Thyroid Adenocarcinoma: PARADIGM pathway analysis of mRNASeq expression data<BR>(primary solid tumor cohort)

Pathway.Name	Avg.Num.Perturbations
Ephrin A reverse signaling	199
Signaling events mediated by Stem cell factor receptor (c-Kit)	123
Signaling events regulated by Ret tyrosine kinase	115
Reelin signaling pathway	102
Wnt signaling	85
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	83
IL4-mediated signaling events	79
PDGFR-alpha signaling pathway	75
Noncanonical Wnt signaling pathway	74
FOXA2 and FOXA3 transcription factor networks	71

Pathway.Name	Avg.Num.Perturbations	Total.Perturbations	Num.Entities	Min.Mean.Truth	Max.Mean.Truth	Min.Mean.Within	Max.Mean.Within	Min.Mean.Any	Max.Mean.Within.1
Ephrin A reverse signaling	199	1395	7	-0.55	0	1000	-1000	-0.028	-1000
Signaling events mediated by Stem cell factor receptor (c-Kit)	123	9596	78	-0.79	0.23	1000	-1000	-0.075	-1000
Signaling events regulated by Ret tyrosine kinase	115	9488	82	-0.48	0.013	1000	-1000	-0.079	-1000
Reelin signaling pathway	102	5729	56	-0.63	0.034	1000	-1000	-0.088	-1000
Wnt signaling	85	598	7	-0.45	0.013	1000	-1000	-0.029	-1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	83	5675	68	-0.88	0.35	1000	-1000	-0.13	-1000
IL4-mediated signaling events	79	7210	91	-1.3	0.66	1000	-1000	-0.12	-1000
PDGFR-alpha signaling pathway	75	3341	44	-0.53	0.033	1000	-1000	-0.065	-1000
Noncanonical Wnt signaling pathway	74	1946	26	-0.45	0.013	1000	-1000	-0.086	-1000
FOXA2 and FOXA3 transcription factor networks	71	3278	46	-0.98	0.02	1000	-1000	-0.07	-1000
Signaling events mediated by the Hedgehog family	70	3690	52	-0.43	0.23	1000	-1000	-0.077	-1000
Nongenotropic Androgen signaling	61	3216	52	-0.33	0.16	1000	-1000	-0.064	-1000
Lissencephaly gene (LIS1) in neuronal migration and development	57	3100	54	-0.63	0.027	1000	-1000	-0.096	-1000
Calcium signaling in the CD4+ TCR pathway	55	1705	31	-0.52	0.013	1000	-1000	-0.082	-1000
Nephrin/Neph1 signaling in the kidney podocyte	53	1813	34	-0.16	0.013	1000	-1000	-0.07	-1000
Glypican 1 network	49	2362	48	-0.4	0.029	1000	-1000	-0.05	-1000
Endothelins	49	4798	96	-0.43	0.013	1000	-1000	-0.082	-1000
HIF-1-alpha transcription factor network	45	3450	76	-0.6	0.04	1000	-1000	-0.11	-1000
Ephrin B reverse signaling	44	2120	48	-0.28	0.19	1000	-1000	-0.076	-1000
Glypican 2 network	44	177	4	-0.079	-0.014	1000	-1000	-0.031	-1000
TCR signaling in naïve CD8+ T cells	42	3998	93	-0.2	0.091	1000	-1000	-0.085	-1000
BMP receptor signaling	41	3326	81	-0.6	0.023	1000	-1000	-0.1	-1000
Glucocorticoid receptor regulatory network	41	4756	114	-0.57	0.37	1000	-1000	-0.079	-1000
IGF1 pathway	41	2377	57	-0.19	0.051	1000	-1000	-0.093	-1000
IL23-mediated signaling events	41	2461	60	-0.34	0.021	1000	-1000	-0.15	-1000
Arf6 signaling events	36	2273	62	-0.32	0.02	1000	-1000	-0.073	-1000
Syndecan-1-mediated signaling events	35	1195	34	-0.21	0.013	1000	-1000	-0.07	-1000
TCGA08_retinoblastoma	35	286	8	-0.12	0.07	1000	-1000	-0.023	-1000
Coregulation of Androgen receptor activity	34	2607	76	-0.78	0.06	1000	-1000	-0.049	-1000
Signaling mediated by p38-alpha and p38-beta	34	1538	44	-0.24	0.013	1000	-1000	-0.053	-1000
Hedgehog signaling events mediated by Gli proteins	30	1980	65	-0.69	0.063	1000	-1000	-0.061	-1000
EPHB forward signaling	29	2479	85	-0.28	0.14	1000	-1000	-0.095	-1000
IL12-mediated signaling events	28	2474	87	-0.42	0.019	1000	-1000	-0.12	-1000
amb2 Integrin signaling	28	2342	82	-0.27	0.013	1000	-1000	-0.091	-1000
Syndecan-4-mediated signaling events	27	1847	67	-0.24	0.013	1000	-1000	-0.088	-1000
IL6-mediated signaling events	26	1985	75	-0.22	0.061	1000	-1000	-0.08	-1000
Ras signaling in the CD4+ TCR pathway	26	454	17	-0.098	0.012	1000	-1000	-0.043	-1000
Thromboxane A2 receptor signaling	25	2654	105	-0.21	0.029	1000	-1000	-0.071	-1000
Osteopontin-mediated events	24	921	38	-0.27	0.013	1000	-1000	-0.1	-1000
EGFR-dependent Endothelin signaling events	24	524	21	-0.11	0.013	1000	-1000	-0.071	-1000
FAS signaling pathway (CD95)	21	1011	47	-0.29	0.025	1000	-1000	-0.042	-1000
IL27-mediated signaling events	21	1092	51	-0.2	0.049	1000	-1000	-0.08	-1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)	20	1750	85	-0.3	0.013	1000	-1000	-0.078	-1000
Visual signal transduction: Rods	20	1060	52	-0.18	0.013	1000	-1000	-0.084	-1000
ErbB2/ErbB3 signaling events	19	1276	65	-0.14	0.027	1000	-1000	-0.067	-1000
Regulation of p38-alpha and p38-beta	19	1046	54	-0.49	0.013	1000	-1000	-0.062	-1000
Plasma membrane estrogen receptor signaling	19	1712	86	-0.2	0.021	1000	-1000	-0.078	-1000
Syndecan-2-mediated signaling events	18	1278	69	-0.21	0.038	1000	-1000	-0.061	-1000
LPA receptor mediated events	18	1887	102	-0.27	0.03	1000	-1000	-0.099	-1000
JNK signaling in the CD4+ TCR pathway	17	293	17	-0.1	0.016	1000	-1000	-0.078	-1000
Integrins in angiogenesis	17	1492	84	-0.22	0.029	1000	-1000	-0.096	-1000
Angiopoietin receptor Tie2-mediated signaling	17	1520	88	-0.32	0.028	1000	-1000	-0.11	-1000
BCR signaling pathway	16	1635	99	-0.18	0.023	1000	-1000	-0.093	-1000
Regulation of nuclear SMAD2/3 signaling	15	2080	136	-0.33	0.067	1000	-1000	-0.079	-1000
p75(NTR)-mediated signaling	15	1962	125	-0.38	0.068	1000	-1000	-0.1	-1000
Fc-epsilon receptor I signaling in mast cells	15	1458	97	-0.22	0.03	1000	-1000	-0.087	-1000
Visual signal transduction: Cones	14	568	38	-0.1	0.013	1000	-1000	-0.072	-1000
IL1-mediated signaling events	14	898	62	-0.13	0.066	1000	-1000	-0.091	-1000
TCGA08_rtk_signaling	14	370	26	-0.25	0.024	1000	-1000	-0.022	-1000
Regulation of Androgen receptor activity	14	1002	70	-0.48	0.034	1000	-1000	-0.067	-1000
Signaling events mediated by PTP1B	13	994	76	-0.26	0.021	1000	-1000	-0.085	-1000
Aurora C signaling	13	94	7	-0.056	0.005	1000	-1000	-0.042	-1000
RXR and RAR heterodimerization with other nuclear receptor	13	694	52	-0.27	0.051	1000	-1000	-0.062	-1000
Effects of Botulinum toxin	13	338	26	-0.18	0.019	1000	-1000	-0.062	-1000
Neurotrophic factor-mediated Trk receptor signaling	13	1669	120	-0.34	0.042	1000	-1000	-0.083	-1000
Aurora B signaling	13	891	67	-0.39	0.014	1000	-1000	-0.064	-1000
LPA4-mediated signaling events	12	146	12	-0.11	0.016	1000	-1000	-0.023	-1000
ErbB4 signaling events	12	894	69	-0.13	0.059	1000	-1000	-0.091	-1000
Syndecan-3-mediated signaling events	12	429	35	-0.17	0.013	1000	-1000	-0.063	-1000
VEGFR1 specific signals	12	675	56	-0.082	0.042	1000	-1000	-0.083	-1000
Presenilin action in Notch and Wnt signaling	11	694	61	-0.22	0.047	1000	-1000	-0.07	-1000
FOXM1 transcription factor network	11	593	51	-0.21	0.04	1000	-1000	-0.15	-1000
Signaling events mediated by HDAC Class III	10	404	40	-0.36	0.024	1000	-1000	-0.051	-1000
IL2 signaling events mediated by STAT5	10	235	22	-0.059	0.04	1000	-1000	-0.046	-1000
Rapid glucocorticoid signaling	10	215	20	-0.095	0.015	1000	-1000	-0.034	-1000
Signaling events mediated by PRL	10	349	34	-0.13	0.013	1000	-1000	-0.052	-1000
Class IB PI3K non-lipid kinase events	10	30	3	-0.001	-1000	1000	-1000	-0.014	-1000
a4b1 and a4b7 Integrin signaling	9	47	5	-0.03	0.006	1000	-1000	-0.032	-1000
Insulin-mediated glucose transport	9	314	32	-0.21	0.037	1000	-1000	-0.066	-1000
IFN-gamma pathway	9	615	68	-0.1	0.041	1000	-1000	-0.1	-1000
Ceramide signaling pathway	9	726	76	-0.18	0.024	1000	-1000	-0.061	-1000
IL2 signaling events mediated by PI3K	9	523	58	-0.058	0.032	1000	-1000	-0.079	-1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha	9	425	45	-0.09	0.039	1000	-1000	-0.081	-1000
Nectin adhesion pathway	8	526	63	-0.25	0.038	1000	-1000	-0.076	-1000
S1P1 pathway	8	308	36	-0.051	0.029	1000	-1000	-0.056	-1000
Retinoic acid receptors-mediated signaling	8	483	58	-0.11	0.033	1000	-1000	-0.07	-1000
Stabilization and expansion of the E-cadherin adherens junction	8	608	74	-0.18	0.086	1000	-1000	-0.09	-1000
Regulation of Telomerase	8	841	102	-0.31	0.053	1000	-1000	-0.099	-1000
Caspase cascade in apoptosis	7	540	74	-0.09	0.029	1000	-1000	-0.054	-1000
Cellular roles of Anthrax toxin	7	306	39	-0.09	0.019	1000	-1000	-0.033	-1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes	7	653	83	-0.21	0.052	1000	-1000	-0.084	-1000
Class I PI3K signaling events	7	558	73	-0.26	0.025	1000	-1000	-0.073	-1000
Insulin Pathway	7	536	74	-0.076	0.037	1000	-1000	-0.096	-1000
BARD1 signaling events	6	363	57	-0.028	0.055	1000	-1000	-0.07	-1000
Sphingosine 1-phosphate (S1P) pathway	6	185	28	-0.2	0.032	1000	-1000	-0.052	-1000
Class I PI3K signaling events mediated by Akt	6	415	68	-0.21	0.051	1000	-1000	-0.057	-1000
S1P3 pathway	6	291	42	-0.2	0.049	1000	-1000	-0.055	-1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha	6	207	33	-0.18	0.035	1000	-1000	-0.065	-1000
mTOR signaling pathway	5	316	53	-0.036	0.023	1000	-1000	-0.06	-1000
TRAIL signaling pathway	5	263	48	-0.081	0.052	1000	-1000	-0.062	-1000
ceramide signaling pathway	5	293	49	-0.09	0.031	1000	-1000	-0.042	-1000
Canonical NF-kappaB pathway	4	184	39	-0.09	0.069	1000	-1000	-0.076	-1000
Arf6 downstream pathway	4	212	43	-0.16	0.086	1000	-1000	-0.041	-1000
Signaling events mediated by HDAC Class I	4	495	104	-0.09	0.06	1000	-1000	-0.072	-1000
FoxO family signaling	4	297	64	-0.21	0.16	1000	-1000	-0.076	-1000
Canonical Wnt signaling pathway	4	251	51	-0.047	0.069	1000	-1000	-0.062	-1000
Paxillin-independent events mediated by a4b1 and a4b7	3	138	37	-0.032	0.033	1000	-1000	-0.068	-1000
S1P5 pathway	3	57	17	-0.013	0.024	1000	-1000	-0.043	-1000
Signaling events mediated by VEGFR1 and VEGFR2	3	420	125	-0.039	0.084	1000	-1000	-0.11	-1000
E-cadherin signaling in the nascent adherens junction	3	299	76	-0.16	0.072	1000	-1000	-0.088	-1000
S1P4 pathway	3	92	25	-0.013	0.032	1000	-1000	-0.047	-1000
Circadian rhythm pathway	2	48	22	-0.05	0.013	1000	-1000	-0.076	-1000
Aurora A signaling	2	134	60	-0.051	0.038	1000	-1000	-0.063	-1000
EPO signaling pathway	2	151	55	-0.05	0.066	1000	-1000	-0.095	-1000
Signaling mediated by p38-gamma and p38-delta	2	32	15	0	0.031	1000	-1000	-0.029	-1000
Paxillin-dependent events mediated by a4b1	2	75	36	-0.03	0.024	1000	-1000	-0.071	-1000
Atypical NF-kappaB pathway	2	86	31	-0.024	0.047	1000	-1000	-0.06	-1000
PDGFR-beta signaling pathway	2	218	97	-0.19	0.066	1000	-1000	-0.091	-1000
p38 MAPK signaling pathway	2	109	44	-0.027	0.028	1000	-1000	-0.063	-1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling	1	32	23	-0.028	0.049	1000	-1000	-0.078	-1000
Signaling events mediated by HDAC Class II	1	132	75	-0.049	0.034	1000	-1000	-0.076	-1000
PLK2 and PLK4 events	1	5	3	0.009	0.021	1000	-1000	-0.02	-1000
PLK1 signaling events	1	108	85	-0.048	0.024	1000	-1000	-0.049	-1000
HIF-2-alpha transcription factor network	1	64	43	-0.2	0.21	1000	-1000	-0.082	-1000
E-cadherin signaling in keratinocytes	1	66	43	-0.006	0.051	1000	-1000	-0.067	-1000
TCGA08_p53	0	0	7	-0.081	0.052	1000	-1000	-0.018	-1000
Sumoylation by RanBP2 regulates transcriptional repression	0	0	27	0	0.03	1000	-1000	-0.055	-1000
Arf6 trafficking events	0	63	71	-0.024	0.045	1000	-1000	-0.085	-1000
E-cadherin signaling events	0	0	5	0	0.013	1000	-1000	-0.043	-1000
Arf1 pathway	0	12	54	-0.005	0.035	1000	-1000	-0.053	-1000
Alternative NF-kappaB pathway	0	0	13	0	0.013	1000	-1000	-0.059	-1000
Total	2952	166020	7203	-30	-990	131000	-131000	-9.3	-131000

Ephrin A reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAPKKK cascade	-0.47	0.33	-9999	-0.65	271	271
EFNA5	-0.14	0.33	-9999	-0.84	66	66
FYN	-0.42	0.32	-9999	-0.6	271	271
neuron projection morphogenesis	-0.47	0.33	-9999	-0.65	271	271
cell-cell signaling	0	0	-9999	-10000	0	0
Ephrin A5/EPHA5	-0.47	0.33	-9999	-0.66	271	271
EPHA5	-0.55	0.41	-9999	-0.86	245	245

×

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K1	-0.21	0.22	-10000	0	-0.4	219	219
CRKL	-0.21	0.24	-10000	0	-0.42	212	212
HRAS	-0.18	0.22	-10000	0	-0.51	29	29
mol:PIP3	-0.21	0.22	-10000	0	-0.4	212	212
SPRED1	0.013	0	-10000	0	-10000	0	0
SPRED2	0.013	0	-10000	0	-10000	0	0
GAB1	-0.23	0.25	-10000	0	-0.45	212	212
FOXO3	-0.19	0.22	-10000	0	-0.38	212	212
AKT1	-0.21	0.23	-10000	0	-0.41	212	212
BAD	-0.19	0.22	-10000	0	-0.38	212	212
megakaryocyte differentiation	-0.24	0.24	-10000	0	-0.45	216	216
GSK3B	-0.19	0.22	-10000	0	-0.38	212	212
RAF1	-0.14	0.18	-10000	0	-0.46	17	17
SHC1	0.013	0	-10000	0	-10000	0	0
STAT3	-0.23	0.25	-10000	0	-0.45	212	212
STAT1	-0.58	0.58	-10000	0	-1.1	212	212
HRAS/SPRED1	-0.17	0.15	-10000	0	-0.46	17	17
cell proliferation	-0.23	0.24	-10000	0	-0.44	213	213
PIK3CA	0.01	0.045	-10000	0	-0.86	1	1
TEC	0.013	0	-10000	0	-10000	0	0
RPS6KB1	-0.23	0.24	-10000	0	-0.44	212	212
HRAS/SPRED2	-0.17	0.15	-10000	0	-0.46	17	17
LYN/TEC/p62DOK	-0.23	0.2	-10000	0	-0.41	212	212
MAPK3	-0.091	0.13	-10000	0	-0.32	14	14
STAP1	-0.25	0.25	-10000	0	-0.47	212	212
GRAP2	-0.045	0.21	-10000	0	-0.79	27	27
JAK2	-0.5	0.45	-10000	0	-0.89	212	212
STAT1 (dimer)	-0.56	0.57	-10000	0	-1.1	212	212
mol:Gleevec	0.007	0.01	-10000	0	-10000	0	0
GRB2/SOCS1/VAV1	-0.24	0.21	-10000	0	-0.42	214	214
actin filament polymerization	-0.23	0.24	-10000	0	-0.44	212	212
LYN	0.013	0	-10000	0	-10000	0	0
STAP1/STAT5A (dimer)	-0.34	0.34	-10000	0	-0.64	212	212
PIK3R1	0.012	0.001	-10000	0	-10000	0	0
CBL/CRKL/GRB2	-0.21	0.19	-10000	0	-0.37	203	203
PI3K	-0.23	0.21	-10000	0	-0.42	212	212
PTEN	0.011	0.045	-10000	0	-0.86	1	1
SCF/KIT/EPO/EPOR	-0.73	0.72	-10000	0	-1.4	212	212
MAPK8	-0.23	0.25	-10000	0	-0.45	213	213
STAT3 (dimer)	-0.23	0.24	-10000	0	-0.44	212	212
positive regulation of transcription	-0.073	0.11	-10000	0	-0.26	13	13
mol:GDP	-0.22	0.19	-10000	0	-0.55	32	32
PIK3C2B	-0.23	0.25	-10000	0	-0.45	212	212
CBL/CRKL	-0.19	0.22	-10000	0	-0.39	212	212
FER	-0.23	0.25	-10000	0	-0.45	213	213
SH2B3	-0.23	0.25	-10000	0	-0.45	212	212
PDPK1	-0.19	0.21	-10000	0	-0.37	212	212
SNAI2	-0.23	0.25	-10000	0	-0.45	212	212
positive regulation of cell proliferation	-0.4	0.42	-10000	0	-0.77	212	212
KITLG	0.001	0.08	-10000	0	-0.89	3	3
cell motility	-0.4	0.42	-10000	0	-0.77	212	212
PTPN6	0.02	0.017	-10000	0	-10000	0	0
EPOR	-0.13	0.17	-10000	0	-0.56	3	3
STAT5A (dimer)	-0.33	0.34	-10000	0	-0.63	212	212
SOCS1	0.01	0.032	-10000	0	-0.3	4	4
cell migration	0.23	0.25	0.45	213	-10000	0	213
SOS1	0.013	0	-10000	0	-10000	0	0
EPO	-0.002	0.021	-10000	0	-0.32	1	1
VAV1	-0.013	0.1	-10000	0	-0.86	2	2
GRB10	-0.23	0.25	-10000	0	-0.45	212	212
PTPN11	0.016	0.014	-10000	0	-10000	0	0
SCF/KIT	-0.26	0.25	-10000	0	-0.48	212	212
GO:0007205	0.011	0.013	-10000	0	-10000	0	0
MAP2K1	-0.1	0.15	-10000	0	-0.36	14	14
CBL	0.013	0	-10000	0	-10000	0	0
KIT	-0.79	0.76	-10000	0	-1.5	212	212
MAP2K2	-0.1	0.15	-10000	0	-0.36	14	14
SHC/Grb2/SOS1	-0.23	0.2	-10000	0	-0.41	212	212
STAT5A	-0.34	0.36	-10000	0	-0.65	212	212
GRB2	0.013	0	-10000	0	-10000	0	0
response to radiation	-0.23	0.24	-10000	0	-0.44	212	212
SHC/GRAP2	-0.043	0.16	-10000	0	-0.66	24	24
PTPRO	-0.25	0.25	-10000	0	-0.46	216	216
SH2B2	-0.23	0.25	-10000	0	-0.45	212	212
DOK1	0.013	0	-10000	0	-10000	0	0
MATK	-0.24	0.26	-10000	0	-0.46	213	213
CREBBP	0.018	0.02	-10000	0	-10000	0	0
BCL2	-0.19	0.39	-10000	0	-1.6	22	22

×

Signaling events regulated by Ret tyrosine kinase

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.091	0.072	-9999	-10000	0	0
Crk/p130 Cas/Paxillin	-0.26	0.2	-9999	-0.43	180	180
JUN	-0.33	0.32	-9999	-0.69	137	137
HRAS	0.012	0.016	-9999	-0.3	1	1
RET51/GFRalpha1/GDNF/GRB10	-0.4	0.34	-9999	-0.64	233	233
RAP1A	0.013	0	-9999	-10000	0	0
FRS2	0.013	0	-9999	-10000	0	0
RAP1A/GDP	0	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/DOK1	-0.4	0.34	-9999	-0.64	233	233
EntrezGene:5979	0	0	-9999	-10000	0	0
PTPN11	0.013	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.013	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/Enigma	-0.31	0.27	-9999	-0.54	215	215
RHOA	0.013	0	-9999	-10000	0	0
RAP1A/GTP	-0.36	0.31	-9999	-0.58	233	233
GRB7	-0.033	0.11	-9999	-0.3	56	56
RET51/GFRalpha1/GDNF	-0.4	0.34	-9999	-0.64	233	233
MAPKKK cascade	-0.32	0.27	-9999	-0.51	233	233
BCAR1	0.013	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/IRS1	-0.36	0.32	-9999	-0.6	224	224
lamellipodium assembly	-0.24	0.19	-9999	-0.39	215	215
RET51/GFRalpha1/GDNF/SHC	-0.4	0.34	-9999	-0.64	233	233
PIK3CA	0.011	0.045	-9999	-0.86	1	1
RET9/GFRalpha1/GDNF/SHC	-0.31	0.27	-9999	-0.54	215	215
RET9/GFRalpha1/GDNF/Shank3	-0.31	0.27	-9999	-0.54	215	215
MAPK3	-0.32	0.31	-9999	-0.54	233	233
DOK1	0.013	0	-9999	-10000	0	0
DOK6	-0.12	0.32	-9999	-0.86	59	59
PXN	0.013	0	-9999	-10000	0	0
neurite development	-0.33	0.29	-9999	-0.7	99	99
DOK5	-0.1	0.3	-9999	-0.86	51	51
GFRA1	-0.48	0.43	-9999	-0.85	216	216
MAPK8	-0.23	0.23	-9999	-0.59	66	66
HRAS/GTP	-0.37	0.32	-9999	-0.59	233	233
tube development	-0.29	0.25	-9999	-0.5	215	215
MAPK1	-0.32	0.31	-9999	-0.54	233	233
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.19	0.19	-9999	-0.35	215	215
Rac1/GDP	0	0	-9999	-10000	0	0
SRC	0.012	0.016	-9999	-10000	0	0
PDLIM7	0.009	0.035	-9999	-0.3	5	5
RET51/GFRalpha1/GDNF/Dok6	-0.45	0.4	-9999	-0.7	241	241
SHC1	0.013	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/Dok4	-0.4	0.34	-9999	-0.64	233	233
RET51/GFRalpha1/GDNF/Dok5	-0.47	0.41	-9999	-0.72	243	243
PRKCA	-0.038	0.2	-9999	-0.86	22	22
HRAS/GDP	-0.001	0.01	-9999	-10000	0	0
CREB1	-0.25	0.24	-9999	-0.44	215	215
PIK3R1	0.013	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.19	0.19	-9999	-0.35	215	215
RET51/GFRalpha1/GDNF/Grb7	-0.42	0.35	-9999	-0.67	233	233
mol:GDP	0	0	-9999	-10000	0	0
RET	-0.17	0.33	-9999	-0.86	66	66
DOK4	0.013	0	-9999	-10000	0	0
JNK cascade	-0.32	0.31	-9999	-0.67	137	137
RET9/GFRalpha1/GDNF/FRS2	-0.31	0.27	-9999	-0.54	215	215
SHANK3	0.013	0	-9999	-10000	0	0
RASA1	0.013	0	-9999	-10000	0	0
NCK1	0.013	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.19	0.19	-9999	-0.35	215	215
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.25	0.24	-9999	-0.42	233	233
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK	-0.25	0.24	-9999	-0.42	233	233
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.29	0.32	-9999	-0.49	233	233
PI3K	-0.37	0.34	-9999	-0.63	215	215
SOS1	0.013	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/Shank3/Grb2	-0.29	0.25	-9999	-0.5	215	215
GRB10	0.013	0	-9999	-10000	0	0
activation of MAPKK activity	-0.23	0.22	-9999	-0.39	215	215
RET51/GFRalpha1/GDNF/FRS2	-0.4	0.34	-9999	-0.64	233	233
GAB1	0.013	0	-9999	-10000	0	0
IRS1	-0.07	0.26	-9999	-0.86	36	36
IRS2	0.013	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.29	0.32	-9999	-0.49	233	233
RET51/GFRalpha1/GDNF/PKC alpha	-0.43	0.39	-9999	-0.69	233	233
GRB2	0.013	0	-9999	-10000	0	0
PRKACA	0.013	0	-9999	-10000	0	0
GDNF	0	0.035	-9999	-0.3	5	5
RAC1	0.013	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/IRS1	-0.45	0.38	-9999	-0.69	242	242
Rac1/GTP	-0.29	0.23	-9999	-0.47	215	215
RET9/GFRalpha1/GDNF	-0.34	0.29	-9999	-0.59	215	215
GFRalpha1/GDNF	-0.38	0.33	-9999	-0.67	215	215

×

Reelin signaling pathway

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
CDK5R1/CDK5	-0.002	0.017	-9999	-10000	0	0
VLDLR	-0.012	0.15	-9999	-0.86	11	11
CRKL	0.013	0	-9999	-10000	0	0
LRPAP1	0.013	0	-9999	-10000	0	0
FYN	0.013	0	-9999	-10000	0	0
ITGA3	0.009	0.035	-9999	-0.3	5	5
RELN/VLDLR/Fyn	-0.44	0.27	-9999	-0.59	284	284
MAPK8IP1/MKK7/MAP3K11/JNK1	-0.003	0.035	-9999	-0.49	2	2
AKT1	-0.24	0.17	-9999	-0.34	284	284
MAP2K7	0.013	0	-9999	-10000	0	0
RAPGEF1	0.013	0	-9999	-10000	0	0
DAB1	0.007	0.006	-9999	-10000	0	0
RELN/LRP8/DAB1	-0.42	0.26	-9999	-0.56	284	284
LRPAP1/LRP8	-0.026	0.13	-9999	-0.66	15	15
RELN/LRP8/DAB1/Fyn	-0.39	0.24	-9999	-0.52	284	284
DAB1/alpha3/beta1 Integrin	-0.37	0.24	-9999	-0.48	286	286
long-term memory	-0.39	0.26	-9999	-0.52	285	285
DAB1/LIS1	-0.38	0.24	-9999	-0.5	286	286
DAB1/CRLK/C3G	-0.36	0.24	-9999	-0.52	146	146
PIK3CA	0.011	0.045	-9999	-0.86	1	1
DAB1/NCK2	-0.38	0.24	-9999	-0.5	286	286
ARHGEF2	0.013	0	-9999	-10000	0	0
mol:Src family inhibitors PP1 and PP2	0	0	-9999	-10000	0	0
GRIN2A	-0.024	0.16	-9999	-0.63	22	22
CDK5R1	0.01	0.028	-9999	-0.3	3	3
RELN	-0.63	0.38	-9999	-0.86	282	282
PIK3R1	0.013	0	-9999	-10000	0	0
RELN/LRP8/Fyn	-0.45	0.28	-9999	-0.6	284	284
GRIN2A/RELN/LRP8/DAB1/Fyn	-0.41	0.27	-9999	-0.54	285	285
MAPK8	0.008	0.063	-9999	-0.86	2	2
RELN/VLDLR/DAB1	-0.41	0.25	-9999	-0.55	284	284
ITGB1	0.013	0	-9999	-10000	0	0
MAP1B	-0.39	0.26	-9999	-0.53	286	286
RELN/LRP8	-0.45	0.28	-9999	-0.6	284	284
GRIN2B/RELN/LRP8/DAB1/Fyn	-0.39	0.24	-9999	-0.52	284	284
PI3K	-0.002	0.034	-9999	-0.66	1	1
mol:PP2	0	0	-9999	-10000	0	0
alpha3/beta1 Integrin	-0.003	0.022	-9999	-10000	0	0
RAP1A	-0.32	0.24	-9999	-0.84	21	21
PAFAH1B1	0.013	0	-9999	-10000	0	0
MAPK8IP1	0.013	0	-9999	-10000	0	0
CRLK/C3G	0	0	-9999	-10000	0	0
GRIN2B	0.003	0.017	-9999	-0.3	1	1
NCK2	0.013	0	-9999	-10000	0	0
neuron differentiation	-0.16	0.13	-9999	-0.51	14	14
neuron adhesion	-0.3	0.23	-9999	-0.75	25	25
LRP8	-0.021	0.17	-9999	-0.86	15	15
GSK3B	-0.22	0.16	-9999	-0.62	10	10
RELN/VLDLR/DAB1/Fyn	-0.39	0.24	-9999	-0.52	284	284
MAP3K11	0.013	0	-9999	-10000	0	0
RELN/VLDLR/DAB1/P13K	-0.27	0.18	-9999	-0.36	284	284
CDK5	0.013	0	-9999	-10000	0	0
MAPT	0.034	0.086	-9999	-0.31	16	16
neuron migration	-0.31	0.22	-9999	-0.43	283	283
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1	-0.16	0.13	-9999	-0.52	14	14
RELN/VLDLR	-0.42	0.27	-9999	-0.56	286	286

×

Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Noncanonical Wnts/FZD	-0.3	0.29	-9999	-0.49	246	246
FZD6	0.013	0	-9999	-10000	0	0
WNT6	0.007	0.039	-9999	-0.3	6	6
WNT4	-0.29	0.41	-9999	-0.84	135	135
FZD3	0.013	0	-9999	-10000	0	0
WNT5A	-0.011	0.14	-9999	-0.86	10	10
WNT11	-0.45	0.43	-9999	-0.86	201	201

×

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	-0.045	0.16	-10000	0	-0.53	26	26
NFATC2	-0.2	0.36	-10000	0	-0.82	78	78
NFATC3	-0.088	0.13	-10000	0	-10000	0	0
CD40LG	-0.71	0.58	-10000	0	-1.2	198	198
ITCH	0.05	0.017	-10000	0	-10000	0	0
CBLB	0.05	0.017	-10000	0	-10000	0	0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment	-0.49	0.51	-10000	0	-1.3	88	88
JUNB	-0.001	0.11	-10000	0	-0.86	6	6
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.001	0.018	-10000	0	-0.34	1	1
T cell anergy	0.03	0.063	-10000	0	-0.5	1	1
TLE4	-0.21	0.42	-10000	0	-0.91	88	88
Jun/NFAT1-c-4/p21SNFT	-0.65	0.62	-10000	0	-1.2	181	181
AP-1/NFAT1-c-4	-0.88	0.8	-10000	0	-1.5	200	200
IKZF1	-0.15	0.32	-10000	0	-0.77	61	61
T-helper 2 cell differentiation	-0.29	0.34	-10000	0	-0.83	83	83
AP-1/NFAT1	-0.42	0.5	-10000	0	-0.95	157	157
CALM1	0.028	0.011	-10000	0	-10000	0	0
EGR2	-0.78	0.86	-10000	0	-1.7	171	171
EGR3	-0.55	0.74	-10000	0	-1.7	92	92
NFAT1/FOXP3	-0.19	0.32	-10000	0	-0.74	75	75
EGR1	-0.18	0.36	-10000	0	-0.86	84	84
JUN	-0.2	0.36	-10000	0	-0.86	88	88
EGR4	-0.055	0.22	-10000	0	-0.84	27	27
mol:Ca2+	0.016	0.012	-10000	0	-10000	0	0
GBP3	-0.14	0.3	-10000	0	-0.74	60	60
FOSL1	-0.033	0.11	-10000	0	-0.3	56	56
NFAT1-c-4/MAF/IRF4	-0.54	0.56	-10000	0	-1.1	169	169
DGKA	-0.13	0.28	-10000	0	-0.7	55	55
CREM	0.013	0	-10000	0	-10000	0	0
NFAT1-c-4/PPARG	-0.53	0.56	-10000	0	-1.1	180	180
CTLA4	-0.22	0.37	-10000	0	-0.85	75	75
NFAT1-c-4 (dimer)/EGR1	-0.63	0.67	-10000	0	-1.3	181	181
NFAT1-c-4 (dimer)/EGR4	-0.56	0.56	-10000	0	-1.1	185	185
FOS	-0.23	0.38	-10000	0	-0.86	103	103
IFNG	-0.39	0.53	-10000	0	-1.2	92	92
T cell activation	-0.42	0.44	-10000	0	-0.99	121	121
MAF	0.013	0	-10000	0	-10000	0	0
T-helper 2 cell lineage commitment	0	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	0.35	0.42	0.8	136	-10000	0	136
TNF	-0.59	0.59	-10000	0	-1.1	184	184
FASLG	-0.72	0.79	-10000	0	-1.5	187	187
TBX21	-0.04	0.19	-10000	0	-0.77	22	22
BATF3	-0.01	0.089	-10000	0	-0.32	26	26
PRKCQ	-0.001	0.11	-10000	0	-0.86	6	6
PTPN1	-0.13	0.28	-10000	0	-0.73	49	49
NFAT1-c-4/ICER1	-0.52	0.55	-10000	0	-1	180	180
GATA3	-0.037	0.2	-10000	0	-0.86	22	22
T-helper 1 cell differentiation	-0.38	0.5	-10000	0	-1.2	92	92
IL2RA	-0.44	0.44	-10000	0	-1.1	95	95
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
CASP3	-0.13	0.28	-10000	0	-0.71	54	54
E2F1	-0.077	0.14	-10000	0	-0.29	119	119
PPARG	-0.002	0.1	-10000	0	-0.61	9	9
SLC3A2	-0.13	0.28	-10000	0	-0.69	57	57
IRF4	-0.092	0.21	-10000	0	-0.4	96	96
PTGS2	-0.7	0.58	-10000	0	-1.2	192	192
CSF2	-0.75	0.55	-10000	0	-1.2	202	202
JunB/Fra1/NFAT1-c-4	-0.52	0.54	-10000	0	-1.1	155	155
IL4	-0.3	0.36	-10000	0	-0.9	77	77
IL5	-0.68	0.55	-10000	0	-1.2	192	192
IL2	-0.44	0.45	-10000	0	-1	121	121
IL3	-0.095	0.063	-10000	0	-10000	0	0
RNF128	0.048	0.049	-10000	0	-0.91	1	1
NFATC1	-0.36	0.42	-10000	0	-0.81	133	133
CDK4	0.21	0.25	0.6	40	-10000	0	40
PTPRK	-0.13	0.28	-10000	0	-0.7	55	55
IL8	-0.7	0.56	-10000	0	-1.2	191	191
POU2F1	0.012	0.016	-10000	0	-10000	0	0

×

IL4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.59	0.45	-10000	0	-1.1	148	148
STAT6 (cleaved dimer)	-0.65	0.46	-10000	0	-1	204	204
IGHG1	-0.2	0.14	-10000	0	-0.36	28	28
IGHG3	-0.58	0.44	-10000	0	-0.95	184	184
AKT1	-0.31	0.26	-10000	0	-0.67	72	72
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1	-0.25	0.25	-10000	0	-0.68	52	52
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1	-0.34	0.28	-10000	0	-0.7	89	89
THY1	-0.59	0.45	-10000	0	-1.1	133	133
MYB	-0.009	0.13	-10000	0	-0.86	8	8
HMGA1	0.013	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3	-0.41	0.32	-10000	0	-0.7	156	156
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP	-0.32	0.26	-10000	0	-0.65	74	74
SP1	0.02	0.006	-10000	0	-10000	0	0
INPP5D	-0.01	0.081	-10000	0	-0.3	28	28
SOCS5	0.029	0.013	-10000	0	-10000	0	0
STAT6 (dimer)/ETS1	-0.62	0.45	-10000	0	-0.98	198	198
SOCS1	-0.4	0.29	-10000	0	-0.72	116	116
SOCS3	-0.38	0.38	-10000	0	-1	65	65
FCER2	-0.56	0.42	-10000	0	-0.96	158	158
PARP14	0.012	0.004	-10000	0	-10000	0	0
CCL17	-0.67	0.49	-10000	0	-1.1	161	161
GRB2	0.013	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP	-0.26	0.22	-10000	0	-0.64	39	39
T cell proliferation	-0.6	0.47	-10000	0	-1.1	159	159
IL4R/JAK1	-0.59	0.45	-10000	0	-1.1	145	145
EGR2	-0.93	0.74	-10000	0	-1.6	187	187
JAK2	-0.015	0.025	-10000	0	-10000	0	0
JAK3	-0.058	0.13	-10000	0	-0.3	87	87
PIK3R1	0.013	0	-10000	0	-10000	0	0
JAK1	0.002	0.009	-10000	0	-10000	0	0
COL1A2	-0.2	0.17	-10000	0	-0.62	15	15
CCL26	-0.61	0.46	-10000	0	-1.1	148	148
IL4R	-0.63	0.48	-10000	0	-1.1	151	151
PTPN6	0.028	0.009	-10000	0	-10000	0	0
IL13RA2	-0.71	0.59	-10000	0	-1.3	156	156
IL13RA1	-0.015	0.025	-10000	0	-10000	0	0
IRF4	-0.3	0.43	-10000	0	-1.2	56	56
ARG1	-0.14	0.12	-10000	0	-10000	0	0
CBL	-0.38	0.3	-10000	0	-0.68	134	134
GTF3A	0.016	0.01	-10000	0	-10000	0	0
PIK3CA	0.011	0.045	-10000	0	-0.86	1	1
IL13RA1/JAK2	-0.022	0.035	-10000	0	-10000	0	0
IRF4/BCL6	-0.28	0.39	-10000	0	-1.2	49	49
CD40LG	-0.096	0.29	-10000	0	-0.81	51	51
MAPK14	-0.39	0.32	-10000	0	-0.73	126	126
mitosis	-0.3	0.24	-10000	0	-0.63	72	72
STAT6	-0.67	0.53	-10000	0	-1.1	182	182
SPI1	0.001	0.07	-10000	0	-0.3	7	7
RPS6KB1	-0.28	0.24	-10000	0	-0.64	53	53
STAT6 (dimer)	-0.67	0.53	-10000	0	-1.1	182	182
STAT6 (dimer)/PARP14	-0.63	0.49	-10000	0	-1.1	175	175
mast cell activation	0.015	0.01	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2	-0.31	0.27	-10000	0	-0.66	86	86
FRAP1	-0.31	0.26	-10000	0	-0.67	72	72
LTA	-0.61	0.47	-10000	0	-1.1	127	127
FES	0.013	0	-10000	0	-10000	0	0
T-helper 1 cell differentiation	0.66	0.51	1.1	182	-10000	0	182
CCL11	-0.58	0.44	-10000	0	-1	147	147
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES	-0.31	0.27	-10000	0	-0.65	82	82
IL2RG	-0.049	0.2	-10000	0	-0.51	47	47
IL10	-0.61	0.48	-10000	0	-1.1	137	137
IRS1	-0.07	0.26	-10000	0	-0.86	36	36
IRS2	0.013	0	-10000	0	-10000	0	0
IL4	-0.14	0.099	-10000	0	-10000	0	0
IL5	-0.6	0.45	-10000	0	-1.1	134	134
IL4/IL4R/JAK1/IL13RA1/JAK2	-0.48	0.34	-10000	0	-0.82	148	148
COL1A1	-0.25	0.24	-10000	0	-0.78	17	17
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1	-0.59	0.47	-10000	0	-1.1	128	128
IL2R gamma/JAK3	-0.078	0.18	-10000	0	-0.5	46	46
TFF3	-1.3	0.64	-10000	0	-1.6	305	305
ALOX15	-0.6	0.46	-10000	0	-1.1	133	133
MYBL1	0.012	0.016	-10000	0	-0.3	1	1
T-helper 2 cell differentiation	-0.51	0.37	-10000	0	-0.84	170	170
SHC1	0.013	0	-10000	0	-10000	0	0
CEBPB	0.017	0.004	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2	-0.3	0.25	-10000	0	-0.64	69	69
mol:PI-3-4-5-P3	-0.31	0.26	-10000	0	-0.67	72	72
PI3K	-0.33	0.28	-10000	0	-0.72	72	72
DOK2	0	0.08	-10000	0	-0.39	12	12
ETS1	0.029	0.01	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2	-0.24	0.21	-10000	0	-0.62	43	43
ITGB3	-0.61	0.48	-10000	0	-1.1	137	137
PIGR	-0.63	0.5	-10000	0	-1.2	142	142
IGHE	0.05	0.037	-10000	0	-10000	0	0
MAPKKK cascade	-0.24	0.2	-10000	0	-0.6	43	43
BCL6	0.011	0.045	-10000	0	-0.85	1	1
OPRM1	-0.6	0.45	-10000	0	-1.1	150	150
RETNLB	-0.6	0.45	-10000	0	-1.1	139	139
SELP	-0.6	0.47	-10000	0	-1.1	142	142
AICDA	-0.58	0.44	-10000	0	-1	141	141

