0.52	15	15
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.09	0.15	-10000	0	-0.41	42	42
PRKACB	0.014	0	-10000	0	-10000	0	0
proBDNF (dimer)/p75 ECD	-0.075	0.15	-10000	0	-0.37	74	74
ChemicalAbstracts:86-01-1	0	0	-10000	0	-10000	0	0
BIRC3	-0.035	0.16	-10000	0	-0.55	32	32
BIRC2	0.014	0	-10000	0	-10000	0	0
neuron projection morphogenesis	-0.087	0.15	0.21	3	-0.37	62	65
BAD	-0.037	0.16	-10000	0	-0.46	18	18
RIPK2	0.014	0	-10000	0	-10000	0	0
NGFR	-0.061	0.19	-10000	0	-0.54	50	50
CYCS	-0.044	0.15	-10000	0	-0.32	58	58
ADAM17	0.006	0.072	-10000	0	-0.6	5	5
NGF (dimer)/p75(NTR)/TRAF6/RIP2	-0.083	0.14	-10000	0	-0.36	58	58
BCL2L11	-0.037	0.16	-10000	0	-0.46	18	18
BDNF (dimer)/p75(NTR)	-0.12	0.2	-10000	0	-0.41	107	107
PI3K	-0.083	0.14	-10000	0	-0.35	58	58
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1	-0.083	0.14	-10000	0	-0.35	58	58
NDNL2	0.014	0	-10000	0	-10000	0	0
YWHAE	0.014	0	-10000	0	-10000	0	0
PRKCI	0.014	0	-10000	0	-10000	0	0
NGF (dimer)/p75(NTR)	-0.11	0.19	-10000	0	-0.41	98	98
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE	-0.083	0.14	-10000	0	-0.35	58	58
TRAF6	0.012	0.032	-10000	0	-0.6	1	1
RAC1	0.014	0	-10000	0	-10000	0	0
PRKCZ	-0.01	0.12	-10000	0	-0.56	15	15
PLG	0.001	0.026	-10000	0	-0.48	1	1
oligodendrocyte cell fate commitment	0	0	-10000	0	-10000	0	0
CASP6	-0.093	0.18	-10000	0	-0.46	42	42
SQSTM1	0.014	0	-10000	0	-10000	0	0
NGFRAP1	0.014	0	-10000	0	-10000	0	0
CASP3	-0.032	0.15	-10000	0	-0.42	18	18
E2F1	-0.008	0.1	-10000	0	-0.5	16	16
CASP9	0.014	0	-10000	0	-10000	0	0
IKK complex	-0.063	0.12	-10000	0	-0.51	10	10
NGF (dimer)/TRKA	-0.073	0.16	-10000	0	-0.41	66	66
MMP7	-0.15	0.25	-10000	0	-0.54	105	105
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.077	0.13	-10000	0	-0.53	8	8
MMP3	-0.032	0.14	-10000	0	-0.48	30	30
APAF-1/Caspase 9	-0.067	0.11	-10000	0	-0.43	12	12

×

Glypican 1 network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer	-0.005	0.047	-10000	0	-0.38	5	5
fibroblast growth factor receptor signaling pathway	-0.005	0.047	-10000	0	-0.38	5	5
LAMA1	-0.054	0.19	-10000	0	-0.58	42	42
PRNP	0.012	0.032	-10000	0	-0.6	1	1
GPC1/SLIT2	-0.099	0.17	-10000	0	-0.38	94	94
SMAD2	0.029	0.049	-10000	0	-0.38	3	3
GPC1/PrPc/Cu2+	-0.003	0.028	-10000	0	-0.31	3	3
GPC1/Laminin alpha1	-0.05	0.14	-10000	0	-0.43	42	42
TDGF1	-0.084	0.22	-10000	0	-0.57	61	61
CRIPTO/GPC1	-0.071	0.16	-10000	0	-0.42	61	61
APP/GPC1	-0.002	0.025	-10000	0	-0.33	2	2
mol:NO	0	0	-10000	0	-10000	0	0
YES1	-0.035	0.15	-10000	0	-0.36	61	61
FLT1	0.012	0.032	-10000	0	-0.6	1	1
GPC1/TGFB/TGFBR1/TGFBR2	-0.007	0.05	-10000	0	-0.42	3	3
SERPINC1	0.007	0.052	-10000	0	-0.48	4	4
FYN	-0.034	0.14	-10000	0	-0.35	61	61
FGR	-0.035	0.15	-10000	0	-0.35	63	63
positive regulation of MAPKKK cascade	-0.074	0.19	-10000	0	-0.47	51	51
SLIT2	-0.13	0.24	-10000	0	-0.54	92	92
GPC1/NRG	-0.12	0.19	-10000	0	-0.4	111	111
NRG1	-0.16	0.26	-10000	0	-0.56	110	110
GPC1/VEGF165 homodimer/VEGFR1 homodimer	-0.014	0.063	-10000	0	-0.29	17	17
LYN	-0.039	0.15	-10000	0	-0.34	67	67
mol:Spermine	0.01	0.026	-10000	0	-0.34	2	2
cell growth	-0.005	0.047	-10000	0	-0.38	5	5
BMP signaling pathway	-0.011	0.036	0.48	2	-10000	0	2
SRC	-0.034	0.14	-10000	0	-0.38	47	47
TGFBR1	0.011	0.041	-10000	0	-0.54	2	2
mol:Cu2+	0	0	-10000	0	-10000	0	0
PLA2G2A	-0.075	0.18	-10000	0	-0.49	59	59
GPC1	0.011	0.037	-10000	0	-0.48	2	2
TGFBR1 (dimer)	0.011	0.041	-10000	0	-0.54	2	2
VEGFA	-0.006	0.098	-10000	0	-0.48	15	15
BLK	-0.1	0.18	-10000	0	-0.42	59	59
HCK	-0.05	0.17	-10000	0	-0.41	51	51
FGF2	0.009	0.052	-10000	0	-0.56	3	3
FGFR1	0.012	0.032	-10000	0	-0.6	1	1
VEGFR1 homodimer	0.012	0.032	-10000	0	-0.6	1	1
TGFBR2	0.007	0.061	-10000	0	-0.5	5	5
cell death	-0.002	0.025	-10000	0	-0.33	2	2
ATIII/GPC1	-0.005	0.042	-10000	0	-0.33	6	6
PLA2G2A/GPC1	-0.057	0.13	-10000	0	-0.35	59	59
LCK	-0.095	0.2	-10000	0	-0.44	70	70
neuron differentiation	-0.12	0.19	-10000	0	-0.4	111	111
PrPc/Cu2+	-0.001	0.023	-10000	0	-0.45	1	1
APP	0.014	0	-10000	0	-10000	0	0
TGFBR2 (dimer)	0.007	0.061	-10000	0	-0.5	5	5

×

PDGFR-alpha signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.063	0.2	-9999	-0.59	45	45
PDGF/PDGFRA/CRKL	-0.05	0.14	-9999	-0.41	45	45
positive regulation of JUN kinase activity	-0.039	0.1	-9999	-0.32	37	37
CRKL	0.014	0	-9999	-10000	0	0
PDGF/PDGFRA/Caveolin-3	-0.057	0.14	-9999	-0.42	49	49
AP1	-0.16	0.31	-9999	-0.9	49	49
mol:IP3	-0.036	0.15	-9999	-0.43	45	45
PLCG1	-0.036	0.15	-9999	-0.43	45	45
PDGF/PDGFRA/alphaV Integrin	-0.051	0.14	-9999	-0.42	45	45
RAPGEF1	0.014	0	-9999	-10000	0	0
CRK	0.014	0	-9999	-10000	0	0
mol:Ca2+	-0.036	0.15	-9999	-0.43	45	45
CAV3	0.001	0.057	-9999	-0.48	5	5
CAV1	-0.045	0.16	-9999	-0.49	43	43
SHC/Grb2/SOS1	-0.039	0.1	-9999	-0.32	37	37
PDGF/PDGFRA/Shf	-0.054	0.15	-9999	-0.44	46	46
FOS	-0.12	0.33	-9999	-0.88	49	49
JUN	-0.02	0.062	-9999	-0.41	8	8
oligodendrocyte development	-0.051	0.14	-9999	-0.42	45	45
GRB2	0.014	0	-9999	-10000	0	0
PIK3R1	0.014	0	-9999	-10000	0	0
mol:DAG	-0.036	0.15	-9999	-0.43	45	45
PDGF/PDGFRA	-0.063	0.2	-9999	-0.59	45	45
actin cytoskeleton reorganization	-0.05	0.14	-9999	-0.41	45	45
SRF	0.027	0.009	-9999	-10000	0	0
SHC1	0.009	0.052	-9999	-0.48	4	4
PI3K	-0.043	0.12	-9999	-0.36	40	40
PDGF/PDGFRA/Crk/C3G	-0.042	0.11	-9999	-0.35	39	39
JAK1	-0.03	0.14	-9999	-0.41	45	45
ELK1/SRF	-0.001	0.11	-9999	-0.32	37	37
SHB	0.014	0	-9999	-10000	0	0
SHF	0.007	0.064	-9999	-0.6	4	4
CSNK2A1	0.013	0.022	-9999	-10000	0	0
GO:0007205	-0.037	0.15	-9999	-0.44	45	45
SOS1	0.014	0	-9999	-10000	0	0
Ras protein signal transduction	-0.039	0.1	-9999	-0.32	37	37
PDGF/PDGFRA/SHB	-0.05	0.14	-9999	-0.41	45	45
PDGF/PDGFRA/Caveolin-1	-0.09	0.18	-9999	-0.4	82	82
ITGAV	0.012	0.032	-9999	-0.6	1	1
ELK1	-0.028	0.14	-9999	-0.4	40	40
PIK3CA	0.012	0.032	-9999	-0.6	1	1
PDGF/PDGFRA/Crk	-0.05	0.14	-9999	-0.41	45	45
JAK-STAT cascade	-0.03	0.14	-9999	-0.41	45	45
cell proliferation	-0.054	0.15	-9999	-0.44	46	46

×

Glucocorticoid receptor regulatory network

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
PCK2	0.018	0.11	-10000	0	-0.89	3	3
SMARCC2	0.015	0.01	-10000	0	-10000	0	0
SMARCC1	0.015	0.01	-10000	0	-10000	0	0
TBX21	-0.1	0.24	-10000	0	-0.71	40	40
SUMO2	0.013	0.013	-10000	0	-10000	0	0
STAT1 (dimer)	0.002	0.1	-10000	0	-0.56	11	11
FKBP4	0.014	0	-10000	0	-10000	0	0
FKBP5	-0.1	0.23	-10000	0	-0.56	75	75
GR alpha/HSP90/FKBP51/HSP90	0.013	0.17	0.3	19	-0.33	33	52
PRL	-0.049	0.095	-10000	0	-0.6	2	2
cortisol/GR alpha (dimer)/TIF2	0.18	0.25	0.51	82	-0.44	4	86
RELA	-0.066	0.097	-10000	0	-0.28	8	8
FGG	0.17	0.16	0.46	40	-0.44	1	41
GR beta/TIF2	0.06	0.16	0.3	30	-0.4	28	58
IFNG	-0.23	0.21	-10000	0	-0.63	40	40
apoptosis	-0.002	0.19	0.6	15	-0.56	2	17
CREB1	0.013	0.023	-10000	0	-10000	0	0
histone acetylation	-0.047	0.12	-10000	0	-0.37	26	26
BGLAP	-0.051	0.13	-10000	0	-0.72	4	4
GR/PKAc	0.09	0.092	0.29	22	-10000	0	22
NF kappa B1 p50/RelA	-0.12	0.18	-10000	0	-0.43	52	52
SMARCD1	0.015	0.01	-10000	0	-10000	0	0
MDM2	0.081	0.078	0.24	38	-10000	0	38
GATA3	-0.094	0.23	-10000	0	-0.53	77	77
AKT1	0.002	0.019	-10000	0	-10000	0	0
CSF2	-0.064	0.099	-10000	0	-10000	0	0
GSK3B	0.013	0.013	-10000	0	-10000	0	0
NR1I3	0.036	0.19	0.59	14	-0.72	2	16
CSN2	0.14	0.13	0.39	27	-10000	0	27
BRG1/BAF155/BAF170/BAF60A	0.039	0.034	-10000	0	-10000	0	0
NFATC1	-0.018	0.14	-10000	0	-0.57	21	21
POU2F1	0.013	0.033	-10000	0	-0.6	1	1
CDKN1A	-0.073	0.33	-10000	0	-1.5	16	16
response to stress	0	0	-10000	0	-10000	0	0
response to UV	0	0.011	-10000	0	-10000	0	0
SFN	-0.11	0.23	-10000	0	-0.52	87	87
GR alpha/HSP90/FKBP51/HSP90/14-3-3	-0.049	0.19	0.28	12	-0.41	26	38
prolactin receptor activity	0	0	-10000	0	-10000	0	0
EGR1	-0.037	0.3	0.57	14	-0.8	33	47
JUN	-0.16	0.19	-10000	0	-0.5	50	50
IL4	-0.084	0.15	-10000	0	-0.54	19	19
CDK5R1	-0.022	0.14	-10000	0	-0.6	21	21
PRKACA	0.014	0	-10000	0	-10000	0	0
cortisol/GR alpha (monomer)/AP-1	-0.16	0.19	-10000	0	-0.47	72	72
GR alpha/HSP90/FKBP51/HSP90/PP5C	0.023	0.16	0.29	19	-0.33	9	28
cortisol/GR alpha (monomer)	0.24	0.26	0.59	93	-10000	0	93
NCOA2	-0.035	0.17	-10000	0	-0.6	29	29
response to hypoxia	0	0	-10000	0	-10000	0	0
FOS	-0.13	0.22	-10000	0	-0.57	66	66
AP-1/NFAT1-c-4	-0.3	0.29	-10000	0	-0.67	96	96
AFP	-0.12	0.18	-10000	0	-0.6	20	20
SUV420H1	0.014	0	-10000	0	-10000	0	0
IRF1	0.12	0.14	0.47	7	-0.5	2	9
TP53	-0.019	0.16	-10000	0	-0.54	26	26
PPP5C	0.014	0	-10000	0	-10000	0	0
KRT17	-0.43	0.48	-10000	0	-0.96	134	134
KRT14	-0.13	0.18	-10000	0	-0.54	33	33
TBP	0.022	0.022	-10000	0	-10000	0	0
CREBBP	0.031	0.059	-10000	0	-10000	0	0
HDAC1	0.006	0.047	-10000	0	-0.6	2	2
HDAC2	0.014	0	-10000	0	-10000	0	0
AP-1	-0.3	0.3	-10000	0	-0.67	96	96
MAPK14	0.013	0.011	-10000	0	-10000	0	0
MAPK10	0.006	0.065	-10000	0	-0.6	4	4
MAPK11	0.008	0.057	-10000	0	-0.6	3	3
KRT5	-0.38	0.42	-10000	0	-0.95	98	98
interleukin-1 receptor activity	0	0	-10000	0	-10000	0	0
NCOA1	0.016	0.011	-10000	0	-10000	0	0
STAT1	0.002	0.1	-10000	0	-0.56	11	11
CGA	-0.069	0.12	-10000	0	-0.48	8	8
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2	0.082	0.11	0.34	18	-10000	0	18
MAPK3	0.013	0.012	-10000	0	-10000	0	0
MAPK1	0.013	0.011	-10000	0	-10000	0	0
ICAM1	-0.2	0.28	-10000	0	-0.72	56	56
NFKB1	-0.067	0.1	-10000	0	-0.39	4	4
MAPK8	-0.14	0.17	-10000	0	-0.42	64	64
MAPK9	0.013	0.011	-10000	0	-10000	0	0
cortisol/GR alpha (dimer)	-0.005	0.2	0.61	15	-0.59	2	17
BAX	-0.003	0.11	-10000	0	-0.49	2	2
POMC	-0.13	0.22	-10000	0	-1.1	10	10
EP300	0.024	0.089	-10000	0	-0.6	4	4
cortisol/GR alpha (dimer)/p53	0.18	0.23	0.5	76	-0.53	2	78
proteasomal ubiquitin-dependent protein catabolic process	0.058	0.068	0.22	19	-10000	0	19
SGK1	0.053	0.24	-10000	0	-1.4	9	9
IL13	-0.23	0.23	-10000	0	-0.66	44	44
IL6	-0.29	0.38	-10000	0	-0.85	95	95
PRKACG	0.005	0.045	-10000	0	-0.48	3	3
IL5	-0.2	0.19	-10000	0	-0.57	35	35
IL2	-0.23	0.21	-10000	0	-0.57	57	57
CDK5	0.014	0.006	-10000	0	-10000	0	0
PRKACB	0.014	0	-10000	0	-10000	0	0
HSP90AA1	0.014	0	-10000	0	-10000	0	0
IL8	-0.33	0.41	-10000	0	-0.82	123	123
CDK5R1/CDK5	-0.02	0.1	-10000	0	-0.43	21	21
NF kappa B1 p50/RelA/PKAc	-0.06	0.14	-10000	0	-0.4	11	11
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90	0.21	0.2	0.48	89	-10000	0	89
SMARCA4	0.015	0.01	-10000	0	-10000	0	0
chromatin remodeling	0.15	0.13	0.36	51	-0.34	2	53
NF kappa B1 p50/RelA/Cbp	-0.059	0.16	-10000	0	-0.46	12	12
JUN (dimer)	-0.16	0.19	-10000	0	-0.5	50	50
YWHAH	-0.009	0.1	-10000	0	-0.48	17	17
VIPR1	-0.13	0.28	-10000	0	-0.74	56	56
NR3C1	0.14	0.14	0.42	48	-10000	0	48
NR4A1	-0.024	0.14	-10000	0	-0.49	31	31
TIF2/SUV420H1	-0.035	0.12	-10000	0	-0.44	29	29
MAPKKK cascade	-0.002	0.19	0.6	15	-0.56	2	17
cortisol/GR alpha (dimer)/Src-1	0.22	0.22	0.51	93	-10000	0	93
PBX1	0.013	0.033	-10000	0	-0.6	1	1
POU1F1	0.004	0.027	-10000	0	-0.48	1	1
SELE	-0.3	0.39	-10000	0	-0.84	100	100
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A	0.15	0.13	0.36	51	-0.35	2	53
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90	0.21	0.2	0.48	89	-10000	0	89
mol:cortisol	0.13	0.15	0.32	97	-10000	0	97
MMP1	-0.11	0.14	-10000	0	-0.53	21	21

×

Osteopontin-mediated 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IKK alpha homodimer	-0.039	0.17	-9999	-0.48	21	21
NF kappa B1 p50/RelA/I kappa B alpha	-0.016	0.16	-9999	-0.49	16	16
alphaV/beta3 Integrin/Osteopontin/Src	-0.069	0.15	-9999	-0.38	66	66
AP1	-0.082	0.23	-9999	-0.58	37	37
ILK	-0.047	0.17	-9999	-0.49	22	22
bone resorption	-0.08	0.24	-9999	-0.55	55	55
PTK2B	-0.01	0.11	-9999	-0.48	18	18
PYK2/p130Cas	-0.095	0.16	-9999	-0.51	33	33
ITGAV	0.015	0.032	-9999	-0.59	1	1
mol:GTP	0	0	-9999	-10000	0	0
CD44/Rho Family GTPase/ROCK2	-0.067	0.16	-9999	-0.42	59	59
alphaV/beta3 Integrin/Osteopontin	-0.095	0.17	-9999	-0.4	71	71
MAP3K1	-0.05	0.17	-9999	-0.49	23	23
JUN	0.003	0.075	-9999	-0.5	8	8
MAPK3	-0.041	0.18	-9999	-0.5	22	22
MAPK1	-0.041	0.18	-9999	-0.5	22	22
Rac1/GDP	0	0	-9999	-10000	0	0
NFKB1	0.013	0.026	-9999	-0.48	1	1
MAPK8	-0.047	0.18	-9999	-0.48	28	28
ITGB3	-0.051	0.18	-9999	-0.51	47	47
NFKBIA	-0.032	0.18	-9999	-0.5	21	21
FOS	-0.087	0.22	-9999	-0.55	66	66
CD44	-0.057	0.19	-9999	-0.55	46	46
CHUK	0.014	0	-9999	-10000	0	0
PLAU	-0.074	0.28	-9999	-0.78	36	36
NF kappa B1 p50/RelA	-0.077	0.13	-9999	-0.53	15	15
BCAR1	0.012	0.032	-9999	-0.6	1	1
RELA	0.014	0	-9999	-10000	0	0
alphaV beta3 Integrin	-0.048	0.12	-9999	-0.36	48	48
mol:GDP	0	0	-9999	-10000	0	0
SYK	-0.062	0.2	-9999	-0.43	64	64
VAV3	-0.11	0.23	-9999	-0.57	49	49
MAP3K14	-0.05	0.18	-9999	-0.5	23	23
ROCK2	-0.011	0.12	-9999	-0.6	15	15
SPP1	-0.081	0.21	-9999	-0.54	65	65
RAC1	0.014	0	-9999	-10000	0	0
Rac1/GTP	-0.13	0.19	-9999	-0.53	46	46
MMP2	-0.073	0.22	-9999	-0.52	45	45

×

Arf6 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CENTA1/KIF3B	-0.018	0.076	-9999	-0.33	20	20
ARNO/beta Arrestin1-2	-0.019	0.074	-9999	-0.55	3	3
EGFR	-0.082	0.21	-9999	-0.55	62	62
EPHA2	-0.018	0.12	-9999	-0.49	23	23
USP6	0.005	0.068	-9999	-0.48	7	7
IQSEC1	0.007	0.061	-9999	-0.5	5	5
EGFR/EGFR/EGF/EGF	-0.11	0.19	-9999	-0.43	89	89
ARRB2	0.009	0.034	-9999	-0.19	10	10
mol:GTP	0.005	0.043	-9999	-0.16	14	14
ARRB1	0.002	0.085	-9999	-0.6	7	7
FBXO8	0.012	0.032	-9999	-0.6	1	1
TSHR	-0.2	0.27	-9999	-0.54	143	143
EGF	-0.044	0.17	-9999	-0.56	37	37
somatostatin receptor activity	0	0	-9999	-0.001	47	47
ARAP2	-0.008	0.11	-9999	-0.6	13	13
mol:GDP	-0.068	0.12	-9999	-0.29	55	55
mol:PI-3-4-5-P3	0	0	-9999	-0.001	21	21
ITGA2B	-0.043	0.17	-9999	-0.57	36	36
ARF6	0.014	0	-9999	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	-0.018	0.068	-9999	-0.41	3	3
ADAP1	-0.017	0.13	-9999	-0.55	20	20
KIF13B	0.014	0	-9999	-10000	0	0
HGF/MET	-0.16	0.22	-9999	-0.42	139	139
PXN	0.014	0	-9999	-10000	0	0
ARF6/GTP	-0.059	0.12	-9999	-0.29	45	45
EGFR/EGFR/EGF/EGF/ARFGEP100	-0.092	0.17	-9999	-0.37	91	91
ADRB2	-0.011	0.12	-9999	-0.6	15	15
receptor agonist activity	0	0	-9999	0	47	47
actin filament binding	0	0	-9999	-0.001	47	47
SRC	0.014	0	-9999	-10000	0	0
ITGB3	-0.054	0.18	-9999	-0.51	47	47
GNAQ	0.014	0	-9999	-10000	0	0
EFA6/PI-4-5-P2	0	0	-9999	-0.001	35	35
ARF6/GDP	-0.005	0.1	-9999	-0.41	11	11
ARF6/GDP/GULP/ACAP1	-0.11	0.17	-9999	-0.44	56	56
alphaIIb/beta3 Integrin/paxillin/GIT1	-0.063	0.13	-9999	-0.36	37	37
ACAP1	-0.033	0.15	-9999	-0.49	34	34
ACAP2	0.012	0.032	-9999	-0.6	1	1
LHCGR/beta Arrestin2	0.003	0.048	-9999	-0.28	10	10
EFNA1	0.011	0.037	-9999	-0.48	2	2
HGF	-0.07	0.19	-9999	-0.5	59	59
CYTH3	0.012	0	-9999	-10000	0	0
CYTH2	0.009	0.002	-9999	-10000	0	0
NCK1	0.012	0.032	-9999	-0.6	1	1
fibronectin binding	0	0	-9999	0	41	41
endosomal lumen acidification	0	0	-9999	0	51	51
microtubule-based process	0	0	-9999	-10000	0	0
GULP1	-0.052	0.19	-9999	-0.58	41	41
GNAQ/ARNO	0.014	0.008	-9999	-10000	0	0
mol:Phosphatidic acid	0	0	-9999	-10000	0	0
PIP3-E	0	0	-9999	0	21	21
MET	-0.14	0.25	-9999	-0.54	101	101
GNA14	-0.006	0.11	-9999	-0.56	13	13
GNA15	-0.007	0.11	-9999	-0.56	13	13
GIT1	0.014	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-0.001	39	39
GNA11	0.002	0.085	-9999	-0.6	7	7
LHCGR	-0.005	0.08	-9999	-0.48	10	10
AGTR1	-0.036	0.16	-9999	-0.55	32	32
desensitization of G-protein coupled receptor protein signaling pathway	0.003	0.048	-9999	-0.28	10	10
IPCEF1/ARNO	-0.054	0.14	-9999	-0.49	10	10
alphaIIb/beta3 Integrin	-0.086	0.17	-9999	-0.4	78	78

×

BCR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
JUN	-0.043	0.14	-10000	0	-0.37	40	40
IKBKB	-0.014	0.078	-10000	0	-0.27	10	10
AKT1	-0.052	0.1	-10000	0	-0.25	36	36
IKBKG	-0.012	0.083	-10000	0	-0.27	15	15
CALM1	-0.057	0.15	0.21	2	-0.4	42	44
PIK3CA	0.012	0.032	-10000	0	-0.6	1	1
MAP3K1	-0.069	0.19	-10000	0	-0.5	44	44
MAP3K7	0.014	0	-10000	0	-10000	0	0
mol:Ca2+	-0.067	0.16	0.21	2	-0.42	42	44
DOK1	0.012	0.032	-10000	0	-0.6	1	1
AP-1	-0.035	0.099	-10000	0	-0.26	22	22
LYN	0.006	0.063	-10000	0	-0.48	6	6
BLNK	-0.056	0.19	-10000	0	-0.58	43	43
SHC1	0.009	0.052	-10000	0	-0.48	4	4
BCR complex	-0.086	0.18	-10000	0	-0.44	73	73
CD22	-0.18	0.22	-10000	0	-0.46	99	99
CAMK2G	-0.046	0.14	-10000	0	-0.47	22	22
CSNK2A1	0.014	0	-10000	0	-10000	0	0
INPP5D	0.008	0.055	-10000	0	-0.51	4	4
SHC/GRB2/SOS1	-0.095	0.17	-10000	0	-0.55	31	31
GO:0007205	-0.069	0.16	0.21	2	-0.43	42	44
SYK	-0.013	0.12	-10000	0	-0.56	17	17
ELK1	-0.057	0.15	0.21	2	-0.4	42	44
NFATC1	-0.069	0.18	-10000	0	-0.47	46	46
B-cell antigen/BCR complex	-0.086	0.18	-10000	0	-0.44	73	73
PAG1/CSK	-0.001	0.023	-10000	0	-0.44	1	1
NFKBIB	0.005	0.029	-10000	0	-10000	0	0
HRAS	-0.052	0.16	-10000	0	-0.39	43	43
NFKBIA	0.006	0.028	-10000	0	-10000	0	0
NF-kappa-B/RelA/I kappa B beta	0.012	0.024	-10000	0	-10000	0	0
RasGAP/Csk	-0.14	0.19	-10000	0	-0.55	39	39
mol:GDP	-0.063	0.15	0.22	2	-0.41	42	44
PTEN	0.014	0	-10000	0	-10000	0	0
CD79B	-0.061	0.19	-10000	0	-0.54	50	50
NF-kappa-B/RelA/I kappa B alpha	0.012	0.024	-10000	0	-10000	0	0
GRB2	0.014	0	-10000	0	-10000	0	0
PI3K/BCAP/CD19	-0.093	0.19	-10000	0	-0.49	56	56
PIK3R1	0.014	0	-10000	0	-10000	0	0
mol:IP3	-0.069	0.16	0.21	2	-0.44	42	44
CSK	0.014	0	-10000	0	-10000	0	0
FOS	-0.093	0.18	-10000	0	-0.48	38	38
CHUK	-0.012	0.083	-10000	0	-0.27	15	15
IBTK	0.014	0	-10000	0	-10000	0	0
CARD11/BCL10/MALT1/TAK1	-0.065	0.14	-10000	0	-0.51	24	24
PTPN6	-0.17	0.22	-10000	0	-0.53	69	69
RELA	0.014	0	-10000	0	-10000	0	0
BCL2A1	-0.007	0.046	-10000	0	-0.1	26	26
VAV2	-0.12	0.19	-10000	0	-0.53	47	47
ubiquitin-dependent protein catabolic process	0.01	0.028	-10000	0	-10000	0	0
BTK	-0.036	0.19	0.37	1	-1.1	10	11
CD19	-0.12	0.19	-10000	0	-0.52	51	51
MAP4K1	-0.025	0.15	-10000	0	-0.58	24	24
CD72	-0.008	0.1	-10000	0	-0.5	16	16
PAG1	0.012	0.032	-10000	0	-0.6	1	1
MAPK14	-0.051	0.16	-10000	0	-0.43	39	39
SH3BP5	0.011	0.046	-10000	0	-0.6	2	2
PIK3AP1	-0.069	0.18	0.24	2	-0.47	49	51
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72	-0.063	0.21	-10000	0	-0.56	39	39
RAF1	-0.041	0.15	-10000	0	-0.45	24	24
RasGAP/p62DOK/SHIP	-0.13	0.19	-10000	0	-0.54	39	39
CD79A	-0.039	0.16	-10000	0	-0.53	36	36
re-entry into mitotic cell cycle	-0.035	0.099	-10000	0	-0.27	21	21
RASA1	0.014	0	-10000	0	-10000	0	0
MAPK3	-0.019	0.12	-10000	0	-0.4	18	18
MAPK1	-0.019	0.12	-10000	0	-0.4	18	18
CD72/SHP1	-0.14	0.22	-10000	0	-0.52	67	67
NFKB1	0.013	0.026	-10000	0	-0.48	1	1
MAPK8	-0.058	0.17	-10000	0	-0.43	45	45
actin cytoskeleton organization	-0.072	0.18	-10000	0	-0.47	43	43
NF-kappa-B/RelA	0.029	0.045	-10000	0	-10000	0	0
Calcineurin	-0.059	0.12	-10000	0	-0.45	21	21
PI3K	-0.14	0.18	-10000	0	-0.46	64	64
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2	-0.083	0.17	0.24	2	-0.48	42	44
SOS1	0.014	0	-10000	0	-10000	0	0
Bam32/HPK1	-0.12	0.28	-10000	0	-0.78	45	45
DAPP1	-0.14	0.29	-10000	0	-0.86	42	42
cytokine secretion	-0.063	0.17	-10000	0	-0.43	46	46
mol:DAG	-0.069	0.16	0.21	2	-0.44	42	44
PLCG2	0.002	0.082	-10000	0	-0.54	8	8
MAP2K1	-0.03	0.14	-10000	0	-0.44	19	19
B-cell antigen/BCR complex/FcgammaRIIB	-0.16	0.22	-10000	0	-0.47	104	104
mol:PI-3-4-5-P3	-0.1	0.12	-10000	0	-0.33	58	58
ETS1	-0.037	0.13	-10000	0	-0.44	21	21
B-cell antigen/BCR complex/LYN/SYK/BLNK	-0.11	0.2	-10000	0	-0.42	81	81
B-cell antigen/BCR complex/LYN	-0.11	0.19	-10000	0	-0.49	57	57
MALT1	0.014	0	-10000	0	-10000	0	0
TRAF6	0.012	0.032	-10000	0	-0.6	1	1
RAC1	-0.077	0.19	-10000	0	-0.5	43	43
B-cell antigen/BCR complex/LYN/SYK	-0.17	0.23	-10000	0	-0.57	69	69
CARD11	-0.068	0.18	-10000	0	-0.47	45	45
FCGR2B	-0.15	0.25	-10000	0	-0.53	107	107
PPP3CA	0.011	0.037	-10000	0	-0.48	2	2
BCL10	0.014	0	-10000	0	-10000	0	0
IKK complex	0.001	0.036	-10000	0	-0.12	1	1
PTPRC	-0.043	0.17	-10000	0	-0.54	38	38
PDPK1	-0.053	0.097	-10000	0	-0.24	38	38
PPP3CB	0.01	0.045	-10000	0	-0.48	3	3
PPP3CC	0.014	0	-10000	0	-10000	0	0
POU2F2	0.012	0.024	-10000	0	-0.099	5	5

×

HIF-1-alpha transcription factor network

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
PKM2	-0.012	0.49	-9999	-1.1	33	33
HDAC7	0.017	0.003	-9999	-10000	0	0
HIF1A/ARNT/Cbp/p300/Src-1	-0.14	0.34	-9999	-0.92	36	36
SMAD4	0.016	0.003	-9999	-10000	0	0
ID2	-0.012	0.49	-9999	-1.1	33	33
AP1	-0.06	0.18	-9999	-0.43	66	66
ABCG2	-0.013	0.49	-9999	-1.1	33	33
HIF1A	0.026	0.089	-9999	-0.55	1	1
TFF3	-0.048	0.5	-9999	-1.1	40	40
GATA2	-0.009	0.12	-9999	-0.56	15	15
AKT1	0.019	0.1	-9999	-10000	0	0
response to hypoxia	0.002	0.11	-9999	-0.24	11	11
MCL1	-0.012	0.49	-9999	-1.1	33	33
NDRG1	-0.016	0.49	-9999	-1.1	34	34
SERPINE1	-0.087	0.54	-9999	-1.1	49	49
FECH	-0.012	0.49	-9999	-1.1	33	33
FURIN	-0.012	0.49	-9999	-1.1	36	36
NCOA2	-0.033	0.17	-9999	-0.6	29	29
EP300	0.032	0.18	-9999	-0.36	23	23
HMOX1	-0.021	0.5	-9999	-1.2	37	37
BHLHE40	-0.02	0.5	-9999	-1.1	37	37
BHLHE41	-0.02	0.5	-9999	-1.1	39	39
HIF1A/ARNT/SMAD3/SMAD4/SP1	-0.014	0.061	-9999	-0.4	4	4
ENG	0.087	0.13	-9999	-0.52	5	5
JUN	0.003	0.076	-9999	-0.5	8	8
RORA	-0.013	0.49	-9999	-1.1	33	33
ABCB1	-0.036	0.068	-9999	-0.6	1	1
TFRC	-0.018	0.49	-9999	-1.1	34	34
CXCR4	-0.023	0.5	-9999	-1.2	36	36
TF	-0.045	0.52	-9999	-1.2	40	40
CITED2	-0.013	0.49	-9999	-1.1	33	33
HIF1A/ARNT	-0.18	0.51	-9999	-1.3	41	41
LDHA	-0.032	0.099	-9999	-0.7	5	5
ETS1	-0.014	0.49	-9999	-1.1	34	34
PGK1	-0.012	0.49	-9999	-1.1	33	33
NOS2	-0.036	0.51	-9999	-1.2	37	37
ITGB2	-0.032	0.51	-9999	-1.1	41	41
ALDOA	-0.012	0.49	-9999	-1.1	33	33
Cbp/p300/CITED2	-0.084	0.5	-9999	-1.2	37	37
FOS	-0.087	0.22	-9999	-0.55	66	66
HK2	-0.024	0.51	-9999	-1.2	36	36
SP1	0.024	0.005	-9999	-10000	0	0
GCK	-0.067	0.48	-9999	-1.3	38	38
HK1	-0.012	0.49	-9999	-1.1	33	33
NPM1	-0.012	0.49	-9999	-1.1	33	33
EGLN1	-0.012	0.49	-9999	-1.1	33	33
CREB1	0.022	0.004	-9999	-10000	0	0
PGM1	-0.012	0.49	-9999	-1.1	33	33
SMAD3	0.014	0.032	-9999	-0.6	1	1
EDN1	-0.053	0.34	-9999	-1	25	25
IGFBP1	-0.079	0.53	-9999	-1.1	47	47
VEGFA	0.02	0.41	-9999	-0.95	24	24
HIF1A/JAB1	-0.007	0.032	-9999	-0.4	1	1
CP	-0.099	0.54	-9999	-1.1	51	51
CXCL12	-0.016	0.49	-9999	-1.1	34	34
COPS5	0.015	0.003	-9999	-10000	0	0
SMAD3/SMAD4	-0.002	0.023	-9999	-0.43	1	1
BNIP3	-0.012	0.49	-9999	-1.1	32	32
EGLN3	-0.014	0.49	-9999	-1.2	33	33
CA9	-0.045	0.52	-9999	-1.2	40	40
TERT	-0.08	0.51	-9999	-1.1	44	44
ENO1	-0.012	0.49	-9999	-1.1	33	33
PFKL	-0.012	0.49	-9999	-1.1	33	33
NCOA1	0.015	0.001	-9999	-10000	0	0
ADM	-0.048	0.52	-9999	-1.2	39	39
ARNT	0.016	0.089	-9999	-0.64	1	1
HNF4A	-0.044	0.14	-9999	-0.48	31	31
ADFP	-0.061	0.47	-9999	-1.1	40	40
SLC2A1	0.028	0.4	-9999	-0.88	22	22
LEP	-0.049	0.48	-9999	-1.1	34	34
HIF1A/ARNT/Cbp/p300	-0.15	0.35	-9999	-0.94	39	39
EPO	0.022	0.37	-9999	-0.97	16	16
CREBBP	0.036	0.17	-9999	-0.34	20	20
HIF1A/ARNT/Cbp/p300/HDAC7	-0.14	0.35	-9999	-0.96	35	35
PFKFB3	-0.013	0.49	-9999	-1.1	33	33
NT5E	-0.019	0.5	-9999	-1.1	38	38

×

TCGA08_p53

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
CDKN2A	-0.076	0.18	-10000	0	-0.42	74	74
TP53	-0.035	0.093	0.19	2	-0.44	11	13
Senescence	-0.035	0.093	0.19	2	-0.44	11	13
Apoptosis	-0.035	0.093	0.19	2	-0.44	11	13
Activated_Oncogenes	0	0	-10000	0	-10000	0	0
MDM2	0.049	0.1	0.25	72	-0.25	2	74
MDM4	0.005	0.068	-10000	0	-0.48	7	7

×

LPA receptor mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.05	0.11	-9999	-0.34	33	33
NF kappa B1 p50/RelA/I kappa B alpha	-0.041	0.089	-9999	-0.4	9	9
AP1	-0.12	0.17	-9999	-0.44	47	47
mol:PIP3	-0.098	0.15	-9999	-0.47	33	33
AKT1	0.019	0.097	-9999	-0.34	7	7
PTK2B	-0.019	0.11	-9999	-0.33	25	25
RHOA	0.006	0.066	-9999	-0.32	6	6
PIK3CB	0.014	0.001	-9999	-10000	0	0
mol:Ca2+	0.004	0.088	-9999	-0.35	7	7
MAGI3	0.002	0.085	-9999	-0.6	7	7
RELA	0.014	0	-9999	-10000	0	0
apoptosis	-0.042	0.13	-9999	-0.35	40	40
HRAS/GDP	-0.001	0.018	-9999	-0.34	1	1
positive regulation of microtubule depolymerization	-0.008	0.11	-9999	-0.35	18	18
NF kappa B1 p50/RelA	-0.069	0.13	-9999	-0.5	17	17
endothelial cell migration	-0.05	0.18	-9999	-0.42	66	66
ADCY4	-0.022	0.15	-9999	-0.42	37	37
ADCY5	-0.026	0.16	-9999	-0.43	41	41
ADCY6	-0.019	0.15	-9999	-0.41	37	37
ADCY7	-0.019	0.15	-9999	-0.41	37	37
ADCY1	-0.048	0.17	-9999	-0.44	45	45
ADCY2	-0.026	0.16	-9999	-0.44	40	40
ADCY3	-0.019	0.15	-9999	-0.41	37	37
ADCY8	-0.044	0.19	-9999	-0.49	42	42
ADCY9	-0.02	0.15	-9999	-0.41	37	37
GSK3B	-0.01	0.1	-9999	-0.34	18	18
arachidonic acid secretion	-0.012	0.14	-9999	-0.38	37	37
GNG2	0.009	0.056	-9999	-0.6	3	3
TRIP6	0.006	0.068	-9999	-0.41	4	4
GNAO1	-0.036	0.14	-9999	-0.35	57	57
HRAS	0.013	0.026	-9999	-0.48	1	1
NFKBIA	-0.011	0.12	-9999	-0.42	15	15
GAB1	0.011	0.041	-9999	-0.54	2	2
mol:GTP	0	0	-9999	-10000	0	0
lamellipodium assembly	-0.005	0.097	-9999	-1	3	3
JUN	0.003	0.075	-9999	-0.5	8	8
LPA/LPA2/NHERF2	-0.015	0.06	-9999	-0.31	13	13
TIAM1	-0.009	0.13	-9999	-1.3	3	3
PIK3R1	0.014	0.001	-9999	-10000	0	0
mol:IP3	0.004	0.089	-9999	-0.36	7	7
PLCB3	0.015	0.06	-9999	-0.33	5	5
FOS	-0.087	0.22	-9999	-0.55	66	66
positive regulation of mitosis	-0.012	0.14	-9999	-0.38	37	37
LPA/LPA1-2-3	-0.081	0.14	-9999	-0.38	45	45
mol:Ca ++	0	0	-9999	-10000	0	0
JNK cascade	0	0	-9999	-10000	0	0
BCAR1	0.012	0.032	-9999	-0.6	1	1
stress fiber formation	-0.022	0.12	-9999	-0.32	31	31
GNAZ	-0.03	0.13	-9999	-0.33	53	53
EGFR/PI3K-beta/Gab1	-0.1	0.16	-9999	-0.49	33	33
positive regulation of dendritic cell cytokine production	-0.081	0.14	-9999	-0.38	45	45
LPA/LPA2/MAGI-3	-0.021	0.078	-9999	-0.36	17	17
ARHGEF1	-0.01	0.12	-9999	-0.32	31	31
GNAI2	-0.029	0.13	-9999	-0.33	52	52
GNAI3	-0.029	0.13	-9999	-0.33	52	52
GNAI1	-0.041	0.15	-9999	-0.35	63	63
LPA/LPA3	-0.04	0.11	-9999	-0.36	36	36
LPA/LPA2	-0.018	0.07	-9999	-0.39	11	11
LPA/LPA1	-0.066	0.15	-9999	-0.36	66	66
HB-EGF/EGFR	-0.14	0.21	-9999	-0.37	150	150
HBEGF	-0.1	0.19	-9999	-0.38	113	113
mol:DAG	0.004	0.089	-9999	-0.36	7	7
cAMP biosynthetic process	-0.024	0.16	-9999	-0.43	37	37
NFKB1	0.013	0.026	-9999	-0.48	1	1
SRC	0.014	0	-9999	-10000	0	0
GNB1	0.014	0.001	-9999	-10000	0	0
LYN	-0.013	0.12	-9999	-0.42	16	16
GNAQ	-0.011	0.085	-9999	-0.31	13	13
LPAR2	-0.003	0.095	-9999	-0.54	11	11
LPAR3	-0.042	0.14	-9999	-0.48	36	36
LPAR1	-0.061	0.19	-9999	-0.56	44	44
IL8	-0.18	0.23	-9999	-0.45	135	135
PTK2	-0.046	0.15	-9999	-0.36	43	43
Rac1/GDP	0	0	-9999	-10000	0	0
CASP3	-0.042	0.13	-9999	-0.35	40	40
EGFR	-0.082	0.21	-9999	-0.55	62	62
PLCG1	-0.011	0.091	-9999	-0.29	19	19
PLD2	-0.046	0.15	-9999	-0.36	43	43
G12/G13	-0.049	0.11	-9999	-0.35	31	31
PI3K-beta	-0.038	0.085	-9999	-0.39	8	8
cell migration	-0.027	0.056	-9999	-0.24	9	9
SLC9A3R2	0.011	0.037	-9999	-0.48	2	2
PXN	-0.023	0.12	-9999	-0.34	29	29
HRAS/GTP	-0.013	0.15	-9999	-0.39	37	37
RAC1	0.014	0	-9999	-10000	0	0
MMP9	-0.15	0.25	-9999	-0.52	111	111
PRKCE	0.002	0.079	-9999	-0.52	8	8
PRKCD	-0.003	0.11	-9999	-0.4	13	13
Gi(beta/gamma)	-0.015	0.14	-9999	-0.38	38	38
mol:LPA	-0.006	0.041	-9999	-0.2	8	8
TRIP6/p130 Cas/FAK1/Paxillin	-0.066	0.13	-9999	-0.43	21	21
MAPKKK cascade	-0.012	0.14	-9999	-0.38	37	37
contractile ring contraction involved in cytokinesis	0.006	0.066	-9999	-0.32	6	6
mol:GDP	0	0	-9999	-10000	0	0
GNA14	-0.021	0.098	-9999	-0.31	22	22
GNA15	-0.022	0.1	-9999	-0.31	24	24
GNA12	0.012	0.032	-9999	-0.6	1	1
GNA13	0.014	0	-9999	-10000	0	0
MAPT	-0.008	0.11	-9999	-0.36	18	18
GNA11	-0.018	0.099	-9999	-0.33	20	20
Rac1/GTP	-0.006	0.11	-9999	-1.1	3	3
MMP2	-0.05	0.18	-9999	-0.42	66	66

×

PLK1 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
regulation of centriole-centriole cohesion	0.038	0.095	0.2	83	-10000	0	83
BUB1B	-0.057	0.14	-10000	0	-0.3	89	89
PLK1	0	0.041	-10000	0	-0.13	18	18
PLK1S1	0.006	0.021	-10000	0	-10000	0	0
KIF2A	0.006	0.049	-10000	0	-0.32	4	4
regulation of mitotic centrosome separation	0	0.041	-10000	0	-0.12	18	18
GOLGA2	0.014	0	-10000	0	-10000	0	0
Hec1/SPC24	-0.13	0.23	-10000	0	-0.42	127	127
WEE1	-0.005	0.086	-10000	0	-0.35	14	14
cytokinesis	-0.11	0.21	-10000	0	-0.43	95	95
PP2A-alpha B56	-0.065	0.23	-10000	0	-0.66	46	46
AURKA	0.002	0.039	-10000	0	-0.15	14	14
PICH/PLK1	-0.024	0.15	-10000	0	-0.43	34	34
CENPE	-0.036	0.13	-10000	0	-0.32	57	57
RhoA/GTP	0	0	-10000	0	-10000	0	0
positive regulation of microtubule depolymerization	0.006	0.049	-10000	0	-0.32	4	4
PPP2CA	0.014	0	-10000	0	-10000	0	0
FZR1	0.014	0	-10000	0	-10000	0	0
TPX2	-0.02	0.082	-10000	0	-0.21	50	50
PAK1	-0.038	0.15	-10000	0	-0.49	38	38
SPC24	-0.12	0.24	-10000	0	-0.54	88	88
FBXW11	0.014	0	-10000	0	-10000	0	0
CLSPN	-0.033	0.1	-10000	0	-0.25	57	57
GORASP1	0.014	0	-10000	0	-10000	0	0
metaphase	0	0.004	-10000	0	-0.013	22	22
mol:GTP	0	0	-10000	0	-10000	0	0
NLP	0	0.021	-10000	0	-0.063	16	16
G2 phase of mitotic cell cycle	0	0.002	-10000	0	-0.009	8	8
STAG2	0.014	0	-10000	0	-10000	0	0
GRASP65/GM130/RAB1/GTP	0.004	0.01	-10000	0	-10000	0	0
spindle elongation	0	0.041	-10000	0	-0.12	18	18
ODF2	0.013	0.003	-10000	0	-10000	0	0
BUB1	-0.1	0.24	-10000	0	-0.73	46	46
TPT1	0.006	0.021	-10000	0	-10000	0	0
CDC25C	-0.05	0.14	-10000	0	-0.34	55	55
CDC25B	0.014	0.003	-10000	0	-10000	0	0
SGOL1	-0.038	0.095	-10000	0	-0.2	83	83
RHOA	0.014	0	-10000	0	-10000	0	0
CCNB1/CDK1	-0.024	0.08	-10000	0	-0.32	17	17
CDC14B	0.012	0.001	-10000	0	-10000	0	0
CDC20	-0.093	0.22	-10000	0	-0.54	70	70
PLK1/PBIP1	-0.05	0.12	-10000	0	-0.32	53	53
mitosis	0.001	0.004	0.021	8	-10000	0	8
FBXO5	0.005	0.044	-10000	0	-0.24	5	5
CDC2	0	0.004	-10000	0	-0.014	20	20
NDC80	-0.13	0.25	-10000	0	-0.55	94	94
metaphase plate congression	0.006	0.025	-10000	0	-0.14	1	1
ERCC6L	-0.049	0.13	-10000	0	-0.43	32	32
NLP/gamma Tubulin	0.004	0.024	-10000	0	-0.1	1	1
microtubule cytoskeleton organization	0.006	0.021	-10000	0	-10000	0	0
G2/M transition DNA damage checkpoint	0	0.002	0.01	3	-10000	0	3
PPP1R12A	0.014	0.001	-10000	0	-10000	0	0
interphase	0	0.002	0.01	3	-10000	0	3
PLK1/PRC1-2	-0.087	0.18	-10000	0	-0.34	116	116
GRASP65/GM130/RAB1/GTP/PLK1	-0.004	0.021	-10000	0	-10000	0	0
RAB1A	0.014	0	-10000	0	-10000	0	0
prophase	0	0	-10000	0	-10000	0	0
Aurora A/BORA	0.007	0.033	-10000	0	-0.19	1	1
mitotic prometaphase	-0.001	0.002	-10000	0	-0.01	13	13
proteasomal ubiquitin-dependent protein catabolic process	0.008	0.06	-10000	0	-10000	0	0
microtubule-based process	-0.092	0.17	-10000	0	-0.33	116	116
Golgi organization	0	0.041	-10000	0	-0.12	18	18
Cohesin/SA2	-0.011	0.027	-10000	0	-0.22	1	1
PPP1CB/MYPT1	0.004	0.009	-10000	0	-10000	0	0
KIF20A	-0.17	0.27	-10000	0	-0.56	116	116
APC/C/CDC20	-0.051	0.14	-10000	0	-0.34	70	70
PPP2R1A	0.014	0	-10000	0	-10000	0	0
chromosome segregation	-0.049	0.11	-10000	0	-0.32	53	53
PRC1	-0.002	0.088	-10000	0	-0.48	12	12
ECT2	0	0.07	-10000	0	-0.33	13	13
C13orf34	0.006	0.034	-10000	0	-0.19	1	1
NUDC	0.006	0.025	-10000	0	-0.14	1	1
regulation of attachment of spindle microtubules to kinetochore	-0.057	0.14	-10000	0	-0.3	89	89
spindle assembly	0.003	0.033	-10000	0	-0.098	15	15
spindle stabilization	0.006	0.021	-10000	0	-10000	0	0
APC/C/HCDH1	0.02	0.001	-10000	0	-10000	0	0
MKLP2/PLK1	-0.092	0.17	-10000	0	-0.34	116	116
CCNB1	-0.012	0.11	-10000	0	-0.48	19	19
PPP1CB	0.014	0.001	-10000	0	-10000	0	0
BTRC	0.014	0	-10000	0	-10000	0	0
ROCK2	-0.006	0.094	-10000	0	-0.44	15	15
TUBG1	0.006	0.021	-10000	0	-10000	0	0
G2/M transition of mitotic cell cycle	-0.026	0.078	-10000	0	-0.32	17	17
MLF1IP	-0.048	0.15	-10000	0	-0.4	53	53
INCENP	0.012	0.005	-10000	0	-10000	0	0

×

IL1-mediated signaling events

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
UBC13/UEV1A	-0.002	0.025	-10000	0	-0.33	2	2
PRKCZ	-0.01	0.12	-10000	0	-0.56	15	15
MAP3K7IP2	0	0	-10000	0	-10000	0	0
ERC1	0.013	0.026	-10000	0	-0.48	1	1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4	-0.076	0.12	-10000	0	-0.43	19	19
IRAK/TOLLIP	0.031	0.02	-10000	0	-10000	0	0
IKBKB	0.014	0	-10000	0	-10000	0	0
IKBKG	0.014	0	-10000	0	-10000	0	0
IL1 alpha/IL1R2	-0.17	0.22	-10000	0	-0.42	152	152
IL1A	-0.1	0.23	-10000	0	-0.54	79	79
IL1B	-0.13	0.22	-10000	0	-0.4	136	136
IRAK/TRAF6/p62/Atypical PKCs	-0.012	0.054	-10000	0	-0.41	1	1
IL1R2	-0.12	0.24	-10000	0	-0.53	91	91
IL1R1	-0.022	0.13	-10000	0	-0.52	25	25
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.041	0.12	0.22	1	-0.42	14	15
TOLLIP	0.014	0	-10000	0	-10000	0	0
TICAM2	-0.002	0.097	-10000	0	-0.58	10	10
MAP3K3	0.014	0	-10000	0	-10000	0	0
TAK1/TAB1/TAB2	0	0	-10000	0	-10000	0	0
IKK complex/ELKS	0.065	0.032	-10000	0	-10000	0	0
JUN	0.034	0.072	-10000	0	-0.48	3	3
MAP3K7	0.014	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/PI3K	-0.13	0.17	-10000	0	-0.54	30	30
IL1 alpha/IL1R1/IL1RAP/MYD88	-0.1	0.16	-10000	0	-0.38	60	60
PIK3R1	0.014	0	-10000	0	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4	-0.097	0.14	-10000	0	-0.5	16	16
IL1 beta fragment/IL1R1/IL1RAP	-0.13	0.21	-10000	0	-0.42	84	84
NFKB1	0.013	0.026	-10000	0	-0.48	1	1
MAPK8	0.032	0.062	-10000	0	-0.56	1	1
IRAK1	0.024	0.023	-10000	0	-10000	0	0
IL1RN/IL1R1	-0.11	0.19	-10000	0	-0.4	103	103
IRAK4	0.013	0.026	-10000	0	-0.48	1	1
PRKCI	0.014	0	-10000	0	-10000	0	0
TRAF6	0.012	0.032	-10000	0	-0.6	1	1
PI3K	-0.001	0.023	-10000	0	-0.44	1	1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.06	0.14	-10000	0	-0.48	19	19
CHUK	0.014	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s	-0.13	0.21	-10000	0	-0.42	84	84
IL1 beta/IL1R2	-0.19	0.22	-10000	0	-0.38	196	196
IRAK/TRAF6/TAK1/TAB1/TAB2	-0.002	0.021	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.12	0.15	-10000	0	-0.49	30	30
IRAK3	0.006	0.069	-10000	0	-0.58	5	5
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4	-0.14	0.18	-10000	0	-0.54	36	36
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.04	0.12	-10000	0	-0.36	13	13
IL1 alpha/IL1R1/IL1RAP	-0.12	0.17	-10000	0	-0.42	58	58
RELA	0.014	0	-10000	0	-10000	0	0
MAP3K7IP1	0	0	-10000	0	-10000	0	0
SQSTM1	0.014	0	-10000	0	-10000	0	0
MYD88	0.008	0.061	-10000	0	-0.57	4	4
IRAK/TRAF6/MEKK3	0.038	0.026	-10000	0	-10000	0	0
IL1RAP	-0.033	0.15	-10000	0	-0.51	33	33
UBE2N	0.014	0	-10000	0	-10000	0	0
IRAK/TRAF6	-0.11	0.15	-10000	0	-0.49	26	26
CASP1	-0.01	0.11	-10000	0	-0.53	16	16
IL1RN/IL1R2	-0.18	0.24	-10000	0	-0.46	143	143
IL1 beta fragment/IL1R1/IL1RAP/MYD88	-0.12	0.2	-10000	0	-0.57	33	33
TMEM189-UBE2V1	0.005	0.037	-10000	0	-0.48	2	2
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.02	0.11	-10000	0	-0.37	13	13
PIK3CA	0.012	0.032	-10000	0	-0.6	1	1
IL1RN	-0.11	0.23	-10000	0	-0.53	86	86
TRAF6/TAK1/TAB1/TAB2	-0.002	0.022	-10000	0	-0.3	1	1
MAP2K6	0.034	0.029	-10000	0	-0.29	1	1

×

Nephrin/Neph1 signaling in the kidney podocyte

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
positive regulation of NF-kappaB transcription factor activity	0.067	0.16	0.4	60	-10000	0	60
KIRREL	-0.039	0.17	-10000	0	-0.6	30	30
Nephrin/NEPH1Par3/Par6/Atypical PKCs	-0.067	0.16	-10000	0	-0.41	60	60
PLCG1	0.014	0	-10000	0	-10000	0	0
ARRB2	0.014	0	-10000	0	-10000	0	0
WASL	0.014	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/CD2AP	-0.049	0.11	-10000	0	-0.34	34	34
ChemicalAbstracts:57-88-5	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP	-0.008	0.1	-10000	0	-0.29	32	32
FYN	-0.028	0.11	-10000	0	-0.33	34	34
mol:Ca2+	-0.049	0.11	-10000	0	-0.34	34	34
mol:DAG	-0.049	0.11	-10000	0	-0.34	34	34
NPHS2	-0.008	0.045	-10000	0	-0.54	2	2
mol:IP3	-0.049	0.11	-10000	0	-0.34	34	34
regulation of endocytosis	-0.018	0.11	-10000	0	-0.3	34	34
Nephrin/NEPH1/podocin/Cholesterol	-0.05	0.12	-10000	0	-0.3	57	57
establishment of cell polarity	-0.067	0.16	-10000	0	-0.4	60	60
Nephrin/NEPH1/podocin/NCK1-2	-0.044	0.1	-10000	0	-0.42	8	8
Nephrin/NEPH1/beta Arrestin2	-0.017	0.11	-10000	0	-0.3	34	34
NPHS1	-0.038	0.15	-10000	0	-0.5	33	33
Nephrin/NEPH1/podocin	-0.031	0.11	-10000	0	-0.33	34	34
TJP1	0.014	0	-10000	0	-10000	0	0
NCK1	0.012	0.032	-10000	0	-0.6	1	1
NCK2	0.014	0	-10000	0	-10000	0	0
heterophilic cell adhesion	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/PLCgamma1	-0.049	0.11	-10000	0	-0.34	34	34
CD2AP	0.014	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/GRB2	-0.049	0.11	-10000	0	-0.34	34	34
GRB2	0.014	0	-10000	0	-10000	0	0
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
TRPC6	-0.047	0.14	-10000	0	-0.33	46	46
cytoskeleton organization	-0.008	0.12	-10000	0	-0.34	32	32
Nephrin/NEPH1	-0.047	0.11	-10000	0	-0.29	60	60
Nephrin/NEPH1/ZO-1	-0.052	0.12	-10000	0	-0.37	33	33

×

Retinoic acid receptors-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.011	0.046	-10000	0	-0.6	2	2
HDAC3	0.014	0	-10000	0	-10000	0	0
VDR	-0.061	0.19	-10000	0	-0.53	50	50
Cbp/p300/PCAF	-0.005	0.041	-10000	0	-0.36	4	4
EP300	0.007	0.064	-10000	0	-0.6	4	4
RARs/AIB1/Cbp/p300/PCAF/9cRA	0.012	0.069	-10000	0	-0.44	4	4
KAT2B	0.013	0.026	-10000	0	-0.48	1	1
MAPK14	0.014	0	-10000	0	-10000	0	0
AKT1	0.004	0.069	0.22	3	-0.3	3	6
RAR alpha/9cRA/Cyclin H	-0.055	0.089	-10000	0	-0.92	1	1
mol:9cRA	0	0	-10000	0	-10000	0	0
RARs/Src-1/Cbp/p300/PCAF/9cRA	0.01	0.061	-10000	0	-0.35	4	4
CDC2	0.001	0	-10000	0	-10000	0	0
response to UV	0.001	0	-10000	0	-10000	0	0
RAR alpha/Jnk1	-0.068	0.11	-10000	0	-0.54	10	10
NCOR2	0.014	0	-10000	0	-10000	0	0
VDR/VDR/Vit D3	-0.053	0.14	-10000	0	-0.39	50	50
RXRs/RARs/NRIP1/9cRA	-0.066	0.2	-10000	0	-0.45	65	65
NCOA2	-0.035	0.17	-10000	0	-0.6	29	29
NCOA3	0.014	0	-10000	0	-10000	0	0
NCOA1	0.014	0	-10000	0	-10000	0	0
VDR/VDR/DNA	-0.061	0.19	-10000	0	-0.53	50	50
RARG	0.014	0.026	-10000	0	-0.48	1	1
RAR gamma1/9cRA	-0.001	0.015	-10000	0	-0.28	1	1
MAPK3	0.015	0	-10000	0	-10000	0	0
MAPK1	0.014	0	-10000	0	-10000	0	0
MAPK8	-0.002	0.1	-10000	0	-0.6	10	10
mol:Vit D3	0	0	-10000	0	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.15	0.22	-10000	0	-0.55	71	71
RARA	-0.056	0.12	-10000	0	-0.26	74	74
negative regulation of phosphoinositide 3-kinase cascade	0	0	-10000	0	-10000	0	0
RARs/TIF2/Cbp/p300/PCAF/9cRA	-0.01	0.11	-10000	0	-0.4	15	15
PRKCA	0.016	0.032	-10000	0	-0.6	1	1
RXRs/RARs/NRIP1/9cRA/HDAC1	-0.078	0.2	-10000	0	-0.46	65	65
RXRG	-0.13	0.22	-10000	0	-0.45	90	90
RXRA	-0.04	0.11	-10000	0	-0.22	74	74
RXRB	-0.08	0.16	-10000	0	-0.35	65	65
VDR/Vit D3/DNA	-0.053	0.14	-10000	0	-0.39	50	50
RBP1	-0.066	0.18	-10000	0	-0.49	58	58
CRBP1/9-cic-RA	-0.056	0.13	-10000	0	-0.35	58	58
RARB	0.013	0.046	-10000	0	-0.6	2	2
PRKCG	-0.2	0.27	-10000	0	-0.53	142	142
MNAT1	0.013	0.026	-10000	0	-0.48	1	1
RAR alpha/RXRs	-0.07	0.21	-10000	0	-0.48	65	65
RXRs/RARs/SMRT(N-CoR2)/9cRA	-0.053	0.17	-10000	0	-0.38	65	65
proteasomal ubiquitin-dependent protein catabolic process	-0.011	0.1	-10000	0	-0.43	5	5
RXRs/RARs/NRIP1/9cRA/HDAC3	-0.078	0.2	-10000	0	-0.46	65	65
positive regulation of DNA binding	-0.052	0.084	-10000	0	-0.82	1	1
NRIP1	-0.069	0.18	-10000	0	-0.6	18	18
RXRs/RARs	-0.085	0.2	-10000	0	-0.46	67	67
RXRs/RXRs/DNA/9cRA	-0.13	0.2	-10000	0	-0.52	65	65
PRKACA	0.014	0	-10000	0	-10000	0	0
CDK7	0.014	0	-10000	0	-10000	0	0
TFIIH	-0.001	0.014	-10000	0	-0.27	1	1
RAR alpha/9cRA	-0.039	0.067	-10000	0	-0.8	1	1
CCNH	0.014	0	-10000	0	-10000	0	0
CREBBP	0.014	0	-10000	0	-10000	0	0
RAR gamma2/9cRA	-0.001	0.014	-10000	0	-10000	0	0

×

BMP receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS	-0.061	0.13	-9999	-0.34	52	52
SMAD6-7/SMURF1	-0.004	0.036	-9999	-0.34	4	4
NOG	-0.062	0.2	-9999	-0.59	46	46
SMAD9	-0.037	0.18	-9999	-0.59	30	30
SMAD4	0.014	0	-9999	-10000	0	0
SMAD5	-0.003	0.12	-9999	-0.47	13	13
BMP7/USAG1	-0.094	0.17	-9999	-0.38	91	91
SMAD5/SKI	0.005	0.12	-9999	-0.45	12	12
SMAD1	0.043	0.032	-9999	-0.32	1	1
BMP2	-0.079	0.22	-9999	-0.6	55	55
SMAD1/SMAD1/SMAD4	-0.004	0.026	-9999	-10000	0	0
BMPR1A	0.014	0	-9999	-10000	0	0
BMPR1B	-0.026	0.15	-9999	-0.6	24	24
BMPR1A-1B/BAMBI	-0.028	0.099	-9999	-0.37	28	28
AHSG	-0.086	0.22	-9999	-0.55	64	64
CER1	-0.011	0.091	-9999	-0.48	13	13
BMP2-4/CER1	-0.08	0.19	-9999	-0.48	57	57
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA	-0.015	0.16	-9999	-0.47	27	27
BMP2-4 (homodimer)	-0.082	0.2	-9999	-0.52	58	58
RGMB	0.002	0.082	-9999	-0.54	8	8
BMP6/BMPR2/BMPR1A-1B	-0.031	0.098	-9999	-0.35	27	27
RGMA	-0.002	0.099	-9999	-0.59	10	10
SMURF1	0.014	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP	-0.022	0.15	-9999	-0.46	27	27
BMP2-4/USAG1	-0.14	0.22	-9999	-0.49	82	82
SMAD6/SMURF1/SMAD5	0.005	0.12	-9999	-0.45	12	12
SOSTDC1	-0.11	0.23	-9999	-0.52	86	86
BMP7/BMPR2/BMPR1A-1B	-0.027	0.089	-9999	-0.32	30	30
SKI	0.014	0	-9999	-10000	0	0
BMP6 (homodimer)	-0.006	0.1	-9999	-0.52	14	14
HFE2	0.005	0.052	-9999	-0.48	4	4
ZFYVE16	0.014	0	-9999	-10000	0	0
MAP3K7	0.014	0	-9999	-10000	0	0
BMP2-4/CHRD	-0.072	0.17	-9999	-0.44	59	59
SMAD5/SMAD5/SMAD4	0.005	0.12	-9999	-0.45	12	12
MAPK1	0.014	0	-9999	-10000	0	0
TAK1/TAB family	-0.048	0.11	-9999	-0.4	25	25
BMP7 (homodimer)	0.004	0.078	-9999	-0.6	6	6
NUP214	0.014	0	-9999	-10000	0	0
BMP6/FETUA	-0.082	0.17	-9999	-0.41	74	74
SMAD1/SKI	0.049	0.03	-9999	-10000	0	0
SMAD6	0.008	0.061	-9999	-0.57	4	4
CTDSP2	0.01	0.045	-9999	-0.48	3	3
BMP2-4/FETUA	-0.13	0.22	-9999	-0.48	81	81
MAP3K7IP1	0	0	-9999	-10000	0	0
GREM1	-0.17	0.27	-9999	-0.55	120	120
BMPR2 (homodimer)	0.014	0	-9999	-10000	0	0
GADD34/PP1CA	-0.004	0.035	-9999	-0.27	6	6
BMPR1A-1B (homodimer)	-0.029	0.11	-9999	-0.44	24	24
CHRDL1	-0.074	0.21	-9999	-0.58	54	54
ENDOFIN/SMAD1	0.049	0.03	-9999	-10000	0	0
SMAD6-7/SMURF1/SMAD1	-0.003	0.03	-9999	-10000	0	0
SMAD6/SMURF1	0.014	0	-9999	-10000	0	0
BAMBI	0.007	0.064	-9999	-0.53	5	5
SMURF2	0.011	0.046	-9999	-0.6	2	2
BMP2-4/CHRDL1	-0.12	0.21	-9999	-0.44	97	97
BMP2-4/GREM1	-0.18	0.23	-9999	-0.46	117	117
SMAD7	0.014	0	-9999	-10000	0	0
SMAD8A/SMAD8A/SMAD4	-0.027	0.17	-9999	-0.55	30	30
SMAD1/SMAD6	0.049	0.03	-9999	-10000	0	0
TAK1/SMAD6	0	0	-9999	-10000	0	0
BMP7	0.004	0.078	-9999	-0.6	6	6
BMP6	-0.006	0.1	-9999	-0.52	14	14
MAP3K7IP2	0	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1	-0.015	0.14	-9999	-0.41	27	27
PPM1A	0.014	0	-9999	-10000	0	0
SMAD1/SMURF2	0.047	0.039	-9999	-0.31	2	2
SMAD7/SMURF1	0	0	-9999	-10000	0	0
CTDSPL	0.012	0.032	-9999	-0.6	1	1
PPP1CA	0.014	0	-9999	-10000	0	0
XIAP	0.014	0	-9999	-10000	0	0
CTDSP1	0.014	0	-9999	-10000	0	0
PPP1R15A	0.006	0.063	-9999	-0.48	6	6
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS	-0.053	0.19	-9999	-0.49	39	39
CHRD	0.011	0.046	-9999	-0.6	2	2
BMPR2	0.014	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM	-0.03	0.16	-9999	-0.5	27	27
BMP4	-0.013	0.12	-9999	-0.6	16	16
FST	-0.064	0.19	-9999	-0.54	52	52
BMP2-4/NOG	-0.11	0.25	-9999	-0.59	66	66
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1	-0.024	0.082	-9999	-0.3	30	30

×

Nongenotropic Androgen signaling

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
PTK2	0.012	0	-10000	0	-10000	0	0
GNB1/GNG2	-0.06	0.13	-10000	0	-0.33	56	56
regulation of S phase of mitotic cell cycle	-0.017	0.1	-10000	0	-0.26	54	54
GNAO1	0.004	0.078	-10000	0	-0.6	6	6
HRAS	0.013	0.026	-10000	0	-0.48	1	1
SHBG/T-DHT	-0.004	0.043	-10000	0	-0.36	5	5
PELP1	0.014	0.001	-10000	0	-10000	0	0
AKT1	0.012	0	-10000	0	-10000	0	0
MAP2K1	-0.02	0.13	-10000	0	-0.38	17	17
T-DHT/AR	-0.08	0.17	-10000	0	-0.42	70	70
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
mol:GTP	-0.001	0.002	-10000	0	-0.006	60	60
GNAI2	0.014	0	-10000	0	-10000	0	0
GNAI3	0.014	0	-10000	0	-10000	0	0
GNAI1	-0.004	0.1	-10000	0	-0.6	11	11
mol:GDP	-0.076	0.16	-10000	0	-0.46	53	53
cell proliferation	-0.031	0.18	-10000	0	-0.55	17	17
PIK3CA	0.012	0.032	-10000	0	-0.6	1	1
FOS	-0.072	0.27	-10000	0	-0.78	40	40
mol:Ca2+	-0.011	0.02	-10000	0	-0.064	24	24
MAPK3	-0.024	0.15	-10000	0	-0.47	17	17
MAPK1	-0.01	0.089	-10000	0	-0.27	14	14
PIK3R1	0.014	0	-10000	0	-10000	0	0
mol:IP3	0	0.002	-10000	0	-0.004	66	66
cAMP biosynthetic process	0.005	0.045	-10000	0	-0.33	5	5
GNG2	0.009	0.056	-10000	0	-0.6	3	3
potassium channel inhibitor activity	0	0.002	-10000	0	-0.004	66	66
HRAS/GTP	-0.057	0.12	-10000	0	-0.31	55	55
actin cytoskeleton reorganization	-0.001	0.015	-10000	0	-0.29	1	1
SRC	0.014	0.001	-10000	0	-10000	0	0
voltage-gated calcium channel activity	0	0.002	-10000	0	-0.004	66	66
PI3K	0	0.02	-10000	0	-0.37	1	1
apoptosis	0.03	0.16	0.43	40	-10000	0	40
T-DHT/AR/PELP1	-0.067	0.14	-10000	0	-0.36	70	70
HRAS/GDP	-0.071	0.16	-10000	0	-0.43	53	53
CREB1	-0.034	0.17	-10000	0	-0.46	40	40
RAC1-CDC42/GTP	-0.001	0.015	-10000	0	-0.29	1	1
AR	-0.099	0.23	-10000	0	-0.57	70	70
GNB1	0.014	0	-10000	0	-10000	0	0
RAF1	-0.025	0.13	-10000	0	-0.35	17	17
RAC1-CDC42/GDP	-0.065	0.14	-10000	0	-0.41	53	53
T-DHT/AR/PELP1/Src	-0.059	0.13	-10000	0	-0.33	58	58
MAP2K2	-0.019	0.13	-10000	0	-0.36	17	17
T-DHT/AR/PELP1/Src/PI3K	-0.018	0.11	-10000	0	-0.26	54	54
GNAZ	0.012	0.032	-10000	0	-0.6	1	1
SHBG	0.006	0.069	-10000	0	-0.58	5	5
Gi family/GNB1/GNG2/GDP	0.018	0.086	-10000	0	-0.47	7	7
mol:T-DHT	0	0.001	-10000	0	-0.003	21	21
RAC1	0.014	0	-10000	0	-10000	0	0
GNRH1	0.003	0.06	-10000	0	-0.4	8	8
Gi family/GTP	-0.013	0.085	-10000	0	-0.37	6	6
CDC42	0.014	0	-10000	0	-10000	0	0

×

PLK2 and PLK4 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
PLK2	-0.016	0.12	-9999	-0.5	21	21
PLK4	-0.005	0.099	-9999	-0.5	14	14
regulation of centriole replication	-0.011	0.12	-9999	-0.37	33	33

×

Paxillin-independent events mediated by a4b1 and a4b7

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
PTK2	-0.032	0.14	-9999	-0.38	45	45
CRKL	0.014	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
DOCK1	0.009	0.056	-9999	-0.6	3	3
ITGA4	-0.048	0.18	-9999	-0.53	42	42
alpha4/beta7 Integrin/MAdCAM1	-0.13	0.18	-9999	-0.41	79	79
EPO	-0.01	0.1	-9999	-0.48	16	16
alpha4/beta7 Integrin	-0.08	0.17	-9999	-0.44	67	67
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.014	0	-9999	-10000	0	0
alpha4/beta1 Integrin	-0.045	0.13	-9999	-0.39	42	42
EPO/EPOR (dimer)	-0.016	0.076	-9999	-0.35	17	17
lamellipodium assembly	0.009	0.023	-9999	-10000	0	0
PIK3CA	0.012	0.032	-9999	-0.6	1	1
PI3K	-0.001	0.023	-9999	-0.44	1	1
ARF6	0.014	0	-9999	-10000	0	0
JAK2	0	0.09	-9999	-0.3	4	4
PXN	0.014	0	-9999	-10000	0	0
PIK3R1	0.014	0	-9999	-10000	0	0
MADCAM1	-0.12	0.24	-9999	-0.54	87	87
cell adhesion	-0.12	0.18	-9999	-0.4	79	79
CRKL/CBL	0	0	-9999	-10000	0	0
ITGB1	0.011	0.037	-9999	-0.48	2	2
SRC	-0.088	0.18	-9999	-0.35	88	88
ITGB7	-0.041	0.17	-9999	-0.54	36	36
RAC1	0.014	0	-9999	-10000	0	0
alpha4/beta1 Integrin/VCAM1	-0.13	0.18	-9999	-0.4	88	88
p130Cas/Crk/Dock1	-0.055	0.16	-9999	-0.51	11	11
VCAM1	-0.14	0.26	-9999	-0.57	97	97
RHOA	0.014	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/GIT1	-0.033	0.093	-9999	-0.34	19	19
BCAR1	-0.075	0.17	-9999	-0.56	10	10
EPOR	0.011	0.037	-9999	-0.48	2	2
mol:GDP	0	0	-9999	-10000	0	0
CBL	0.014	0	-9999	-10000	0	0
GIT1	0.014	0	-9999	-10000	0	0
Rac1/GTP	0.009	0.024	-9999	-10000	0	0

×

RXR and RAR heterodimerization with other nuclear receptor

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	-0.001	0.17	-9999	-1.3	6	6
VDR	-0.061	0.19	-9999	-0.53	50	50
FAM120B	0.014	0	-9999	-10000	0	0
RXRs/LXRs/DNA/9cRA	-0.044	0.16	-9999	-0.47	19	19
RXRs/LXRs/DNA/Oxysterols	-0.071	0.22	-9999	-0.46	64	64
MED1	0.014	0	-9999	-10000	0	0
mol:9cRA	-0.008	0.024	-9999	-10000	0	0
RARs/THRs/DNA/Src-1	0.027	0.056	-9999	-10000	0	0
RXRs/NUR77	-0.037	0.15	-9999	-0.35	55	55
RXRs/PPAR	-0.016	0.12	-9999	-0.29	49	49
NCOR2	0.014	0	-9999	-10000	0	0
VDR/VDR/Vit D3	-0.053	0.14	-9999	-0.39	50	50
RARs/VDR/DNA/Vit D3	-0.038	0.095	-9999	-0.32	23	23
RARA	0.014	0	-9999	-10000	0	0
NCOA1	0.014	0	-9999	-10000	0	0
VDR/VDR/DNA	-0.061	0.19	-9999	-0.53	50	50
RARs/RARs/DNA/9cRA	0.017	0.032	-9999	-0.29	3	3
RARG	0.013	0.026	-9999	-0.48	1	1
RPS6KB1	0.02	0.066	-9999	-0.4	6	6
RARs/THRs/DNA/SMRT	0.027	0.056	-9999	-10000	0	0
THRA	0.011	0.046	-9999	-0.6	2	2
mol:Bile acids	0	0	-9999	-10000	0	0
VDR/Vit D3/DNA	-0.053	0.14	-9999	-0.39	50	50
RXRs/PPAR/9cRA/PGJ2/DNA	-0.035	0.13	-9999	-0.35	44	44
NR1H4	-0.12	0.23	-9999	-0.52	91	91
RXRs/LXRs/DNA	-0.022	0.14	-9999	-0.44	15	15
NR1H2	0.011	0.017	-9999	-10000	0	0
NR1H3	0.01	0.02	-9999	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.055	0.16	-9999	-0.36	65	65
NR4A1	-0.023	0.13	-9999	-0.5	26	26
mol:ATRA	0	0	-9999	-10000	0	0
RXRs/FXR/9cRA/MED1	-0.064	0.14	-9999	-0.32	59	59
RXRG	-0.065	0.2	-9999	-0.6	45	45
RXR alpha/CCPG	0.017	0.013	-9999	-10000	0	0
RXRA	0.011	0.016	-9999	-10000	0	0
RXRB	0.009	0.019	-9999	-10000	0	0
THRB	-0.011	0.12	-9999	-0.53	17	17
PPARG	-0.013	0.12	-9999	-0.57	17	17
PPARD	0.014	0	-9999	-10000	0	0
TNF	-0.18	0.41	-9999	-1	57	57
mol:Oxysterols	-0.006	0.021	-9999	-10000	0	0
cholesterol transport	-0.07	0.22	-9999	-0.45	64	64
PPARA	0.014	0	-9999	-10000	0	0
mol:Vit D3	0	0	-9999	-10000	0	0
RARB	0.011	0.046	-9999	-0.6	2	2
RXRs/NUR77/BCL2	-0.024	0.12	-9999	-0.3	50	50
SREBF1	-0.074	0.27	-9999	-0.95	20	20
RXRs/RXRs/DNA/9cRA	-0.035	0.14	-9999	-0.35	44	44
ABCA1	-0.072	0.26	-9999	-0.9	20	20
RARs/THRs	-0.015	0.062	-9999	-10000	0	0
RXRs/FXR	-0.091	0.19	-9999	-0.39	82	82
BCL2	0.006	0.072	-9999	-0.6	5	5

×

Angiopoietin receptor Tie2-mediated signaling

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
AKT1	-0.079	0.28	-10000	0	-0.91	26	26
NCK1/PAK1/Dok-R	-0.094	0.13	-10000	0	-0.41	35	35
NCK1/Dok-R	-0.11	0.31	-10000	0	-1.1	25	25
PIK3CA	0.012	0.032	-10000	0	-0.6	1	1
mol:beta2-estradiol	0.015	0.063	0.22	22	-10000	0	22
RELA	0.014	0	-10000	0	-10000	0	0
SHC1	0.008	0.052	-10000	0	-0.48	4	4
Rac/GDP	0	0	-10000	0	-10000	0	0
F2	0.016	0.077	0.25	11	-0.44	3	14
TNIP2	0.014	0	-10000	0	-10000	0	0
NF kappa B/RelA	-0.1	0.26	-10000	0	-1	25	25
FN1	-0.002	0.088	-10000	0	-0.48	12	12
PLD2	-0.078	0.31	-10000	0	-1.1	25	25
PTPN11	0.014	0	-10000	0	-10000	0	0
GRB14	-0.17	0.26	-10000	0	-0.53	123	123
ELK1	-0.055	0.28	-10000	0	-1	25	25
GRB7	-0.036	0.14	-10000	0	-0.48	34	34
PAK1	-0.038	0.15	-10000	0	-0.49	38	38
Tie2/Ang1/alpha5/beta1 Integrin	-0.12	0.29	-10000	0	-1	29	29
CDKN1A	-0.099	0.29	-10000	0	-0.69	53	53
ITGA5	-0.011	0.11	-10000	0	-0.49	18	18
mol:GTP	0	0	-10000	0	-10000	0	0
RasGAP/Dok-R	-0.11	0.31	-10000	0	-1.1	25	25
CRK	0.014	0	-10000	0	-10000	0	0
mol:NO	-0.052	0.22	-10000	0	-0.66	27	27
PLG	-0.086	0.31	-10000	0	-1.2	25	25
mol:GDP	0	0	-10000	0	-10000	0	0
chemokinesis	-0.07	0.26	-10000	0	-0.86	27	27
GRB2	0.014	0	-10000	0	-10000	0	0
PIK3R1	0.014	0.002	-10000	0	-10000	0	0
ANGPT2	-0.1	0.27	-10000	0	-0.71	44	44
BMX	-0.11	0.32	-10000	0	-1.2	25	25
ANGPT1	-0.13	0.35	-10000	0	-1.3	24	24
tube development	-0.077	0.26	-10000	0	-0.66	42	42
ANGPT4	-0.047	0.18	-10000	0	-0.55	39	39
response to hypoxia	-0.007	0.021	-10000	0	-10000	0	0
Tie2/Ang1/GRB14	-0.17	0.35	-10000	0	-1.2	27	27
alpha5/beta1 Integrin	-0.019	0.082	-10000	0	-0.36	19	19
FGF2	0.01	0.052	-10000	0	-0.56	3	3
STAT5A (dimer)	-0.1	0.31	-10000	0	-0.76	48	48
mol:L-citrulline	-0.052	0.22	-10000	0	-0.66	27	27
AGTR1	-0.036	0.16	-10000	0	-0.55	32	32
MAPK14	-0.085	0.31	-10000	0	-1.1	25	25
Tie2/SHP2	-0.039	0.16	-10000	0	-1.1	6	6
TEK	-0.019	0.19	-10000	0	-1.2	7	7
RPS6KB1	-0.066	0.27	-10000	0	-0.86	26	26
Angiotensin II/AT1	-0.026	0.12	-10000	0	-0.41	32	32
Tie2/Ang1/GRB2	-0.081	0.32	-10000	0	-1.2	25	25
MAPK3	-0.062	0.29	-10000	0	-1	25	25
MAPK1	-0.062	0.29	-10000	0	-1	25	25
Tie2/Ang1/GRB7	-0.11	0.33	-10000	0	-1.2	26	26
NFKB1	0.013	0.026	-10000	0	-0.48	1	1
MAPK8	-0.086	0.32	-10000	0	-1.2	25	25
PI3K	-0.089	0.31	-10000	0	-1	26	26
FES	-0.085	0.31	-10000	0	-1.1	25	25
Crk/Dok-R	-0.11	0.31	-10000	0	-1.1	25	25
Tie2/Ang1/ABIN2	-0.081	0.32	-10000	0	-1.2	25	25
blood circulation	0	0	-10000	0	-10000	0	0
negative regulation of caspase activity	-0.069	0.26	-10000	0	-0.76	30	30
STAT5A	0	0.09	-10000	0	-0.6	8	8
mol:ROS	0	0	-10000	0	-10000	0	0
PTK2	-0.066	0.27	-10000	0	-0.86	26	26
Tie2/Ang2	-0.12	0.34	-10000	0	-0.91	42	42
Tie2/Ang1	-0.094	0.34	-10000	0	-1.3	25	25
FOXO1	-0.075	0.27	-10000	0	-0.76	37	37
ELF1	0.018	0.037	-10000	0	-0.65	1	1
ELF2	-0.082	0.31	-10000	0	-1.1	25	25
mol:Choline	-0.072	0.3	-10000	0	-1.1	25	25
cell migration	-0.053	0.072	-10000	0	-0.24	29	29
FYN	-0.09	0.29	-10000	0	-0.75	42	42
DOK2	-0.071	0.2	-10000	0	-0.53	57	57
negative regulation of cell cycle	-0.086	0.26	-10000	0	-0.62	54	54
ETS1	-0.005	0.079	-10000	0	-0.5	4	4
PXN	-0.045	0.23	-10000	0	-0.7	26	26
ITGB1	0.011	0.037	-10000	0	-0.48	2	2
NOS3	-0.062	0.25	-10000	0	-0.75	27	27
RAC1	0.014	0	-10000	0	-10000	0	0
TNF	-0.16	0.27	-10000	0	-0.56	109	109
MAPKKK cascade	-0.072	0.3	-10000	0	-1.1	25	25
RASA1	0.014	0	-10000	0	-10000	0	0
Tie2/Ang1/Shc	-0.086	0.33	-10000	0	-1.2	25	25
NCK1	0.012	0.032	-10000	0	-0.6	1	1
vasculogenesis	-0.044	0.2	-10000	0	-0.58	27	27
mol:Phosphatidic acid	-0.072	0.3	-10000	0	-1.1	25	25
mol:Angiotensin II	-0.001	0.007	-10000	0	-10000	0	0
mol:NADP	-0.052	0.22	-10000	0	-0.66	27	27
Rac1/GTP	-0.11	0.22	-10000	0	-0.8	26	26
MMP2	-0.096	0.32	-10000	0	-1.1	25	25

×

Syndecan-2-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Syndecan-2/Fibronectin	0.002	0.09	-9999	-0.31	27	27
EPHB2	0.001	0.084	-9999	-0.52	9	9
Syndecan-2/TACI	-0.011	0.084	-9999	-0.32	24	24
LAMA1	-0.054	0.19	-9999	-0.58	42	42
Syndecan-2/alpha2 ITGB1	-0.026	0.15	-9999	-0.37	39	39
HRAS	0.013	0.026	-9999	-0.48	1	1
Syndecan-2/CASK	-0.014	0.068	-9999	-0.33	16	16
ITGA5	-0.011	0.11	-9999	-0.49	18	18
BAX	0.02	0.085	-9999	-10000	0	0
EPB41	0.009	0.052	-9999	-0.56	3	3
positive regulation of cell-cell adhesion	-0.013	0.059	-9999	-0.29	16	16
LAMA3	-0.031	0.16	-9999	-0.56	29	29
EZR	0.004	0.078	-9999	-0.6	6	6
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
CAV2	-0.014	0.12	-9999	-0.49	20	20
Syndecan-2/MMP2	-0.011	0.11	-9999	-0.32	39	39
RP11-540L11.1	0	0	-9999	-10000	0	0
alpha2 ITGB1	-0.039	0.12	-9999	-0.38	37	37
dendrite morphogenesis	0.004	0.091	-9999	-0.34	23	23
Syndecan-2/GM-CSF	-0.013	0.068	-9999	-0.33	16	16
determination of left/right symmetry	0.004	0.084	-9999	-0.38	16	16
Syndecan-2/PKC delta	-0.006	0.12	-9999	-0.39	29	29
GNB2L1	0.014	0	-9999	-10000	0	0
MAPK3	0.013	0.065	-9999	-0.29	16	16
MAPK1	0.013	0.065	-9999	-0.29	16	16
Syndecan-2/RACK1	-0.011	0.056	-9999	-0.3	8	8
NF1	0.009	0.056	-9999	-0.6	3	3
FGFR/FGF/Syndecan-2	0.004	0.084	-9999	-0.38	16	16
ITGA2	-0.039	0.16	-9999	-0.54	35	35
MAPK8	0.011	0.095	-9999	-0.33	26	26
Syndecan-2/alpha2/beta1 Integrin	-0.039	0.16	-9999	-0.36	58	58
Syndecan-2/Kininogen	-0.019	0.09	-9999	-0.3	33	33
ITGB1	0.011	0.037	-9999	-0.48	2	2
SRC	0.027	0.06	-9999	-0.28	8	8
Syndecan-2/CASK/Protein 4.1	-0.015	0.072	-9999	-0.32	17	17
extracellular matrix organization	0.005	0.086	-9999	-0.33	22	22
actin cytoskeleton reorganization	0.002	0.089	-9999	-0.31	27	27
Syndecan-2/Caveolin-2/Ras	0.004	0.094	-9999	-0.34	14	14
Syndecan-2/Laminin alpha3	-0.016	0.12	-9999	-0.35	42	42
Syndecan-2/RasGAP	-0.011	0.052	-9999	-0.28	8	8
alpha5/beta1 Integrin	-0.019	0.082	-9999	-0.36	19	19
PRKCD	-0.015	0.13	-9999	-0.6	17	17
Syndecan-2 dimer	0.004	0.092	-9999	-0.34	23	23
GO:0007205	0.004	0	-9999	-10000	0	0
DNA mediated transformation	0	0	-9999	-10000	0	0
Syndecan-2/RasGAP/Src	0.034	0.058	-9999	-10000	0	0
RHOA	0.014	0	-9999	-10000	0	0
SDCBP	0.014	0	-9999	-10000	0	0
TNFRSF13B	-0.006	0.076	-9999	-0.48	9	9
RASA1	0.014	0	-9999	-10000	0	0
alpha2/beta1 Integrin	-0.039	0.12	-9999	-0.38	37	37
Syndecan-2/Synbindin	0.012	0.071	-9999	-0.32	16	16
TGFB1	0.004	0.078	-9999	-0.6	6	6
CASP3	0.004	0.11	-9999	-0.39	21	21
FN1	-0.002	0.088	-9999	-0.48	12	12
Syndecan-2/IL8	-0.096	0.17	-9999	-0.32	127	127
SDC2	0.004	0.084	-9999	-0.38	16	16
KNG1	-0.018	0.1	-9999	-0.48	17	17
Syndecan-2/Neurofibromin	0.009	0.082	-9999	-0.34	18	18
TRAPPC4	0.014	0	-9999	-10000	0	0
CSF2	0.001	0.003	-9999	-10000	0	0
Syndecan-2/TGFB1	0.005	0.086	-9999	-0.33	22	22
Syndecan-2/Syntenin/PI-4-5-P2	-0.012	0.06	-9999	-0.29	16	16
Syndecan-2/Ezrin	0.015	0.092	-9999	-0.46	10	10
PRKACA	0.019	0.075	-9999	-0.34	11	11
angiogenesis	-0.095	0.17	-9999	-0.32	127	127
MMP2	-0.022	0.14	-9999	-0.53	24	24
IL8	-0.16	0.26	-9999	-0.53	117	117
calcineurin-NFAT signaling pathway	-0.011	0.084	-9999	-0.32	24	24

×

Fc-epsilon receptor I signaling in mast cells

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
PPAP2A	0.013	0.026	-9999	-0.48	1	1
LAT2	-0.051	0.17	-9999	-0.58	23	23
AP1	-0.099	0.17	-9999	-0.53	35	35
mol:PIP3	-0.065	0.2	-9999	-0.57	28	28
IKBKB	-0.03	0.11	-9999	-0.3	22	22
AKT1	-0.035	0.14	-9999	-0.47	10	10
IKBKG	-0.03	0.11	-9999	-0.28	28	28
MS4A2	-0.03	0.12	-9999	-0.48	24	24
mol:Sphingosine-1-phosphate	0	0	-9999	-10000	0	0
PIK3CA	0.012	0.032	-9999	-0.6	1	1
MAP3K1	-0.015	0.15	-9999	-0.54	19	19
mol:Ca2+	-0.045	0.15	-9999	-0.41	28	28
LYN	0.005	0.065	-9999	-0.49	6	6
CBLB	-0.037	0.14	-9999	-0.43	22	22
SHC1	0.009	0.052	-9999	-0.48	4	4
RasGAP/p62DOK	-0.02	0.074	-9999	-0.33	12	12
positive regulation of cell migration	0	0	-9999	-10000	0	0
INPP5D	0.008	0.055	-9999	-0.51	4	4
PLD2	-0.07	0.16	-9999	-0.36	50	50
PTPN13	-0.028	0.14	-9999	-0.56	13	13
PTPN11	0.011	0.008	-9999	-10000	0	0
GO:0007205	0	0	-9999	-10000	0	0
regulation of mast cell degranulation	-0.003	0.12	-9999	-0.33	14	14
SYK	-0.014	0.12	-9999	-0.57	17	17
GRB2	0.014	0.001	-9999	-10000	0	0
LAT/PLCgamma1/GRB2/SLP76/GADs	-0.11	0.17	-9999	-0.59	27	27
LAT	-0.056	0.15	-9999	-0.38	42	42
PAK2	-0.026	0.17	-9999	-0.6	21	21
NFATC2	-0.11	0.2	-9999	-0.57	48	48
HRAS	-0.038	0.19	-9999	-0.66	22	22
GAB2	0.012	0.032	-9999	-0.6	1	1
PLA2G1B	0.04	0.023	-9999	-10000	0	0
Fc epsilon R1	-0.12	0.18	-9999	-0.4	86	86
Antigen/IgE/Fc epsilon R1	-0.11	0.17	-9999	-0.39	73	73
mol:GDP	-0.047	0.2	-9999	-0.68	24	24
JUN	0.003	0.075	-9999	-0.5	8	8
mol:Ca++	0	0	-9999	-10000	0	0
PIK3R1	0.014	0.001	-9999	-10000	0	0
FOS	-0.087	0.22	-9999	-0.55	66	66
Antigen/IgE/Fc epsilon R1/LYN/SYK	-0.062	0.13	-9999	-0.47	21	21
CHUK	-0.03	0.11	-9999	-0.28	28	28
KLRG1	-0.041	0.13	-9999	-0.48	17	17
VAV1	-0.053	0.18	-9999	-0.55	29	29
calcium-dependent protein kinase C activity	0	0	-9999	-10000	0	0
CBL	-0.036	0.13	-9999	-0.45	20	20
negative regulation of mast cell degranulation	-0.033	0.14	-9999	-0.5	17	17
BTK	-0.068	0.19	-9999	-0.73	20	20
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK	-0.11	0.19	-9999	-0.54	35	35
GAB2/PI3K/SHP2	-0.082	0.13	-9999	-0.46	17	17
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP	-0.053	0.15	-9999	-0.41	32	32
RAF1	0.029	0.026	-9999	-10000	0	0
Fc epsilon R1/FcgammaRIIB/SHIP	-0.18	0.22	-9999	-0.45	108	108
FCER1G	-0.017	0.13	-9999	-0.57	19	19
FCER1A	-0.14	0.25	-9999	-0.53	104	104
Antigen/IgE/Fc epsilon R1/Fyn	-0.1	0.16	-9999	-0.37	65	65
MAPK3	0.039	0.023	-9999	-10000	0	0
MAPK1	0.039	0.023	-9999	-10000	0	0
NFKB1	0.013	0.026	-9999	-0.48	1	1
MAPK8	-0.003	0.11	-9999	-0.59	10	10
DUSP1	-0.022	0.14	-9999	-0.54	24	24
NF-kappa-B/RelA	-0.033	0.05	-9999	-0.25	2	2
actin cytoskeleton reorganization	-0.033	0.13	-9999	-0.44	20	20
mol:Glucocorticoid Dexamethasone	0	0	-9999	-10000	0	0
PI3K	-0.068	0.16	-9999	-0.62	21	21
FER	-0.054	0.16	-9999	-0.42	40	40
RELA	0.014	0	-9999	-10000	0	0
ITK	-0.072	0.13	-9999	-0.36	47	47
SOS1	0.014	0	-9999	-10000	0	0
PLCG1	-0.045	0.2	-9999	-0.69	23	23
cytokine secretion	-0.024	0.037	-9999	-10000	0	0
SPHK1	-0.056	0.16	-9999	-0.46	32	32
PTK2	-0.035	0.14	-9999	-0.47	19	19
NTAL/PLCgamma1/GRB2/SLP76/GADs	-0.1	0.18	-9999	-0.65	25	25
EDG1	0	0	-9999	-10000	0	0
mol:DAG	-0.051	0.19	-9999	-0.54	27	27
MAP2K2	0.035	0.022	-9999	-10000	0	0
MAP2K1	0.034	0.026	-9999	-10000	0	0
MAP2K7	0.014	0	-9999	-10000	0	0
KLRG1/SHP2	-0.046	0.12	-9999	-0.47	16	16
MAP2K4	0.02	0.015	-9999	-10000	0	0
Fc epsilon R1/FcgammaRIIB	-0.19	0.23	-9999	-0.47	117	117
mol:Choline	-0.069	0.16	-9999	-0.36	50	50
SHC/Grb2/SOS1	-0.057	0.11	-9999	-0.49	15	15
FYN	0.014	0	-9999	-10000	0	0
DOK1	0.012	0.032	-9999	-0.6	1	1
PXN	-0.024	0.13	-9999	-0.5	13	13
HCLS1	-0.055	0.18	-9999	-0.57	26	26
PRKCB	-0.054	0.14	-9999	-0.38	35	35
FCGR2B	-0.15	0.25	-9999	-0.53	107	107
IGHE	-0.001	0.006	-9999	-10000	0	0
KLRG1/SHIP	-0.034	0.14	-9999	-0.51	17	17
LCP2	-0.004	0.094	-9999	-0.49	13	13
PLA2G4A	-0.051	0.15	-9999	-0.43	35	35
RASA1	0.014	0	-9999	-10000	0	0
mol:Phosphatidic acid	-0.069	0.16	-9999	-0.36	50	50
IKK complex	-0.009	0.086	-9999	-0.23	15	15
WIPF1	0.014	0	-9999	-10000	0	0

×

Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Noncanonical Wnts/FZD	-0.035	0.14	-9999	-0.42	21	21
FZD6	-0.012	0.11	-9999	-0.49	19	19
WNT6	-0.041	0.16	-9999	-0.53	37	37
WNT4	-0.04	0.16	-9999	-0.52	37	37
FZD3	0.009	0.056	-9999	-0.6	3	3
WNT5A	-0.012	0.12	-9999	-0.57	16	16
WNT11	-0.016	0.13	-9999	-0.54	20	20