×

PDGFR-alpha signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRA	-0.26	0.4	-9999	-0.87	116	116
PDGF/PDGFRA/CRKL	-0.2	0.3	-9999	-0.66	116	116
positive regulation of JUN kinase activity	-0.16	0.24	-9999	-0.51	116	116
CRKL	0.013	0	-9999	-10000	0	0
PDGF/PDGFRA/Caveolin-3	-0.21	0.31	-9999	-0.67	116	116
AP1	-0.53	0.66	-9999	-1.5	106	106
mol:IP3	-0.2	0.32	-9999	-0.68	116	116
PLCG1	-0.2	0.32	-9999	-0.68	116	116
PDGF/PDGFRA/alphaV Integrin	-0.2	0.31	-9999	-0.66	116	116
RAPGEF1	0.013	0	-9999	-10000	0	0
CRK	0.013	0	-9999	-10000	0	0
mol:Ca2+	-0.2	0.32	-9999	-0.68	116	116
CAV3	-0.002	0.034	-9999	-0.3	5	5
CAV1	-0.012	0.15	-9999	-0.86	11	11
SHC/Grb2/SOS1	-0.16	0.24	-9999	-0.52	116	116
PDGF/PDGFRA/Shf	-0.2	0.3	-9999	-0.66	116	116
FOS	-0.48	0.63	-9999	-1.4	106	106
JUN	-0.18	0.3	-9999	-0.73	88	88
oligodendrocyte development	-0.2	0.31	-9999	-0.66	116	116
GRB2	0.013	0	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
mol:DAG	-0.2	0.32	-9999	-0.68	116	116
PDGF/PDGFRA	-0.26	0.4	-9999	-0.87	116	116
actin cytoskeleton reorganization	-0.2	0.3	-9999	-0.66	116	116
SRF	0.033	0.012	-9999	-10000	0	0
SHC1	0.013	0	-9999	-10000	0	0
PI3K	-0.18	0.26	-9999	-0.57	117	117
PDGF/PDGFRA/Crk/C3G	-0.17	0.26	-9999	-0.57	116	116
JAK1	-0.19	0.31	-9999	-0.66	116	116
ELK1/SRF	-0.15	0.24	-9999	-0.52	116	116
SHB	0.013	0	-9999	-10000	0	0
SHF	0.012	0.016	-9999	-0.3	1	1
CSNK2A1	0.027	0.028	-9999	-10000	0	0
GO:0007205	-0.21	0.33	-9999	-0.7	116	116
SOS1	0.013	0	-9999	-10000	0	0
Ras protein signal transduction	-0.16	0.24	-9999	-0.51	116	116
PDGF/PDGFRA/SHB	-0.2	0.3	-9999	-0.66	116	116
PDGF/PDGFRA/Caveolin-1	-0.22	0.33	-9999	-0.69	121	121
ITGAV	0.011	0.045	-9999	-0.86	1	1
ELK1	-0.19	0.3	-9999	-0.63	116	116
PIK3CA	0.011	0.045	-9999	-0.86	1	1
PDGF/PDGFRA/Crk	-0.2	0.3	-9999	-0.66	116	116
JAK-STAT cascade	-0.19	0.31	-9999	-0.66	116	116
cell proliferation	-0.2	0.3	-9999	-0.66	116	116

×

Noncanonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC2	-0.097	0.29	-9999	-0.86	48	48
GNB1/GNG2	-0.28	0.25	-9999	-0.62	102	102
mol:DAG	-0.23	0.24	-9999	-0.57	97	97
PLCG1	-0.24	0.25	-9999	-0.6	97	97
YES1	-0.28	0.28	-9999	-0.65	102	102
FZD3	0.013	0	-9999	-10000	0	0
FZD6	0.013	0	-9999	-10000	0	0
G protein	-0.26	0.23	-9999	-0.6	97	97
MAP3K7	-0.19	0.21	-9999	-0.47	97	97
mol:Ca2+	-0.23	0.24	-9999	-0.55	97	97
mol:IP3	-0.23	0.24	-9999	-0.57	97	97
NLK	-0.012	0.01	-9999	-10000	0	0
GNB1	0.013	0	-9999	-10000	0	0
CAMK2A	-0.21	0.22	-9999	-0.51	97	97
MAP3K7IP1	0	0	-9999	-10000	0	0
Noncanonical Wnts/FZD	-0.3	0.29	-9999	-0.49	246	246
CSNK1A1	0.013	0	-9999	-10000	0	0
GNAS	-0.28	0.28	-9999	-0.65	102	102
GO:0007205	-0.23	0.24	-9999	-0.56	97	97
WNT6	0.007	0.039	-9999	-0.3	6	6
WNT4	-0.29	0.41	-9999	-0.84	135	135
NFAT1/CK1 alpha	-0.31	0.26	-9999	-0.63	116	116
GNG2	0.013	0	-9999	-10000	0	0
WNT5A	-0.011	0.14	-9999	-0.86	10	10
WNT11	-0.45	0.43	-9999	-0.86	201	201
CDC42	-0.26	0.26	-9999	-0.61	102	102

×

FOXA2 and FOXA3 transcription factor networks

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
ACADVL	-0.55	0.56	-9999	-1.1	153	153
PCK1	-0.35	0.5	-9999	-1.3	59	59
HNF4A	-0.71	0.68	-9999	-1.3	185	185
KCNJ11	-0.52	0.56	-9999	-1.1	142	142
AKT1	-0.039	0.13	-9999	-10000	0	0
response to starvation	-0.017	0.035	-9999	-10000	0	0
DLK1	-0.52	0.56	-9999	-1.1	143	143
NKX2-1	-0.17	0.21	-9999	-10000	0	0
ACADM	-0.55	0.56	-9999	-1.1	152	152
TAT	-0.2	0.22	-9999	-0.73	3	3
CEBPB	0.013	0.004	-9999	-10000	0	0
CEBPA	0.004	0.089	-9999	-0.86	4	4
TTR	-0.19	0.22	-9999	-0.77	22	22
PKLR	-0.56	0.56	-9999	-1.1	157	157
APOA1	-0.98	0.91	-9999	-1.8	198	198
CPT1C	-0.56	0.56	-9999	-1.1	167	167
ALAS1	-0.17	0.21	-9999	-10000	0	0
TFRC	-0.26	0.29	-9999	-0.74	22	22
FOXF1	-0.01	0.089	-9999	-0.86	4	4
NF1	0.02	0.001	-9999	-10000	0	0
HNF1A (dimer)	0.015	0.006	-9999	-10000	0	0
CPT1A	-0.55	0.56	-9999	-1.1	151	151
HMGCS1	-0.55	0.56	-9999	-1.1	152	152
NR3C1	0.019	0.015	-9999	-10000	0	0
CPT1B	-0.55	0.56	-9999	-1.1	156	156
chromatin remodeling	0	0	-9999	-10000	0	0
SP1	0.013	0.005	-9999	-10000	0	0
GCK	-0.71	0.72	-9999	-1.4	173	173
CREB1	0.001	0.052	-9999	-10000	0	0
IGFBP1	-0.19	0.2	-9999	-0.57	1	1
PDX1	-0.18	0.22	-9999	-0.6	1	1
UCP2	-0.55	0.56	-9999	-1.1	153	153
ALDOB	-0.52	0.56	-9999	-1.1	142	142
AFP	-0.044	0.11	-9999	-0.43	14	14
BDH1	-0.55	0.56	-9999	-1.1	151	151
HADH	-0.51	0.56	-9999	-1.1	138	138
F2	-0.66	0.65	-9999	-1.3	163	163
HNF1A	0.015	0.006	-9999	-10000	0	0
G6PC	-0.002	0.087	-9999	-10000	0	0
SLC2A2	-0.24	0.27	-9999	-10000	0	0
INS	-0.008	0.017	-9999	-10000	0	0
FOXA1	-0.06	0.14	-9999	-0.34	61	61
FOXA3	-0.065	0.17	-9999	-0.47	27	27
FOXA2	-0.59	0.63	-9999	-1.2	164	164
ABCC8	-0.82	0.78	-9999	-1.5	197	197
ALB	-0.094	0.32	-9999	-1.3	23	23

×

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	-0.13	0.27	-10000	0	-0.72	27	27
IHH	-0.23	0.39	-10000	0	-0.88	102	102
SHH Np/Cholesterol/GAS1	-0.12	0.22	-10000	0	-0.54	79	79
LRPAP1	0.013	0	-10000	0	-10000	0	0
dorsoventral neural tube patterning	0.12	0.22	0.54	79	-10000	0	79
SMO/beta Arrestin2	-0.11	0.26	-10000	0	-0.5	104	104
SMO	-0.12	0.27	-10000	0	-0.54	105	105
AKT1	-0.032	0.12	-10000	0	-0.33	1	1
ARRB2	0.013	0	-10000	0	-10000	0	0
BOC	-0.005	0.12	-10000	0	-0.86	8	8
ADRBK1	0.013	0	-10000	0	-10000	0	0
heart looping	-0.12	0.26	-10000	0	-0.53	105	105
STIL	-0.092	0.21	-10000	0	-0.6	16	16
DHH N/PTCH2	-0.1	0.24	-10000	0	-0.67	59	59
DHH N/PTCH1	-0.12	0.24	-10000	0	-0.48	107	107
PIK3CA	0.011	0.045	-10000	0	-0.86	1	1
DHH	0.006	0.077	-10000	0	-0.86	3	3
PTHLH	-0.18	0.38	-10000	0	-1.2	27	27
determination of left/right symmetry	-0.12	0.26	-10000	0	-0.53	105	105
PIK3R1	0.013	0	-10000	0	-10000	0	0
skeletal system development	-0.17	0.38	-10000	0	-1.2	27	27
IHH N/Hhip	-0.43	0.42	-10000	0	-0.78	213	213
DHH N/Hhip	-0.28	0.33	-10000	0	-0.67	157	157
mol:Cholesterol	0	0	-10000	0	-10000	0	0
heart development	-0.12	0.26	-10000	0	-0.53	105	105
pancreas development	-0.35	0.42	-10000	0	-0.85	158	158
HHAT	0.011	0.045	-10000	0	-0.86	1	1
PI3K	-0.002	0.034	-10000	0	-0.66	1	1
EntrezGene:84976	0	0	-10000	0	-10000	0	0
GAS1	-0.17	0.35	-10000	0	-0.86	78	78
somite specification	-0.12	0.26	-10000	0	-0.53	105	105
SHH Np/Cholesterol/PTCH1	-0.1	0.22	-10000	0	-0.43	105	105
SHH Np/Cholesterol/PTCH2	-0.086	0.2	-10000	0	-0.54	58	58
SHH Np/Cholesterol/Megalin	-0.14	0.24	-10000	0	-0.55	98	98
SHH	0.007	0.05	-10000	0	-0.66	1	1
catabolic process	-0.13	0.27	-10000	0	-0.54	104	104
SMO/Vitamin D3	-0.11	0.24	-10000	0	-0.47	105	105
SHH Np/Cholesterol/Hhip	-0.23	0.26	-10000	0	-0.54	157	157
LRP2	-0.21	0.38	-10000	0	-0.86	97	97
receptor-mediated endocytosis	-0.21	0.24	-10000	0	-0.74	37	37
SHH Np/Cholesterol/BOC	-0.017	0.086	-10000	0	-0.55	9	9
SHH Np/Cholesterol/CDO	-0.16	0.24	-10000	0	-0.54	110	110
mesenchymal cell differentiation	0.23	0.26	0.53	157	-10000	0	157
mol:Vitamin D3	-0.1	0.22	-10000	0	-0.44	105	105
IHH N/PTCH2	-0.25	0.36	-10000	0	-0.68	144	144
CDON	-0.24	0.39	-10000	0	-0.86	109	109
IHH N/PTCH1	-0.14	0.27	-10000	0	-0.55	104	104
Megalin/LRPAP1	-0.17	0.29	-10000	0	-0.66	97	97
PTCH2	-0.12	0.31	-10000	0	-0.86	57	57
SHH Np/Cholesterol	-0.006	0.037	-10000	0	-0.54	1	1
PTCH1	-0.13	0.27	-10000	0	-0.54	104	104
HHIP	-0.35	0.42	-10000	0	-0.85	158	158

×

Nongenotropic Androgen signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.012	0.001	-10000	0	-10000	0	0
GNB1/GNG2	-0.21	0.26	-10000	0	-0.53	149	149
regulation of S phase of mitotic cell cycle	-0.12	0.18	-10000	0	-0.35	150	150
GNAO1	-0.013	0.14	-10000	0	-0.86	10	10
HRAS	0.012	0.016	-10000	0	-0.3	1	1
SHBG/T-DHT	-0.012	0.085	-10000	0	-0.59	8	8
PELP1	0.012	0.001	-10000	0	-10000	0	0
AKT1	0.012	0.001	-10000	0	-10000	0	0
MAP2K1	-0.16	0.24	-10000	0	-0.46	149	149
T-DHT/AR	-0.26	0.33	-10000	0	-0.67	149	149
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
mol:GTP	-0.001	0.003	-10000	0	-0.005	103	103
GNAI2	0.013	0	-10000	0	-10000	0	0
GNAI3	0.013	0	-10000	0	-10000	0	0
GNAI1	0.01	0.045	-10000	0	-0.86	1	1
mol:GDP	-0.25	0.31	-10000	0	-0.64	149	149
cell proliferation	-0.2	0.29	-10000	0	-0.7	57	57
PIK3CA	0.011	0.045	-10000	0	-0.86	1	1
FOS	-0.25	0.4	-10000	0	-0.89	103	103
mol:Ca2+	-0.026	0.031	-10000	0	-0.073	66	66
MAPK3	-0.18	0.27	-10000	0	-0.62	62	62
MAPK1	-0.083	0.13	-10000	0	-0.31	56	56
PIK3R1	0.013	0	-10000	0	-10000	0	0
mol:IP3	-0.001	0.002	-10000	0	-0.004	103	103
cAMP biosynthetic process	0.011	0.088	-10000	0	-0.55	8	8
GNG2	0.013	0	-10000	0	-10000	0	0
potassium channel inhibitor activity	-0.001	0.002	-10000	0	-0.004	103	103
HRAS/GTP	-0.2	0.24	-10000	0	-0.5	149	149
actin cytoskeleton reorganization	-0.001	0.024	-10000	0	-0.47	1	1
SRC	0.012	0.016	-10000	0	-10000	0	0
voltage-gated calcium channel activity	-0.001	0.002	-10000	0	-0.004	103	103
PI3K	-0.002	0.03	-10000	0	-0.58	1	1
apoptosis	0.16	0.25	0.52	103	-10000	0	103
T-DHT/AR/PELP1	-0.23	0.29	-10000	0	-0.59	149	149
HRAS/GDP	-0.24	0.3	-10000	0	-0.61	150	150
CREB1	-0.18	0.28	-10000	0	-0.57	103	103
RAC1-CDC42/GTP	-0.001	0.024	-10000	0	-0.48	1	1
AR	-0.33	0.42	-10000	0	-0.86	149	149
GNB1	0.013	0	-10000	0	-10000	0	0
RAF1	-0.17	0.25	-10000	0	-0.48	149	149
RAC1-CDC42/GDP	-0.23	0.28	-10000	0	-0.58	149	149
T-DHT/AR/PELP1/Src	-0.21	0.26	-10000	0	-0.54	149	149
MAP2K2	-0.16	0.24	-10000	0	-0.46	149	149
T-DHT/AR/PELP1/Src/PI3K	-0.12	0.19	-10000	0	-0.35	150	150
GNAZ	0.013	0	-10000	0	-10000	0	0
SHBG	-0.005	0.12	-10000	0	-0.86	8	8
Gi family/GNB1/GNG2/GDP	-0.016	0.11	-10000	0	-0.56	11	11
mol:T-DHT	0	0.001	0.002	56	-0.003	46	102
RAC1	0.013	0	-10000	0	-10000	0	0
GNRH1	0.01	0.035	-10000	0	-0.67	1	1
Gi family/GTP	-0.091	0.13	-10000	0	-0.52	11	11
CDC42	0.013	0	-10000	0	-10000	0	0

×

Lissencephaly gene (LIS1) in neuronal migration and development

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
DYNC1H1	0.013	0	-9999	-10000	0	0
VLDLR	-0.012	0.15	-9999	-0.86	11	11
LRPAP1	0.013	0	-9999	-10000	0	0
NUDC	0.013	0	-9999	-10000	0	0
RELN/LRP8	-0.45	0.28	-9999	-0.6	284	284
CaM/Ca2+	0	0	-9999	-10000	0	0
KATNA1	0.013	0	-9999	-10000	0	0
GO:0030286	0	0	-9999	-10000	0	0
ABL1	-0.4	0.26	-9999	-0.54	284	284
IQGAP1/CaM	0	0	-9999	-10000	0	0
DAB1	0.007	0.006	-9999	-10000	0	0
IQGAP1	0.013	0	-9999	-10000	0	0
PLA2G7	-0.12	0.32	-9999	-0.86	59	59
CALM1	0.013	0	-9999	-10000	0	0
DYNLT1	0.013	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
LRPAP1/LRP8	-0.026	0.13	-9999	-0.66	15	15
UniProt:Q4QZ09	0	0	-9999	-10000	0	0
CLIP1	0.013	0	-9999	-10000	0	0
CDK5R1	0.01	0.028	-9999	-0.3	3	3
LIS1/Poliovirus Protein 3A	0	0	-9999	-10000	0	0
CDK5R2	0.003	0.028	-9999	-0.3	3	3
mol:PP1	0	0	-9999	-10000	0	0
RELN/VLDLR/DAB1	-0.44	0.27	-9999	-0.59	284	284
YWHAE	0.013	0	-9999	-10000	0	0
NDEL1/14-3-3 E	-0.3	0.21	-9999	-0.76	13	13
MAP1B	0	0.005	-9999	-10000	0	0
RAC1	0	0	-9999	-10000	0	0
p35/CDK5	-0.34	0.24	-9999	-0.47	284	284
RELN	-0.63	0.38	-9999	-0.86	282	282
PAFAH/LIS1	-0.066	0.22	-9999	-0.57	59	59
LIS1/CLIP170	0.027	0	-9999	-10000	0	0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain	-0.24	0.15	-9999	-0.57	13	13
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3	-0.25	0.18	-9999	-0.36	139	139
GO:0005869	0	0	-9999	-10000	0	0
NDEL1	-0.32	0.23	-9999	-0.46	186	186
LIS1/IQGAP1	0.027	0	-9999	-10000	0	0
RHOA	0	0	-9999	-10000	0	0
PAFAH1B1	0.024	0	-9999	-10000	0	0
PAFAH1B3	0.011	0.023	-9999	-10000	0	0
PAFAH1B2	0.008	0.063	-9999	-0.86	2	2
MAP1B/LIS1/Dynein heavy chain	0.026	0.004	-9999	-10000	0	0
NDEL1/Katanin 60/Dynein heavy chain	-0.3	0.18	-9999	-0.72	13	13
LRP8	-0.021	0.17	-9999	-0.86	15	15
NDEL1/Katanin 60	-0.3	0.21	-9999	-0.76	13	13
P39/CDK5	-0.35	0.24	-9999	-0.48	284	284
LIS1/NudC/Dynein intermediate chain/microtubule organizing center	0.027	0	-9999	-10000	0	0
CDK5	-0.37	0.25	-9999	-0.5	284	284
PPP2R5D	0.013	0	-9999	-10000	0	0
LIS1/CLIP170/Dynein Complex/Dynactin Complex	0	0	-9999	-10000	0	0
CSNK2A1	0.013	0	-9999	-10000	0	0
RELN/VLDLR/DAB1/LIS1	-0.38	0.23	-9999	-0.51	284	284
RELN/VLDLR	-0.42	0.27	-9999	-0.56	286	286
CDC42	0	0	-9999	-10000	0	0

×

Calcium signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC1	-0.009	0.079	-9999	-0.6	6	6
NFATC2	-0.078	0.2	-9999	-0.61	48	48
NFATC3	0.001	0.027	-9999	-10000	0	0
CD40LG	-0.42	0.41	-9999	-0.88	143	143
PTGS2	-0.41	0.41	-9999	-0.89	134	134
JUNB	-0.001	0.11	-9999	-0.86	6	6
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.006	0.013	-9999	-10000	0	0
CaM/Ca2+	-0.006	0.013	-9999	-10000	0	0
CALM1	0.008	0.008	-9999	-10000	0	0
JUN	-0.2	0.37	-9999	-0.86	88	88
mol:Ca2+	-0.01	0.011	-9999	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0	0.002	-9999	-10000	0	0
FOSL1	-0.033	0.11	-9999	-0.3	56	56
CREM	0.013	0	-9999	-10000	0	0
Jun/NFAT1-c-4/p21SNFT	-0.25	0.28	-9999	-0.6	124	124
FOS	-0.23	0.39	-9999	-0.86	103	103
IFNG	-0.42	0.41	-9999	-0.86	152	152
AP-1/NFAT1-c-4	-0.52	0.52	-9999	-1.1	135	135
FASLG	-0.4	0.39	-9999	-0.85	140	140
NFAT1-c-4/ICER1	-0.096	0.19	-9999	-0.54	53	53
IL2RA	-0.39	0.39	-9999	-0.85	131	131
FKBP12/FK506	0	0	-9999	-10000	0	0
CSF2	-0.46	0.37	-9999	-0.81	171	171
JunB/Fra1/NFAT1-c-4	-0.12	0.19	-9999	-0.53	58	58
IL4	-0.38	0.37	-9999	-0.82	131	131
IL2	-0.013	0.026	-9999	-10000	0	0
IL3	-0.031	0.03	-9999	-10000	0	0
FKBP1A	0.013	0	-9999	-10000	0	0
BATF3	-0.01	0.089	-9999	-0.32	26	26
mol:FK506	0	0	-9999	-10000	0	0
POU2F1	0.012	0.016	-9999	-10000	0	0

×

Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity	0.16	0.3	0.7	86	-10000	0	86
KIRREL	-0.052	0.21	-10000	0	-0.88	23	23
Nephrin/NEPH1Par3/Par6/Atypical PKCs	-0.16	0.3	-10000	0	-0.7	86	86
PLCG1	0.013	0	-10000	0	-10000	0	0
ARRB2	0.013	0	-10000	0	-10000	0	0
WASL	0.013	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/CD2AP	-0.12	0.23	-10000	0	-0.54	86	86
ChemicalAbstracts:57-88-5	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP	-0.069	0.19	-10000	0	-0.4	86	86
FYN	-0.1	0.23	-10000	0	-0.51	86	86
mol:Ca2+	-0.12	0.23	-10000	0	-0.54	86	86
mol:DAG	-0.12	0.23	-10000	0	-0.54	86	86
NPHS2	-0.014	0.034	-10000	0	-10000	0	0
mol:IP3	-0.12	0.23	-10000	0	-0.54	86	86
regulation of endocytosis	-0.11	0.21	-10000	0	-0.48	86	86
Nephrin/NEPH1/podocin/Cholesterol	-0.12	0.24	-10000	0	-0.55	86	86
establishment of cell polarity	-0.16	0.3	-10000	0	-0.7	86	86
Nephrin/NEPH1/podocin/NCK1-2	-0.11	0.22	-10000	0	-0.5	86	86
Nephrin/NEPH1/beta Arrestin2	-0.11	0.21	-10000	0	-0.49	86	86
NPHS1	-0.16	0.33	-10000	0	-0.86	68	68
Nephrin/NEPH1/podocin	-0.12	0.22	-10000	0	-0.52	86	86
TJP1	0.013	0	-10000	0	-10000	0	0
NCK1	0.013	0	-10000	0	-10000	0	0
NCK2	0.013	0	-10000	0	-10000	0	0
heterophilic cell adhesion	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/PLCgamma1	-0.12	0.23	-10000	0	-0.54	86	86
CD2AP	0.013	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/GRB2	-0.12	0.23	-10000	0	-0.54	86	86
GRB2	0.013	0	-10000	0	-10000	0	0
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
TRPC6	-0.1	0.24	-10000	0	-0.52	88	88
cytoskeleton organization	-0.094	0.25	-10000	0	-0.54	86	86
Nephrin/NEPH1	-0.12	0.23	-10000	0	-0.53	86	86
Nephrin/NEPH1/ZO-1	-0.13	0.25	-10000	0	-0.58	86	86

×

Glypican 1 network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer	-0.002	0.03	-10000	0	-0.57	1	1
fibroblast growth factor receptor signaling pathway	-0.002	0.03	-10000	0	-0.57	1	1
LAMA1	-0.052	0.23	-10000	0	-0.84	29	29
PRNP	0.013	0	-10000	0	-10000	0	0
GPC1/SLIT2	-0.091	0.23	-10000	0	-0.66	52	52
SMAD2	0.029	0.039	-10000	0	-0.52	1	1
GPC1/PrPc/Cu2+	0	0.008	-10000	0	-10000	0	0
GPC1/Laminin alpha1	-0.05	0.17	-10000	0	-0.66	28	28
TDGF1	-0.35	0.43	-10000	0	-0.86	159	159
CRIPTO/GPC1	-0.28	0.33	-10000	0	-0.66	159	159
APP/GPC1	-0.001	0.01	-10000	0	-10000	0	0
mol:NO	0	0	-10000	0	-10000	0	0
YES1	-0.22	0.3	-10000	0	-0.57	159	159
FLT1	0.013	0	-10000	0	-10000	0	0
GPC1/TGFB/TGFBR1/TGFBR2	-0.006	0.039	-10000	0	-0.57	1	1
SERPINC1	0.012	0.003	-10000	0	-10000	0	0
FYN	-0.22	0.3	-10000	0	-0.57	159	159
FGR	-0.23	0.3	-10000	0	-0.57	159	159
positive regulation of MAPKKK cascade	-0.29	0.33	-10000	0	-0.65	160	160
SLIT2	-0.11	0.3	-10000	0	-0.86	52	52
GPC1/NRG	-0.066	0.2	-10000	0	-0.66	37	37
NRG1	-0.073	0.26	-10000	0	-0.84	38	38
GPC1/VEGF165 homodimer/VEGFR1 homodimer	-0.003	0.042	-10000	0	-0.57	2	2
LYN	-0.22	0.3	-10000	0	-0.57	159	159
mol:Spermine	0.011	0.011	-10000	0	-10000	0	0
cell growth	-0.002	0.03	-10000	0	-0.57	1	1
BMP signaling pathway	-0.012	0.016	0.3	1	-10000	0	1
SRC	-0.22	0.3	-10000	0	-0.57	159	159
TGFBR1	0.004	0.052	-10000	0	-0.3	11	11
mol:Cu2+	0	0	-10000	0	-10000	0	0
PLA2G2A	-0.25	0.38	-10000	0	-0.7	141	141
GPC1	0.012	0.016	-10000	0	-0.3	1	1
TGFBR1 (dimer)	0.004	0.052	-10000	0	-0.3	11	11
VEGFA	0.008	0.063	-10000	0	-0.86	2	2
BLK	-0.4	0.4	-10000	0	-0.71	216	216
HCK	-0.23	0.3	-10000	0	-0.58	159	159
FGF2	0.013	0	-10000	0	-10000	0	0
FGFR1	0.011	0.045	-10000	0	-0.86	1	1
VEGFR1 homodimer	0.013	0	-10000	0	-10000	0	0
TGFBR2	0.011	0.045	-10000	0	-0.86	1	1
cell death	0	0.01	-10000	0	-10000	0	0
ATIII/GPC1	-0.001	0.01	-10000	0	-10000	0	0
PLA2G2A/GPC1	-0.2	0.29	-10000	0	-0.66	101	101
LCK	-0.24	0.3	-10000	0	-0.58	163	163
neuron differentiation	-0.065	0.2	-10000	0	-0.66	37	37
PrPc/Cu2+	0	0	-10000	0	-10000	0	0
APP	0.013	0	-10000	0	-10000	0	0
TGFBR2 (dimer)	0.011	0.044	-10000	0	-0.85	1	1

×

Endothelins

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
AKT1	-0.058	0.15	-9999	-0.59	9	9
PTK2B	0.013	0.001	-9999	-10000	0	0
mol:Ca2+	-0.14	0.28	-9999	-0.7	45	45
EDN1	-0.049	0.13	-9999	-0.84	6	6
EDN3	-0.43	0.43	-9999	-0.86	191	191
EDN2	-0.01	0.11	-9999	-0.4	21	21
HRAS/GDP	-0.12	0.24	-9999	-0.54	67	67
ETA receptor/Endothelin-1/Gq/GTP/PLC beta	-0.092	0.18	-9999	-0.4	73	73
ADCY4	-0.1	0.2	-9999	-0.54	54	54
ADCY5	-0.18	0.27	-9999	-0.6	94	94
ADCY6	-0.1	0.2	-9999	-0.54	54	54
ADCY7	-0.1	0.2	-9999	-0.54	54	54
ADCY1	-0.11	0.22	-9999	-0.57	56	56
ADCY2	-0.15	0.25	-9999	-0.59	81	81
ADCY3	-0.1	0.2	-9999	-0.54	54	54
ADCY8	-0.2	0.21	-9999	-0.56	74	74
ADCY9	-0.1	0.2	-9999	-0.54	54	54
arachidonic acid secretion	-0.19	0.32	-9999	-0.65	106	106
ETB receptor/Endothelin-1/Gq/GTP	-0.1	0.21	-9999	-0.44	93	93
GNAO1	-0.013	0.14	-9999	-0.86	10	10
HRAS	0.01	0.017	-9999	-0.3	1	1
ETA receptor/Endothelin-1/G12/GTP	-0.026	0.16	-9999	-0.55	9	9
ETA receptor/Endothelin-1/Gs/GTP	-0.093	0.23	-9999	-0.57	55	55
mol:GTP	-0.003	0.009	-9999	-10000	0	0
COL3A1	-0.076	0.17	-9999	-0.5	31	31
EDNRB	0.002	0.091	-9999	-0.74	5	5
response to oxidative stress	0	0	-9999	-10000	0	0
CYSLTR2	-0.16	0.24	-9999	-0.64	44	44
CYSLTR1	-0.064	0.17	-9999	-0.72	12	12
SLC9A1	-0.025	0.075	-9999	-0.32	6	6
mol:GDP	-0.13	0.26	-9999	-0.56	75	75
SLC9A3	-0.054	0.19	-9999	-0.81	17	17
RAF1	-0.17	0.3	-9999	-0.6	96	96
JUN	-0.29	0.52	-9999	-1.2	92	92
JAK2	-0.058	0.15	-9999	-0.59	9	9
mol:IP3	-0.12	0.23	-9999	-0.49	87	87
ETA receptor/Endothelin-1	-0.046	0.2	-9999	-0.54	18	18
PLCB1	0.008	0.045	-9999	-0.86	1	1
PLCB2	0.003	0.045	-9999	-0.3	8	8
ETA receptor/Endothelin-3	-0.36	0.35	-9999	-0.7	192	192
FOS	-0.28	0.48	-9999	-1	104	104
Gai/GDP	-0.002	0.11	-9999	-0.65	10	10
CRK	0.013	0.001	-9999	-10000	0	0
mol:Ca ++	-0.13	0.24	-9999	-0.58	51	51
BCAR1	0.013	0.002	-9999	-10000	0	0
PRKCB1	-0.12	0.22	-9999	-0.48	87	87
GNAQ	0.011	0.008	-9999	-10000	0	0
GNAZ	0.013	0	-9999	-10000	0	0
GNAL	-0.095	0.29	-9999	-0.86	47	47
Gs family/GDP	-0.2	0.26	-9999	-0.57	103	103
ETA receptor/Endothelin-1/Gq/GTP	-0.12	0.21	-9999	-0.46	85	85
MAPK14	-0.069	0.17	-9999	-0.39	53	53
TRPC6	-0.15	0.29	-9999	-0.75	44	44
GNAI2	0.013	0	-9999	-10000	0	0
GNAI3	0.013	0	-9999	-10000	0	0
GNAI1	0.011	0.045	-9999	-0.86	1	1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta	-0.081	0.18	-9999	-0.4	71	71
ETB receptor/Endothelin-2	-0.023	0.1	-9999	-0.66	8	8
ETB receptor/Endothelin-3	-0.34	0.34	-9999	-0.67	193	193
ETB receptor/Endothelin-1	-0.025	0.12	-9999	-0.66	10	10
MAPK3	-0.25	0.44	-9999	-0.9	108	108
MAPK1	-0.25	0.44	-9999	-0.89	109	109
Rac1/GDP	-0.11	0.24	-9999	-0.53	66	66
cAMP biosynthetic process	-0.15	0.22	-9999	-0.57	62	62
MAPK8	-0.17	0.32	-9999	-0.62	98	98
SRC	0.012	0.016	-9999	-10000	0	0
ETB receptor/Endothelin-1/Gi/GTP	0.008	0.074	-9999	-0.28	18	18
p130Cas/CRK/Src/PYK2	-0.15	0.29	-9999	-0.61	76	76
mol:K +	0	0	-9999	-10000	0	0
G12/GDP	-0.11	0.24	-9999	-0.53	66	66
COL1A2	-0.045	0.17	-9999	-0.7	8	8
EntrezGene:2778	0	0	-9999	-10000	0	0
ETA receptor/Endothelin-2	-0.029	0.11	-9999	-0.6	7	7
mol:DAG	-0.12	0.23	-9999	-0.5	87	87
MAP2K2	-0.2	0.35	-9999	-0.69	111	111
MAP2K1	-0.2	0.35	-9999	-0.69	111	111
EDNRA	-0.043	0.099	-9999	-0.53	5	5
positive regulation of muscle contraction	-0.043	0.13	-9999	-0.54	8	8
Gq family/GDP	-0.2	0.3	-9999	-0.69	91	91
HRAS/GTP	-0.14	0.26	-9999	-0.57	78	78
PRKCH	-0.11	0.22	-9999	-0.5	73	73
RAC1	0.013	0	-9999	-10000	0	0
PRKCA	-0.14	0.26	-9999	-0.56	89	89
PRKCB	-0.13	0.22	-9999	-0.52	71	71
PRKCE	-0.11	0.23	-9999	-0.52	72	72
PRKCD	-0.11	0.22	-9999	-0.51	70	70
PRKCG	-0.12	0.23	-9999	-0.52	70	70
regulation of vascular smooth muscle contraction	-0.32	0.56	-9999	-1.2	104	104
PRKCQ	-0.12	0.24	-9999	-0.52	75	75
PLA2G4A	-0.21	0.36	-9999	-0.72	106	106
GNA14	-0.2	0.37	-9999	-0.86	91	91
GNA15	-0.02	0.098	-9999	-0.31	35	35
GNA12	0.013	0	-9999	-10000	0	0
GNA11	0.003	0.077	-9999	-0.86	3	3
Rac1/GTP	-0.026	0.16	-9999	-0.55	9	9
MMP1	-0.088	0.15	-9999	-10000	0	0

×

HIF-1-alpha transcription factor network

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
PKM2	-0.21	0.42	-9999	-0.98	41	41
HDAC7	0.015	0.002	-9999	-10000	0	0
HIF1A/ARNT/Cbp/p300/Src-1	-0.3	0.34	-9999	-0.83	90	90
SMAD4	0.014	0.002	-9999	-10000	0	0
ID2	-0.21	0.42	-9999	-0.97	42	42
AP1	-0.31	0.48	-9999	-0.98	120	120
ABCG2	-0.21	0.43	-9999	-0.94	54	54
HIF1A	-0.014	0.066	-9999	-10000	0	0
TFF3	-0.6	0.53	-9999	-1.1	163	163
GATA2	0.014	0.016	-9999	-0.3	1	1
AKT1	-0.043	0.1	-9999	-10000	0	0
response to hypoxia	-0.064	0.11	-9999	-0.24	20	20
MCL1	-0.21	0.42	-9999	-0.95	47	47
NDRG1	-0.21	0.42	-9999	-0.95	47	47
SERPINE1	-0.22	0.43	-9999	-0.97	47	47
FECH	-0.21	0.42	-9999	-0.95	47	47
FURIN	-0.21	0.42	-9999	-0.95	46	46
NCOA2	-0.039	0.21	-9999	-0.86	23	23
EP300	-0.07	0.18	-9999	-0.34	86	86
HMOX1	-0.21	0.43	-9999	-0.94	53	53
BHLHE40	-0.22	0.43	-9999	-0.96	51	51
BHLHE41	-0.21	0.43	-9999	-0.97	45	45
HIF1A/ARNT/SMAD3/SMAD4/SP1	-0.017	0.035	-9999	-10000	0	0
ENG	0.04	0.089	-9999	-10000	0	0
JUN	-0.19	0.37	-9999	-0.86	88	88
RORA	-0.21	0.43	-9999	-0.96	47	47
ABCB1	-0.076	0.18	-9999	-1.5	5	5
TFRC	-0.21	0.42	-9999	-0.95	47	47
CXCR4	-0.21	0.42	-9999	-0.95	47	47
TF	-0.27	0.5	-9999	-1.1	71	71
CITED2	-0.24	0.47	-9999	-1	58	58
HIF1A/ARNT	-0.31	0.38	-9999	-1	57	57
LDHA	-0.041	0.05	-9999	-10000	0	0
ETS1	-0.21	0.42	-9999	-0.93	53	53
PGK1	-0.21	0.42	-9999	-0.96	44	44
NOS2	-0.23	0.43	-9999	-0.96	52	52
ITGB2	-0.22	0.43	-9999	-0.96	51	51
ALDOA	-0.21	0.42	-9999	-0.94	50	50
Cbp/p300/CITED2	-0.34	0.51	-9999	-1.1	85	85
FOS	-0.22	0.39	-9999	-0.86	103	103
HK2	-0.21	0.43	-9999	-0.94	52	52
SP1	0.022	0.006	-9999	-10000	0	0
GCK	-0.42	0.73	-9999	-1.5	110	110
HK1	-0.21	0.42	-9999	-0.96	44	44
NPM1	-0.21	0.42	-9999	-0.97	43	43
EGLN1	-0.21	0.42	-9999	-0.98	40	40
CREB1	0.021	0	-9999	-10000	0	0
PGM1	-0.21	0.42	-9999	-0.93	51	51
SMAD3	0.014	0.002	-9999	-10000	0	0
EDN1	-0.18	0.32	-9999	-0.76	52	52
IGFBP1	-0.22	0.43	-9999	-0.98	44	44
VEGFA	-0.17	0.39	-9999	-0.76	62	62
HIF1A/JAB1	-0.013	0.02	-9999	-10000	0	0
CP	-0.39	0.57	-9999	-1.1	117	117
CXCL12	-0.26	0.49	-9999	-1.1	64	64
COPS5	0.014	0.001	-9999	-10000	0	0
SMAD3/SMAD4	0	0.002	-9999	-10000	0	0
BNIP3	-0.21	0.42	-9999	-0.96	45	45
EGLN3	-0.22	0.44	-9999	-0.99	51	51
CA9	-0.22	0.42	-9999	-0.96	49	49
TERT	-0.22	0.42	-9999	-0.95	50	50
ENO1	-0.21	0.42	-9999	-0.94	50	50
PFKL	-0.21	0.42	-9999	-0.96	44	44
NCOA1	0.013	0	-9999	-10000	0	0
ADM	-0.24	0.44	-9999	-0.96	56	56
ARNT	-0.015	0.066	-9999	-10000	0	0
HNF4A	-0.027	0.065	-9999	-0.33	9	9
ADFP	-0.22	0.42	-9999	-0.92	57	57
SLC2A1	-0.17	0.38	-9999	-0.76	61	61
LEP	-0.22	0.42	-9999	-0.95	51	51
HIF1A/ARNT/Cbp/p300	-0.32	0.36	-9999	-0.86	90	90
EPO	-0.14	0.3	-9999	-0.98	10	10
CREBBP	-0.07	0.18	-9999	-0.34	85	85
HIF1A/ARNT/Cbp/p300/HDAC7	-0.29	0.34	-9999	-0.82	89	89
PFKFB3	-0.21	0.43	-9999	-0.96	47	47
NT5E	-0.22	0.43	-9999	-0.98	46	46

×

Ephrin B reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EFNB2	0.013	0	-10000	0	-10000	0	0
EPHB2	0.006	0.077	-10000	0	-0.86	3	3
EFNB1	-0.011	0.15	-10000	0	-0.66	18	18
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	-0.24	0.25	-10000	0	-0.55	143	143
Ephrin B2/EPHB1-2	-0.18	0.25	-10000	0	-0.53	129	129
neuron projection morphogenesis	-0.22	0.24	-10000	0	-0.52	143	143
Ephrin B1/EPHB1-2/Tiam1	-0.25	0.28	-10000	0	-0.59	143	143
DNM1	-0.03	0.18	-10000	0	-0.83	19	19
cell-cell signaling	-0.001	0.002	-10000	0	-10000	0	0
MAP2K4	0.012	0.044	-10000	0	-0.81	1	1
YES1	-0.001	0.053	-10000	0	-1	1	1
Ephrin B1/EPHB1-2/NCK2	-0.18	0.26	-10000	0	-0.51	143	143
PI3K	0.011	0.068	-10000	0	-1.3	1	1
mol:GDP	-0.25	0.27	-10000	0	-0.58	143	143
ITGA2B	-0.095	0.29	-10000	0	-0.86	47	47
endothelial cell proliferation	0	0	-10000	0	-10000	0	0
FYN	-0.001	0.053	-10000	0	-1	1	1
MAP3K7	-0.004	0.045	-10000	0	-0.86	1	1
FGR	-0.003	0.054	-10000	0	-1	1	1
TIAM1	-0.16	0.16	-10000	0	-0.3	210	210
PIK3R1	0.013	0	-10000	0	-10000	0	0
RGS3	0.013	0	-10000	0	-10000	0	0
cell adhesion	-0.049	0.21	-10000	0	-0.54	53	53
LYN	-0.001	0.053	-10000	0	-1	1	1
Ephrin B1/EPHB1-2/Src Family Kinases	-0.005	0.05	-10000	0	-0.97	1	1
Ephrin B1/EPHB1-2	-0.012	0.048	-10000	0	-0.93	1	1
SRC	-0.003	0.054	-10000	0	-1	1	1
ITGB3	-0.015	0.15	-10000	0	-0.86	12	12
EPHB1	-0.28	0.41	-10000	0	-0.86	127	127
EPHB4	0.013	0	-10000	0	-10000	0	0
RAC1	0.013	0	-10000	0	-10000	0	0
Ephrin B2/EPHB4	0	0	-10000	0	-10000	0	0
alphaIIb/beta3 Integrin	-0.1	0.26	-10000	0	-0.72	53	53
BLK	-0.059	0.098	-10000	0	-1	1	1
HCK	-0.004	0.054	-10000	0	-1	1	1
regulation of stress fiber formation	0.19	0.25	0.5	143	-10000	0	143
MAPK8	0.018	0.069	-10000	0	-0.84	2	2
Ephrin B1/EPHB1-2/RGS3	-0.18	0.26	-10000	0	-0.51	143	143
endothelial cell migration	0	0.04	-10000	0	-0.76	1	1
NCK2	0.013	0	-10000	0	-10000	0	0
PTPN13	0.013	0.052	-10000	0	-0.97	1	1
regulation of focal adhesion formation	0.19	0.25	0.5	143	-10000	0	143
chemotaxis	0.19	0.25	0.5	143	-10000	0	143
PIK3CA	0.011	0.045	-10000	0	-0.86	1	1
Rac1/GTP	-0.23	0.25	-10000	0	-0.54	143	143
angiogenesis	-0.012	0.048	-10000	0	-0.92	1	1
LCK	-0.006	0.057	-10000	0	-1	1	1

×

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	-0.079	0.14	-9999	-0.3	112	112
GPC2	-0.014	0.088	-9999	-0.3	33	33
GPC2/Midkine	-0.072	0.11	-9999	-0.38	16	16
neuron projection morphogenesis	-0.072	0.11	-9999	-0.37	16	16

×

TCR signaling in naïve CD8+ T cells

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GRB2/SOS1/SHC	-0.12	0.23	-10000	0	-0.6	62	62
FYN	-0.11	0.34	-10000	0	-0.8	63	63
LAT/GRAP2/SLP76	-0.13	0.27	-10000	0	-0.65	72	72
IKBKB	0.013	0	-10000	0	-10000	0	0
AKT1	-0.056	0.22	-10000	0	-0.47	71	71
B2M	0.012	0.006	-10000	0	-10000	0	0
IKBKG	-0.031	0.05	-10000	0	-0.19	7	7
MAP3K8	0.004	0.089	-10000	0	-0.86	4	4
mol:Ca2+	-0.033	0.052	-10000	0	-0.13	82	82
integrin-mediated signaling pathway	0	0	-10000	0	-10000	0	0
LAT/GRAP2/SLP76/VAV1/PI3K Class IA	-0.1	0.32	-10000	0	-0.72	72	72
TRPV6	-0.19	0.36	-10000	0	-0.82	87	87
CD28	-0.044	0.19	-10000	0	-0.58	36	36
SHC1	-0.11	0.34	-10000	0	-0.78	67	67
receptor internalization	-0.14	0.38	-10000	0	-0.81	76	76
PRF1	-0.11	0.34	-10000	0	-0.88	52	52
KRAS	0.013	0	-10000	0	-10000	0	0
GRB2	0.013	0	-10000	0	-10000	0	0
COT/AKT1	-0.037	0.18	-10000	0	-0.38	64	64
LAT	-0.12	0.35	-10000	0	-0.8	67	67
EntrezGene:6955	0	0.003	-10000	0	-10000	0	0
CD3D	-0.097	0.28	-10000	0	-0.74	55	55
CD3E	-0.065	0.24	-10000	0	-0.87	30	30
CD3G	-0.14	0.33	-10000	0	-0.81	71	71
RASGRP2	0	0.03	-10000	0	-0.19	4	4
RASGRP1	-0.052	0.22	-10000	0	-0.46	74	74
HLA-A	0.01	0.023	-10000	0	-10000	0	0
RASSF5	0.013	0	-10000	0	-10000	0	0
RAP1A/GTP/RAPL	0	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
mol:GDP	0.01	0.068	-10000	0	-0.12	48	48
PDK1/CARD11/BCL10/MALT1/TRAF6	-0.057	0.09	-10000	0	-0.25	50	50
PRKCA	-0.066	0.14	-10000	0	-0.32	73	73
GRAP2	-0.045	0.21	-10000	0	-0.79	27	27
mol:IP3	-0.052	0.24	0.28	68	-0.46	69	137
EntrezGene:6957	0	0.004	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.15	0.42	-10000	0	-0.94	66	66
ORAI1	0.091	0.16	0.4	80	-10000	0	80
CSK	-0.12	0.35	-10000	0	-0.81	67	67
B7 family/CD28	-0.2	0.35	-10000	0	-0.74	92	92
CHUK	0.013	0	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8/LCK/ZAP-70	-0.15	0.42	-10000	0	-0.92	73	73
PTPN6	-0.12	0.35	-10000	0	-0.82	66	66
VAV1	-0.12	0.34	-10000	0	-0.78	71	71
Monovalent TCR/CD3	-0.16	0.42	-10000	0	-0.76	90	90
CBL	0.013	0	-10000	0	-10000	0	0
LCK	-0.12	0.36	-10000	0	-0.82	66	66
PAG1	-0.12	0.35	-10000	0	-0.81	67	67
RAP1A	0.013	0	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8/LCK	-0.15	0.42	-10000	0	-0.97	66	66
CD80	-0.086	0.27	-10000	0	-0.83	44	44
CD86	-0.008	0.092	-10000	0	-0.35	21	21
PDK1/CARD11/BCL10/MALT1	-0.07	0.11	-10000	0	-0.29	56	56
HRAS	0.012	0.016	-10000	0	-0.3	1	1
GO:0035030	-0.11	0.3	-10000	0	-0.58	92	92
CD8A	-0.048	0.22	-10000	0	-0.86	26	26
CD8B	-0.099	0.28	-10000	0	-0.74	57	57
PTPRC	-0.032	0.17	-10000	0	-0.55	29	29
PDK1/PKC theta	-0.072	0.27	-10000	0	-0.59	70	70
CSK/PAG1	-0.11	0.34	-10000	0	-0.8	64	64
SOS1	0.013	0	-10000	0	-10000	0	0
peptide-MHC class I	0.013	0.019	-10000	0	-10000	0	0
GRAP2/SLP76	-0.15	0.32	-10000	0	-0.76	74	74
STIM1	0.049	0.083	-10000	0	-10000	0	0
RAS family/GTP	0.007	0.091	-10000	0	-0.18	40	40
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin	-0.16	0.43	-10000	0	-0.9	76	76
mol:DAG	-0.071	0.18	-10000	0	-0.41	73	73
RAP1A/GDP	0.006	0.03	-10000	0	-10000	0	0
PLCG1	0.013	0	-10000	0	-10000	0	0
CD247	-0.029	0.18	-10000	0	-0.65	24	24
cytotoxic T cell degranulation	-0.1	0.32	-10000	0	-0.83	52	52
RAP1A/GTP	-0.003	0.009	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	-0.076	0.26	-10000	0	-0.57	72	72
LAT/GRAP2/SLP76/VAV1/PLCgamma1	-0.081	0.3	0.3	64	-0.61	72	136
NRAS	0.013	0	-10000	0	-10000	0	0
ZAP70	-0.028	0.17	-10000	0	-0.66	23	23
GRB2/SOS1	0	0	-10000	0	-10000	0	0
LAT/GRAP2/SLP76/VAV1	-0.12	0.26	-10000	0	-0.61	74	74
MALT1	0.013	0	-10000	0	-10000	0	0
TRAF6	0.011	0.045	-10000	0	-0.86	1	1
CD8 heterodimer	-0.11	0.3	-10000	0	-0.79	57	57
CARD11	-0.079	0.17	-10000	0	-0.33	101	101
PRKCB	-0.06	0.13	-10000	0	-0.31	63	63
PRKCE	-0.052	0.12	-10000	0	-0.3	57	57
PRKCQ	-0.095	0.31	-10000	0	-0.68	71	71
LCP2	0.004	0.052	-10000	0	-10000	0	0
BCL10	0.013	0	-10000	0	-10000	0	0
regulation of survival gene product expression	-0.042	0.19	-10000	0	-0.4	70	70
IKK complex	0.01	0.069	-10000	0	-0.12	32	32
RAS family/GDP	-0.005	0.01	-10000	0	-10000	0	0
MAP3K14	-0.017	0.14	-10000	0	-0.3	52	52
PDPK1	-0.049	0.21	-10000	0	-0.45	69	69
TCR/CD3/MHC I/CD8/Fyn	-0.17	0.45	-10000	0	-1	66	66

×

BMP receptor signaling

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
BMP7/BMPR2/BMPR1A-1B/FS	-0.3	0.36	-9999	-0.64	174	174
SMAD6-7/SMURF1	0	0	-9999	-10000	0	0
NOG	-0.056	0.23	-9999	-0.76	34	34
SMAD9	-0.22	0.29	-9999	-0.62	119	119
SMAD4	0.013	0	-9999	-10000	0	0
SMAD5	-0.11	0.21	-9999	-0.38	132	132
BMP7/USAG1	-0.35	0.33	-9999	-0.66	199	199
SMAD5/SKI	-0.094	0.2	-9999	-0.55	21	21
SMAD1	0.016	0.047	-9999	-10000	0	0
BMP2	-0.015	0.15	-9999	-0.86	12	12
SMAD1/SMAD1/SMAD4	-0.002	0.003	-9999	-10000	0	0
BMPR1A	0.013	0	-9999	-10000	0	0
BMPR1B	-0.29	0.41	-9999	-0.86	132	132
BMPR1A-1B/BAMBI	-0.21	0.28	-9999	-0.58	132	132
AHSG	-0.011	0.071	-9999	-0.3	22	22
CER1	0	0.002	-9999	-10000	0	0
BMP2-4/CER1	-0.038	0.14	-9999	-0.58	24	24
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA	-0.086	0.2	-9999	-0.65	25	25
BMP2-4 (homodimer)	-0.044	0.16	-9999	-0.66	24	24
RGMB	0.013	0	-9999	-10000	0	0
BMP6/BMPR2/BMPR1A-1B	-0.18	0.25	-9999	-0.52	132	132
RGMA	-0.017	0.16	-9999	-0.86	13	13
SMURF1	0.013	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP	-0.096	0.19	-9999	-0.59	23	23
BMP2-4/USAG1	-0.34	0.31	-9999	-0.6	213	213
SMAD6/SMURF1/SMAD5	-0.094	0.2	-9999	-0.55	21	21
SOSTDC1	-0.44	0.43	-9999	-0.86	199	199
BMP7/BMPR2/BMPR1A-1B	-0.18	0.25	-9999	-0.52	132	132
SKI	0.013	0	-9999	-10000	0	0
BMP6 (homodimer)	0.013	0	-9999	-10000	0	0
HFE2	0.001	0.031	-9999	-0.3	4	4
ZFYVE16	0.013	0	-9999	-10000	0	0
MAP3K7	0.013	0	-9999	-10000	0	0
BMP2-4/CHRD	-0.05	0.16	-9999	-0.59	31	31
SMAD5/SMAD5/SMAD4	-0.094	0.2	-9999	-0.55	21	21
MAPK1	0.013	0	-9999	-10000	0	0
TAK1/TAB family	-0.1	0.14	-9999	-0.5	23	23
BMP7 (homodimer)	0.013	0	-9999	-10000	0	0
NUP214	0.013	0	-9999	-10000	0	0
BMP6/FETUA	-0.011	0.044	-9999	-10000	0	0
SMAD1/SKI	0.023	0.044	-9999	-10000	0	0
SMAD6	0.013	0	-9999	-10000	0	0
CTDSP2	0.013	0	-9999	-10000	0	0
BMP2-4/FETUA	-0.047	0.15	-9999	-0.6	24	24
MAP3K7IP1	0	0	-9999	-10000	0	0
GREM1	-0.2	0.36	-9999	-0.74	108	108
BMPR2 (homodimer)	0.013	0	-9999	-10000	0	0
GADD34/PP1CA	-0.011	0.077	-9999	-0.57	7	7
BMPR1A-1B (homodimer)	-0.23	0.32	-9999	-0.66	132	132
CHRDL1	-0.6	0.39	-9999	-0.86	269	269
ENDOFIN/SMAD1	0.023	0.044	-9999	-10000	0	0
SMAD6-7/SMURF1/SMAD1	-0.007	0.01	-9999	-10000	0	0
SMAD6/SMURF1	0.013	0	-9999	-10000	0	0
BAMBI	0	0.072	-9999	-0.86	1	1
SMURF2	0.013	0	-9999	-10000	0	0
BMP2-4/CHRDL1	-0.44	0.3	-9999	-0.61	274	274
BMP2-4/GREM1	-0.17	0.29	-9999	-0.64	96	96
SMAD7	0.013	0	-9999	-10000	0	0
SMAD8A/SMAD8A/SMAD4	-0.18	0.28	-9999	-0.58	119	119
SMAD1/SMAD6	0.023	0.044	-9999	-10000	0	0
TAK1/SMAD6	0	0	-9999	-10000	0	0
BMP7	0.013	0	-9999	-10000	0	0
BMP6	0.013	0	-9999	-10000	0	0
MAP3K7IP2	0	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1	-0.073	0.16	-9999	-0.51	23	23
PPM1A	0.013	0	-9999	-10000	0	0
SMAD1/SMURF2	0.023	0.044	-9999	-10000	0	0
SMAD7/SMURF1	0	0	-9999	-10000	0	0
CTDSPL	0.013	0	-9999	-10000	0	0
PPP1CA	0.013	0	-9999	-10000	0	0
XIAP	0.013	0	-9999	-10000	0	0
CTDSP1	0.013	0	-9999	-10000	0	0
PPP1R15A	-0.003	0.12	-9999	-0.86	7	7
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS	-0.22	0.33	-9999	-0.83	70	70
CHRD	-0.005	0.12	-9999	-0.86	8	8
BMPR2	0.013	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM	-0.1	0.2	-9999	-0.63	23	23
BMP4	-0.018	0.16	-9999	-0.72	16	16
FST	-0.22	0.38	-9999	-0.82	104	104
BMP2-4/NOG	-0.083	0.2	-9999	-0.58	51	51
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1	-0.17	0.23	-9999	-0.49	132	132

×

Glucocorticoid receptor regulatory network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PCK2	0.046	0.094	0.33	8	-10000	0	8
SMARCC2	0.013	0.013	-10000	0	-10000	0	0
SMARCC1	0.013	0.013	-10000	0	-10000	0	0
TBX21	-0.16	0.29	-10000	0	-0.87	37	37
SUMO2	0.014	0.012	-10000	0	-10000	0	0
STAT1 (dimer)	0.014	0.051	-10000	0	-0.3	10	10
FKBP4	0.013	0	-10000	0	-10000	0	0
FKBP5	0.004	0.089	-10000	0	-0.86	4	4
GR alpha/HSP90/FKBP51/HSP90	0.13	0.13	0.35	31	-0.54	4	35
PRL	-0.088	0.12	-10000	0	-0.52	1	1
cortisol/GR alpha (dimer)/TIF2	0.27	0.29	0.59	122	-0.56	8	130
RELA	-0.043	0.09	-10000	0	-0.31	1	1
FGG	0.25	0.19	0.52	83	-10000	0	83
GR beta/TIF2	0.1	0.21	0.38	32	-0.59	23	55
IFNG	-0.49	0.51	-10000	0	-1.1	113	113
apoptosis	0.03	0.24	0.52	41	-0.53	1	42
CREB1	0.012	0.02	-10000	0	-10000	0	0
histone acetylation	-0.078	0.16	-10000	0	-0.41	45	45
BGLAP	-0.099	0.15	-10000	0	-0.52	11	11
GR/PKAc	0.13	0.1	0.36	19	-10000	0	19
NF kappa B1 p50/RelA	-0.084	0.16	-10000	0	-0.47	21	21
SMARCD1	0.013	0.013	-10000	0	-10000	0	0
MDM2	0.12	0.095	0.28	72	-10000	0	72
GATA3	-0.034	0.2	-10000	0	-0.86	22	22
AKT1	0	0	-10000	0	-10000	0	0
CSF2	-0.2	0.16	-10000	0	-0.49	56	56
GSK3B	0.014	0.012	-10000	0	-10000	0	0
NR1I3	0.057	0.23	0.5	35	-0.78	4	39
CSN2	0.2	0.14	0.45	41	-10000	0	41
BRG1/BAF155/BAF170/BAF60A	0.006	0.043	-10000	0	-10000	0	0
NFATC1	0.001	0.11	-10000	0	-0.86	6	6
POU2F1	0.013	0.016	-10000	0	-10000	0	0
CDKN1A	0.024	0.051	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
response to UV	0.001	0.012	-10000	0	-10000	0	0
SFN	-0.21	0.17	-10000	0	-0.32	254	254
GR alpha/HSP90/FKBP51/HSP90/14-3-3	0.052	0.16	0.35	12	-0.48	11	23
prolactin receptor activity	0	0	-10000	0	-10000	0	0
EGR1	-0.087	0.45	0.49	34	-0.89	84	118
JUN	-0.33	0.31	-10000	0	-0.7	127	127
IL4	-0.13	0.17	-10000	0	-0.66	16	16
CDK5R1	0.01	0.029	-10000	0	-0.3	3	3
PRKACA	0.013	0	-10000	0	-10000	0	0
cortisol/GR alpha (monomer)/AP-1	-0.38	0.43	-10000	0	-0.87	138	138
GR alpha/HSP90/FKBP51/HSP90/PP5C	0.13	0.12	0.35	24	-0.49	4	28
cortisol/GR alpha (monomer)	0.37	0.3	0.71	134	-10000	0	134
NCOA2	-0.04	0.21	-10000	0	-0.86	23	23
response to hypoxia	0	0	-10000	0	-10000	0	0
FOS	-0.27	0.38	-10000	0	-0.88	103	103
AP-1/NFAT1-c-4	-0.57	0.5	-10000	0	-1	170	170
AFP	-0.22	0.22	-10000	0	-0.58	77	77
SUV420H1	0.013	0	-10000	0	-10000	0	0
IRF1	0.2	0.15	0.48	41	-10000	0	41
TP53	0.032	0.021	-10000	0	-10000	0	0
PPP5C	0.013	0	-10000	0	-10000	0	0
KRT17	-0.48	0.4	-10000	0	-0.96	107	107
KRT14	-0.22	0.17	-10000	0	-0.58	17	17
TBP	0.022	0.006	-10000	0	-10000	0	0
CREBBP	0.055	0.061	-10000	0	-10000	0	0
HDAC1	0.01	0.005	-10000	0	-10000	0	0
HDAC2	0.028	0.013	-10000	0	-10000	0	0
AP-1	-0.57	0.51	-10000	0	-1	170	170
MAPK14	0.014	0.011	-10000	0	-10000	0	0
MAPK10	0.014	0.012	-10000	0	-10000	0	0
MAPK11	0.014	0.012	-10000	0	-10000	0	0
KRT5	-0.56	0.56	-10000	0	-1.2	127	127
interleukin-1 receptor activity	0.016	0.013	-10000	0	-10000	0	0
NCOA1	0.017	0.001	-10000	0	-10000	0	0
STAT1	0.014	0.052	-10000	0	-0.3	10	10
CGA	-0.13	0.16	-10000	0	-0.56	15	15
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2	0.23	0.14	0.37	141	-10000	0	141
MAPK3	0.014	0.012	-10000	0	-10000	0	0
MAPK1	0.014	0.011	-10000	0	-10000	0	0
ICAM1	-0.28	0.27	-10000	0	-0.7	75	75
NFKB1	-0.043	0.09	-10000	0	-0.31	1	1
MAPK8	-0.18	0.18	-10000	0	-0.47	76	76
MAPK9	0.014	0.011	-10000	0	-10000	0	0
cortisol/GR alpha (dimer)	0.025	0.24	0.52	41	-0.56	1	42
BAX	0.029	0.028	-10000	0	-10000	0	0
POMC	-0.56	0.71	-10000	0	-1.5	112	112
EP300	0.055	0.061	-10000	0	-10000	0	0
cortisol/GR alpha (dimer)/p53	0.33	0.24	0.61	128	-10000	0	128
proteasomal ubiquitin-dependent protein catabolic process	0.088	0.072	0.24	25	-10000	0	25
SGK1	0.098	0.22	-10000	0	-1.4	7	7
IL13	-0.3	0.27	-10000	0	-0.87	41	41
IL6	-0.44	0.57	-10000	0	-1.3	104	104
PRKACG	0.002	0.005	-10000	0	-10000	0	0
IL5	-0.26	0.22	-10000	0	-0.78	29	29
IL2	-0.36	0.28	-10000	0	-0.76	83	83
CDK5	0.012	0.007	-10000	0	-10000	0	0
PRKACB	0.013	0	-10000	0	-10000	0	0
HSP90AA1	0.013	0	-10000	0	-10000	0	0
IL8	-0.28	0.32	-10000	0	-0.81	65	65
CDK5R1/CDK5	0.006	0.025	-10000	0	-10000	0	0
NF kappa B1 p50/RelA/PKAc	-0.039	0.12	-10000	0	-0.49	1	1
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90	0.31	0.22	0.57	119	-10000	0	119
SMARCA4	0.013	0.013	-10000	0	-10000	0	0
chromatin remodeling	0.2	0.15	0.42	77	-10000	0	77
NF kappa B1 p50/RelA/Cbp	0.002	0.16	-10000	0	-0.48	7	7
JUN (dimer)	-0.33	0.3	-10000	0	-0.7	127	127
YWHAH	0.013	0	-10000	0	-10000	0	0
VIPR1	-0.26	0.43	-10000	0	-1.1	71	71
NR3C1	0.22	0.19	0.51	82	-10000	0	82
NR4A1	-0.33	0.43	-10000	0	-0.78	166	166
TIF2/SUV420H1	-0.04	0.16	-10000	0	-0.66	23	23
MAPKKK cascade	0.03	0.24	0.52	41	-0.53	1	42
cortisol/GR alpha (dimer)/Src-1	0.32	0.24	0.59	132	-10000	0	132
PBX1	0.011	0.045	-10000	0	-0.86	1	1
POU1F1	0.006	0.008	-10000	0	-10000	0	0
SELE	-0.36	0.51	-10000	0	-1.2	78	78
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A	0.2	0.15	0.42	75	-10000	0	75
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90	0.31	0.22	0.57	119	-10000	0	119
mol:cortisol	0.21	0.19	0.4	155	-10000	0	155
MMP1	-0.21	0.15	-10000	0	-10000	0	0

×

IGF1 pathway

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
NCK2	0.013	0	-10000	0	-10000	0	0
PTK2	0.013	0	-10000	0	-10000	0	0
CRKL	-0.12	0.24	-10000	0	-0.48	109	109
GRB2/SOS1/SHC	0	0	-10000	0	-10000	0	0
HRAS	0.012	0.016	-10000	0	-0.3	1	1
IRS1/Crk	-0.12	0.24	-10000	0	-0.48	109	109
IGF-1R heterotetramer/IGF1/PTP1B	-0.12	0.23	-10000	0	-0.55	81	81
AKT1	-0.082	0.22	-10000	0	-0.81	9	9
BAD	-0.069	0.2	-10000	0	-0.73	9	9
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	-0.12	0.24	-10000	0	-0.48	109	109
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.14	0.23	-10000	0	-0.48	109	109
RAF1	-0.059	0.19	-10000	0	-0.68	9	9
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos	-0.13	0.22	-10000	0	-0.45	109	109
YWHAZ	0.013	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.15	0.25	-10000	0	-0.52	109	109
PIK3CA	0.011	0.045	-10000	0	-0.86	1	1
RPS6KB1	-0.082	0.22	-10000	0	-0.81	9	9
GNB2L1	0.013	0	-10000	0	-10000	0	0
positive regulation of MAPKKK cascade	-0.052	0.16	-10000	0	-0.55	9	9
PXN	0.013	0	-10000	0	-10000	0	0
PIK3R1	0.013	0	-10000	0	-10000	0	0
cell adhesion	0	0	-10000	0	-10000	0	0
GRB2/SOS1	0	0	-10000	0	-10000	0	0
HRAS/GTP	-0.12	0.19	-10000	0	-0.43	81	81
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc	-0.099	0.18	-10000	0	-0.44	81	81
IGF-1R heterotetramer	-0.017	0.048	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS/Nck	-0.14	0.23	-10000	0	-0.48	109	109
Crk/p130 Cas/Paxillin	-0.12	0.2	-10000	0	-0.46	81	81
IGF1R	-0.017	0.048	-10000	0	-10000	0	0
IGF1	-0.19	0.36	-10000	0	-0.84	86	86
IRS2/Crk	-0.11	0.23	-10000	0	-0.45	109	109
PI3K	-0.13	0.22	-10000	0	-0.49	81	81
apoptosis	0.051	0.18	0.6	9	-10000	0	9
HRAS/GDP	-0.001	0.01	-10000	0	-10000	0	0
PRKCD	-0.099	0.24	-10000	0	-0.55	81	81
RAF1/14-3-3 E	-0.043	0.17	-10000	0	-0.55	9	9
BAD/14-3-3	-0.055	0.19	-10000	0	-0.65	9	9
PRKCZ	-0.082	0.22	-10000	0	-0.81	9	9
Crk/p130 Cas/Paxillin/FAK1	-0.096	0.16	-10000	0	-0.66	9	9
PTPN1	0.013	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1	-0.11	0.26	-10000	0	-0.59	81	81
BCAR1	0.013	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1/SHC/GRB10	-0.11	0.2	-10000	0	-0.49	81	81
mol:GDP	0	0	-10000	0	-10000	0	0
SOS1	0.013	0	-10000	0	-10000	0	0
IRS1/NCK2	-0.12	0.24	-10000	0	-0.48	109	109
GRB10	0.013	0	-10000	0	-10000	0	0
PTPN11	-0.12	0.24	-10000	0	-0.48	109	109
IRS1	-0.14	0.26	-10000	0	-0.52	109	109
IRS2	-0.12	0.24	-10000	0	-0.48	109	109
IGF-1R heterotetramer/IGF1	-0.16	0.28	-10000	0	-0.69	81	81
GRB2	0.013	0	-10000	0	-10000	0	0
PDPK1	-0.095	0.23	-10000	0	-0.46	81	81
YWHAE	0.013	0	-10000	0	-10000	0	0
PRKD1	-0.099	0.24	-10000	0	-0.55	81	81
SHC1	0.013	0	-10000	0	-10000	0	0

×

IL23-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCL2	-0.21	0.54	-9999	-1.3	57	57
IL23A	-0.22	0.55	-9999	-1.3	63	63
NF kappa B1 p50/RelA/I kappa B alpha	-0.29	0.46	-9999	-1.2	65	65
positive regulation of T cell mediated cytotoxicity	-0.24	0.6	-9999	-1.3	67	67
ITGA3	-0.2	0.5	-9999	-1.2	58	58
IL17F	-0.1	0.34	-9999	-0.75	48	48
IL12B	0.001	0.085	-9999	-0.44	9	9
STAT1 (dimer)	-0.23	0.56	-9999	-1.3	67	67
CD4	-0.19	0.49	-9999	-1.1	62	62
IL23	-0.23	0.52	-9999	-1.2	63	63
IL23R	-0.004	0.097	-9999	-10000	0	0
IL1B	-0.23	0.57	-9999	-1.3	63	63
T-helper cell lineage commitment	0	0	-9999	-10000	0	0
IL24	-0.19	0.49	-9999	-1.1	60	60
TYK2	0.013	0.022	-9999	-10000	0	0
STAT4	-0.034	0.16	-9999	-0.44	39	39
STAT3	0.013	0	-9999	-10000	0	0
IL18RAP	-0.04	0.2	-9999	-0.86	22	22
IL12RB1	-0.024	0.12	-9999	-0.52	9	9
PIK3CA	0.011	0.045	-9999	-0.86	1	1
IL12Rbeta1/TYK2	-0.011	0.094	-9999	-0.71	3	3
IL23R/JAK2	-0.001	0.12	-9999	-10000	0	0
positive regulation of chronic inflammatory response	-0.24	0.6	-9999	-1.3	67	67
natural killer cell activation	0.001	0.009	-9999	-10000	0	0
JAK2	0.021	0.026	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
NFKB1	0.013	0.004	-9999	-10000	0	0
RELA	0.013	0.004	-9999	-10000	0	0
positive regulation of dendritic cell antigen processing and presentation	-0.21	0.49	-9999	-1.1	64	64
ALOX12B	-0.21	0.5	-9999	-1.1	63	63
CXCL1	-0.22	0.52	-9999	-1.2	58	58
T cell proliferation	-0.24	0.6	-9999	-1.3	67	67
NFKBIA	0.013	0.004	-9999	-10000	0	0
IL17A	-0.06	0.28	-9999	-0.59	39	39
PI3K	-0.3	0.47	-9999	-1.2	66	66
IFNG	-0.021	0.054	-9999	-0.13	55	55
STAT3 (dimer)	-0.28	0.43	-9999	-1.1	64	64
IL18R1	-0.031	0.14	-9999	-0.4	39	39
IL23/IL23R/JAK2/TYK2/SOCS3	-0.1	0.32	-9999	-0.75	43	43
IL18/IL18R	-0.077	0.19	-9999	-0.62	35	35
macrophage activation	-0.015	0.018	-9999	-0.044	65	65
TNF	-0.26	0.61	-9999	-1.4	74	74
STAT3/STAT4	-0.31	0.48	-9999	-1.2	69	69
STAT4 (dimer)	-0.25	0.57	-9999	-1.3	69	69
IL18	-0.035	0.15	-9999	-0.39	44	44
IL19	-0.19	0.49	-9999	-1.2	57	57
STAT5A (dimer)	-0.23	0.56	-9999	-1.3	66	66
STAT1	0.005	0.05	-9999	-0.3	10	10
SOCS3	-0.05	0.22	-9999	-0.84	28	28
CXCL9	-0.27	0.6	-9999	-1.3	77	77
MPO	-0.19	0.5	-9999	-1.1	61	61
positive regulation of humoral immune response	-0.24	0.6	-9999	-1.3	67	67
IL23/IL23R/JAK2/TYK2	-0.28	0.71	-9999	-1.5	67	67
IL6	-0.34	0.67	-9999	-1.4	99	99
STAT5A	0.013	0	-9999	-10000	0	0
IL2	0.001	0.017	-9999	-10000	0	0
positive regulation of tyrosine phosphorylation of STAT protein	0.001	0.009	-9999	-10000	0	0
CD3E	-0.22	0.55	-9999	-1.3	62	62
keratinocyte proliferation	-0.24	0.6	-9999	-1.3	67	67
NOS2	-0.2	0.5	-9999	-1.1	63	63

×

Arf6 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CENTA1/KIF3B	0	0	-9999	-10000	0	0
ARNO/beta Arrestin1-2	-0.042	0.12	-9999	-0.51	10	10
EGFR	0.001	0.099	-9999	-0.86	5	5
EPHA2	0.011	0.023	-9999	-0.3	2	2
USP6	0.01	0.028	-9999	-0.3	3	3
IQSEC1	0.013	0	-9999	-10000	0	0
EGFR/EGFR/EGF/EGF	-0.1	0.24	-9999	-0.66	56	56
ARRB2	-0.041	0.15	-9999	-0.46	42	42
mol:GTP	0.02	0.012	-9999	-10000	0	0
ARRB1	0.011	0.045	-9999	-0.86	1	1
FBXO8	0.013	0	-9999	-10000	0	0
TSHR	0.008	0.063	-9999	-0.86	2	2
EGF	-0.11	0.3	-9999	-0.86	51	51
somatostatin receptor activity	0	0	-9999	-0.001	101	101
ARAP2	0.011	0.045	-9999	-0.86	1	1
mol:GDP	-0.12	0.14	-9999	-0.31	99	99
mol:PI-3-4-5-P3	0	0	-9999	-0.001	90	90
ITGA2B	-0.095	0.29	-9999	-0.86	47	47
ARF6	0.013	0	-9999	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	-0.001	0.009	-9999	-10000	0	0
ADAP1	0.013	0	-9999	-10000	0	0
KIF13B	0.013	0	-9999	-10000	0	0
HGF/MET	-0.16	0.24	-9999	-0.73	51	51
PXN	0.013	0	-9999	-10000	0	0
ARF6/GTP	-0.12	0.15	-9999	-0.32	102	102
EGFR/EGFR/EGF/EGF/ARFGEP100	-0.087	0.2	-9999	-0.57	56	56
ADRB2	-0.01	0.14	-9999	-0.86	10	10
receptor agonist activity	0	0	-9999	0	107	107
actin filament binding	0	0	-9999	-0.001	98	98
SRC	0.012	0.016	-9999	-10000	0	0
ITGB3	-0.015	0.15	-9999	-0.86	12	12
GNAQ	0.013	0	-9999	-10000	0	0
EFA6/PI-4-5-P2	0	0.001	-9999	-0.001	92	92
ARF6/GDP	0.001	0.069	-9999	-0.34	2	2
ARF6/GDP/GULP/ACAP1	-0.19	0.2	-9999	-0.52	82	82
alphaIIb/beta3 Integrin/paxillin/GIT1	-0.081	0.21	-9999	-0.58	53	53
ACAP1	-0.001	0.081	-9999	-0.86	2	2
ACAP2	0.013	0	-9999	-10000	0	0
LHCGR/beta Arrestin2	-0.081	0.22	-9999	-0.71	42	42
EFNA1	0.013	0	-9999	-10000	0	0
HGF	-0.1	0.3	-9999	-0.86	51	51
CYTH3	0.01	0.035	-9999	-0.67	1	1
CYTH2	0.007	0.002	-9999	-10000	0	0
NCK1	0.013	0	-9999	-10000	0	0
fibronectin binding	0	0	-9999	0	90	90
endosomal lumen acidification	0	0	-9999	-0.001	104	104
microtubule-based process	0	0	-9999	-10000	0	0
GULP1	-0.14	0.33	-9999	-0.86	68	68
GNAQ/ARNO	0.008	0.009	-9999	-10000	0	0
mol:Phosphatidic acid	0	0	-9999	-10000	0	0
PIP3-E	0	0	-9999	0	21	21
MET	-0.11	0.15	-9999	-0.3	154	154
GNA14	-0.2	0.37	-9999	-0.86	91	91
GNA15	-0.017	0.099	-9999	-0.31	35	35
GIT1	0.013	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-0.001	97	97
GNA11	0.006	0.077	-9999	-0.86	3	3
LHCGR	-0.093	0.27	-9999	-0.86	42	42
AGTR1	-0.32	0.42	-9999	-0.86	146	146
desensitization of G-protein coupled receptor protein signaling pathway	-0.08	0.22	-9999	-0.7	42	42
IPCEF1/ARNO	-0.064	0.16	-9999	-0.46	56	56
alphaIIb/beta3 Integrin	-0.1	0.26	-9999	-0.72	53	53