×

IL6-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.039	0.23	-10000	0	-0.76	8	8
CRP	-0.047	0.23	-10000	0	-0.7	11	11
cell cycle arrest	-0.06	0.26	-10000	0	-0.67	27	27
TIMP1	-0.081	0.27	-10000	0	-0.68	30	30
IL6ST	-0.039	0.17	-10000	0	-0.6	31	31
Rac1/GDP	-0.075	0.21	-10000	0	-0.54	35	35
AP1	-0.016	0.14	-10000	0	-0.49	11	11
GAB2	0.013	0.032	-10000	0	-0.6	1	1
TNFSF11	-0.049	0.24	-10000	0	-0.75	9	9
HSP90B1	0	0.17	-10000	0	-0.92	11	11
GAB1	0.012	0.041	-10000	0	-0.54	2	2
MAPK14	-0.11	0.24	-10000	0	-0.54	64	64
AKT1	0.058	0.034	-10000	0	-0.46	1	1
FOXO1	0.061	0.043	-10000	0	-0.43	1	1
MAP2K6	-0.093	0.22	-10000	0	-0.52	48	48
mol:GTP	0	0.002	-10000	0	-10000	0	0
MAP2K4	-0.061	0.22	-10000	0	-0.55	33	33
MITF	-0.074	0.2	-10000	0	-0.49	41	41
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TYK2	0.014	0	-10000	0	-10000	0	0
A2M	0.02	0.04	-10000	0	-10000	0	0
CEBPB	0	0.12	-10000	0	-0.57	14	14
GRB2/SOS1/GAB family/SHP2	0	0.084	-10000	0	-0.82	1	1
STAT3	-0.065	0.26	-10000	0	-0.71	27	27
STAT1	-0.008	0.034	-10000	0	-10000	0	0
CEBPD	-0.081	0.33	-10000	0	-0.96	31	31
PIK3CA	0.014	0.032	-10000	0	-0.6	1	1
PI3K	0.023	0.024	-10000	0	-0.44	1	1
JUN	0.003	0.075	-10000	0	-0.5	8	8
PIAS3/MITF	-0.063	0.18	-10000	0	-0.5	33	33
MAPK11	-0.11	0.25	-10000	0	-0.54	68	68
STAT3 (dimer)/FOXO1	0.011	0.21	-10000	0	-0.63	9	9
GRB2/SOS1/GAB family	-0.079	0.14	-10000	0	-0.52	20	20
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK	-0.075	0.19	-10000	0	-0.52	33	33
GRB2	0.015	0.001	-10000	0	-10000	0	0
JAK2	0.014	0	-10000	0	-10000	0	0
LBP	-0.036	0.23	-10000	0	-0.69	17	17
PIK3R1	0.016	0	-10000	0	-10000	0	0
JAK1	0.013	0.009	-10000	0	-10000	0	0
MYC	-0.067	0.3	-10000	0	-0.98	22	22
FGG	-0.047	0.23	-10000	0	-0.73	9	9
macrophage differentiation	-0.06	0.26	-10000	0	-0.67	27	27
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4	-0.11	0.18	-10000	0	-0.54	33	33
JUNB	-0.063	0.28	-10000	0	-0.81	23	23
FOS	-0.087	0.22	-10000	0	-0.55	66	66
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4	-0.085	0.2	0.29	1	-0.47	51	52
STAT1/PIAS1	-0.061	0.19	0.29	1	-0.46	42	43
GRB2/SOS1/GAB family/SHP2/PI3K	0.044	0.037	-10000	0	-0.39	2	2
STAT3 (dimer)	-0.063	0.26	-10000	0	-0.7	27	27
PRKCD	-0.062	0.25	-10000	0	-0.65	32	32
IL6R	-0.019	0.13	-10000	0	-0.57	20	20
SOCS3	-0.16	0.36	-10000	0	-1	41	41
gp130 (dimer)/JAK1/JAK1/LMO4	-0.006	0.11	-10000	0	-0.36	31	31
Rac1/GTP	-0.076	0.21	-10000	0	-0.52	41	41
HCK	-0.013	0.12	-10000	0	-0.53	18	18
MAPKKK cascade	0.023	0.073	-10000	0	-0.91	1	1
bone resorption	-0.045	0.23	-10000	0	-0.69	10	10
IRF1	-0.046	0.24	-10000	0	-0.78	9	9
mol:GDP	-0.087	0.21	-10000	0	-0.51	47	47
SOS1	0.015	0.001	-10000	0	-10000	0	0
VAV1	-0.089	0.22	-10000	0	-0.52	47	47
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3	-0.11	0.24	-10000	0	-0.58	50	50
PTPN11	-0.002	0.017	-10000	0	-10000	0	0
IL6/IL6RA	-0.11	0.21	-10000	0	-0.42	109	109
gp130 (dimer)/TYK2/TYK2/LMO4	-0.009	0.11	-10000	0	-0.36	31	31
gp130 (dimer)/JAK2/JAK2/LMO4	-0.009	0.11	-10000	0	-0.36	31	31
IL6	-0.13	0.24	-10000	0	-0.53	99	99
PIAS3	0.014	0	-10000	0	-10000	0	0
PTPRE	0.012	0.037	-10000	0	-0.61	1	1
PIAS1	0.007	0.064	-10000	0	-0.6	4	4
RAC1	0.015	0.001	-10000	0	-10000	0	0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4	-0.075	0.17	0.27	1	-0.44	39	40
LMO4	0.014	0.011	-10000	0	-10000	0	0
STAT3 (dimer)/PIAS3	-0.12	0.21	0.35	1	-0.66	28	29
MCL1	0.063	0.031	-10000	0	-10000	0	0

×

Rapid glucocorticoid signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma	-0.035	0.1	-10000	0	-0.33	38	38
MAPK9	0.009	0	-10000	0	-10000	0	0
adrenocorticotropin secretion	-0.13	0.2	-10000	0	-0.4	127	127
GNB1/GNG2	-0.003	0.034	-10000	0	-0.37	3	3
GNB1	0.014	0	-10000	0	-10000	0	0
regulation of calcium ion transport via voltage-gated calcium channel activity	0	0	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
MAPK14	0.009	0	-10000	0	-10000	0	0
Gs family/GTP	-0.036	0.11	-10000	0	-0.35	38	38
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	0.009	0.027	0.088	38	-10000	0	38
GNAL	-0.05	0.19	-10000	0	-0.6	38	38
GNG2	0.009	0.056	-10000	0	-0.6	3	3
CRH	-0.18	0.27	-10000	0	-0.54	127	127
mol:cortisol	0	0	-10000	0	-10000	0	0
MAPK8	-0.001	0.062	-10000	0	-0.37	10	10
MAPK11	0.006	0.034	-10000	0	-0.37	3	3

×

LPA4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ADCY4	0.007	0.069	-9999	-0.31	16	16
ADCY5	0.002	0.091	-9999	-0.39	17	17
ADCY6	0.014	0.05	-9999	-0.32	8	8
ADCY7	0.014	0.05	-9999	-0.32	8	8
ADCY1	-0.056	0.15	-9999	-0.34	77	77
ADCY2	0.003	0.085	-9999	-0.37	17	17
ADCY3	0.014	0.05	-9999	-0.32	8	8
ADCY8	-0.035	0.14	-9999	-0.36	54	54
PRKCE	0.004	0.058	-9999	-0.38	8	8
ADCY9	0.012	0.06	-9999	-0.35	9	9
mol:DAG	0	0	-9999	-10000	0	0
cAMP biosynthetic process	-0.011	0.11	-9999	-0.36	18	18

×

Coregulation of Androgen receptor activity

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NRIP1	0.013	0.004	-9999	-10000	0	0
SVIL	-0.009	0.1	-9999	-0.49	16	16
ZNF318	0.019	0.018	-9999	-10000	0	0
JMJD2C	-0.003	0.02	-9999	-0.076	24	24
T-DHT/AR/Ubc9	-0.063	0.16	-9999	-0.37	70	70
CARM1	0.014	0.001	-9999	-10000	0	0
PRDX1	-0.008	0.11	-9999	-0.6	13	13
PELP1	0.015	0.003	-9999	-10000	0	0
CTNNB1	0.013	0.004	-9999	-10000	0	0
AKT1	0.015	0.005	-9999	-10000	0	0
PTK2B	-0.011	0.11	-9999	-0.48	18	18
MED1	0.015	0.005	-9999	-10000	0	0
MAK	-0.037	0.16	-9999	-0.49	40	40
response to oxidative stress	0	0.001	-9999	-10000	0	0
HIP1	-0.004	0.1	-9999	-0.6	10	10
GSN	0.002	0.08	-9999	-0.57	7	7
NCOA2	-0.035	0.17	-9999	-0.6	29	29
NCOA6	0.013	0.004	-9999	-10000	0	0
DNA-PK	0.008	0.026	-9999	-10000	0	0
NCOA4	0.014	0.001	-9999	-10000	0	0
PIAS3	0.013	0.004	-9999	-10000	0	0
cell proliferation	-0.041	0.1	-9999	-0.56	6	6
XRCC5	0.015	0.004	-9999	-10000	0	0
UBE3A	0.012	0.009	-9999	-10000	0	0
T-DHT/AR/SNURF	-0.075	0.18	-9999	-0.39	77	77
FHL2	-0.043	0.21	-9999	-0.88	16	16
RANBP9	0.013	0.004	-9999	-10000	0	0
JMJD1A	-0.009	0.052	-9999	-0.11	72	72
CDK6	-0.036	0.16	-9999	-0.54	33	33
TGFB1I1	0.001	0.082	-9999	-0.54	8	8
T-DHT/AR/CyclinD1	-0.084	0.18	-9999	-0.4	83	83
XRCC6	0.015	0.004	-9999	-10000	0	0
T-DHT/AR	-0.071	0.18	-9999	-0.4	67	67
CTDSP1	0.013	0.004	-9999	-10000	0	0
CTDSP2	0.013	0.046	-9999	-0.48	3	3
BRCA1	0.011	0.037	-9999	-0.48	2	2
TCF4	0.015	0.033	-9999	-0.6	1	1
CDKN2A	-0.1	0.24	-9999	-0.57	74	74
SRF	0.017	0.027	-9999	-10000	0	0
NKX3-1	-0.054	0.17	-9999	-0.98	7	7
KLK3	-0.019	0.12	-9999	-10000	0	0
TMF1	0.013	0.004	-9999	-10000	0	0
HNRNPA1	0.016	0.006	-9999	-10000	0	0
AOF2	-0.002	0.008	-9999	-10000	0	0
APPL1	0.028	0.01	-9999	-10000	0	0
T-DHT/AR/Caspase 8	-0.074	0.17	-9999	-0.38	81	81
AR	-0.11	0.24	-9999	-0.59	70	70
UBA3	0.013	0.004	-9999	-10000	0	0
PATZ1	0.016	0.006	-9999	-10000	0	0
PAWR	-0.034	0.15	-9999	-0.52	32	32
PRKDC	0.015	0.004	-9999	-10000	0	0
PA2G4	0.016	0.007	-9999	-10000	0	0
UBE2I	0.014	0	-9999	-10000	0	0
T-DHT/AR/Cyclin D3/CDK11 p58	-0.057	0.15	-9999	-0.34	71	71
RPS6KA3	0.012	0.032	-9999	-0.6	1	1
T-DHT/AR/ARA70	-0.064	0.16	-9999	-0.37	70	70
LATS2	0.003	0.084	-9999	-0.52	9	9
T-DHT/AR/PRX1	-0.067	0.17	-9999	-0.37	77	77
Cyclin D3/CDK11 p58	0	0.018	-9999	-0.34	1	1
VAV3	-0.11	0.22	-9999	-0.51	84	84
KLK2	-0.063	0.12	-9999	-0.47	15	15
CASP8	-0.006	0.1	-9999	-0.49	15	15
T-DHT/AR/TIF2/CARM1	-0.077	0.18	-9999	-0.39	80	80
TMPRSS2	-0.14	0.31	-9999	-0.68	72	72
CCND1	-0.019	0.13	-9999	-0.53	22	22
PIAS1	0.005	0.065	-9999	-0.6	4	4
mol:T-DHT	-0.011	0.031	-9999	-0.079	38	38
CDC2L1	0	0.001	-9999	-10000	0	0
PIAS4	0.01	0.015	-9999	-10000	0	0
T-DHT/AR/CDK6	-0.093	0.19	-9999	-0.39	94	94
CMTM2	-0.006	0.11	-9999	-0.56	13	13
SNURF	-0.005	0.1	-9999	-0.6	11	11
ZMIZ1	0.006	0.026	-9999	-10000	0	0
CCND3	0.013	0.026	-9999	-0.48	1	1
TGIF1	-0.005	0.1	-9999	-0.53	14	14
FKBP4	0.013	0.004	-9999	-10000	0	0

×

Ephrin B reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EFNB2	0.003	0.077	-10000	0	-0.51	8	8
EPHB2	0.001	0.084	-10000	0	-0.52	9	9
EFNB1	-0.078	0.18	-10000	0	-0.38	93	93
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	-0.087	0.15	-10000	0	-0.59	17	17
Ephrin B2/EPHB1-2	-0.035	0.12	-10000	0	-0.35	43	43
neuron projection morphogenesis	-0.084	0.15	-10000	0	-0.56	17	17
Ephrin B1/EPHB1-2/Tiam1	-0.066	0.18	-10000	0	-0.4	56	56
DNM1	-0.12	0.24	-10000	0	-0.52	92	92
cell-cell signaling	-0.001	0.002	-10000	0	-10000	0	0
MAP2K4	0.01	0.083	-10000	0	-0.74	4	4
YES1	-0.008	0.11	-10000	0	-1	4	4
Ephrin B1/EPHB1-2/NCK2	-0.066	0.18	-10000	0	-0.4	56	56
PI3K	0.012	0.083	-10000	0	-0.66	5	5
mol:GDP	-0.088	0.17	-10000	0	-0.4	56	56
ITGA2B	-0.043	0.17	-10000	0	-0.56	36	36
endothelial cell proliferation	-0.007	0.045	-10000	0	-0.3	8	8
FYN	-0.007	0.1	-10000	0	-0.96	4	4
MAP3K7	-0.007	0.083	-10000	0	-0.79	4	4
FGR	-0.007	0.1	-10000	0	-0.96	4	4
TIAM1	0.012	0.032	-10000	0	-0.6	1	1
PIK3R1	0.014	0	-10000	0	-10000	0	0
RGS3	0.01	0.045	-10000	0	-0.48	3	3
cell adhesion	-0.035	0.15	-10000	0	-0.62	9	9
LYN	-0.008	0.1	-10000	0	-0.96	4	4
Ephrin B1/EPHB1-2/Src Family Kinases	-0.011	0.097	-10000	0	-0.92	4	4
Ephrin B1/EPHB1-2	-0.013	0.09	-10000	0	-0.85	4	4
SRC	-0.007	0.1	-10000	0	-0.96	4	4
ITGB3	-0.054	0.18	-10000	0	-0.51	47	47
EPHB1	-0.039	0.17	-10000	0	-0.6	31	31
EPHB4	0.014	0	-10000	0	-10000	0	0
RAC1	0.014	0	-10000	0	-10000	0	0
Ephrin B2/EPHB4	-0.004	0.046	-10000	0	-0.31	8	8
alphaIIb/beta3 Integrin	-0.086	0.17	-10000	0	-0.4	78	78
BLK	-0.023	0.11	-10000	0	-0.98	4	4
HCK	-0.012	0.11	-10000	0	-1.1	4	4
regulation of stress fiber formation	0.087	0.17	0.39	56	-10000	0	56
MAPK8	0.009	0.098	-10000	0	-0.44	13	13
Ephrin B1/EPHB1-2/RGS3	-0.068	0.18	-10000	0	-0.4	56	56
endothelial cell migration	-0.008	0.081	-10000	0	-0.55	6	6
NCK2	0.014	0	-10000	0	-10000	0	0
PTPN13	0.003	0.082	-10000	0	-0.68	5	5
regulation of focal adhesion formation	0.087	0.17	0.39	56	-10000	0	56
chemotaxis	0.089	0.17	0.47	34	-10000	0	34
PIK3CA	0.012	0.032	-10000	0	-0.6	1	1
Rac1/GTP	-0.086	0.15	-10000	0	-0.58	17	17
angiogenesis	-0.013	0.089	-10000	0	-0.84	4	4
LCK	-0.026	0.11	-10000	0	-0.99	4	4

×

IL2 signaling events mediated by STAT5

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GAB2	0.013	0.032	-9999	-0.6	1	1
ELF1	-0.021	0.1	-9999	-0.36	13	13
CCNA2	-0.051	0.18	-9999	-0.54	43	43
PIK3CA	0.013	0.032	-9999	-0.6	1	1
JAK3	-0.058	0.19	-9999	-0.53	49	49
PIK3R1	0.015	0.001	-9999	-10000	0	0
JAK1	0.015	0.001	-9999	-10000	0	0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	-0.031	0.16	-9999	-0.43	23	23
SHC1	0.009	0.052	-9999	-0.48	4	4
SP1	0.015	0.048	-9999	-0.35	4	4
IL2RA	-0.054	0.2	-9999	-0.5	56	56
IL2RB	-0.099	0.22	-9999	-0.53	76	76
SOS1	0.015	0.001	-9999	-10000	0	0
IL2RG	-0.036	0.16	-9999	-0.51	35	35
G1/S transition of mitotic cell cycle	-0.04	0.2	-9999	-0.53	37	37
PTPN11	0.015	0.001	-9999	-10000	0	0
CCND2	0.017	0.1	-9999	-0.58	10	10
LCK	-0.087	0.21	-9999	-0.53	68	68
GRB2	0.015	0.001	-9999	-10000	0	0
IL2	0.001	0.002	-9999	-10000	0	0
CDK6	-0.036	0.16	-9999	-0.54	33	33
CCND3	-0.017	0.14	-9999	-0.5	6	6

×

Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.014	0	-10000	0	-10000	0	0
RAS family/GTP/Tiam1	0.028	0.042	-10000	0	-0.51	1	1
NT3 (dimer)/TRKC	-0.015	0.08	-10000	0	-0.4	14	14
NT3 (dimer)/TRKB	-0.07	0.15	-10000	0	-0.36	71	71
SHC/Grb2/SOS1/GAB1/PI3K	0.037	0.034	-10000	0	-0.44	1	1
RAPGEF1	0.014	0	-10000	0	-10000	0	0
BDNF	-0.087	0.21	-10000	0	-0.5	71	71
PIK3CA	0.012	0.032	-10000	0	-0.6	1	1
DYNLT1	0.011	0.046	-10000	0	-0.6	2	2
NTRK1	-0.006	0.1	-10000	0	-0.52	14	14
NTRK2	-0.015	0.13	-10000	0	-0.6	17	17
NTRK3	0.009	0.056	-10000	0	-0.6	3	3
NT-4/5 (dimer)/TRKB	-0.071	0.15	-10000	0	-0.38	57	57
neuron apoptosis	0.13	0.17	0.42	70	-10000	0	70
SHC 2-3/Grb2	-0.14	0.18	-10000	0	-0.46	70	70
SHC1	0.009	0.052	-10000	0	-0.48	4	4
SHC2	-0.07	0.11	-10000	0	-0.4	21	21
SHC3	-0.16	0.24	-10000	0	-0.56	78	78
STAT3 (dimer)	0.006	0.07	-10000	0	-0.35	9	9
NT3 (dimer)/TRKA	-0.065	0.14	-10000	0	-0.34	69	69
RIN/GDP	-0.035	0.11	-10000	0	-0.27	13	13
GIPC1	0.014	0	-10000	0	-10000	0	0
KRAS	0.013	0.026	-10000	0	-0.48	1	1
DNAJA3	-0.066	0.12	-10000	0	-0.35	30	30
RIN/GTP	-0.16	0.2	-10000	0	-0.41	139	139
CCND1	-0.003	0.16	-10000	0	-0.58	22	22
MAGED1	0.014	0	-10000	0	-10000	0	0
PTPN11	0.014	0	-10000	0	-10000	0	0
RICS	0	0	-10000	0	-10000	0	0
NT-4/5 (dimer)	-0.012	0.09	-10000	0	-0.48	13	13
SHC/GRB2/SOS1	-0.003	0.028	-10000	0	-0.27	4	4
GRB2	0.014	0	-10000	0	-10000	0	0
NGF (dimer)/TRKA/MATK	-0.12	0.19	-10000	0	-0.38	113	113
TRKA/NEDD4-2	-0.026	0.1	-10000	0	-0.39	25	25
ELMO1	-0.001	0.096	-10000	0	-0.6	9	9
RhoG/GTP/ELMO1/DOCK1	-0.012	0.067	-10000	0	-0.37	12	12
NGF	-0.072	0.2	-10000	0	-0.55	55	55
HRAS	0.013	0.026	-10000	0	-0.48	1	1
DOCK1	0.009	0.056	-10000	0	-0.6	3	3
GAB2	0.012	0.032	-10000	0	-0.6	1	1
RIT2	-0.2	0.28	-10000	0	-0.56	139	139
RIT1	0.014	0	-10000	0	-10000	0	0
FRS2	0.011	0.041	-10000	0	-0.54	2	2
DNM1	-0.12	0.24	-10000	0	-0.52	92	92
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.014	0	-10000	0	-10000	0	0
SH2B1 (homopentamer)	0	0	-10000	0	-10000	0	0
RhoG/GTP	-0.072	0.12	-10000	0	-0.36	39	39
mol:GDP	0.045	0.069	-10000	0	-0.46	2	2
NGF (dimer)	-0.072	0.2	-10000	0	-0.55	55	55
RhoG/GDP	-0.011	0.069	-10000	0	-0.45	9	9
RIT1/GDP	0.041	0.05	-10000	0	-0.29	2	2
TIAM1	0.012	0.032	-10000	0	-0.6	1	1
PIK3R1	0.014	0	-10000	0	-10000	0	0
BDNF (dimer)/TRKB	-0.077	0.14	-10000	0	-0.4	33	33
KIDINS220/CRKL/C3G	0	0	-10000	0	-10000	0	0
SHC/RasGAP	-0.004	0.035	-10000	0	-0.33	4	4
FRS2 family/SHP2	-0.002	0.024	-10000	0	-0.32	2	2
SHC/GRB2/SOS1/GAB1	-0.004	0.039	-10000	0	-0.57	1	1
RIT1/GTP	0	0	-10000	0	-10000	0	0
NT3 (dimer)	-0.008	0.091	-10000	0	-0.48	13	13
RAP1/GDP	-0.006	0.025	-10000	0	-0.24	2	2
KIDINS220/CRKL	0.014	0	-10000	0	-10000	0	0
BDNF (dimer)	-0.087	0.21	-10000	0	-0.5	71	71
ubiquitin-dependent protein catabolic process	-0.071	0.15	-10000	0	-0.36	72	72
Schwann cell development	-0.02	0.027	-10000	0	-10000	0	0
EHD4	0.007	0.058	-10000	0	-0.48	5	5
FRS2 family/GRB2/SOS1	-0.002	0.021	-10000	0	-0.32	1	1
FRS2 family/SHP2/CRK family/C3G/GAB2	0.042	0.02	-10000	0	-10000	0	0
RAP1B	0.013	0.026	-10000	0	-0.48	1	1
RAP1A	0.014	0	-10000	0	-10000	0	0
CDC42/GTP	-0.063	0.12	-10000	0	-0.48	13	13
ABL1	0.014	0	-10000	0	-10000	0	0
SH2B family/GRB2/SOS1	0	0	-10000	0	-10000	0	0
Rap1/GTP	-0.023	0.044	-10000	0	-10000	0	0
STAT3	0.006	0.07	-10000	0	-0.34	9	9
axon guidance	-0.061	0.12	-10000	0	-0.46	13	13
MAPK3	-0.08	0.19	-10000	0	-0.4	73	73
MAPK1	-0.08	0.19	-10000	0	-0.4	73	73
CDC42/GDP	0.041	0.05	-10000	0	-0.29	2	2
NTF3	-0.008	0.091	-10000	0	-0.48	13	13
NTF4	-0.012	0.09	-10000	0	-0.48	13	13
NGF (dimer)/TRKA/FAIM	-0.062	0.14	-10000	0	-0.34	67	67
PI3K	-0.001	0.023	-10000	0	-0.44	1	1
FRS3	0.014	0	-10000	0	-10000	0	0
FAIM	0.012	0.032	-10000	0	-0.6	1	1
GAB1	0.011	0.041	-10000	0	-0.54	2	2
RASGRF1	-0.11	0.16	-10000	0	-0.37	75	75
SOS1	0.014	0	-10000	0	-10000	0	0
MCF2L	0.012	0.075	-10000	0	-0.33	15	15
RGS19	0.013	0.026	-10000	0	-0.48	1	1
CDC42	0.014	0	-10000	0	-10000	0	0
RAS family/GTP	0.015	0.073	-10000	0	-10000	0	0
Rac1/GDP	0.041	0.05	-10000	0	-0.29	2	2
NGF (dimer)/TRKA/GRIT	-0.063	0.14	-10000	0	-0.35	66	66
neuron projection morphogenesis	-0.035	0.13	-10000	0	-0.47	6	6
NGF (dimer)/TRKA/NEDD4-2	-0.071	0.15	-10000	0	-0.36	72	72
MAP2K1	0.038	0.042	-10000	0	-0.53	1	1
NGFR	-0.061	0.19	-10000	0	-0.54	50	50
NGF (dimer)/TRKA/GIPC/GAIP	-0.057	0.14	-10000	0	-0.31	69	69
RAS family/GTP/PI3K	0.032	0.019	-10000	0	-0.26	1	1
FRS2 family/SHP2/GRB2/SOS1	-0.001	0.019	-10000	0	-0.3	1	1
NRAS	0.014	0	-10000	0	-10000	0	0
GRB2/SOS1	0	0	-10000	0	-10000	0	0
PRKCI	0.014	0	-10000	0	-10000	0	0
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
RAC1	0.014	0	-10000	0	-10000	0	0
PRKCZ	-0.01	0.12	-10000	0	-0.56	15	15
MAPKKK cascade	-0.076	0.19	-10000	0	-0.6	39	39
RASA1	0.014	0	-10000	0	-10000	0	0
TRKA/c-Abl	-0.014	0.072	-10000	0	-0.37	14	14
SQSTM1	0.014	0	-10000	0	-10000	0	0
BDNF (dimer)/TRKB/GIPC	-0.067	0.13	-10000	0	-0.36	33	33
NGF (dimer)/TRKA/p62/Atypical PKCs	-0.061	0.13	-10000	0	-0.35	46	46
MATK	-0.087	0.22	-10000	0	-0.55	66	66
NEDD4L	-0.004	0.098	-10000	0	-0.53	12	12
RAS family/GDP	-0.005	0.023	-10000	0	-0.26	1	1
NGF (dimer)/TRKA	-0.072	0.12	-10000	0	-0.31	64	64
Rac1/GTP	-0.063	0.095	-10000	0	-0.32	25	25
FRS2 family/SHP2/CRK family	-0.001	0.019	-10000	0	-10000	0	0

×

ErbB2/ErbB3 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
USP8	0.018	0.006	-9999	-10000	0	0
RAS family/GTP	-0.068	0.15	-9999	-0.51	19	19
NFATC4	-0.057	0.13	-9999	-0.37	23	23
ERBB2IP	0.014	0.032	-9999	-0.6	1	1
HSP90 (dimer)	0.014	0	-9999	-10000	0	0
mammary gland morphogenesis	-0.087	0.16	-9999	-0.48	19	19
JUN	-0.021	0.1	-9999	-0.37	16	16
HRAS	0.012	0.026	-9999	-0.48	1	1
DOCK7	-0.082	0.16	-9999	-0.48	21	21
ErbB2/ErbB3/neuregulin 1 beta/SHC	-0.13	0.18	-9999	-0.38	96	96
AKT1	0.011	0.004	-9999	-10000	0	0
BAD	0.02	0.003	-9999	-10000	0	0
MAPK10	-0.048	0.077	-9999	-0.25	17	17
mol:GTP	-0.001	0.002	-9999	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta	-0.092	0.17	-9999	-0.52	19	19
RAF1	-0.059	0.15	-9999	-0.48	20	20
ErbB2/ErbB3/neuregulin 2	-0.046	0.12	-9999	-0.36	36	36
STAT3	0.004	0.005	-9999	-10000	0	0
cell migration	-0.02	0.096	-9999	-0.25	15	15
mol:PI-3-4-5-P3	-0.002	0.003	-9999	-10000	0	0
cell proliferation	-0.14	0.26	-9999	-0.61	59	59
FOS	-0.11	0.21	-9999	-0.46	66	66
NRAS	0.014	0.001	-9999	-10000	0	0
mol:Ca2+	-0.087	0.16	-9999	-0.48	19	19
MAPK3	-0.11	0.22	-9999	-0.5	57	57
MAPK1	-0.11	0.22	-9999	-0.5	57	57
JAK2	-0.076	0.15	-9999	-0.46	18	18
NF2	-0.003	0.006	-9999	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1	-0.089	0.18	-9999	-0.34	95	95
NRG1	-0.16	0.26	-9999	-0.56	110	110
GRB2/SOS1	0	0	-9999	-10000	0	0
MAPK8	-0.075	0.15	-9999	-0.4	24	24
MAPK9	-0.046	0.073	-9999	-0.24	14	14
ERBB2	-0.006	0.046	-9999	-0.36	6	6
ERBB3	-0.063	0.2	-9999	-0.57	47	47
SHC1	0.008	0.052	-9999	-0.48	4	4
RAC1	0.014	0	-9999	-10000	0	0
apoptosis	-0.001	0.011	-9999	-10000	0	0
STAT3 (dimer)	0.009	0.009	-9999	-10000	0	0
RNF41	0.023	0.009	-9999	-10000	0	0
FRAP1	0.009	0.003	-9999	-10000	0	0
RAC1-CDC42/GTP	-0.072	0.1	-9999	-0.33	21	21
ErbB2/ErbB2/HSP90 (dimer)	-0.005	0.037	-9999	-0.29	6	6
CHRNA1	-0.13	0.25	-9999	-0.59	64	64
myelination	-0.05	0.13	-9999	-0.35	23	23
PPP3CB	-0.073	0.14	-9999	-0.42	19	19
KRAS	0.012	0.026	-9999	-0.48	1	1
RAC1-CDC42/GDP	-0.062	0.16	-9999	-0.5	20	20
NRG2	0.012	0.032	-9999	-0.6	1	1
mol:GDP	-0.088	0.18	-9999	-0.34	95	95
SOS1	0.014	0.001	-9999	-10000	0	0
MAP2K2	-0.057	0.15	-9999	-0.44	24	24
SRC	0.014	0	-9999	-10000	0	0
mol:cAMP	-0.001	0.002	-9999	-10000	0	0
PTPN11	-0.077	0.15	-9999	-0.46	18	18
MAP2K1	-0.12	0.21	-9999	-0.54	36	36
heart morphogenesis	-0.087	0.16	-9999	-0.48	19	19
RAS family/GDP	-0.065	0.15	-9999	-0.51	19	19
GRB2	0.014	0.001	-9999	-10000	0	0
PRKACA	-0.006	0.009	-9999	-10000	0	0
CHRNE	0	0.048	-9999	-0.19	19	19
HSP90AA1	0.014	0	-9999	-10000	0	0
activation of caspase activity	-0.01	0.004	-9999	-10000	0	0
nervous system development	-0.087	0.16	-9999	-0.48	19	19
CDC42	0.014	0	-9999	-10000	0	0

×

JNK signaling in the CD4+ TCR 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1	-0.081	0.16	-9999	-0.39	60	60
MAP4K1	-0.025	0.15	-9999	-0.58	24	24
MAP3K8	0	0.083	-9999	-0.49	10	10
PRKCB	-0.063	0.19	-9999	-0.52	53	53
DBNL	0.014	0	-9999	-10000	0	0
CRKL	0.014	0	-9999	-10000	0	0
MAP3K1	-0.007	0.11	-9999	-0.43	8	8
JUN	-0.029	0.17	-9999	-0.59	24	24
MAP3K7	-0.006	0.11	-9999	-0.43	8	8
GRAP2	-0.049	0.17	-9999	-0.52	43	43
CRK	0.014	0	-9999	-10000	0	0
MAP2K4	0	0.11	-9999	-0.4	11	11
LAT	-0.024	0.15	-9999	-0.6	23	23
LCP2	-0.004	0.094	-9999	-0.49	13	13
MAPK8	-0.033	0.17	-9999	-0.63	23	23
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family	-0.016	0.12	-9999	-0.46	8	8
LAT/GRAP2/SLP76/HPK1/HIP-55	-0.075	0.15	-9999	-0.55	15	15

×

S1P5 pathway

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
mol:S1P	0	0	-10000	0	-10000	0	0
telencephalon oligodendrocyte cell migration	0.053	0.1	0.54	7	-10000	0	7
GNAI2	0.014	0	-10000	0	-10000	0	0
S1P/S1P5/G12	-0.084	0.15	-10000	0	-0.34	90	90
mol:GDP	0	0	-10000	0	-10000	0	0
GNAO1	0.004	0.078	-10000	0	-0.6	6	6
RhoA/GTP	-0.054	0.11	-10000	0	-0.55	7	7
negative regulation of cAMP metabolic process	-0.033	0.13	-10000	0	-0.29	55	55
GNAZ	0.012	0.032	-10000	0	-0.6	1	1
GNAI3	0.014	0	-10000	0	-10000	0	0
GNA12	0.012	0.032	-10000	0	-0.6	1	1
S1PR5	-0.12	0.24	-10000	0	-0.55	90	90
mol:GTP	0	0	-10000	0	-10000	0	0
S1P/S1P5/Gi	-0.034	0.14	-10000	0	-0.3	55	55
RhoA/GDP	0	0	-10000	0	-10000	0	0
RHOA	0.014	0	-10000	0	-10000	0	0
GNAI1	-0.004	0.1	-10000	0	-0.6	11	11

×

FAS signaling pathway (CD95)

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
SPTAN1	0.007	0.057	0.25	5	-10000	0	5
RFC1	0.007	0.057	0.21	15	-10000	0	15
PRKDC	0.007	0.057	0.22	14	-10000	0	14
RIPK1	0.016	0.003	-10000	0	-10000	0	0
CASP7	-0.006	0.075	0.24	11	-0.31	6	17
FASLG/FAS/FADD/FAF1	-0.009	0.085	0.23	13	-0.31	10	23
MAP2K4	-0.005	0.12	-10000	0	-0.36	9	9
mol:ceramide	-0.004	0.096	-10000	0	-0.39	7	7
GSN	0	0.071	0.25	4	-0.33	6	10
FASLG/FAS/FADD/FAF1/Caspase 8	-0.003	0.093	-10000	0	-0.34	10	10
FAS	-0.009	0.1	-10000	0	-0.55	13	13
BID	0.003	0.084	0.3	11	-0.28	15	26
MAP3K1	0.008	0.091	0.21	9	-0.29	8	17
MAP3K7	0.012	0.004	-10000	0	-10000	0	0
RB1	0.006	0.06	0.22	14	-0.36	1	15
CFLAR	0.014	0.026	-10000	0	-0.47	1	1
HGF/MET	-0.14	0.19	-10000	0	-0.36	141	141
ARHGDIB	0.004	0.065	0.22	14	-0.36	3	17
FADD	0.011	0.007	-10000	0	-10000	0	0
actin filament polymerization	0	0.07	0.33	6	-0.25	4	10
NFKB1	-0.04	0.067	-10000	0	-10000	0	0
MAPK8	-0.031	0.17	-10000	0	-0.42	41	41
DFFA	0.007	0.057	0.25	5	-10000	0	5
DNA fragmentation during apoptosis	0.007	0.057	0.25	5	-10000	0	5
FAS/FADD/MET	-0.099	0.16	-10000	0	-0.34	108	108
CFLAR/RIP1	0.013	0.02	-10000	0	-0.32	1	1
FAIM3	-0.03	0.15	-10000	0	-0.53	30	30
FAF1	0.012	0.007	-10000	0	-10000	0	0
PARP1	0.006	0.059	0.25	5	-0.28	1	6
DFFB	0.007	0.057	0.25	5	-10000	0	5
CHUK	-0.034	0.058	-10000	0	-10000	0	0
FASLG	-0.031	0.13	-10000	0	-0.49	27	27
FAS/FADD	0.002	0.078	-10000	0	-0.4	13	13
HGF	-0.069	0.19	-10000	0	-0.5	59	59
LMNA	0.004	0.06	0.23	5	-0.36	2	7
CASP6	0.005	0.063	0.25	5	-0.39	2	7
CASP10	0.011	0.007	-10000	0	-10000	0	0
CASP3	0.007	0.067	0.25	16	-10000	0	16
PTPN13	0.006	0.069	-10000	0	-0.58	5	5
CASP8	0.008	0.11	0.3	26	-0.33	15	41
IL6	-0.15	0.38	-10000	0	-1.3	31	31
MET	-0.14	0.25	-10000	0	-0.54	101	101
ICAD/CAD	0.007	0.053	0.23	5	-10000	0	5
FASLG/FAS/FADD/FAF1/Caspase 10	-0.004	0.096	-10000	0	-0.4	7	7
activation of caspase activity by cytochrome c	0.003	0.084	0.3	11	-0.28	15	26
PAK2	0.007	0.057	0.25	5	-10000	0	5
BCL2	0.006	0.072	-10000	0	-0.6	5	5

×

Regulation of nuclear SMAD2/3 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
EP300	0.007	0.066	-10000	0	-0.6	4	4
HSPA8	0.012	0.033	-10000	0	-0.6	1	1
SMAD3/SMAD4/ER alpha	-0.028	0.11	0.22	3	-0.4	19	22
AKT1	0.009	0.023	-10000	0	-10000	0	0
GSC	-0.17	0.49	-10000	0	-1.4	48	48
NKX2-5	-0.087	0.2	-10000	0	-0.49	70	70
muscle cell differentiation	0.14	0.18	0.51	52	-10000	0	52
SMAD2-3/SMAD4/SP1	-0.006	0.11	-10000	0	-0.54	3	3
SMAD4	-0.016	0.065	-10000	0	-0.4	1	1
CBFB	0.014	0	-10000	0	-10000	0	0
SAP18	0.014	0.002	-10000	0	-10000	0	0
Cbp/p300/MSG1	-0.022	0.11	-10000	0	-0.37	21	21
SMAD3/SMAD4/VDR	-0.034	0.12	-10000	0	-0.39	11	11
MYC	-0.008	0.13	-10000	0	-0.57	17	17
CDKN2B	-0.12	0.44	-10000	0	-1.4	38	38
AP1	-0.027	0.16	-10000	0	-0.62	12	12
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1	0.044	0.057	-10000	0	-0.4	1	1
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1	-0.005	0.13	-10000	0	-0.38	20	20
SP3	0.016	0.006	-10000	0	-10000	0	0
CREB1	0.014	0	-10000	0	-10000	0	0
FOXH1	-0.017	0.1	-10000	0	-0.54	12	12
SMAD3/SMAD4/GR	-0.01	0.061	-10000	0	-0.36	2	2
GATA3	-0.12	0.23	-10000	0	-0.56	77	77
SKI/SIN3/HDAC complex/NCoR1	0.046	0.031	-10000	0	-10000	0	0
MEF2C/TIF2	-0.077	0.18	-10000	0	-0.49	35	35
endothelial cell migration	0.22	0.49	1.4	53	-10000	0	53
MAX	0.023	0.019	-10000	0	-10000	0	0
RBBP7	0.014	0.002	-10000	0	-10000	0	0
RBBP4	0.014	0.002	-10000	0	-10000	0	0
RUNX2	-0.006	0.1	-10000	0	-0.52	14	14
RUNX3	-0.03	0.15	-10000	0	-0.54	29	29
RUNX1	-0.051	0.18	-10000	0	-0.53	44	44
CTBP1	0.014	0	-10000	0	-10000	0	0
NR3C1	0.023	0.019	-10000	0	-10000	0	0
VDR	-0.061	0.19	-10000	0	-0.53	50	50
CDKN1A	-0.056	0.3	-10000	0	-1.3	17	17
KAT2B	0.012	0.027	-10000	0	-0.48	1	1
SMAD2/SMAD2/SMAD4/FOXH1	-0.027	0.12	-10000	0	-0.36	17	17
DCP1A	0.014	0	-10000	0	-10000	0	0
SKI	0.014	0.002	-10000	0	-10000	0	0
SERPINE1	-0.23	0.5	-10000	0	-1.4	53	53
SMAD3/SMAD4/ATF2	-0.028	0.084	-10000	0	-0.4	11	11
SMAD3/SMAD4/ATF3	-0.049	0.12	-10000	0	-0.38	33	33
SAP30	0.012	0.032	-10000	0	-0.6	1	1
Cbp/p300/PIAS3	0.013	0.06	-10000	0	-0.35	4	4
JUN	-0.021	0.16	-10000	0	-0.61	12	12
SMAD3/SMAD4/IRF7	-0.036	0.097	-10000	0	-0.39	14	14
TFE3	0.008	0.029	-10000	0	-10000	0	0
COL1A2	-0.043	0.17	-10000	0	-0.47	39	39
mesenchymal cell differentiation	0.031	0.09	0.38	16	-10000	0	16
DLX1	-0.16	0.26	-10000	0	-0.54	113	113
TCF3	0.011	0.046	-10000	0	-0.6	2	2
FOS	-0.085	0.22	-10000	0	-0.55	66	66
SMAD3/SMAD4/Max	-0.01	0.061	-10000	0	-0.36	2	2
Cbp/p300/SNIP1	0.005	0.044	-10000	0	-0.36	4	4
ZBTB17	0.018	0.018	-10000	0	-10000	0	0
LAMC1	0.001	0.11	-10000	0	-0.48	12	12
TGIF2/HDAC complex/SMAD3/SMAD4	-0.023	0.078	-10000	0	-0.45	7	7
IRF7	-0.016	0.12	-10000	0	-0.51	21	21
ESR1	-0.015	0.13	-10000	0	-0.54	20	20
HNF4A	-0.035	0.14	-10000	0	-0.48	31	31
MEF2C	-0.058	0.17	-10000	0	-0.49	21	21
SMAD2-3/SMAD4	-0.034	0.073	-10000	0	-0.38	4	4
Cbp/p300/Src-1	0.009	0.049	-10000	0	-0.36	4	4
IGHV3OR16-13	-0.014	0.032	-10000	0	-10000	0	0
TGIF2/HDAC complex	0.006	0.069	-10000	0	-0.58	5	5
CREBBP	0.014	0.012	-10000	0	-10000	0	0
SKIL	0.002	0.085	-10000	0	-0.6	7	7
HDAC1	0.011	0.046	-10000	0	-0.6	2	2
HDAC2	0.014	0.002	-10000	0	-10000	0	0
SNIP1	0.014	0.005	-10000	0	-10000	0	0
GCN5L2	-0.001	0.016	-10000	0	-10000	0	0
SMAD3/SMAD4/TFE3	-0.01	0.082	-10000	0	-0.38	4	4
MSG1/HSC70	-0.021	0.12	-10000	0	-0.37	38	38
SMAD2	-0.003	0.047	-10000	0	-10000	0	0
SMAD3	-0.006	0.06	-10000	0	-0.41	2	2
SMAD3/E2F4-5/DP1/p107/SMAD4	0.007	0.078	-10000	0	-0.4	3	3
SMAD2/SMAD2/SMAD4	-0.004	0.034	-10000	0	-10000	0	0
NCOR1	0.012	0.032	-10000	0	-0.6	1	1
NCOA2	-0.035	0.17	-10000	0	-0.6	29	29
NCOA1	0.014	0	-10000	0	-10000	0	0
MYOD/E2A	-0.13	0.19	-10000	0	-0.39	122	122
SMAD2-3/SMAD4/SP1/MIZ-1	0.004	0.11	-10000	0	-0.48	4	4
IFNB1	-0.01	0.098	-10000	0	-0.41	6	6
SMAD3/SMAD4/MEF2C	-0.064	0.17	-10000	0	-0.47	24	24
CITED1	-0.04	0.16	-10000	0	-0.52	37	37
SMAD2-3/SMAD4/ARC105	-0.009	0.074	-10000	0	-0.47	1	1
RBL1	-0.011	0.12	-10000	0	-0.59	15	15
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB	-0.027	0.19	-10000	0	-0.54	39	39
RUNX1-3/PEBPB2	-0.062	0.14	-10000	0	-0.42	38	38
SMAD7	-0.009	0.14	-10000	0	-0.61	5	5
MYC/MIZ-1	-0.002	0.1	-10000	0	-0.42	15	15
SMAD3/SMAD4	-0.044	0.19	0.3	24	-0.42	46	70
IL10	-0.14	0.28	-10000	0	-0.62	79	79
PIASy/HDAC complex	0.016	0.013	-10000	0	-10000	0	0
PIAS3	0.013	0.007	-10000	0	-10000	0	0
CDK2	0.001	0.086	-10000	0	-0.53	9	9
IL5	-0.083	0.19	-10000	0	-0.5	34	34
CDK4	0.001	0.082	-10000	0	-0.48	10	10
PIAS4	0.016	0.013	-10000	0	-10000	0	0
ATF3	-0.036	0.16	-10000	0	-0.52	34	34
SMAD3/SMAD4/SP1	-0.008	0.1	-10000	0	-0.46	4	4
FOXG1	-0.011	0.12	-10000	0	-0.59	16	16
FOXO3	0.017	0.031	-10000	0	-10000	0	0
FOXO1	0.014	0.05	-10000	0	-0.42	3	3
FOXO4	0.016	0.041	-10000	0	-0.52	1	1
heart looping	-0.058	0.16	-10000	0	-0.48	21	21
CEBPB	-0.011	0.12	-10000	0	-0.58	14	14
SMAD3/SMAD4/DLX1	-0.12	0.17	-10000	0	-0.39	92	92
MYOD1	-0.17	0.26	-10000	0	-0.55	120	120
SMAD3/SMAD4/HNF4	-0.045	0.1	-10000	0	-0.35	21	21
SMAD3/SMAD4/GATA3	-0.12	0.19	-10000	0	-0.48	54	54
SnoN/SIN3/HDAC complex/NCoR1	0.002	0.084	-10000	0	-0.6	7	7
SMAD3/SMAD4/RUNX1-3/PEBPB2	-0.06	0.15	-10000	0	-0.44	31	31
SMAD3/SMAD4/SP1-3	0.01	0.097	-10000	0	-0.49	3	3
MED15	0.014	0	-10000	0	-10000	0	0
SP1	0.005	0.04	-10000	0	-10000	0	0
SIN3B	0.014	0.002	-10000	0	-10000	0	0
SIN3A	0.014	0.002	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5	-0.07	0.16	-10000	0	-0.4	26	26
ITGB5	0.021	0.11	-10000	0	-0.72	3	3
TGIF/SIN3/HDAC complex/CtBP	0.044	0.043	-10000	0	-0.45	1	1
SMAD3/SMAD4/AR	-0.088	0.16	-10000	0	-0.4	65	65
AR	-0.099	0.23	-10000	0	-0.57	70	70
negative regulation of cell growth	-0.01	0.12	-10000	0	-0.44	14	14
SMAD3/SMAD4/MYOD	-0.13	0.17	-10000	0	-0.42	76	76
E2F5	0.009	0.056	-10000	0	-0.6	3	3
E2F4	0.014	0	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF	-0.009	0.098	-10000	0	-0.35	4	4
SMAD2-3/SMAD4/FOXO1-3a-4	-0.009	0.13	-10000	0	-0.37	29	29
TFDP1	0.014	0	-10000	0	-10000	0	0
SMAD3/SMAD4/AP1	-0.026	0.16	-10000	0	-0.62	12	12
SMAD3/SMAD4/RUNX2	-0.031	0.09	-10000	0	-0.38	16	16
TGIF2	0.006	0.069	-10000	0	-0.58	5	5
TGIF1	-0.007	0.11	-10000	0	-0.53	14	14
ATF2	-0.003	0.1	-10000	0	-0.6	10	10