×

Syndecan-1-mediated 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
TGFB1	0.007	0.042	-9999	-10000	0	0
CCL5	-0.043	0.21	-9999	-0.72	29	29
SDCBP	0.013	0	-9999	-10000	0	0
FGFR/FGF2/Syndecan-1	-0.1	0.16	-9999	-0.47	39	39
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
Syndecan-1/Laminin-5	-0.089	0.16	-9999	-0.52	25	25
Syndecan-1/Syntenin	-0.089	0.16	-9999	-0.67	14	14
MAPK3	-0.066	0.14	-9999	-0.63	12	12
HGF/MET	-0.16	0.24	-9999	-0.73	51	51
TGFB1/TGF beta receptor Type II	0.007	0.042	-9999	-10000	0	0
BSG	0.012	0.016	-9999	-10000	0	0
keratinocyte migration	-0.088	0.15	-9999	-0.51	25	25
Syndecan-1/RANTES	-0.12	0.22	-9999	-0.75	32	32
Syndecan-1/CD147	-0.09	0.14	-9999	-0.68	12	12
Syndecan-1/Syntenin/PIP2	-0.096	0.14	-9999	-0.65	14	14
LAMA5	0.013	0	-9999	-10000	0	0
positive regulation of cell-cell adhesion	-0.094	0.14	-9999	-0.62	14	14
MMP7	-0.17	0.22	-9999	-0.36	186	186
HGF	-0.1	0.3	-9999	-0.86	51	51
Syndecan-1/CASK	-0.097	0.15	-9999	-0.45	39	39
Syndecan-1/HGF/MET	-0.21	0.23	-9999	-0.67	61	61
regulation of cell adhesion	-0.056	0.14	-9999	-0.6	12	12
HPSE	-0.021	0.14	-9999	-0.86	9	9
positive regulation of cell migration	-0.1	0.16	-9999	-0.47	39	39
SDC1	-0.1	0.16	-9999	-0.48	39	39
Syndecan-1/Collagen	-0.1	0.16	-9999	-0.47	39	39
PPIB	0.013	0	-9999	-10000	0	0
MET	-0.11	0.15	-9999	-0.3	154	154
PRKACA	0.013	0	-9999	-10000	0	0
MMP9	-0.086	0.24	-9999	-0.54	68	68
MAPK1	-0.066	0.14	-9999	-0.63	12	12
homophilic cell adhesion	-0.1	0.16	-9999	-0.47	39	39
MMP1	-0.14	0.15	-9999	-0.3	180	180

×

TCGA08_retinoblastoma

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2B	-0.12	0.15	-10000	0	-10000	0	0
CDKN2C	0.026	0.034	-10000	0	-0.29	3	3
CDKN2A	-0.12	0.16	-10000	0	-0.3	164	164
CCND2	0.067	0.069	0.16	114	-10000	0	114
RB1	-0.066	0.068	-10000	0	-0.23	1	1
CDK4	0.067	0.068	0.24	1	-10000	0	1
CDK6	0.07	0.073	0.24	1	-0.19	1	2
G1/S progression	0.058	0.075	0.23	1	-10000	0	1

×

Coregulation of Androgen receptor activity

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NRIP1	-0.014	0.062	-10000	0	-0.35	10	10
SVIL	-0.006	0.03	-10000	0	-10000	0	0
ZNF318	0.06	0.082	-10000	0	-10000	0	0
JMJD2C	-0.065	0.069	-10000	0	-0.12	215	215
T-DHT/AR/Ubc9	-0.28	0.3	-10000	0	-0.65	149	149
CARM1	0.011	0.003	-10000	0	-10000	0	0
PRDX1	0.015	0.004	-10000	0	-10000	0	0
PELP1	0.02	0.01	-10000	0	-10000	0	0
CTNNB1	-0.002	0.023	-10000	0	-10000	0	0
AKT1	0.025	0.019	-10000	0	-10000	0	0
PTK2B	0.004	0.015	-10000	0	-10000	0	0
MED1	0.024	0.019	-10000	0	-10000	0	0
MAK	0.048	0.13	-10000	0	-0.83	5	5
response to oxidative stress	0.002	0.004	-10000	0	-10000	0	0
HIP1	-0.008	0.053	-10000	0	-0.86	1	1
GSN	-0.006	0.03	-10000	0	-10000	0	0
NCOA2	-0.042	0.21	-10000	0	-0.86	23	23
NCOA6	-0.005	0.028	-10000	0	-10000	0	0
DNA-PK	0.057	0.082	0.26	1	-10000	0	1
NCOA4	0.011	0.004	-10000	0	-10000	0	0
PIAS3	-0.002	0.023	-10000	0	-10000	0	0
cell proliferation	-0.014	0.15	-10000	0	-1.1	5	5
XRCC5	0.024	0.017	-10000	0	-10000	0	0
UBE3A	-0.015	0.046	-10000	0	-10000	0	0
T-DHT/AR/SNURF	-0.3	0.33	-10000	0	-0.68	154	154
FHL2	-0.16	0.37	-10000	0	-1.4	31	31
RANBP9	-0.005	0.028	-10000	0	-10000	0	0
JMJD1A	0.002	0.037	-10000	0	-0.12	28	28
CDK6	0.012	0.045	-10000	0	-0.85	1	1
TGFB1I1	-0.006	0.03	-10000	0	-10000	0	0
T-DHT/AR/CyclinD1	-0.29	0.31	-10000	0	-0.66	151	151
XRCC6	0.024	0.017	-10000	0	-10000	0	0
T-DHT/AR	-0.33	0.33	-10000	0	-0.66	172	172
CTDSP1	0.008	0.006	-10000	0	-10000	0	0
CTDSP2	0.045	0.05	-10000	0	-10000	0	0
BRCA1	-0.006	0.03	-10000	0	-10000	0	0
TCF4	0.035	0.034	-10000	0	-10000	0	0
CDKN2A	-0.1	0.15	-10000	0	-10000	0	0
SRF	0.026	0.04	-10000	0	-10000	0	0
NKX3-1	-0.13	0.15	-10000	0	-1.3	3	3
KLK3	-0.43	0.7	-10000	0	-1.6	102	102
TMF1	0.009	0.006	-10000	0	-10000	0	0
HNRNPA1	0.03	0.027	-10000	0	-10000	0	0
AOF2	-0.021	0.033	-10000	0	-0.075	102	102
APPL1	0.051	0.042	-10000	0	-10000	0	0
T-DHT/AR/Caspase 8	-0.27	0.3	-10000	0	-0.64	149	149
AR	-0.37	0.43	-10000	0	-0.9	149	149
UBA3	0.008	0.006	-10000	0	-10000	0	0
PATZ1	0.03	0.027	-10000	0	-10000	0	0
PAWR	0.009	0.006	-10000	0	-10000	0	0
PRKDC	0.024	0.017	-10000	0	-10000	0	0
PA2G4	0.035	0.035	-10000	0	-10000	0	0
UBE2I	0.013	0	-10000	0	-10000	0	0
T-DHT/AR/Cyclin D3/CDK11 p58	-0.25	0.29	-10000	0	-0.6	149	149
RPS6KA3	-0.006	0.03	-10000	0	-10000	0	0
T-DHT/AR/ARA70	-0.28	0.31	-10000	0	-0.65	149	149
LATS2	0.03	0.027	-10000	0	-10000	0	0
T-DHT/AR/PRX1	-0.25	0.28	-10000	0	-0.59	149	149
Cyclin D3/CDK11 p58	0	0	-10000	0	-10000	0	0
VAV3	-0.011	0.091	-10000	0	-0.86	4	4
KLK2	-0.78	0.64	-10000	0	-1.3	215	215
CASP8	0.017	0.007	-10000	0	-10000	0	0
T-DHT/AR/TIF2/CARM1	-0.29	0.33	-10000	0	-0.67	154	154
TMPRSS2	-0.18	0.32	-10000	0	-1.2	28	28
CCND1	0	0.05	-10000	0	-0.3	10	10
PIAS1	-0.015	0.046	-10000	0	-10000	0	0
mol:T-DHT	-0.033	0.043	-10000	0	-0.084	132	132
CDC2L1	0.001	0.002	-10000	0	-10000	0	0
PIAS4	-0.034	0.075	-10000	0	-10000	0	0
T-DHT/AR/CDK6	-0.28	0.31	-10000	0	-0.65	149	149
CMTM2	0.014	0.023	-10000	0	-0.29	2	2
SNURF	-0.022	0.17	-10000	0	-0.86	15	15
ZMIZ1	-0.013	0.038	-10000	0	-10000	0	0
CCND3	0.014	0.002	-10000	0	-10000	0	0
TGIF1	0.03	0.027	-10000	0	-10000	0	0
FKBP4	-0.005	0.028	-10000	0	-10000	0	0

×

Signaling mediated by p38-alpha and p38-beta

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
PTGS2	-0.13	0.42	-9999	-1.4	38	38
MKNK1	0.013	0	-9999	-10000	0	0
MAPK14	-0.042	0.11	-9999	-0.33	38	38
ATF2/c-Jun	-0.23	0.44	-9999	-1	88	88
MAPK11	-0.042	0.11	-9999	-0.39	16	16
MITF	-0.036	0.14	-9999	-0.4	38	38
MAPKAPK5	-0.036	0.14	-9999	-0.4	38	38
KRT8	-0.036	0.14	-9999	-0.4	38	38
MAPKAPK3	0.013	0	-9999	-10000	0	0
MAPKAPK2	0.013	0	-9999	-10000	0	0
p38alpha-beta/CK2	-0.059	0.17	-9999	-0.51	38	38
CEBPB	-0.036	0.14	-9999	-0.4	38	38
SLC9A1	-0.036	0.14	-9999	-0.4	38	38
mol:GDP	0	0	-9999	-10000	0	0
ATF2	-0.072	0.19	-9999	-0.44	53	53
p38alpha-beta/MNK1	-0.034	0.14	-9999	-0.5	16	16
JUN	-0.23	0.44	-9999	-1	88	88
PPARGC1A	-0.24	0.25	-9999	-0.47	200	200
USF1	-0.036	0.14	-9999	-0.4	38	38
RAB5/GDP/GDI1	-0.043	0.087	-9999	-0.35	16	16
NOS2	-0.057	0.16	-9999	-0.54	16	16
DDIT3	-0.039	0.14	-9999	-0.41	38	38
RAB5A	0.013	0	-9999	-10000	0	0
HSPB1	-0.019	0.11	-9999	-0.39	16	16
p38alpha-beta/HBP1	-0.034	0.14	-9999	-0.5	16	16
CREB1	-0.049	0.16	-9999	-0.43	43	43
RAB5/GDP	0	0	-9999	-10000	0	0
EIF4E	-0.022	0.12	-9999	-0.43	16	16
RPS6KA4	-0.036	0.14	-9999	-0.4	38	38
PLA2G4A	-0.055	0.2	-9999	-0.61	36	36
GDI1	-0.036	0.14	-9999	-0.4	38	38
TP53	-0.047	0.17	-9999	-0.5	38	38
RPS6KA5	-0.071	0.2	-9999	-0.46	60	60
ESR1	-0.072	0.21	-9999	-0.53	47	47
HBP1	0.013	0	-9999	-10000	0	0
MEF2C	-0.036	0.14	-9999	-0.4	38	38
MEF2A	-0.036	0.14	-9999	-0.4	38	38
EIF4EBP1	-0.049	0.16	-9999	-0.43	44	44
KRT19	-0.11	0.23	-9999	-0.57	51	51
ELK4	-0.036	0.14	-9999	-0.4	38	38
ATF6	-0.036	0.14	-9999	-0.4	38	38
ATF1	-0.049	0.16	-9999	-0.44	38	38
p38alpha-beta/MAPKAPK2	-0.034	0.14	-9999	-0.5	16	16
p38alpha-beta/MAPKAPK3	-0.034	0.14	-9999	-0.5	16	16

×

Hedgehog signaling events mediated by Gli proteins

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
HDAC1	0.014	0.001	-9999	-10000	0	0
HDAC2	0.014	0.001	-9999	-10000	0	0
GNB1/GNG2	0	0	-9999	-10000	0	0
forebrain development	-0.33	0.28	-9999	-0.56	201	201
GNAO1	-0.017	0.14	-9999	-0.86	10	10
SMO/beta Arrestin2	0.012	0.012	-9999	-10000	0	0
SMO	0.007	0.007	-9999	-10000	0	0
ARRB2	0.007	0.007	-9999	-10000	0	0
GLI3/SPOP	0.048	0.043	-9999	-10000	0	0
mol:GTP	-0.002	0.003	-9999	-10000	0	0
GSK3B	0.013	0	-9999	-10000	0	0
GNAI2	0.01	0.006	-9999	-10000	0	0
SIN3/HDAC complex	0.008	0.033	-9999	-0.52	1	1
GNAI1	0.007	0.045	-9999	-0.86	1	1
XPO1	0.008	0.008	-9999	-10000	0	0
GLI1/Su(fu)	-0.25	0.19	-9999	-0.52	105	105
SAP30	0.012	0.045	-9999	-0.86	1	1
mol:GDP	0.007	0.007	-9999	-10000	0	0
MIM/GLI2A	-0.009	0.044	-9999	-0.29	1	1
IFT88	0.013	0	-9999	-10000	0	0
GNAI3	0.01	0.005	-9999	-10000	0	0
GLI2	0.032	0.062	-9999	-10000	0	0
GLI3	0.042	0.045	-9999	-0.31	6	6
CSNK1D	0.013	0	-9999	-10000	0	0
CSNK1E	0.013	0	-9999	-10000	0	0
SAP18	0.014	0.001	-9999	-10000	0	0
embryonic digit morphogenesis	0.013	0	-9999	-10000	0	0
GNG2	0.013	0	-9999	-10000	0	0
Gi family/GTP	0.009	0.065	-9999	-0.34	11	11
SIN3B	0.014	0.001	-9999	-10000	0	0
SIN3A	0.014	0.001	-9999	-10000	0	0
GLI3/Su(fu)	0.03	0.044	-9999	-10000	0	0
GLI2/Su(fu)	0.021	0.058	-9999	-10000	0	0
FOXA2	-0.69	0.67	-9999	-1.4	189	189
neural tube patterning	-0.33	0.28	-9999	-0.56	201	201
SPOP	0.013	0	-9999	-10000	0	0
Su(fu)/PIAS1	0.017	0.018	-9999	-10000	0	0
GNB1	0.013	0	-9999	-10000	0	0
CSNK1G2	0.013	0	-9999	-10000	0	0
CSNK1G3	0.013	0	-9999	-10000	0	0
MTSS1	-0.009	0.044	-9999	-0.29	1	1
embryonic limb morphogenesis	-0.33	0.28	-9999	-0.56	201	201
SUFU	0.016	0.016	-9999	-10000	0	0
LGALS3	-0.1	0.15	-9999	-0.3	139	139
catabolic process	0.063	0.06	-9999	-0.4	1	1
GLI3A/CBP	-0.2	0.2	-9999	-0.39	201	201
KIF3A	0.013	0	-9999	-10000	0	0
GLI1	-0.34	0.29	-9999	-0.57	201	201
RAB23	0.006	0.077	-9999	-0.86	3	3
CSNK1A1	0.013	0	-9999	-10000	0	0
IFT172	0.013	0	-9999	-10000	0	0
RBBP7	0.014	0.001	-9999	-10000	0	0
Su(fu)/Galectin3	-0.034	0.073	-9999	-10000	0	0
GNAZ	0.01	0.005	-9999	-10000	0	0
RBBP4	0.014	0.001	-9999	-10000	0	0
CSNK1G1	0.013	0	-9999	-10000	0	0
PIAS1	0.013	0	-9999	-10000	0	0
PRKACA	0.013	0	-9999	-10000	0	0
GLI2/SPOP	0.037	0.058	-9999	-10000	0	0
STK36	0.008	0.008	-9999	-10000	0	0
Gi family/GNB1/GNG2/GDP	0.015	0.055	-9999	-0.28	4	4
PTCH1	-0.29	0.26	-9999	-0.62	105	105
MIM/GLI1	-0.47	0.39	-9999	-0.77	196	196
CREBBP	-0.2	0.2	-9999	-0.39	201	201
Su(fu)/SIN3/HDAC complex	0.057	0.017	-9999	-10000	0	0

×

EPHB forward 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
Ephrin A5/EPHB2	-0.1	0.22	-10000	0	-0.59	66	66
cell-cell adhesion	0.14	0.19	0.56	8	-10000	0	8
Ephrin B/EPHB2/RasGAP	-0.013	0.068	-10000	0	-0.49	7	7
ITSN1	0.013	0	-10000	0	-10000	0	0
PIK3CA	0.011	0.045	-10000	0	-0.86	1	1
SHC1	0.013	0	-10000	0	-10000	0	0
Ephrin B1/EPHB3	-0.094	0.076	-10000	0	-10000	0	0
Ephrin B1/EPHB1	-0.2	0.28	-10000	0	-0.58	127	127
HRAS/GDP	-0.13	0.18	-10000	0	-0.5	10	10
Ephrin B/EPHB1/GRB7	-0.19	0.25	-10000	0	-0.53	130	130
Endophilin/SYNJ1	0.025	0.072	-10000	0	-0.46	7	7
KRAS	0.013	0	-10000	0	-10000	0	0
Ephrin B/EPHB1/Src	-0.17	0.24	-10000	0	-0.5	130	130
endothelial cell migration	-0.001	0.025	-10000	0	-0.49	1	1
GRB2	0.013	0	-10000	0	-10000	0	0
GRB7	-0.033	0.11	-10000	0	-0.3	56	56
PAK1	0.033	0.073	-10000	0	-0.46	7	7
HRAS	0.012	0.016	-10000	0	-0.3	1	1
RRAS	0.025	0.073	-10000	0	-0.47	7	7
DNM1	-0.029	0.18	-10000	0	-0.83	19	19
cell-cell signaling	0	0	-10000	0	-10000	0	0
CRK	-0.14	0.24	-10000	0	-0.48	130	130
lamellipodium assembly	-0.14	0.19	-10000	0	-0.56	8	8
Ephrin B/EPHB1/Src/p52 SHC/GRB2	-0.091	0.18	-10000	0	-0.34	127	127
PIK3R1	0.013	0	-10000	0	-10000	0	0
EPHB2	0.006	0.077	-10000	0	-0.86	3	3
EPHB3	-0.18	0.15	-10000	0	-10000	0	0
EPHB1	-0.28	0.41	-10000	0	-0.86	127	127
EPHB4	0.013	0	-10000	0	-10000	0	0
mol:GDP	-0.06	0.18	-10000	0	-0.47	8	8
Ephrin B/EPHB2	-0.014	0.07	-10000	0	-0.5	7	7
Ephrin B/EPHB3	-0.079	0.08	-10000	0	-0.6	4	4
JNK cascade	-0.14	0.25	-10000	0	-0.48	129	129
Ephrin B/EPHB1	-0.18	0.24	-10000	0	-0.51	130	130
RAP1/GDP	-0.045	0.16	-10000	0	-0.47	3	3
EFNB2	0.013	0	-10000	0	-10000	0	0
EFNB3	-0.009	0.11	-10000	0	-0.42	19	19
EFNB1	0.013	0	-10000	0	-10000	0	0
Ephrin B2/EPHB1-2	-0.18	0.26	-10000	0	-0.54	129	129
RAP1B	0.013	0	-10000	0	-10000	0	0
RAP1A	0.013	0	-10000	0	-10000	0	0
CDC42/GTP	-0.14	0.2	-10000	0	-0.53	13	13
Rap1/GTP	-0.14	0.19	-10000	0	-0.57	8	8
axon guidance	-0.1	0.22	-10000	0	-0.59	66	66
MAPK3	-0.066	0.16	-10000	0	-0.55	1	1
MAPK1	-0.066	0.16	-10000	0	-0.55	1	1
Rac1/GDP	-0.036	0.17	-10000	0	-0.45	6	6
actin cytoskeleton reorganization	-0.1	0.14	-10000	0	-0.57	2	2
CDC42/GDP	-0.036	0.17	-10000	0	-0.42	8	8
PI3K	-0.001	0.026	-10000	0	-0.5	1	1
EFNA5	-0.14	0.33	-10000	0	-0.84	66	66
Ephrin B2/EPHB4	0	0	-10000	0	-10000	0	0
Ephrin B/EPHB2/Intersectin/N-WASP	0.028	0.054	-10000	0	-0.34	7	7
CDC42	0.013	0	-10000	0	-10000	0	0
RAS family/GTP	-0.14	0.19	-10000	0	-0.54	9	9
PTK2	0.037	0.052	-10000	0	-10000	0	0
MAP4K4	-0.14	0.25	-10000	0	-0.49	129	129
SRC	0.012	0.016	-10000	0	-10000	0	0
KALRN	0.013	0	-10000	0	-10000	0	0
Intersectin/N-WASP	0	0	-10000	0	-10000	0	0
neuron projection morphogenesis	-0.057	0.18	-10000	0	-0.56	2	2
MAP2K1	-0.077	0.17	-10000	0	-0.4	8	8
WASL	0.013	0	-10000	0	-10000	0	0
Ephrin B1/EPHB1-2/NCK1	-0.18	0.25	-10000	0	-0.53	129	129
cell migration	-0.072	0.19	-10000	0	-0.43	8	8
NRAS	0.013	0	-10000	0	-10000	0	0
SYNJ1	0.025	0.073	-10000	0	-0.47	7	7
PXN	0.013	0	-10000	0	-10000	0	0
TF	-0.035	0.19	-10000	0	-0.47	56	56
HRAS/GTP	-0.15	0.21	-10000	0	-0.6	9	9
Ephrin B1/EPHB1-2	-0.18	0.26	-10000	0	-0.54	129	129
cell adhesion mediated by integrin	0.012	0.07	0.53	4	-10000	0	4
RAC1	0.013	0	-10000	0	-10000	0	0
mol:GTP	-0.16	0.22	-10000	0	-0.46	132	132
RAC1-CDC42/GTP	-0.19	0.21	-10000	0	-0.51	96	96
RASA1	0.013	0	-10000	0	-10000	0	0
RAC1-CDC42/GDP	-0.045	0.16	-10000	0	-0.47	3	3
ruffle organization	-0.1	0.22	-10000	0	-0.57	8	8
NCK1	0.013	0	-10000	0	-10000	0	0
receptor internalization	0.009	0.13	-10000	0	-0.49	23	23
Ephrin B/EPHB2/KALRN	-0.013	0.068	-10000	0	-0.49	7	7
ROCK1	-0.068	0.077	-10000	0	-10000	0	0
RAS family/GDP	-0.08	0.11	-10000	0	-0.54	2	2
Rac1/GTP	-0.15	0.2	-10000	0	-0.6	8	8
Ephrin B/EPHB1/Src/Paxillin	-0.096	0.18	-10000	0	-0.35	130	130

×

IL12-mediated signaling events

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
IL12/IL12R/TYK2/JAK2/SOCS1	-0.019	0.14	-10000	0	-0.45	15	15
TBX21	-0.12	0.44	-10000	0	-1.1	48	48
B2M	0.012	0.008	-10000	0	-10000	0	0
TYK2	0.015	0.02	-10000	0	-10000	0	0
IL12RB1	-0.022	0.12	-10000	0	-0.48	11	11
GADD45B	-0.1	0.39	-10000	0	-0.99	46	46
IL12RB2	-0.013	0.15	-10000	0	-0.74	14	14
GADD45G	-0.075	0.34	-10000	0	-0.89	37	37
natural killer cell activation	0.002	0.022	-10000	0	-10000	0	0
RELB	0.013	0	-10000	0	-10000	0	0
RELA	0.013	0	-10000	0	-10000	0	0
IL18	-0.032	0.15	-10000	0	-0.38	44	44
IL2RA	-0.04	0.18	-10000	0	-0.86	16	16
IFNG	-0.11	0.28	-10000	0	-0.73	60	60
STAT3 (dimer)	-0.072	0.32	-10000	0	-0.78	45	45
HLA-DRB5	-0.052	0.14	-10000	0	-0.86	2	2
FASLG	-0.14	0.47	-10000	0	-1.2	52	52
NF kappa B2 p52/RelB	-0.17	0.32	-10000	0	-0.93	46	46
CD4	0	0.055	-10000	0	-0.3	12	12
SOCS1	0.01	0.032	-10000	0	-0.3	4	4
EntrezGene:6955	-0.007	0.015	-10000	0	-10000	0	0
CD3D	-0.1	0.28	-10000	0	-0.73	56	56
CD3E	-0.068	0.24	-10000	0	-0.74	38	38
CD3G	-0.15	0.33	-10000	0	-0.82	71	71
IL12Rbeta2/JAK2	0.002	0.12	-10000	0	-0.66	11	11
CCL3	-0.11	0.43	-10000	0	-1.2	35	35
CCL4	-0.15	0.52	-10000	0	-1.4	47	47
HLA-A	0.01	0.024	-10000	0	-0.32	1	1
IL18/IL18R	-0.04	0.21	-10000	0	-0.6	37	37
NOS2	-0.09	0.35	-10000	0	-0.87	42	42
IL12/IL12R/TYK2/JAK2/SPHK2	-0.018	0.14	-10000	0	-0.45	15	15
IL1R1	-0.086	0.37	-10000	0	-0.98	39	39
IL4	0.002	0.022	-10000	0	-10000	0	0
JAK2	0.015	0.02	-10000	0	-10000	0	0
EntrezGene:6957	-0.007	0.014	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.24	0.54	-10000	0	-1.1	79	79
RAB7A	-0.044	0.29	-10000	0	-0.7	37	37
lysosomal transport	-0.039	0.28	-10000	0	-0.65	39	39
FOS	-0.42	0.66	-10000	0	-1.3	123	123
STAT4 (dimer)	-0.081	0.35	-10000	0	-0.83	46	46
STAT5A (dimer)	-0.22	0.36	-10000	0	-0.89	67	67
GZMA	-0.1	0.41	-10000	0	-1.1	37	37
GZMB	-0.1	0.39	-10000	0	-1	41	41
HLX	0.006	0.045	-10000	0	-10000	0	0
LCK	-0.11	0.42	-10000	0	-1.1	46	46
TCR/CD3/MHC II/CD4	-0.19	0.34	-10000	0	-0.74	74	74
IL2/IL2R	-0.08	0.23	-10000	0	-0.73	33	33
MAPK14	-0.073	0.35	-10000	0	-0.8	52	52
CCR5	-0.092	0.38	-10000	0	-1	37	37
IL1B	-0.05	0.23	-10000	0	-0.78	32	32
STAT6	-0.004	0.11	-10000	0	-0.25	12	12
STAT4	-0.034	0.16	-10000	0	-0.44	39	39
STAT3	0.013	0	-10000	0	-10000	0	0
STAT1	0.005	0.05	-10000	0	-0.3	10	10
NFKB1	0.013	0	-10000	0	-10000	0	0
NFKB2	0.013	0	-10000	0	-10000	0	0
IL12B	0.001	0.08	-10000	0	-0.44	9	9
CD8A	-0.048	0.22	-10000	0	-0.86	26	26
CD8B	-0.1	0.28	-10000	0	-0.73	57	57
T-helper 1 cell differentiation	0	0	-10000	0	-10000	0	0
natural killer cell mediated cytotoxicity	0.019	0.14	0.45	15	-10000	0	15
IL2RB	-0.018	0.14	-10000	0	-0.54	21	21
proteasomal ubiquitin-dependent protein catabolic process	-0.069	0.32	-10000	0	-0.75	46	46
IL2RG	-0.052	0.2	-10000	0	-0.51	47	47
IL12	-0.053	0.21	-10000	0	-0.66	39	39
STAT5A	0.013	0	-10000	0	-10000	0	0
CD247	-0.033	0.18	-10000	0	-0.66	24	24
IL2	0.004	0.006	-10000	0	-10000	0	0
SPHK2	0.013	0	-10000	0	-10000	0	0
FRAP1	0	0	-10000	0	-10000	0	0
IL12A	-0.071	0.26	-10000	0	-0.82	39	39
IL12/IL12R/TYK2/JAK2	-0.12	0.47	-10000	0	-1.1	48	48
MAP2K3	-0.075	0.35	-10000	0	-0.79	51	51
RIPK2	0.013	0	-10000	0	-10000	0	0
MAP2K6	-0.081	0.36	-10000	0	-0.82	52	52
regulation of dendritic cell antigen processing and presentation	0	0	-10000	0	-10000	0	0
HLA-DRA	-0.033	0.12	-10000	0	-0.34	47	47
IL18RAP	-0.037	0.2	-10000	0	-0.86	22	22
IL12Rbeta1/TYK2	-0.006	0.093	-10000	0	-0.67	3	3
EOMES	-0.14	0.41	-10000	0	-1.5	30	30
STAT1 (dimer)	-0.13	0.36	-10000	0	-0.78	67	67
T cell proliferation	-0.054	0.27	-10000	0	-0.61	43	43
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
IL18R1	-0.028	0.14	-10000	0	-0.4	39	39
CD8-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.15	0.24	-10000	0	-0.67	51	51
ATF2	-0.068	0.33	-10000	0	-0.75	50	50

×

amb2 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2	-0.043	0.12	-9999	-0.51	14	14
alphaM/beta2 Integrin/GPIbA	-0.053	0.14	-9999	-0.55	20	20
alphaM/beta2 Integrin/proMMP-9	-0.096	0.2	-9999	-0.6	42	42
PLAUR	-0.086	0.14	-9999	-0.3	121	121
HMGB1	0.001	0.024	-9999	-10000	0	0
alphaM/beta2 Integrin/Talin	-0.036	0.1	-9999	-0.68	4	4
AGER	-0.078	0.25	-9999	-0.88	33	33
RAP1A	0.013	0	-9999	-10000	0	0
SELPLG	-0.008	0.077	-9999	-0.3	25	25
mol:LDL	0	0	-9999	-10000	0	0
alphaM/beta2 Integrin/RAGE/HMGB1	-0.13	0.21	-9999	-0.66	37	37
mol:GTP	0	0	-9999	-10000	0	0
MMP9	-0.086	0.24	-9999	-0.54	68	68
CYR61	-0.26	0.4	-9999	-0.86	119	119
TLN1	0.013	0	-9999	-10000	0	0
Rap1/GTP	-0.073	0.094	-9999	-0.46	6	6
RHOA	0.013	0	-9999	-10000	0	0
P-selectin oligomer	-0.006	0.12	-9999	-0.65	11	11
MYH2	-0.1	0.12	-9999	-0.41	32	32
MST1R	-0.005	0.11	-9999	-0.86	6	6
leukocyte activation during inflammatory response	-0.04	0.093	-9999	-0.59	4	4
APOB	-0.007	0.069	-9999	-0.3	20	20
mol:GDP	0	0	-9999	-10000	0	0
complement component iC3b receptor activity	0	0	-9999	-10000	0	0
MMP2	0.001	0.093	-9999	-0.62	7	7
JAM3	0.013	0	-9999	-10000	0	0
GP1BA	-0.015	0.14	-9999	-0.59	17	17
alphaM/beta2 Integrin/CTGF	-0.12	0.23	-9999	-0.62	61	61
alphaM/beta2 Integrin	-0.097	0.11	-9999	-0.37	34	34
JAM3 homodimer	0.013	0	-9999	-10000	0	0
ICAM2	0.013	0	-9999	-10000	0	0
ICAM1	-0.094	0.15	-9999	-0.3	131	131
phagocytosis triggered by activation of immune response cell surface activating receptor	-0.096	0.11	-9999	-0.36	34	34
cell adhesion	-0.053	0.14	-9999	-0.55	20	20
NFKB1	-0.15	0.31	-9999	-0.86	39	39
THY1	0.01	0.028	-9999	-0.3	3	3
RhoA/GDP	0	0	-9999	-10000	0	0
Lipoprotein(a)	-0.012	0.046	-9999	-0.32	2	2
alphaM/beta2 Integrin/LRP/tPA	-0.036	0.1	-9999	-0.56	8	8
IL6	-0.27	0.48	-9999	-1.1	86	86
ITGB2	-0.024	0.093	-9999	-0.32	28	28
elevation of cytosolic calcium ion concentration	-0.13	0.16	-9999	-0.52	31	31
alphaM/beta2 Integrin/JAM2/JAM3	-0.035	0.11	-9999	-0.68	6	6
JAM2	0.003	0.09	-9999	-0.86	4	4
alphaM/beta2 Integrin/ICAM1	-0.076	0.14	-9999	-0.54	16	16
alphaM/beta2 Integrin/uPA/Plg	-0.092	0.12	-9999	-0.5	17	17
RhoA/GTP	-0.11	0.13	-9999	-0.43	34	34
positive regulation of phagocytosis	-0.072	0.12	-9999	-0.48	11	11
Ron/MSP	-0.015	0.092	-9999	-0.66	7	7
alphaM/beta2 Integrin/uPAR/uPA	-0.13	0.16	-9999	-0.52	31	31
alphaM/beta2 Integrin/uPAR	-0.084	0.13	-9999	-0.53	18	18
PLAU	-0.12	0.15	-9999	-0.3	167	167
PLAT	0.003	0.075	-9999	-0.42	9	9
actin filament polymerization	-0.1	0.12	-9999	-0.4	32	32
MST1	0.01	0.047	-9999	-0.58	2	2
alphaM/beta2 Integrin/lipoprotein(a)	-0.04	0.094	-9999	-0.6	4	4
TNF	-0.2	0.4	-9999	-1	59	59
RAP1B	0.013	0	-9999	-10000	0	0
alphaM/beta2 Integrin/uPA	-0.1	0.13	-9999	-0.53	18	18
fibrinolysis	-0.091	0.12	-9999	-0.49	17	17
HCK	-0.007	0.076	-9999	-0.3	24	24
dendritic cell antigen processing and presentation	-0.096	0.11	-9999	-0.36	34	34
VTN	-0.085	0.27	-9999	-0.8	46	46
alphaM/beta2 Integrin/CYR61	-0.22	0.29	-9999	-0.63	120	120
LPA	-0.003	0.046	-9999	-0.3	9	9
LRP1	0.011	0.045	-9999	-0.86	1	1
cell migration	-0.09	0.2	-9999	-0.6	40	40
FN1	-0.21	0.14	-9999	-0.3	273	273
alphaM/beta2 Integrin/Thy1	-0.037	0.1	-9999	-0.48	10	10
MPO	0.001	0.091	-9999	-0.67	6	6
KNG1	-0.01	0.068	-9999	-10000	0	0
RAP1/GDP	0	0	-9999	-10000	0	0
ROCK1	-0.096	0.12	-9999	-0.45	19	19
ELA2	0	0	-9999	-10000	0	0
PLG	0	0.022	-9999	-10000	0	0
CTGF	-0.12	0.31	-9999	-0.86	57	57
alphaM/beta2 Integrin/Hck	-0.046	0.12	-9999	-0.52	16	16
ITGAM	-0.024	0.1	-9999	-0.35	26	26
alphaM/beta2 Integrin/P-Selectin/PSGL1	-0.05	0.13	-9999	-0.53	20	20
HP	-0.071	0.16	-9999	-0.33	93	93
leukocyte adhesion	-0.1	0.17	-9999	-0.63	22	22
SELP	-0.006	0.12	-9999	-0.65	11	11

×

Syndecan-4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.075	0.058	-9999	-10000	0	0
Syndecan-4/Syndesmos	-0.12	0.17	-9999	-0.66	29	29
positive regulation of JNK cascade	-0.17	0.2	-9999	-0.6	55	55
Syndecan-4/ADAM12	-0.16	0.18	-9999	-0.66	29	29
CCL5	-0.043	0.21	-9999	-0.72	29	29
Rac1/GDP	0	0	-9999	-10000	0	0
DNM2	0.013	0	-9999	-10000	0	0
ITGA5	0.013	0	-9999	-10000	0	0
SDCBP	0.013	0	-9999	-10000	0	0
PLG	0.002	0.025	-9999	-0.3	1	1
ADAM12	-0.067	0.14	-9999	-0.3	97	97
mol:GTP	0	0	-9999	-10000	0	0
NUDT16L1	0.013	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
Syndecan-4/PKC alpha	-0.063	0.045	-9999	-0.23	2	2
Syndecan-4/Laminin alpha1	-0.16	0.21	-9999	-0.7	36	36
Syndecan-4/CXCL12/CXCR4	-0.17	0.22	-9999	-0.64	54	54
Syndecan-4/Laminin alpha3	-0.14	0.19	-9999	-0.66	35	35
MDK	-0.079	0.14	-9999	-0.3	112	112
Syndecan-4/FZD7	-0.13	0.18	-9999	-0.65	31	31
Syndecan-4/Midkine	-0.16	0.18	-9999	-0.66	29	29
FZD7	0.004	0.089	-9999	-0.86	4	4
Syndecan-4/FGFR1/FGF	-0.12	0.16	-9999	-0.61	30	30
THBS1	-0.011	0.083	-9999	-0.3	29	29
integrin-mediated signaling pathway	-0.17	0.18	-9999	-0.67	29	29
positive regulation of MAPKKK cascade	-0.17	0.2	-9999	-0.6	55	55
Syndecan-4/TACI	-0.24	0.26	-9999	-0.63	100	100
CXCR4	0.01	0.032	-9999	-0.3	4	4
cell adhesion	-0.073	0.1	-9999	-0.46	22	22
Syndecan-4/Dynamin	-0.12	0.17	-9999	-0.66	29	29
Syndecan-4/TSP1	-0.13	0.18	-9999	-0.66	29	29
Syndecan-4/GIPC	-0.12	0.17	-9999	-0.66	29	29
Syndecan-4/RANTES	-0.15	0.22	-9999	-0.78	34	34
ITGB1	0.013	0	-9999	-10000	0	0
LAMA1	-0.052	0.23	-9999	-0.84	29	29
LAMA3	-0.023	0.16	-9999	-0.6	22	22
RAC1	0.013	0	-9999	-10000	0	0
PRKCA	0.001	0.2	-9999	-0.78	22	22
Syndecan-4/alpha-Actinin	-0.12	0.17	-9999	-0.66	29	29
TFPI	-0.04	0.21	-9999	-0.86	23	23
F2	-0.001	0.033	-9999	-0.31	4	4
alpha5/beta1 Integrin	0	0	-9999	-10000	0	0
positive regulation of cell adhesion	-0.16	0.21	-9999	-0.68	39	39
ACTN1	0.012	0.016	-9999	-10000	0	0
TNC	-0.12	0.16	-9999	-0.86	3	3
Syndecan-4/CXCL12	-0.18	0.23	-9999	-0.67	55	55
FGF6	0	0.001	-9999	-10000	0	0
RHOA	0.013	0	-9999	-10000	0	0
CXCL12	-0.086	0.28	-9999	-0.86	43	43
TNFRSF13B	-0.19	0.36	-9999	-0.82	91	91
FGF2	0.013	0	-9999	-10000	0	0
FGFR1	0.011	0.045	-9999	-0.86	1	1
Syndecan-4/PI-4-5-P2	-0.13	0.17	-9999	-0.67	29	29
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.21	0.14	-9999	-0.3	245	245
cell migration	-0.021	0.017	-9999	-10000	0	0
PRKCD	0.008	0.015	-9999	-10000	0	0
vasculogenesis	-0.13	0.17	-9999	-0.63	29	29
SDC4	-0.14	0.18	-9999	-0.71	29	29
Syndecan-4/Tenascin C	-0.18	0.19	-9999	-0.71	29	29
Syndecan-4/PI-4-5-P2/PKC alpha	-0.05	0.035	-9999	-10000	0	0
Syndecan-4/Syntenin	-0.12	0.17	-9999	-0.66	29	29
MMP9	-0.087	0.24	-9999	-0.54	67	67
Rac1/GTP	-0.075	0.11	-9999	-0.47	22	22
cytoskeleton organization	-0.12	0.17	-9999	-0.63	29	29
GIPC1	0.013	0	-9999	-10000	0	0
Syndecan-4/TFPI	-0.15	0.21	-9999	-0.66	45	45