×

Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
DYNC1H1	0.014	0	-9999	-10000	0	0
VLDLR	-0.002	0.099	-9999	-0.59	10	10
LRPAP1	0.014	0	-9999	-10000	0	0
NUDC	0.014	0	-9999	-10000	0	0
RELN/LRP8	-0.085	0.15	-9999	-0.37	50	50
CaM/Ca2+	-0.001	0.023	-9999	-0.45	1	1
KATNA1	0.014	0	-9999	-10000	0	0
GO:0030286	0	0	-9999	-10000	0	0
ABL1	-0.048	0.14	-9999	-0.33	50	50
IQGAP1/CaM	-0.007	0.052	-9999	-0.38	7	7
DAB1	-0.091	0.23	-9999	-0.58	65	65
IQGAP1	0.005	0.068	-9999	-0.52	6	6
PLA2G7	-0.033	0.16	-9999	-0.55	30	30
CALM1	0.012	0.032	-9999	-0.6	1	1
DYNLT1	0.011	0.046	-9999	-0.6	2	2
mol:Ca2+	0	0	-9999	-10000	0	0
LRPAP1/LRP8	-0.001	0.023	-9999	-0.44	1	1
UniProt:Q4QZ09	0	0	-9999	-10000	0	0
CLIP1	0.012	0.032	-9999	-0.6	1	1
CDK5R1	-0.021	0.14	-9999	-0.6	21	21
LIS1/Poliovirus Protein 3A	0.018	0	-9999	-10000	0	0
CDK5R2	-0.1	0.24	-9999	-0.57	73	73
mol:PP1	0	0	-9999	-10000	0	0
RELN/VLDLR/DAB1	-0.16	0.21	-9999	-0.39	145	145
YWHAE	0.014	0	-9999	-10000	0	0
NDEL1/14-3-3 E	-0.067	0.2	-9999	-0.6	26	26
MAP1B	-0.001	0.017	-9999	-0.32	1	1
RAC1	-0.002	0.017	-9999	-10000	0	0
p35/CDK5	-0.044	0.16	-9999	-0.58	12	12
RELN	-0.13	0.25	-9999	-0.54	96	96
PAFAH/LIS1	0	0.099	-9999	-0.36	18	18
LIS1/CLIP170	0.028	0.021	-9999	-0.36	1	1
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain	-0.079	0.13	-9999	-0.48	24	24
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3	-0.086	0.21	-9999	-0.7	24	24
GO:0005869	0	0	-9999	-10000	0	0
NDEL1	-0.08	0.21	-9999	-0.59	32	32
LIS1/IQGAP1	0.024	0.043	-9999	-0.36	2	2
RHOA	-0.002	0.017	-9999	-10000	0	0
PAFAH1B1	0.025	0	-9999	-10000	0	0
PAFAH1B3	0.014	0	-9999	-10000	0	0
PAFAH1B2	-0.01	0.12	-9999	-0.6	14	14
MAP1B/LIS1/Dynein heavy chain	0.027	0.011	-9999	-10000	0	0
NDEL1/Katanin 60/Dynein heavy chain	-0.099	0.16	-9999	-0.57	26	26
LRP8	0.012	0.032	-9999	-0.6	1	1
NDEL1/Katanin 60	-0.067	0.2	-9999	-0.6	26	26
P39/CDK5	-0.086	0.18	-9999	-0.54	23	23
LIS1/NudC/Dynein intermediate chain/microtubule organizing center	0.029	0	-9999	-10000	0	0
CDK5	-0.036	0.14	-9999	-0.3	50	50
PPP2R5D	0.014	0	-9999	-10000	0	0
LIS1/CLIP170/Dynein Complex/Dynactin Complex	-0.001	0.016	-9999	-0.31	1	1
CSNK2A1	0.014	0	-9999	-10000	0	0
RELN/VLDLR/DAB1/LIS1	-0.1	0.2	-9999	-0.37	101	101
RELN/VLDLR	-0.084	0.14	-9999	-0.34	59	59
CDC42	-0.002	0.017	-9999	-10000	0	0

×

Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved)	-0.049	0.16	-10000	0	-0.72	15	15
HDAC1	0.009	0.046	-10000	0	-0.59	2	2
AES	0.014	0.004	-10000	0	-10000	0	0
FBXW11	0.014	0	-10000	0	-10000	0	0
DTX1	0.004	0.076	-10000	0	-0.58	6	6
LRP6/FZD1	-0.005	0.039	-10000	0	-0.33	5	5
TLE1	0.014	0.004	-10000	0	-10000	0	0
AP1	-0.023	0.12	-10000	0	-0.3	44	44
NCSTN	0.014	0	-10000	0	-10000	0	0
ADAM10	-0.001	0.096	-10000	0	-0.6	9	9
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4	0.027	0.071	-10000	0	-10000	0	0
NICD/RBPSUH	-0.022	0.12	-10000	0	-0.6	15	15
WIF1	-0.27	0.28	-10000	0	-0.54	189	189
NOTCH1	-0.026	0.13	-10000	0	-0.63	15	15
PSENEN	0.014	0	-10000	0	-10000	0	0
KREMEN2	-0.051	0.18	-10000	0	-0.52	45	45
DKK1	-0.12	0.23	-10000	0	-0.53	87	87
beta catenin/beta TrCP1	0.016	0.043	0.42	1	-10000	0	1
APH1B	0.014	0	-10000	0	-10000	0	0
APH1A	0.014	0	-10000	0	-10000	0	0
AXIN1	-0.002	0.045	0.21	2	-0.26	2	4
CtBP/CBP/TCF1/TLE1/AES	0.032	0.046	0.28	3	-0.27	2	5
PSEN1	0.014	0	-10000	0	-10000	0	0
FOS	-0.087	0.22	-10000	0	-0.55	66	66
JUN	0.003	0.075	-10000	0	-0.5	8	8
MAP3K7	0.014	0.005	-10000	0	-10000	0	0
CTNNB1	0.009	0.046	0.34	2	-10000	0	2
MAPK3	0.014	0	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	-0.11	0.17	-10000	0	-0.34	113	113
HNF1A	0.012	0.033	-10000	0	-0.6	1	1
CTBP1	0.014	0.004	-10000	0	-10000	0	0
MYC	-0.037	0.29	-10000	0	-1.4	15	15
NKD1	0	0.09	-10000	0	-0.56	9	9
FZD1	0.009	0.052	-10000	0	-0.48	4	4
NOTCH1 precursor/Deltex homolog 1	-0.027	0.13	-10000	0	-0.62	15	15
apoptosis	-0.023	0.12	-10000	0	-0.3	44	44
Delta 1/NOTCHprecursor	-0.047	0.16	-10000	0	-0.72	15	15
DLL1	-0.037	0.17	-10000	0	-0.6	30	30
PPARD	0.02	0.026	-10000	0	-10000	0	0
Gamma Secretase	0	0	-10000	0	-10000	0	0
APC	-0.004	0.067	0.21	2	-0.5	3	5
DVL1	-0.021	0.025	-10000	0	-10000	0	0
CSNK2A1	0.014	0.003	-10000	0	-10000	0	0
MAP3K7IP1	-0.001	0.005	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	-0.11	0.17	-10000	0	-0.34	119	119
LRP6	0.013	0.026	-10000	0	-0.48	1	1
CSNK1A1	0.014	0.003	-10000	0	-10000	0	0
NLK	0.016	0.016	-10000	0	-10000	0	0
CCND1	-0.026	0.24	-10000	0	-1.4	9	9
WNT1	-0.024	0.13	-10000	0	-0.48	26	26
Axin1/APC/beta catenin	0.016	0.063	0.34	2	-0.53	1	3
DKK2	-0.11	0.23	-10000	0	-0.54	80	80
NOTCH1 precursor/DVL1	-0.024	0.11	-10000	0	-0.57	15	15
GSK3B	0.014	0.001	-10000	0	-10000	0	0
FRAT1	0.009	0.049	-10000	0	-0.52	3	3
NOTCH/Deltex homolog 1	-0.029	0.13	-10000	0	-0.62	15	15
PPP2R5D	-0.005	0.045	0.26	9	-10000	0	9
MAPK1	0.014	0	-10000	0	-10000	0	0
WNT1/LRP6/FZD1	-0.16	0.17	-10000	0	-0.38	99	99
RBPJ	0.014	0	-10000	0	-10000	0	0
CREBBP	0.017	0.005	-10000	0	-10000	0	0

×

IL27-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.004	0.078	-10000	0	-0.6	6	6
CD4-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
cytokine production during immune response	0.011	0.11	0.43	7	-10000	0	7
IL27/IL27R/JAK1	-0.045	0.16	-10000	0	-0.55	8	8
TBX21	-0.067	0.22	-10000	0	-0.56	30	30
IL12B	-0.001	0.051	-10000	0	-0.49	4	4
IL12A	-0.012	0.1	-10000	0	-0.43	20	20
IL6ST	-0.039	0.17	-10000	0	-0.61	31	31
IL27RA/JAK1	0.017	0.036	-10000	0	-10000	0	0
IL27	-0.016	0.11	-10000	0	-0.48	20	20
TYK2	0.014	0.003	-10000	0	-10000	0	0
T-helper cell lineage commitment	-0.055	0.12	-10000	0	-0.73	2	2
T-helper 2 cell differentiation	0.011	0.11	0.43	7	-10000	0	7
T cell proliferation during immune response	0.011	0.11	0.43	7	-10000	0	7
MAPKKK cascade	-0.011	0.11	-10000	0	-0.43	7	7
STAT3	0.014	0	-10000	0	-10000	0	0
STAT2	0.011	0.037	-10000	0	-0.48	2	2
STAT1	-0.002	0.085	-10000	0	-0.48	11	11
IL12RB1	-0.034	0.16	-10000	0	-0.55	31	31
positive regulation of tyrosine phosphorylation of STAT protein	0	0	-10000	0	-10000	0	0
IL12RB2	-0.1	0.25	-10000	0	-0.54	48	48
IL27/IL27R/JAK2/TYK2	-0.011	0.11	-10000	0	-0.44	7	7
positive regulation of T cell mediated cytotoxicity	-0.011	0.11	-10000	0	-0.43	7	7
STAT1 (dimer)	-0.077	0.25	0.52	18	-0.66	14	32
JAK2	0.015	0.004	-10000	0	-10000	0	0
JAK1	0.013	0.004	-10000	0	-10000	0	0
STAT2 (dimer)	-0.004	0.11	-10000	0	-0.41	7	7
T cell proliferation	-0.076	0.16	-10000	0	-0.5	13	13
IL12/IL12R/TYK2/JAK2	-0.007	0.095	-10000	0	-0.57	4	4
IL17A	-0.055	0.12	-10000	0	-0.73	2	2
mast cell activation	0.011	0.11	0.43	7	-10000	0	7
IFNG	0	0.022	-10000	0	-0.089	4	4
T cell differentiation	-0.004	0.005	-10000	0	-0.022	3	3
STAT3 (dimer)	-0.003	0.1	-10000	0	-0.41	7	7
STAT5A (dimer)	-0.01	0.12	-10000	0	-0.45	11	11
STAT4 (dimer)	-0.098	0.17	-10000	0	-0.46	23	23
STAT4	-0.17	0.26	-10000	0	-0.54	124	124
T cell activation	-0.009	0.007	0.061	2	-10000	0	2
IL27R/JAK2/TYK2	-0.018	0.097	-10000	0	-10000	0	0
GATA3	-0.14	0.39	-10000	0	-1.4	31	31
IL18	-0.021	0.11	-10000	0	-0.38	31	31
positive regulation of mast cell cytokine production	-0.003	0.1	-10000	0	-0.4	7	7
IL27/EBI3	-0.023	0.13	-10000	0	-0.4	35	35
IL27RA	0.013	0.034	-10000	0	-10000	0	0
IL6	-0.13	0.24	-10000	0	-0.52	99	99
STAT5A	0.001	0.09	-10000	0	-0.6	8	8
monocyte differentiation	0	0	-10000	0	-10000	0	0
IL2	-0.001	0.02	-10000	0	-10000	0	0
IL1B	-0.13	0.2	-10000	0	-0.39	128	128
EBI3	-0.016	0.13	-10000	0	-0.57	18	18
TNF	-0.11	0.19	-10000	0	-0.39	109	109

×

E-cadherin signaling in the nascent adherens junction

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	-0.042	0.17	-9999	-0.46	47	47
KLHL20	-0.028	0.058	-9999	-0.27	7	7
CYFIP2	0.008	0.055	-9999	-0.51	4	4
Rac1/GDP	0.003	0.12	-9999	-10000	0	0
ENAH	-0.043	0.17	-9999	-0.46	47	47
AP1M1	0.014	0	-9999	-10000	0	0
RAP1B	0.013	0.026	-9999	-0.48	1	1
RAP1A	0.014	0	-9999	-10000	0	0
CTNNB1	0.014	0	-9999	-10000	0	0
CDC42/GTP	-0.038	0.07	-9999	-10000	0	0
ABI1/Sra1/Nap1	-0.019	0.04	-9999	-0.18	8	8
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin	-0.1	0.16	-9999	-0.4	59	59
RAPGEF1	-0.02	0.15	-9999	-0.39	47	47
CTNND1	0.014	0	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.08	0.16	-9999	-0.48	47	47
CRK	-0.031	0.16	-9999	-0.43	47	47
E-cadherin/gamma catenin/alpha catenin	-0.09	0.15	-9999	-0.33	100	100
alphaE/beta7 Integrin	-0.038	0.12	-9999	-0.39	36	36
IQGAP1	0.005	0.068	-9999	-0.52	6	6
NCKAP1	0.014	0	-9999	-10000	0	0
Rap1/GTP/I-afadin	-0.002	0.022	-9999	-0.29	2	2
DLG1	-0.042	0.17	-9999	-0.46	47	47
ChemicalAbstracts:7440-70-2	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.028	0.05	-9999	-10000	0	0
MLLT4	0.012	0.032	-9999	-0.6	1	1
ARF6/GTP/NME1/Tiam1	0	0.018	-9999	-0.33	1	1
PI3K	-0.035	0.064	-9999	-10000	0	0
ARF6	0.014	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
E-cadherin/gamma catenin	-0.11	0.18	-9999	-0.4	100	100
TIAM1	0.012	0.032	-9999	-0.6	1	1
E-cadherin(dimer)/Ca2+	-0.069	0.12	-9999	-0.31	47	47
AKT1	-0.02	0.036	-9999	-10000	0	0
PIK3R1	0.014	0	-9999	-10000	0	0
CDH1	-0.13	0.25	-9999	-0.54	95	95
RhoA/GDP	0.003	0.12	-9999	-10000	0	0
actin cytoskeleton organization	-0.021	0.043	-9999	-0.19	7	7
CDC42/GDP	0.003	0.12	-9999	-10000	0	0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin	-0.037	0.11	-9999	-0.28	51	51
ITGB7	-0.041	0.17	-9999	-0.54	36	36
RAC1	0.014	0	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/p120 catenin	-0.073	0.12	-9999	-0.32	47	47
E-cadherin/Ca2+/beta catenin/alpha catenin	-0.071	0.12	-9999	-0.31	47	47
mol:GDP	-0.008	0.13	-9999	-10000	0	0
CDC42/GTP/IQGAP1	-0.005	0.04	-9999	-0.31	6	6
JUP	0.001	0.086	-9999	-0.57	8	8
p120 catenin/RhoA/GDP	-0.046	0.091	-9999	-10000	0	0
RAC1/GTP/IQGAP1	-0.005	0.04	-9999	-0.31	6	6
PIP5K1C/AP1M1	0	0	-9999	-10000	0	0
RHOA	0.014	0	-9999	-10000	0	0
CDC42	0.014	0	-9999	-10000	0	0
CTNNA1	0.014	0	-9999	-10000	0	0
positive regulation of S phase of mitotic cell cycle	0.008	0.065	-9999	-0.21	22	22
NME1	0.014	0	-9999	-10000	0	0
clathrin coat assembly	0	0	-9999	-10000	0	0
TJP1	-0.042	0.17	-9999	-0.46	47	47
regulation of cell-cell adhesion	-0.034	0.062	-9999	-10000	0	0
WASF2	-0.009	0.021	-9999	-10000	0	0
Rap1/GTP	-0.045	0.08	-9999	-10000	0	0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin	-0.099	0.16	-9999	-0.39	63	63
CCND1	0.008	0.08	-9999	-0.26	22	22
VAV2	-0.025	0.16	-9999	-0.42	47	47
RAP1/GDP	-0.043	0.085	-9999	-10000	0	0
adherens junction assembly	-0.04	0.17	-9999	-0.45	47	47
homophilic cell adhesion	0	0	-9999	-10000	0	0
ABI1	0.014	0	-9999	-10000	0	0
PIP5K1C	0.014	0	-9999	-10000	0	0
regulation of heterotypic cell-cell adhesion	-0.061	0.17	-9999	-0.55	20	20
E-cadherin/beta catenin	-0.073	0.14	-9999	-0.39	47	47
mol:GTP	0	0	-9999	-10000	0	0
SRC	-0.044	0.17	-9999	-0.46	47	47
PIK3CA	0.012	0.032	-9999	-0.6	1	1
Rac1/GTP	-0.046	0.094	-9999	-0.46	7	7
E-cadherin/beta catenin/alpha catenin	-0.083	0.14	-9999	-0.36	47	47
ITGAE	0.014	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.082	0.17	-9999	-0.5	47	47

×

Cellular roles of Anthrax toxin

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ANTXR1	0.009	0.056	-10000	0	-0.6	3	3
ANTXR2	-0.001	0.089	-10000	0	-0.5	11	11
negative regulation of myeloid dendritic cell antigen processing and presentation	-0.002	0.013	-10000	0	-0.065	14	14
monocyte activation	-0.16	0.26	-10000	0	-0.54	98	98
MAP2K2	-0.001	0.004	-10000	0	-10000	0	0
MAP2K1	-0.003	0.019	-10000	0	-0.32	1	1
MAP2K7	-0.002	0.01	-10000	0	-10000	0	0
MAP2K6	-0.003	0.02	-10000	0	-0.33	1	1
CYAA	0.006	0.055	-10000	0	-0.27	14	14
MAP2K4	-0.003	0.025	-10000	0	-0.32	2	2
IL1B	-0.087	0.14	-10000	0	-0.28	128	128
Channel	-0.011	0.055	-10000	0	-0.29	14	14
NLRP1	-0.004	0.023	-10000	0	-0.29	2	2
CALM1	0.012	0.032	-10000	0	-0.6	1	1
negative regulation of phagocytosis	-0.004	0.032	-10000	0	-0.55	1	1
mol:Ca2+	0	0	-10000	0	-10000	0	0
regulation of endothelial cell proliferation	0.002	0.013	0.065	14	-10000	0	14
MAPK3	-0.002	0.01	-10000	0	-10000	0	0
MAPK1	-0.002	0.01	-10000	0	-10000	0	0
PGR	-0.031	0.096	-10000	0	-0.33	33	33
PA/Cellular Receptors	-0.012	0.061	-10000	0	-0.32	14	14
apoptosis	-0.002	0.013	-10000	0	-0.065	14	14
LOC728358	0	0	-10000	0	-10000	0	0
Lethal toxin (unfolded)	0.007	0.054	-10000	0	-0.26	14	14
macrophage activation	0.019	0.012	-10000	0	-10000	0	0
TNF	-0.15	0.25	-10000	0	-0.54	109	109
VCAM1	-0.16	0.27	-10000	0	-0.54	98	98
platelet activation	-0.004	0.032	-10000	0	-0.55	1	1
MAPKKK cascade	-0.014	0.019	0.17	2	-10000	0	2
IL18	-0.01	0.089	-10000	0	-0.29	31	31
negative regulation of macrophage activation	-0.002	0.013	-10000	0	-0.065	14	14
LEF	-0.002	0.013	-10000	0	-0.065	14	14
CASP1	-0.005	0.025	-10000	0	-0.26	2	2
mol:cAMP	-0.004	0.032	-10000	0	-0.55	1	1
necrosis	-0.002	0.013	-10000	0	-0.065	14	14
intracellular pH reduction	0	0	-10000	0	-10000	0	0
PAGA	0	0	-10000	0	-10000	0	0
Edema toxin (unfolded)	0.007	0.056	-10000	0	-0.27	14	14
mol:Epigallocatechin-3-gallate (EGCG)	0	0	-10000	0	-10000	0	0

×

Syndecan-3-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	0.014	0	-9999	-10000	0	0
Syndecan-3/Src/Cortactin	-0.005	0.048	-9999	-0.84	1	1
Syndecan-3/Neurocan	-0.02	0.084	-9999	-0.33	20	20
POMC	-0.005	0.1	-9999	-0.53	13	13
EGFR	-0.082	0.21	-9999	-0.55	62	62
Syndecan-3/EGFR	-0.047	0.11	-9999	-0.32	35	35
AGRP	0.002	0.057	-9999	-0.48	5	5
NCSTN	0.014	0	-9999	-10000	0	0
PSENEN	0.014	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
APH1B	0.014	0	-9999	-10000	0	0
APH1A	0.014	0	-9999	-10000	0	0
NCAN	-0.024	0.15	-9999	-0.59	23	23
long-term memory	-0.002	0.03	-9999	-0.56	1	1
Syndecan-3/IL8	-0.083	0.12	-9999	-0.31	46	46
PSEN1	0.014	0	-9999	-10000	0	0
Src/Cortactin	0	0	-9999	-10000	0	0
FYN	0.014	0	-9999	-10000	0	0
limb bud formation	-0.002	0.034	-9999	-0.63	1	1
MC4R	-0.11	0.24	-9999	-0.56	78	78
SRC	0.014	0	-9999	-10000	0	0
PTN	0.007	0.061	-9999	-0.5	5	5
FGFR/FGF/Syndecan-3	-0.002	0.034	-9999	-0.64	1	1
neuron projection morphogenesis	-0.02	0.082	-9999	-0.71	2	2
Syndecan-3/AgRP	-0.005	0.042	-9999	-0.61	1	1
Syndecan-3/AgRP/MC4R	-0.061	0.12	-9999	-0.3	53	53
Fyn/Cortactin	0	0	-9999	-10000	0	0
SDC3	-0.002	0.035	-9999	-0.64	1	1
GO:0007205	0	0	-9999	-10000	0	0
positive regulation of leukocyte migration	-0.082	0.12	-9999	-0.3	46	46
IL8	-0.16	0.26	-9999	-0.53	117	117
Syndecan-3/Fyn/Cortactin	-0.002	0.031	-9999	-0.58	1	1
Syndecan-3/CASK	-0.002	0.033	-9999	-0.61	1	1
alpha-MSH/MC4R	-0.099	0.18	-9999	-0.41	87	87
Gamma Secretase	0	0	-9999	-10000	0	0

×

Noncanonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC2	-0.074	0.21	-9999	-0.56	56	56
GNB1/GNG2	-0.019	0.13	-9999	-0.42	18	18
mol:DAG	-0.008	0.12	-9999	-0.47	8	8
PLCG1	-0.009	0.13	-9999	-0.49	8	8
YES1	-0.026	0.14	-9999	-0.44	19	19
FZD3	0.009	0.056	-9999	-0.6	3	3
FZD6	-0.012	0.11	-9999	-0.49	19	19
G protein	-0.01	0.13	-9999	-0.49	8	8
MAP3K7	-0.11	0.16	-9999	-0.42	36	36
mol:Ca2+	-0.008	0.12	-9999	-0.45	8	8
mol:IP3	-0.008	0.12	-9999	-0.47	8	8
NLK	-0.007	0.012	-9999	-10000	0	0
GNB1	0.014	0	-9999	-10000	0	0
CAMK2A	-0.12	0.17	-9999	-0.46	36	36
MAP3K7IP1	0	0	-9999	-10000	0	0
Noncanonical Wnts/FZD	-0.035	0.14	-9999	-0.42	21	21
CSNK1A1	0.014	0	-9999	-10000	0	0
GNAS	-0.024	0.13	-9999	-0.41	18	18
GO:0007205	-0.008	0.12	-9999	-0.46	8	8
WNT6	-0.041	0.16	-9999	-0.53	37	37
WNT4	-0.04	0.16	-9999	-0.52	37	37
NFAT1/CK1 alpha	-0.084	0.14	-9999	-0.47	27	27
GNG2	0.009	0.056	-9999	-0.6	3	3
WNT5A	-0.012	0.12	-9999	-0.57	16	16
WNT11	-0.016	0.13	-9999	-0.54	20	20
CDC42	-0.017	0.13	-9999	-0.41	19	19

×

Signaling events mediated by PTP1B

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.01	0.045	-10000	0	-0.48	3	3
Jak2/Leptin Receptor	-0.01	0.11	0.2	16	-0.46	10	26
PTP1B/AKT1	-0.008	0.089	-10000	0	-0.36	7	7
FYN	0.014	0	-10000	0	-10000	0	0
p210 bcr-abl/PTP1B	-0.017	0.098	-10000	0	-0.33	14	14
EGFR	-0.083	0.22	-10000	0	-0.56	62	62
EGF/EGFR	-0.094	0.17	-10000	0	-0.42	61	61
CSF1	-0.01	0.12	-10000	0	-0.6	14	14
AKT1	0.014	0.002	-10000	0	-10000	0	0
INSR	0.014	0.002	-10000	0	-10000	0	0
PTP1B/N-cadherin	-0.009	0.096	-10000	0	-0.39	8	8
Insulin Receptor/Insulin	-0.027	0.063	-10000	0	-0.34	5	5
HCK	-0.013	0.12	-10000	0	-0.53	18	18
CRK	0.014	0	-10000	0	-10000	0	0
TYK2	-0.008	0.093	-10000	0	-0.34	10	10
EGF	-0.045	0.18	-10000	0	-0.56	37	37
YES1	0.011	0.046	-10000	0	-0.6	2	2
CAV1	-0.03	0.13	-10000	0	-0.39	23	23
TXN	0.011	0.027	-10000	0	-0.49	1	1
PTP1B/IRS1/GRB2	-0.004	0.087	-10000	0	-0.37	6	6
cell migration	0.017	0.098	0.33	14	-10000	0	14
STAT3	0.014	0.001	-10000	0	-10000	0	0
PRLR	-0.018	0.14	-10000	0	-0.55	22	22
ITGA2B	-0.043	0.17	-10000	0	-0.57	36	36
CSF1R	-0.023	0.14	-10000	0	-0.57	23	23
Prolactin Receptor/Prolactin	-0.017	0.1	-10000	0	-0.4	23	23
FGR	0.011	0.037	-10000	0	-0.48	2	2
PTP1B/p130 Cas	-0.009	0.094	-10000	0	-0.33	12	12
Crk/p130 Cas	-0.005	0.089	-10000	0	-0.36	7	7
DOK1	0	0.09	-10000	0	-0.36	8	8
JAK2	0	0.087	-10000	0	-0.35	9	9
Jak2/Leptin Receptor/Leptin	-0.11	0.18	-10000	0	-0.45	68	68
PIK3R1	0.014	0	-10000	0	-10000	0	0
PTPN1	-0.017	0.099	-10000	0	-0.33	14	14
LYN	0.006	0.063	-10000	0	-0.48	6	6
CDH2	0.012	0.032	-10000	0	-0.6	1	1
SRC	0.011	0.039	-10000	0	-10000	0	0
ITGB3	-0.054	0.18	-10000	0	-0.51	47	47
CAT1/PTP1B	-0.062	0.14	-10000	0	-0.39	32	32
CAPN1	0.015	0.002	-10000	0	-10000	0	0
CSK	0.014	0	-10000	0	-10000	0	0
PI3K	-0.021	0.059	-10000	0	-0.4	2	2
mol:H2O2	0	0.004	-10000	0	-10000	0	0
STAT3 (dimer)	-0.11	0.18	-10000	0	-0.45	70	70
negative regulation of transcription	0.001	0.087	-10000	0	-0.35	9	9
FCGR2A	-0.035	0.16	-10000	0	-0.54	32	32
FER	-0.023	0.15	-10000	0	-0.61	21	21
alphaIIb/beta3 Integrin	-0.083	0.17	-10000	0	-0.4	78	78
BLK	-0.095	0.21	-10000	0	-0.5	76	76
Insulin Receptor/Insulin/Shc	-0.005	0.047	-10000	0	-0.31	8	8
RHOA	0.015	0.002	-10000	0	-10000	0	0
LEPR	-0.001	0.097	-10000	0	-0.55	11	11
BCAR1	0.012	0.032	-10000	0	-0.6	1	1
p210 bcr-abl/Grb2	0.014	0	-10000	0	-10000	0	0
mol:NADPH	0	0.004	-10000	0	-10000	0	0
TRPV6	-0.068	0.15	-10000	0	-0.42	35	35
PRL	0.002	0.025	-10000	0	-0.47	1	1
SOCS3	-0.15	0.38	-10000	0	-1.4	28	28
SPRY2	0.005	0.071	-10000	0	-0.5	7	7
Insulin Receptor/Insulin/IRS1	-0.001	0.037	-10000	0	-0.36	3	3
CSF1/CSF1R	-0.035	0.15	-10000	0	-0.48	22	22
Ras protein signal transduction	0.021	0.03	-10000	0	-10000	0	0
IRS1	0.014	0	-10000	0	-10000	0	0
INS	-0.006	0.06	-10000	0	-0.57	4	4
LEP	-0.004	0.062	-10000	0	-0.48	6	6
STAT5B	-0.004	0.088	-10000	0	-0.31	10	10
STAT5A	-0.008	0.091	-10000	0	-0.31	12	12
GRB2	0.014	0	-10000	0	-10000	0	0
PDGFB-D/PDGFRB	-0.01	0.098	-10000	0	-0.38	10	10
CSN2	0	0.041	-10000	0	-10000	0	0
PIK3CA	0.012	0.032	-10000	0	-0.6	1	1
LAT	-0.046	0.16	-10000	0	-0.49	38	38
YBX1	0.021	0.032	-10000	0	-0.59	1	1
LCK	-0.088	0.21	-10000	0	-0.53	68	68
SHC1	0.009	0.052	-10000	0	-0.48	4	4
NOX4	-0.066	0.19	-10000	0	-0.52	54	54

×

Signaling events mediated by HDAC Class III

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
EP300	0.007	0.064	-10000	0	-0.6	4	4
HDAC4	0.014	0	-10000	0	-10000	0	0
induction of apoptosis	0	0	-10000	0	-10000	0	0
regulation of S phase of mitotic cell cycle	-0.027	0.041	0.34	3	-10000	0	3
CDKN1A	-0.059	0.18	-10000	0	-0.48	48	48
KAT2B	0.013	0.026	-10000	0	-0.48	1	1
BAX	0.014	0	-10000	0	-10000	0	0
FOXO3	0.005	0.048	0.46	4	-10000	0	4
FOXO1	0.009	0.052	-10000	0	-0.56	3	3
FOXO4	0.02	0.037	-10000	0	-0.3	5	5
response to UV	0	0	-10000	0	-10000	0	0
XRCC6	0.014	0	-10000	0	-10000	0	0
TAT	-0.069	0.2	-10000	0	-0.53	56	56
mol:Lysophosphatidic acid	0	0	-10000	0	-10000	0	0
MYOD1	-0.12	0.2	-10000	0	-0.39	120	120
PPARGC1A	-0.017	0.13	-10000	0	-0.58	19	19
FHL2	-0.027	0.14	-10000	0	-0.52	28	28
response to nutrient levels	0	0	-10000	0	-10000	0	0
KU70/SIRT1	0.014	0.037	-10000	0	-10000	0	0
HIST2H4A	0.027	0.042	-10000	0	-0.34	3	3
SIRT1/FOXO3a	0.015	0.044	0.29	4	-10000	0	4
SIRT1	0.017	0.047	0.2	14	-10000	0	14
response to hypoxia	0	0	-10000	0	-10000	0	0
SIRT1/MEF2D/HDAC4	0.012	0.042	-10000	0	-10000	0	0
SIRT1/Histone H1b	0.003	0.068	-10000	0	-0.26	13	13
apoptosis	-0.013	0.036	-10000	0	-10000	0	0
SIRT1/PGC1A	-0.007	0.089	-10000	0	-0.36	19	19
p53/SIRT1	0.025	0.13	0.3	47	-0.42	11	58
SIRT1/FOXO4	0.012	0.05	-10000	0	-0.25	5	5
FOXO1/FHL2/SIRT1	-0.012	0.087	-10000	0	-0.27	30	30
HIST1H1E	0.009	0.067	-10000	0	-0.31	13	13
SIRT1/p300	0.009	0.06	-10000	0	-0.44	4	4
muscle cell differentiation	0.096	0.16	0.37	64	-10000	0	64
TP53	-0.002	0.12	-10000	0	-0.57	12	12
KU70/SIRT1/BAX	0.013	0.036	-10000	0	-10000	0	0
CREBBP	0.014	0	-10000	0	-10000	0	0
MEF2D	0.011	0.037	-10000	0	-0.48	2	2
HIV-1 Tat/SIRT1	-0.045	0.14	-10000	0	-0.37	56	56
ACSS2	0.03	0.025	-10000	0	-10000	0	0
SIRT1/PCAF/MYOD	-0.096	0.16	-10000	0	-0.37	64	64

×

IL2 signaling events mediated by PI3K

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
BCL2L1	-0.04	0.16	-10000	0	-0.52	10	10
UGCG	-0.026	0.14	-10000	0	-0.66	16	16
AKT1/mTOR/p70S6K/Hsp90/TERT	-0.038	0.16	-10000	0	-0.42	28	28
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucosylceramide	-0.025	0.14	-10000	0	-0.65	16	16
mol:DAG	-0.005	0.051	-10000	0	-0.97	1	1
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.07	0.12	-10000	0	-0.47	17	17
FRAP1	-0.028	0.18	-10000	0	-0.54	18	18
FOXO3	-0.021	0.17	-10000	0	-0.55	14	14
AKT1	-0.032	0.18	-10000	0	-0.48	28	28
GAB2	0.013	0.033	-10000	0	-0.61	1	1
SMPD1	0.004	0.036	-10000	0	-10000	0	0
SGMS1	0.002	0.05	-10000	0	-0.67	1	1
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
mol:GDP	0.022	0.022	-10000	0	-0.39	1	1
CALM1	0.012	0.032	-10000	0	-0.6	1	1
cell proliferation	-0.018	0.11	-10000	0	-0.3	33	33
EIF3A	0.014	0	-10000	0	-10000	0	0
PI3K	0.023	0.026	-10000	0	-0.45	1	1
RPS6KB1	-0.003	0.063	-10000	0	-0.23	1	1
mol:sphingomyelin	-0.005	0.051	-10000	0	-0.97	1	1
natural killer cell activation	0	0.002	-10000	0	-0.012	7	7
JAK3	-0.057	0.19	-10000	0	-0.53	49	49
PIK3R1	0.016	0.004	-10000	0	-10000	0	0
JAK1	0.016	0.003	-10000	0	-10000	0	0
NFKB1	0.013	0.026	-10000	0	-0.48	1	1
MYC	-0.04	0.24	-10000	0	-0.93	18	18
MYB	-0.083	0.34	-10000	0	-1	34	34
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	-0.041	0.17	-10000	0	-0.4	44	44
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.014	0.06	-10000	0	-0.28	1	1
mol:PI-3-4-5-P3	-0.039	0.17	-10000	0	-0.39	44	44
Rac1/GDP	0.028	0.021	-10000	0	-0.34	1	1
T cell proliferation	-0.037	0.18	-10000	0	-0.48	27	27
SHC1	0.009	0.052	-10000	0	-0.48	4	4
RAC1	0.014	0	-10000	0	-10000	0	0
positive regulation of cyclin-dependent protein kinase activity	-0.001	0.02	-10000	0	-0.05	48	48
PRKCZ	-0.04	0.18	-10000	0	-0.51	27	27
NF kappa B1 p50/RelA	-0.064	0.12	-10000	0	-0.49	15	15
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K	-0.054	0.17	-10000	0	-0.42	46	46
HSP90AA1	0.014	0	-10000	0	-10000	0	0
RELA	0.014	0	-10000	0	-10000	0	0
IL2RA	-0.069	0.19	-10000	0	-0.51	55	55
IL2RB	-0.097	0.22	-10000	0	-0.53	76	76
TERT	-0.079	0.2	-10000	0	-0.56	55	55
E2F1	-0.025	0.14	-10000	0	-0.42	34	34
SOS1	0.014	0.003	-10000	0	-10000	0	0
RPS6	0.013	0.026	-10000	0	-0.48	1	1
mol:cAMP	0	0.01	0.024	48	-10000	0	48
PTPN11	0.014	0.004	-10000	0	-10000	0	0
IL2RG	-0.034	0.16	-10000	0	-0.51	35	35
actin cytoskeleton organization	-0.037	0.18	-10000	0	-0.48	27	27
GRB2	0.014	0.003	-10000	0	-10000	0	0
IL2	0.003	0.004	-10000	0	-10000	0	0
PIK3CA	0.015	0.033	-10000	0	-0.61	1	1
Rac1/GTP	0.032	0.025	-10000	0	-0.33	1	1
LCK	-0.085	0.21	-10000	0	-0.53	68	68
BCL2	-0.015	0.17	-10000	0	-0.62	13	13

×

Canonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.004	0.05	-10000	0	-0.58	2	2
AES	0.01	0.022	-10000	0	-10000	0	0
FBXW11	0.014	0	-10000	0	-10000	0	0
mol:GTP	0	0.001	-10000	0	-10000	0	0
LRP6/FZD1	-0.002	0.04	-10000	0	-0.33	5	5
SMAD4	0.014	0	-10000	0	-10000	0	0
DKK2	-0.11	0.23	-10000	0	-0.54	80	80
TLE1	0.009	0.023	0.2	1	-10000	0	1
MACF1	0.015	0	-10000	0	-10000	0	0
CTNNB1	0.062	0.085	-10000	0	-10000	0	0
WIF1	-0.27	0.28	-10000	0	-0.54	189	189
beta catenin/RanBP3	0.019	0.11	0.4	23	-10000	0	23
KREMEN2	-0.051	0.18	-10000	0	-0.52	45	45
DKK1	-0.12	0.23	-10000	0	-0.53	87	87
beta catenin/beta TrCP1	0.067	0.08	-10000	0	-10000	0	0
FZD1	0.009	0.051	-10000	0	-0.48	4	4
AXIN2	-0.001	0.1	-10000	0	-0.84	3	3
AXIN1	0.015	0.001	-10000	0	-10000	0	0
RAN	0.014	0.001	-10000	0	-10000	0	0
Axin1/APC/GSK3/beta catenin	0.025	0.036	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4	0.091	0.051	0.3	2	-10000	0	2
Axin1/APC/GSK3	0.008	0.036	0.26	3	-10000	0	3
Axin1/APC/GSK3/beta catenin/Macf1	0.054	0.065	-10000	0	-10000	0	0
HNF1A	0.005	0.04	-10000	0	-0.61	1	1
CTBP1	0.007	0.025	-10000	0	-10000	0	0
MYC	-0.05	0.3	-10000	0	-1.5	15	15
RANBP3	0.014	0.001	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	-0.11	0.17	-10000	0	-0.34	113	113
NKD1	0	0.09	-10000	0	-0.56	9	9
TCF4	0.005	0.038	-10000	0	-0.56	1	1
TCF3	0.004	0.046	-10000	0	-0.54	2	2
WNT1/LRP6/FZD1/Axin1	-0.018	0.069	-10000	0	-0.49	1	1
Ran/GTP	0.002	0.005	-10000	0	-10000	0	0
CtBP/CBP/TCF/TLE1/AES	0.034	0.13	0.5	21	-10000	0	21
LEF1	0	0.061	-10000	0	-0.48	5	5
DVL1	0.06	0.046	-10000	0	-10000	0	0
CSNK2A1	0.014	0	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES	0.086	0.08	-10000	0	-0.41	3	3
DKK1/LRP6/Kremen 2	-0.11	0.17	-10000	0	-0.34	119	119
LRP6	0.013	0.026	-10000	0	-0.48	1	1
CSNK1A1	0.009	0.025	-10000	0	-10000	0	0
NLK	0.011	0.038	-10000	0	-0.5	2	2
CCND1	-0.038	0.25	-10000	0	-1.5	9	9
WNT1	-0.024	0.13	-10000	0	-0.48	26	26
GSK3A	0.015	0.001	-10000	0	-10000	0	0
GSK3B	0.014	0.001	-10000	0	-10000	0	0
FRAT1	0.01	0.049	-10000	0	-0.52	3	3
PPP2R5D	0.041	0.047	0.3	9	-10000	0	9
APC	0.021	0.075	-10000	0	-0.38	2	2
WNT1/LRP6/FZD1	0.097	0.1	0.24	79	-10000	0	79
CREBBP	0.007	0.024	-10000	0	-10000	0	0

×

ErbB4 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
ErbB4/ErbB4/HBEGF/HBEGF	0.018	0.068	-10000	0	-0.36	3	3
epithelial cell differentiation	-0.041	0.085	-10000	0	-0.43	6	6
ITCH	0.019	0.013	-10000	0	-10000	0	0
WWP1	0.025	0.05	-10000	0	-10000	0	0
FYN	0.014	0	-10000	0	-10000	0	0
EGFR	-0.082	0.21	-10000	0	-0.55	62	62
PRL	0	0.026	-10000	0	-0.48	1	1
neuron projection morphogenesis	-0.027	0.14	-10000	0	-0.42	6	6
PTPRZ1	0.001	0.086	-10000	0	-0.57	8	8
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC	-0.085	0.12	-10000	0	-0.43	10	10
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta	-0.073	0.16	-10000	0	-0.34	81	81
ADAM17	0.01	0.072	-10000	0	-0.6	5	5
ErbB4/ErbB4	0.022	0.064	-10000	0	-0.42	1	1
ErbB4/ErbB4/neuregulin 3/neuregulin 3	-0.004	0.12	-10000	0	-0.38	28	28
NCOR1	0.012	0.032	-10000	0	-0.6	1	1
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn	-0.061	0.15	-10000	0	-0.38	18	18
GRIN2B	-0.15	0.21	-10000	0	-0.51	60	60
ErbB4/ErbB2/betacellulin	-0.033	0.14	-10000	0	-0.42	17	17
STAT1	-0.001	0.085	-10000	0	-0.48	11	11
HBEGF	0.005	0.068	-10000	0	-0.48	7	7
PRLR	-0.02	0.14	-10000	0	-0.55	22	22
E4ICDs/ETO2	0.019	0.068	-10000	0	-0.38	4	4
axon guidance	-0.013	0.077	-10000	0	-10000	0	0
NEDD4	0.008	0.074	-10000	0	-0.51	7	7
Prolactin receptor/Prolactin receptor/Prolactin	-0.025	0.098	-10000	0	-0.4	23	23
CBFA2T3	0.006	0.066	-10000	0	-0.55	5	5
ErbB4/ErbB2/HBEGF	0.022	0.078	-10000	0	-0.36	7	7
MAPK3	-0.036	0.14	-10000	0	-0.44	6	6
STAT1 (dimer)	0.015	0.074	-10000	0	-0.39	3	3
MAPK1	-0.036	0.14	-10000	0	-0.44	6	6
JAK2	0.014	0	-10000	0	-10000	0	0
ErbB4/ErbB2/neuregulin 1 beta	-0.066	0.16	-10000	0	-0.39	22	22
NRG1	-0.11	0.2	-10000	0	-0.41	114	114
NRG3	-0.031	0.16	-10000	0	-0.6	27	27
NRG2	0.012	0.032	-10000	0	-0.6	1	1
NRG4	-0.049	0.17	-10000	0	-0.5	44	44
heart development	-0.013	0.077	-10000	0	-10000	0	0
neural crest cell migration	-0.065	0.16	-10000	0	-0.39	22	22
ERBB2	0.014	0.072	-10000	0	-0.37	12	12
WWOX/E4ICDs	0.023	0.054	-10000	0	-0.36	1	1
SHC1	0.009	0.052	-10000	0	-0.48	4	4
ErbB4/EGFR/neuregulin 4	-0.058	0.16	-10000	0	-0.48	25	25
apoptosis	0.041	0.12	0.42	28	-10000	0	28
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta	0.022	0.059	-10000	0	-0.42	2	2
ErbB4/ErbB2/epiregulin	0.007	0.085	-10000	0	-0.38	8	8
ErbB4/ErbB4/betacellulin/betacellulin	-0.041	0.14	-10000	0	-0.37	41	41
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2	-0.028	0.079	-10000	0	-0.47	4	4
MDM2	0.026	0.059	-10000	0	-0.36	1	1
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta	-0.092	0.14	-10000	0	-0.39	11	11
STAT5A	-0.011	0.092	-10000	0	-0.44	6	6
ErbB4/EGFR/neuregulin 1 beta	-0.11	0.2	-10000	0	-0.5	39	39
DLG4	0.006	0.063	-10000	0	-0.48	6	6
GRB2/SHC	-0.004	0.035	-10000	0	-0.33	4	4
E4ICDs/TAB2/NCoR1	-0.013	0.044	-10000	0	-0.4	2	2
STAT5A (dimer)	-0.043	0.09	-10000	0	-0.46	6	6
MAP3K7IP2	0	0	-10000	0	-10000	0	0
STAT5B (dimer)	-0.005	0.071	-10000	0	-10000	0	0
LRIG1	-0.004	0.1	-10000	0	-0.6	11	11
EREG	-0.009	0.098	-10000	0	-0.48	15	15
BTC	-0.088	0.22	-10000	0	-0.55	65	65
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta	-0.013	0.077	-10000	0	-10000	0	0
ERBB4	0.022	0.064	-10000	0	-0.42	1	1
STAT5B	0.014	0	-10000	0	-10000	0	0
YAP1	-0.033	0.13	-10000	0	-0.61	17	17
GRB2	0.014	0	-10000	0	-10000	0	0
ErbB4/ErbB2/neuregulin 4	-0.008	0.11	-10000	0	-0.39	13	13
glial cell differentiation	0.013	0.044	0.39	2	-10000	0	2
WWOX	0.014	0	-10000	0	-10000	0	0
cell proliferation	-0.1	0.18	-10000	0	-0.51	30	30

×

Ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	-0.005	0.1	-10000	0	-0.34	30	30
MAP4K4	-0.021	0.12	-10000	0	-0.43	12	12
BAG4	-0.006	0.11	-10000	0	-0.6	12	12
PKC zeta/ceramide	-0.01	0.069	0.16	3	-0.27	15	18
NFKBIA	0.014	0	-10000	0	-10000	0	0
BIRC3	-0.035	0.16	-10000	0	-0.55	32	32
BAX	0.006	0.025	-10000	0	-10000	0	0
RIPK1	0.014	0	-10000	0	-10000	0	0
AKT1	0.022	0.013	-10000	0	-10000	0	0
BAD	0.004	0.047	0.16	6	-10000	0	6
SMPD1	-0.024	0.087	-10000	0	-0.2	49	49
RB1	0.003	0.051	0.16	6	-0.41	1	7
FADD/Caspase 8	-0.012	0.12	-10000	0	-0.41	14	14
MAP2K4	0.009	0.051	-10000	0	-0.24	4	4
NSMAF	0.014	0	-10000	0	-10000	0	0
response to UV	0	0	-10000	0	-10000	0	0
RAF1	0.011	0.044	-10000	0	-10000	0	0
EGF	-0.044	0.17	-10000	0	-0.56	37	37
mol:ceramide	-0.006	0.05	0.14	28	-10000	0	28
MADD	0.014	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
mol:Free Fatty acid	-0.005	0.1	-10000	0	-0.34	30	30
ASAH1	0.014	0	-10000	0	-10000	0	0
negative regulation of cell cycle	0.002	0.051	0.16	6	-0.41	1	7
cell proliferation	0.001	0.085	-10000	0	-0.4	9	9
BID	-0.009	0.09	-10000	0	-0.36	9	9
MAP3K1	0.002	0.05	0.16	6	-0.25	2	8
EIF2A	0.014	0.058	-10000	0	-0.29	6	6
TRADD	0.011	0.041	-10000	0	-0.54	2	2
CRADD	0.014	0	-10000	0	-10000	0	0
MAPK3	0.023	0.042	-10000	0	-10000	0	0
response to heat	0	0	-10000	0	-10000	0	0
MAPK1	0.023	0.042	-10000	0	-10000	0	0
Cathepsin D/ceramide	0.002	0.044	0.15	5	-10000	0	5
FADD	-0.02	0.12	-10000	0	-0.45	11	11
KSR1	0.004	0.047	0.17	5	-10000	0	5
MAPK8	0	0.071	0.17	2	-0.24	18	20
PRKRA	0.004	0.047	0.16	6	-10000	0	6
PDGFA	-0.027	0.14	-10000	0	-0.49	30	30
TRAF2	0.014	0	-10000	0	-10000	0	0
IGF1	-0.007	0.11	-10000	0	-0.55	14	14
mol:GD3	0	0	-10000	0	-10000	0	0
ganglioside biosynthetic process	-0.006	0.05	0.14	28	-10000	0	28
CTSD	0.013	0.026	-10000	0	-0.48	1	1
regulation of nitric oxide biosynthetic process	-0.001	0.017	-10000	0	-0.33	1	1
response to radiation	0	0	-10000	0	-10000	0	0
ERK1/PKC delta	0.003	0.092	-10000	0	-0.44	9	9
PRKCD	-0.015	0.13	-10000	0	-0.6	17	17
PRKCZ	-0.01	0.12	-10000	0	-0.56	15	15
mol:GW4869	0	0	-10000	0	-10000	0	0
mol:sphingosine	-0.005	0.1	-10000	0	-0.34	30	30
RelA/NF kappa B1	-0.001	0.017	-10000	0	-0.33	1	1
mol:glutathione	0	0	-10000	0	-10000	0	0
PAWR	-0.033	0.15	-10000	0	-0.52	32	32
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD	-0.03	0.12	-10000	0	-0.48	11	11
TNFR1A/BAG4/TNF-alpha	-0.11	0.17	-10000	0	-0.34	120	120
mol:Sphingosine-1-phosphate	-0.005	0.1	-10000	0	-0.34	30	30
MAP2K1	0.018	0.044	-10000	0	-10000	0	0
mol:C11AG	0	0	-10000	0	-10000	0	0
RELA	0.014	0	-10000	0	-10000	0	0
CYCS	0.008	0.039	0.19	4	-10000	0	4
TNFRSF1A	0.005	0.068	-10000	0	-0.52	6	6
NFKB1	0.013	0.026	-10000	0	-0.48	1	1
TNFR1A/BAG4	-0.02	0.093	-10000	0	-0.44	17	17
EIF2AK2	0.006	0.061	-10000	0	-0.31	6	6
TNF-alpha/TNFR1A/FAN	-0.099	0.15	-10000	0	-0.32	113	113
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
CASP8	-0.003	0.083	-10000	0	-0.34	6	6
MAP2K2	0.019	0.042	-10000	0	-10000	0	0
SMPD3	-0.046	0.13	-10000	0	-0.38	28	28
TNF	-0.15	0.25	-10000	0	-0.54	109	109
PKC zeta/PAR4	-0.048	0.14	-10000	0	-0.4	44	44
mol:PHOSPHOCHOLINE	0.004	0.074	0.2	30	-10000	0	30
NF kappa B1/RelA/I kappa B alpha	-0.033	0.097	-10000	0	-0.61	3	3
AIFM1	0.008	0.039	0.19	4	-10000	0	4
BCL2	0.006	0.072	-10000	0	-0.6	5	5