×

IL6-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-0.05	0.2	-9999	-0.62	20	20
CRP	-0.055	0.2	-9999	-0.69	12	12
cell cycle arrest	-0.069	0.23	-9999	-0.73	21	21
TIMP1	-0.14	0.2	-9999	-0.59	25	25
IL6ST	-0.078	0.26	-9999	-0.86	39	39
Rac1/GDP	-0.082	0.24	-9999	-0.59	44	44
AP1	-0.21	0.34	-9999	-0.7	111	111
GAB2	0.013	0.001	-9999	-10000	0	0
TNFSF11	-0.092	0.21	-9999	-0.65	19	19
HSP90B1	0.023	0.041	-9999	-10000	0	0
GAB1	0.013	0	-9999	-10000	0	0
MAPK14	-0.098	0.3	-9999	-0.82	43	43
AKT1	0.055	0.022	-9999	-10000	0	0
FOXO1	0.061	0.021	-9999	-10000	0	0
MAP2K6	-0.099	0.28	-9999	-0.72	46	46
mol:GTP	0	0.001	-9999	-10000	0	0
MAP2K4	-0.072	0.22	-9999	-0.7	23	23
MITF	-0.085	0.25	-9999	-0.62	43	43
positive regulation of NF-kappaB transcription factor activity	0	0	-9999	-10000	0	0
TYK2	0.013	0	-9999	-10000	0	0
A2M	0.024	0.006	-9999	-10000	0	0
CEBPB	0.021	0.002	-9999	-10000	0	0
GRB2/SOS1/GAB family/SHP2	-0.025	0.078	-9999	-10000	0	0
STAT3	-0.081	0.24	-9999	-0.79	21	21
STAT1	-0.011	0.021	-9999	-10000	0	0
CEBPD	-0.051	0.2	-9999	-0.63	18	18
PIK3CA	0.012	0.045	-9999	-0.86	1	1
PI3K	-0.002	0.034	-9999	-0.66	1	1
JUN	-0.19	0.37	-9999	-0.86	88	88
PIAS3/MITF	-0.074	0.24	-9999	-0.59	41	41
MAPK11	-0.098	0.3	-9999	-0.82	43	43
STAT3 (dimer)/FOXO1	-0.001	0.19	-9999	-0.6	11	11
GRB2/SOS1/GAB family	-0.11	0.19	-9999	-0.7	19	19
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK	-0.12	0.25	-9999	-0.49	79	79
GRB2	0.013	0	-9999	-10000	0	0
JAK2	0.013	0	-9999	-10000	0	0
LBP	-0.06	0.19	-9999	-0.6	11	11
PIK3R1	0.014	0	-9999	-10000	0	0
JAK1	0.013	0.005	-9999	-10000	0	0
MYC	-0.062	0.25	-9999	-0.85	19	19
FGG	-0.058	0.2	-9999	-0.63	20	20
macrophage differentiation	-0.069	0.23	-9999	-0.73	21	21
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4	-0.18	0.28	-9999	-0.57	116	116
JUNB	-0.058	0.23	-9999	-0.78	18	18
FOS	-0.22	0.39	-9999	-0.86	103	103
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4	-0.095	0.27	-9999	-0.56	64	64
STAT1/PIAS1	-0.076	0.23	-9999	-0.53	46	46
GRB2/SOS1/GAB family/SHP2/PI3K	0.036	0.028	-9999	-0.32	1	1
STAT3 (dimer)	-0.078	0.23	-9999	-0.76	21	21
PRKCD	-0.06	0.22	-9999	-0.68	20	20
IL6R	-0.01	0.14	-9999	-0.86	10	10
SOCS3	-0.12	0.4	-9999	-1.1	42	42
gp130 (dimer)/JAK1/JAK1/LMO4	-0.043	0.18	-9999	-0.57	39	39
Rac1/GTP	-0.1	0.23	-9999	-0.59	43	43
HCK	-0.007	0.076	-9999	-0.3	24	24
MAPKKK cascade	0.012	0.06	-9999	-10000	0	0
bone resorption	-0.088	0.21	-9999	-0.61	20	20
IRF1	-0.05	0.2	-9999	-0.64	17	17
mol:GDP	-0.093	0.25	-9999	-0.62	46	46
SOS1	0.013	0.001	-9999	-10000	0	0
VAV1	-0.096	0.26	-9999	-0.63	46	46
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3	-0.11	0.3	-9999	-0.78	45	45
PTPN11	-0.008	0.018	-9999	-10000	0	0
IL6/IL6RA	-0.17	0.3	-9999	-0.68	91	91
gp130 (dimer)/TYK2/TYK2/LMO4	-0.048	0.18	-9999	-0.57	39	39
gp130 (dimer)/JAK2/JAK2/LMO4	-0.048	0.18	-9999	-0.57	39	39
IL6	-0.2	0.36	-9999	-0.86	84	84
PIAS3	0.013	0	-9999	-10000	0	0
PTPRE	-0.098	0.15	-9999	-0.31	55	55
PIAS1	0.013	0	-9999	-10000	0	0
RAC1	0.013	0.001	-9999	-10000	0	0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4	-0.094	0.25	-9999	-0.46	96	96
LMO4	0.011	0.01	-9999	-10000	0	0
STAT3 (dimer)/PIAS3	-0.094	0.22	-9999	-0.77	21	21
MCL1	0.06	0.02	-9999	-10000	0	0

×

Ras signaling in the CD4+ TCR pathway

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
ERK1-2/ELK1	-0.098	0.22	-9999	-0.41	112	112
MAP3K8	0.001	0.089	-9999	-0.86	4	4
FOS	-0.06	0.16	-9999	-0.5	22	22
PRKCA	-0.04	0.2	-9999	-0.86	22	22
PTPN7	-0.042	0.16	-9999	-0.41	48	48
HRAS	0.011	0.016	-9999	-0.3	1	1
PRKCB	-0.031	0.11	-9999	-0.31	48	48
NRAS	0.012	0.002	-9999	-10000	0	0
RAS family/GTP	0	0.007	-9999	-10000	0	0
MAPK3	-0.031	0.12	-9999	-0.58	9	9
MAP2K1	-0.03	0.15	-9999	-0.56	23	23
ELK1	0.007	0.011	-9999	-10000	0	0
BRAF	-0.049	0.13	-9999	-0.56	23	23
mol:GTP	-0.002	0.003	-9999	-0.006	103	103
MAPK1	-0.031	0.12	-9999	-0.44	16	16
RAF1	-0.049	0.13	-9999	-0.56	23	23
KRAS	0.012	0.002	-9999	-10000	0	0

×

Thromboxane A2 receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGM2	-0.036	0.11	-10000	0	-0.3	56	56
GNB1/GNG2	-0.046	0.067	-10000	0	-0.2	39	39
AKT1	-0.017	0.1	-10000	0	-0.21	32	32
EGF	-0.11	0.3	-10000	0	-0.86	51	51
mol:TXA2	0	0.001	-10000	0	-10000	0	0
FGR	0.006	0.068	-10000	0	-0.59	1	1
mol:Ca2+	-0.049	0.14	-10000	0	-0.31	57	57
LYN	0.007	0.067	-10000	0	-0.59	1	1
RhoA/GTP	-0.032	0.045	-10000	0	-0.13	17	17
mol:PGI2	0	0	-10000	0	-10000	0	0
SYK	-0.05	0.16	-10000	0	-0.35	55	55
GNG2	0.013	0	-10000	0	-10000	0	0
ARRB2	0.013	0	-10000	0	-10000	0	0
TP alpha/Gq family/GDP/G beta5/gamma2	-0.024	0.11	-10000	0	-0.54	4	4
G beta5/gamma2	-0.062	0.092	-10000	0	-0.27	39	39
PRKCH	-0.057	0.16	-10000	0	-0.37	54	54
DNM1	-0.029	0.18	-10000	0	-0.83	19	19
TXA2/TP beta/beta Arrestin3	-0.017	0.067	-10000	0	-0.31	18	18
mol:GTP	0	0.001	-10000	0	-10000	0	0
PTGDR	-0.022	0.17	-10000	0	-0.86	15	15
G12 family/GTP	-0.081	0.11	-10000	0	-0.31	55	55
ADRBK1	0.013	0	-10000	0	-10000	0	0
ADRBK2	0.013	0	-10000	0	-10000	0	0
RhoA/GTP/ROCK1	0	0	-10000	0	-10000	0	0
mol:GDP	0.021	0.1	0.37	10	-10000	0	10
mol:NADP	0.013	0	-10000	0	-10000	0	0
RAB11A	0.013	0	-10000	0	-10000	0	0
PRKG1	-0.21	0.38	-10000	0	-0.86	98	98
mol:IP3	-0.066	0.18	-10000	0	-0.39	57	57
cell morphogenesis	0	0	-10000	0	-10000	0	0
PLCB2	-0.095	0.23	-10000	0	-0.54	57	57
mol:cGMP	0	0.001	-10000	0	-10000	0	0
BLK	-0.12	0.2	-10000	0	-0.41	113	113
mol:PDG2	0	0	-10000	0	-10000	0	0
HCK	0	0.07	-10000	0	-0.59	1	1
RHOA	0.013	0	-10000	0	-10000	0	0
PTGIR	0.004	0.089	-10000	0	-0.86	4	4
PRKCB1	-0.066	0.17	-10000	0	-0.39	57	57
GNAQ	0.013	0	-10000	0	-10000	0	0
mol:L-citrulline	0.013	0	-10000	0	-10000	0	0
TXA2/TXA2-R family	-0.092	0.23	-10000	0	-0.54	58	58
LCK	-0.002	0.086	-10000	0	-0.53	5	5
TXA2/TP beta/beta Arrestin3/RAB11/GDP	-0.017	0.079	-10000	0	-0.84	1	1
TXA2-R family/G12 family/GDP/G beta/gamma	0.029	0.025	-10000	0	-10000	0	0
TXA2/TP beta/beta Arrestin2/RAB11/GDP	-0.017	0.077	-10000	0	-0.84	1	1
MAPK14	-0.024	0.11	-10000	0	-0.23	54	54
TGM2/GTP	-0.079	0.2	-10000	0	-0.44	59	59
MAPK11	-0.024	0.11	-10000	0	-0.23	54	54
ARHGEF1	-0.019	0.088	-10000	0	-0.18	32	32
GNAI2	0.013	0	-10000	0	-10000	0	0
JNK cascade	-0.063	0.18	-10000	0	-0.4	58	58
RAB11/GDP	0.013	0.001	-10000	0	-10000	0	0
ICAM1	-0.059	0.15	-10000	0	-0.3	62	62
cAMP biosynthetic process	-0.064	0.16	-10000	0	-0.37	55	55
Gq family/GTP/EBP50	-0.045	0.12	-10000	0	-0.33	15	15
actin cytoskeleton reorganization	0	0	-10000	0	-10000	0	0
SRC	0.007	0.067	-10000	0	-0.59	1	1
GNB5	0.013	0	-10000	0	-10000	0	0
GNB1	0.013	0	-10000	0	-10000	0	0
EGF/EGFR	-0.021	0.1	-10000	0	-0.39	3	3
VCAM1	-0.043	0.14	-10000	0	-0.3	58	58
TP beta/Gq family/GDP/G beta5/gamma2	-0.024	0.11	-10000	0	-0.54	4	4
platelet activation	-0.032	0.15	-10000	0	-0.31	55	55
PGI2/IP	-0.007	0.069	-10000	0	-0.67	4	4
PRKACA	-0.003	0.1	-10000	0	-0.43	18	18
Gq family/GDP/G beta5/gamma2	-0.026	0.11	-10000	0	-0.5	4	4
TXA2/TP beta/beta Arrestin2	-0.034	0.14	-10000	0	-0.68	18	18
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TBXA2R	0.009	0.097	-10000	0	-0.4	18	18
mol:DAG	-0.075	0.19	-10000	0	-0.44	57	57
EGFR	0.001	0.099	-10000	0	-0.86	5	5
TXA2/TP alpha	-0.089	0.22	-10000	0	-0.5	55	55
Gq family/GTP	-0.078	0.13	-10000	0	-0.31	94	94
YES1	0.007	0.067	-10000	0	-0.59	1	1
GNAI2/GTP	-0.015	0.07	-10000	0	-0.72	1	1
PGD2/DP	-0.027	0.13	-10000	0	-0.67	15	15
SLC9A3R1	0.011	0.023	-10000	0	-0.3	2	2
FYN	0.007	0.067	-10000	0	-0.59	1	1
mol:NO	0.013	0	-10000	0	-10000	0	0
GNA15	-0.017	0.099	-10000	0	-0.31	35	35
PGK/cGMP	-0.15	0.26	-10000	0	-0.58	98	98
RhoA/GDP	0.013	0.001	-10000	0	-10000	0	0
TP alpha/TGM2/GDP/G beta/gamma	-0.029	0.086	-10000	0	-0.56	4	4
NOS3	0.013	0	-10000	0	-10000	0	0
RAC1	0.013	0	-10000	0	-10000	0	0
PRKCA	-0.073	0.18	-10000	0	-0.39	70	70
PRKCB	-0.067	0.16	-10000	0	-0.37	60	60
PRKCE	-0.06	0.17	-10000	0	-0.38	56	56
PRKCD	-0.06	0.17	-10000	0	-0.39	56	56
PRKCG	-0.065	0.17	-10000	0	-0.4	56	56
muscle contraction	-0.081	0.21	-10000	0	-0.5	58	58
PRKCZ	-0.05	0.16	-10000	0	-0.35	55	55
ARR3	0.004	0.006	-10000	0	-10000	0	0
TXA2/TP beta	-0.017	0.079	-10000	0	-0.86	1	1
PRKCQ	-0.06	0.17	-10000	0	-0.37	60	60
MAPKKK cascade	-0.082	0.2	-10000	0	-0.47	58	58
SELE	-0.063	0.18	-10000	0	-0.43	56	56
TP beta/GNAI2/GDP/G beta/gamma	-0.016	0.076	-10000	0	-0.83	1	1
ROCK1	0.013	0	-10000	0	-10000	0	0
GNA14	-0.2	0.37	-10000	0	-0.86	91	91
chemotaxis	-0.1	0.26	-10000	0	-0.62	58	58
GNA12	0.013	0	-10000	0	-10000	0	0
GNA13	0.013	0	-10000	0	-10000	0	0
GNA11	0.006	0.077	-10000	0	-0.86	3	3
Rac1/GTP	0	0	-10000	0	-10000	0	0

×

Osteopontin-mediated events

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
IKK alpha homodimer	-0.032	0.16	-9999	-0.51	30	30
NF kappa B1 p50/RelA/I kappa B alpha	-0.052	0.12	-9999	-0.62	6	6
alphaV/beta3 Integrin/Osteopontin/Src	-0.064	0.15	-9999	-0.65	20	20
AP1	-0.27	0.37	-9999	-0.88	90	90
ILK	-0.035	0.16	-9999	-0.54	30	30
bone resorption	-0.054	0.14	-9999	-0.67	7	7
PTK2B	0.013	0	-9999	-10000	0	0
PYK2/p130Cas	-0.053	0.14	-9999	-0.49	30	30
ITGAV	0.011	0.045	-9999	-0.85	1	1
mol:GTP	0	0	-9999	-10000	0	0
CD44/Rho Family GTPase/ROCK2	-0.014	0.095	-9999	-0.66	8	8
alphaV/beta3 Integrin/Osteopontin	-0.07	0.17	-9999	-0.6	30	30
MAP3K1	-0.032	0.17	-9999	-0.55	30	30
JUN	-0.19	0.37	-9999	-0.86	88	88
MAPK3	-0.031	0.16	-9999	-0.51	30	30
MAPK1	-0.031	0.16	-9999	-0.51	30	30
Rac1/GDP	0	0	-9999	-10000	0	0
NFKB1	0.013	0	-9999	-10000	0	0
MAPK8	-0.023	0.16	-9999	-0.52	31	31
ITGB3	-0.014	0.15	-9999	-0.85	12	12
NFKBIA	-0.024	0.16	-9999	-0.49	30	30
FOS	-0.22	0.39	-9999	-0.86	103	103
CD44	0.013	0	-9999	-10000	0	0
CHUK	0.013	0	-9999	-10000	0	0
PLAU	-0.097	0.18	-9999	-0.72	5	5
NF kappa B1 p50/RelA	-0.057	0.12	-9999	-0.6	6	6
BCAR1	0.013	0	-9999	-10000	0	0
RELA	0.013	0	-9999	-10000	0	0
alphaV beta3 Integrin	-0.022	0.12	-9999	-0.7	12	12
mol:GDP	0	0	-9999	-10000	0	0
SYK	-0.032	0.17	-9999	-0.55	30	30
VAV3	-0.026	0.17	-9999	-0.52	33	33
MAP3K14	-0.039	0.17	-9999	-0.55	30	30
ROCK2	-0.005	0.12	-9999	-0.86	8	8
SPP1	-0.078	0.21	-9999	-0.43	78	78
RAC1	0.013	0	-9999	-10000	0	0
Rac1/GTP	-0.054	0.14	-9999	-0.47	33	33
MMP2	-0.18	0.3	-9999	-0.68	80	80

×

EGFR-dependent Endothelin signaling events

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HRAS	0.012	0.016	-9999	-0.3	1	1
EGFR	0.001	0.099	-9999	-0.86	5	5
EGF/EGFR	-0.081	0.18	-9999	-0.48	62	62
EGF/EGFR dimer/SHC/GRB2/SOS1	-0.074	0.17	-9999	-0.49	56	56
mol:GTP	0	0	-9999	-10000	0	0
EDNRA	0.007	0.055	-9999	-0.86	1	1
response to oxidative stress	0	0	-9999	-10000	0	0
EGF	-0.11	0.3	-9999	-0.86	51	51
EGF/EGFR dimer/SHC	-0.087	0.2	-9999	-0.57	56	56
mol:GDP	-0.073	0.17	-9999	-0.48	56	56
mol:Ca2+	0	0	-9999	-10000	0	0
EDN1	0.001	0.1	-9999	-0.76	6	6
GRB2/SOS1	0	0	-9999	-10000	0	0
HRAS/GTP	-0.067	0.16	-9999	-0.45	56	56
SHC1	0.013	0	-9999	-10000	0	0
HRAS/GDP	-0.069	0.16	-9999	-0.46	56	56
FRAP1	-0.037	0.18	-9999	-0.47	56	56
EGF/EGFR dimer	-0.1	0.24	-9999	-0.66	56	56
SOS1	0.013	0	-9999	-10000	0	0
GRB2	0.013	0	-9999	-10000	0	0
ETA receptor/Endothelin-1	-0.013	0.085	-9999	-0.66	6	6

×

FAS signaling pathway (CD95)

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPTAN1	0.021	0.072	0.3	22	-10000	0	22
RFC1	0.021	0.072	0.3	22	-10000	0	22
PRKDC	0.021	0.072	0.3	22	-10000	0	22
RIPK1	0.014	0.005	-10000	0	-10000	0	0
CASP7	-0.014	0.047	-10000	0	-10000	0	0
FASLG/FAS/FADD/FAF1	-0.031	0.1	0.26	1	-0.39	25	26
MAP2K4	-0.032	0.16	-10000	0	-0.54	14	14
mol:ceramide	-0.028	0.15	-10000	0	-0.51	25	25
GSN	0.021	0.072	0.3	22	-10000	0	22
FASLG/FAS/FADD/FAF1/Caspase 8	-0.024	0.13	-10000	0	-0.49	25	25
FAS	0.01	0.006	-10000	0	-10000	0	0
BID	-0.033	0.08	0.32	3	-10000	0	3
MAP3K1	-0.002	0.099	-10000	0	-0.29	14	14
MAP3K7	0.01	0.006	-10000	0	-10000	0	0
RB1	0.021	0.072	0.3	22	-10000	0	22
CFLAR	0.014	0.005	-10000	0	-10000	0	0
HGF/MET	-0.14	0.21	-10000	0	-0.63	52	52
ARHGDIB	0.017	0.075	0.3	21	-10000	0	21
FADD	0.01	0.006	-10000	0	-10000	0	0
actin filament polymerization	-0.021	0.072	-10000	0	-0.3	22	22
NFKB1	-0.056	0.091	-10000	0	-0.29	14	14
MAPK8	-0.064	0.22	-10000	0	-0.46	80	80
DFFA	0.021	0.072	0.3	22	-10000	0	22
DNA fragmentation during apoptosis	0.021	0.072	0.3	22	-10000	0	22
FAS/FADD/MET	-0.061	0.073	-10000	0	-10000	0	0
CFLAR/RIP1	0	0	-10000	0	-10000	0	0
FAIM3	-0.005	0.097	-10000	0	-0.39	18	18
FAF1	0.01	0.007	-10000	0	-10000	0	0
PARP1	0.021	0.072	0.3	22	-10000	0	22
DFFB	0.021	0.072	0.3	22	-10000	0	22
CHUK	-0.048	0.08	-10000	0	-10000	0	0
FASLG	-0.062	0.22	-10000	0	-0.63	43	43
FAS/FADD	0	0.001	-10000	0	-10000	0	0
HGF	-0.1	0.3	-10000	0	-0.86	51	51
LMNA	0.019	0.065	0.27	22	-10000	0	22
CASP6	0.021	0.072	0.3	22	-10000	0	22
CASP10	0.01	0.006	-10000	0	-10000	0	0
CASP3	0.025	0.087	0.35	25	-10000	0	25
PTPN13	0.011	0.045	-10000	0	-0.86	1	1
CASP8	0.009	0.049	0.46	3	-10000	0	3
IL6	-0.29	0.59	-10000	0	-1.4	84	84
MET	-0.11	0.15	-10000	0	-0.3	154	154
ICAD/CAD	0.02	0.067	0.28	22	-10000	0	22
FASLG/FAS/FADD/FAF1/Caspase 10	-0.029	0.15	-10000	0	-0.52	25	25
activation of caspase activity by cytochrome c	-0.033	0.08	0.32	3	-10000	0	3
PAK2	0.021	0.072	0.3	22	-10000	0	22
BCL2	-0.037	0.2	-10000	0	-0.86	22	22

×

IL27-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.009	0.042	-10000	0	-10000	0	0
CD4-positive alpha-beta T cell lineage commitment	0	0.001	-10000	0	-10000	0	0
cytokine production during immune response	0.049	0.13	0.41	25	-10000	0	25
IL27/IL27R/JAK1	-0.098	0.18	-10000	0	-0.61	26	26
TBX21	-0.074	0.21	-10000	0	-0.65	26	26
IL12B	-0.002	0.075	-10000	0	-0.42	9	9
IL12A	-0.057	0.2	-10000	0	-0.67	36	36
IL6ST	-0.078	0.27	-10000	0	-0.86	39	39
IL27RA/JAK1	0.014	0.025	-10000	0	-10000	0	0
IL27	0.001	0.036	-10000	0	-0.3	5	5
TYK2	0.012	0.006	-10000	0	-10000	0	0
T-helper cell lineage commitment	-0.074	0.16	-10000	0	-10000	0	0
T-helper 2 cell differentiation	0.049	0.13	0.41	25	-10000	0	25
T cell proliferation during immune response	0.049	0.13	0.41	25	-10000	0	25
MAPKKK cascade	-0.049	0.13	-10000	0	-0.41	25	25
STAT3	0.013	0	-10000	0	-10000	0	0
STAT2	0.013	0	-10000	0	-10000	0	0
STAT1	0.005	0.05	-10000	0	-0.3	10	10
IL12RB1	-0.025	0.12	-10000	0	-0.86	3	3
positive regulation of tyrosine phosphorylation of STAT protein	0	0	-10000	0	-10000	0	0
IL12RB2	-0.07	0.2	-10000	0	-0.63	20	20
IL27/IL27R/JAK2/TYK2	-0.05	0.14	-10000	0	-0.42	25	25
positive regulation of T cell mediated cytotoxicity	-0.049	0.13	-10000	0	-0.41	25	25
STAT1 (dimer)	-0.091	0.23	0.52	14	-0.81	10	24
JAK2	0.014	0.007	-10000	0	-10000	0	0
JAK1	0.013	0.002	-10000	0	-10000	0	0
STAT2 (dimer)	-0.039	0.13	-10000	0	-0.52	6	6
T cell proliferation	-0.16	0.24	-10000	0	-0.54	89	89
IL12/IL12R/TYK2/JAK2	-0.049	0.15	-10000	0	-0.68	8	8
IL17A	-0.075	0.16	-10000	0	-10000	0	0
mast cell activation	0.049	0.13	0.41	25	-10000	0	25
IFNG	-0.017	0.047	-10000	0	-0.13	48	48
T cell differentiation	-0.005	0.008	-10000	0	-0.022	46	46
STAT3 (dimer)	-0.039	0.13	-10000	0	-0.52	6	6
STAT5A (dimer)	-0.039	0.13	-10000	0	-0.52	6	6
STAT4 (dimer)	-0.064	0.15	-10000	0	-0.51	20	20
STAT4	-0.034	0.16	-10000	0	-0.44	39	39
T cell activation	-0.011	0.005	-10000	0	-10000	0	0
IL27R/JAK2/TYK2	-0.044	0.16	-10000	0	-0.53	27	27
GATA3	-0.058	0.36	-10000	0	-1.5	22	22
IL18	-0.022	0.11	-10000	0	-0.28	44	44
positive regulation of mast cell cytokine production	-0.039	0.13	-10000	0	-0.51	6	6
IL27/EBI3	-0.093	0.11	-10000	0	-0.42	6	6
IL27RA	0.006	0.026	-10000	0	-10000	0	0
IL6	-0.2	0.36	-10000	0	-0.86	84	84
STAT5A	0.013	0	-10000	0	-10000	0	0
monocyte differentiation	-0.001	0.003	-10000	0	-10000	0	0
IL2	0.001	0.013	-10000	0	-10000	0	0
IL1B	-0.039	0.17	-10000	0	-0.58	32	32
EBI3	-0.14	0.16	-10000	0	-0.3	182	182
TNF	-0.069	0.22	-10000	0	-0.62	48	48

×

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

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
MET/RANBP9	-0.077	0.093	-10000	0	-10000	0	0
CRKL	-0.029	0.11	-10000	0	-0.33	22	22
mol:PIP3	-0.018	0.038	0.71	1	-10000	0	1
AKT1	0.001	0.038	0.46	1	-0.56	1	2
PTK2B	0.013	0	-10000	0	-10000	0	0
RAPGEF1	-0.02	0.1	-10000	0	-10000	0	0
RANBP10	0.013	0	-10000	0	-10000	0	0
PIK3CA	0.011	0.045	-10000	0	-0.86	1	1
HGF/MET/SHIP2	-0.14	0.21	-10000	0	-0.64	51	51
MAP3K5	-0.019	0.11	-10000	0	-0.49	5	5
HGF/MET/CIN85/CBL/ENDOPHILINS	-0.12	0.19	-10000	0	-0.58	51	51
AP1	-0.3	0.45	-10000	0	-0.92	120	120
mol:SU11274	0	0	-10000	0	-10000	0	0
SHC1	0.013	0	-10000	0	-10000	0	0
apoptosis	-0.27	0.4	-10000	0	-0.85	120	120
STAT3 (dimer)	-0.037	0.13	-10000	0	-0.39	22	22
GAB1/CRKL/SHP2/PI3K	-0.038	0.086	-10000	0	-0.4	1	1
INPP5D	-0.01	0.081	-10000	0	-0.3	28	28
CBL/CRK	-0.02	0.1	-10000	0	-10000	0	0
PTPN11	0.013	0	-10000	0	-10000	0	0
GO:0007205	0	0	-10000	0	-10000	0	0
PLCG1	0.013	0	-10000	0	-10000	0	0
PTEN	0.011	0.045	-10000	0	-0.86	1	1
ELK1	-0.051	0.061	-10000	0	-10000	0	0
mol:SU5416	0	0	-10000	0	-10000	0	0
SHP2/GRB2/SOS1GAB1	-0.037	0.071	-10000	0	-0.25	22	22
PAK1	0.01	0.035	0.43	1	-0.52	1	2
HGF/MET/RANBP10	-0.14	0.21	-10000	0	-0.64	51	51
HRAS	-0.055	0.16	-10000	0	-0.44	51	51
DOCK1	-0.021	0.11	-10000	0	-0.45	1	1
GAB1	-0.039	0.12	-10000	0	-0.31	51	51
CRK	-0.029	0.11	-10000	0	-0.33	22	22
mol:PHA665752	0	0	-10000	0	-10000	0	0
mol:GDP	-0.1	0.21	-10000	0	-0.62	51	51
JUN	-0.19	0.37	-10000	0	-0.86	88	88
EntrezGene:200958	0	0	-10000	0	-10000	0	0
HGF/MET	-0.069	0.1	-10000	0	-0.3	51	51
PIK3R1	0.013	0	-10000	0	-10000	0	0
cell morphogenesis	-0.007	0.13	-10000	0	-10000	0	0
GRB2/SHC	-0.053	0.085	-10000	0	-0.3	22	22
FOS	-0.22	0.39	-10000	0	-0.86	103	103
GLMN	0	0	-10000	0	-10000	0	0
cell motility	-0.051	0.061	-10000	0	-10000	0	0
HGF/MET/MUC20	-0.14	0.21	-10000	0	-0.64	51	51
cell migration	-0.052	0.084	-10000	0	-0.3	22	22
GRB2	0.013	0	-10000	0	-10000	0	0
CBL	0.013	0	-10000	0	-10000	0	0
MET/RANBP10	-0.077	0.093	-10000	0	-10000	0	0
HGF/MET/Paxillin/FAK1/FAK12/RasGAP	-0.049	0.14	-10000	0	-0.38	51	51
MET/MUC20	-0.082	0.099	-10000	0	-0.2	154	154
RAP1B	-0.011	0.1	-10000	0	-10000	0	0
RAP1A	-0.011	0.1	-10000	0	-10000	0	0
HGF/MET/RANBP9	-0.14	0.21	-10000	0	-0.64	51	51
RAF1	-0.044	0.15	-10000	0	-0.46	22	22
STAT3	-0.038	0.13	-10000	0	-0.4	22	22
cell proliferation	-0.044	0.17	-10000	0	-0.47	51	51
RPS6KB1	-0.015	0.039	-10000	0	-10000	0	0
MAPK3	-0.051	0.055	-10000	0	-10000	0	0
MAPK1	-0.051	0.055	-10000	0	-10000	0	0
RANBP9	0.013	0	-10000	0	-10000	0	0
MAPK8	0.001	0.11	-10000	0	-0.48	6	6
SRC	-0.038	0.13	-10000	0	-0.39	22	22
PI3K	-0.054	0.088	-10000	0	-0.48	1	1
MET/Glomulin	-0.062	0.09	-10000	0	-10000	0	0
SOS1	0.013	0	-10000	0	-10000	0	0
MAP2K1	-0.033	0.14	-10000	0	-0.42	22	22
MET	-0.11	0.15	-10000	0	-0.3	154	154
MAP4K1	-0.027	0.12	-10000	0	-0.55	4	4
PTK2	0.013	0	-10000	0	-10000	0	0
MAP2K2	-0.033	0.14	-10000	0	-0.42	22	22
BAD	0.01	0.035	0.43	1	-0.52	1	2
MAP2K4	-0.009	0.1	-10000	0	-0.44	5	5
SHP2/GRB2/SOS1/GAB1	-0.054	0.09	-10000	0	-10000	0	0
INPPL1	0.013	0	-10000	0	-10000	0	0
PXN	0.013	0	-10000	0	-10000	0	0
SH3KBP1	0.013	0	-10000	0	-10000	0	0
HGS	-0.047	0.1	-10000	0	-0.32	22	22
PLCgamma1/PKC	0	0	-10000	0	-10000	0	0
HGF	-0.1	0.3	-10000	0	-0.86	51	51
RASA1	0.013	0	-10000	0	-10000	0	0
NCK1	0.013	0	-10000	0	-10000	0	0
PTPRJ	0.013	0	-10000	0	-10000	0	0
NCK/PLCgamma1	-0.056	0.095	-10000	0	-0.33	22	22
PDPK1	-0.008	0.041	0.53	1	-0.6	1	2
HGF/MET/SHIP	-0.15	0.21	-10000	0	-0.64	51	51

×

Visual signal transduction: Rods

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:K +	0.013	0	-9999	-10000	0	0
GNAT1/GTP	-0.001	0.01	-9999	-10000	0	0
Metarhodopsin II/Arrestin	0	0.009	-9999	-10000	0	0
PDE6G/GNAT1/GTP	-0.016	0.065	-9999	-0.58	3	3
mol:GTP	0	0	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
GNAT1	0.004	0.017	-9999	-0.3	1	1
GRK1	-0.071	0.26	-9999	-0.86	36	36
CNG Channel	-0.028	0.09	-9999	-0.56	7	7
mol:Na +	-0.026	0.093	-9999	-0.48	13	13
mol:ADP	-0.07	0.25	-9999	-0.85	36	36
RGS9-1/Gbeta5/R9AP	-0.1	0.23	-9999	-0.59	66	66
mol:GDP	0	0	-9999	-10000	0	0
cGMP/CNG Channel	-0.026	0.096	-9999	-0.49	13	13
CNGB1	-0.002	0.064	-9999	-0.3	17	17
RDH5	-0.18	0.15	-9999	-0.3	238	238
SAG	0.003	0.005	-9999	-10000	0	0
mol:Ca2+	0.013	0.099	-9999	-0.64	2	2
Na + (4 Units)	-0.023	0.086	-9999	-0.62	2	2
RGS9	-0.085	0.27	-9999	-0.83	44	44
GNB1/GNGT1	-0.003	0.022	-9999	-10000	0	0
GNAT1/GDP	-0.091	0.2	-9999	-0.52	66	66
GUCY2D	-0.01	0.12	-9999	-0.86	6	6
GNGT1	-0.004	0.034	-9999	-0.3	5	5
GUCY2F	0.001	0.003	-9999	-10000	0	0
GNB5	0.013	0	-9999	-10000	0	0
mol:GMP (4 units)	0.004	0.068	-9999	-0.5	3	3
mol:11-cis-retinal	-0.18	0.15	-9999	-0.3	238	238
mol:cGMP	-0.017	0.08	-9999	-0.51	9	9
GNB1	0.013	0	-9999	-10000	0	0
Rhodopsin	-0.12	0.094	-9999	-10000	0	0
SLC24A1	0.013	0	-9999	-10000	0	0
CNGA1	-0.002	0.1	-9999	-0.61	9	9
Metarhodopsin II	-0.052	0.16	-9999	-0.54	36	36
mol:Ca ++	0	0	-9999	-10000	0	0
GC1/GCAP Family	-0.018	0.085	-9999	-0.54	9	9
RGS9BP	-0.047	0.22	-9999	-0.86	26	26
Metarhodopsin II/Transducin	0.011	0.012	-9999	-10000	0	0
GCAP Family/Ca ++	-0.005	0.05	-9999	-0.55	3	3
PDE6A/B	-0.011	0.044	-9999	-10000	0	0
mol:Pi	-0.1	0.22	-9999	-0.59	66	66
mol:all-trans-retinal	0	0	-9999	-10000	0	0
Transducin	-0.002	0.017	-9999	-10000	0	0
PDE6B	0.013	0	-9999	-10000	0	0
PDE6A	-0.007	0.072	-9999	-10000	0	0
PDE6G	-0.015	0.11	-9999	-0.36	28	28
RHO	0.006	0.017	-9999	-0.3	1	1
PDE6	-0.1	0.2	-9999	-0.5	68	68
GUCA1A	0.004	0.028	-9999	-0.3	3	3
GC2/GCAP Family	-0.005	0.05	-9999	-0.55	3	3
GUCA1C	0	0	-9999	-10000	0	0
GUCA1B	0.006	0.077	-9999	-0.86	3	3

×

ErbB2/ErbB3 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
USP8	0.02	0.005	-9999	-10000	0	0
RAS family/GTP	-0.045	0.11	-9999	-0.58	3	3
NFATC4	-0.005	0.12	-9999	-0.59	2	2
ERBB2IP	0.013	0.003	-9999	-10000	0	0
HSP90 (dimer)	0.013	0	-9999	-10000	0	0
mammary gland morphogenesis	-0.051	0.14	-9999	-0.43	45	45
JUN	0.003	0.094	-9999	-0.28	6	6
HRAS	0.012	0.016	-9999	-0.3	1	1
DOCK7	-0.018	0.14	-9999	-0.4	45	45
ErbB2/ErbB3/neuregulin 1 beta/SHC	-0.062	0.17	-9999	-0.52	45	45
AKT1	0.012	0.003	-9999	-10000	0	0
BAD	0.021	0.003	-9999	-10000	0	0
MAPK10	-0.024	0.064	-9999	-0.29	1	1
mol:GTP	-0.001	0.002	-9999	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta	-0.032	0.16	-9999	-0.46	45	45
RAF1	-0.008	0.13	-9999	-0.56	3	3
ErbB2/ErbB3/neuregulin 2	-0.076	0.19	-9999	-0.55	52	52
STAT3	0	0.003	-9999	-10000	0	0
cell migration	0.022	0.081	-9999	-0.28	2	2
mol:PI-3-4-5-P3	0	0.002	-9999	-10000	0	0
cell proliferation	-0.14	0.34	-9999	-0.68	92	92
FOS	-0.12	0.29	-9999	-0.52	120	120
NRAS	0.012	0.001	-9999	-10000	0	0
mol:Ca2+	-0.051	0.14	-9999	-0.43	45	45
MAPK3	-0.09	0.26	-9999	-0.51	89	89
MAPK1	-0.09	0.26	-9999	-0.51	89	89
JAK2	-0.018	0.14	-9999	-0.4	45	45
NF2	-0.002	0.006	-9999	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1	-0.024	0.14	-9999	-0.39	45	45
NRG1	-0.075	0.26	-9999	-0.84	38	38
GRB2/SOS1	0	0	-9999	-10000	0	0
MAPK8	-0.011	0.13	-9999	-0.35	46	46
MAPK9	-0.024	0.064	-9999	-0.29	1	1
ERBB2	0	0	-9999	-10000	0	0
ERBB3	-0.013	0.13	-9999	-0.86	9	9
SHC1	0.012	0.003	-9999	-10000	0	0
RAC1	0.013	0	-9999	-10000	0	0
apoptosis	0.003	0.011	-9999	-10000	0	0
STAT3 (dimer)	0	0.003	-9999	-10000	0	0
RNF41	0.027	0.008	-9999	-10000	0	0
FRAP1	0.01	0.003	-9999	-10000	0	0
RAC1-CDC42/GTP	-0.034	0.092	-9999	-0.44	1	1
ErbB2/ErbB2/HSP90 (dimer)	0	0	-9999	-10000	0	0
CHRNA1	-0.061	0.21	-9999	-0.39	78	78
myelination	0.005	0.12	-9999	-0.53	2	2
PPP3CB	-0.016	0.13	-9999	-0.37	45	45
KRAS	0.012	0.001	-9999	-10000	0	0
RAC1-CDC42/GDP	-0.039	0.11	-9999	-0.92	1	1
NRG2	-0.088	0.28	-9999	-0.82	46	46
mol:GDP	-0.023	0.14	-9999	-0.39	45	45
SOS1	0.012	0.001	-9999	-10000	0	0
MAP2K2	-0.011	0.14	-9999	-0.43	18	18
SRC	0.012	0.016	-9999	-10000	0	0
mol:cAMP	-0.001	0.002	-9999	-10000	0	0
PTPN11	-0.018	0.14	-9999	-0.4	45	45
MAP2K1	-0.083	0.24	-9999	-0.62	24	24
heart morphogenesis	-0.051	0.14	-9999	-0.43	45	45
RAS family/GDP	-0.039	0.11	-9999	-0.68	2	2
GRB2	0.012	0.001	-9999	-10000	0	0
PRKACA	-0.003	0.009	-9999	-10000	0	0
CHRNE	0.011	0.032	-9999	-0.13	10	10
HSP90AA1	0.013	0	-9999	-10000	0	0
activation of caspase activity	-0.012	0.003	-9999	-10000	0	0
nervous system development	-0.051	0.14	-9999	-0.43	45	45
CDC42	0.013	0	-9999	-10000	0	0