×

TRAIL signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TNFSF10	-0.019	0.13	-10000	0	-0.54	22	22
positive regulation of NF-kappaB transcription factor activity	-0.034	0.11	-10000	0	-0.37	34	34
MAP2K4	0.027	0.068	-10000	0	-0.34	2	2
IKBKB	0.014	0	-10000	0	-10000	0	0
TNFRSF10B	0.012	0.032	-10000	0	-0.6	1	1
TNFRSF10A	-0.029	0.15	-10000	0	-0.56	27	27
SMPD1	0.009	0.049	-10000	0	-0.22	11	11
IKBKG	0.014	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
TNFRSF10D	-0.003	0.092	-10000	0	-0.5	12	12
TRAIL/TRAILR2	-0.024	0.094	-10000	0	-0.38	23	23
TRAIL/TRAILR3	-0.048	0.13	-10000	0	-0.4	44	44
TRAIL/TRAILR1	-0.053	0.14	-10000	0	-0.41	47	47
TRAIL/TRAILR4	-0.035	0.11	-10000	0	-0.37	34	34
TRAIL/TRAILR1/DAP3/GTP	-0.04	0.1	-10000	0	-0.31	47	47
IKK complex	-0.012	0.031	-10000	0	-10000	0	0
RIPK1	0.014	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
DAP3/GTP	0	0	-10000	0	-10000	0	0
MAPK3	0	0.097	-10000	0	-0.38	22	22
MAP3K1	0.021	0.067	-10000	0	-0.28	1	1
TRAILR4 (trimer)	-0.003	0.092	-10000	0	-0.5	12	12
TRADD	0.011	0.041	-10000	0	-0.54	2	2
TRAILR1 (trimer)	-0.028	0.15	-10000	0	-0.56	27	27
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2	0.008	0.086	-10000	0	-0.27	2	2
CFLAR	0.013	0.026	-10000	0	-0.48	1	1
MAPK1	0	0.097	-10000	0	-0.38	22	22
TRAIL/TRAILR1/FADD/TRADD/RIP	-0.037	0.095	-10000	0	-0.31	31	31
mol:ceramide	0.009	0.049	-10000	0	-0.22	11	11
FADD	0.014	0	-10000	0	-10000	0	0
MAPK8	0.025	0.088	-10000	0	-0.37	7	7
TRAF2	0.014	0	-10000	0	-10000	0	0
TRAILR3 (trimer)	-0.023	0.14	-10000	0	-0.53	25	25
CHUK	0.014	0	-10000	0	-10000	0	0
TRAIL/TRAILR1/FADD	-0.044	0.12	-10000	0	-0.34	47	47
DAP3	0.014	0	-10000	0	-10000	0	0
CASP10	-0.023	0.089	0.28	1	-0.36	12	13
JNK cascade	-0.034	0.11	-10000	0	-0.37	34	34
TRAIL (trimer)	-0.019	0.13	-10000	0	-0.54	22	22
TNFRSF10C	-0.023	0.14	-10000	0	-0.53	25	25
TRAIL/TRAILR1/DAP3/GTP/FADD	-0.036	0.097	-10000	0	-0.32	30	30
TRAIL/TRAILR2/FADD	-0.02	0.078	-10000	0	-0.32	23	23
cell death	0.009	0.049	-10000	0	-0.22	11	11
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2	0.026	0.059	-10000	0	-10000	0	0
TRAILR2 (trimer)	0.012	0.032	-10000	0	-0.6	1	1
CASP8	-0.004	0.058	-10000	0	-0.81	1	1
negative regulation of caspase activity	0	0	-10000	0	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP	-0.017	0.065	-10000	0	-10000	0	0

×

S1P1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	-0.018	0.087	-9999	-0.38	19	19
PDGFRB	0.009	0.045	-9999	-0.49	3	3
SPHK1	-0.041	0.14	-9999	-0.79	12	12
mol:S1P	-0.04	0.13	-9999	-0.66	13	13
S1P1/S1P/Gi	-0.023	0.16	-9999	-0.38	46	46
GNAO1	0.002	0.079	-9999	-0.61	6	6
PDGFB-D/PDGFRB/PLCgamma1	-0.012	0.15	-9999	-0.54	11	11
PLCG1	-0.016	0.16	-9999	-0.55	11	11
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.009	0.045	-9999	-0.49	3	3
GNAI2	0.012	0.006	-9999	-10000	0	0
GNAI3	0.012	0.006	-9999	-10000	0	0
GNAI1	-0.006	0.11	-9999	-0.6	11	11
mol:GDP	0	0	-9999	-10000	0	0
EDG1	-0.002	0.077	-9999	-0.32	19	19
S1P1/S1P	-0.049	0.12	-9999	-0.48	19	19
negative regulation of cAMP metabolic process	-0.022	0.16	-9999	-0.37	46	46
MAPK3	-0.041	0.22	-9999	-0.55	46	46
calcium-dependent phospholipase C activity	-0.001	0.003	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
RhoA/GDP	0	0	-9999	-10000	0	0
KDR	0.004	0.069	-9999	-0.52	6	6
PLCB2	-0.017	0.14	-9999	-0.48	20	20
RAC1	0.014	0	-9999	-10000	0	0
RhoA/GTP	-0.041	0.097	-9999	-0.43	16	16
receptor internalization	-0.047	0.11	-9999	-0.44	20	20
PTGS2	-0.1	0.36	-9999	-1	46	46
Rac1/GTP	-0.041	0.097	-9999	-0.43	16	16
RHOA	0.014	0	-9999	-10000	0	0
VEGFA	-0.007	0.098	-9999	-0.48	15	15
negative regulation of T cell proliferation	-0.022	0.16	-9999	-0.37	46	46
GO:0007205	0	0	-9999	-10000	0	0
GNAZ	0.011	0.033	-9999	-0.61	1	1
MAPK1	-0.041	0.22	-9999	-0.55	46	46
S1P1/S1P/PDGFB-D/PDGFRB	-0.01	0.14	-9999	-0.51	16	16
ABCC1	0.011	0.037	-9999	-0.49	2	2

×

TCGA08_rtk_signaling

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
PDGFRA	-0.059	0.2	-10000	0	-0.58	45	45
HRAS	0.013	0.026	-10000	0	-0.48	1	1
EGFR	-0.082	0.21	-10000	0	-0.55	62	62
AKT	0.019	0.051	-10000	0	-0.38	4	4
FOXO3	0.014	0	-10000	0	-10000	0	0
AKT1	0.014	0	-10000	0	-10000	0	0
FOXO1	0.009	0.052	-10000	0	-0.56	3	3
AKT3	0.006	0.072	-10000	0	-0.6	5	5
FOXO4	0.012	0.032	-10000	0	-0.6	1	1
MET	-0.14	0.25	-10000	0	-0.54	101	101
PIK3CA	0.012	0.032	-10000	0	-0.6	1	1
PIK3CB	0.014	0	-10000	0	-10000	0	0
NRAS	0.014	0	-10000	0	-10000	0	0
PIK3CG	-0.061	0.19	-10000	0	-0.53	51	51
PIK3R3	0.013	0.026	-10000	0	-0.48	1	1
PIK3R2	0.014	0	-10000	0	-10000	0	0
NF1	0.009	0.056	-10000	0	-0.6	3	3
RAS	-0.052	0.11	0.23	1	-0.29	36	37
ERBB2	0.005	0.068	-10000	0	-0.48	7	7
proliferation/survival/translation	-0.008	0.054	0.22	8	-10000	0	8
PI3K	-0.045	0.11	-10000	0	-0.26	50	50
PIK3R1	0.014	0	-10000	0	-10000	0	0
KRAS	0.013	0.026	-10000	0	-0.48	1	1
FOXO	0.029	0.03	-10000	0	-10000	0	0
AKT2	0.014	0	-10000	0	-10000	0	0
PTEN	0.014	0	-10000	0	-10000	0	0

×

Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization	-0.03	0.11	-10000	0	-0.26	54	54
epithelial cell differentiation	-0.068	0.12	-10000	0	-0.3	47	47
CYFIP2	0.008	0.055	-10000	0	-0.51	4	4
ENAH	0.004	0.1	-10000	0	-0.37	1	1
EGFR	-0.082	0.21	-10000	0	-0.55	62	62
EPHA2	-0.018	0.12	-10000	0	-0.49	23	23
MYO6	-0.033	0.13	-10000	0	-10000	0	0
CTNNB1	0.014	0	-10000	0	-10000	0	0
ABI1/Sra1/Nap1	-0.003	0.031	-10000	0	-0.36	1	1
AQP5	-0.14	0.19	-10000	0	-0.52	54	54
CTNND1	0.014	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	-0.032	0.12	-10000	0	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.036	0.13	-10000	0	-0.58	1	1
EGF	-0.044	0.17	-10000	0	-0.56	37	37
NCKAP1	0.014	0	-10000	0	-10000	0	0
AQP3	-0.085	0.14	-10000	0	-0.53	19	19
cortical microtubule organization	-0.068	0.12	-10000	0	-0.3	47	47
GO:0000145	-0.031	0.12	-10000	0	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.069	0.12	-10000	0	-0.31	47	47
MLLT4	0.012	0.032	-10000	0	-0.6	1	1
ARF6/GDP	-0.061	0.096	-10000	0	-0.41	6	6
ARF6	0.014	0	-10000	0	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	-0.018	0.068	-10000	0	-0.41	3	3
mol:Ca2+	0	0	-10000	0	-10000	0	0
VASP	-0.032	0.12	-10000	0	-0.38	1	1
PVRL2	0.011	0.041	-10000	0	-0.54	2	2
ZYX	-0.037	0.13	-10000	0	-10000	0	0
ARF6/GTP	-0.016	0.061	-10000	0	-0.53	1	1
CDH1	-0.13	0.25	-10000	0	-0.54	95	95
EGFR/EGFR/EGF/EGF	-0.13	0.16	-10000	0	-0.52	31	31
RhoA/GDP	-0.063	0.11	-10000	0	-10000	0	0
actin cytoskeleton organization	-0.028	0.12	-10000	0	-10000	0	0
IGF-1R heterotetramer	0.014	0	-10000	0	-10000	0	0
GIT1	0.014	0	-10000	0	-10000	0	0
IGF1R	0.014	0	-10000	0	-10000	0	0
IGF1	-0.007	0.11	-10000	0	-0.55	14	14
DIAPH1	0.001	0.04	-10000	0	-0.68	1	1
Wnt receptor signaling pathway	0.068	0.12	0.3	47	-10000	0	47
RHOA	0.014	0	-10000	0	-10000	0	0
RhoA/GTP	-0.061	0.097	-10000	0	-0.41	6	6
CTNNA1	0.014	0	-10000	0	-10000	0	0
VCL	-0.029	0.13	-10000	0	-10000	0	0
EFNA1	0.011	0.037	-10000	0	-0.48	2	2
LPP	-0.045	0.14	-10000	0	-0.43	4	4
Ephrin A1/EPHA2	-0.073	0.11	-10000	0	-0.46	5	5
SEC6/SEC8	-0.055	0.097	-10000	0	-0.48	3	3
MGAT3	-0.037	0.13	-10000	0	-0.59	1	1
HGF/MET	-0.16	0.17	-10000	0	-0.49	49	49
HGF	-0.069	0.19	-10000	0	-0.5	59	59
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN	-0.03	0.11	-10000	0	-0.26	54	54
actin cable formation	0.016	0.1	-10000	0	-0.33	2	2
KIAA1543	-0.063	0.17	-10000	0	-0.54	17	17
KIFC3	-0.034	0.13	-10000	0	-0.59	1	1
NCK1	0.012	0.032	-10000	0	-0.6	1	1
EXOC3	0.014	0	-10000	0	-10000	0	0
ACTN1	-0.048	0.14	-10000	0	-0.46	4	4
NCK1/GIT1	-0.001	0.023	-10000	0	-0.44	1	1
mol:GDP	-0.068	0.12	-10000	0	-0.3	47	47
EXOC4	0.014	0	-10000	0	-10000	0	0
STX4	-0.033	0.13	-10000	0	-10000	0	0
PIP5K1C	-0.033	0.13	-10000	0	-10000	0	0
LIMA1	0.002	0.085	-10000	0	-0.6	7	7
ABI1	0.014	0	-10000	0	-10000	0	0
ROCK1	-0.006	0.11	-10000	0	-0.37	4	4
adherens junction assembly	-0.043	0.16	-10000	0	-0.51	17	17
IGF-1R heterotetramer/IGF1	-0.069	0.12	-10000	0	-0.56	5	5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	-0.003	0.037	-10000	0	-0.4	3	3
MET	-0.14	0.25	-10000	0	-0.54	101	101
PLEKHA7	-0.039	0.14	-10000	0	-0.57	3	3
mol:GTP	-0.018	0.067	-10000	0	-0.4	3	3
establishment of epithelial cell apical/basal polarity	-0.001	0.12	-10000	0	-0.45	3	3
cortical actin cytoskeleton stabilization	-0.03	0.11	-10000	0	-0.26	54	54
regulation of cell-cell adhesion	-0.028	0.12	-10000	0	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton	-0.03	0.11	-10000	0	-0.26	54	54

×

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

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
MAP4K1	0.009	0.12	-10000	0	-0.4	13	13
CRKL	0.021	0.11	-10000	0	-0.42	13	13
HRAS	0.002	0.14	-10000	0	-0.45	13	13
mol:PIP3	0.003	0.099	-10000	0	-0.37	14	14
SPRED1	0.014	0	-10000	0	-10000	0	0
SPRED2	0.01	0.045	-10000	0	-0.48	3	3
GAB1	0.014	0.11	-10000	0	-0.44	14	14
FOXO3	0.026	0.097	-10000	0	-0.37	11	11
AKT1	0.019	0.1	-10000	0	-0.39	13	13
BAD	0.026	0.097	-10000	0	-0.37	11	11
megakaryocyte differentiation	0.003	0.13	-10000	0	-0.38	27	27
GSK3B	0.026	0.097	-10000	0	-0.37	11	11
RAF1	0.013	0.12	-10000	0	-0.37	11	11
SHC1	0.009	0.052	-10000	0	-0.48	4	4
STAT3	0.015	0.11	-10000	0	-0.41	14	14
STAT1	0.01	0.22	-10000	0	-0.92	16	16
HRAS/SPRED1	0.01	0.11	-10000	0	-0.38	10	10
cell proliferation	0.007	0.12	-10000	0	-0.4	22	22
PIK3CA	0.013	0.032	-10000	0	-0.6	1	1
TEC	-0.004	0.1	-10000	0	-0.54	12	12
RPS6KB1	0.015	0.11	-10000	0	-0.36	21	21
HRAS/SPRED2	0.009	0.12	-10000	0	-0.38	12	12
LYN/TEC/p62DOK	-0.035	0.11	-10000	0	-0.45	17	17
MAPK3	0.025	0.088	-10000	0	-0.27	6	6
STAP1	-0.003	0.13	-10000	0	-0.41	20	20
GRAP2	-0.049	0.17	-10000	0	-0.52	43	43
JAK2	-0.045	0.17	-10000	0	-0.79	14	14
STAT1 (dimer)	0.011	0.22	-10000	0	-0.9	16	16
mol:Gleevec	-0.002	0.005	-10000	0	-10000	0	0
GRB2/SOCS1/VAV1	-0.056	0.12	-10000	0	-0.44	20	20
actin filament polymerization	0.008	0.12	-10000	0	-0.38	21	21
LYN	0.006	0.063	-10000	0	-0.48	6	6
STAP1/STAT5A (dimer)	-0.004	0.17	-10000	0	-0.63	19	19
PIK3R1	0.014	0	-10000	0	-10000	0	0
CBL/CRKL/GRB2	0.032	0.097	-10000	0	-0.39	11	11
PI3K	0.024	0.1	-10000	0	-0.4	12	12
PTEN	0.014	0	-10000	0	-10000	0	0
SCF/KIT/EPO/EPOR	0.002	0.26	-10000	0	-1.2	13	13
MAPK8	0.006	0.13	-10000	0	-0.41	22	22
STAT3 (dimer)	0.015	0.11	-10000	0	-0.41	14	14
positive regulation of transcription	0.026	0.076	-10000	0	-0.24	2	2
mol:GDP	-0.062	0.12	-10000	0	-0.43	22	22
PIK3C2B	0.01	0.12	-10000	0	-0.4	17	17
CBL/CRKL	0.029	0.1	-10000	0	-0.39	13	13
FER	-0.003	0.15	-10000	0	-0.44	28	28
SH2B3	0.014	0.11	-10000	0	-0.41	14	14
PDPK1	0.011	0.097	-10000	0	-0.36	13	13
SNAI2	-0.002	0.13	-10000	0	-0.4	23	23
positive regulation of cell proliferation	0.012	0.18	-10000	0	-0.72	16	16
KITLG	0	0.11	-10000	0	-0.6	11	11
cell motility	0.012	0.18	-10000	0	-0.72	16	16
PTPN6	-0.012	0.096	-10000	0	-0.53	12	12
EPOR	0.039	0.077	-10000	0	-10000	0	0
STAT5A (dimer)	0.007	0.16	-10000	0	-0.63	17	17
SOCS1	-0.034	0.15	-10000	0	-0.51	34	34
cell migration	0.036	0.16	0.37	47	-10000	0	47
SOS1	0.014	0	-10000	0	-10000	0	0
EPO	-0.008	0.1	-10000	0	-0.48	16	16
VAV1	-0.022	0.14	-10000	0	-0.56	23	23
GRB10	0.014	0.11	-10000	0	-0.4	15	15
PTPN11	0.012	0.005	-10000	0	-10000	0	0
SCF/KIT	0.007	0.11	0.23	5	-0.38	22	27
GO:0007205	-0.002	0.006	-10000	0	-10000	0	0
MAP2K1	0.021	0.096	-10000	0	-0.29	9	9
CBL	0.014	0	-10000	0	-10000	0	0
KIT	0	0.25	-10000	0	-1.3	12	12
MAP2K2	0.022	0.096	-10000	0	-0.29	10	10
SHC/Grb2/SOS1	-0.025	0.089	-10000	0	-0.4	13	13
STAT5A	0.006	0.17	-10000	0	-0.65	17	17
GRB2	0.014	0	-10000	0	-10000	0	0
response to radiation	-0.001	0.13	-10000	0	-0.39	23	23
SHC/GRAP2	-0.047	0.13	-10000	0	-0.38	45	45
PTPRO	0.002	0.13	-10000	0	-0.39	27	27
SH2B2	0.007	0.12	-10000	0	-0.38	21	21
DOK1	0.012	0.032	-10000	0	-0.6	1	1
MATK	-0.037	0.16	-10000	0	-0.37	47	47
CREBBP	0.039	0.012	-10000	0	-10000	0	0
BCL2	0.026	0.18	-10000	0	-1.4	5	5

×

Paxillin-dependent events mediated by a4b1

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
CRKL	0.014	0	-10000	0	-10000	0	0
Rac1/GDP	0.006	0.016	-10000	0	-10000	0	0
DOCK1	0.009	0.056	-10000	0	-0.6	3	3
ITGA4	-0.048	0.18	-10000	0	-0.53	42	42
RAC1	0.014	0	-10000	0	-10000	0	0
alpha4/beta7 Integrin	-0.08	0.17	-10000	0	-0.44	67	67
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.014	0	-10000	0	-10000	0	0
alpha4/beta1 Integrin	-0.037	0.1	-10000	0	-0.38	19	19
alpha4/beta7 Integrin/Paxillin	-0.03	0.14	-10000	0	-0.37	44	44
lamellipodium assembly	0.003	0.041	-10000	0	-0.38	1	1
PIK3CA	0.012	0.032	-10000	0	-0.6	1	1
PI3K	-0.001	0.023	-10000	0	-0.44	1	1
ARF6	0.014	0	-10000	0	-10000	0	0
TLN1	0.014	0	-10000	0	-10000	0	0
PXN	0.025	0	-10000	0	-10000	0	0
PIK3R1	0.014	0	-10000	0	-10000	0	0
ARF6/GTP	-0.027	0.076	-10000	0	-0.42	2	2
cell adhesion	-0.03	0.085	-10000	0	-0.31	19	19
CRKL/CBL	0	0	-10000	0	-10000	0	0
alpha4/beta1 Integrin/Paxillin	-0.001	0.1	-10000	0	-0.34	19	19
ITGB1	0.011	0.037	-10000	0	-0.48	2	2
ITGB7	-0.041	0.17	-10000	0	-0.54	36	36
ARF6/GDP	0.006	0.016	-10000	0	-10000	0	0
alpha4/beta1 Integrin/Paxillin/VCAM1	-0.075	0.17	-10000	0	-0.32	88	88
p130Cas/Crk/Dock1	-0.004	0.038	-10000	0	-0.36	4	4
VCAM1	-0.14	0.26	-10000	0	-0.57	97	97
alpha4/beta1 Integrin/Paxillin/Talin	0.009	0.099	-10000	0	-0.32	19	19
alpha4/beta1 Integrin/Paxillin/GIT1	0.009	0.099	-10000	0	-0.46	2	2
BCAR1	0.012	0.032	-10000	0	-0.6	1	1
mol:GDP	0.03	0.085	0.45	2	-10000	0	2
CBL	0.014	0	-10000	0	-10000	0	0
PRKACA	0.014	0	-10000	0	-10000	0	0
GIT1	0.014	0	-10000	0	-10000	0	0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton	0.009	0.099	-10000	0	-0.32	19	19
Rac1/GTP	0.003	0.044	-10000	0	-0.42	1	1

×

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BAG4	-0.006	0.11	-9999	-0.6	12	12
Caspase 8 (4 units)	-0.014	0.087	-9999	-0.36	14	14
NEF	-0.005	0.032	-9999	-10000	0	0
NFKBIA	0.009	0.029	-9999	-10000	0	0
BIRC3	-0.003	0.17	-9999	-0.54	32	32
CYCS	0.022	0.088	-9999	-0.32	11	11
RIPK1	0.014	0	-9999	-10000	0	0
CD247	-0.027	0.15	-9999	-0.6	23	23
MAP2K7	0.016	0.077	-9999	-0.33	1	1
protein ubiquitination	0.019	0.095	-9999	-0.4	6	6
CRADD	0.014	0	-9999	-10000	0	0
DAXX	0.014	0	-9999	-10000	0	0
FAS	-0.006	0.1	-9999	-0.55	13	13
BID	0.014	0.092	-9999	-0.33	14	14
NF-kappa-B/RelA/I kappa B alpha	-0.023	0.076	-9999	-0.52	1	1
TRADD	0.011	0.041	-9999	-0.54	2	2
MAP3K5	0.009	0.056	-9999	-0.6	3	3
CFLAR	0.013	0.026	-9999	-0.48	1	1
FADD	0.014	0	-9999	-10000	0	0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin	-0.023	0.077	-9999	-0.52	1	1
MAPK8	0.016	0.089	-9999	-0.55	1	1
APAF1	0.014	0	-9999	-10000	0	0
TRAF1	0.002	0.085	-9999	-0.6	7	7
TRAF2	0.014	0	-9999	-10000	0	0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG	0.007	0.095	-9999	-0.31	22	22
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD	0	0.12	-9999	-0.53	7	7
CHUK	0.018	0.1	-9999	-0.44	6	6
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8	-0.021	0.074	-9999	-0.32	13	13
TCRz/NEF	-0.041	0.13	-9999	-0.42	36	36
TNF	-0.15	0.25	-9999	-0.54	109	109
FASLG	-0.031	0.17	-9999	-0.54	34	34
NFKB1	0.007	0.042	-9999	-0.58	1	1
TNFR1A/BAG4/TNF-alpha	-0.11	0.17	-9999	-0.34	120	120
CASP6	-0.02	0.066	-9999	-0.52	2	2
CASP7	0.029	0.17	-9999	-0.52	25	25
RELA	0.009	0.029	-9999	-10000	0	0
CASP2	0.014	0	-9999	-10000	0	0
CASP3	0.029	0.16	-9999	-0.52	25	25
TNFRSF1A	0.005	0.068	-9999	-0.52	6	6
TNFR1A/BAG4	-0.02	0.093	-9999	-0.44	17	17
CASP8	-0.007	0.1	-9999	-0.49	15	15
CASP9	0.014	0	-9999	-10000	0	0
MAP3K14	0.009	0.11	-9999	-0.48	7	7
APAF-1/Caspase 9	-0.041	0.11	-9999	-0.41	27	27
BCL2	0.019	0.091	-9999	-0.5	2	2

×

Sphingosine 1-phosphate (S1P) pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.014	0	-9999	-10000	0	0
SPHK1	-0.025	0.14	-9999	-0.54	26	26
GNAI2	0.014	0	-9999	-10000	0	0
mol:S1P	0.007	0.066	-9999	-0.3	12	12
GNAO1	0.004	0.078	-9999	-0.6	6	6
mol:Sphinganine-1-P	-0.004	0.1	-9999	-0.38	26	26
growth factor activity	0	0	-9999	-10000	0	0
S1P/S1P2/G12/G13	0.025	0.068	-9999	-0.44	4	4
GNAI3	0.014	0	-9999	-10000	0	0
G12/G13	-0.001	0.023	-9999	-0.44	1	1
S1PR3	-0.044	0.17	-9999	-0.51	41	41
S1PR2	0.008	0.061	-9999	-0.57	4	4
EDG1	0	0	-9999	-10000	0	0
S1P1/S1P	-0.014	0.051	-9999	-0.26	12	12
S1PR5	-0.12	0.24	-9999	-0.55	90	90
S1PR4	0	0.083	-9999	-0.49	10	10
GNAI1	-0.004	0.1	-9999	-0.6	11	11
S1P/S1P5/G12	-0.058	0.15	-9999	-0.34	56	56
S1P/S1P3/Gq	-0.008	0.12	-9999	-0.45	12	12
S1P/S1P4/Gi	0.023	0.077	-9999	-0.38	7	7
GNAQ	0.014	0	-9999	-10000	0	0
GNAZ	0.012	0.032	-9999	-0.6	1	1
GNA14	-0.006	0.11	-9999	-0.56	13	13
GNA15	-0.006	0.11	-9999	-0.56	13	13
GNA12	0.012	0.032	-9999	-0.6	1	1
GNA13	0.014	0	-9999	-10000	0	0
GNA11	0.002	0.085	-9999	-0.6	7	7
ABCC1	0.011	0.037	-9999	-0.48	2	2

×

Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.013	0.026	-10000	0	-0.48	1	1
NFATC1	0.033	0.092	-10000	0	-0.44	2	2
NFATC2	0.009	0.078	-10000	0	-0.28	13	13
NFATC3	0.009	0.076	-10000	0	-0.41	10	10
YWHAE	0.014	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/CABIN1	-0.064	0.16	-10000	0	-0.51	27	27
Exportin 1/Ran/NUP214	0	0	-10000	0	-10000	0	0
mol:DAG	0	0.002	-10000	0	-10000	0	0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV	-0.14	0.18	-10000	0	-0.48	57	57
BCL2/BAX	-0.006	0.051	-10000	0	-0.44	5	5
CaM/Ca2+/Calcineurin A alpha-beta B1	0.01	0.024	-10000	0	-0.45	1	1
CaM/Ca2+	0.01	0.024	-10000	0	-0.45	1	1
BAX	0.014	0	-10000	0	-10000	0	0
MAPK14	0.014	0.004	-10000	0	-10000	0	0
BAD	0.014	0	-10000	0	-10000	0	0
CABIN1/MEF2D	-0.055	0.16	-10000	0	-0.48	28	28
Calcineurin A alpha-beta B1/BCL2	0.006	0.072	-10000	0	-0.6	5	5
FKBP8	0.014	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	0.054	0.15	0.48	28	-10000	0	28
KPNB1	0.014	0	-10000	0	-10000	0	0
KPNA2	0.013	0.026	-10000	0	-0.48	1	1
XPO1	0.014	0	-10000	0	-10000	0	0
SFN	-0.11	0.23	-10000	0	-0.52	87	87
MAP3K8	0	0.083	-10000	0	-0.5	10	10
NFAT4/CK1 alpha	-0.011	0.048	-10000	0	-0.33	1	1
MEF2D/NFAT1/Cbp/p300	0.022	0.11	-10000	0	-0.46	8	8
CABIN1	-0.064	0.16	-10000	0	-0.51	27	27
CALM1	0.012	0.032	-10000	0	-0.6	1	1
RAN	0.014	0	-10000	0	-10000	0	0
MAP3K1	0.011	0.037	-10000	0	-0.48	2	2
CAMK4	-0.17	0.27	-10000	0	-0.57	113	113
mol:Ca2+	0	0.004	-10000	0	-10000	0	0
MAPK3	0.014	0	-10000	0	-10000	0	0
YWHAH	-0.009	0.1	-10000	0	-0.48	17	17
Calcineurin A alpha-beta B1/AKAP79/PKA	-0.017	0.11	-10000	0	-0.34	37	37
YWHAB	0.014	0	-10000	0	-10000	0	0
MAPK8	-0.003	0.1	-10000	0	-0.6	10	10
MAPK9	0.014	0	-10000	0	-10000	0	0
YWHAG	0.002	0.077	-10000	0	-0.48	9	9
FKBP1A	0.014	0	-10000	0	-10000	0	0
NFAT1-c-4/YWHAQ	0.04	0.099	-10000	0	-0.43	5	5
PRKCH	0.014	0	-10000	0	-10000	0	0
CABIN1/Cbp/p300	-0.004	0.045	-10000	0	-0.44	4	4
CASP3	0.012	0.026	-10000	0	-0.48	1	1
PIM1	0.009	0.052	-10000	0	-0.48	4	4
Calcineurin A alpha-beta B1/FKBP12/FK506	0.01	0.003	-10000	0	-10000	0	0
apoptosis	-0.002	0.022	-10000	0	-0.34	1	1
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1	0.006	0.076	-10000	0	-0.3	4	4
PRKCB	-0.063	0.19	-10000	0	-0.52	53	53
PRKCE	0.002	0.08	-10000	0	-0.53	8	8
JNK2/NFAT4	0.017	0.07	-10000	0	-0.37	10	10
BAD/BCL-XL	-0.001	0.017	-10000	0	-0.33	1	1
PRKCD	-0.015	0.13	-10000	0	-0.6	17	17
NUP214	0.014	0	-10000	0	-10000	0	0
PRKCZ	-0.01	0.12	-10000	0	-0.56	15	15
PRKCA	0.012	0.032	-10000	0	-0.6	1	1
PRKCG	-0.2	0.27	-10000	0	-0.54	142	142
PRKCQ	-0.007	0.11	-10000	0	-0.58	13	13
FKBP38/BCL2	-0.006	0.051	-10000	0	-0.44	5	5
EP300	0.007	0.064	-10000	0	-0.6	4	4
PRKCB1	0	0	-10000	0	-10000	0	0
CSNK2A1	0.014	0	-10000	0	-10000	0	0
NFATc/JNK1	0.029	0.099	-10000	0	-0.49	1	1
CaM/Ca2+/FKBP38	0.018	0.021	-10000	0	-0.37	1	1
FKBP12/FK506	0	0	-10000	0	-10000	0	0
CSNK1A1	0.02	0.021	-10000	0	-0.37	1	1
CaM/Ca2+/CAMK IV	-0.097	0.18	-10000	0	-0.35	114	114
NFATc/ERK1	0.039	0.088	-10000	0	-0.49	1	1
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV	-0.14	0.18	-10000	0	-0.48	57	57
NR4A1	0.013	0.15	-10000	0	-0.45	29	29
GSK3B	0.014	0.004	-10000	0	-10000	0	0
positive T cell selection	0.009	0.076	-10000	0	-0.41	10	10
NFAT1/CK1 alpha	-0.02	0.05	-10000	0	-0.39	2	2
RCH1/ KPNB1	-0.001	0.017	-10000	0	-0.33	1	1
YWHAQ	0.014	0	-10000	0	-10000	0	0
PRKACA	0.014	0.004	-10000	0	-10000	0	0
AKAP5	-0.037	0.15	-10000	0	-0.49	37	37
MEF2D	0.012	0.037	-10000	0	-0.49	2	2
mol:FK506	0	0	-10000	0	-10000	0	0
YWHAZ	0.014	0	-10000	0	-10000	0	0
NFATc/p38 alpha	0.037	0.088	-10000	0	-0.49	1	1
CREBBP	0.014	0.002	-10000	0	-10000	0	0
BCL2	0.006	0.072	-10000	0	-0.6	5	5

×

Integrins in angiogenesis

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	-0.02	0.086	-9999	-0.38	19	19
alphaV beta3 Integrin	-0.042	0.11	-9999	-0.4	15	15
PTK2	-0.012	0.15	-9999	-0.49	15	15
IGF1R	0.014	0	-9999	-10000	0	0
PI4KB	0.014	0	-9999	-10000	0	0
MFGE8	0.009	0.056	-9999	-0.6	3	3
SRC	0.014	0	-9999	-10000	0	0
CDKN1B	-0.03	0.095	-9999	-0.5	11	11
VEGFA	-0.006	0.098	-9999	-0.48	15	15
ILK	-0.03	0.095	-9999	-0.5	11	11
ROCK1	0.014	0	-9999	-10000	0	0
AKT1	0.007	0.097	-9999	-0.46	11	11
PTK2B	-0.021	0.14	-9999	-0.5	14	14
alphaV/beta3 Integrin/JAM-A	-0.016	0.14	-9999	-0.57	7	7
CBL	0.014	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
alphaV beta3 Integrin/ANGPTL3	-0.04	0.1	-9999	-0.32	29	29
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.011	0.056	-9999	-0.32	8	8
VEGF/Rho/ROCK/alphaV/beta3 Integrin	0.01	0.087	-9999	-0.37	4	4
alphaV/beta3 Integrin/Syndecan-1	-0.062	0.14	-9999	-0.46	26	26
PI4KA	0.006	0.063	-9999	-0.48	6	6
IGF-1R heterotetramer/IGF1/IRS1	-0.045	0.11	-9999	-0.48	12	12
PI4 Kinase	-0.005	0.042	-9999	-0.33	6	6
PIK3CA	0.012	0.032	-9999	-0.6	1	1
alphaV/beta3 Integrin/Osteopontin	-0.095	0.17	-9999	-0.42	60	60
RPS6KB1	0.009	0.12	-9999	-0.45	12	12
TLN1	0.014	0	-9999	-10000	0	0
MAPK3	0.001	0.14	-9999	-0.48	16	16
GPR124	0.01	0.045	-9999	-0.48	3	3
MAPK1	0.001	0.14	-9999	-0.48	16	16
PXN	0.014	0	-9999	-10000	0	0
PIK3R1	0.014	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Tumstatin	-0.077	0.15	-9999	-0.44	34	34
cell adhesion	-0.035	0.089	-9999	-0.34	13	13
ANGPTL3	0.006	0.007	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Src	-0.016	0.072	-9999	-0.45	4	4
IGF-1R heterotetramer	0.014	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
TGFBR2	0.007	0.061	-9999	-0.5	5	5
ITGB3	-0.054	0.18	-9999	-0.51	47	47
IGF1	-0.007	0.11	-9999	-0.55	14	14
RAC1	0.014	0	-9999	-10000	0	0
regulation of cell-matrix adhesion	-0.041	0.1	-9999	-0.38	14	14
apoptosis	0.012	0.032	-9999	-0.6	1	1
CD47	0.014	0	-9999	-10000	0	0
alphaV/beta3 Integrin/CD47	-0.039	0.1	-9999	-0.36	13	13
VCL	0.005	0.071	-9999	-0.54	6	6
alphaV/beta3 Integrin/Del1	-0.087	0.17	-9999	-0.44	46	46
CSF1	-0.01	0.12	-9999	-0.6	14	14
PIK3C2A	-0.032	0.1	-9999	-0.52	12	12
PI4 Kinase/Pyk2	-0.058	0.13	-9999	-0.44	23	23
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	-0.049	0.12	-9999	-0.42	27	27
FAK1/Vinculin	-0.003	0.13	-9999	-0.44	13	13
alphaV beta3/Integrin/ppsTEM5	-0.041	0.11	-9999	-0.38	14	14
RHOA	0.014	0	-9999	-10000	0	0
VTN	-0.011	0.12	-9999	-0.55	16	16
BCAR1	0.012	0.032	-9999	-0.6	1	1
FGF2	0.009	0.052	-9999	-0.56	3	3
F11R	0.011	0.071	-9999	-0.36	13	13
alphaV/beta3 Integrin/Lactadherin	-0.042	0.11	-9999	-0.36	16	16
alphaV/beta3 Integrin/TGFBR2	-0.043	0.11	-9999	-0.42	16	16
alphaV/beta3 Integrin/c-FMS/Cbl/Cas	-0.014	0.066	-9999	-0.32	16	16
HSP90AA1	0.014	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Talin	-0.035	0.092	-9999	-0.33	13	13
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.002	0.088	-9999	-0.48	12	12
alphaV/beta3 Integrin/Pyk2	-0.021	0.14	-9999	-0.5	14	14
SDC1	-0.027	0.14	-9999	-0.49	30	30
VAV3	-0.036	0.14	-9999	-0.36	26	26
PTPN11	0.014	0	-9999	-10000	0	0
IRS1	0.014	0	-9999	-10000	0	0
FAK1/Paxillin	0	0.12	-9999	-0.39	13	13
cell migration	0.007	0.12	-9999	-0.44	8	8
ITGAV	0.012	0.032	-9999	-0.6	1	1
PI3K	-0.045	0.1	-9999	-0.51	7	7
SPP1	-0.084	0.21	-9999	-0.54	65	65
KDR	0.005	0.068	-9999	-0.52	6	6
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Caspase 8	0.012	0.032	-9999	-0.6	1	1
COL4A3	-0.053	0.18	-9999	-0.53	45	45
angiogenesis	0.003	0.14	-9999	-0.5	16	16
Rac1/GTP	-0.06	0.11	-9999	-0.5	6	6
EDIL3	-0.069	0.21	-9999	-0.58	51	51
cell proliferation	-0.043	0.11	-9999	-0.42	16	16

×

EPHB forward signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Ephrin A5/EPHB2	-0.064	0.14	-10000	0	-0.35	67	67
cell-cell adhesion	0.036	0.1	0.49	11	-10000	0	11
Ephrin B/EPHB2/RasGAP	-0.02	0.083	-10000	0	-0.4	12	12
ITSN1	0.014	0	-10000	0	-10000	0	0
PIK3CA	0.012	0.032	-10000	0	-0.6	1	1
SHC1	0.009	0.052	-10000	0	-0.48	4	4
Ephrin B1/EPHB3	-0.004	0.033	-10000	0	-0.28	5	5
Ephrin B1/EPHB1	-0.034	0.11	-10000	0	-0.38	33	33
HRAS/GDP	-0.032	0.098	-10000	0	-0.48	9	9
Ephrin B/EPHB1/GRB7	-0.06	0.14	-10000	0	-0.41	36	36
Endophilin/SYNJ1	0.018	0.09	-10000	0	-0.38	13	13
KRAS	0.013	0.026	-10000	0	-0.48	1	1
Ephrin B/EPHB1/Src	-0.04	0.12	-10000	0	-0.58	8	8
endothelial cell migration	-0.006	0.039	-10000	0	-0.3	3	3
GRB2	0.014	0	-10000	0	-10000	0	0
GRB7	-0.036	0.14	-10000	0	-0.48	34	34
PAK1	-0.005	0.13	-10000	0	-0.47	15	15
HRAS	0.013	0.026	-10000	0	-0.48	1	1
RRAS	0.019	0.092	-10000	0	-0.39	13	13
DNM1	-0.12	0.24	-10000	0	-0.52	92	92
cell-cell signaling	0	0	-10000	0	-10000	0	0
CRK	-0.001	0.12	-10000	0	-0.55	8	8
lamellipodium assembly	-0.036	0.1	-10000	0	-0.49	11	11
Ephrin B/EPHB1/Src/p52 SHC/GRB2	0.007	0.11	-10000	0	-0.51	8	8
PIK3R1	0.014	0	-10000	0	-10000	0	0
EPHB2	0.001	0.084	-10000	0	-0.52	9	9
EPHB3	0.011	0.037	-10000	0	-0.48	2	2
EPHB1	-0.038	0.17	-10000	0	-0.6	31	31
EPHB4	0.014	0	-10000	0	-10000	0	0
mol:GDP	-0.031	0.094	-10000	0	-0.44	11	11
Ephrin B/EPHB2	-0.021	0.085	-10000	0	-0.41	12	12
Ephrin B/EPHB3	-0.016	0.068	-10000	0	-0.36	9	9
JNK cascade	0.004	0.12	-10000	0	-0.34	33	33
Ephrin B/EPHB1	-0.041	0.12	-10000	0	-0.37	36	36
RAP1/GDP	-0.026	0.08	-10000	0	-0.42	7	7
EFNB2	0.003	0.077	-10000	0	-0.51	8	8
EFNB3	0	0.092	-10000	0	-0.58	9	9
EFNB1	0.01	0.045	-10000	0	-0.48	3	3
Ephrin B2/EPHB1-2	-0.041	0.12	-10000	0	-0.35	43	43
RAP1B	0.013	0.026	-10000	0	-0.48	1	1
RAP1A	0.014	0	-10000	0	-10000	0	0
CDC42/GTP	-0.037	0.11	-10000	0	-0.52	11	11
Rap1/GTP	-0.036	0.1	-10000	0	-0.49	11	11
axon guidance	-0.064	0.14	-10000	0	-0.35	67	67
MAPK3	0.022	0.1	-10000	0	-0.43	9	9
MAPK1	0.022	0.1	-10000	0	-0.43	9	9
Rac1/GDP	0.02	0.1	-10000	0	-0.41	10	10
actin cytoskeleton reorganization	-0.027	0.08	-10000	0	-0.4	9	9
CDC42/GDP	0.02	0.1	-10000	0	-0.4	11	11
PI3K	-0.006	0.039	-10000	0	-0.3	3	3
EFNA5	-0.081	0.21	-10000	0	-0.55	62	62
Ephrin B2/EPHB4	-0.007	0.045	-10000	0	-0.3	8	8
Ephrin B/EPHB2/Intersectin/N-WASP	0.024	0.071	-10000	0	-0.41	5	5
CDC42	0.014	0	-10000	0	-10000	0	0
RAS family/GTP	-0.035	0.1	-10000	0	-0.48	11	11
PTK2	0.009	0.027	-10000	0	-10000	0	0
MAP4K4	0.004	0.12	-10000	0	-0.35	33	33
SRC	0.014	0	-10000	0	-10000	0	0
KALRN	0.001	0.081	-10000	0	-0.48	10	10
Intersectin/N-WASP	0	0	-10000	0	-10000	0	0
neuron projection morphogenesis	0.018	0.12	-10000	0	-0.44	7	7
MAP2K1	0.015	0.11	-10000	0	-0.46	9	9
WASL	0.014	0	-10000	0	-10000	0	0
Ephrin B1/EPHB1-2/NCK1	-0.037	0.11	-10000	0	-0.37	33	33
cell migration	0.017	0.12	-10000	0	-0.52	8	8
NRAS	0.014	0	-10000	0	-10000	0	0
SYNJ1	0.018	0.091	-10000	0	-0.38	13	13
PXN	0.014	0	-10000	0	-10000	0	0
TF	-0.01	0.14	-10000	0	-0.58	8	8
HRAS/GTP	-0.039	0.11	-10000	0	-0.53	11	11
Ephrin B1/EPHB1-2	-0.037	0.11	-10000	0	-0.36	38	38
cell adhesion mediated by integrin	0.009	0.067	0.32	11	-10000	0	11
RAC1	0.014	0	-10000	0	-10000	0	0
mol:GTP	-0.042	0.12	-10000	0	-0.57	11	11
RAC1-CDC42/GTP	-0.036	0.11	-10000	0	-0.5	12	12
RASA1	0.014	0	-10000	0	-10000	0	0
RAC1-CDC42/GDP	-0.026	0.08	-10000	0	-0.41	8	8
ruffle organization	0.023	0.12	-10000	0	-0.49	11	11
NCK1	0.012	0.032	-10000	0	-0.6	1	1
receptor internalization	-0.041	0.15	-10000	0	-0.59	11	11
Ephrin B/EPHB2/KALRN	-0.026	0.09	-10000	0	-0.52	6	6
ROCK1	0.024	0.032	-10000	0	-0.24	5	5
RAS family/GDP	-0.025	0.076	-10000	0	-0.43	6	6
Rac1/GTP	-0.038	0.11	-10000	0	-0.52	11	11
Ephrin B/EPHB1/Src/Paxillin	0.004	0.11	-10000	0	-0.48	8	8

×

Aurora A signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Aurora A/GADD45A	0.007	0.089	-9999	-0.3	21	21
BIRC5	-0.13	0.25	-9999	-0.55	95	95
NFKBIA	0.031	0.045	-9999	-0.28	1	1
CPEB1	-0.001	0.096	-9999	-0.6	9	9
AKT1	0.031	0.045	-9999	-0.28	1	1
NDEL1	0.014	0	-9999	-10000	0	0
Aurora A/BRCA1	0.003	0.048	-9999	-0.34	3	3
NDEL1/TACC3	-0.009	0.081	-9999	-0.36	12	12
GADD45A	-0.017	0.12	-9999	-0.49	23	23
GSK3B	0.018	0.014	-9999	-10000	0	0
PAK1/Aurora A	-0.006	0.099	-9999	-0.3	12	12
MDM2	0.011	0.037	-9999	-0.48	2	2
JUB	-0.016	0.13	-9999	-0.57	19	19
TPX2	-0.035	0.15	-9999	-0.38	54	54
TP53	0.02	0.064	-9999	-0.28	11	11
DLG7	0.02	0.045	-9999	-0.3	1	1
AURKAIP1	0.013	0.026	-9999	-0.48	1	1
ARHGEF7	0.014	0	-9999	-10000	0	0
G2 phase of mitotic cell cycle	0	0	-9999	-10000	0	0
Aurora A/NDEL1/TACC3	-0.007	0.087	-9999	-0.38	12	12
G2/M transition of mitotic cell cycle	0.003	0.047	-9999	-0.34	3	3
AURKA	0.025	0.057	-9999	-0.35	1	1
AURKB	-0.079	0.13	-9999	-0.29	83	83
CDC25B	0.024	0.046	-9999	-0.28	1	1
G2/M transition checkpoint	-0.012	0.075	-9999	-0.3	16	16
mRNA polyadenylation	-0.004	0.066	-9999	-0.33	10	10
Aurora A/CPEB	-0.004	0.067	-9999	-0.34	10	10
Aurora A/TACC1/TRAP/chTOG	0.011	0.046	-9999	-10000	0	0
BRCA1	0.011	0.037	-9999	-0.48	2	2
centrosome duplication	-0.006	0.098	-9999	-0.3	12	12
regulation of centrosome cycle	-0.017	0.075	-9999	-0.36	12	12
spindle assembly	0.003	0.041	-9999	-10000	0	0
TDRD7	0.011	0.046	-9999	-0.6	2	2
Aurora A/RasGAP/Survivin	-0.069	0.12	-9999	-0.32	45	45
CENPA	-0.052	0.12	-9999	-0.32	50	50
Aurora A/PP2A	0.026	0.043	-9999	-0.28	1	1
meiosis	0	0	-9999	-10000	0	0
protein catabolic process	0.032	0.043	-9999	-0.27	1	1
negative regulation of DNA binding	0.02	0.064	-9999	-0.28	11	11
prophase	0	0	-9999	-10000	0	0
GIT1/beta-PIX	0	0	-9999	-10000	0	0
RASA1	0.014	0	-9999	-10000	0	0
Ajuba/Aurora A	-0.012	0.076	-9999	-0.3	16	16
mitotic prometaphase	0.021	0.038	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.025	0.057	-9999	-0.35	1	1
TACC1	0.014	0	-9999	-10000	0	0
TACC3	-0.016	0.12	-9999	-0.49	22	22
Aurora A/Antizyme1	0.009	0.043	-9999	-10000	0	0
Aurora A/RasGAP	0.026	0.043	-9999	-0.28	1	1
OAZ1	0.014	0	-9999	-10000	0	0
RAN	0.014	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
PRKACA	0.018	0.014	-9999	-10000	0	0
GIT1	0.014	0	-9999	-10000	0	0
GIT1/beta-PIX/PAK1	-0.029	0.086	-9999	-0.36	3	3
Importin alpha/Importin beta/TPX2	-0.035	0.15	-9999	-0.38	54	54
PPP2R5D	0.014	0	-9999	-10000	0	0
Aurora A/TPX2	-0.011	0.13	-9999	-0.36	31	31
PAK1	-0.038	0.15	-9999	-0.49	38	38
CKAP5	0.014	0	-9999	-10000	0	0