×

Regulation of p38-alpha and p38-beta

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
RIP1/MEKK3	0	0	-9999	-10000	0	0
response to insulin stimulus	0	0	-9999	-10000	0	0
RIPK1	0.013	0	-9999	-10000	0	0
response to stress	0	0	-9999	-10000	0	0
MAP2K6	-0.002	0.11	-9999	-0.86	6	6
mol:GTP	0	0	-9999	-10000	0	0
MAP2K4	0.013	0	-9999	-10000	0	0
RAC1-CDC42/GTP/PAK family	-0.15	0.16	-9999	-0.29	218	218
response to UV	0	0	-9999	-10000	0	0
YES1	0.013	0	-9999	-10000	0	0
interleukin-1 receptor activity	0	0	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
MAP3K3	0.013	0	-9999	-10000	0	0
FYN	0.013	0	-9999	-10000	0	0
MAP3K12	0.013	0	-9999	-10000	0	0
FGR	0.01	0.032	-9999	-10000	0	0
p38 alpha/TAB1	-0.048	0.067	-9999	-0.3	2	2
PRKG1	-0.21	0.38	-9999	-0.86	98	98
DUSP8	0.001	0.086	-9999	-0.86	3	3
PGK/cGMP/p38 alpha	-0.16	0.21	-9999	-0.49	100	100
apoptosis	-0.047	0.065	-9999	-0.29	2	2
RAL/GTP	0	0	-9999	-10000	0	0
LYN	0.013	0	-9999	-10000	0	0
DUSP1	-0.13	0.32	-9999	-0.86	62	62
PAK1	0.013	0	-9999	-10000	0	0
SRC	0.012	0.016	-9999	-10000	0	0
RAC1/OSM/MEKK3/MKK3	0	0	-9999	-10000	0	0
TRAF6	0.011	0.045	-9999	-0.86	1	1
RAC1	0.013	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	0.013	0	-9999	-10000	0	0
RAC1-CDC42/GTP	0	0	-9999	-10000	0	0
MAPK11	-0.063	0.12	-9999	-0.38	6	6
BLK	-0.26	0.39	-9999	-0.86	113	113
HCK	-0.007	0.076	-9999	-0.3	24	24
MAP2K3	0.013	0	-9999	-10000	0	0
DUSP16	0.013	0	-9999	-10000	0	0
DUSP10	0.009	0.05	-9999	-0.48	3	3
TRAF6/MEKK3	-0.001	0.028	-9999	-0.54	1	1
MAP3K7IP1	0	0	-9999	-10000	0	0
MAPK14	-0.029	0.09	-9999	-0.32	2	2
positive regulation of innate immune response	-0.062	0.13	-9999	-0.41	5	5
LCK	-0.012	0.11	-9999	-0.4	23	23
p38alpha-beta/MKP7	-0.053	0.13	-9999	-0.46	2	2
p38alpha-beta/MKP5	-0.054	0.13	-9999	-0.54	3	3
PGK/cGMP	-0.17	0.29	-9999	-0.67	98	98
PAK2	0.013	0	-9999	-10000	0	0
p38alpha-beta/MKP1	-0.12	0.2	-9999	-0.5	56	56
CDC42	0.013	0	-9999	-10000	0	0
RALB	0.013	0	-9999	-10000	0	0
RALA	0.013	0	-9999	-10000	0	0
PAK3	-0.49	0.43	-9999	-0.86	218	218

×

Plasma membrane estrogen receptor 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
GNB1/GNG2	-0.033	0.12	-10000	0	-0.52	18	18
ER alpha/Gai/GDP/Gbeta gamma	0.008	0.14	-10000	0	-0.49	24	24
AKT1	-0.009	0.19	-10000	0	-0.86	18	18
PIK3CA	0.011	0.045	-10000	0	-0.86	1	1
E2/ER alpha (dimer)/PELP1/Src/PI3K	-0.011	0.19	-10000	0	-0.87	18	18
mol:Ca2+	-0.1	0.23	-10000	0	-0.5	92	92
IGF1R	0.013	0	-10000	0	-10000	0	0
E2/ER alpha (dimer)/Striatin	-0.057	0.17	-10000	0	-0.61	29	29
SHC1	0.013	0	-10000	0	-10000	0	0
apoptosis	0.007	0.18	0.81	18	-10000	0	18
RhoA/GTP	-0.026	0.091	-10000	0	-0.44	17	17
E2/ER alpha (dimer)/PELP1/Src/p130 Cas	-0.034	0.13	-10000	0	-0.6	17	17
regulation of stress fiber formation	-0.021	0.1	0.44	1	-10000	0	1
E2/ERA-ERB (dimer)	-0.041	0.14	-10000	0	-0.61	18	18
KRAS	0.013	0	-10000	0	-10000	0	0
G13/GTP	-0.034	0.12	-10000	0	-0.54	17	17
pseudopodium formation	0.021	0.1	-10000	0	-0.44	1	1
E2/ER alpha (dimer)/PELP1	-0.038	0.12	-10000	0	-0.58	17	17
GRB2	0.013	0	-10000	0	-10000	0	0
GNG2	0.013	0	-10000	0	-10000	0	0
GNAO1	-0.013	0.14	-10000	0	-0.86	10	10
HRAS	0.012	0.016	-10000	0	-0.3	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
mol:NO	0.016	0.14	-10000	0	-0.61	17	17
E2/ER beta (dimer)	-0.004	0.049	-10000	0	-0.67	2	2
mol:GDP	-0.034	0.13	-10000	0	-0.6	18	18
mol:NADP	0.016	0.14	-10000	0	-0.61	17	17
PIK3R1	0.013	0	-10000	0	-10000	0	0
mol:IP3	-0.11	0.24	-10000	0	-0.53	92	92
IGF-1R heterotetramer	0.013	0	-10000	0	-10000	0	0
PLCB1	-0.12	0.25	-10000	0	-0.55	92	92
PLCB2	-0.12	0.25	-10000	0	-0.55	91	91
IGF1	-0.18	0.36	-10000	0	-0.82	86	86
mol:L-citrulline	0.016	0.14	-10000	0	-0.61	17	17
RHOA	0.013	0	-10000	0	-10000	0	0
Gai/GDP	-0.022	0.13	-10000	0	-0.81	10	10
JNK cascade	-0.004	0.048	-10000	0	-0.67	2	2
BCAR1	0.013	0	-10000	0	-10000	0	0
ESR2	0.008	0.063	-10000	0	-0.86	2	2
GNAQ	0.013	0	-10000	0	-10000	0	0
ESR1	-0.049	0.19	-10000	0	-0.51	45	45
Gq family/GDP/Gbeta gamma	-0.055	0.16	-10000	0	-0.63	4	4
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1	0.02	0.08	-10000	0	-0.34	17	17
E2/ER alpha (dimer)/PELP1/Src/p52 SHC	-0.034	0.13	-10000	0	-0.6	17	17
GNAZ	0.013	0	-10000	0	-10000	0	0
E2/ER alpha (dimer)	-0.045	0.14	-10000	0	-0.67	17	17
STRN	-0.017	0.16	-10000	0	-0.86	13	13
GNAL	-0.095	0.29	-10000	0	-0.86	47	47
PELP1	0.013	0	-10000	0	-10000	0	0
MAPK11	0.016	0.043	-10000	0	-0.58	2	2
GNAI2	0.013	0	-10000	0	-10000	0	0
GNAI3	0.013	0	-10000	0	-10000	0	0
GNAI1	0.011	0.045	-10000	0	-0.86	1	1
HBEGF	-0.002	0.16	-10000	0	-0.52	22	22
cAMP biosynthetic process	-0.091	0.2	-10000	0	-0.52	61	61
SRC	0.016	0.14	-10000	0	-0.51	17	17
PI3K	-0.002	0.034	-10000	0	-0.66	1	1
GNB1	0.013	0	-10000	0	-10000	0	0
G13/GDP/Gbeta gamma	-0.029	0.11	-10000	0	-0.52	18	18
SOS1	0.013	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1	-0.098	0.18	-10000	0	-0.54	28	28
Gs family/GTP	-0.093	0.2	-10000	0	-0.53	61	61
EntrezGene:2778	0	0	-10000	0	-10000	0	0
RAS family/GTP	0	0.007	-10000	0	-10000	0	0
vasodilation	0.017	0.14	-10000	0	-0.58	17	17
mol:DAG	-0.11	0.24	-10000	0	-0.53	92	92
Gs family/GDP/Gbeta gamma	-0.073	0.16	-10000	0	-0.43	61	61
MSN	0.02	0.11	-10000	0	-0.48	1	1
Gq family/GTP	-0.15	0.25	-10000	0	-0.58	91	91
mol:PI-3-4-5-P3	-0.009	0.18	-10000	0	-0.82	18	18
NRAS	0.013	0	-10000	0	-10000	0	0
mol:E2	0	0	-10000	0	-10000	0	0
cell adhesion	-0.017	0.14	0.58	17	-10000	0	17
GRB2/SOS1	0	0	-10000	0	-10000	0	0
RhoA/GDP	-0.031	0.12	-10000	0	-0.55	18	18
NOS3	0.014	0.15	-10000	0	-0.65	17	17
GNA11	0.006	0.077	-10000	0	-0.86	3	3
MAPKKK cascade	0.006	0.18	-10000	0	-0.59	29	29
E2/ER alpha (dimer)/PELP1/Src	-0.037	0.14	-10000	0	-0.64	17	17
ruffle organization	0.021	0.1	-10000	0	-0.44	1	1
ROCK2	0.012	0.12	-10000	0	-0.44	8	8
GNA14	-0.2	0.37	-10000	0	-0.86	91	91
GNA15	-0.017	0.099	-10000	0	-0.31	35	35
GNA13	0.013	0	-10000	0	-10000	0	0
MMP9	-0.026	0.19	-10000	0	-0.52	42	42
MMP2	0.018	0.14	-10000	0	-0.49	20	20

×

Syndecan-2-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Syndecan-2/Fibronectin	-0.11	0.1	-9999	-0.68	5	5
EPHB2	0.006	0.077	-9999	-0.86	3	3
Syndecan-2/TACI	-0.13	0.26	-9999	-0.59	88	88
LAMA1	-0.052	0.23	-9999	-0.84	29	29
Syndecan-2/alpha2 ITGB1	-0.069	0.11	-9999	-0.5	17	17
HRAS	0.012	0.016	-9999	-0.3	1	1
Syndecan-2/CASK	-0.008	0.066	-9999	-0.58	5	5
ITGA5	0.013	0	-9999	-10000	0	0
BAX	0.032	0.074	-9999	-0.5	7	7
EPB41	0.013	0	-9999	-10000	0	0
positive regulation of cell-cell adhesion	-0.007	0.06	-9999	-0.52	5	5
LAMA3	-0.023	0.16	-9999	-0.6	22	22
EZR	0.013	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
CAV2	0.008	0.063	-9999	-0.86	2	2
Syndecan-2/MMP2	0.01	0.092	-9999	-0.57	9	9
RP11-540L11.1	0	0	-9999	-10000	0	0
alpha2 ITGB1	-0.077	0.093	-9999	-10000	0	0
dendrite morphogenesis	0.013	0.086	-9999	-0.57	8	8
Syndecan-2/GM-CSF	-0.1	0.097	-9999	-0.6	5	5
determination of left/right symmetry	0.012	0.078	-9999	-0.66	5	5
Syndecan-2/PKC delta	0.017	0.068	-9999	-0.57	5	5
GNB2L1	0.013	0	-9999	-10000	0	0
MAPK3	-0.078	0.09	-9999	-0.55	5	5
MAPK1	-0.078	0.09	-9999	-0.55	5	5
Syndecan-2/RACK1	-0.007	0.057	-9999	-0.5	5	5
NF1	0.013	0	-9999	-10000	0	0
FGFR/FGF/Syndecan-2	0.012	0.078	-9999	-0.66	5	5
ITGA2	-0.11	0.15	-9999	-0.3	154	154
MAPK8	0.025	0.081	-9999	-0.57	7	7
Syndecan-2/alpha2/beta1 Integrin	-0.087	0.15	-9999	-0.54	31	31
Syndecan-2/Kininogen	-0.004	0.076	-9999	-0.58	5	5
ITGB1	0.013	0	-9999	-10000	0	0
SRC	0.031	0.058	-9999	-0.46	5	5
Syndecan-2/CASK/Protein 4.1	-0.007	0.06	-9999	-0.53	5	5
extracellular matrix organization	0.014	0.071	-9999	-0.57	5	5
actin cytoskeleton reorganization	-0.11	0.1	-9999	-0.68	5	5
Syndecan-2/Caveolin-2/Ras	-0.01	0.079	-9999	-0.6	6	6
Syndecan-2/Laminin alpha3	-0.006	0.13	-9999	-0.57	17	17
Syndecan-2/RasGAP	-0.006	0.054	-9999	-0.47	5	5
alpha5/beta1 Integrin	0	0	-9999	-10000	0	0
PRKCD	0.013	0	-9999	-10000	0	0
Syndecan-2 dimer	0.013	0.086	-9999	-0.57	8	8
GO:0007205	0.004	0	-9999	-10000	0	0
DNA mediated transformation	0	0	-9999	-10000	0	0
Syndecan-2/RasGAP/Src	0.038	0.057	-9999	-0.45	5	5
RHOA	0.013	0	-9999	-10000	0	0
SDCBP	0.013	0	-9999	-10000	0	0
TNFRSF13B	-0.19	0.36	-9999	-0.82	91	91
RASA1	0.013	0	-9999	-10000	0	0
alpha2/beta1 Integrin	-0.077	0.093	-9999	-10000	0	0
Syndecan-2/Synbindin	0.017	0.068	-9999	-0.57	5	5
TGFB1	0.007	0.042	-9999	-10000	0	0
CASP3	0.027	0.063	-9999	-0.52	5	5
FN1	-0.21	0.14	-9999	-0.3	273	273
Syndecan-2/IL8	-0.036	0.12	-9999	-0.57	13	13
SDC2	0.012	0.078	-9999	-0.66	5	5
KNG1	-0.01	0.068	-9999	-10000	0	0
Syndecan-2/Neurofibromin	0.017	0.068	-9999	-0.57	5	5
TRAPPC4	0.013	0	-9999	-10000	0	0
CSF2	-0.19	0.14	-9999	-0.3	251	251
Syndecan-2/TGFB1	0.014	0.072	-9999	-0.57	5	5
Syndecan-2/Syntenin/PI-4-5-P2	-0.007	0.06	-9999	-0.53	5	5
Syndecan-2/Ezrin	-0.007	0.059	-9999	-0.52	5	5
PRKACA	0.027	0.063	-9999	-0.52	5	5
angiogenesis	-0.036	0.12	-9999	-0.57	13	13
MMP2	0.001	0.093	-9999	-0.62	7	7
IL8	-0.079	0.17	-9999	-0.86	8	8
calcineurin-NFAT signaling pathway	-0.13	0.26	-9999	-0.58	88	88

×

LPA receptor mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.046	0.15	-9999	-0.55	31	31
NF kappa B1 p50/RelA/I kappa B alpha	-0.023	0.042	-9999	-10000	0	0
AP1	-0.27	0.39	-9999	-0.74	137	137
mol:PIP3	-0.045	0.14	-9999	-0.68	7	7
AKT1	-0.029	0.097	-9999	-0.56	3	3
PTK2B	-0.001	0.085	-9999	-0.27	31	31
RHOA	0.03	0.047	-9999	-0.27	1	1
PIK3CB	0.013	0.001	-9999	-10000	0	0
mol:Ca2+	0.003	0.073	-9999	-10000	0	0
MAGI3	0.011	0.044	-9999	-0.85	1	1
RELA	0.013	0	-9999	-10000	0	0
apoptosis	-0.016	0.14	-9999	-0.46	31	31
HRAS/GDP	-0.001	0.01	-9999	-10000	0	0
positive regulation of microtubule depolymerization	0.008	0.091	-9999	-0.52	3	3
NF kappa B1 p50/RelA	-0.052	0.12	-9999	-0.54	8	8
endothelial cell migration	-0.029	0.2	-9999	-0.65	32	32
ADCY4	-0.016	0.2	-9999	-0.64	31	31
ADCY5	-0.052	0.22	-9999	-0.67	35	35
ADCY6	-0.016	0.2	-9999	-0.64	31	31
ADCY7	-0.016	0.2	-9999	-0.64	31	31
ADCY1	-0.019	0.2	-9999	-0.64	31	31
ADCY2	-0.041	0.22	-9999	-0.68	32	32
ADCY3	-0.016	0.2	-9999	-0.64	31	31
ADCY8	-0.055	0.2	-9999	-0.67	31	31
ADCY9	-0.016	0.2	-9999	-0.64	31	31
GSK3B	0.007	0.081	-9999	-0.31	7	7
arachidonic acid secretion	-0.009	0.18	-9999	-0.59	31	31
GNG2	0.013	0.001	-9999	-10000	0	0
TRIP6	0.026	0.008	-9999	-10000	0	0
GNAO1	-0.041	0.21	-9999	-0.63	39	39
HRAS	0.012	0.016	-9999	-0.3	1	1
NFKBIA	0.009	0.077	-9999	-10000	0	0
GAB1	0.013	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
lamellipodium assembly	-0.03	0.1	-9999	-0.98	4	4
JUN	-0.19	0.37	-9999	-0.86	88	88
LPA/LPA2/NHERF2	-0.001	0.006	-9999	-10000	0	0
TIAM1	-0.04	0.12	-9999	-1.2	4	4
PIK3R1	0.013	0.001	-9999	-10000	0	0
mol:IP3	0.003	0.074	-9999	-10000	0	0
PLCB3	0.03	0.007	-9999	-10000	0	0
FOS	-0.22	0.39	-9999	-0.86	103	103
positive regulation of mitosis	-0.009	0.18	-9999	-0.59	31	31
LPA/LPA1-2-3	-0.053	0.16	-9999	-0.56	31	31
mol:Ca ++	0	0	-9999	-10000	0	0
JNK cascade	0	0	-9999	-10000	0	0
BCAR1	0.013	0	-9999	-10000	0	0
stress fiber formation	0.002	0.11	-9999	-0.36	31	31
GNAZ	-0.023	0.18	-9999	-0.59	32	32
EGFR/PI3K-beta/Gab1	-0.047	0.14	-9999	-0.73	7	7
positive regulation of dendritic cell cytokine production	-0.052	0.16	-9999	-0.56	31	31
LPA/LPA2/MAGI-3	-0.002	0.032	-9999	-0.62	1	1
ARHGEF1	-0.003	0.16	-9999	-0.51	31	31
GNAI2	-0.023	0.18	-9999	-0.59	32	32
GNAI3	-0.023	0.18	-9999	-0.59	32	32
GNAI1	-0.025	0.18	-9999	-0.59	33	33
LPA/LPA3	-0.01	0.043	-9999	-0.26	1	1
LPA/LPA2	-0.001	0.008	-9999	-10000	0	0
LPA/LPA1	-0.059	0.19	-9999	-0.68	32	32
HB-EGF/EGFR	-0.056	0.17	-9999	-0.57	34	34
HBEGF	-0.06	0.19	-9999	-0.64	31	31
mol:DAG	0.003	0.074	-9999	-10000	0	0
cAMP biosynthetic process	-0.029	0.2	-9999	-0.6	39	39
NFKB1	0.013	0	-9999	-10000	0	0
SRC	0.012	0.016	-9999	-10000	0	0
GNB1	0.013	0.001	-9999	-10000	0	0
LYN	0.009	0.077	-9999	-10000	0	0
GNAQ	0.018	0.028	-9999	-10000	0	0
LPAR2	0.013	0	-9999	-10000	0	0
LPAR3	-0.004	0.066	-9999	-0.3	18	18
LPAR1	-0.055	0.24	-9999	-0.87	31	31
IL8	-0.13	0.2	-9999	-0.49	47	47
PTK2	-0.013	0.16	-9999	-0.52	31	31
Rac1/GDP	0	0	-9999	-10000	0	0
CASP3	-0.018	0.14	-9999	-0.46	31	31
EGFR	0.001	0.099	-9999	-0.86	5	5
PLCG1	-0.017	0.084	-9999	-0.3	7	7
PLD2	-0.013	0.16	-9999	-0.52	31	31
G12/G13	-0.047	0.15	-9999	-0.55	31	31
PI3K-beta	-0.034	0.11	-9999	-0.44	20	20
cell migration	-0.016	0.059	-9999	-0.28	4	4
SLC9A3R2	0.013	0	-9999	-10000	0	0
PXN	0.001	0.12	-9999	-0.37	31	31
HRAS/GTP	-0.024	0.19	-9999	-0.61	31	31
RAC1	0.013	0	-9999	-10000	0	0
MMP9	-0.086	0.24	-9999	-0.54	68	68
PRKCE	0.006	0.077	-9999	-0.86	3	3
PRKCD	0.01	0.071	-9999	-10000	0	0
Gi(beta/gamma)	-0.009	0.19	-9999	-0.6	31	31
mol:LPA	0.003	0.016	-9999	-0.22	1	1
TRIP6/p130 Cas/FAK1/Paxillin	-0.032	0.14	-9999	-0.48	25	25
MAPKKK cascade	-0.009	0.18	-9999	-0.59	31	31
contractile ring contraction involved in cytokinesis	0.029	0.047	-9999	-0.26	1	1
mol:GDP	0	0	-9999	-10000	0	0
GNA14	-0.094	0.2	-9999	-0.46	91	91
GNA15	0.006	0.057	-9999	-0.45	1	1
GNA12	0.013	0	-9999	-10000	0	0
GNA13	0.013	0	-9999	-10000	0	0
MAPT	0.008	0.093	-9999	-0.55	3	3
GNA11	0.014	0.05	-9999	-0.44	3	3
Rac1/GTP	-0.031	0.11	-9999	-1.1	4	4
MMP2	-0.029	0.2	-9999	-0.65	32	32

×

JNK signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1	-0.062	0.18	-9999	-0.58	34	34
MAP4K1	-0.024	0.14	-9999	-0.86	7	7
MAP3K8	0.004	0.089	-9999	-0.86	4	4
PRKCB	-0.028	0.11	-9999	-0.31	48	48
DBNL	0.013	0	-9999	-10000	0	0
CRKL	0.013	0	-9999	-10000	0	0
MAP3K1	0.009	0.12	-9999	-0.54	6	6
JUN	-0.1	0.24	-9999	-0.51	90	90
MAP3K7	0.009	0.12	-9999	-0.54	6	6
GRAP2	-0.045	0.21	-9999	-0.79	27	27
CRK	0.013	0	-9999	-10000	0	0
MAP2K4	0.016	0.11	-9999	-0.52	6	6
LAT	0.003	0.09	-9999	-0.74	5	5
LCP2	0.004	0.052	-9999	-10000	0	0
MAPK8	0.011	0.076	-9999	-0.71	3	3
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family	0	0.12	-9999	-0.39	25	25
LAT/GRAP2/SLP76/HPK1/HIP-55	-0.058	0.17	-9999	-0.56	32	32

×

Integrins in angiogenesis

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	-0.009	0.075	-9999	-0.66	5	5
alphaV beta3 Integrin	-0.02	0.11	-9999	-0.62	12	12
PTK2	0.009	0.16	-9999	-0.57	12	12
IGF1R	0.013	0	-9999	-10000	0	0
PI4KB	0.013	0	-9999	-10000	0	0
MFGE8	-0.026	0.1	-9999	-10000	0	0
SRC	0.012	0.016	-9999	-10000	0	0
CDKN1B	-0.076	0.2	-9999	-0.64	41	41
VEGFA	0.008	0.063	-9999	-0.86	2	2
ILK	-0.076	0.2	-9999	-0.64	41	41
ROCK1	0.013	0	-9999	-10000	0	0
AKT1	-0.07	0.18	-9999	-0.59	41	41
PTK2B	0.017	0.12	-9999	-0.55	16	16
alphaV/beta3 Integrin/JAM-A	-0.071	0.18	-9999	-0.51	52	52
CBL	0.013	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
alphaV beta3 Integrin/ANGPTL3	-0.02	0.11	-9999	-0.62	12	12
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.16	0.26	-9999	-0.56	109	109
VEGF/Rho/ROCK/alphaV/beta3 Integrin	-0.004	0.12	-9999	-0.56	3	3
alphaV/beta3 Integrin/Syndecan-1	-0.021	0.11	-9999	-0.62	12	12
PI4KA	0.013	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.22	0.26	-9999	-0.65	79	79
PI4 Kinase	0	0	-9999	-10000	0	0
PIK3CA	0.011	0.045	-9999	-0.86	1	1
alphaV/beta3 Integrin/Osteopontin	-0.071	0.17	-9999	-0.62	30	30
RPS6KB1	-0.19	0.25	-9999	-0.6	79	79
TLN1	0.013	0	-9999	-10000	0	0
MAPK3	-0.095	0.17	-9999	-0.81	12	12
GPR124	0.013	0	-9999	-10000	0	0
MAPK1	-0.095	0.17	-9999	-0.81	12	12
PXN	0.013	0	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Tumstatin	-0.039	0.16	-9999	-0.67	22	22
cell adhesion	-0.03	0.11	-9999	-0.57	12	12
ANGPTL3	0.006	0.017	-9999	-0.3	1	1
VEGFR2 homodimer/VEGFA homodimer/Src	-0.008	0.066	-9999	-0.57	5	5
IGF-1R heterotetramer	0.013	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
TGFBR2	0.011	0.045	-9999	-0.86	1	1
ITGB3	-0.015	0.15	-9999	-0.86	12	12
IGF1	-0.18	0.36	-9999	-0.82	86	86
RAC1	0.013	0	-9999	-10000	0	0
regulation of cell-matrix adhesion	-0.019	0.11	-9999	-0.61	12	12
apoptosis	0.011	0.044	-9999	-0.85	1	1
CD47	0.013	0	-9999	-10000	0	0
alphaV/beta3 Integrin/CD47	-0.02	0.11	-9999	-0.62	12	12
VCL	0.013	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Del1	-0.033	0.12	-9999	-0.61	15	15
CSF1	0.004	0.089	-9999	-0.86	4	4
PIK3C2A	-0.076	0.2	-9999	-0.64	41	41
PI4 Kinase/Pyk2	-0.064	0.16	-9999	-0.82	3	3
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	-0.025	0.12	-9999	-0.59	16	16
FAK1/Vinculin	0.018	0.13	-9999	-0.53	5	5
alphaV beta3/Integrin/ppsTEM5	-0.02	0.11	-9999	-0.62	12	12
RHOA	0.013	0	-9999	-10000	0	0
VTN	-0.085	0.27	-9999	-0.8	46	46
BCAR1	0.013	0	-9999	-10000	0	0
FGF2	0.013	0	-9999	-10000	0	0
F11R	0.024	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Lactadherin	-0.038	0.12	-9999	-0.62	12	12
alphaV/beta3 Integrin/TGFBR2	-0.021	0.12	-9999	-0.61	13	13
alphaV/beta3 Integrin/c-FMS/Cbl/Cas	-0.007	0.06	-9999	-0.52	5	5
HSP90AA1	0.013	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Talin	-0.018	0.1	-9999	-0.57	12	12
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.21	0.14	-9999	-0.3	273	273
alphaV/beta3 Integrin/Pyk2	-0.023	0.12	-9999	-0.55	16	16
SDC1	0.01	0.028	-9999	-0.3	3	3
VAV3	0.029	0.081	-9999	-0.49	9	9
PTPN11	0.013	0	-9999	-10000	0	0
IRS1	-0.07	0.26	-9999	-0.86	36	36
FAK1/Paxillin	0.018	0.13	-9999	-0.53	5	5
cell migration	0.028	0.12	-9999	-0.47	5	5
ITGAV	0.011	0.045	-9999	-0.86	1	1
PI3K	-0.065	0.16	-9999	-0.46	52	52
SPP1	-0.079	0.21	-9999	-0.43	78	78
KDR	0.006	0.077	-9999	-0.86	3	3
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Caspase 8	0.011	0.044	-9999	-0.85	1	1
COL4A3	-0.017	0.16	-9999	-0.86	13	13
angiogenesis	-0.087	0.19	-9999	-0.62	30	30
Rac1/GTP	-0.011	0.068	-9999	-0.44	9	9
EDIL3	-0.013	0.11	-9999	-0.36	26	26
cell proliferation	-0.021	0.11	-9999	-0.61	13	13

×

Angiopoietin receptor Tie2-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	0.01	0.21	-10000	0	-0.94	16	16
NCK1/PAK1/Dok-R	-0.028	0.09	-10000	0	-0.42	17	17
NCK1/Dok-R	-0.065	0.23	-10000	0	-1.1	16	16
PIK3CA	0.01	0.045	-10000	0	-0.86	1	1
mol:beta2-estradiol	-0.003	0.047	0.25	12	-10000	0	12
RELA	0.013	0	-10000	0	-10000	0	0
SHC1	0.013	0.001	-10000	0	-10000	0	0
Rac/GDP	0	0	-10000	0	-10000	0	0
F2	-0.005	0.058	0.26	3	-0.32	4	7
TNIP2	0.013	0	-10000	0	-10000	0	0
NF kappa B/RelA	-0.057	0.21	-10000	0	-1	16	16
FN1	-0.21	0.14	-10000	0	-0.3	273	273
PLD2	0.002	0.26	-10000	0	-1.2	16	16
PTPN11	0.013	0	-10000	0	-10000	0	0
GRB14	-0.022	0.17	-10000	0	-0.86	15	15
ELK1	0.017	0.23	-10000	0	-1	16	16
GRB7	-0.033	0.11	-10000	0	-0.3	56	56
PAK1	0.013	0	-10000	0	-10000	0	0
Tie2/Ang1/alpha5/beta1 Integrin	-0.098	0.23	-10000	0	-1.2	16	16
CDKN1A	-0.011	0.17	-10000	0	-0.64	15	15
ITGA5	0.013	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
RasGAP/Dok-R	-0.065	0.23	-10000	0	-1.1	16	16
CRK	0.013	0	-10000	0	-10000	0	0
mol:NO	0.026	0.16	-10000	0	-0.68	16	16
PLG	-0.006	0.26	-10000	0	-1.2	16	16
mol:GDP	0	0	-10000	0	-10000	0	0
chemokinesis	0.008	0.2	-10000	0	-0.9	16	16
GRB2	0.013	0	-10000	0	-10000	0	0
PIK3R1	0.013	0.002	-10000	0	-10000	0	0
ANGPT2	-0.11	0.23	-10000	0	-0.82	17	17
BMX	-0.011	0.27	-10000	0	-1.2	17	17
ANGPT1	-0.039	0.29	-10000	0	-1.5	14	14
tube development	-0.017	0.18	-10000	0	-0.72	16	16
ANGPT4	-0.063	0.24	-10000	0	-0.86	31	31
response to hypoxia	0	0.016	-10000	0	-10000	0	0
Tie2/Ang1/GRB14	-0.024	0.28	-10000	0	-1.2	16	16
alpha5/beta1 Integrin	0	0	-10000	0	-10000	0	0
FGF2	0.012	0.002	-10000	0	-10000	0	0
STAT5A (dimer)	-0.02	0.2	-10000	0	-0.82	16	16
mol:L-citrulline	0.026	0.16	-10000	0	-0.68	16	16
AGTR1	-0.32	0.42	-10000	0	-0.85	146	146
MAPK14	-0.01	0.25	-10000	0	-1.2	16	16
Tie2/SHP2	-0.019	0.098	-10000	0	-1.2	2	2
TEK	0.022	0.12	-10000	0	-1.4	2	2
RPS6KB1	0.01	0.21	-10000	0	-0.9	16	16
Angiotensin II/AT1	-0.25	0.33	-10000	0	-0.67	146	146
Tie2/Ang1/GRB2	-0.004	0.26	-10000	0	-1.2	16	16
MAPK3	0.012	0.24	-10000	0	-1.1	16	16
MAPK1	0.012	0.24	-10000	0	-1.1	16	16
Tie2/Ang1/GRB7	-0.024	0.27	-10000	0	-1.2	16	16
NFKB1	0.013	0	-10000	0	-10000	0	0
MAPK8	-0.001	0.26	-10000	0	-1.1	17	17
PI3K	-0.004	0.24	-10000	0	-1.1	16	16
FES	-0.009	0.25	-10000	0	-1.2	16	16
Crk/Dok-R	-0.065	0.23	-10000	0	-1.1	16	16
Tie2/Ang1/ABIN2	-0.004	0.26	-10000	0	-1.2	16	16
blood circulation	0	0	-10000	0	-10000	0	0
negative regulation of caspase activity	0.014	0.19	-10000	0	-0.83	16	16
STAT5A	0.013	0	-10000	0	-10000	0	0
mol:ROS	0	0	-10000	0	-10000	0	0
PTK2	0.01	0.21	-10000	0	-0.9	16	16
Tie2/Ang2	-0.038	0.23	-10000	0	-1	16	16
Tie2/Ang1	-0.009	0.27	-10000	0	-1.3	16	16
FOXO1	0.021	0.2	-10000	0	-0.83	16	16
ELF1	0.019	0.045	-10000	0	-0.85	1	1
ELF2	-0.001	0.25	-10000	0	-1.1	16	16
mol:Choline	0.005	0.24	-10000	0	-1.1	16	16
cell migration	-0.022	0.055	-10000	0	-10000	0	0
FYN	-0.023	0.2	-10000	0	-0.82	16	16
DOK2	0	0.08	-10000	0	-0.39	12	12
negative regulation of cell cycle	-0.007	0.16	-10000	0	-0.58	15	15
ETS1	0.015	0.044	-10000	0	-10000	0	0
PXN	0.022	0.17	-10000	0	-0.73	16	16
ITGB1	0.013	0	-10000	0	-10000	0	0
NOS3	0.022	0.18	-10000	0	-0.78	16	16
RAC1	0.013	0	-10000	0	-10000	0	0
TNF	-0.089	0.28	-10000	0	-0.8	48	48
MAPKKK cascade	0.005	0.24	-10000	0	-1.1	16	16
RASA1	0.013	0	-10000	0	-10000	0	0
Tie2/Ang1/Shc	-0.007	0.26	-10000	0	-1.2	16	16
NCK1	0.013	0	-10000	0	-10000	0	0
vasculogenesis	0.028	0.15	-10000	0	-0.6	16	16
mol:Phosphatidic acid	0.005	0.24	-10000	0	-1.1	16	16
mol:Angiotensin II	0.001	0.002	-10000	0	-10000	0	0
mol:NADP	0.026	0.16	-10000	0	-0.68	16	16
Rac1/GTP	-0.05	0.17	-10000	0	-0.83	16	16
MMP2	-0.004	0.26	-10000	0	-1.2	16	16

×

BCR signaling pathway

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
JUN	-0.1	0.18	-9999	-0.46	48	48
IKBKB	-0.016	0.067	-9999	-0.28	4	4
AKT1	-0.036	0.1	-9999	-0.27	17	17
IKBKG	-0.014	0.07	-9999	-0.3	4	4
CALM1	-0.029	0.082	-9999	-0.36	2	2
PIK3CA	0.011	0.045	-9999	-0.86	1	1
MAP3K1	-0.066	0.18	-9999	-0.66	13	13
MAP3K7	0.013	0	-9999	-10000	0	0
mol:Ca2+	-0.038	0.086	-9999	-0.38	2	2
DOK1	0.013	0	-9999	-10000	0	0
AP-1	-0.08	0.14	-9999	-0.28	89	89
LYN	0.013	0	-9999	-10000	0	0
BLNK	0.013	0	-9999	-10000	0	0
SHC1	0.013	0	-9999	-10000	0	0
BCR complex	-0.16	0.24	-9999	-0.52	103	103
CD22	-0.14	0.23	-9999	-0.7	37	37
CAMK2G	-0.02	0.078	-9999	-0.33	2	2
CSNK2A1	0.013	0	-9999	-10000	0	0
INPP5D	-0.01	0.081	-9999	-0.3	28	28
SHC/GRB2/SOS1	-0.092	0.15	-9999	-10000	0	0
GO:0007205	-0.039	0.087	-9999	-0.39	2	2
SYK	0.013	0	-9999	-10000	0	0
ELK1	-0.029	0.083	-9999	-0.36	2	2
NFATC1	-0.063	0.16	-9999	-0.54	15	15
B-cell antigen/BCR complex	-0.16	0.24	-9999	-0.52	103	103
PAG1/CSK	0	0	-9999	-10000	0	0
NFKBIB	0.003	0.026	-9999	-0.1	1	1
HRAS	-0.032	0.096	-9999	-0.35	2	2
NFKBIA	0.003	0.026	-9999	-0.1	1	1
NF-kappa-B/RelA/I kappa B beta	0.009	0.022	-9999	-10000	0	0
RasGAP/Csk	-0.13	0.2	-9999	-0.53	64	64
mol:GDP	-0.035	0.08	-9999	-0.35	2	2
PTEN	0.011	0.045	-9999	-0.86	1	1
CD79B	-0.032	0.11	-9999	-10000	0	0
NF-kappa-B/RelA/I kappa B alpha	0.009	0.021	-9999	-10000	0	0
GRB2	0.013	0	-9999	-10000	0	0
PI3K/BCAP/CD19	-0.078	0.18	-9999	-0.45	51	51
PIK3R1	0.013	0	-9999	-10000	0	0
mol:IP3	-0.045	0.084	-9999	-0.39	2	2
CSK	0.013	0	-9999	-10000	0	0
FOS	-0.15	0.23	-9999	-0.5	105	105
CHUK	-0.014	0.07	-9999	-0.3	4	4
IBTK	0.013	0	-9999	-10000	0	0
CARD11/BCL10/MALT1/TAK1	-0.063	0.091	-9999	-0.51	6	6
PTPN6	-0.13	0.21	-9999	-0.65	37	37
RELA	0.013	0	-9999	-10000	0	0
BCL2A1	0.004	0.034	-9999	-0.13	13	13
VAV2	-0.13	0.19	-9999	-0.87	9	9
ubiquitin-dependent protein catabolic process	0.008	0.025	-9999	-0.095	1	1
BTK	-0.004	0.12	-9999	-1.2	3	3
CD19	-0.14	0.2	-9999	-0.5	52	52
MAP4K1	-0.024	0.14	-9999	-0.86	7	7
CD72	0.01	0.032	-9999	-0.3	4	4
PAG1	0.013	0	-9999	-10000	0	0
MAPK14	-0.048	0.16	-9999	-0.54	13	13
SH3BP5	0.013	0	-9999	-10000	0	0
PIK3AP1	-0.03	0.086	-9999	-0.33	2	2
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72	-0.053	0.16	-9999	-0.45	48	48
RAF1	-0.022	0.092	-9999	-10000	0	0
RasGAP/p62DOK/SHIP	-0.13	0.2	-9999	-0.51	64	64
CD79A	-0.18	0.3	-9999	-0.5	142	142
re-entry into mitotic cell cycle	-0.078	0.14	-9999	-0.28	89	89
RASA1	0.013	0	-9999	-10000	0	0
MAPK3	-0.004	0.081	-9999	-10000	0	0
MAPK1	-0.004	0.081	-9999	-10000	0	0
CD72/SHP1	-0.097	0.21	-9999	-0.7	24	24
NFKB1	0.013	0	-9999	-10000	0	0
MAPK8	-0.05	0.16	-9999	-0.54	15	15
actin cytoskeleton organization	-0.08	0.18	-9999	-0.7	9	9
NF-kappa-B/RelA	0.023	0.042	-9999	-10000	0	0
Calcineurin	-0.03	0.057	-9999	-10000	0	0
PI3K	-0.12	0.16	-9999	-0.57	21	21
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2	-0.049	0.083	-9999	-0.35	2	2
SOS1	0.013	0	-9999	-10000	0	0
Bam32/HPK1	-0.095	0.24	-9999	-1	14	14
DAPP1	-0.12	0.25	-9999	-1.3	11	11
cytokine secretion	-0.059	0.15	-9999	-0.5	15	15
mol:DAG	-0.045	0.084	-9999	-0.39	2	2
PLCG2	0.013	0	-9999	-10000	0	0
MAP2K1	-0.013	0.087	-9999	-10000	0	0
B-cell antigen/BCR complex/FcgammaRIIB	-0.16	0.24	-9999	-0.62	64	64
mol:PI-3-4-5-P3	-0.09	0.12	-9999	-0.4	18	18
ETS1	-0.01	0.074	-9999	-10000	0	0
B-cell antigen/BCR complex/LYN/SYK/BLNK	-0.11	0.17	-9999	-0.49	51	51
B-cell antigen/BCR complex/LYN	-0.12	0.2	-9999	-0.52	55	55
MALT1	0.013	0	-9999	-10000	0	0
TRAF6	0.011	0.045	-9999	-0.86	1	1
RAC1	-0.085	0.19	-9999	-0.77	9	9
B-cell antigen/BCR complex/LYN/SYK	-0.14	0.23	-9999	-0.6	55	55
CARD11	-0.071	0.12	-9999	-0.58	7	7
FCGR2B	-0.029	0.18	-9999	-0.77	20	20
PPP3CA	0.013	0	-9999	-10000	0	0
BCL10	0.013	0	-9999	-10000	0	0
IKK complex	0.001	0.034	-9999	-0.14	1	1
PTPRC	-0.03	0.17	-9999	-0.55	29	29
PDPK1	-0.039	0.099	-9999	-0.27	17	17
PPP3CB	0.013	0	-9999	-10000	0	0
PPP3CC	0.013	0	-9999	-10000	0	0
POU2F2	0.009	0.023	-9999	-10000	0	0

×

Regulation of nuclear SMAD2/3 signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EP300	0.02	0.015	-10000	0	-10000	0	0
HSPA8	0.008	0.045	-10000	0	-0.86	1	1
SMAD3/SMAD4/ER alpha	-0.053	0.14	-10000	0	-0.62	17	17
AKT1	0.009	0.008	-10000	0	-10000	0	0
GSC	-0.21	0.56	-10000	0	-1.6	56	56
NKX2-5	0.001	0.031	-10000	0	-0.29	4	4
muscle cell differentiation	0.026	0.046	-10000	0	-10000	0	0
SMAD2-3/SMAD4/SP1	0.003	0.079	-10000	0	-10000	0	0
SMAD4	-0.015	0.059	-10000	0	-10000	0	0
CBFB	0.013	0	-10000	0	-10000	0	0
SAP18	0.011	0.004	-10000	0	-10000	0	0
Cbp/p300/MSG1	-0.11	0.079	-10000	0	-0.57	4	4
SMAD3/SMAD4/VDR	0.01	0.045	-10000	0	-10000	0	0
MYC	0.004	0.13	-10000	0	-0.86	8	8
CDKN2B	-0.074	0.14	-10000	0	-10000	0	0
AP1	-0.28	0.53	-10000	0	-1	120	120
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1	0.032	0.042	-10000	0	-10000	0	0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1	-0.001	0.066	-10000	0	-10000	0	0
SP3	0.016	0.002	-10000	0	-10000	0	0
CREB1	0.013	0	-10000	0	-10000	0	0
FOXH1	-0.005	0.058	-10000	0	-0.29	9	9
SMAD3/SMAD4/GR	-0.018	0.046	-10000	0	-10000	0	0
GATA3	-0.038	0.2	-10000	0	-0.85	22	22
SKI/SIN3/HDAC complex/NCoR1	0.041	0.023	-10000	0	-10000	0	0
MEF2C/TIF2	-0.047	0.13	-10000	0	-0.52	14	14
endothelial cell migration	-0.009	0.11	1.4	1	-10000	0	1
MAX	0.013	0.006	-10000	0	-10000	0	0
RBBP7	0.011	0.004	-10000	0	-10000	0	0
RBBP4	0.011	0.004	-10000	0	-10000	0	0
RUNX2	-0.078	0.15	-10000	0	-0.31	107	107
RUNX3	-0.01	0.11	-10000	0	-0.4	21	21
RUNX1	-0.13	0.16	-10000	0	-0.3	178	178
CTBP1	0.013	0	-10000	0	-10000	0	0
NR3C1	0.013	0.006	-10000	0	-10000	0	0
VDR	0.012	0.016	-10000	0	-10000	0	0
CDKN1A	0.024	0.07	-10000	0	-10000	0	0
KAT2B	0.015	0.005	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1	-0.037	0.088	-10000	0	-10000	0	0
DCP1A	0.013	0	-10000	0	-10000	0	0
SKI	0.011	0.004	-10000	0	-10000	0	0
SERPINE1	0.008	0.11	-10000	0	-1.5	1	1
SMAD3/SMAD4/ATF2	-0.031	0.099	-10000	0	-0.63	8	8
SMAD3/SMAD4/ATF3	-0.17	0.28	-10000	0	-0.66	91	91
SAP30	0.009	0.045	-10000	0	-0.86	1	1
Cbp/p300/PIAS3	0.033	0.045	-10000	0	-10000	0	0
JUN	-0.27	0.53	-10000	0	-0.98	120	120
SMAD3/SMAD4/IRF7	-0.017	0.045	-10000	0	-10000	0	0
TFE3	0.018	0.006	-10000	0	-10000	0	0
COL1A2	-0.004	0.11	-10000	0	-1.2	1	1
mesenchymal cell differentiation	0.067	0.095	0.52	3	-10000	0	3
DLX1	-0.044	0.22	-10000	0	-0.86	25	25
TCF3	0.013	0	-10000	0	-10000	0	0
FOS	-0.24	0.42	-10000	0	-0.92	103	103
SMAD3/SMAD4/Max	-0.018	0.046	-10000	0	-10000	0	0
Cbp/p300/SNIP1	0.008	0.021	-10000	0	-10000	0	0
ZBTB17	0.02	0.011	-10000	0	-10000	0	0
LAMC1	0.023	0.054	-10000	0	-10000	0	0
TGIF2/HDAC complex/SMAD3/SMAD4	-0.018	0.045	-10000	0	-10000	0	0
IRF7	0.014	0.004	-10000	0	-10000	0	0
ESR1	-0.05	0.19	-10000	0	-0.51	45	45
HNF4A	-0.004	0.046	-10000	0	-0.3	9	9
MEF2C	0.007	0.085	-10000	0	-10000	0	0
SMAD2-3/SMAD4	-0.033	0.055	-10000	0	-10000	0	0
Cbp/p300/Src-1	0.024	0.031	-10000	0	-10000	0	0
IGHV3OR16-13	-0.017	0.022	-10000	0	-10000	0	0
TGIF2/HDAC complex	0.013	0	-10000	0	-10000	0	0
CREBBP	0.017	0.01	-10000	0	-10000	0	0
SKIL	0.013	0	-10000	0	-10000	0	0
HDAC1	0.011	0.004	-10000	0	-10000	0	0
HDAC2	0.011	0.004	-10000	0	-10000	0	0
SNIP1	0.011	0.005	-10000	0	-10000	0	0
GCN5L2	0.006	0.012	-10000	0	-10000	0	0
SMAD3/SMAD4/TFE3	-0.013	0.045	-10000	0	-10000	0	0
MSG1/HSC70	-0.16	0.098	-10000	0	-0.69	5	5
SMAD2	-0.003	0.04	-10000	0	-10000	0	0
SMAD3	-0.006	0.048	-10000	0	-10000	0	0
SMAD3/E2F4-5/DP1/p107/SMAD4	0.013	0.064	-10000	0	-0.4	3	3
SMAD2/SMAD2/SMAD4	0.012	0.025	-10000	0	-10000	0	0
NCOR1	0.011	0.004	-10000	0	-10000	0	0
NCOA2	-0.04	0.21	-10000	0	-0.86	23	23
NCOA1	0.013	0	-10000	0	-10000	0	0
MYOD/E2A	-0.002	0.019	-10000	0	-10000	0	0
SMAD2-3/SMAD4/SP1/MIZ-1	0.01	0.075	-10000	0	-10000	0	0
IFNB1	0.014	0.056	-10000	0	-10000	0	0
SMAD3/SMAD4/MEF2C	-0.004	0.086	-10000	0	-10000	0	0
CITED1	-0.24	0.14	-10000	0	-0.3	307	307
SMAD2-3/SMAD4/ARC105	-0.024	0.045	-10000	0	-10000	0	0
RBL1	-0.003	0.12	-10000	0	-0.86	7	7
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB	-0.005	0.078	-10000	0	-10000	0	0
RUNX1-3/PEBPB2	-0.082	0.099	-10000	0	-0.61	4	4
SMAD7	-0.12	0.28	-10000	0	-0.61	74	74
MYC/MIZ-1	0.015	0.11	-10000	0	-0.67	8	8
SMAD3/SMAD4	0.062	0.1	0.31	32	-10000	0	32
IL10	-0.032	0.2	-10000	0	-0.63	31	31
PIASy/HDAC complex	0.007	0.009	-10000	0	-10000	0	0
PIAS3	0.015	0.006	-10000	0	-10000	0	0
CDK2	0.018	0.011	-10000	0	-10000	0	0
IL5	-0.022	0.15	-10000	0	-0.53	22	22
CDK4	0.018	0.012	-10000	0	-10000	0	0
PIAS4	0.007	0.009	-10000	0	-10000	0	0
ATF3	-0.2	0.37	-10000	0	-0.86	91	91
SMAD3/SMAD4/SP1	-0.019	0.053	-10000	0	-10000	0	0
FOXG1	-0.013	0.11	-10000	0	-0.47	16	16
FOXO3	0.017	0.015	-10000	0	-10000	0	0
FOXO1	0.017	0.015	-10000	0	-10000	0	0
FOXO4	0.017	0.015	-10000	0	-10000	0	0
heart looping	0.007	0.085	-10000	0	-10000	0	0
CEBPB	0.009	0.007	-10000	0	-10000	0	0
SMAD3/SMAD4/DLX1	-0.059	0.16	-10000	0	-0.63	25	25
MYOD1	-0.002	0.031	-10000	0	-0.3	4	4
SMAD3/SMAD4/HNF4	-0.025	0.054	-10000	0	-0.4	1	1
SMAD3/SMAD4/GATA3	-0.057	0.15	-10000	0	-0.57	26	26
SnoN/SIN3/HDAC complex/NCoR1	0.013	0	-10000	0	-10000	0	0
SMAD3/SMAD4/RUNX1-3/PEBPB2	-0.076	0.097	-10000	0	-0.55	4	4
SMAD3/SMAD4/SP1-3	-0.009	0.045	-10000	0	-10000	0	0
MED15	0.013	0	-10000	0	-10000	0	0
SP1	0.014	0.021	-10000	0	-10000	0	0
SIN3B	0.011	0.004	-10000	0	-10000	0	0
SIN3A	0.011	0.004	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5	-0.029	0.08	-10000	0	-10000	0	0
ITGB5	0.034	0.061	-10000	0	-10000	0	0
TGIF/SIN3/HDAC complex/CtBP	0.042	0.022	-10000	0	-10000	0	0
SMAD3/SMAD4/AR	-0.26	0.3	-10000	0	-0.63	149	149
AR	-0.33	0.42	-10000	0	-0.86	149	149
negative regulation of cell growth	-0.041	0.13	-10000	0	-0.53	2	2
SMAD3/SMAD4/MYOD	-0.024	0.05	-10000	0	-10000	0	0
E2F5	0.013	0	-10000	0	-10000	0	0
E2F4	0.013	0	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF	-0.019	0.057	-10000	0	-10000	0	0
SMAD2-3/SMAD4/FOXO1-3a-4	0.001	0.064	-10000	0	-10000	0	0
TFDP1	0.013	0	-10000	0	-10000	0	0
SMAD3/SMAD4/AP1	-0.3	0.54	-10000	0	-1	117	117
SMAD3/SMAD4/RUNX2	-0.067	0.096	-10000	0	-0.52	3	3
TGIF2	0.013	0	-10000	0	-10000	0	0
TGIF1	0.013	0	-10000	0	-10000	0	0
ATF2	-0.005	0.12	-10000	0	-0.86	8	8

×

p75(NTR)-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Sortilin/TRAF6	-0.002	0.034	-9999	-0.66	1	1
Necdin/E2F1	-0.063	0.1	-9999	-0.81	2	2
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E	-0.038	0.12	-9999	-0.52	18	18
NGF (dimer)/p75(NTR)/BEX1	-0.3	0.3	-9999	-0.6	184	184
NT-4/5 (dimer)/p75(NTR)	-0.077	0.19	-9999	-0.69	29	29
IKBKB	0.013	0	-9999	-10000	0	0
AKT1	-0.005	0.13	-9999	-0.52	19	19
IKBKG	0.013	0	-9999	-10000	0	0
BDNF	-0.02	0.16	-9999	-0.72	17	17
MGDIs/NGR/p75(NTR)/LINGO1	-0.049	0.13	-9999	-0.6	16	16
FURIN	0.013	0	-9999	-10000	0	0
proBDNF (dimer)/p75(NTR)/Sortilin	-0.064	0.16	-9999	-0.59	28	28
LINGO1	0	0.062	-9999	-0.3	16	16
Sortilin/TRAF6/NRIF	-0.001	0.022	-9999	-0.43	1	1
proBDNF (dimer)	-0.02	0.16	-9999	-0.72	17	17
NTRK1	0	0.054	-9999	-0.3	12	12
RTN4R	0.013	0	-9999	-10000	0	0
neuron apoptosis	-0.016	0.15	-9999	-0.52	23	23
IRAK1	0.013	0	-9999	-10000	0	0
SHC1	-0.024	0.14	-9999	-0.6	18	18
ARHGDIA	0.013	0	-9999	-10000	0	0
RhoA/GTP	0	0	-9999	-10000	0	0
Gamma Secretase	0	0	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1	-0.042	0.12	-9999	-0.55	18	18
MAGEH1	0.013	0	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/Necdin	-0.045	0.13	-9999	-0.55	20	20
Mammalian IAPs/DIABLO	-0.029	0.12	-9999	-0.52	19	19
proNGF (dimer)	0.005	0.078	-9999	-0.85	3	3
MAGED1	0.013	0	-9999	-10000	0	0
APP	0.013	0	-9999	-10000	0	0
NT-4/5 (dimer)	-0.021	0.16	-9999	-0.85	12	12
ZNF274	0.013	0	-9999	-10000	0	0
RhoA/GDP/RHOGDI	-0.039	0.12	-9999	-0.52	18	18
NGF	0.005	0.079	-9999	-0.86	3	3
cell cycle arrest	0.042	0.17	-9999	-0.5	18	18
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK	0.007	0.092	-9999	-0.56	2	2
NT-4/5 (dimer)/p75(NTR)/TRAF6	-0.066	0.17	-9999	-0.62	29	29
NCSTN	0.013	0	-9999	-10000	0	0
mol:GTP	-0.048	0.14	-9999	-0.6	18	18
PSENEN	0.013	0	-9999	-10000	0	0
mol:ceramide	-0.013	0.13	-9999	-0.54	18	18
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs	0.019	0.076	-9999	-0.45	2	2
p75(NTR)/beta APP	-0.052	0.14	-9999	-0.66	16	16
BEX1	-0.38	0.43	-9999	-0.86	170	170
mol:GDP	-0.034	0.14	-9999	-0.61	18	18
NGF (dimer)	-0.091	0.13	-9999	-0.54	24	24
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI	-0.043	0.12	-9999	-0.55	16	16
PIK3R1	0.013	0	-9999	-10000	0	0
RAC1/GTP	-0.041	0.12	-9999	-0.53	18	18
MYD88	0.013	0	-9999	-10000	0	0
CHUK	0.013	0	-9999	-10000	0	0
NGF (dimer)/p75(NTR)/PKA	-0.048	0.14	-9999	-0.6	18	18
RHOB	0.011	0.045	-9999	-0.86	1	1
RHOA	0.013	0	-9999	-10000	0	0
MAGE-G1/E2F1	-0.06	0.088	-9999	-10000	0	0
NT3 (dimer)	-0.052	0.21	-9999	-0.63	38	38
TP53	-0.011	0.14	-9999	-0.48	29	29
PRDM4	-0.013	0.13	-9999	-0.55	18	18
BDNF (dimer)	-0.13	0.17	-9999	-0.57	33	33
PIK3CA	0.011	0.045	-9999	-0.86	1	1
SORT1	0.013	0	-9999	-10000	0	0
activation of caspase activity	-0.038	0.11	-9999	-0.51	18	18
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.044	0.13	-9999	-0.56	19	19
RHOC	0.013	0	-9999	-10000	0	0
XIAP	0.013	0	-9999	-10000	0	0
MAPK10	0.018	0.13	-9999	-0.46	17	17
DIABLO	0.013	0	-9999	-10000	0	0
SMPD2	-0.013	0.13	-9999	-0.55	18	18
APH1B	0.013	0	-9999	-10000	0	0
APH1A	0.013	0	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin	-0.048	0.14	-9999	-0.6	18	18
PSEN1	0.013	0	-9999	-10000	0	0
APAF-1/Pro-Caspase 9	0	0	-9999	-10000	0	0
NT3 (dimer)/p75(NTR)	-0.099	0.21	-9999	-0.7	37	37
MAPK8	0.017	0.14	-9999	-0.47	17	17
MAPK9	0.018	0.13	-9999	-0.63	3	3
APAF1	0.013	0	-9999	-10000	0	0
NTF3	-0.052	0.21	-9999	-0.64	38	38
NTF4	-0.021	0.16	-9999	-0.86	12	12
NDN	0.008	0.063	-9999	-0.86	2	2
RAC1/GDP	0	0	-9999	-10000	0	0
RhoA-B-C/GDP	-0.036	0.11	-9999	-0.5	18	18
p75 CTF/Sortilin/TRAF6/NRIF	-0.003	0.053	-9999	-1	1	1
RhoA-B-C/GTP	-0.047	0.13	-9999	-0.6	18	18
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.053	0.14	-9999	-0.51	29	29
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.058	0.15	-9999	-0.55	29	29
PRKACB	0.013	0	-9999	-10000	0	0
proBDNF (dimer)/p75 ECD	-0.026	0.13	-9999	-0.66	14	14
ChemicalAbstracts:86-01-1	0	0	-9999	-10000	0	0
BIRC3	-0.038	0.19	-9999	-0.68	28	28
BIRC2	0.013	0	-9999	-10000	0	0
neuron projection morphogenesis	0.068	0.18	-9999	-0.5	18	18
BAD	0.026	0.13	-9999	-0.45	17	17
RIPK2	0.013	0	-9999	-10000	0	0
NGFR	-0.064	0.2	-9999	-0.86	16	16
CYCS	-0.004	0.13	-9999	-0.51	18	18
ADAM17	0.011	0.045	-9999	-0.86	1	1
NGF (dimer)/p75(NTR)/TRAF6/RIP2	-0.044	0.13	-9999	-0.56	19	19
BCL2L11	0.026	0.13	-9999	-0.45	17	17
BDNF (dimer)/p75(NTR)	-0.077	0.18	-9999	-0.68	28	28
PI3K	-0.043	0.13	-9999	-0.56	19	19
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1	-0.042	0.12	-9999	-0.55	18	18
NDNL2	0.013	0	-9999	-10000	0	0
YWHAE	0.013	0	-9999	-10000	0	0
PRKCI	0.013	0	-9999	-10000	0	0
NGF (dimer)/p75(NTR)	-0.058	0.16	-9999	-0.69	18	18
ChemicalAbstracts:146-91-8	0	0	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE	-0.042	0.12	-9999	-0.55	18	18
TRAF6	0.011	0.045	-9999	-0.86	1	1
RAC1	0.013	0	-9999	-10000	0	0
PRKCZ	0.013	0	-9999	-10000	0	0
PLG	0	0.022	-9999	-10000	0	0
oligodendrocyte cell fate commitment	0	0	-9999	-10000	0	0
CASP6	-0.024	0.16	-9999	-0.52	30	30
SQSTM1	0.013	0	-9999	-10000	0	0
NGFRAP1	0.013	0	-9999	-10000	0	0
CASP3	0.028	0.12	-9999	-0.42	17	17
E2F1	-0.085	0.14	-9999	-0.3	119	119
CASP9	0.013	0	-9999	-10000	0	0
IKK complex	-0.014	0.065	-9999	-0.56	3	3
NGF (dimer)/TRKA	-0.012	0.068	-9999	-0.66	3	3
MMP7	-0.17	0.22	-9999	-0.36	186	186
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.04	0.12	-9999	-0.52	19	19
MMP3	-0.039	0.11	-9999	-0.3	55	55
APAF-1/Caspase 9	-0.043	0.12	-9999	-0.7	5	5

×

Fc-epsilon receptor I signaling in mast cells

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PPAP2A	0.012	0.016	-9999	-0.3	1	1
LAT2	-0.017	0.099	-9999	-0.33	5	5
AP1	-0.21	0.29	-9999	-0.6	123	123
mol:PIP3	-0.018	0.16	-9999	-0.45	23	23
IKBKB	0.003	0.092	-9999	-0.28	10	10
AKT1	-0.016	0.14	-9999	-0.5	4	4
IKBKG	0.003	0.092	-9999	-0.29	8	8
MS4A2	-0.068	0.13	-9999	-0.3	94	94
mol:Sphingosine-1-phosphate	0	0	-9999	-10000	0	0
PIK3CA	0.011	0.045	-9999	-0.86	1	1
MAP3K1	0.012	0.097	-9999	-0.42	5	5
mol:Ca2+	-0.009	0.12	-9999	-0.34	23	23
LYN	0.01	0.007	-9999	-10000	0	0
CBLB	-0.011	0.088	-9999	-0.33	3	3
SHC1	0.013	0	-9999	-10000	0	0
RasGAP/p62DOK	-0.087	0.2	-9999	-0.53	62	62
positive regulation of cell migration	0	0	-9999	-10000	0	0
INPP5D	-0.01	0.081	-9999	-0.3	28	28
PLD2	-0.049	0.15	-9999	-0.48	27	27
PTPN13	0.002	0.085	-9999	-0.5	1	1
PTPN11	0.012	0.006	-9999	-10000	0	0
GO:0007205	0	0	-9999	-10000	0	0
regulation of mast cell degranulation	0.018	0.1	-9999	-0.32	3	3
SYK	0.01	0.007	-9999	-10000	0	0
GRB2	0.013	0	-9999	-10000	0	0
LAT/PLCgamma1/GRB2/SLP76/GADs	-0.063	0.13	-9999	-0.44	33	33
LAT	-0.017	0.1	-9999	-0.45	7	7
PAK2	0.003	0.1	-9999	-0.46	6	6
NFATC2	-0.12	0.26	-9999	-0.78	48	48
HRAS	-0.006	0.11	-9999	-0.51	6	6
GAB2	0.013	0	-9999	-10000	0	0
PLA2G1B	0.03	0.017	-9999	-10000	0	0
Fc epsilon R1	-0.1	0.17	-9999	-0.52	43	43
Antigen/IgE/Fc epsilon R1	-0.091	0.16	-9999	-0.48	43	43
mol:GDP	-0.013	0.12	-9999	-0.54	7	7
JUN	-0.19	0.37	-9999	-0.86	88	88
mol:Ca++	0	0	-9999	-10000	0	0
PIK3R1	0.013	0.001	-9999	-10000	0	0
FOS	-0.22	0.39	-9999	-0.86	103	103
Antigen/IgE/Fc epsilon R1/LYN/SYK	-0.044	0.078	-9999	-0.34	4	4
CHUK	0.003	0.092	-9999	-0.29	8	8
KLRG1	-0.023	0.11	-9999	-0.4	12	12
VAV1	-0.022	0.11	-9999	-0.49	6	6
calcium-dependent protein kinase C activity	0	0	-9999	-10000	0	0
CBL	-0.011	0.088	-9999	-0.33	3	3
negative regulation of mast cell degranulation	-0.023	0.11	-9999	-0.39	12	12
BTK	-0.042	0.097	-9999	-0.51	7	7
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK	-0.051	0.19	-9999	-0.53	37	37
GAB2/PI3K/SHP2	-0.063	0.12	-9999	-0.53	5	5
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP	-0.019	0.095	-9999	-0.3	27	27
RAF1	0.018	0.021	-9999	-10000	0	0
Fc epsilon R1/FcgammaRIIB/SHIP	-0.11	0.21	-9999	-0.6	45	45
FCER1G	-0.009	0.08	-9999	-0.3	26	26
FCER1A	-0.076	0.23	-9999	-0.57	57	57
Antigen/IgE/Fc epsilon R1/Fyn	-0.081	0.15	-9999	-0.5	33	33
MAPK3	0.029	0.017	-9999	-10000	0	0
MAPK1	0.029	0.017	-9999	-10000	0	0
NFKB1	0.013	0	-9999	-10000	0	0
MAPK8	0.016	0.057	-9999	-0.61	2	2
DUSP1	-0.13	0.32	-9999	-0.86	62	62
NF-kappa-B/RelA	-0.018	0.041	-9999	-10000	0	0
actin cytoskeleton reorganization	-0.005	0.083	-9999	-10000	0	0
mol:Glucocorticoid Dexamethasone	0	0	-9999	-10000	0	0
PI3K	-0.039	0.094	-9999	-0.51	6	6
FER	-0.014	0.094	-9999	-0.39	5	5
RELA	0.013	0	-9999	-10000	0	0
ITK	-0.074	0.18	-9999	-0.55	46	46
SOS1	0.013	0	-9999	-10000	0	0
PLCG1	-0.01	0.12	-9999	-0.54	7	7
cytokine secretion	-0.014	0.03	-9999	-10000	0	0
SPHK1	-0.014	0.09	-9999	-0.33	3	3
PTK2	-0.005	0.085	-9999	-10000	0	0
NTAL/PLCgamma1/GRB2/SLP76/GADs	-0.065	0.14	-9999	-0.46	32	32
EDG1	0	0	-9999	-10000	0	0
mol:DAG	-0.011	0.15	-9999	-0.43	22	22
MAP2K2	0.025	0.018	-9999	-10000	0	0
MAP2K1	0.025	0.018	-9999	-10000	0	0
MAP2K7	0.013	0	-9999	-10000	0	0
KLRG1/SHP2	-0.047	0.091	-9999	-0.41	11	11
MAP2K4	0.02	0.007	-9999	-10000	0	0
Fc epsilon R1/FcgammaRIIB	-0.11	0.22	-9999	-0.64	42	42
mol:Choline	-0.049	0.15	-9999	-0.48	27	27
SHC/Grb2/SOS1	-0.031	0.065	-9999	-10000	0	0
FYN	0.013	0	-9999	-10000	0	0
DOK1	0.013	0	-9999	-10000	0	0
PXN	0.003	0.081	-9999	-10000	0	0
HCLS1	-0.013	0.093	-9999	-0.36	4	4
PRKCB	-0.01	0.12	-9999	-0.37	16	16
FCGR2B	-0.029	0.18	-9999	-0.77	20	20
IGHE	-0.001	0.006	-9999	-10000	0	0
KLRG1/SHIP	-0.024	0.11	-9999	-0.4	12	12
LCP2	0.004	0.052	-9999	-10000	0	0
PLA2G4A	-0.042	0.16	-9999	-0.53	26	26
RASA1	0.013	0	-9999	-10000	0	0
mol:Phosphatidic acid	-0.049	0.15	-9999	-0.48	27	27
IKK complex	0.018	0.074	-9999	-0.23	1	1
WIPF1	0.013	0	-9999	-10000	0	0

×

Visual signal transduction: Cones

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Cone Metarhodopsin II/Cone Transducin	-0.017	0.089	-9999	-0.51	12	12
RGS9BP	-0.047	0.22	-9999	-0.86	26	26
mol:GTP	0	0	-9999	-10000	0	0
GRK1	-0.071	0.26	-9999	-0.86	36	36
mol:Na +	-0.019	0.052	-9999	-10000	0	0
mol:ADP	-0.048	0.2	-9999	-0.67	36	36
GNAT2	0.009	0.023	-9999	-0.3	2	2
RGS9-1/Gbeta5/R9AP	-0.1	0.23	-9999	-0.59	66	66
mol:GDP	0	0	-9999	-10000	0	0
PDE6H/GNAT2/GTP	-0.001	0.012	-9999	-10000	0	0
GRK7	0.007	0.006	-9999	-10000	0	0
CNGB3	0.003	0.005	-9999	-10000	0	0
Cone Metarhodopsin II/X-Arrestin	0	0	-9999	-10000	0	0
mol:Ca2+	-0.011	0.059	-9999	-10000	0	0
Cone PDE6	-0.09	0.2	-9999	-0.51	66	66
Cone Metarhodopsin II	-0.052	0.16	-9999	-0.54	36	36
Na + (4 Units)	-0.022	0.053	-9999	-10000	0	0
GNAT2/GDP	-0.09	0.2	-9999	-0.51	66	66
GNB5	0.013	0	-9999	-10000	0	0
mol:GMP (4 units)	0.011	0.014	-9999	-10000	0	0
Cone Transducin	-0.018	0.094	-9999	-0.53	12	12
SLC24A2	-0.009	0.061	-9999	-0.3	16	16
GNB3/GNGT2	-0.022	0.12	-9999	-0.66	12	12
GNB3	-0.015	0.15	-9999	-0.86	12	12
GNAT2/GTP	-0.001	0.015	-9999	-10000	0	0
CNGA3	-0.023	0.099	-9999	-0.3	44	44
ARR3	0.004	0.006	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
cGMP/Cone CNG Channel	-0.019	0.052	-9999	-10000	0	0
mol:Pi	-0.1	0.22	-9999	-0.59	66	66
Cone CNG Channel	-0.014	0.039	-9999	-10000	0	0
mol:all-trans-retinal	0	0	-9999	-10000	0	0
mol:K +	-0.009	0.061	-9999	-0.3	16	16
RGS9	-0.085	0.27	-9999	-0.83	44	44
PDE6C	0.004	0.006	-9999	-10000	0	0
GNGT2	0.011	0.023	-9999	-10000	0	0
mol:cGMP (4 units)	0	0	-9999	-10000	0	0
PDE6H	0.004	0.006	-9999	-10000	0	0

×

IL1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
UBC13/UEV1A	0	0	-9999	-10000	0	0
PRKCZ	0.013	0	-9999	-10000	0	0
MAP3K7IP2	0	0	-9999	-10000	0	0
ERC1	0.013	0	-9999	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4	-0.029	0.067	-9999	-0.32	6	6
IRAK/TOLLIP	0.029	0.004	-9999	-10000	0	0
IKBKB	0.013	0	-9999	-10000	0	0
IKBKG	0.013	0	-9999	-10000	0	0
IL1 alpha/IL1R2	-0.13	0.27	-9999	-0.7	63	63
IL1A	-0.059	0.24	-9999	-0.8	33	33
IL1B	-0.031	0.19	-9999	-0.66	29	29
IRAK/TRAF6/p62/Atypical PKCs	-0.001	0.023	-9999	-0.45	1	1
IL1R2	-0.094	0.26	-9999	-0.62	64	64
IL1R1	0.013	0	-9999	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.023	0.056	-9999	-0.3	1	1
TOLLIP	0.013	0	-9999	-10000	0	0
TICAM2	0.006	0.077	-9999	-0.86	3	3
MAP3K3	0.013	0	-9999	-10000	0	0
TAK1/TAB1/TAB2	0	0	-9999	-10000	0	0
IKK complex/ELKS	0.066	0.023	-9999	-10000	0	0
JUN	-0.073	0.22	-9999	-0.45	92	92
MAP3K7	0.013	0	-9999	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/PI3K	-0.065	0.14	-9999	-0.5	28	28
IL1 alpha/IL1R1/IL1RAP/MYD88	-0.078	0.15	-9999	-0.54	30	30
PIK3R1	0.013	0	-9999	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4	-0.07	0.14	-9999	-0.5	30	30
IL1 beta fragment/IL1R1/IL1RAP	-0.077	0.15	-9999	-0.56	28	28
NFKB1	0.013	0	-9999	-10000	0	0
MAPK8	0.029	0.079	-9999	-0.49	8	8
IRAK1	0.023	0.004	-9999	-10000	0	0
IL1RN/IL1R1	-0.042	0.11	-9999	-0.66	8	8
IRAK4	0.013	0	-9999	-10000	0	0
PRKCI	0.013	0	-9999	-10000	0	0
TRAF6	0.011	0.045	-9999	-0.86	1	1
PI3K	-0.002	0.034	-9999	-0.66	1	1
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.002	0.086	-9999	-0.35	6	6
CHUK	0.013	0	-9999	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s	-0.077	0.15	-9999	-0.56	28	28
IL1 beta/IL1R2	-0.11	0.24	-9999	-0.63	61	61
IRAK/TRAF6/TAK1/TAB1/TAB2	-0.001	0.024	-9999	-0.47	1	1
NF kappa B1 p50/RelA	-0.055	0.12	-9999	-0.58	6	6
IRAK3	0.011	0.045	-9999	-0.86	1	1
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4	-0.068	0.14	-9999	-0.52	30	30
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.019	0.11	-9999	-0.35	30	30
IL1 alpha/IL1R1/IL1RAP	-0.089	0.16	-9999	-0.59	30	30
RELA	0.013	0	-9999	-10000	0	0
MAP3K7IP1	0	0	-9999	-10000	0	0
SQSTM1	0.013	0	-9999	-10000	0	0
MYD88	0.013	0	-9999	-10000	0	0
IRAK/TRAF6/MEKK3	-0.001	0.026	-9999	-0.5	1	1
IL1RAP	-0.076	0.14	-9999	-0.3	109	109
UBE2N	0.013	0	-9999	-10000	0	0
IRAK/TRAF6	-0.052	0.12	-9999	-0.52	9	9
CASP1	0.006	0.069	-9999	-0.52	5	5
IL1RN/IL1R2	-0.12	0.23	-9999	-0.64	52	52
IL1 beta fragment/IL1R1/IL1RAP/MYD88	-0.069	0.14	-9999	-0.53	28	28
TMEM189-UBE2V1	0.004	0.006	-9999	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.007	0.08	-9999	-0.34	3	3
PIK3CA	0.011	0.045	-9999	-0.86	1	1
IL1RN	-0.051	0.16	-9999	-0.37	63	63
TRAF6/TAK1/TAB1/TAB2	-0.001	0.025	-9999	-0.49	1	1
MAP2K6	0.024	0.067	-9999	-0.46	7	7

×

TCGA08_rtk_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
PDGFRA	-0.25	0.4	-10000	0	-0.86	116	116
HRAS	0.012	0.016	-10000	0	-0.3	1	1
EGFR	0.001	0.099	-10000	0	-0.86	5	5
AKT	0.017	0.025	-10000	0	-10000	0	0
FOXO3	0.013	0	-10000	0	-10000	0	0
AKT1	0.013	0	-10000	0	-10000	0	0
FOXO1	0.013	0	-10000	0	-10000	0	0
AKT3	0.013	0	-10000	0	-10000	0	0
FOXO4	0.013	0	-10000	0	-10000	0	0
MET	-0.11	0.15	-10000	0	-0.3	154	154
PIK3CA	0.011	0.045	-10000	0	-0.86	1	1
PIK3CB	0.013	0	-10000	0	-10000	0	0
NRAS	0.013	0	-10000	0	-10000	0	0
PIK3CG	-0.009	0.13	-10000	0	-0.75	11	11
PIK3R3	0.011	0.045	-10000	0	-0.86	1	1
PIK3R2	0.013	0	-10000	0	-10000	0	0
NF1	0.013	0	-10000	0	-10000	0	0
RAS	-0.063	0.1	-10000	0	-0.28	37	37
ERBB2	0.013	0	-10000	0	-10000	0	0
proliferation/survival/translation	-0.024	0.022	-10000	0	-10000	0	0
PI3K	-0.041	0.098	0.23	1	-0.23	41	42
PIK3R1	0.013	0	-10000	0	-10000	0	0
KRAS	0.013	0	-10000	0	-10000	0	0
FOXO	0.024	0.026	0.2	1	-10000	0	1
AKT2	0.013	0	-10000	0	-10000	0	0
PTEN	0.011	0.045	-10000	0	-0.86	1	1

×

Regulation of Androgen receptor activity

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
HDAC1	0.021	0.005	-9999	-10000	0	0
SMARCC1	0.013	0.014	-9999	-10000	0	0
REL	-0.018	0.18	-9999	-0.85	16	16
HDAC7	-0.022	0.12	-9999	-0.57	7	7
JUN	-0.19	0.36	-9999	-0.86	88	88
EP300	0.012	0.001	-9999	-10000	0	0
KAT2B	0.011	0.004	-9999	-10000	0	0
KAT5	0.014	0.001	-9999	-10000	0	0
MAPK14	0	0.087	-9999	-0.67	6	6
FOXO1	0.012	0.001	-9999	-10000	0	0
T-DHT/AR	-0.035	0.12	-9999	-0.59	8	8
MAP2K6	-0.007	0.11	-9999	-0.86	6	6
BRM/BAF57	-0.001	0.003	-9999	-10000	0	0
MAP2K4	0.008	0.007	-9999	-10000	0	0
SMARCA2	0.009	0.006	-9999	-10000	0	0
PDE9A	0.012	0.053	-9999	-10000	0	0
NCOA2	-0.047	0.21	-9999	-0.86	23	23
CEBPA	0.005	0.089	-9999	-0.86	4	4
EHMT2	0.009	0.006	-9999	-10000	0	0
cell proliferation	-0.059	0.13	-9999	-0.5	5	5
NR0B1	-0.002	0.038	-9999	-10000	0	0
EGR1	-0.18	0.36	-9999	-0.86	84	84
RXRs/9cRA	-0.12	0.056	-9999	-0.53	2	2
AR/RACK1/Src	-0.11	0.14	-9999	-0.62	7	7
AR/GR	-0.12	0.18	-9999	-0.36	96	96
GNB2L1	0.006	0.007	-9999	-10000	0	0
PKN1	0.011	0.004	-9999	-10000	0	0
RCHY1	0.013	0	-9999	-10000	0	0
epidermal growth factor receptor activity	-0.006	0.005	-9999	-10000	0	0
MAPK8	0.007	0.051	-9999	-0.66	2	2
T-DHT/AR/TIF2/CARM1	-0.1	0.19	-9999	-0.66	27	27
SRC	0.005	0.083	-9999	-0.5	8	8
NR3C1	0.013	0	-9999	-10000	0	0
KLK3	-0.39	0.57	-9999	-1.3	102	102
APPBP2	0.013	0.004	-9999	-10000	0	0
TRIM24	0.009	0.006	-9999	-10000	0	0
T-DHT/AR/TIP60	-0.044	0.12	-9999	-0.61	8	8
TMPRSS2	-0.059	0.32	-9999	-1.3	24	24
RXRG	-0.26	0.11	-9999	-0.86	2	2
mol:9cRA	-0.002	0.002	-9999	-10000	0	0
RXRA	0.012	0.001	-9999	-10000	0	0
RXRB	0.012	0.001	-9999	-10000	0	0
CARM1	0.006	0.007	-9999	-10000	0	0
NR2C2	0.005	0.077	-9999	-0.86	3	3
KLK2	-0.48	0.43	-9999	-0.84	216	216
AR	-0.14	0.2	-9999	-0.38	151	151
SENP1	0.012	0.002	-9999	-10000	0	0
HSP90AA1	0.013	0	-9999	-10000	0	0
MDM2	0.022	0.014	-9999	-10000	0	0
SRY	0.009	0.014	-9999	-10000	0	0
GATA2	0.012	0.016	-9999	-0.3	1	1
MYST2	0.014	0.002	-9999	-10000	0	0
HOXB13	-0.016	0.057	-9999	-0.31	11	11
T-DHT/AR/RACK1/Src	-0.068	0.12	-9999	-0.6	8	8
positive regulation of transcription	0.012	0.016	-9999	-0.3	1	1
DNAJA1	0.013	0.004	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.034	0.004	-9999	-10000	0	0
NCOA1	0.012	0.009	-9999	-10000	0	0
SPDEF	-0.024	0.097	-9999	-0.3	40	40
T-DHT/AR/TIF2	-0.037	0.12	-9999	-0.41	22	22
T-DHT/AR/Hsp90	-0.046	0.11	-9999	-0.61	8	8
GSK3B	0.009	0.006	-9999	-10000	0	0
NR2C1	0.014	0.003	-9999	-10000	0	0
mol:T-DHT	0.003	0.086	-9999	-0.54	8	8
SIRT1	0.012	0.001	-9999	-10000	0	0
ZMIZ2	0.022	0.015	-9999	-10000	0	0
POU2F1	0.03	0.02	-9999	-10000	0	0
T-DHT/AR/DAX-1	-0.064	0.11	-9999	-0.61	8	8
CREBBP	0.011	0.004	-9999	-10000	0	0
SMARCE1	0.009	0.006	-9999	-10000	0	0