×

Regulation of Telomerase

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Telomerase catalytic core complex	-0.12	0.38	-9999	-1.1	39	39
RAD9A	0.014	0	-9999	-10000	0	0
AP1	-0.062	0.18	-9999	-0.43	66	66
IFNAR2	0.013	0.006	-9999	-10000	0	0
AKT1	0	0.051	-9999	-0.23	10	10
ER alpha/Oestrogen	-0.013	0.094	-9999	-0.4	20	20
NFX1/SIN3/HDAC complex	0.041	0.029	-9999	-10000	0	0
EGF	-0.045	0.17	-9999	-0.56	37	37
SMG5	0.014	0	-9999	-10000	0	0
SMG6	0.014	0	-9999	-10000	0	0
SP3/HDAC2	0.019	0.012	-9999	-10000	0	0
TERT/c-Abl	-0.12	0.34	-9999	-1	39	39
SAP18	0.013	0.004	-9999	-10000	0	0
MRN complex	0	0	-9999	-10000	0	0
WT1	-0.041	0.14	-9999	-0.48	35	35
WRN	0.009	0.056	-9999	-0.6	3	3
SP1	0.013	0.009	-9999	-10000	0	0
SP3	0.012	0.006	-9999	-10000	0	0
TERF2IP	0.014	0	-9999	-10000	0	0
Telomerase/Nucleolin	-0.12	0.29	-9999	-0.91	39	39
Mad/Max	0.019	0.009	-9999	-10000	0	0
TERT	-0.13	0.4	-9999	-1.2	39	39
CCND1	-0.11	0.36	-9999	-0.99	47	47
MAX	0.012	0.006	-9999	-10000	0	0
RBBP7	0.013	0.004	-9999	-10000	0	0
RBBP4	0.013	0.004	-9999	-10000	0	0
TERF2	0	0	-9999	-10000	0	0
PTGES3	0.014	0	-9999	-10000	0	0
SIN3A	0.013	0.004	-9999	-10000	0	0
Telomerase/911	0.034	0.038	-9999	-10000	0	0
CDKN1B	0.014	0.068	-9999	-10000	0	0
RAD1	0.014	0	-9999	-10000	0	0
XRCC5	0.014	0	-9999	-10000	0	0
XRCC6	0.014	0	-9999	-10000	0	0
SAP30	0.011	0.032	-9999	-0.6	1	1
TRF2/PARP2	0	0	-9999	-10000	0	0
UBE3A	0.012	0.005	-9999	-10000	0	0
JUN	0.001	0.075	-9999	-0.5	8	8
E6	-0.001	0.005	-9999	-10000	0	0
HPV-16 E6/E6AP	0.009	0.007	-9999	-10000	0	0
FOS	-0.089	0.22	-9999	-0.55	66	66
IFN-gamma/IRF1	-0.009	0.077	-9999	-0.33	15	15
PARP2	0.014	0	-9999	-10000	0	0
BLM	-0.053	0.18	-9999	-0.53	45	45
Telomerase	-0.035	0.1	-9999	-0.4	19	19
IRF1	-0.004	0.1	-9999	-0.47	16	16
ESR1	-0.017	0.13	-9999	-0.54	20	20
KU/TER	0	0	-9999	-10000	0	0
ATM/TRF2	0.022	0	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	0.046	0.03	-9999	-10000	0	0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex	0.046	0.031	-9999	-10000	0	0
HDAC1	0.01	0.046	-9999	-0.6	2	2
HDAC2	0.012	0.009	-9999	-10000	0	0
ATM	0	0	-9999	-10000	0	0
SMAD3	0.018	0.063	-9999	-0.43	7	7
ABL1	0.014	0	-9999	-10000	0	0
MXD1	0.012	0.006	-9999	-10000	0	0
MRE11A	0.014	0	-9999	-10000	0	0
HUS1	0.014	0	-9999	-10000	0	0
RPS6KB1	0.014	0	-9999	-10000	0	0
TERT/NF kappa B1/14-3-3	-0.13	0.32	-9999	-1	38	38
NR2F2	-0.011	0.12	-9999	-0.52	19	19
MAPK3	0.011	0.008	-9999	-10000	0	0
MAPK1	0.011	0.008	-9999	-10000	0	0
TGFB1/TGF beta receptor Type II	0.005	0.078	-9999	-0.6	6	6
NFKB1	0.013	0.026	-9999	-0.48	1	1
HNRNPC	0.014	0	-9999	-10000	0	0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis	0	0	-9999	-10000	0	0
NBN	0.014	0	-9999	-10000	0	0
EGFR	-0.083	0.21	-9999	-0.55	62	62
mol:Oestrogen	-0.001	0.003	-9999	-10000	0	0
EGF/EGFR	-0.092	0.2	-9999	-0.44	89	89
MYC	-0.016	0.13	-9999	-0.59	17	17
IL2	-0.003	0.014	-9999	-10000	0	0
KU	0	0	-9999	-10000	0	0
RAD50	0.014	0	-9999	-10000	0	0
HSP90AA1	0.014	0	-9999	-10000	0	0
TGFB1	0.005	0.078	-9999	-0.6	6	6
TRF2/BLM	-0.043	0.12	-9999	-0.35	45	45
FRAP1	0	0	-9999	-10000	0	0
KU/TERT	-0.1	0.35	-9999	-1	39	39
SP1/HDAC2	0.019	0.017	-9999	-10000	0	0
PINX1	0.014	0	-9999	-10000	0	0
Telomerase/EST1A	-0.12	0.29	-9999	-0.91	39	39
Smad3/Myc	0.005	0.099	-9999	-0.38	21	21
911 complex	0	0	-9999	-10000	0	0
IFNG	0.002	0.051	-9999	-0.48	4	4
Telomerase/PinX1	-0.12	0.29	-9999	-0.92	38	38
Telomerase/AKT1/mTOR/p70S6K	0.01	0.073	-9999	-10000	0	0
SIN3B	0.013	0.004	-9999	-10000	0	0
YWHAE	0.014	0	-9999	-10000	0	0
Telomerase/EST1B	-0.12	0.29	-9999	-0.92	38	38
response to DNA damage stimulus	0.004	0	-9999	-10000	0	0
MRN complex/TRF2/Rap1	0	0	-9999	-10000	0	0
TRF2/WRN	-0.003	0.037	-9999	-0.4	3	3
Telomerase/hnRNP C1/C2	-0.12	0.29	-9999	-0.91	39	39
E2F1	-0.01	0.11	-9999	-0.5	16	16
ZNFX1	0.013	0.004	-9999	-10000	0	0
PIF1	-0.048	0.18	-9999	-0.54	41	41
NCL	0.014	0	-9999	-10000	0	0
DKC1	0.014	0	-9999	-10000	0	0
telomeric DNA binding	0	0	-9999	-10000	0	0

×

E-cadherin signaling in keratinocytes

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
keratinocyte differentiation	0.016	0.071	-10000	0	-0.39	2	2
adherens junction organization	-0.037	0.12	-10000	0	-0.38	18	18
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	-0.022	0.12	-10000	0	-0.44	5	5
FMN1	-0.069	0.16	-10000	0	-0.5	21	21
mol:IP3	0.007	0.071	-10000	0	-0.4	2	2
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin	-0.021	0.12	-10000	0	-0.55	3	3
CTNNB1	0.016	0.004	-10000	0	-10000	0	0
AKT1	0.009	0.08	-10000	0	-0.44	2	2
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin	-0.038	0.16	-10000	0	-0.41	48	48
CTNND1	0.014	0.002	-10000	0	-10000	0	0
mol:PI-4-5-P2	-0.011	0.11	-10000	0	-0.51	3	3
VASP	-0.012	0.11	-10000	0	-0.52	3	3
ZYX	-0.016	0.11	-10000	0	-0.52	3	3
JUB	-0.027	0.13	-10000	0	-0.5	7	7
EGFR(dimer)	-0.06	0.15	-10000	0	-0.43	17	17
E-cadherin/beta catenin-gamma catenin	-0.088	0.15	-10000	0	-0.32	100	100
mol:PI-3-4-5-P3	-0.033	0.066	-10000	0	-0.41	3	3
PIK3CA	0.013	0.032	-10000	0	-0.6	1	1
PI3K	-0.034	0.067	-10000	0	-0.42	3	3
FYN	0.016	0.07	-10000	0	-0.33	2	2
mol:Ca2+	0.007	0.07	-10000	0	-0.39	2	2
JUP	0.003	0.086	-10000	0	-0.57	8	8
PIK3R1	0.014	0.002	-10000	0	-10000	0	0
mol:DAG	0.007	0.071	-10000	0	-0.4	2	2
CDH1	-0.13	0.24	-10000	0	-0.54	95	95
RhoA/GDP	-0.022	0.12	-10000	0	-0.44	5	5
establishment of polarity of embryonic epithelium	-0.011	0.11	-10000	0	-0.51	3	3
SRC	0.014	0	-10000	0	-10000	0	0
RAC1	0.014	0	-10000	0	-10000	0	0
RHOA	0.014	0	-10000	0	-10000	0	0
EGFR	-0.082	0.21	-10000	0	-0.55	62	62
CASR	0.004	0.079	-10000	0	-0.37	2	2
RhoA/GTP	-0.022	0.046	-10000	0	-0.36	2	2
AKT2	0.009	0.08	-10000	0	-0.44	2	2
actin cable formation	-0.06	0.16	-10000	0	-0.48	21	21
apoptosis	0.029	0.059	0.37	3	-10000	0	3
CTNNA1	0.014	0.002	-10000	0	-10000	0	0
mol:GDP	-0.032	0.13	-10000	0	-0.41	11	11
PIP5K1A	-0.011	0.11	-10000	0	-0.52	3	3
PLCG1	0.007	0.072	-10000	0	-0.41	2	2
Rac1/GTP	-0.079	0.12	-10000	0	-0.39	17	17
homophilic cell adhesion	0	0.002	-10000	0	-10000	0	0

×

S1P4 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
mol:S1P	0	0	-9999	-10000	0	0
GNAO1	0.004	0.078	-9999	-0.6	6	6
CDC42/GTP	-0.013	0.056	-9999	-0.4	4	4
PLCG1	0.028	0.068	-9999	-0.41	4	4
mol:GTP	0	0	-9999	-10000	0	0
GNAI2	0.014	0	-9999	-10000	0	0
GNAI3	0.014	0	-9999	-10000	0	0
G12/G13	-0.001	0.023	-9999	-0.44	1	1
cell migration	-0.013	0.055	-9999	-0.39	4	4
S1PR5	-0.12	0.24	-9999	-0.55	90	90
S1PR4	0	0.083	-9999	-0.49	10	10
MAPK3	0.028	0.068	-9999	-0.41	4	4
MAPK1	0.028	0.068	-9999	-0.41	4	4
S1P/S1P5/Gi	-0.034	0.14	-9999	-0.3	55	55
GNAI1	-0.004	0.1	-9999	-0.6	11	11
CDC42/GDP	0	0	-9999	-10000	0	0
S1P/S1P5/G12	-0.084	0.15	-9999	-0.34	90	90
RHOA	0.026	0.047	-9999	-0.3	2	2
S1P/S1P4/Gi	0.021	0.072	-9999	-0.35	8	8
mol:GDP	0	0	-9999	-10000	0	0
GNAZ	0.012	0.032	-9999	-0.6	1	1
S1P/S1P4/G12/G13	-0.008	0.045	-9999	-0.33	2	2
GNA12	0.012	0.032	-9999	-0.6	1	1
GNA13	0.014	0	-9999	-10000	0	0
CDC42	0.014	0	-9999	-10000	0	0

×

BARD1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BARD1/CSTF1	-0.025	0.1	-10000	0	-0.43	21	21
ATM	0.014	0	-10000	0	-10000	0	0
UBE2D3	0.014	0	-10000	0	-10000	0	0
PRKDC	0.014	0	-10000	0	-10000	0	0
ATR	0.014	0	-10000	0	-10000	0	0
UBE2L3	0.014	0	-10000	0	-10000	0	0
FANCD2	0.017	0.054	-10000	0	-0.35	4	4
protein ubiquitination	-0.025	0.092	-10000	0	-0.33	26	26
XRCC5	0.014	0	-10000	0	-10000	0	0
XRCC6	0.014	0	-10000	0	-10000	0	0
M/R/N Complex	0	0	-10000	0	-10000	0	0
MRE11A	0.014	0	-10000	0	-10000	0	0
DNA-PK	0	0	-10000	0	-10000	0	0
FA complex/FANCD2/Ubiquitin	-0.012	0.052	-10000	0	-0.42	3	3
FANCF	0.014	0	-10000	0	-10000	0	0
BRCA1	0.011	0.037	-10000	0	-0.48	2	2
CCNE1	0.011	0.037	-10000	0	-0.48	2	2
CDK2/Cyclin E1	-0.011	0.068	-10000	0	-0.4	10	10
FANCG	0.014	0	-10000	0	-10000	0	0
BRCA1/BACH1/BARD1	-0.026	0.1	-10000	0	-0.44	22	22
FANCE	0.014	0	-10000	0	-10000	0	0
FANCC	0.011	0.041	-10000	0	-0.54	2	2
NBN	0.014	0	-10000	0	-10000	0	0
FANCA	-0.021	0.13	-10000	0	-0.52	24	24
DNA repair	0.019	0.14	-10000	0	-0.5	12	12
BRCA1/BARD1/ubiquitin	-0.026	0.1	-10000	0	-0.44	22	22
BARD1/DNA-PK	-0.018	0.074	-10000	0	-0.32	19	19
FANCL	0.014	0	-10000	0	-10000	0	0
mRNA polyadenylation	0.025	0.099	0.43	21	-10000	0	21
BRCA1/BARD1/CTIP/M/R/N Complex	0.027	0.069	-10000	0	-0.36	2	2
BRCA1/BACH1/BARD1/TopBP1	-0.022	0.088	-10000	0	-0.37	20	20
BRCA1/BARD1/P53	-0.03	0.1	-10000	0	-0.35	29	29
BARD1/CSTF1/BRCA1	-0.022	0.088	-10000	0	-0.36	22	22
BRCA1/BACH1	0.011	0.036	-10000	0	-0.48	2	2
BARD1	-0.021	0.14	-10000	0	-0.59	21	21
PCNA	0.013	0.026	-10000	0	-0.48	1	1
BRCA1/BARD1/UbcH5C	-0.022	0.088	-10000	0	-0.37	20	20
BRCA1/BARD1/UbcH7	-0.022	0.088	-10000	0	-0.36	22	22
BRCA1/BARD1/RAD51/PCNA	-0.052	0.13	-10000	0	-0.38	33	33
BARD1/DNA-PK/P53	-0.026	0.09	-10000	0	-0.32	28	28
BRCA1/BARD1/Ubiquitin	-0.026	0.1	-10000	0	-0.44	22	22
BRCA1/BARD1/CTIP	0.012	0.095	-10000	0	-0.36	20	20
FA complex	0.03	0.054	-10000	0	-10000	0	0
BARD1/EWS	-0.025	0.1	-10000	0	-0.43	21	21
RBBP8	0.022	0.032	-10000	0	-0.34	3	3
TP53	-0.006	0.11	-10000	0	-0.59	12	12
TOPBP1	0.014	0	-10000	0	-10000	0	0
G1/S transition of mitotic cell cycle	0.03	0.1	0.35	29	-10000	0	29
BRCA1/BARD1	-0.026	0.094	-10000	0	-0.33	26	26
CSTF1	0.014	0	-10000	0	-10000	0	0
BARD1/EWS-Fli1	-0.025	0.1	-10000	0	-0.44	21	21
CDK2	0.001	0.086	-10000	0	-0.54	9	9
UniProt:Q9BZD1	0	0	-10000	0	-10000	0	0
RAD51	-0.05	0.17	-10000	0	-0.52	44	44
RAD50	0.014	0	-10000	0	-10000	0	0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme	-0.026	0.1	-10000	0	-0.44	22	22
EWSR1	0.014	0	-10000	0	-10000	0	0

×

Insulin-mediated glucose transport

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
Insulin responsive Vesicles	-0.035	0.09	0.16	2	-0.38	11	13
CaM/Ca2+	-0.001	0.023	-10000	0	-0.45	1	1
AKT1	0.014	0	-10000	0	-10000	0	0
AKT2	0.014	0	-10000	0	-10000	0	0
STXBP4	0.014	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucose	0.025	0.13	0.24	40	-0.43	10	50
YWHAZ	0.014	0	-10000	0	-10000	0	0
CALM1	0.012	0.032	-10000	0	-0.6	1	1
YWHAQ	0.014	0	-10000	0	-10000	0	0
TBC1D4	0.025	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
YWHAH	-0.009	0.1	-10000	0	-0.48	17	17
YWHAB	0.014	0	-10000	0	-10000	0	0
SNARE/Synip	0	0	-10000	0	-10000	0	0
YWHAG	0.002	0.077	-10000	0	-0.48	9	9
ASIP	-0.086	0.22	-10000	0	-0.55	64	64
PRKCI	0.014	0	-10000	0	-10000	0	0
AS160/CaM/Ca2+	-0.001	0.023	-10000	0	-0.45	1	1
RHOQ	0.014	0	-10000	0	-10000	0	0
GYS1	0.034	0	-10000	0	-10000	0	0
PRKCZ	-0.01	0.12	-10000	0	-0.56	15	15
TRIP10	0.005	0.071	-10000	0	-0.54	6	6
TC10/GTP/CIP4/Exocyst	-0.005	0.042	-10000	0	-0.33	6	6
AS160/14-3-3	0.004	0.087	-10000	0	-0.36	4	4
VAMP2	0.014	0	-10000	0	-10000	0	0
SLC2A4	0.024	0.14	0.27	20	-0.49	10	30
STX4	0.014	0	-10000	0	-10000	0	0
GSK3B	0.028	0	-10000	0	-10000	0	0
SFN	-0.11	0.23	-10000	0	-0.52	87	87
LNPEP	-0.021	0.14	-10000	0	-0.6	21	21
YWHAE	0.014	0	-10000	0	-10000	0	0

×

Signaling mediated by p38-gamma and p38-delta

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
EEF2K	0.006	0.094	-9999	-0.32	27	27
SNTA1	-0.014	0.12	-9999	-0.56	18	18
response to hypoxia	0	0	-9999	-10000	0	0
STMN1	0.005	0.096	-9999	-0.32	28	28
MAPK12	0.028	0.037	-9999	-0.3	3	3
CCND1	0.007	0.073	-9999	-0.42	9	9
p38 gamma/SNTA1	0.018	0.076	-9999	-0.3	15	15
MAP2K3	0.011	0.037	-9999	-0.48	2	2
PKN1	0.014	0	-9999	-10000	0	0
G2/M transition checkpoint	0.028	0.036	-9999	-0.3	3	3
MAP2K6	0.022	0.035	-9999	-0.33	2	2
MAPT	0.009	0.09	-9999	-0.32	20	20
MAPK13	-0.006	0.11	-9999	-0.39	27	27
hyperosmotic response	0	0	-9999	-10000	0	0
ZAK	0.014	0.033	-9999	-0.22	7	7

×

Regulation of p38-alpha and p38-beta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
RIP1/MEKK3	0	0	-9999	-10000	0	0
response to insulin stimulus	0	0	-9999	-10000	0	0
RIPK1	0.014	0	-9999	-10000	0	0
response to stress	0	0	-9999	-10000	0	0
MAP2K6	0.012	0.032	-9999	-0.6	1	1
mol:GTP	0	0	-9999	-10000	0	0
MAP2K4	0.011	0.037	-9999	-0.48	2	2
RAC1-CDC42/GTP/PAK family	-0.032	0.1	-9999	-0.22	72	72
response to UV	0	0	-9999	-10000	0	0
YES1	0.011	0.046	-9999	-0.6	2	2
interleukin-1 receptor activity	0	0	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
MAP3K3	0.014	0	-9999	-10000	0	0
FYN	0.014	0	-9999	-10000	0	0
MAP3K12	0.014	0	-9999	-10000	0	0
FGR	0.011	0.037	-9999	-0.48	2	2
p38 alpha/TAB1	-0.024	0.057	-9999	-0.4	3	3
PRKG1	-0.048	0.18	-9999	-0.58	38	38
DUSP8	-0.001	0.091	-9999	-0.54	10	10
PGK/cGMP/p38 alpha	-0.047	0.091	-9999	-0.31	25	25
apoptosis	-0.023	0.054	-9999	-0.39	3	3
RAL/GTP	0	0	-9999	-10000	0	0
LYN	0.006	0.063	-9999	-0.48	6	6
DUSP1	-0.022	0.14	-9999	-0.54	24	24
PAK1	-0.038	0.15	-9999	-0.49	38	38
SRC	0.014	0	-9999	-10000	0	0
RAC1/OSM/MEKK3/MKK3	-0.001	0.018	-9999	-10000	0	0
TRAF6	0.012	0.032	-9999	-0.6	1	1
RAC1	0.014	0	-9999	-10000	0	0
epidermal growth factor receptor activity	0	0	-9999	-10000	0	0
mol:LPS	0	0	-9999	-10000	0	0
mol:cGMP	0	0	-9999	-10000	0	0
CCM2	0.014	0	-9999	-10000	0	0
RAC1-CDC42/GTP	0	0	-9999	-10000	0	0
MAPK11	-0.001	0.097	-9999	-0.39	7	7
BLK	-0.095	0.21	-9999	-0.5	76	76
HCK	-0.013	0.12	-9999	-0.53	18	18
MAP2K3	0.011	0.037	-9999	-0.48	2	2
DUSP16	0.014	0	-9999	-10000	0	0
DUSP10	-0.009	0.11	-9999	-0.55	15	15
TRAF6/MEKK3	-0.001	0.018	-9999	-0.34	1	1
MAP3K7IP1	0	0	-9999	-10000	0	0
MAPK14	0.009	0.08	-9999	-0.39	4	4
positive regulation of innate immune response	0.004	0.11	-9999	-0.42	7	7
LCK	-0.088	0.21	-9999	-0.53	68	68
p38alpha-beta/MKP7	0.011	0.1	-9999	-0.47	4	4
p38alpha-beta/MKP5	0.001	0.11	-9999	-0.44	7	7
PGK/cGMP	-0.045	0.13	-9999	-0.43	38	38
PAK2	0.014	0	-9999	-10000	0	0
p38alpha-beta/MKP1	-0.005	0.12	-9999	-0.46	6	6
CDC42	0.014	0	-9999	-10000	0	0
RALB	0.014	0	-9999	-10000	0	0
RALA	0.014	0	-9999	-10000	0	0
PAK3	-0.11	0.24	-9999	-0.56	80	80

×

Plasma membrane estrogen receptor signaling

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
GNB1/GNG2	-0.026	0.082	-10000	0	-0.31	21	21
ER alpha/Gai/GDP/Gbeta gamma	0.021	0.1	-10000	0	-0.4	15	15
AKT1	0.012	0.13	-10000	0	-0.72	11	11
PIK3CA	0.012	0.032	-10000	0	-0.6	1	1
E2/ER alpha (dimer)/PELP1/Src/PI3K	0.011	0.13	-10000	0	-0.73	11	11
mol:Ca2+	-0.005	0.14	-10000	0	-0.49	16	16
IGF1R	0.014	0	-10000	0	-10000	0	0
E2/ER alpha (dimer)/Striatin	-0.039	0.12	-10000	0	-0.36	40	40
SHC1	0.009	0.052	-10000	0	-0.48	4	4
apoptosis	-0.013	0.13	0.69	11	-10000	0	11
RhoA/GTP	-0.013	0.053	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas	-0.024	0.085	-10000	0	-0.4	15	15
regulation of stress fiber formation	-0.011	0.11	0.39	10	-10000	0	10
E2/ERA-ERB (dimer)	-0.029	0.097	-10000	0	-0.34	31	31
KRAS	0.013	0.026	-10000	0	-0.48	1	1
G13/GTP	-0.016	0.068	-10000	0	-0.3	20	20
pseudopodium formation	0.011	0.11	-10000	0	-0.39	10	10
E2/ER alpha (dimer)/PELP1	-0.018	0.075	-10000	0	-0.33	20	20
GRB2	0.014	0	-10000	0	-10000	0	0
GNG2	0.009	0.056	-10000	0	-0.6	3	3
GNAO1	0.004	0.078	-10000	0	-0.6	6	6
HRAS	0.013	0.026	-10000	0	-0.48	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
mol:NO	0.023	0.1	-10000	0	-0.45	11	11
E2/ER beta (dimer)	-0.013	0.073	-10000	0	-0.4	12	12
mol:GDP	-0.024	0.085	-10000	0	-0.37	18	18
mol:NADP	0.023	0.1	-10000	0	-0.45	11	11
PIK3R1	0.014	0	-10000	0	-10000	0	0
mol:IP3	-0.006	0.14	-10000	0	-0.51	16	16
IGF-1R heterotetramer	0.014	0	-10000	0	-10000	0	0
PLCB1	-0.001	0.12	-10000	0	-0.47	12	12
PLCB2	-0.004	0.13	-10000	0	-0.55	13	13
IGF1	-0.007	0.11	-10000	0	-0.55	14	14
mol:L-citrulline	0.023	0.1	-10000	0	-0.45	11	11
RHOA	0.014	0	-10000	0	-10000	0	0
Gai/GDP	-0.019	0.1	-10000	0	-0.76	6	6
JNK cascade	-0.013	0.072	-10000	0	-0.4	12	12
BCAR1	0.012	0.032	-10000	0	-0.6	1	1
ESR2	-0.004	0.1	-10000	0	-0.55	12	12
GNAQ	0.014	0	-10000	0	-10000	0	0
ESR1	-0.016	0.13	-10000	0	-0.54	20	20
Gq family/GDP/Gbeta gamma	0.013	0.11	-10000	0	-0.44	17	17
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1	0.03	0.058	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC	-0.025	0.089	-10000	0	-0.42	15	15
GNAZ	0.012	0.032	-10000	0	-0.6	1	1
E2/ER alpha (dimer)	-0.022	0.091	-10000	0	-0.4	20	20
STRN	-0.021	0.14	-10000	0	-0.6	21	21
GNAL	-0.05	0.19	-10000	0	-0.6	38	38
PELP1	0.014	0	-10000	0	-10000	0	0
MAPK11	0.006	0.073	-10000	0	-0.34	15	15
GNAI2	0.014	0	-10000	0	-10000	0	0
GNAI3	0.014	0	-10000	0	-10000	0	0
GNAI1	-0.004	0.1	-10000	0	-0.6	11	11
HBEGF	-0.014	0.13	-10000	0	-0.48	9	9
cAMP biosynthetic process	-0.054	0.12	-10000	0	-0.33	54	54
SRC	0.029	0.098	-10000	0	-0.38	15	15
PI3K	-0.001	0.023	-10000	0	-0.44	1	1
GNB1	0.014	0	-10000	0	-10000	0	0
G13/GDP/Gbeta gamma	-0.023	0.075	-10000	0	-0.35	11	11
SOS1	0.014	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1	-0.027	0.084	-10000	0	-0.47	5	5
Gs family/GTP	-0.054	0.12	-10000	0	-0.33	53	53
EntrezGene:2778	0	0	-10000	0	-10000	0	0
RAS family/GTP	-0.001	0.018	-10000	0	-10000	0	0
vasodilation	0.023	0.1	-10000	0	-0.43	11	11
mol:DAG	-0.006	0.14	-10000	0	-0.51	16	16
Gs family/GDP/Gbeta gamma	-0.045	0.1	-10000	0	-0.38	18	18
MSN	0.01	0.11	-10000	0	-0.43	10	10
Gq family/GTP	0	0.1	-10000	0	-0.5	9	9
mol:PI-3-4-5-P3	0.012	0.13	-10000	0	-0.7	11	11
NRAS	0.014	0	-10000	0	-10000	0	0
mol:E2	0	0	-10000	0	-10000	0	0
cell adhesion	-0.023	0.1	0.43	11	-10000	0	11
GRB2/SOS1	0	0	-10000	0	-10000	0	0
RhoA/GDP	-0.023	0.079	-10000	0	-0.34	18	18
NOS3	0.022	0.11	-10000	0	-0.48	11	11
GNA11	0.002	0.085	-10000	0	-0.6	7	7
MAPKKK cascade	0.016	0.14	-10000	0	-0.42	30	30
E2/ER alpha (dimer)/PELP1/Src	-0.025	0.088	-10000	0	-0.42	15	15
ruffle organization	0.011	0.11	-10000	0	-0.39	10	10
ROCK2	0.025	0.09	-10000	0	-0.5	3	3
GNA14	-0.006	0.11	-10000	0	-0.56	13	13
GNA15	-0.006	0.11	-10000	0	-0.56	13	13
GNA13	0.014	0	-10000	0	-10000	0	0
MMP9	-0.043	0.15	-10000	0	-0.47	13	13
MMP2	0.019	0.12	-10000	0	-0.48	8	8

×

Regulation of Androgen receptor activity

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.022	0.034	-9999	-0.44	2	2
SMARCC1	0.009	0.013	-9999	-10000	0	0
REL	-0.031	0.16	-9999	-0.57	29	29
HDAC7	0.021	0.1	-9999	-0.37	7	7
JUN	0.002	0.075	-9999	-0.5	8	8
EP300	0.007	0.064	-9999	-0.6	4	4
KAT2B	0.013	0.026	-9999	-0.48	1	1
KAT5	0.014	0	-9999	-10000	0	0
MAPK14	0.022	0.027	-9999	-0.43	1	1
FOXO1	0.009	0.052	-9999	-0.56	3	3
T-DHT/AR	0.017	0.11	-9999	-0.4	7	7
MAP2K6	0.012	0.033	-9999	-0.6	1	1
BRM/BAF57	0.004	0.025	-9999	-0.44	1	1
MAP2K4	0.011	0.037	-9999	-0.49	2	2
SMARCA2	0.012	0.032	-9999	-0.6	1	1
PDE9A	-0.025	0.099	-9999	-0.9	2	2
NCOA2	-0.035	0.17	-9999	-0.6	29	29
CEBPA	-0.015	0.13	-9999	-0.56	19	19
EHMT2	0.013	0.004	-9999	-10000	0	0
cell proliferation	0.028	0.13	-9999	-0.44	10	10
NR0B1	-0.084	0.22	-9999	-0.55	63	63
EGR1	-0.1	0.23	-9999	-0.53	79	79
RXRs/9cRA	-0.035	0.11	-9999	-0.33	45	45
AR/RACK1/Src	-0.012	0.079	-9999	-0.37	8	8
AR/GR	-0.014	0.12	-9999	-0.37	16	16
GNB2L1	0.014	0.001	-9999	-10000	0	0
PKN1	0.014	0	-9999	-10000	0	0
RCHY1	0.014	0	-9999	-10000	0	0
epidermal growth factor receptor activity	0	0.002	-9999	-10000	0	0
MAPK8	0.009	0.081	-9999	-0.42	12	12
T-DHT/AR/TIF2/CARM1	-0.006	0.14	-9999	-0.51	19	19
SRC	0.028	0.066	-9999	-0.29	10	10
NR3C1	0.014	0	-9999	-10000	0	0
KLK3	-0.047	0.14	-9999	-0.46	18	18
APPBP2	0.014	0.005	-9999	-10000	0	0
TRIM24	0.012	0.026	-9999	-0.48	1	1
T-DHT/AR/TIP60	0.012	0.087	-9999	-0.37	11	11
TMPRSS2	-0.13	0.32	-9999	-1.1	32	32
RXRG	-0.061	0.2	-9999	-0.6	45	45
mol:9cRA	0	0.001	-9999	-10000	0	0
RXRA	0.014	0.001	-9999	-10000	0	0
RXRB	0.014	0.001	-9999	-10000	0	0
CARM1	0.014	0.001	-9999	-10000	0	0
NR2C2	0.002	0.085	-9999	-0.6	7	7
KLK2	-0.011	0.15	-9999	-0.49	13	13
AR	-0.022	0.13	-9999	-0.3	53	53
SENP1	0.014	0.001	-9999	-10000	0	0
HSP90AA1	0.014	0	-9999	-10000	0	0
MDM2	0.013	0.037	-9999	-0.48	2	2
SRY	-0.011	0.086	-9999	-0.48	12	12
GATA2	-0.01	0.12	-9999	-0.56	15	15
MYST2	0.014	0.001	-9999	-10000	0	0
HOXB13	-0.05	0.16	-9999	-0.49	41	41
T-DHT/AR/RACK1/Src	0.019	0.087	-9999	-0.38	8	8
positive regulation of transcription	-0.01	0.12	-9999	-0.56	15	15
DNAJA1	0.014	0.005	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.03	0.024	-9999	-0.25	2	2
NCOA1	0.017	0.005	-9999	-10000	0	0
SPDEF	-0.044	0.17	-9999	-0.53	39	39
T-DHT/AR/TIF2	0.011	0.13	-9999	-0.62	10	10
T-DHT/AR/Hsp90	0.012	0.087	-9999	-0.37	12	12
GSK3B	0.014	0.003	-9999	-10000	0	0
NR2C1	0.014	0.001	-9999	-10000	0	0
mol:T-DHT	0.022	0.07	-9999	-0.32	12	12
SIRT1	0.014	0	-9999	-10000	0	0
ZMIZ2	0.015	0.005	-9999	-10000	0	0
POU2F1	0.023	0.036	-9999	-0.6	1	1
T-DHT/AR/DAX-1	-0.04	0.15	-9999	-0.39	34	34
CREBBP	0.014	0	-9999	-10000	0	0
SMARCE1	0.013	0.003	-9999	-10000	0	0

×

Nectin adhesion 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.01	0.045	-9999	-0.48	3	3
alphaV beta3 Integrin	-0.048	0.12	-9999	-0.36	48	48
PTK2	-0.034	0.12	-9999	-0.53	15	15
positive regulation of JNK cascade	-0.011	0.053	-9999	-0.33	9	9
CDC42/GDP	0.043	0.085	-9999	-0.45	9	9
Rac1/GDP	0.045	0.085	-9999	-0.44	9	9
RAP1B	0.013	0.026	-9999	-0.48	1	1
RAP1A	0.014	0	-9999	-10000	0	0
CTNNB1	0.014	0	-9999	-10000	0	0
CDC42/GTP	-0.013	0.066	-9999	-0.41	9	9
nectin-3/I-afadin	-0.011	0.068	-9999	-0.44	9	9
RAPGEF1	0.037	0.095	-9999	-0.51	9	9
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.029	0.11	-9999	-0.59	9	9
PDGFB-D/PDGFRB	0.01	0.045	-9999	-0.48	3	3
TLN1	0.031	0.036	-9999	-0.35	1	1
Rap1/GTP	-0.012	0.057	-9999	-0.35	9	9
IQGAP1	0.005	0.068	-9999	-0.52	6	6
Rap1/GTP/I-afadin	-0.002	0.022	-9999	-0.29	2	2
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin	-0.011	0.068	-9999	-0.44	9	9
PVR	0.014	0	-9999	-10000	0	0
Necl-5(dimer)	0.014	0	-9999	-10000	0	0
mol:GDP	0.04	0.1	-9999	-0.56	9	9
MLLT4	0.012	0.032	-9999	-0.6	1	1
PIK3CA	0.012	0.032	-9999	-0.6	1	1
PI3K	-0.01	0.056	-9999	-0.54	1	1
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin	-0.016	0.081	-9999	-0.44	13	13
positive regulation of lamellipodium assembly	-0.011	0.056	-9999	-0.35	9	9
PVRL1	-0.006	0.11	-9999	-0.6	12	12
PVRL3	0.001	0.09	-9999	-0.6	8	8
PVRL2	0.011	0.041	-9999	-0.54	2	2
PIK3R1	0.014	0	-9999	-10000	0	0
CDH1	-0.13	0.25	-9999	-0.54	95	95
CLDN1	-0.017	0.12	-9999	-0.52	21	21
JAM-A/CLDN1	-0.03	0.095	-9999	-0.36	20	20
SRC	-0.024	0.11	-9999	-0.67	9	9
ITGB3	-0.054	0.18	-9999	-0.51	47	47
nectin-1(dimer)/I-afadin/I-afadin	-0.016	0.081	-9999	-0.44	13	13
FARP2	0.034	0.1	-9999	-0.55	9	9
RAC1	0.014	0	-9999	-10000	0	0
CTNNA1	0.014	0	-9999	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer)	-0.009	0.057	-9999	-0.36	9	9
nectin-1/I-afadin	-0.016	0.081	-9999	-0.44	13	13
nectin-2/I-afadin	-0.003	0.037	-9999	-0.4	3	3
RAC1/GTP/IQGAP1/filamentous actin	-0.005	0.04	-9999	-0.31	6	6
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin	-0.021	0.092	-9999	-0.4	19	19
CDC42/GTP/IQGAP1/filamentous actin	-0.005	0.04	-9999	-0.31	6	6
F11R	0	0.083	-9999	-0.49	10	10
positive regulation of filopodium formation	-0.011	0.053	-9999	-0.33	9	9
alphaV/beta3 Integrin/Talin	0.01	0.1	-9999	-0.44	5	5
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	-0.003	0.037	-9999	-0.4	3	3
nectin-2(dimer)/I-afadin/I-afadin	-0.003	0.037	-9999	-0.4	3	3
PIP5K1C	0.024	0.039	-9999	-0.38	1	1
VAV2	0.033	0.1	-9999	-0.56	9	9
RAP1/GDP	-0.013	0.066	-9999	-0.41	9	9
ITGAV	0.012	0.032	-9999	-0.6	1	1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin	-0.011	0.061	-9999	-0.36	11	11
nectin-3(dimer)/I-afadin/I-afadin	-0.011	0.068	-9999	-0.44	9	9
Rac1/GTP	-0.013	0.068	-9999	-0.42	9	9
PTPRM	0.015	0.042	-9999	-0.24	9	9
E-cadherin/beta catenin/alpha catenin	-0.074	0.13	-9999	-0.61	6	6
adherens junction assembly	0	0	-9999	-10000	0	0
CDC42	0.014	0	-9999	-10000	0	0

×

ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K4	-0.014	0.12	-10000	0	-0.45	11	11
BAG4	-0.006	0.11	-10000	0	-0.6	12	12
BAD	0.009	0.044	-10000	0	-0.19	1	1
NFKBIA	0.014	0	-10000	0	-10000	0	0
BIRC3	-0.035	0.16	-10000	0	-0.55	32	32
BAX	0.009	0.044	-10000	0	-0.19	1	1
EnzymeConsortium:3.1.4.12	-0.003	0.032	-10000	0	-0.099	11	11
IKBKB	-0.005	0.11	-10000	0	-0.42	11	11
MAP2K2	0.019	0.048	-10000	0	-10000	0	0
MAP2K1	0.018	0.05	-10000	0	-0.3	1	1
SMPD1	0.004	0.032	-10000	0	-0.14	1	1
GO:0005551	0	0	-10000	0	-10000	0	0
FADD/Caspase 8	-0.008	0.12	-10000	0	-0.42	12	12
MAP2K4	0.013	0.05	-10000	0	-0.29	1	1
protein ubiquitination	-0.004	0.12	-10000	0	-0.42	11	11
EnzymeConsortium:2.7.1.37	0.02	0.055	-10000	0	-0.29	1	1
response to UV	0	0.001	-10000	0	-0.002	2	2
RAF1	0.014	0.047	-10000	0	-10000	0	0
CRADD	0.014	0	-10000	0	-10000	0	0
mol:ceramide	0.001	0.045	-10000	0	-0.16	6	6
I-kappa-B-alpha/RELA/p50/ubiquitin	0	0	-10000	0	-10000	0	0
MADD	0.014	0	-10000	0	-10000	0	0
MAP3K1	0.007	0.047	-10000	0	-0.2	3	3
TRADD	0.011	0.041	-10000	0	-0.54	2	2
RELA/p50	0.014	0	-10000	0	-10000	0	0
MAPK3	0.021	0.049	-10000	0	-10000	0	0
MAPK1	0.021	0.049	-10000	0	-10000	0	0
p50/RELA/I-kappa-B-alpha	0	0	-10000	0	-10000	0	0
FADD	-0.013	0.12	-10000	0	-0.45	11	11
KSR1	0.008	0.046	-10000	0	-0.21	1	1
MAPK8	0.012	0.068	-10000	0	-0.28	11	11
TRAF2	0.014	0	-10000	0	-10000	0	0
response to radiation	0	0	-10000	0	-10000	0	0
CHUK	-0.005	0.11	-10000	0	-0.42	11	11
TNF R/SODD	-0.019	0.094	-10000	0	-0.44	17	17
TNF	-0.15	0.25	-10000	0	-0.54	109	109
CYCS	0.012	0.044	0.14	3	-0.19	1	4
IKBKG	-0.005	0.11	-10000	0	-0.42	11	11
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD	-0.022	0.12	-10000	0	-0.48	11	11
RELA	0.014	0	-10000	0	-10000	0	0
RIPK1	0.014	0	-10000	0	-10000	0	0
AIFM1	0.012	0.044	0.14	3	-0.19	1	4
TNF/TNF R/SODD	-0.11	0.17	-10000	0	-0.34	120	120
TNFRSF1A	0.005	0.068	-10000	0	-0.52	6	6
response to heat	0	0	-10000	0	-10000	0	0
CASP8	0.007	0.056	-10000	0	-0.72	1	1
NSMAF	-0.013	0.12	-10000	0	-0.44	11	11
response to hydrogen peroxide	0	0.001	-10000	0	-0.002	2	2
BCL2	0.006	0.072	-10000	0	-0.6	5	5

×

Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A	-0.1	0.23	-9999	-0.56	72	72
oxygen homeostasis	0	0	-9999	-10000	0	0
TCEB2	0.014	0	-9999	-10000	0	0
TCEB1	0.014	0	-9999	-10000	0	0
HIF1A/p53	0.022	0.058	-9999	-0.28	11	11
HIF1A	0.025	0.019	-9999	-10000	0	0
COPS5	0.014	0	-9999	-10000	0	0
VHL/Elongin B/Elongin C/RBX1/CUL2	0	0	-9999	-10000	0	0
FIH (dimer)	0.014	0	-9999	-10000	0	0
CDKN2A	-0.1	0.24	-9999	-0.57	74	74
ARNT/IPAS	-0.081	0.16	-9999	-0.4	73	73
HIF1AN	0.014	0	-9999	-10000	0	0
GNB2L1	0.014	0	-9999	-10000	0	0
HIF1A/ARNT	0.032	0.025	-9999	-0.3	1	1
CUL2	0.014	0	-9999	-10000	0	0
OS9	0.006	0.063	-9999	-0.48	6	6
RACK1/Elongin B/Elongin C	0	0	-9999	-10000	0	0
response to hypoxia	0	0	-9999	-10000	0	0
HIF1A/Hsp90	0.032	0.019	-9999	-10000	0	0
PHD1-3/OS9	-0.008	0.048	-9999	-0.32	5	5
HIF1A/RACK1/Elongin B/Elongin C	-0.001	0.01	-9999	-10000	0	0
VHL	0.014	0	-9999	-10000	0	0
HSP90AA1	0.014	0	-9999	-10000	0	0
HIF1A/JAB1	0.032	0.019	-9999	-10000	0	0
EGLN3	0.006	0.072	-9999	-0.6	5	5
EGLN2	0.014	0	-9999	-10000	0	0
EGLN1	0.014	0	-9999	-10000	0	0
TP53	-0.006	0.11	-9999	-0.59	12	12
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A	0.041	0.005	-9999	-10000	0	0
ARNT	0.013	0.026	-9999	-0.48	1	1
ARD1A	0	0	-9999	-10000	0	0
RBX1	0.014	0	-9999	-10000	0	0
HIF1A/p19ARF	-0.028	0.12	-9999	-0.28	59	59

×

Class I PI3K signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ARF5/GTP	-0.014	0.046	-9999	-10000	0	0
DAPP1	-0.03	0.14	-9999	-0.42	27	27
Src family/SYK family/BLNK-LAT/BTK-ITK	-0.084	0.22	-9999	-0.57	41	41
mol:DAG	-0.027	0.11	-9999	-0.29	20	20
HRAS	0.013	0.026	-9999	-0.48	1	1
RAP1A	0.014	0.003	-9999	-10000	0	0
ARF5/GDP	0.029	0.056	-9999	-0.29	4	4
PLCG2	0.002	0.082	-9999	-0.54	8	8
PLCG1	0.014	0	-9999	-10000	0	0
ARF5	0.014	0	-9999	-10000	0	0
mol:GTP	-0.016	0.053	-9999	-10000	0	0
ARF1/GTP	-0.013	0.043	-9999	-10000	0	0
RHOA	0.014	0	-9999	-10000	0	0
YES1	0.011	0.046	-9999	-0.6	2	2
RAP1A/GTP	-0.015	0.053	-9999	-10000	0	0
ADAP1	-0.028	0.081	-9999	-0.49	4	4
ARAP3	-0.016	0.053	-9999	-10000	0	0
INPPL1	0.014	0	-9999	-10000	0	0
PREX1	0.002	0.085	-9999	-0.6	7	7
ARHGEF6	0.009	0.056	-9999	-0.6	3	3
ARHGEF7	0.014	0	-9999	-10000	0	0
ARF1	0.014	0	-9999	-10000	0	0
NRAS	0.014	0.003	-9999	-10000	0	0
FYN	0.014	0	-9999	-10000	0	0
ARF6	0.014	0	-9999	-10000	0	0
FGR	0.011	0.037	-9999	-0.48	2	2
mol:Ca2+	-0.004	0.058	-9999	-10000	0	0
mol:IP4	0	0	-9999	-10000	0	0
TIAM1	0.012	0.032	-9999	-0.6	1	1
ZAP70	-0.059	0.19	-9999	-0.53	49	49
mol:IP3	-0.01	0.077	-9999	-0.21	7	7
LYN	0.006	0.063	-9999	-0.48	6	6
ARF1/GDP	0.029	0.056	-9999	-0.29	4	4
RhoA/GDP	-0.015	0.044	-9999	-10000	0	0
PDK1/Src/Hsp90	-0.001	0.019	-9999	-0.36	1	1
BLNK	-0.056	0.19	-9999	-0.58	43	43
actin cytoskeleton reorganization	0.042	0.075	-9999	-0.39	3	3
SRC	0.014	0	-9999	-10000	0	0
PLEKHA2	0.029	0.034	-9999	-0.3	4	4
RAC1	0.014	0	-9999	-10000	0	0
PTEN	0.003	0.009	-9999	-10000	0	0
HSP90AA1	0.014	0	-9999	-10000	0	0
ARF6/GTP	-0.014	0.046	-9999	-10000	0	0
RhoA/GTP	-0.014	0.049	-9999	-10000	0	0
Src family/SYK family/BLNK-LAT	-0.079	0.2	-9999	-0.53	39	39
BLK	-0.095	0.21	-9999	-0.5	76	76
PDPK1	0.012	0.032	-9999	-0.6	1	1
CYTH1	-0.014	0.049	-9999	-10000	0	0
HCK	-0.013	0.12	-9999	-0.53	18	18
CYTH3	-0.014	0.049	-9999	-10000	0	0
CYTH2	-0.014	0.049	-9999	-10000	0	0
KRAS	0.013	0.026	-9999	-0.48	1	1
GO:0030676	0	0	-9999	-10000	0	0
FOXO3	0.025	0.085	-9999	-0.45	9	9
SGK1	-0.02	0.08	-9999	-0.5	9	9
INPP5D	0.008	0.055	-9999	-0.51	4	4
mol:GDP	0.022	0.059	-9999	-0.31	4	4
SOS1	0.014	0	-9999	-10000	0	0
SYK	-0.013	0.12	-9999	-0.56	17	17
ARF6/GDP	-0.015	0.044	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.016	0.053	-9999	-10000	0	0
ARAP3/RAP1A/GTP	-0.016	0.053	-9999	-10000	0	0
VAV1	-0.022	0.14	-9999	-0.56	23	23
mol:PI-3-4-P2	0.021	0.04	-9999	-0.36	4	4
RAS family/GTP/PI3K Class I	0.016	0.063	-9999	-10000	0	0
PLEKHA1	0.024	0.049	-9999	-0.28	9	9
Rac1/GDP	0.029	0.056	-9999	-0.29	4	4
LAT	-0.024	0.15	-9999	-0.6	23	23
Rac1/GTP	0.024	0.085	-9999	-0.49	6	6
ITK	-0.067	0.12	-9999	-0.42	18	18
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma	-0.044	0.14	-9999	-0.42	21	21
LCK	-0.088	0.21	-9999	-0.53	68	68
BTK	-0.025	0.07	-9999	-0.41	1	1

×

p38 MAPK signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TRAF6/ASK1	0.011	0.034	-10000	0	-0.31	4	4
TRAF2/ASK1	-0.003	0.034	-10000	0	-0.37	3	3
ATM	0.014	0	-10000	0	-10000	0	0
MAP2K3	0.018	0.053	-10000	0	-0.32	1	1
response to stress	0	0	-10000	0	-10000	0	0
MAP2K6	0.017	0.071	-10000	0	-0.45	3	3
hyperosmotic response	0	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
GADD45G	-0.037	0.16	-10000	0	-0.54	34	34
TXN	0.009	0.011	-10000	0	-0.2	1	1
CALM1	0.012	0.032	-10000	0	-0.6	1	1
GADD45A	-0.017	0.12	-10000	0	-0.49	23	23
GADD45B	-0.028	0.14	-10000	0	-0.52	29	29
MAP3K1	0.011	0.037	-10000	0	-0.48	2	2
MAP3K6	0.006	0.063	-10000	0	-0.48	6	6
MAP3K7	0.014	0	-10000	0	-10000	0	0
MAP3K4	0.014	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
ASK1/ASK2	-0.009	0.058	-10000	0	-0.37	9	9
TAK1/TAB family	0.001	0.019	0.19	3	-0.18	1	4
RAC1/OSM/MEKK3	0	0	-10000	0	-10000	0	0
TRAF2	0.014	0	-10000	0	-10000	0	0
RAC1/OSM/MEKK3/MKK3	-0.008	0.024	-10000	0	-10000	0	0
TRAF6	0.008	0.02	-10000	0	-0.37	1	1
RAC1	0.014	0	-10000	0	-10000	0	0
mol:LPS	0	0	-10000	0	-10000	0	0
CAMK2B	-0.074	0.2	-10000	0	-0.54	58	58
CCM2	0.014	0	-10000	0	-10000	0	0
CaM/Ca2+/CAMKIIB	-0.053	0.12	-10000	0	-0.33	58	58
MAPK11	0.009	0.056	-10000	0	-0.6	3	3
response to DNA damage stimulus	0	0	-10000	0	-10000	0	0
CaM/Ca2+/CAMKIIB/ASK1	-0.049	0.12	-10000	0	-0.31	58	58
OSM/MEKK3	0	0	-10000	0	-10000	0	0
TAOK1	-0.024	0.12	-10000	0	-0.36	41	41
TAOK2	0.019	0	-10000	0	-10000	0	0
TAOK3	0.019	0	-10000	0	-10000	0	0
MAP3K7IP1	0	0	-10000	0	-10000	0	0
MAPK14	0.014	0	-10000	0	-10000	0	0
MAP3K7IP2	0	0	-10000	0	-10000	0	0
MAP3K5	0.009	0.056	-10000	0	-0.6	3	3
MAP3K10	0.005	0.068	-10000	0	-0.48	7	7
MAP3K3	0.014	0	-10000	0	-10000	0	0
TRX/ASK1	0.014	0.04	-10000	0	-0.42	3	3
GADD45/MTK1/MTK1	-0.059	0.13	-10000	0	-0.38	37	37

×

Canonical NF-kappaB 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FBXW11	0.018	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.086	0.03	-9999	-10000	0	0
ERC1	0.013	0.026	-9999	-0.48	1	1
RIP2/NOD2	-0.018	0.081	-9999	-0.38	17	17
NFKBIA	0.05	0.014	-9999	-10000	0	0
BIRC2	0.014	0	-9999	-10000	0	0
IKBKB	0.014	0	-9999	-10000	0	0
RIPK2	0.014	0	-9999	-10000	0	0
IKBKG	-0.006	0.031	-9999	-10000	0	0
IKK complex/A20	-0.067	0.1	-9999	-0.45	7	7
NEMO/A20/RIP2	0.014	0	-9999	-10000	0	0
XPO1	0.014	0	-9999	-10000	0	0
NEMO/ATM	0.047	0.04	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
RAN	0.014	0	-9999	-10000	0	0
Exportin 1/RanGTP	0	0	-9999	-10000	0	0
IKK complex/ELKS	-0.005	0.025	-9999	-10000	0	0
BCL10/MALT1/TRAF6	-0.001	0.019	-9999	-0.36	1	1
NOD2	-0.012	0.12	-9999	-0.54	17	17
NFKB1	0.016	0.026	-9999	-0.47	1	1
RELA	0.018	0	-9999	-10000	0	0
MALT1	0.014	0	-9999	-10000	0	0
cIAP1/UbcH5C	0	0	-9999	-10000	0	0
ATM	0.014	0	-9999	-10000	0	0
TNF/TNFR1A	-0.12	0.18	-9999	-0.38	113	113
TRAF6	0.012	0.032	-9999	-0.6	1	1
PRKCA	0.012	0.032	-9999	-0.6	1	1
CHUK	0.014	0	-9999	-10000	0	0
UBE2D3	0.014	0	-9999	-10000	0	0
TNF	-0.15	0.25	-9999	-0.54	109	109
NF kappa B1 p50/RelA	-0.001	0.013	-9999	-10000	0	0
BCL10	0.014	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.049	0.014	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.018	0	-9999	-10000	0	0
TNFRSF1A	0.005	0.068	-9999	-0.52	6	6
IKK complex	0.054	0.039	-9999	-10000	0	0
CYLD	0.014	0	-9999	-10000	0	0
IKK complex/PKC alpha	-0.005	0.027	-9999	-10000	0	0

×

Circadian rhythm pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
chromatin modification	0.033	0.08	-10000	0	-0.54	4	4
CLOCK	-0.028	0.16	-10000	0	-0.6	27	27
TIMELESS/CRY2	0.028	0.072	-10000	0	-10000	0	0
DEC1/BMAL1	0.008	0.06	-10000	0	-0.35	10	10
ATR	0.014	0	-10000	0	-10000	0	0
NR1D1	0.027	0.094	-10000	0	-0.93	2	2
ARNTL	0.013	0.05	-10000	0	-0.53	3	3
TIMELESS	0.026	0.075	-10000	0	-0.44	1	1
NPAS2	0.004	0.087	-10000	0	-0.57	8	8
CRY2	0.011	0.046	-10000	0	-0.6	2	2
mol:CO	-0.012	0.016	0.074	12	-10000	0	12
CHEK1	0.009	0.052	-10000	0	-0.48	4	4
mol:HEME	0.012	0.016	-10000	0	-0.074	12	12
PER1	0.004	0.078	-10000	0	-0.6	6	6
BMAL/CLOCK/NPAS2	0.005	0.13	-10000	0	-0.39	33	33
BMAL1/CLOCK	0.012	0.14	-10000	0	-0.64	6	6
S phase of mitotic cell cycle	0.033	0.08	-10000	0	-0.54	4	4
TIMELESS/CHEK1/ATR	0.034	0.081	-10000	0	-0.54	4	4
mol:NADPH	0.012	0.016	-10000	0	-0.074	12	12
PER1/TIMELESS	0.024	0.08	-10000	0	-10000	0	0
PER1-2 / CRY1-2	0	0	-10000	0	-10000	0	0
DEC1	-0.001	0.067	-10000	0	-0.48	7	7

×

Atypical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL3/RelA	-0.01	0.057	-9999	-0.33	11	11
FBXW11	0.014	0	-9999	-10000	0	0
NF kappa B1 p50/c-Rel	-0.001	0.1	-9999	-0.37	22	22
NF kappa B1 p50/RelA/I kappa B alpha	0.013	0.081	-9999	-0.4	2	2
NFKBIA	-0.011	0.09	-9999	-0.23	42	42
MAPK14	0.014	0	-9999	-10000	0	0
NF kappa B1 p105/p50	0.028	0.016	-9999	-10000	0	0
ARRB2	0.019	0	-9999	-10000	0	0
REL	-0.032	0.16	-9999	-0.57	29	29
response to oxidative stress	0	0	-9999	-10000	0	0
BCL3/NF kappa B1 p50	0.019	0.057	-9999	-0.54	1	1
response to UV	0	0	-9999	-10000	0	0
NF kappa B1 p105/RelA	0.028	0.016	-9999	-10000	0	0
PIK3CA	0.012	0.032	-9999	-0.6	1	1
NF kappa B1 p50 dimer	0.021	0.019	-9999	-0.33	1	1
PIK3R1	0.014	0	-9999	-10000	0	0
NFKB1	0.024	0.019	-9999	-0.34	1	1
RELA	0.014	0	-9999	-10000	0	0
positive regulation of anti-apoptosis	-0.003	0.087	-9999	-0.44	1	1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2	0.018	0.079	-9999	-0.49	1	1
SRC	0.014	0	-9999	-10000	0	0
PI3K	-0.001	0.023	-9999	-0.44	1	1
NF kappa B1 p50/RelA	-0.004	0.088	-9999	-0.45	1	1
IKBKB	0.014	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.014	0	-9999	-10000	0	0
SYK	-0.013	0.12	-9999	-0.56	17	17
I kappa B alpha/PIK3R1	-0.003	0.084	-9999	-0.55	1	1
cell death	0.017	0.077	-9999	-0.46	1	1
NF kappa B1 p105/c-Rel	-0.001	0.1	-9999	-0.37	22	22
LCK	-0.088	0.21	-9999	-0.53	68	68
BCL3	-0.001	0.085	-9999	-0.48	11	11

×

S1P3 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.01	0.045	-9999	-0.48	3	3
mol:S1P	0.001	0.003	-9999	-10000	0	0
S1P1/S1P/Gi	0.023	0.07	-9999	-0.31	13	13
GNAO1	0.006	0.079	-9999	-0.61	6	6
S1P/S1P3/G12/G13	-0.004	0.098	-9999	-0.27	41	41
AKT1	0.024	0.045	-9999	-0.3	2	2
AKT3	0.019	0.17	-9999	-1.3	5	5
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.01	0.045	-9999	-0.48	3	3
GNAI2	0.016	0.002	-9999	-10000	0	0
GNAI3	0.016	0.002	-9999	-10000	0	0
GNAI1	-0.003	0.11	-9999	-0.61	11	11
mol:GDP	0	0	-9999	-10000	0	0
S1PR3	-0.043	0.16	-9999	-0.5	41	41
S1PR2	0.008	0.061	-9999	-0.57	4	4
EDG1	0	0	-9999	-10000	0	0
mol:Ca2+	0.012	0.1	-9999	-0.52	7	7
MAPK3	0.02	0.099	-9999	-0.49	7	7
MAPK1	0.02	0.099	-9999	-0.49	7	7
JAK2	0.018	0.1	-9999	-0.47	8	8
CXCR4	0.007	0.12	-9999	-0.45	10	10
FLT1	0.016	0.033	-9999	-0.62	1	1
RhoA/GDP	0	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
SRC	0.02	0.099	-9999	-0.49	7	7
S1P/S1P3/Gi	0.012	0.1	-9999	-0.52	7	7
RAC1	0.014	0	-9999	-10000	0	0
RhoA/GTP	-0.025	0.08	-9999	-0.47	7	7
VEGFA	-0.003	0.099	-9999	-0.48	15	15
S1P/S1P2/Gi	0.028	0.074	-9999	-0.36	7	7
VEGFR1 homodimer/VEGFA homodimer	0.014	0.077	-9999	-0.34	16	16
RHOA	0.014	0	-9999	-10000	0	0
S1P/S1P3/Gq	-0.01	0.11	-9999	-0.31	32	32
GNAQ	0.014	0	-9999	-10000	0	0
GNAZ	0.014	0.032	-9999	-0.6	1	1
G12/G13	-0.001	0.023	-9999	-0.44	1	1
GNA14	-0.006	0.11	-9999	-0.56	13	13
GNA15	-0.006	0.11	-9999	-0.56	13	13
GNA12	0.012	0.032	-9999	-0.6	1	1
GNA13	0.014	0	-9999	-10000	0	0
GNA11	0.002	0.085	-9999	-0.6	7	7
Rac1/GTP	-0.025	0.08	-9999	-0.47	7	7

×

Signaling events mediated by PRL

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
CCNE1	0.011	0.037	-10000	0	-0.48	2	2
mol:Halofuginone	0.005	0.001	-10000	0	-10000	0	0
ITGA1	-0.012	0.12	-10000	0	-0.52	18	18
CDKN1A	-0.024	0.12	-10000	0	-0.42	19	19
PRL-3/alpha Tubulin	-0.004	0.035	-10000	0	-0.33	4	4
mol:Ca2+	-0.019	0.093	0.22	2	-0.43	17	19
AGT	-0.014	0.13	-10000	0	-0.59	17	17
CCNA2	-0.05	0.15	-10000	0	-0.5	9	9
TUBA1B	0.014	0	-10000	0	-10000	0	0
EGR1	-0.059	0.16	-10000	0	-0.37	79	79
CDK2/Cyclin E1	-0.014	0.12	-10000	0	-0.39	22	22
MAPK3	0.021	0.037	-10000	0	-0.33	4	4
PRL-2 /Rab GGTase beta	0	0	-10000	0	-10000	0	0
MAPK1	0.021	0.037	-10000	0	-0.33	4	4
PTP4A1	-0.026	0.13	-10000	0	-10000	0	0
PTP4A3	0.009	0.052	-10000	0	-0.48	4	4
PTP4A2	0.014	0	-10000	0	-10000	0	0
ITGB1	0.019	0.046	-10000	0	-0.33	6	6
SRC	0.014	0	-10000	0	-10000	0	0
RAC1	0.005	0.059	-10000	0	-10000	0	0
Rab GGTase beta/Rab GGTase alpha	0	0	-10000	0	-10000	0	0
PRL-1/ATF-5	-0.02	0.12	-10000	0	-10000	0	0
RABGGTA	0.014	0	-10000	0	-10000	0	0
BCAR1	0.001	0.033	0.22	4	-0.45	1	5
RHOC	0.004	0.063	-10000	0	-0.39	1	1
RHOA	0.005	0.059	-10000	0	-10000	0	0
cell motility	0.008	0.063	-10000	0	-10000	0	0
PRL-1/alpha Tubulin	-0.017	0.12	-10000	0	-10000	0	0
PRL-3/alpha1 Integrin	-0.022	0.09	-10000	0	-0.38	21	21
ROCK1	0.008	0.064	-10000	0	-10000	0	0
RABGGTB	0.014	0	-10000	0	-10000	0	0
CDK2	0.001	0.086	-10000	0	-0.54	9	9
mitosis	-0.025	0.13	-10000	0	-10000	0	0
ATF5	0.009	0.052	-10000	0	-0.48	4	4

×

EPO signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.06	0.093	-9999	-0.84	1	1
CRKL	0.033	0.075	-9999	-0.42	4	4
mol:DAG	0.04	0.072	-9999	-0.45	2	2
HRAS	0.054	0.08	-9999	-0.78	1	1
MAPK8	0.013	0.099	-9999	-0.41	12	12
RAP1A	0.033	0.075	-9999	-0.42	4	4
GAB1	0.032	0.083	-9999	-0.49	4	4
MAPK14	0.023	0.07	-9999	-0.37	2	2
EPO	-0.007	0.1	-9999	-0.48	16	16
PLCG1	0.04	0.074	-9999	-0.46	2	2
EPOR/TRPC2/IP3 Receptors	0.013	0.038	-9999	-0.49	2	2
RAPGEF1	0.014	0	-9999	-10000	0	0
EPO/EPOR (dimer)/SOCS3	-0.062	0.16	-9999	-0.4	40	40
GAB1/SHC/GRB2/SOS1	-0.016	0.067	-9999	-0.61	2	2
EPO/EPOR (dimer)	0.008	0.081	-9999	-0.35	17	17
IRS2	0.033	0.083	-9999	-0.49	4	4
STAT1	0.043	0.091	-9999	-0.48	4	4
STAT5B	0.045	0.077	-9999	-0.49	2	2
cell proliferation	0.022	0.093	-9999	-0.39	11	11
GAB1/SHIP/PIK3R1/SHP2/SHC	-0.017	0.07	-9999	-0.66	2	2
TEC	0.024	0.099	-9999	-0.44	9	9
SOCS3	-0.11	0.23	-9999	-0.52	85	85
STAT1 (dimer)	0.043	0.09	-9999	-0.48	4	4
JAK2	0.015	0.007	-9999	-10000	0	0
PIK3R1	0.014	0	-9999	-10000	0	0
EPO/EPOR (dimer)/JAK2	0.039	0.083	-9999	-0.44	4	4
EPO/EPOR	0.008	0.081	-9999	-0.35	17	17
LYN	0.008	0.063	-9999	-0.48	6	6
TEC/VAV2	0.033	0.097	-9999	-0.42	9	9
elevation of cytosolic calcium ion concentration	0.013	0.038	-9999	-0.49	2	2
SHC1	0.009	0.052	-9999	-0.48	4	4
EPO/EPOR (dimer)/LYN	0.021	0.08	-9999	-0.34	8	8
mol:IP3	0.04	0.072	-9999	-0.45	2	2
PI3K regualtory subunit polypeptide 1/IRS2/SHIP	0.042	0.086	-9999	-0.48	5	5
SH2B3	0.012	0.038	-9999	-0.49	2	2
NFKB1	0.022	0.071	-9999	-0.45	1	1
EPO/EPOR (dimer)/JAK2/SOCS3	-0.041	0.077	-9999	-0.26	7	7
PTPN6	0.026	0.079	-9999	-0.44	4	4
TEC/VAV2/GRB2	0.039	0.094	-9999	-0.42	8	8
EPOR	0.013	0.038	-9999	-0.49	2	2
INPP5D	0.008	0.055	-9999	-0.51	4	4
mol:GDP	-0.016	0.068	-9999	-0.62	2	2
SOS1	0.014	0	-9999	-10000	0	0
PLCG2	0.002	0.082	-9999	-0.54	8	8
CRKL/CBL/C3G	0.047	0.071	-9999	-0.38	4	4
VAV2	0.033	0.075	-9999	-0.42	4	4
CBL	0.033	0.075	-9999	-0.42	4	4
SHC/Grb2/SOS1	-0.016	0.064	-9999	-0.42	5	5
STAT5A	0.036	0.11	-9999	-0.53	7	7
GRB2	0.014	0	-9999	-10000	0	0
STAT5 (dimer)	0.055	0.11	-9999	-0.53	7	7
LYN/PLCgamma2	0.008	0.086	-9999	-0.49	10	10
PTPN11	0.014	0	-9999	-10000	0	0
BTK	0.021	0.11	-9999	-0.48	11	11
BCL2	0.053	0.14	-9999	-0.96	5	5

×

IFN-gamma pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2	0.034	0.028	-9999	-10000	0	0
positive regulation of NF-kappaB transcription factor activity	0	0.002	-9999	-10000	0	0
CRKL	0.014	0	-9999	-10000	0	0
STAT1 (dimer)/Cbp/p300	0.045	0.09	-9999	-0.43	6	6
IFN-gammaR/JAK1/JAK1/JAK2/JAK2	0	0.002	-9999	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class I	-0.054	0.075	-9999	-0.32	13	13
CaM/Ca2+	-0.003	0.023	-9999	-10000	0	0
RAP1A	0.014	0	-9999	-10000	0	0
STAT1 (dimer)/SHP2	0.035	0.06	-9999	-0.37	1	1
AKT1	0.052	0.029	-9999	-10000	0	0
MAP2K1	0.049	0.035	-9999	-10000	0	0
MAP3K11	0.042	0.027	-9999	-10000	0	0
IFNGR1	0.016	0.002	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKII	-0.14	0.2	-9999	-0.47	78	78
Rap1/GTP	-0.002	0.014	-9999	-10000	0	0
CRKL/C3G	0	0	-9999	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP	0.001	0.024	-9999	-10000	0	0
CEBPB	0.061	0.1	-9999	-0.54	5	5
STAT3	0.014	0	-9999	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1	-0.006	0.18	-9999	-1	9	9
STAT1	0.035	0.06	-9999	-0.33	3	3
CALM1	0.013	0.032	-9999	-0.6	1	1
IFN-gamma (dimer)	0.001	0.05	-9999	-0.47	4	4
PIK3CA	0.013	0.032	-9999	-0.6	1	1
STAT1 (dimer)/PIAS1	0.039	0.066	-9999	-0.34	1	1
CEBPB/PTGES2/Cbp/p300	-0.015	0.058	-9999	-0.36	5	5
mol:Ca2+	0.018	0.029	-9999	-10000	0	0
MAPK3	0.056	0.043	-9999	-10000	0	0
STAT1 (dimer)	-0.07	0.11	-9999	-0.46	13	13
MAPK1	0.056	0.043	-9999	-10000	0	0
JAK2	0.016	0.002	-9999	-10000	0	0
PIK3R1	0.014	0	-9999	-10000	0	0
JAK1	0.016	0.002	-9999	-10000	0	0
CAMK2D	0.013	0.032	-9999	-0.6	1	1
DAPK1	0.052	0.12	-9999	-0.63	11	11
SMAD7	0.006	0.064	-9999	-0.19	3	3
CBL/CRKL/C3G	0.037	0.031	-9999	-10000	0	0
PI3K	-0.003	0.022	-9999	-10000	0	0
IFNG	0.001	0.05	-9999	-0.47	4	4
apoptosis	0.032	0.092	-9999	-0.45	11	11
CAMK2G	0.013	0.032	-9999	-0.6	1	1
STAT3 (dimer)	0.014	0	-9999	-10000	0	0
CAMK2A	-0.24	0.28	-9999	-0.54	171	171
CAMK2B	-0.074	0.2	-9999	-0.54	58	58
FRAP1	0.051	0.027	-9999	-10000	0	0
PRKCD	0.04	0.071	-9999	-10000	0	0
RAP1B	0.013	0.026	-9999	-0.48	1	1
negative regulation of cell growth	-0.054	0.075	-9999	-0.32	13	13
PTPN2	0.014	0	-9999	-10000	0	0
EP300	0.008	0.064	-9999	-0.6	4	4
IRF1	0.034	0.14	-9999	-0.55	11	11
STAT1 (dimer)/PIASy	0.042	0.061	-9999	-10000	0	0
SOCS1	-0.053	0.21	-9999	-1.4	7	7
mol:GDP	-0.001	0.015	-9999	-10000	0	0
CASP1	-0.001	0.084	-9999	-0.28	16	16
PTGES2	0.014	0	-9999	-10000	0	0
IRF9	0.05	0.049	-9999	-0.24	4	4
mol:PI-3-4-5-P3	-0.003	0.021	-9999	-10000	0	0
RAP1/GDP	-0.002	0.014	-9999	-10000	0	0
CBL	0.041	0.026	-9999	-10000	0	0
MAP3K1	0.041	0.032	-9999	-10000	0	0
PIAS1	0.007	0.064	-9999	-0.6	4	4
PIAS4	0.014	0.002	-9999	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class II	-0.054	0.075	-9999	-0.32	13	13
PTPN11	0.034	0.027	-9999	-10000	0	0
CREBBP	0.014	0.001	-9999	-10000	0	0
RAPGEF1	0.014	0	-9999	-10000	0	0

×

Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaV beta3 Integrin	-0.048	0.12	-9999	-0.36	48	48
AKT1	0.075	0.08	-9999	-0.52	2	2
PTK2B	-0.001	0.14	-9999	-0.49	16	16
VEGFR2 homodimer/Frs2	0.029	0.073	-9999	-0.6	3	3
CAV1	-0.045	0.16	-9999	-0.49	43	43
CALM1	0.012	0.032	-9999	-0.6	1	1
VEGFR2 homodimer/VEGFA homodimer/Frs2	-0.018	0.08	-9999	-0.6	4	4
endothelial cell proliferation	0.062	0.1	-9999	-0.44	4	4
mol:Ca2+	0.039	0.089	-9999	-0.54	4	4
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac	-0.019	0.083	-9999	-0.59	5	5
RP11-342D11.1	0.029	0.089	-9999	-0.55	4	4
CDH5	0.01	0.045	-9999	-0.48	3	3
VEGFA homodimer	-0.011	0.049	-9999	-10000	0	0
SHC1	0.009	0.052	-9999	-0.48	4	4
SHC2	0.011	0.041	-9999	-0.54	2	2
HRAS/GDP	-0.018	0.072	-9999	-0.49	5	5
SH2D2A	-0.075	0.2	-9999	-0.53	59	59
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS	-0.021	0.072	-9999	-0.47	4	4
VEGFR2 homodimer/VEGFA homodimer/TsAd	-0.059	0.13	-9999	-0.59	9	9
VEGFR1 homodimer	0.012	0.032	-9999	-0.6	1	1
SHC/GRB2/SOS1	-0.019	0.078	-9999	-0.52	6	6
GRB10	0.038	0.095	-9999	-0.56	5	5
PTPN11	0.014	0	-9999	-10000	0	0
GRB2	0.014	0	-9999	-10000	0	0
PAK1	-0.038	0.15	-9999	-0.49	38	38
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin	-0.019	0.089	-9999	-0.65	5	5
HRAS	0.013	0.026	-9999	-0.48	1	1
VEGF/Rho/ROCK1/Integrin Complex	0.026	0.08	-9999	-0.38	4	4
HIF1A	0.013	0.026	-9999	-0.48	1	1
FRS2	0.011	0.041	-9999	-0.54	2	2
oxygen and reactive oxygen species metabolic process	-0.019	0.082	-9999	-0.58	5	5
mol:GTP	0	0	-9999	-10000	0	0
FLT4	0	0.087	-9999	-0.52	10	10
Nck/Pak	-0.037	0.11	-9999	-0.34	39	39
VEGFR2 homodimer/VEGFA homodimer/Fyn	-0.016	0.077	-9999	-0.6	4	4
mol:GDP	-0.019	0.076	-9999	-0.5	6	6
mol:NADP	0.062	0.081	-9999	-0.42	4	4
eNOS/Hsp90	0.066	0.078	-9999	-0.4	4	4
PIK3R1	0.014	0	-9999	-10000	0	0
mol:IP3	0.039	0.09	-9999	-0.55	4	4
HIF1A/ARNT	-0.002	0.025	-9999	-0.33	2	2
SHB	0.014	0	-9999	-10000	0	0
VEGFA	-0.004	0.098	-9999	-0.48	15	15
VEGFC	-0.002	0.091	-9999	-0.51	11	11
FAK1/Vinculin	0.034	0.12	-9999	-0.6	6	6
mol:Ca ++	0	0	-9999	-10000	0	0
RHOA	0.014	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	-0.046	0.12	-9999	-0.5	15	15
PTPN6	-0.004	0.098	-9999	-0.53	12	12
EPAS1	0.021	0.036	-9999	-0.34	2	2
mol:L-citrulline	0.062	0.081	-9999	-0.42	4	4
ITGAV	0.012	0.032	-9999	-0.6	1	1
PIK3CA	0.012	0.032	-9999	-0.6	1	1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2	-0.016	0.074	-9999	-0.57	4	4
VEGFR2 homodimer/VEGFA homodimer	-0.021	0.083	-9999	-0.6	4	4
VEGFR2/3 heterodimer	0.023	0.098	-9999	-0.61	6	6
VEGFB	0.014	0	-9999	-10000	0	0
MAPK11	0.039	0.095	-9999	-0.54	5	5
VEGFR2 homodimer	0.03	0.078	-9999	-0.54	6	6
FLT1	0.012	0.032	-9999	-0.6	1	1
NEDD4	0.006	0.073	-9999	-0.51	7	7
MAPK3	0.031	0.096	-9999	-0.49	4	4
MAPK1	0.031	0.096	-9999	-0.49	4	4
VEGFA145/NRP2	-0.02	0.085	-9999	-0.37	20	20
VEGFR1/2 heterodimer	0.03	0.071	-9999	-0.6	3	3
KDR	0.03	0.078	-9999	-0.54	6	6
VEGFA165/NRP1/VEGFR2 homodimer	0.033	0.097	-9999	-0.52	5	5
SRC	0.014	0	-9999	-10000	0	0
platelet activating factor biosynthetic process	0.033	0.097	-9999	-0.48	5	5
PI3K	0.062	0.09	-9999	-0.57	3	3
VEGFR2 homodimer/VEGFA homodimer/NCK1	-0.017	0.079	-9999	-0.6	4	4
FES	0.035	0.099	-9999	-0.61	4	4
GAB1	-0.016	0.077	-9999	-0.63	4	4
VEGFR2 homodimer/VEGFA homodimer/Src	-0.016	0.077	-9999	-0.6	4	4
CTNNB1	0.014	0	-9999	-10000	0	0
SOS1	0.014	0	-9999	-10000	0	0
ARNT	0.013	0.026	-9999	-0.48	1	1
eNOS/Caveolin-1	0.041	0.11	-9999	-0.49	5	5
VEGFR2 homodimer/VEGFA homodimer/Yes	-0.018	0.08	-9999	-0.6	4	4
PI3K/GAB1	0.076	0.084	-9999	-0.48	4	4
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak	-0.036	0.091	-9999	-0.55	5	5
PRKACA	0.014	0	-9999	-10000	0	0
VEGFR2/3 heterodimer/VEGFC homodimer	-0.02	0.099	-9999	-0.64	6	6
HSP90AA1	0.014	0	-9999	-10000	0	0
CDC42	0.039	0.091	-9999	-0.56	4	4
actin cytoskeleton reorganization	-0.059	0.13	-9999	-0.59	9	9
PTK2	0.031	0.11	-9999	-0.6	4	4
EDG1	0.029	0.089	-9999	-0.55	4	4
mol:DAG	0.039	0.09	-9999	-0.55	4	4
CaM/Ca2+	-0.018	0.069	-9999	-0.5	4	4
MAP2K3	0.036	0.11	-9999	-0.55	6	6
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4	0.038	0.097	-9999	-0.57	5	5
PLCG1	0.039	0.091	-9999	-0.56	4	4
VEGFR2 homodimer/VEGFA homodimer/Src/Shb	-0.015	0.072	-9999	-0.57	4	4
IQGAP1	0.005	0.068	-9999	-0.52	6	6
YES1	0.011	0.046	-9999	-0.6	2	2
VEGFR2 homodimer/VEGFA homodimer/SHP2	-0.016	0.077	-9999	-0.6	4	4
VEGFR2 homodimer/VEGFA homodimer/SHP1	-0.025	0.093	-9999	-0.57	6	6
cell migration	0.057	0.12	-9999	-0.6	6	6
mol:PI-3-4-5-P3	0.061	0.085	-9999	-0.53	3	3
FYN	0.014	0	-9999	-10000	0	0
VEGFB/NRP1	0.036	0.085	-9999	-0.51	4	4
mol:NO	0.062	0.081	-9999	-0.42	4	4
PXN	0.014	0	-9999	-10000	0	0
HRAS/GTP	-0.018	0.072	-9999	-0.49	5	5
VEGFR2 homodimer/VEGFA homodimer/GRB10	0.038	0.097	-9999	-0.57	5	5
VHL	0.014	0	-9999	-10000	0	0
ITGB3	-0.054	0.18	-9999	-0.51	47	47
NOS3	0.063	0.089	-9999	-0.48	4	4
VEGFR2 homodimer/VEGFA homodimer/Sck	-0.018	0.083	-9999	-0.6	5	5
RAC1	0.014	0	-9999	-10000	0	0
PRKCA	0.045	0.087	-9999	-0.51	4	4
PRKCB	0.007	0.14	-9999	-0.49	12	12
VCL	0.005	0.071	-9999	-0.54	6	6
VEGFA165/NRP1	0.029	0.09	-9999	-0.55	4	4
VEGFR1/2 heterodimer/VEGFA homodimer	-0.017	0.079	-9999	-0.6	4	4
VEGFA165/NRP2	-0.02	0.085	-9999	-0.37	20	20
MAPKKK cascade	0.06	0.094	-9999	-0.53	4	4
NRP2	0.005	0.074	-9999	-0.56	6	6
VEGFC homodimer	-0.002	0.091	-9999	-0.51	11	11
NCK1	0.012	0.032	-9999	-0.6	1	1
ROCK1	0.014	0	-9999	-10000	0	0
FAK1/Paxillin	0.038	0.11	-9999	-0.56	4	4
MAP3K13	0.03	0.11	-9999	-0.55	5	5
PDPK1	0.066	0.08	-9999	-0.47	3	3

×

VEGFR1 specific signals

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR1 homodimer/VEGFB homodimer	0.033	0.043	-9999	-0.73	1	1
VEGFR1 homodimer/NRP1	0.022	0.043	-9999	-0.74	1	1
mol:DAG	-0.017	0.13	-9999	-0.66	1	1
VEGFR1 homodimer/NRP1/VEGFR 121	-0.012	0.06	-9999	-0.68	1	1
CaM/Ca2+	-0.01	0.12	-9999	-0.63	1	1
HIF1A	0.021	0.032	-9999	-0.4	2	2
GAB1	0.011	0.041	-9999	-0.54	2	2
AKT1	0.007	0.12	-9999	-0.57	2	2
PLCG1	-0.018	0.13	-9999	-0.67	1	1
NOS3	0.008	0.13	-9999	-0.48	3	3
CBL	0.014	0	-9999	-10000	0	0
mol:NO	0.009	0.12	-9999	-0.46	3	3
FLT1	0.03	0.049	-9999	-0.57	2	2
PGF	-0.088	0.22	-9999	-0.56	65	65
VEGFR1 homodimer/NRP2/VEGFR121	0.023	0.081	-9999	-0.58	2	2
CALM1	0.012	0.032	-9999	-0.6	1	1
PIK3CA	0.012	0.032	-9999	-0.6	1	1
eNOS/Hsp90	0.016	0.12	-9999	-0.49	2	2
endothelial cell proliferation	-0.031	0.16	-9999	-0.51	15	15
mol:Ca2+	-0.017	0.13	-9999	-0.66	1	1
MAPK3	0.001	0.12	-9999	-0.58	1	1
MAPK1	0.001	0.12	-9999	-0.58	1	1
PIK3R1	0.014	0	-9999	-10000	0	0
PLGF homodimer	-0.088	0.22	-9999	-0.56	65	65
PRKACA	0.014	0	-9999	-10000	0	0
RP11-342D11.1	0	0	-9999	-10000	0	0
CAV1	-0.045	0.16	-9999	-0.49	43	43
VEGFA homodimer	-0.006	0.098	-9999	-0.48	15	15
VEGFR1 homodimer/VEGFA homodimer	0.02	0.073	-9999	-0.73	1	1
platelet activating factor biosynthetic process	0.008	0.11	-9999	-0.55	1	1
PI3K	-0.009	0.13	-9999	-0.62	2	2
PRKCA	-0.008	0.12	-9999	-0.62	1	1
PRKCB	-0.048	0.16	-9999	-0.55	13	13
VEGFR1 homodimer/PLGF homodimer	-0.032	0.14	-9999	-0.37	42	42
VEGFA	-0.006	0.098	-9999	-0.48	15	15
VEGFB	0.014	0	-9999	-10000	0	0
mol:IP3	-0.017	0.13	-9999	-0.66	1	1
RASA1	0.041	0.04	-9999	-0.67	1	1
NRP2	0.005	0.074	-9999	-0.56	6	6
VEGFR1 homodimer	0.03	0.049	-9999	-0.57	2	2
VEGFB homodimer	0.014	0	-9999	-10000	0	0
NCK1	0.012	0.032	-9999	-0.6	1	1
eNOS/Caveolin-1	-0.011	0.14	-9999	-0.48	6	6
PTPN11	0.014	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.049	0.11	-9999	-0.61	2	2
mol:L-citrulline	0.009	0.12	-9999	-0.46	3	3
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP	0.036	0.063	-9999	-0.64	1	1
VEGFR1 homodimer/VEGFA homodimer/NCK1	0.027	0.069	-9999	-0.68	1	1
CD2AP	0.014	0	-9999	-10000	0	0
PI3K/GAB1	-0.047	0.1	-9999	-0.59	2	2
PDPK1	-0.001	0.12	-9999	-0.58	2	2
VEGFR1 homodimer/VEGFA homodimer/SHP2	0.028	0.067	-9999	-0.68	1	1
mol:NADP	0.009	0.12	-9999	-0.46	3	3
HSP90AA1	0.014	0	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	-0.011	0.053	-9999	-0.63	1	1
VEGFR1 homodimer/NRP2	0.027	0.063	-9999	-0.43	5	5

×

Class IB PI3K non-lipid kinase events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
cAMP biosynthetic process	-0.004	0.076	0.58	6	-10000	0	6
PI3K Class IB/PDE3B	0.004	0.076	-10000	0	-0.58	6	6
PDE3B	0.004	0.076	-10000	0	-0.58	6	6

×

Hedgehog signaling events mediated by Gli proteins

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.011	0.046	-9999	-0.6	2	2
HDAC2	0.014	0.001	-9999	-10000	0	0
GNB1/GNG2	-0.01	0.058	-9999	-0.36	9	9
forebrain development	-0.009	0.16	-9999	-0.45	31	31
GNAO1	0.004	0.079	-9999	-0.61	6	6
SMO/beta Arrestin2	0.014	0.062	-9999	-0.42	7	7
SMO	0.003	0.083	-9999	-0.59	7	7
ARRB2	0.014	0.004	-9999	-10000	0	0
GLI3/SPOP	0.04	0.07	-9999	-0.6	1	1
mol:GTP	0	0.002	-9999	-10000	0	0
GSK3B	0.014	0	-9999	-10000	0	0
GNAI2	0.014	0.003	-9999	-10000	0	0
SIN3/HDAC complex	0.003	0.021	-9999	-0.32	1	1
GNAI1	-0.004	0.11	-9999	-0.6	11	11
XPO1	0.015	0.005	-9999	-10000	0	0
GLI1/Su(fu)	-0.045	0.11	-9999	-0.56	9	9
SAP30	0.012	0.032	-9999	-0.6	1	1
mol:GDP	0.003	0.083	-9999	-0.59	7	7
MIM/GLI2A	0.011	0.054	-9999	-0.57	3	3
IFT88	0.014	0	-9999	-10000	0	0
GNAI3	0.014	0.002	-9999	-10000	0	0
GLI2	0.045	0.032	-9999	-10000	0	0
GLI3	0.034	0.073	-9999	-0.64	1	1
CSNK1D	0.014	0	-9999	-10000	0	0
CSNK1E	0.014	0	-9999	-10000	0	0
SAP18	0.014	0.001	-9999	-10000	0	0
embryonic digit morphogenesis	0.014	0	-9999	-10000	0	0
GNG2	0.009	0.056	-9999	-0.6	3	3
Gi family/GTP	0.021	0.077	-9999	-0.35	7	7
SIN3B	0.014	0.001	-9999	-10000	0	0
SIN3A	0.014	0.001	-9999	-10000	0	0
GLI3/Su(fu)	0.053	0.054	-9999	-0.44	1	1
GLI2/Su(fu)	0.055	0.048	-9999	-10000	0	0
FOXA2	-0.036	0.13	-9999	-1.2	2	2
neural tube patterning	-0.009	0.16	-9999	-0.45	31	31
SPOP	0.014	0	-9999	-10000	0	0
Su(fu)/PIAS1	0.026	0.047	-9999	-0.32	4	4
GNB1	0.014	0	-9999	-10000	0	0
CSNK1G2	0.014	0	-9999	-10000	0	0
CSNK1G3	0.014	0	-9999	-10000	0	0
MTSS1	0.011	0.054	-9999	-0.57	3	3
embryonic limb morphogenesis	-0.009	0.16	-9999	-0.45	31	31
SUFU	0.026	0.033	-9999	-10000	0	0
LGALS3	-0.025	0.14	-9999	-0.48	29	29
catabolic process	0.064	0.065	-9999	-0.5	1	1
GLI3A/CBP	-0.019	0.11	-9999	-0.35	25	25
KIF3A	0.012	0.032	-9999	-0.6	1	1
GLI1	-0.01	0.16	-9999	-0.46	31	31
RAB23	0.012	0.032	-9999	-0.6	1	1
CSNK1A1	0.014	0	-9999	-10000	0	0
IFT172	0.009	0.056	-9999	-0.6	3	3
RBBP7	0.014	0.001	-9999	-10000	0	0
Su(fu)/Galectin3	0.009	0.085	-9999	-0.45	3	3
GNAZ	0.013	0.032	-9999	-0.6	1	1
RBBP4	0.014	0.001	-9999	-10000	0	0
CSNK1G1	0.013	0.026	-9999	-0.48	1	1
PIAS1	0.007	0.064	-9999	-0.6	4	4
PRKACA	0.014	0	-9999	-10000	0	0
GLI2/SPOP	0.049	0.03	-9999	-10000	0	0
STK36	0.015	0.005	-9999	-10000	0	0
Gi family/GNB1/GNG2/GDP	0.027	0.078	-9999	-0.47	4	4
PTCH1	-0.011	0.2	-9999	-0.94	10	10
MIM/GLI1	-0.01	0.18	-9999	-0.56	17	17
CREBBP	-0.019	0.11	-9999	-0.34	25	25
Su(fu)/SIN3/HDAC complex	0.051	0.027	-9999	-0.29	1	1

×

HIF-2-alpha transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MMP14	-0.051	0.21	-10000	0	-1.1	12	12
oxygen homeostasis	0.008	0.017	-10000	0	-10000	0	0
TCEB2	0.014	0	-10000	0	-10000	0	0
TCEB1	0.014	0	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C/HIF2A	-0.003	0.045	-10000	0	-0.32	3	3
EPO	0.099	0.23	-10000	0	-0.72	10	10
FIH (dimer)	0.022	0.017	-10000	0	-10000	0	0
APEX1	0.021	0.017	-10000	0	-10000	0	0
SERPINE1	0.019	0.33	-10000	0	-0.77	16	16
FLT1	0.001	0.09	-10000	0	-1.6	1	1
ADORA2A	0.099	0.23	-10000	0	-0.72	9	9
germ cell development	0.09	0.24	-10000	0	-0.71	10	10
SLC11A2	0.1	0.23	-10000	0	-0.73	9	9
BHLHE40	0.092	0.25	-10000	0	-0.82	11	11
HIF1AN	0.022	0.017	-10000	0	-10000	0	0
HIF2A/ARNT/SIRT1	-0.022	0.086	-10000	0	-0.48	5	5
ETS1	0.025	0.058	-10000	0	-0.52	4	4
CITED2	0.002	0.041	-10000	0	-10000	0	0
KDR	-0.006	0.11	-10000	0	-0.96	4	4
PGK1	0.1	0.23	-10000	0	-0.73	9	9
SIRT1	0.014	0.001	-10000	0	-10000	0	0
response to hypoxia	0	0.002	-10000	0	-10000	0	0
HIF2A/ARNT	0.11	0.27	-10000	0	-0.88	10	10
EPAS1	0.073	0.11	-10000	0	-0.36	4	4
SP1	0.018	0.018	-10000	0	-10000	0	0
ABCG2	0.1	0.24	-10000	0	-0.77	9	9
EFNA1	0.1	0.23	-10000	0	-0.75	9	9
FXN	0.1	0.23	-10000	0	-0.7	10	10
POU5F1	0.089	0.25	-10000	0	-0.75	10	10
neuron apoptosis	-0.11	0.26	0.84	10	-10000	0	10
EP300	0.007	0.064	-10000	0	-0.6	4	4
EGLN3	0.013	0.075	-10000	0	-0.61	5	5
EGLN2	0.022	0.017	-10000	0	-10000	0	0
EGLN1	0.022	0.017	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C	0	0	-10000	0	-10000	0	0
VHL	0.014	0	-10000	0	-10000	0	0
ARNT	0.019	0.033	-10000	0	-0.51	1	1
SLC2A1	0.1	0.23	-10000	0	-0.71	10	10
TWIST1	0.073	0.27	-10000	0	-0.73	18	18
ELK1	0.023	0.002	-10000	0	-10000	0	0
HIF2A/ARNT/Cbp/p300	-0.023	0.087	-10000	0	-0.46	7	7
VEGFA	0.094	0.25	-10000	0	-0.82	11	11
CREBBP	0.014	0	-10000	0	-10000	0	0

×

Signaling events mediated by HDAC Class I

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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NF kappa B/RelA	-0.081	0.13	-10000	0	-0.36	51	51
Ran/GTP/Exportin 1/HDAC1	-0.001	0.02	-10000	0	-0.27	2	2
NF kappa B1 p50/RelA/I kappa B alpha	-0.031	0.13	-10000	0	-0.32	49	49
SUMO1	0.014	0	-10000	0	-10000	0	0
ZFPM1	0.013	0.026	-10000	0	-0.48	1	1
NPC/RanGAP1/SUMO1/Ubc9	0.024	0	-10000	0	-10000	0	0
FKBP3	0.014	0	-10000	0	-10000	0	0
Histones	-0.036	0.061	-10000	0	-0.4	1	1
YY1/LSF	0.03	0.035	-10000	0	-0.35	1	1
SMG5	0.014	0	-10000	0	-10000	0	0
RAN	0.014	0	-10000	0	-10000	0	0
I kappa B alpha/HDAC3	-0.037	0.12	-10000	0	-0.45	2	2
I kappa B alpha/HDAC1	-0.021	0.087	-10000	0	-0.31	4	4
SAP18	0.014	0	-10000	0	-10000	0	0
RELA	-0.028	0.11	-10000	0	-0.26	51	51
HDAC1/Smad7	-0.002	0.027	-10000	0	-0.36	2	2
RANGAP1	0.014	0	-10000	0	-10000	0	0
HDAC3/TR2	-0.019	0.085	-10000	0	-0.3	2	2
NuRD/MBD3 Complex	0.05	0.019	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.02	0.1	-10000	0	-0.35	4	4
EntrezGene:23225	0	0	-10000	0	-10000	0	0
GATA2	-0.01	0.12	-10000	0	-0.56	15	15
GATA1	0.003	0.057	-10000	0	-0.48	5	5
Mad/Max	0	0	-10000	0	-10000	0	0
NuRD/MBD3 Complex/GATA1/Fog1	0.059	0.025	-10000	0	-10000	0	0
RBBP7	0.014	0	-10000	0	-10000	0	0
NPC	0	0	-10000	0	-10000	0	0
RBBP4	0.014	0	-10000	0	-10000	0	0
MAX	0.014	0	-10000	0	-10000	0	0
EntrezGene:9972	0	0	-10000	0	-10000	0	0
FBXW11	0.014	0	-10000	0	-10000	0	0
NFKBIA	-0.03	0.095	-10000	0	-0.34	2	2
KAT2B	0.013	0.026	-10000	0	-0.48	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
SIN3/HDAC complex	0.046	0.022	-10000	0	-10000	0	0
SIN3 complex	-0.001	0.017	-10000	0	-0.32	1	1
SMURF1	0.014	0	-10000	0	-10000	0	0
CHD3	0.012	0.032	-10000	0	-0.6	1	1
SAP30	0.012	0.032	-10000	0	-0.6	1	1
EntrezGene:23636	0	0	-10000	0	-10000	0	0
NCOR1	0.012	0.032	-10000	0	-0.6	1	1
YY1/HDAC3	-0.005	0.084	-10000	0	-0.31	2	2
YY1/HDAC2	0.031	0.029	-10000	0	-10000	0	0
YY1/HDAC1	0.028	0.041	-10000	0	-0.35	2	2
NuRD/MBD2 Complex (MeCP1)	0.05	0.019	-10000	0	-10000	0	0
PPARG	-0.085	0.13	-10000	0	-0.35	61	61
HDAC8/hEST1B	-0.001	0.019	-10000	0	-0.36	1	1
UBE2I	0.014	0	-10000	0	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.014	0	-10000	0	-10000	0	0
TNFRSF1A	0.005	0.068	-10000	0	-0.52	6	6
HDAC3/SMRT (N-CoR2)	-0.019	0.085	-10000	0	-0.3	2	2
MBD3L2	0	0.001	-10000	0	-10000	0	0
ubiquitin-dependent protein catabolic process	-0.002	0.027	-10000	0	-0.36	2	2
CREBBP	0.014	0	-10000	0	-10000	0	0
NuRD/MBD3/MBD3L2 Complex	0.054	0.02	-10000	0	-10000	0	0
HDAC1	0.011	0.046	-10000	0	-0.6	2	2
HDAC3	-0.03	0.095	-10000	0	-0.34	2	2
HDAC2	0.014	0	-10000	0	-10000	0	0
YY1	0.029	0.035	-10000	0	-0.29	4	4
HDAC8	0.012	0.032	-10000	0	-0.6	1	1
SMAD7	0.014	0	-10000	0	-10000	0	0
NCOR2	0.014	0	-10000	0	-10000	0	0
MXD1	0.014	0	-10000	0	-10000	0	0
STAT3	0.024	0.039	-10000	0	-0.35	4	4
NFKB1	0.013	0.026	-10000	0	-0.48	1	1
EntrezGene:8021	0	0	-10000	0	-10000	0	0
RANBP2	0.014	0	-10000	0	-10000	0	0
YY1/LSF/HDAC1	0.034	0.041	-10000	0	-0.31	3	3
YY1/SAP30/HDAC1	0.034	0.041	-10000	0	-0.31	3	3
EP300	0.007	0.064	-10000	0	-0.6	4	4
STAT3 (dimer non-phopshorylated)	0.024	0.039	-10000	0	-0.35	4	4
proteasomal ubiquitin-dependent protein catabolic process	-0.029	0.094	-10000	0	-0.33	2	2
histone deacetylation	0.05	0.019	-10000	0	-10000	0	0
STAT3 (dimer non-phopshorylated)/HDAC3	-0.009	0.084	-10000	0	-0.36	2	2
nuclear export	0.001	0.019	0.36	1	-10000	0	1
PRKACA	0.014	0	-10000	0	-10000	0	0
GATAD2B	0.014	0	-10000	0	-10000	0	0
GATAD2A	0.014	0	-10000	0	-10000	0	0
GATA2/HDAC3	-0.032	0.11	-10000	0	-0.38	11	11
GATA1/HDAC1	-0.007	0.05	-10000	0	-0.36	7	7
GATA1/HDAC3	-0.031	0.086	-10000	0	-0.34	3	3
CHD4	0.014	0	-10000	0	-10000	0	0
TNF-alpha/TNFR1A	-0.12	0.18	-10000	0	-0.38	113	113
SIN3/HDAC complex/Mad/Max	0.05	0.019	-10000	0	-10000	0	0
NuRD Complex	0.059	0.02	-10000	0	-10000	0	0
positive regulation of chromatin silencing	-0.036	0.06	-10000	0	-0.39	1	1
SIN3B	0.014	0	-10000	0	-10000	0	0
MTA2	0.014	0	-10000	0	-10000	0	0
SIN3A	0.014	0	-10000	0	-10000	0	0
XPO1	0.014	0	-10000	0	-10000	0	0
SUMO1/HDAC1	0.031	0.024	-10000	0	-0.3	2	2
HDAC complex	-0.002	0.024	-10000	0	-0.32	2	2
GATA1/Fog1	-0.005	0.042	-10000	0	-0.33	6	6
FKBP25/HDAC1/HDAC2	-0.002	0.027	-10000	0	-0.36	2	2
TNF	-0.15	0.25	-10000	0	-0.54	109	109
negative regulation of cell growth	0.05	0.019	-10000	0	-10000	0	0
NuRD/MBD2/PRMT5 Complex	0.05	0.019	-10000	0	-10000	0	0
Ran/GTP/Exportin 1	0	0	-10000	0	-10000	0	0
NF kappa B/RelA/I kappa B alpha	-0.039	0.14	-10000	0	-0.34	51	51
SIN3/HDAC complex/NCoR1	0.048	0.022	-10000	0	-10000	0	0
TFCP2	0.012	0.032	-10000	0	-0.6	1	1
NR2C1	0.014	0	-10000	0	-10000	0	0
MBD3	0.014	0	-10000	0	-10000	0	0
MBD2	0.014	0	-10000	0	-10000	0	0

×

Insulin Pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CBL/APS/CAP	-0.012	0.059	-9999	-0.58	1	1
TC10/GTP	-0.009	0.053	-9999	-0.56	1	1
Insulin Receptor/Insulin/IRS1/Shp2	-0.003	0.029	-9999	-0.3	3	3
HRAS	0.013	0.026	-9999	-0.48	1	1
APS homodimer	-0.001	0.094	-9999	-0.59	9	9
GRB14	-0.17	0.26	-9999	-0.53	123	123
FOXO3	-0.025	0.09	-9999	-0.57	9	9
AKT1	-0.035	0.13	-9999	-0.43	4	4
INSR	0.016	0.003	-9999	-10000	0	0
Insulin Receptor/Insulin	0.036	0.03	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
GRB10	0.012	0.032	-9999	-0.6	1	1
SORBS1	0.007	0.064	-9999	-0.6	4	4
CRK	0.014	0	-9999	-10000	0	0
PTPN1	0.035	0.03	-9999	-10000	0	0
CAV1	-0.005	0.095	-9999	-0.38	6	6
CBL/APS/CAP/Crk-II/C3G	-0.01	0.059	-9999	-0.62	1	1
Insulin Receptor/Insulin/IRS1/NCK2	-0.003	0.029	-9999	-0.3	3	3
mol:GDP	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.003	0.029	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B	0.038	0.033	-9999	-10000	0	0
RPS6KB1	-0.024	0.12	-9999	-0.42	3	3
PARD6A	0.014	0	-9999	-10000	0	0
CBL	0.014	0	-9999	-10000	0	0
tumor necrosis factor-mediated signaling pathway	0	0	-9999	-10000	0	0
DOK1	-0.001	0.044	-9999	-0.83	1	1
PIK3R1	0.014	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/Shc	-0.061	0.09	-9999	-0.41	3	3
HRAS/GTP	-0.007	0.038	-9999	-0.42	1	1
Insulin Receptor	0.016	0.003	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC	-0.005	0.035	-9999	-10000	0	0
PRKCI	-0.022	0.054	-9999	-0.53	3	3
Insulin Receptor/Insulin/GRB14/PDK1	-0.078	0.11	-9999	-0.47	4	4
SHC1	0.009	0.052	-9999	-0.48	4	4
negative regulation of MAPKKK cascade	-0.002	0.041	-9999	-0.51	2	2
PI3K	-0.003	0.029	-9999	-10000	0	0
NCK2	0.014	0	-9999	-10000	0	0
RHOQ	0.014	0	-9999	-10000	0	0
mol:H2O2	0	0.003	-9999	-10000	0	0
HRAS/GDP	-0.001	0.018	-9999	-0.34	1	1
AKT2	-0.035	0.13	-9999	-0.43	4	4
PRKCZ	-0.039	0.11	-9999	-0.58	13	13
SH2B2	-0.001	0.094	-9999	-0.59	9	9
SHC/SHIP	0.028	0.051	-9999	-0.39	2	2
F2RL2	-0.093	0.21	-9999	-0.5	76	76
TRIP10	0.005	0.071	-9999	-0.54	6	6
Insulin Receptor/Insulin/Shc	-0.006	0.04	-9999	-0.28	7	7
TC10/GTP/CIP4/Exocyst	-0.005	0.042	-9999	-0.33	6	6
Insulin Receptor/Insulin/SHC/GRB2/Sos1	-0.005	0.035	-9999	-10000	0	0
RAPGEF1	0.014	0	-9999	-10000	0	0
RASA1	0.014	0	-9999	-10000	0	0
NCK1	0.012	0.032	-9999	-0.6	1	1
CBL/APS/CAP/Crk-II	-0.011	0.064	-9999	-0.35	11	11
TC10/GDP	0	0	-9999	-10000	0	0
Insulin Receptor/Insulin/SHC/GRB10	-0.007	0.043	-9999	-0.31	4	4
INPP5D	0.023	0.047	-9999	-0.35	4	4
SOS1	0.014	0	-9999	-10000	0	0
SGK1	-0.027	0.14	-9999	-0.88	9	9
mol:cAMP	0	0	-9999	-10000	0	0
PTPN11	0.014	0	-9999	-10000	0	0
IRS1	0.014	0	-9999	-10000	0	0
p62DOK/RasGAP	-0.002	0.041	-9999	-0.71	1	1
INS	-0.003	0.06	-9999	-0.57	4	4
mol:PI-3-4-P2	0.023	0.046	-9999	-0.35	4	4
GRB2	0.014	0	-9999	-10000	0	0
EIF4EBP1	-0.031	0.13	-9999	-0.43	10	10
PTPRA	0.016	0.003	-9999	-10000	0	0
PIK3CA	0.012	0.032	-9999	-0.6	1	1
TC10/GTP/CIP4	-0.005	0.042	-9999	-0.33	6	6
PDPK1	0.012	0.032	-9999	-0.6	1	1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos	0.032	0.032	-9999	-10000	0	0
Insulin Receptor/Insulin/IRS1	-0.003	0.03	-9999	-0.31	3	3
Insulin Receptor/Insulin/IRS3	-0.004	0.043	-9999	-0.41	4	4
Par3/Par6	-0.054	0.1	-9999	-0.32	18	18

×

Signaling events mediated by HDAC Class II

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G beta1gamma2/HDAC5	-0.003	0.029	-9999	-0.32	3	3
HDAC3	0.014	0	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	0	0	-9999	-10000	0	0
GATA1/HDAC4	-0.005	0.039	-9999	-0.33	5	5
GATA1/HDAC5	-0.005	0.039	-9999	-0.33	5	5
GATA2/HDAC5	-0.017	0.081	-9999	-0.4	15	15
HDAC5/BCL6/BCoR	-0.001	0.014	-9999	-0.27	1	1
HDAC9	0.004	0.076	-9999	-0.53	7	7
Glucocorticoid receptor/Hsp90/HDAC6	0	0	-9999	-10000	0	0
HDAC4/ANKRA2	0	0	-9999	-10000	0	0
HDAC5/YWHAB	0	0	-9999	-10000	0	0
NPC/RanGAP1/SUMO1/Ubc9	0.024	0	-9999	-10000	0	0
GATA2	-0.01	0.12	-9999	-0.56	15	15
HDAC4/RFXANK	-0.001	0.017	-9999	-0.33	1	1
BCOR	0.013	0.026	-9999	-0.48	1	1
mol:GTP	0	0	-9999	-10000	0	0
HDAC10	0.014	0	-9999	-10000	0	0
HDAC5	0.014	0	-9999	-10000	0	0
GNB1/GNG2	-0.004	0.039	-9999	-0.44	3	3
Histones	0.041	0.026	-9999	-10000	0	0
ADRBK1	0.014	0	-9999	-10000	0	0
HDAC4	0.014	0	-9999	-10000	0	0
XPO1	0.014	0	-9999	-10000	0	0
HDAC5/ANKRA2	0	0	-9999	-10000	0	0
HDAC4/Ubc9	0	0	-9999	-10000	0	0
HDAC7	0.014	0	-9999	-10000	0	0
HDAC5/14-3-3 E	0	0	-9999	-10000	0	0
TUBA1B	0.014	0	-9999	-10000	0	0
HDAC6	0.014	0	-9999	-10000	0	0
HDAC5/RFXANK	-0.001	0.017	-9999	-0.33	1	1
CAMK4	-0.17	0.27	-9999	-0.57	113	113
Tubulin/HDAC6	-0.001	0.019	-9999	-0.36	1	1
SUMO1	0.014	0	-9999	-10000	0	0
EntrezGene:9972	0	0	-9999	-10000	0	0
YWHAB	0.014	0	-9999	-10000	0	0
GATA1	0.003	0.057	-9999	-0.48	5	5
EntrezGene:8021	0	0	-9999	-10000	0	0
YWHAE	0.014	0	-9999	-10000	0	0
NR3C1	0.014	0	-9999	-10000	0	0
SUMO1/HDAC4	0.033	0	-9999	-10000	0	0
SRF	0.014	0	-9999	-10000	0	0
HDAC4/YWHAB	0	0	-9999	-10000	0	0
Tubulin	-0.001	0.023	-9999	-0.44	1	1
HDAC4/14-3-3 E	0	0	-9999	-10000	0	0
GNB1	0.014	0	-9999	-10000	0	0
RANGAP1	0.014	0	-9999	-10000	0	0
BCL6/BCoR	-0.001	0.017	-9999	-0.33	1	1
HDAC4/HDAC3/SMRT (N-CoR2)	0	0	-9999	-10000	0	0
HDAC4/SRF	-0.11	0.16	-9999	-0.34	113	113
HDAC4/ER alpha	-0.021	0.089	-9999	-0.39	20	20
EntrezGene:23225	0	0	-9999	-10000	0	0
positive regulation of chromatin silencing	0.041	0.026	-9999	-10000	0	0
cell motility	-0.001	0.019	-9999	-0.36	1	1
EntrezGene:23636	0	0	-9999	-10000	0	0
UBE2I	0.014	0	-9999	-10000	0	0
HDAC7/HDAC3	0	0	-9999	-10000	0	0
BCL6	0.014	0	-9999	-10000	0	0
HDAC4/CaMK II delta B	0.014	0	-9999	-10000	0	0
Hsp90/HDAC6	0	0	-9999	-10000	0	0
ESR1	-0.016	0.13	-9999	-0.54	20	20
HDAC6/HDAC11	0	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0	0	-9999	-10000	0	0
NPC	0	0	-9999	-10000	0	0
MEF2C	-0.005	0.095	-9999	-0.48	14	14
RAN	0.014	0	-9999	-10000	0	0
HDAC4/MEF2C	-0.008	0.041	-9999	-10000	0	0
GNG2	0.009	0.056	-9999	-0.6	3	3
NCOR2	0.014	0	-9999	-10000	0	0
TUBB2A	0.012	0.032	-9999	-0.6	1	1
HDAC11	0.014	0	-9999	-10000	0	0
HSP90AA1	0.014	0	-9999	-10000	0	0
RANBP2	0.014	0	-9999	-10000	0	0
ANKRA2	0.014	0	-9999	-10000	0	0
RFXANK	0.013	0.026	-9999	-0.48	1	1
nuclear import	-0.032	0	-9999	-10000	0	0

×

FoxO family signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G6PC	0.011	0.17	-9999	-1.4	4	4
PLK1	0.057	0.2	-9999	-0.97	6	6
CDKN1B	0.1	0.11	-9999	-10000	0	0
FOXO3	0.071	0.14	-9999	-0.58	4	4
KAT2B	0.022	0.028	-9999	-0.46	1	1
FOXO1/SIRT1	-0.005	0.07	-9999	-0.41	4	4
CAT	0.075	0.13	-9999	-0.59	1	1
CTNNB1	0.014	0	-9999	-10000	0	0
AKT1	0.025	0.016	-9999	-10000	0	0
FOXO1	0.026	0.085	-9999	-0.35	10	10
MAPK10	0.037	0.04	-9999	-0.32	4	4
mol:GTP	0.002	0.002	-9999	-10000	0	0
FOXO4	0.095	0.067	-9999	-10000	0	0
response to oxidative stress	0.011	0.019	-9999	-10000	0	0
FOXO3A/SIRT1	0.018	0.12	-9999	-0.53	4	4
XPO1	0.015	0.001	-9999	-10000	0	0
EP300	0.009	0.065	-9999	-0.6	4	4
BCL2L11	0.033	0.08	-9999	-1.4	1	1
FOXO1/SKP2	0.022	0.097	-9999	-0.41	11	11
mol:GDP	0.011	0.019	-9999	-10000	0	0
RAN	0.016	0.001	-9999	-10000	0	0
GADD45A	0.082	0.14	-9999	-0.47	9	9
YWHAQ	0.014	0	-9999	-10000	0	0
FOXO1/14-3-3 family	0.043	0.072	-9999	-10000	0	0
MST1	-0.023	0.16	-9999	-0.54	30	30
CSNK1D	0.014	0	-9999	-10000	0	0
CSNK1E	0.014	0	-9999	-10000	0	0
FOXO4/14-3-3 family	0.012	0.1	-9999	-0.51	1	1
YWHAB	0.014	0	-9999	-10000	0	0
MAPK8	0.032	0.059	-9999	-0.31	10	10
MAPK9	0.041	0.014	-9999	-10000	0	0
YWHAG	0.002	0.077	-9999	-0.48	9	9
YWHAE	0.014	0	-9999	-10000	0	0
YWHAZ	0.014	0	-9999	-10000	0	0
SIRT1	0.009	0.011	-9999	-10000	0	0
SOD2	0.1	0.15	-9999	-0.68	2	2
RBL2	0.09	0.11	-9999	-10000	0	0
RAL/GDP	0.031	0.017	-9999	-10000	0	0
CHUK	0.023	0.013	-9999	-10000	0	0
Ran/GTP	0.014	0.005	-9999	-10000	0	0
CSNK1G2	0.014	0	-9999	-10000	0	0
RAL/GTP	0.038	0.018	-9999	-10000	0	0
CSNK1G1	0.013	0.026	-9999	-0.48	1	1
FASLG	0.003	0.1	-9999	-0.44	1	1
SKP2	0.002	0.084	-9999	-0.56	8	8
USP7	0.016	0.001	-9999	-10000	0	0
IKBKB	0.023	0.013	-9999	-10000	0	0
CCNB1	0.066	0.16	-9999	-0.7	3	3
FOXO1-3a-4/beta catenin	0.13	0.12	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.022	0.096	-9999	-0.41	11	11
CSNK1A1	0.014	0	-9999	-10000	0	0
SGK1	0.007	0.099	-9999	-0.58	10	10
CSNK1G3	0.014	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.025	0.008	-9999	-10000	0	0
ZFAND5	0.097	0.061	-9999	-10000	0	0
SFN	-0.11	0.23	-9999	-0.52	87	87
CDK2	0	0.086	-9999	-0.53	9	9
FOXO3A/14-3-3	0.025	0.092	-9999	-0.36	3	3
CREBBP	0.014	0.013	-9999	-10000	0	0
FBXO32	0.061	0.18	-9999	-1.1	4	4
BCL6	0.09	0.11	-9999	-10000	0	0
RALB	0.015	0.001	-9999	-10000	0	0
RALA	0.015	0.001	-9999	-10000	0	0
YWHAH	-0.009	0.1	-9999	-0.48	17	17

×

PDGFR-beta signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate	-0.014	0.076	-9999	-0.36	9	9
PDGFB-D/PDGFRB/SLAP	-0.004	0.1	-9999	-0.4	21	21
PDGFB-D/PDGFRB/APS/CBL	-0.01	0.065	-9999	-0.38	10	10
AKT1	0.059	0.037	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
mol:Sphingosine-1-phosphate	0.01	0.085	-9999	-0.38	7	7
PIK3CA	0.012	0.032	-9999	-0.6	1	1
FGR	0.001	0.03	-9999	-10000	0	0
mol:Ca2+	0.02	0.041	-9999	-10000	0	0
MYC	0.004	0.18	-9999	-0.82	15	15
SHC1	0.009	0.052	-9999	-0.48	4	4
HRAS/GDP	0.036	0.027	-9999	-10000	0	0
LRP1/PDGFRB/PDGFB	-0.001	0.025	-9999	-10000	0	0
GRB10	0.012	0.032	-9999	-0.6	1	1
PTPN11	0.014	0	-9999	-10000	0	0
GO:0007205	0.02	0.041	-9999	-10000	0	0
PTEN	0.014	0	-9999	-10000	0	0
GRB2	0.014	0	-9999	-10000	0	0
GRB7	-0.036	0.14	-9999	-0.48	34	34
PDGFB-D/PDGFRB/SHP2	0.017	0.033	-9999	-0.33	3	3
PDGFB-D/PDGFRB/GRB10	0.015	0.04	-9999	-0.36	4	4
cell cycle arrest	-0.005	0.099	-9999	-0.4	21	21
HRAS	0.013	0.026	-9999	-0.48	1	1
HIF1A	0.063	0.036	-9999	-10000	0	0
GAB1	0.008	0.071	-9999	-0.4	2	2
mol:GTP	0	0	-9999	-10000	0	0
DNM2	0.012	0.073	-9999	-0.39	2	2
PDGFB-D/PDGFRB	0.01	0.032	-9999	-0.29	1	1
mol:GDP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/LMW-PTP	0.017	0.033	-9999	-0.33	3	3
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB	-0.024	0.086	-9999	-0.41	10	10
positive regulation of MAPKKK cascade	0.017	0.032	-9999	-0.33	3	3
PIK3R1	0.014	0	-9999	-10000	0	0
mol:IP3	0.02	0.042	-9999	-10000	0	0
E5	0	0.001	-9999	-10000	0	0
CSK	0.014	0.001	-9999	-10000	0	0
PDGFB-D/PDGFRB/GRB7	-0.019	0.11	-9999	-0.35	36	36
SHB	0.014	0	-9999	-10000	0	0
BLK	-0.042	0.11	-9999	-0.54	13	13
PTPN2	0.014	0.003	-9999	-10000	0	0
PDGFB-D/PDGFRB/SNX15	0.017	0.033	-9999	-0.33	3	3
BCAR1	0.012	0.032	-9999	-0.6	1	1
VAV2	0.01	0.085	-9999	-0.38	5	5
CBL	0.014	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/DEP1	0.016	0.037	-9999	-0.33	4	4
LCK	-0.055	0.15	-9999	-0.52	29	29
PDGFRB	0.01	0.045	-9999	-0.48	3	3
ACP1	0.014	0	-9999	-10000	0	0
HCK	-0.012	0.094	-9999	-0.59	8	8
ABL1	0.01	0.061	-9999	-0.34	2	2
PDGFB-D/PDGFRB/CBL	0.008	0.068	-9999	-0.41	1	1
PTPN1	0.014	0.003	-9999	-10000	0	0
SNX15	0.014	0	-9999	-10000	0	0
STAT3	0.014	0	-9999	-10000	0	0
STAT1	-0.001	0.085	-9999	-0.48	11	11
cell proliferation	0.008	0.16	-9999	-0.72	15	15
SLA	-0.015	0.12	-9999	-0.55	19	19
actin cytoskeleton reorganization	0.048	0.036	-9999	-10000	0	0
SRC	0.002	0.028	-9999	-10000	0	0
PI3K	-0.004	0.03	-9999	-10000	0	0
PDGFB-D/PDGFRB/GRB7/SHC	-0.029	0.096	-9999	-0.3	38	38
SH2B2	-0.001	0.094	-9999	-0.59	9	9
PLCgamma1/SPHK1	0.01	0.087	-9999	-0.39	7	7
LYN	0	0.033	-9999	-10000	0	0
LRP1	0.014	0	-9999	-10000	0	0
SOS1	0.014	0	-9999	-10000	0	0
STAT5B	0.014	0	-9999	-10000	0	0
STAT5A	0.001	0.09	-9999	-0.6	8	8
NCK1-2/p130 Cas	0.004	0.034	-9999	-10000	0	0
SPHK1	-0.025	0.14	-9999	-0.54	26	26
EDG1	0	0.002	-9999	-10000	0	0
mol:DAG	0.02	0.042	-9999	-10000	0	0
PLCG1	0.02	0.042	-9999	-10000	0	0
NHERF/PDGFRB	-0.004	0.042	-9999	-0.37	2	2
YES1	-0.001	0.051	-9999	-0.57	2	2
cell migration	-0.005	0.042	-9999	-0.37	2	2
SHC/Grb2/SOS1	0.004	0.042	-9999	-0.44	2	2
SLC9A3R2	0.011	0.037	-9999	-0.48	2	2
SLC9A3R1	0.011	0.046	-9999	-0.6	2	2
NHERF1-2/PDGFRB/PTEN	0.007	0.042	-9999	-0.33	2	2
FYN	0.003	0.028	-9999	-10000	0	0
DOK1	0.032	0.032	-9999	-0.34	1	1
HRAS/GTP	-0.001	0.018	-9999	-0.34	1	1
PDGFB	0.014	0	-9999	-10000	0	0
RAC1	0.015	0.11	-9999	-0.43	16	16
PRKCD	0.016	0.082	-9999	-0.33	17	17
FER	0.012	0.089	-9999	-0.33	21	21
MAPKKK cascade	-0.004	0.037	-9999	-0.44	2	2
RASA1	0.033	0.026	-9999	-10000	0	0
NCK1	0.012	0.032	-9999	-0.6	1	1
NCK2	0.014	0	-9999	-10000	0	0
p62DOK/Csk	0.039	0.029	-9999	-0.3	1	1
PDGFB-D/PDGFRB/SHB	0.017	0.033	-9999	-0.33	3	3
chemotaxis	0.01	0.06	-9999	-0.33	2	2
STAT1-3-5/STAT1-3-5	-0.013	0.053	-9999	-10000	0	0
Bovine Papilomavirus E5/PDGFRB	0.007	0.032	-9999	-0.35	3	3
PTPRJ	0.013	0.026	-9999	-0.48	1	1

×

Class I PI3K signaling events mediated by Akt

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
BCL2L1	0.024	0.019	-10000	0	-0.34	1	1
BAD/BCL-XL/YWHAZ	0.035	0.014	-10000	0	-10000	0	0
CDKN1B	0.04	0.007	-10000	0	-10000	0	0
CDKN1A	0.005	0.093	-10000	0	-0.28	16	16
FRAP1	0	0	-10000	0	-10000	0	0
PRKDC	0.014	0	-10000	0	-10000	0	0
FOXO3	0.04	0.007	-10000	0	-10000	0	0
AKT1	0	0.006	-10000	0	-10000	0	0
BAD	0.014	0	-10000	0	-10000	0	0
AKT3	0.012	0.061	-10000	0	-0.46	5	5
mol:GTP	0	0	-10000	0	-10000	0	0
FOXO4	0.039	0.018	-10000	0	-0.28	1	1
AKT1/ASK1	0.036	0.033	-10000	0	-0.32	3	3
BAD/YWHAZ	0	0	-10000	0	-10000	0	0
RICTOR	0.014	0	-10000	0	-10000	0	0
RAF1	0.014	0	-10000	0	-10000	0	0
JNK cascade	0.003	0.028	0.31	3	-10000	0	3
TSC1	0.04	0.007	-10000	0	-10000	0	0
YWHAZ	0.014	0	-10000	0	-10000	0	0
AKT1/RAF1	0.04	0.007	-10000	0	-10000	0	0
EP300	0.007	0.064	-10000	0	-0.6	4	4
mol:GDP	0.033	0.008	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	0	0	-10000	0	-10000	0	0
TSC2	0.04	0.007	-10000	0	-10000	0	0
YWHAQ	0.014	0	-10000	0	-10000	0	0
TBC1D4	0.026	0.017	-10000	0	-0.3	1	1
MAP3K5	0.009	0.056	-10000	0	-0.6	3	3
MAPKAP1	0.014	0	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.013	0.059	0.27	1	-10000	0	1
YWHAH	-0.009	0.1	-10000	0	-0.48	17	17
AKT1S1	0.04	0.007	-10000	0	-10000	0	0
CASP9	0.04	0.007	-10000	0	-10000	0	0
YWHAB	0.014	0	-10000	0	-10000	0	0
p27Kip1/KPNA1	0.047	0.007	-10000	0	-10000	0	0
GBL	0	0	-10000	0	-10000	0	0
PDK1/Src/Hsp90	-0.001	0.019	-10000	0	-0.36	1	1
YWHAE	0.014	0	-10000	0	-10000	0	0
SRC	0.014	0	-10000	0	-10000	0	0
AKT2/p21CIP1	-0.029	0.075	-10000	0	-10000	0	0
KIAA1303	0	0	-10000	0	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL	0.02	0.002	-10000	0	-10000	0	0
CHUK	0.04	0.007	-10000	0	-10000	0	0
BAD/BCL-XL	0.054	0.014	-10000	0	-10000	0	0
mTORC2	0	0	-10000	0	-10000	0	0
AKT2	0.018	0.02	-10000	0	-0.36	1	1
FOXO1-3a-4/14-3-3 family	0.031	0.063	-10000	0	-0.29	1	1
PDPK1	0.012	0.032	-10000	0	-0.6	1	1
MDM2	0.039	0.019	-10000	0	-10000	0	0
MAPKKK cascade	-0.04	0.007	-10000	0	-10000	0	0
MDM2/Cbp/p300	0.049	0.039	-10000	0	-0.38	1	1
TSC1/TSC2	0.047	0.007	-10000	0	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.046	0.038	-10000	0	-0.36	1	1
glucose import	-0.013	0.11	-10000	0	-0.28	53	53
mTOR/RHEB/GDP/Raptor/GBL/PRAS40	0.034	0.005	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
SLC2A4	-0.013	0.11	-10000	0	-0.28	53	53
GSK3A	0.04	0.007	-10000	0	-10000	0	0
FOXO1	0.038	0.028	-10000	0	-0.28	2	2
GSK3B	0.04	0.007	-10000	0	-10000	0	0
SFN	-0.11	0.23	-10000	0	-0.52	87	87
G1/S transition of mitotic cell cycle	0.047	0.007	-10000	0	-10000	0	0
p27Kip1/14-3-3 family	0.008	0.085	-10000	0	-0.37	4	4
PRKACA	0.014	0	-10000	0	-10000	0	0
KPNA1	0.014	0	-10000	0	-10000	0	0
HSP90AA1	0.014	0	-10000	0	-10000	0	0
YWHAG	0.002	0.077	-10000	0	-0.48	9	9
RHEB	0.014	0	-10000	0	-10000	0	0
CREBBP	0.014	0	-10000	0	-10000	0	0

×

Arf6 trafficking events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SLC2A4	-0.066	0.2	-9999	-0.55	52	52
CLTC	0.031	0.015	-9999	-10000	0	0
calcium ion-dependent exocytosis	0.016	0.046	-9999	-10000	0	0
Dynamin 2/GTP	0	0	-9999	-10000	0	0
EXOC4	0.014	0	-9999	-10000	0	0
CD59	0.026	0.021	-9999	-10000	0	0
CPE	0.009	0.066	-9999	-0.37	11	11
CTNNB1	0.014	0	-9999	-10000	0	0
membrane fusion	0.015	0.048	-9999	-10000	0	0
CTNND1	0.035	0	-9999	-10000	0	0
DNM2	0.014	0	-9999	-10000	0	0
mol:PI-4-5-P2	0.028	0.025	-9999	-10000	0	0
TSHR	-0.12	0.17	-9999	-0.33	143	143
INS	0.006	0.05	-9999	-0.52	3	3
BIN1	0.014	0	-9999	-10000	0	0
mol:Choline	0.015	0.048	-9999	-10000	0	0
growth hormone secretagogue receptor activity	0	0	-9999	-10000	0	0
mol:GDP	0.02	0	-9999	-10000	0	0
membrane depolarization	0	0	-9999	-10000	0	0
ARF6	0.014	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
JUP	0.021	0.04	-9999	-0.29	2	2
ASAP2/amphiphysin II	0	0	-9999	-10000	0	0
ARF6/GTP	0	0	-9999	-10000	0	0
CDH1	-0.024	0.093	-9999	-0.29	10	10
clathrin-independent pinocytosis	0	0	-9999	-10000	0	0
MAPK8IP3	0.014	0	-9999	-10000	0	0
positive regulation of endocytosis	0	0	-9999	-10000	0	0
EXOC2	0.014	0	-9999	-10000	0	0
substrate adhesion-dependent cell spreading	0.047	0	-9999	-10000	0	0
insulin receptor binding	0	0	-9999	-10000	0	0
SPAG9	0.014	0	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	0.029	0.053	-9999	-10000	0	0
positive regulation of phagocytosis	0.02	0	-9999	-10000	0	0
ARF6/GTP/JIP3	0	0	-9999	-10000	0	0
ACAP1	0.013	0.042	-9999	-0.29	1	1
mol:GTP	0	0	-9999	-10000	0	0
CHRM2	-0.02	0.085	-9999	-0.29	3	3
clathrin heavy chain/ACAP1	0.032	0.03	-9999	-10000	0	0
JIP4/KLC1	0	0	-9999	-10000	0	0
EXOC1	0.014	0	-9999	-10000	0	0
exocyst	0.047	0	-9999	-10000	0	0
RALA/GTP	0	0	-9999	-10000	0	0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex	0	0	-9999	-10000	0	0
receptor recycling	0	0	-9999	-10000	0	0
CTNNA1	0.035	0	-9999	-10000	0	0
NME1	0.021	0	-9999	-10000	0	0
clathrin coat assembly	0.031	0.015	-9999	-10000	0	0
IL2RA	-0.001	0.063	-9999	-0.29	1	1
VAMP3	0.021	0	-9999	-10000	0	0
GLUT4/clathrin heavy chain/ACAP1	-0.037	0.083	-9999	-0.35	4	4
EXOC6	0.014	0	-9999	-10000	0	0
PLD1	-0.021	0.072	-9999	-0.29	24	24
PLD2	0	0	-9999	-10000	0	0
EXOC5	0.014	0	-9999	-10000	0	0
PIP5K1C	0.028	0.025	-9999	-10000	0	0
SDC1	0.014	0.045	-9999	-10000	0	0
ARF6/GDP	0.02	0	-9999	-10000	0	0
EXOC7	0.014	0	-9999	-10000	0	0
E-cadherin/beta catenin	-0.029	0.054	-9999	-10000	0	0
mol:Phosphatidic acid	0.015	0.048	-9999	-10000	0	0
endocytosis	0	0	-9999	-10000	0	0
SCAMP2	0.014	0	-9999	-10000	0	0
ADRB2	0.025	0.066	-9999	-0.33	4	4
EXOC3	0.014	0	-9999	-10000	0	0
ASAP2	0.014	0	-9999	-10000	0	0
Dynamin 2/GDP	0.028	0	-9999	-10000	0	0
KLC1	0.014	0	-9999	-10000	0	0
AVPR2	0.027	0.052	-9999	-10000	0	0
RALA	0.014	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.022	0.047	-9999	-10000	0	0

×

IGF1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NCK2	0.014	0	-9999	-10000	0	0
PTK2	0.014	0	-9999	-10000	0	0
CRKL	0.019	0.053	-9999	-0.29	8	8
GRB2/SOS1/SHC	-0.003	0.028	-9999	-0.27	4	4
HRAS	0.013	0.026	-9999	-0.48	1	1
IRS1/Crk	0.019	0.053	-9999	-0.3	8	8
IGF-1R heterotetramer/IGF1/PTP1B	-0.011	0.058	-9999	-0.34	8	8
AKT1	0.039	0.051	-9999	-10000	0	0
BAD	0.045	0.049	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.019	0.053	-9999	-0.29	8	8
IGF-1R heterotetramer/IGF1/IRS1/Shp2	0.019	0.053	-9999	-0.3	8	8
RAF1	0.049	0.049	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos	0.027	0.051	-9999	-10000	0	0
YWHAZ	0.014	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	0.01	0.058	-9999	-0.33	8	8
PIK3CA	0.012	0.032	-9999	-0.6	1	1
RPS6KB1	0.039	0.051	-9999	-10000	0	0
GNB2L1	0.014	0	-9999	-10000	0	0
positive regulation of MAPKKK cascade	0.042	0.044	-9999	-10000	0	0
PXN	0.014	0	-9999	-10000	0	0
PIK3R1	0.014	0	-9999	-10000	0	0
cell adhesion	0	0	-9999	-10000	0	0
GRB2/SOS1	0	0	-9999	-10000	0	0
HRAS/GTP	-0.01	0.047	-9999	-0.35	2	2
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc	-0.011	0.054	-9999	-0.42	2	2
IGF-1R heterotetramer	0.012	0.013	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS/Nck	0.019	0.054	-9999	-0.3	8	8
Crk/p130 Cas/Paxillin	-0.009	0.043	-9999	-10000	0	0
IGF1R	0.012	0.013	-9999	-10000	0	0
IGF1	-0.007	0.11	-9999	-0.55	14	14
IRS2/Crk	0.026	0.056	-9999	-0.47	1	1
PI3K	0.026	0.053	-9999	-0.3	1	1
apoptosis	-0.049	0.044	-9999	-10000	0	0
HRAS/GDP	-0.001	0.018	-9999	-0.34	1	1
PRKCD	0.018	0.11	-9999	-0.53	8	8
RAF1/14-3-3 E	0.054	0.044	-9999	-10000	0	0
BAD/14-3-3	0.051	0.046	-9999	-10000	0	0
PRKCZ	0.027	0.079	-9999	-0.43	2	2
Crk/p130 Cas/Paxillin/FAK1	-0.007	0.034	-9999	-10000	0	0
PTPN1	0.014	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1	0.026	0.07	-9999	-0.4	8	8
BCAR1	0.012	0.032	-9999	-0.6	1	1
IGF-1R heterotetramer/IGF1/SHC/GRB10	-0.013	0.063	-9999	-0.33	11	11
mol:GDP	0	0	-9999	-10000	0	0
SOS1	0.014	0	-9999	-10000	0	0
IRS1/NCK2	0.019	0.053	-9999	-0.29	8	8
GRB10	0.012	0.032	-9999	-0.6	1	1
PTPN11	0.019	0.053	-9999	-0.29	8	8
IRS1	0.011	0.058	-9999	-0.33	8	8
IRS2	0.018	0.059	-9999	-0.32	9	9
IGF-1R heterotetramer/IGF1	0.004	0.081	-9999	-0.4	14	14
GRB2	0.014	0	-9999	-10000	0	0
PDPK1	0.032	0.053	-9999	-10000	0	0
YWHAE	0.014	0	-9999	-10000	0	0
PRKD1	0.033	0.066	-9999	-0.37	8	8
SHC1	0.009	0.052	-9999	-0.48	4	4

×

Arf6 downstream pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLAUR	0.013	0.13	-10000	0	-1.1	2	2
regulation of axonogenesis	-0.005	0.069	-10000	0	-10000	0	0
myoblast fusion	-0.003	0.062	0.41	2	-10000	0	2
mol:GTP	-0.01	0.036	-10000	0	-0.23	2	2
regulation of calcium-dependent cell-cell adhesion	-0.026	0.043	0.34	1	-10000	0	1
ARF1/GTP	-0.006	0.023	-10000	0	-10000	0	0
mol:GM1	0.003	0.03	-10000	0	-10000	0	0
mol:Choline	-0.006	0.1	-10000	0	-0.35	24	24
lamellipodium assembly	-0.017	0.058	-10000	0	-0.45	2	2
MAPK3	0.016	0.057	-10000	0	-0.34	2	2
ARF6/GTP/NME1/Tiam1	0.027	0.044	-10000	0	-0.35	1	1
ARF1	0.014	0	-10000	0	-10000	0	0
ARF6/GDP	0.003	0.063	-10000	0	-0.41	2	2
ARF1/GDP	0.013	0.058	-10000	0	-0.38	2	2
ARF6	0.007	0.021	-10000	0	-10000	0	0
RAB11A	0.014	0	-10000	0	-10000	0	0
TIAM1	0.013	0.033	-10000	0	-0.6	1	1
fibronectin binding	0	0	-10000	0	-10000	0	0
MAPK1	0.016	0.057	-10000	0	-0.34	2	2
actin filament bundle formation	-0.012	0.057	0.37	2	-10000	0	2
KALRN	-0.018	0.055	-10000	0	-0.32	2	2
RAB11FIP3/RAB11A	0	0	-10000	0	-10000	0	0
RhoA/GDP	0.012	0.057	-10000	0	-0.38	2	2
NME1	0.015	0.004	-10000	0	-10000	0	0
Rac1/GDP	0.012	0.057	-10000	0	-0.38	2	2
substrate adhesion-dependent cell spreading	-0.01	0.036	-10000	0	-0.23	2	2
cortical actin cytoskeleton organization	-0.017	0.058	-10000	0	-0.45	2	2
RAC1	0.014	0	-10000	0	-10000	0	0
liver development	-0.01	0.036	-10000	0	-0.23	2	2
ARF6/GTP	-0.01	0.036	-10000	0	-0.23	2	2
RhoA/GTP	-0.006	0.023	-10000	0	-10000	0	0
mol:GDP	-0.017	0.057	-10000	0	-0.42	2	2
ARF6/GTP/RAB11FIP3/RAB11A	-0.004	0.018	-10000	0	-10000	0	0
RHOA	0.014	0	-10000	0	-10000	0	0
PLD1	-0.019	0.11	-10000	0	-0.38	30	30
RAB11FIP3	0.014	0	-10000	0	-10000	0	0
tube morphogenesis	-0.017	0.058	-10000	0	-0.45	2	2
ruffle organization	0.005	0.069	-10000	0	-10000	0	0
regulation of epithelial cell migration	-0.01	0.036	-10000	0	-0.23	2	2
PLD2	0.015	0.03	-10000	0	-10000	0	0
PIP5K1A	0.005	0.069	-10000	0	-10000	0	0
mol:Phosphatidic acid	-0.006	0.1	-10000	0	-0.35	24	24
Rac1/GTP	-0.017	0.058	-10000	0	-0.45	2	2

×

Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SMAD4	0.014	0	-9999	-10000	0	0
SMAD2	0.015	0.018	-9999	-0.25	1	1
SMAD3	0.043	0.023	-9999	-10000	0	0
SMAD3/SMAD4	0.05	0.01	-9999	-10000	0	0
SMAD4/Ubc9/PIASy	0	0	-9999	-10000	0	0
SMAD2/SMAD2/SMAD4	-0.001	0.014	-9999	-10000	0	0
PPM1A	0.014	0	-9999	-10000	0	0
CALM1	0.012	0.032	-9999	-0.6	1	1
SMAD2/SMAD4	0.022	0.016	-9999	-10000	0	0
MAP3K1	0.011	0.037	-9999	-0.48	2	2
TRAP-1/SMAD4	-0.017	0.084	-9999	-0.44	14	14
MAPK3	0.014	0	-9999	-10000	0	0
MAPK1	0.014	0	-9999	-10000	0	0
NUP214	0.014	0	-9999	-10000	0	0
CTDSP1	0.014	0	-9999	-10000	0	0
CTDSP2	0.01	0.045	-9999	-0.48	3	3
CTDSPL	0.012	0.032	-9999	-0.6	1	1
KPNB1	0.014	0	-9999	-10000	0	0
TGFBRAP1	-0.01	0.12	-9999	-0.6	14	14
UBE2I	0.014	0	-9999	-10000	0	0
NUP153	0.014	0	-9999	-10000	0	0
KPNA2	0.013	0.026	-9999	-0.48	1	1
PIAS4	0.014	0	-9999	-10000	0	0

×

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	0	-9999	-10000	0	0
FBXW11	0.014	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.014	0	-9999	-10000	0	0
CHUK	0.014	0	-9999	-10000	0	0
NF kappa B2 p100/RelB	-0.005	0.038	-9999	-0.46	1	1
NFKB1	0.013	0.026	-9999	-0.48	1	1
MAP3K14	0.014	0	-9999	-10000	0	0
NF kappa B1 p50/RelB	-0.004	0.043	-9999	-0.47	3	3
RELB	0.01	0.049	-9999	-0.52	3	3
NFKB2	0.008	0.055	-9999	-0.51	4	4
NF kappa B2 p52/RelB	-0.006	0.047	-9999	-0.36	6	6
regulation of B cell activation	-0.006	0.047	-9999	-0.36	6	6

×

mTOR signaling pathway

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
GBL	0	0	-9999	-10000	0	0
MKNK1	0.007	0.064	-9999	-0.6	4	4
mol:PIP3	-0.001	0.015	-9999	-0.29	1	1
FRAP1	0.016	0.008	-9999	-10000	0	0
AKT1	0.03	0.019	-9999	-0.28	1	1
INSR	0.014	0	-9999	-10000	0	0
Insulin Receptor/Insulin	-0.004	0.037	-9999	-0.35	4	4
mol:GTP	-0.001	0.014	-9999	-10000	0	0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit	0	0.005	-9999	-10000	0	0
TSC2	0.014	0	-9999	-10000	0	0
RHEB/GDP	-0.001	0.012	-9999	-10000	0	0
TSC1	0.014	0	-9999	-10000	0	0
Insulin Receptor/IRS1	0.018	0.001	-9999	-10000	0	0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA	0	0.006	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
EIF3A	0.014	0	-9999	-10000	0	0
RPS6KB1	0.03	0.013	-9999	-10000	0	0
MAP3K5	0.008	0.036	-9999	-0.39	3	3
PIK3R1	0.014	0	-9999	-10000	0	0
apoptosis	0.008	0.036	-9999	-0.39	3	3
mol:LY294002	0	0	-9999	-10000	0	0
EIF4B	0.036	0.012	-9999	-10000	0	0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	-0.001	0.012	-9999	-10000	0	0
eIF4E/eIF4G1/eIF4A1	-0.002	0.019	-9999	-10000	0	0
KIAA1303	0	0	-9999	-10000	0	0
PI3K	0.026	0.017	-9999	-0.3	1	1
mTOR/RHEB/GTP/Raptor/GBL	0.034	0.01	-9999	-10000	0	0
FKBP1A	0.014	0	-9999	-10000	0	0
RHEB/GTP	-0.001	0.012	-9999	-10000	0	0
mol:Amino Acids	0	0	-9999	-10000	0	0
FKBP12/Rapamycin	0.011	0.001	-9999	-10000	0	0
PDPK1	-0.002	0.021	-9999	-0.28	2	2
EIF4E	0.014	0	-9999	-10000	0	0
ASK1/PP5C	0.019	0.057	-9999	-0.61	3	3
mTOR/RHEB/GTP/Raptor/GBL/eIF4E	0.019	0	-9999	-10000	0	0
TSC1/TSC2	-0.001	0.014	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
RPS6	0.013	0.026	-9999	-0.48	1	1
PPP5C	0.014	0	-9999	-10000	0	0
EIF4G1	0.014	0	-9999	-10000	0	0
IRS1	0.009	0.001	-9999	-10000	0	0
INS	-0.006	0.06	-9999	-0.57	4	4
PTEN	0.014	0	-9999	-10000	0	0
PDK2	-0.001	0.014	-9999	-0.27	1	1
EIF4EBP1	-0.007	0.15	-9999	-1.1	6	6
PIK3CA	0.013	0.032	-9999	-0.6	1	1
PPP2R5D	0.023	0.007	-9999	-10000	0	0
peptide biosynthetic process	0.015	0.034	-9999	-0.31	4	4
RHEB	0.014	0	-9999	-10000	0	0
EIF4A1	0.014	0	-9999	-10000	0	0
mol:Rapamycin	0	0	-9999	-10000	0	0
EEF2	0.015	0.034	-9999	-0.31	4	4
eIF4E/4E-BP1	0.002	0.14	-9999	-1	6	6

×

Sumoylation by RanBP2 regulates transcriptional repression

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.011	0.046	-9999	-0.6	2	2
Ran/GTP/Exportin 1/HDAC4	0	0	-9999	-10000	0	0
MDM2/SUMO1	0.032	0.018	-9999	-10000	0	0
HDAC4	0.014	0	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC1	-0.001	0.018	-9999	-10000	0	0
SUMO1	0.014	0	-9999	-10000	0	0
NPC/RanGAP1/SUMO1	0.019	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
XPO1	0.031	0	-9999	-10000	0	0
EntrezGene:23636	0	0	-9999	-10000	0	0
RAN	0.014	0	-9999	-10000	0	0
EntrezGene:8021	0	0	-9999	-10000	0	0
RANBP2	0.014	0	-9999	-10000	0	0
SUMO1/HDAC4	0.033	0	-9999	-10000	0	0
SUMO1/HDAC1	0.031	0.024	-9999	-0.3	2	2
RANGAP1	0.014	0	-9999	-10000	0	0
MDM2/SUMO1/SUMO1	-0.005	0.038	-9999	-0.32	4	4
NPC/RanGAP1/SUMO1/RanBP2/Ubc9	0.024	0	-9999	-10000	0	0
Ran/GTP	0.029	0	-9999	-10000	0	0
EntrezGene:23225	0	0	-9999	-10000	0	0
MDM2	0.011	0.037	-9999	-0.48	2	2
UBE2I	0.014	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.036	0	-9999	-10000	0	0
NPC	0	0	-9999	-10000	0	0
PIAS2	0.014	0	-9999	-10000	0	0
PIAS1	0.007	0.064	-9999	-0.6	4	4
EntrezGene:9972	0	0	-9999	-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	-0.001	0.01	-9999	-10000	0	0
EntrezGene:79658	0	0	-9999	-10000	0	0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A	0.023	0	-9999	-10000	0	0
AP2	0	0	-9999	-10000	0	0
mol:DAG	0	0	-9999	-10000	0	0
Arfaptin 2/Rac/GTP	0	0	-9999	-10000	0	0
CLTB	0.014	0	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ER cargo protein	0.028	0	-9999	-10000	0	0
CD4	0.004	0.073	-9999	-0.52	7	7
CLTA	0.014	0	-9999	-10000	0	0
mol:GTP	0.002	0	-9999	-10000	0	0
ARFGAP1	0.011	0.019	-9999	-0.34	1	1
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
ARF1/GTP	0	0	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ARF-GAP1/ER cargo protein	0.029	0.013	-9999	-10000	0	0
mol:Choline	0	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
ARF1	0.014	0	-9999	-10000	0	0
DDEF1	0	0	-9999	-10000	0	0
ARF1/GDP	-0.001	0.012	-9999	-0.24	1	1
AP2M1	0.014	0	-9999	-10000	0	0
EntrezGene:1313	0	0	-9999	-10000	0	0
actin filament polymerization	0.018	0	-9999	-10000	0	0
Rac/GTP	0	0	-9999	-10000	0	0
ARF1/GTP/GGA3/ARF-GAP1	0.026	0.014	-9999	-0.23	1	1
ARFIP2	0.012	0	-9999	-10000	0	0
COPA	0.014	0	-9999	-10000	0	0
RAC1	0.014	0	-9999	-10000	0	0
ARF1/GTP/coatomer protein complex	0.028	0	-9999	-10000	0	0
ARF1/GTP/ARHGAP10	0	0	-9999	-10000	0	0
GGA3	0.014	0	-9999	-10000	0	0
ARF1/GTP/Membrin	0	0	-9999	-10000	0	0
AP2A1	0.014	0	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ARF-GAP1	0.03	0.008	-9999	-10000	0	0
ARF1/GDP/Membrin	0.02	0	-9999	-10000	0	0
Arfaptin 2/Rac/GDP	0	0	-9999	-10000	0	0
CYTH2	0.014	0	-9999	-10000	0	0
ARF1/GTP/GGA3	0	0	-9999	-10000	0	0
mol:ATP	0	0	-9999	-10000	0	0
Rac/GDP	0	0	-9999	-10000	0	0
mol:Brefeldin A	0	0	-9999	-10000	0	0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP	0.036	0.024	-9999	-10000	0	0
PLD2	0	0	-9999	-10000	0	0
ARF-GAP1/v-SNARE	0.011	0.019	-9999	-0.34	1	1
PIP5K1A	0	0	-9999	-10000	0	0
ARF1/GTP/Membrin/GBF1/p115	0	0	-9999	-10000	0	0
mol:Phosphatic acid	0	0	-9999	-10000	0	0
mol:Phosphatidic acid	0	0	-9999	-10000	0	0
KDEL Receptor/Ligand/ARF-GAP1	0.011	0.019	-9999	-0.34	1	1
GOSR2	0	0	-9999	-10000	0	0
USO1	0	0	-9999	-10000	0	0
GBF1	0	0	-9999	-10000	0	0
ARF1/GTP/Arfaptin 2	0	0	-9999	-10000	0	0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex	-0.006	0.041	-9999	-0.3	7	7

pid_entity	TCGA.TM.A7CF	TCGA.TM.A7C5	TCGA.TM.A7C4	TCGA.TM.A7C3
109_MAP3K5	0.059	0.059	0.059	0.059
47_PPARGC1A	0.014	0.014	0.014	0.014
105_BMP4	0.014	0.014	0.014	0.014
105_BMP6	0.014	0.014	0.014	0.014
105_BMP7	0.014	0.014	0.014	0.014
105_BMP2	0.014	0.014	0.014	0.014
131_RELN/VLDLR	0	-0.32	0	0
30_TGFB1/TGF beta receptor Type II	0.021	0.017	0.021	0.013
84_STAT5B	-0.046	0.048	0.051	0.049
84_STAT5A	-0.046	0.048	0.051	0.049