×

Signaling events mediated by PTP1B

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
PDGFRB	0.013	0	-10000	0	-10000	0	0
Jak2/Leptin Receptor	-0.019	0.1	-10000	0	-0.49	6	6
PTP1B/AKT1	-0.002	0.065	-10000	0	-0.41	2	2
FYN	0.013	0	-10000	0	-10000	0	0
p210 bcr-abl/PTP1B	-0.01	0.071	-10000	0	-0.39	3	3
EGFR	0	0.1	-10000	0	-0.86	5	5
EGF/EGFR	-0.085	0.19	-10000	0	-0.52	56	56
CSF1	0.004	0.089	-10000	0	-0.86	4	4
AKT1	0.013	0.001	-10000	0	-10000	0	0
INSR	0.013	0.001	-10000	0	-10000	0	0
PTP1B/N-cadherin	-0.093	0.13	-10000	0	-0.51	19	19
Insulin Receptor/Insulin	-0.014	0.043	-10000	0	-10000	0	0
HCK	-0.007	0.076	-10000	0	-0.3	24	24
CRK	0.013	0	-10000	0	-10000	0	0
TYK2	-0.002	0.067	-10000	0	-0.42	2	2
EGF	-0.11	0.3	-10000	0	-0.86	51	51
YES1	0.013	0	-10000	0	-10000	0	0
CAV1	-0.018	0.11	-10000	0	-0.49	4	4
TXN	0.011	0.017	-10000	0	-10000	0	0
PTP1B/IRS1/GRB2	-0.063	0.15	-10000	0	-0.5	38	38
cell migration	0.01	0.071	0.39	3	-10000	0	3
STAT3	0.013	0.001	-10000	0	-10000	0	0
PRLR	-0.043	0.19	-10000	0	-0.86	18	18
ITGA2B	-0.095	0.29	-10000	0	-0.86	47	47
CSF1R	0.009	0.035	-10000	0	-10000	0	0
Prolactin Receptor/Prolactin	-0.037	0.15	-10000	0	-0.67	18	18
FGR	0.01	0.032	-10000	0	-10000	0	0
PTP1B/p130 Cas	-0.002	0.067	-10000	0	-0.42	2	2
Crk/p130 Cas	-0.016	0.05	-10000	0	-0.4	2	2
DOK1	0.007	0.063	-10000	0	-0.38	2	2
JAK2	-0.007	0.084	-10000	0	-0.39	6	6
Jak2/Leptin Receptor/Leptin	-0.066	0.16	-10000	0	-0.61	27	27
PIK3R1	0.013	0	-10000	0	-10000	0	0
PTPN1	-0.01	0.071	-10000	0	-0.4	3	3
LYN	0.013	0	-10000	0	-10000	0	0
CDH2	-0.18	0.21	-10000	0	-0.86	16	16
SRC	0.012	0.029	-10000	0	-10000	0	0
ITGB3	-0.016	0.15	-10000	0	-0.86	12	12
CAT1/PTP1B	-0.093	0.15	-10000	0	-0.4	38	38
CAPN1	0.013	0.004	-10000	0	-10000	0	0
CSK	0.013	0	-10000	0	-10000	0	0
PI3K	-0.014	0.045	-10000	0	-0.63	1	1
mol:H2O2	0	0.004	-10000	0	-10000	0	0
STAT3 (dimer)	-0.066	0.17	-10000	0	-0.65	27	27
negative regulation of transcription	-0.006	0.084	-10000	0	-0.38	7	7
FCGR2A	-0.007	0.085	-10000	0	-0.32	23	23
FER	0.007	0.064	-10000	0	-0.87	2	2
alphaIIb/beta3 Integrin	-0.1	0.26	-10000	0	-0.72	53	53
BLK	-0.26	0.39	-10000	0	-0.86	113	113
Insulin Receptor/Insulin/Shc	0	0	-10000	0	-10000	0	0
RHOA	0.013	0.004	-10000	0	-10000	0	0
LEPR	0	0.1	-10000	0	-0.85	5	5
BCAR1	0.013	0	-10000	0	-10000	0	0
p210 bcr-abl/Grb2	0.013	0	-10000	0	-10000	0	0
mol:NADPH	0	0.004	-10000	0	-10000	0	0
TRPV6	-0.13	0.19	-10000	0	-0.49	37	37
PRL	0.001	0.017	-10000	0	-0.29	1	1
SOCS3	-0.098	0.39	-10000	0	-1.5	27	27
SPRY2	0.011	0.017	-10000	0	-10000	0	0
Insulin Receptor/Insulin/IRS1	-0.056	0.17	-10000	0	-0.59	36	36
CSF1/CSF1R	-0.023	0.075	-10000	0	-0.49	6	6
Ras protein signal transduction	0.02	0.023	-10000	0	-10000	0	0
IRS1	-0.07	0.26	-10000	0	-0.86	36	36
INS	0	0.001	-10000	0	-10000	0	0
LEP	-0.009	0.067	-10000	0	-0.3	19	19
STAT5B	-0.005	0.07	-10000	0	-0.36	3	3
STAT5A	-0.005	0.07	-10000	0	-0.36	3	3
GRB2	0.013	0	-10000	0	-10000	0	0
PDGFB-D/PDGFRB	-0.002	0.067	-10000	0	-0.42	2	2
CSN2	-0.006	0.052	-10000	0	-10000	0	0
PIK3CA	0.011	0.045	-10000	0	-0.86	1	1
LAT	0.001	0.072	-10000	0	-0.55	5	5
YBX1	0.021	0.002	-10000	0	-10000	0	0
LCK	-0.012	0.11	-10000	0	-0.4	23	23
SHC1	0.013	0	-10000	0	-10000	0	0
NOX4	-0.12	0.15	-10000	0	-0.3	156	156

×

Aurora C signaling

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
INCENP	0.013	0	-9999	-10000	0	0
Aurora C/Aurora B/INCENP	-0.033	0.061	-9999	-10000	0	0
metaphase	0	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
H3F3B	-0.009	0.017	-9999	-10000	0	0
AURKB	-0.056	0.13	-9999	-0.3	84	84
AURKC	0.005	0.05	-9999	-0.3	10	10

×

RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1	0.036	0.038	-9999	-10000	0	0
VDR	0.012	0.016	-9999	-10000	0	0
FAM120B	0.013	0	-9999	-10000	0	0
RXRs/LXRs/DNA/9cRA	-0.051	0.1	-9999	-0.34	33	33
RXRs/LXRs/DNA/Oxysterols	-0.042	0.15	-9999	-0.45	43	43
MED1	0.013	0	-9999	-10000	0	0
mol:9cRA	0	0.017	-9999	-10000	0	0
RARs/THRs/DNA/Src-1	0.024	0.074	-9999	-0.34	15	15
RXRs/NUR77	-0.27	0.27	-9999	-0.66	116	116
RXRs/PPAR	-0.048	0.061	-9999	-0.4	7	7
NCOR2	0.013	0	-9999	-10000	0	0
VDR/VDR/Vit D3	-0.001	0.01	-9999	-10000	0	0
RARs/VDR/DNA/Vit D3	-0.013	0.082	-9999	-0.51	10	10
RARA	0.013	0	-9999	-10000	0	0
NCOA1	0.013	0	-9999	-10000	0	0
VDR/VDR/DNA	0.012	0.016	-9999	-10000	0	0
RARs/RARs/DNA/9cRA	-0.013	0.081	-9999	-0.5	10	10
RARG	0.013	0	-9999	-10000	0	0
RPS6KB1	0.051	0.031	-9999	-10000	0	0
RARs/THRs/DNA/SMRT	0.024	0.074	-9999	-0.34	15	15
THRA	0.013	0	-9999	-10000	0	0
mol:Bile acids	0	0	-9999	-10000	0	0
VDR/Vit D3/DNA	-0.001	0.01	-9999	-10000	0	0
RXRs/PPAR/9cRA/PGJ2/DNA	-0.11	0.078	-9999	-0.58	2	2
NR1H4	0	0.035	-9999	-0.3	5	5
RXRs/LXRs/DNA	-0.087	0.086	-9999	-0.56	2	2
NR1H2	0.015	0.012	-9999	-10000	0	0
NR1H3	0.015	0.014	-9999	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.095	0.064	-9999	-0.53	2	2
NR4A1	-0.25	0.4	-9999	-0.85	116	116
mol:ATRA	0	0	-9999	-10000	0	0
RXRs/FXR/9cRA/MED1	-0.042	0.045	-9999	-0.31	2	2
RXRG	-0.26	0.11	-9999	-0.38	34	34
RXR alpha/CCPG	0	0.003	-9999	-10000	0	0
RXRA	0.015	0.012	-9999	-10000	0	0
RXRB	0.014	0.014	-9999	-10000	0	0
THRB	0.001	0.099	-9999	-0.86	5	5
PPARG	-0.002	0.1	-9999	-0.61	9	9
PPARD	0.013	0	-9999	-10000	0	0
TNF	-0.13	0.41	-9999	-1.3	43	43
mol:Oxysterols	0.001	0.016	-9999	-10000	0	0
cholesterol transport	-0.041	0.15	-9999	-0.44	43	43
PPARA	0.013	0	-9999	-10000	0	0
mol:Vit D3	0	0	-9999	-10000	0	0
RARB	-0.01	0.14	-9999	-0.86	10	10
RXRs/NUR77/BCL2	-0.19	0.2	-9999	-0.46	129	129
SREBF1	-0.031	0.14	-9999	-0.63	1	1
RXRs/RXRs/DNA/9cRA	-0.11	0.078	-9999	-0.58	2	2
ABCA1	-0.031	0.14	-9999	-0.63	1	1
RARs/THRs	-0.019	0.095	-9999	-0.49	15	15
RXRs/FXR	-0.11	0.066	-9999	-0.56	2	2
BCL2	-0.038	0.2	-9999	-0.86	22	22

×

Effects of Botulinum toxin

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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
STX1A	0.012	0	-9999	-10000	0	0
UniProt:P19321	0	0	-9999	-10000	0	0
RIMS1/UNC13B	-0.001	0.01	-9999	-10000	0	0
STXBP1	0.013	0	-9999	-10000	0	0
ACh/CHRNA1	-0.015	0.067	-9999	-0.25	10	10
RAB3GAP2/RIMS1/UNC13B	0	0.007	-9999	-10000	0	0
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	0.011	0.016	-9999	-0.3	1	1
mol:ACh	-0.008	0.041	-9999	-0.16	22	22
RAB3GAP2	0.013	0	-9999	-10000	0	0
STX1A/SNAP25/VAMP2	-0.014	0.044	-9999	-10000	0	0
UniProt:P10844	0	0	-9999	-10000	0	0
muscle contraction	-0.015	0.067	-9999	-0.25	10	10
UNC13B	0.013	0	-9999	-10000	0	0
CHRNA1	-0.017	0.096	-9999	-0.32	33	33
UniProt:P10845	0	0	-9999	-10000	0	0
ACh/Synaptotagmin 1	-0.12	0.17	-9999	-0.41	57	57
SNAP25	-0.033	0.097	-9999	-0.39	22	22
VAMP2	0.007	0	-9999	-10000	0	0
SYT1	-0.18	0.24	-9999	-0.38	183	183
UniProt:Q00496	0	0	-9999	-10000	0	0
STXIA/STXBP1	0.019	0	-9999	-10000	0	0
STX1A/SNAP25 fragment 1/VAMP2	-0.014	0.044	-9999	-10000	0	0

×

Neurotrophic factor-mediated Trk receptor signaling

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
CRKL	0.013	0	-10000	0	-10000	0	0
RAS family/GTP/Tiam1	-0.063	0.086	-10000	0	-0.35	19	19
NT3 (dimer)/TRKC	-0.094	0.21	-10000	0	-0.71	34	34
NT3 (dimer)/TRKB	-0.088	0.19	-10000	0	-0.61	40	40
SHC/Grb2/SOS1/GAB1/PI3K	0.038	0.019	-10000	0	-0.34	1	1
RAPGEF1	0.013	0	-10000	0	-10000	0	0
BDNF	-0.02	0.16	-10000	0	-0.72	17	17
PIK3CA	0.011	0.045	-10000	0	-0.86	1	1
DYNLT1	0.013	0	-10000	0	-10000	0	0
NTRK1	0	0.054	-10000	0	-0.3	12	12
NTRK2	0.006	0.077	-10000	0	-0.86	3	3
NTRK3	-0.059	0.18	-10000	0	-0.4	66	66
NT-4/5 (dimer)/TRKB	-0.069	0.17	-10000	0	-0.61	31	31
neuron apoptosis	0.042	0.097	0.45	10	-10000	0	10
SHC 2-3/Grb2	-0.045	0.11	-10000	0	-0.49	10	10
SHC1	0.013	0	-10000	0	-10000	0	0
SHC2	-0.03	0.095	-10000	0	-0.68	4	4
SHC3	-0.049	0.11	-10000	0	-0.62	8	8
STAT3 (dimer)	0.017	0.025	-10000	0	-10000	0	0
NT3 (dimer)/TRKA	-0.089	0.19	-10000	0	-0.62	37	37
RIN/GDP	-0.01	0.066	-10000	0	-0.28	3	3
GIPC1	0.013	0	-10000	0	-10000	0	0
KRAS	0.013	0	-10000	0	-10000	0	0
DNAJA3	-0.033	0.099	-10000	0	-0.46	16	16
RIN/GTP	0	0	-10000	0	-10000	0	0
CCND1	0.025	0.045	-10000	0	-10000	0	0
MAGED1	0.013	0	-10000	0	-10000	0	0
PTPN11	0.013	0	-10000	0	-10000	0	0
RICS	0	0	-10000	0	-10000	0	0
NT-4/5 (dimer)	-0.021	0.16	-10000	0	-0.85	12	12
SHC/GRB2/SOS1	0	0	-10000	0	-10000	0	0
GRB2	0.013	0	-10000	0	-10000	0	0
NGF (dimer)/TRKA/MATK	-0.019	0.087	-10000	0	-0.58	8	8
TRKA/NEDD4-2	-0.006	0.033	-10000	0	-10000	0	0
ELMO1	-0.34	0.43	-10000	0	-0.86	152	152
RhoG/GTP/ELMO1/DOCK1	-0.24	0.29	-10000	0	-0.59	152	152
NGF	0.005	0.079	-10000	0	-0.86	3	3
HRAS	0.012	0.016	-10000	0	-0.3	1	1
DOCK1	0.011	0.045	-10000	0	-0.86	1	1
GAB2	0.013	0	-10000	0	-10000	0	0
RIT2	0.002	0.005	-10000	0	-10000	0	0
RIT1	0.013	0	-10000	0	-10000	0	0
FRS2	0.013	0	-10000	0	-10000	0	0
DNM1	-0.029	0.18	-10000	0	-0.83	19	19
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.013	0	-10000	0	-10000	0	0
SH2B1 (homopentamer)	0	0	-10000	0	-10000	0	0
RhoG/GTP	-0.22	0.24	-10000	0	-0.49	165	165
mol:GDP	-0.017	0.095	-10000	0	-0.41	4	4
NGF (dimer)	0.005	0.078	-10000	0	-0.85	3	3
RhoG/GDP	-0.27	0.33	-10000	0	-0.67	152	152
RIT1/GDP	-0.005	0.066	-10000	0	-0.29	2	2
TIAM1	-0.16	0.16	-10000	0	-0.3	210	210
PIK3R1	0.013	0	-10000	0	-10000	0	0
BDNF (dimer)/TRKB	-0.025	0.13	-10000	0	-0.65	14	14
KIDINS220/CRKL/C3G	0	0	-10000	0	-10000	0	0
SHC/RasGAP	0	0	-10000	0	-10000	0	0
FRS2 family/SHP2	0	0	-10000	0	-10000	0	0
SHC/GRB2/SOS1/GAB1	0	0	-10000	0	-10000	0	0
RIT1/GTP	0	0	-10000	0	-10000	0	0
NT3 (dimer)	-0.052	0.21	-10000	0	-0.63	38	38
RAP1/GDP	-0.019	0.045	-10000	0	-10000	0	0
KIDINS220/CRKL	0.013	0	-10000	0	-10000	0	0
BDNF (dimer)	-0.02	0.16	-10000	0	-0.72	17	17
ubiquitin-dependent protein catabolic process	-0.01	0.057	-10000	0	-0.57	3	3
Schwann cell development	-0.043	0.033	-10000	0	-10000	0	0
EHD4	0.013	0	-10000	0	-10000	0	0
FRS2 family/GRB2/SOS1	0	0	-10000	0	-10000	0	0
FRS2 family/SHP2/CRK family/C3G/GAB2	0.042	0	-10000	0	-10000	0	0
RAP1B	0.013	0	-10000	0	-10000	0	0
RAP1A	0.013	0	-10000	0	-10000	0	0
CDC42/GTP	-0.074	0.17	-10000	0	-0.7	13	13
ABL1	0.013	0	-10000	0	-10000	0	0
SH2B family/GRB2/SOS1	0	0	-10000	0	-10000	0	0
Rap1/GTP	-0.008	0.04	-10000	0	-10000	0	0
STAT3	0.017	0.025	-10000	0	-10000	0	0
axon guidance	-0.07	0.16	-10000	0	-0.65	13	13
MAPK3	0.015	0.085	-10000	0	-0.52	8	8
MAPK1	0.015	0.085	-10000	0	-0.52	8	8
CDC42/GDP	-0.005	0.066	-10000	0	-0.27	3	3
NTF3	-0.052	0.21	-10000	0	-0.64	38	38
NTF4	-0.021	0.16	-10000	0	-0.86	12	12
NGF (dimer)/TRKA/FAIM	-0.01	0.057	-10000	0	-0.58	3	3
PI3K	-0.002	0.034	-10000	0	-0.66	1	1
FRS3	0.013	0	-10000	0	-10000	0	0
FAIM	0.013	0	-10000	0	-10000	0	0
GAB1	0.013	0	-10000	0	-10000	0	0
RASGRF1	-0.12	0.12	-10000	0	-0.5	22	22
SOS1	0.013	0	-10000	0	-10000	0	0
MCF2L	-0.057	0.19	-10000	0	-0.62	33	33
RGS19	0.013	0	-10000	0	-10000	0	0
CDC42	0.013	0	-10000	0	-10000	0	0
RAS family/GTP	0.004	0.044	-10000	0	-10000	0	0
Rac1/GDP	-0.005	0.066	-10000	0	-0.29	2	2
NGF (dimer)/TRKA/GRIT	-0.01	0.059	-10000	0	-0.58	3	3
neuron projection morphogenesis	-0.001	0.1	-10000	0	-0.69	1	1
NGF (dimer)/TRKA/NEDD4-2	-0.01	0.057	-10000	0	-0.58	3	3
MAP2K1	0.042	0	-10000	0	-10000	0	0
NGFR	-0.064	0.2	-10000	0	-0.86	16	16
NGF (dimer)/TRKA/GIPC/GAIP	0.013	0.092	-10000	0	-0.36	20	20
RAS family/GTP/PI3K	0.031	0.024	-10000	0	-0.43	1	1
FRS2 family/SHP2/GRB2/SOS1	0	0	-10000	0	-10000	0	0
NRAS	0.013	0	-10000	0	-10000	0	0
GRB2/SOS1	0	0	-10000	0	-10000	0	0
PRKCI	0.013	0	-10000	0	-10000	0	0
ChemicalAbstracts:146-91-8	0	0	-10000	0	-10000	0	0
RAC1	0.013	0	-10000	0	-10000	0	0
PRKCZ	0.013	0	-10000	0	-10000	0	0
MAPKKK cascade	-0.009	0.063	-10000	0	-0.62	3	3
RASA1	0.013	0	-10000	0	-10000	0	0
TRKA/c-Abl	-0.006	0.033	-10000	0	-10000	0	0
SQSTM1	0.013	0	-10000	0	-10000	0	0
BDNF (dimer)/TRKB/GIPC	-0.023	0.12	-10000	0	-0.6	14	14
NGF (dimer)/TRKA/p62/Atypical PKCs	-0.007	0.047	-10000	0	-0.49	3	3
MATK	-0.002	0.1	-10000	0	-0.61	9	9
NEDD4L	0.013	0	-10000	0	-10000	0	0
RAS family/GDP	-0.016	0.044	-10000	0	-10000	0	0
NGF (dimer)/TRKA	-0.036	0.11	-10000	0	-0.47	19	19
Rac1/GTP	-0.19	0.15	-10000	0	-0.36	153	153
FRS2 family/SHP2/CRK family	0	0	-10000	0	-10000	0	0

×

Aurora B 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Condensin I complex	-0.002	0.079	-9999	-10000	0	0
STMN1	-0.019	0.089	-9999	-0.38	1	1
Aurora B/RasGAP/Survivin	-0.025	0.11	-9999	-0.57	1	1
Chromosomal passenger complex/Cul3 protein complex	0.008	0.068	-9999	-0.29	9	9
BIRC5	-0.021	0.1	-9999	-0.32	39	39
DES	-0.39	0.3	-9999	-0.62	234	234
Aurora C/Aurora B/INCENP	-0.01	0.073	-9999	-10000	0	0
Aurora B/TACC1	-0.018	0.071	-9999	-10000	0	0
Aurora B/PP2A	-0.024	0.086	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CBX5	0.005	0.024	-9999	-10000	0	0
mitotic metaphase/anaphase transition	0.001	0.003	-9999	-10000	0	0
NDC80	-0.054	0.15	-9999	-0.37	57	57
Cul3 protein complex	-0.016	0.085	-9999	-0.57	8	8
KIF2C	-0.002	0.041	-9999	-10000	0	0
PEBP1	0.01	0.005	-9999	-10000	0	0
KIF20A	-0.048	0.12	-9999	-0.3	74	74
mol:GDP	0	0	-9999	-10000	0	0
Aurora B/RasGAP	-0.024	0.086	-9999	-10000	0	0
SEPT1	0.009	0.035	-9999	-0.3	5	5
SMC2	0.013	0	-9999	-10000	0	0
SMC4	0.013	0	-9999	-10000	0	0
NSUN2/NPM1/Nucleolin	0.007	0.042	-9999	-10000	0	0
PSMA3	0.013	0	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	-0.001	0.002	-9999	-10000	0	0
H3F3B	-0.005	0.052	-9999	-10000	0	0
AURKB	-0.047	0.13	-9999	-0.3	84	84
AURKC	0.005	0.05	-9999	-0.3	10	10
CDCA8	0.009	0.029	-9999	-0.31	3	3
cytokinesis	-0.068	0.078	-9999	-0.41	3	3
Aurora B/Septin1	-0.028	0.097	-9999	-0.4	6	6
AURKA	0.012	0.002	-9999	-10000	0	0
INCENP	0.011	0.006	-9999	-10000	0	0
KLHL13	-0.014	0.13	-9999	-0.55	18	18
BUB1	-0.11	0.15	-9999	-0.3	147	147
hSgo1/Aurora B/Survivin	-0.028	0.12	-9999	-0.43	16	16
EVI5	0.014	0.001	-9999	-10000	0	0
RhoA/GTP	-0.031	0.071	-9999	-0.34	3	3
SGOL1	-0.002	0.066	-9999	-0.3	18	18
CENPA	-0.008	0.069	-9999	-0.24	6	6
NCAPG	-0.026	0.1	-9999	-0.3	47	47
Aurora B/HC8 Proteasome	-0.024	0.086	-9999	-10000	0	0
NCAPD2	0.013	0	-9999	-10000	0	0
Aurora B/PP1-gamma	-0.024	0.086	-9999	-10000	0	0
RHOA	0.013	0	-9999	-10000	0	0
NCAPH	-0.04	0.12	-9999	-0.3	65	65
NPM1	-0.01	0.045	-9999	-10000	0	0
RASA1	0.013	0	-9999	-10000	0	0
KLHL9	0.013	0	-9999	-10000	0	0
mitotic prometaphase	-0.001	0.003	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	-0.024	0.086	-9999	-10000	0	0
PPP1CC	0.013	0	-9999	-10000	0	0
Centraspindlin	-0.035	0.079	-9999	-0.34	11	11
RhoA/GDP	0	0	-9999	-10000	0	0
NSUN2	-0.01	0.045	-9999	-10000	0	0
MYLK	-0.005	0.052	-9999	-10000	0	0
KIF23	-0.006	0.074	-9999	-10000	0	0
VIM	-0.018	0.088	-9999	-10000	0	0
RACGAP1	0.012	0.003	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
NCL	-0.01	0.045	-9999	-10000	0	0
Chromosomal passenger complex	-0.015	0.08	-9999	-0.23	22	22
Chromosomal passenger complex/EVI5	0.013	0.12	-9999	-0.41	4	4
TACC1	0.013	0	-9999	-10000	0	0
PPP2R5D	0.013	0	-9999	-10000	0	0
CUL3	0.013	0	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0

×

LPA4-mediated signaling events

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
ADCY4	0.016	0.053	-9999	-0.58	3	3
ADCY5	-0.07	0.22	-9999	-0.58	56	56
ADCY6	0.016	0.053	-9999	-0.58	3	3
ADCY7	0.016	0.053	-9999	-0.58	3	3
ADCY1	0.007	0.086	-9999	-0.6	7	7
ADCY2	-0.045	0.19	-9999	-0.6	37	37
ADCY3	0.016	0.053	-9999	-0.58	3	3
ADCY8	-0.11	0.096	-9999	-0.72	3	3
PRKCE	0.007	0.061	-9999	-0.67	3	3
ADCY9	0.016	0.053	-9999	-0.58	3	3
mol:DAG	0	0	-9999	-10000	0	0
cAMP biosynthetic process	-0.056	0.11	-9999	-0.37	25	25

×

ErbB4 signaling events

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
ErbB4/ErbB4/HBEGF/HBEGF	-0.014	0.089	-10000	0	-10000	0	0
epithelial cell differentiation	-0.044	0.099	-10000	0	-0.5	8	8
ITCH	0.024	0.021	-10000	0	-10000	0	0
WWP1	-0.003	0.08	-10000	0	-10000	0	0
FYN	0.013	0	-10000	0	-10000	0	0
EGFR	0.001	0.099	-10000	0	-0.86	5	5
PRL	0.001	0.016	-10000	0	-0.3	1	1
neuron projection morphogenesis	-0.002	0.15	-10000	0	-0.55	8	8
PTPRZ1	-0.019	0.15	-10000	0	-0.86	10	10
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC	-0.063	0.14	-10000	0	-0.62	8	8
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta	-0.05	0.18	-10000	0	-0.56	37	37
ADAM17	0.022	0.049	-10000	0	-0.85	1	1
ErbB4/ErbB4	-0.013	0.1	-10000	0	-10000	0	0
ErbB4/ErbB4/neuregulin 3/neuregulin 3	-0.051	0.18	-10000	0	-0.59	29	29
NCOR1	0.013	0	-10000	0	-10000	0	0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn	-0.072	0.16	-10000	0	-0.53	37	37
GRIN2B	-0.035	0.17	-10000	0	-0.5	37	37
ErbB4/ErbB2/betacellulin	-0.033	0.098	-10000	0	-0.66	7	7
STAT1	0.005	0.05	-10000	0	-0.3	10	10
HBEGF	0	0.062	-10000	0	-0.3	16	16
PRLR	-0.043	0.19	-10000	0	-0.58	36	36
E4ICDs/ETO2	-0.007	0.087	-10000	0	-10000	0	0
axon guidance	-0.001	0.083	-10000	0	-10000	0	0
NEDD4	0.024	0.021	-10000	0	-10000	0	0
Prolactin receptor/Prolactin receptor/Prolactin	-0.042	0.15	-10000	0	-0.67	18	18
CBFA2T3	0.012	0.016	-10000	0	-10000	0	0
ErbB4/ErbB2/HBEGF	-0.028	0.056	-10000	0	-0.67	1	1
MAPK3	-0.011	0.15	-10000	0	-0.57	8	8
STAT1 (dimer)	-0.011	0.091	-10000	0	-10000	0	0
MAPK1	-0.011	0.15	-10000	0	-0.57	8	8
JAK2	0.013	0	-10000	0	-10000	0	0
ErbB4/ErbB2/neuregulin 1 beta	-0.072	0.16	-10000	0	-0.53	37	37
NRG1	-0.039	0.21	-10000	0	-0.68	37	37
NRG3	-0.054	0.23	-10000	0	-0.86	29	29
NRG2	-0.088	0.28	-10000	0	-0.82	46	46
NRG4	0.007	0.039	-10000	0	-0.3	6	6
heart development	-0.001	0.083	-10000	0	-10000	0	0
neural crest cell migration	-0.072	0.16	-10000	0	-0.52	37	37
ERBB2	0.029	0.037	-10000	0	-0.65	1	1
WWOX/E4ICDs	-0.007	0.086	-10000	0	-10000	0	0
SHC1	0.013	0	-10000	0	-10000	0	0
ErbB4/EGFR/neuregulin 4	-0.041	0.091	-10000	0	-0.59	5	5
apoptosis	0.059	0.14	0.47	29	-10000	0	29
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta	-0.074	0.2	-10000	0	-0.59	43	43
ErbB4/ErbB2/epiregulin	-0.075	0.083	-10000	0	-0.67	1	1
ErbB4/ErbB4/betacellulin/betacellulin	-0.017	0.12	-10000	0	-0.69	7	7
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2	-0.058	0.12	-10000	0	-0.51	18	18
MDM2	-0.002	0.088	-10000	0	-10000	0	0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta	-0.067	0.16	-10000	0	-0.53	37	37
STAT5A	0.008	0.078	-10000	0	-10000	0	0
ErbB4/EGFR/neuregulin 1 beta	-0.079	0.17	-10000	0	-0.54	41	41
DLG4	0.013	0	-10000	0	-10000	0	0
GRB2/SHC	0	0	-10000	0	-10000	0	0
E4ICDs/TAB2/NCoR1	-0.034	0.064	-10000	0	-10000	0	0
STAT5A (dimer)	-0.047	0.11	-10000	0	-0.54	8	8
MAP3K7IP2	0	0	-10000	0	-10000	0	0
STAT5B (dimer)	0.006	0.076	-10000	0	-10000	0	0
LRIG1	0.006	0.077	-10000	0	-0.86	3	3
EREG	-0.13	0.15	-10000	0	-0.3	176	176
BTC	-0.003	0.12	-10000	0	-0.86	7	7
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta	-0.001	0.083	-10000	0	-10000	0	0
ERBB4	-0.013	0.1	-10000	0	-10000	0	0
STAT5B	0.013	0	-10000	0	-10000	0	0
YAP1	-0.011	0.021	-10000	0	-10000	0	0
GRB2	0.013	0	-10000	0	-10000	0	0
ErbB4/ErbB2/neuregulin 4	-0.026	0.055	-10000	0	-0.54	1	1
glial cell differentiation	0.034	0.063	-10000	0	-10000	0	0
WWOX	0.013	0	-10000	0	-10000	0	0
cell proliferation	-0.023	0.18	-10000	0	-0.47	40	40

×

Syndecan-3-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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	0.013	0	-9999	-10000	0	0
Syndecan-3/Src/Cortactin	-0.046	0.14	-9999	-0.45	38	38
Syndecan-3/Neurocan	-0.045	0.14	-9999	-0.49	34	34
POMC	-0.17	0.35	-9999	-0.84	80	80
EGFR	0.001	0.099	-9999	-0.86	5	5
Syndecan-3/EGFR	-0.007	0.056	-9999	-0.49	5	5
AGRP	-0.003	0.056	-9999	-0.3	13	13
NCSTN	0.013	0	-9999	-10000	0	0
PSENEN	0.013	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
APH1B	0.013	0	-9999	-10000	0	0
APH1A	0.013	0	-9999	-10000	0	0
NCAN	-0.067	0.25	-9999	-0.82	36	36
long-term memory	0	0.003	-9999	-10000	0	0
Syndecan-3/IL8	-0.038	0.082	-9999	-0.49	8	8
PSEN1	0.013	0	-9999	-10000	0	0
Src/Cortactin	-0.001	0.01	-9999	-10000	0	0
FYN	0.013	0	-9999	-10000	0	0
limb bud formation	0	0.004	-9999	-10000	0	0
MC4R	0.001	0.038	-9999	-0.3	6	6
SRC	0.012	0.016	-9999	-10000	0	0
PTN	-0.075	0.26	-9999	-0.84	39	39
FGFR/FGF/Syndecan-3	0	0.004	-9999	-10000	0	0
neuron projection morphogenesis	-0.082	0.17	-9999	-0.44	71	71
Syndecan-3/AgRP	-0.004	0.021	-9999	-10000	0	0
Syndecan-3/AgRP/MC4R	-0.005	0.023	-9999	-10000	0	0
Fyn/Cortactin	0	0	-9999	-10000	0	0
SDC3	0	0.004	-9999	-10000	0	0
GO:0007205	0	0	-9999	-10000	0	0
positive regulation of leukocyte migration	-0.037	0.081	-9999	-0.48	8	8
IL8	-0.079	0.17	-9999	-0.86	8	8
Syndecan-3/Fyn/Cortactin	0	0.003	-9999	-10000	0	0
Syndecan-3/CASK	0	0.004	-9999	-10000	0	0
alpha-MSH/MC4R	-0.14	0.27	-9999	-0.67	78	78
Gamma Secretase	0	0	-9999	-10000	0	0

×

VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer	0.033	0	-9999	-10000	0	0
VEGFR1 homodimer/NRP1	0	0	-9999	-10000	0	0
mol:DAG	-0.018	0.17	-9999	-0.51	41	41
VEGFR1 homodimer/NRP1/VEGFR 121	-0.003	0.038	-9999	-0.53	2	2
CaM/Ca2+	-0.011	0.16	-9999	-0.48	41	41
HIF1A	0.021	0	-9999	-10000	0	0
GAB1	0.013	0	-9999	-10000	0	0
AKT1	0.005	0.16	-9999	-0.92	1	1
PLCG1	-0.018	0.17	-9999	-0.52	41	41
NOS3	0.012	0.16	-9999	-10000	0	0
CBL	0.013	0	-9999	-10000	0	0
mol:NO	0.013	0.15	-9999	-10000	0	0
FLT1	0.032	0	-9999	-10000	0	0
PGF	-0.082	0.27	-9999	-0.84	42	42
VEGFR1 homodimer/NRP2/VEGFR121	-0.014	0.05	-9999	-0.52	2	2
CALM1	0.013	0	-9999	-10000	0	0
PIK3CA	0.011	0.045	-9999	-0.86	1	1
eNOS/Hsp90	0.019	0.15	-9999	-10000	0	0
endothelial cell proliferation	-0.039	0.2	-9999	-0.54	41	41
mol:Ca2+	-0.018	0.17	-9999	-0.51	41	41
MAPK3	-0.028	0.2	-9999	-0.48	59	59
MAPK1	-0.028	0.2	-9999	-0.54	22	22
PIK3R1	0.013	0	-9999	-10000	0	0
PLGF homodimer	-0.082	0.27	-9999	-0.84	42	42
PRKACA	0.013	0	-9999	-10000	0	0
RP11-342D11.1	0	0	-9999	-10000	0	0
CAV1	-0.012	0.15	-9999	-0.86	11	11
VEGFA homodimer	0.008	0.063	-9999	-0.85	2	2
VEGFR1 homodimer/VEGFA homodimer	0.03	0.044	-9999	-0.57	2	2
platelet activating factor biosynthetic process	-0.02	0.19	-9999	-0.87	4	4
PI3K	-0.054	0.15	-9999	-0.48	42	42
PRKCA	-0.038	0.21	-9999	-0.51	59	59
PRKCB	-0.027	0.17	-9999	-0.48	42	42
VEGFR1 homodimer/PLGF homodimer	-0.032	0.19	-9999	-0.57	41	41
VEGFA	0.008	0.063	-9999	-0.86	2	2
VEGFB	0.013	0	-9999	-10000	0	0
mol:IP3	-0.018	0.17	-9999	-0.51	41	41
RASA1	0.042	0	-9999	-10000	0	0
NRP2	-0.017	0.092	-9999	-10000	0	0
VEGFR1 homodimer	0.032	0	-9999	-10000	0	0
VEGFB homodimer	0.013	0	-9999	-10000	0	0
NCK1	0.013	0	-9999	-10000	0	0
eNOS/Caveolin-1	0.006	0.17	-9999	-0.84	2	2
PTPN11	0.013	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.053	0.15	-9999	-0.48	42	42
mol:L-citrulline	0.013	0.15	-9999	-10000	0	0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP	-0.003	0.035	-9999	-0.48	2	2
VEGFR1 homodimer/VEGFA homodimer/NCK1	-0.003	0.038	-9999	-0.52	2	2
CD2AP	0.013	0	-9999	-10000	0	0
PI3K/GAB1	-0.05	0.14	-9999	-10000	0	0
PDPK1	-0.004	0.16	-9999	-0.93	1	1
VEGFR1 homodimer/VEGFA homodimer/SHP2	-0.003	0.038	-9999	-0.52	2	2
mol:NADP	0.013	0.15	-9999	-10000	0	0
HSP90AA1	0.013	0	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	-0.003	0.035	-9999	-0.48	2	2
VEGFR1 homodimer/NRP2	0.017	0.051	-9999	-10000	0	0

×

Presenilin action in Notch and Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Delta 1/NOTCH/NOTCH(cleaved)	-0.008	0.079	-10000	0	-0.77	4	4
HDAC1	0.002	0.008	-10000	0	-10000	0	0
AES	0.012	0.002	-10000	0	-10000	0	0
FBXW11	0.013	0	-10000	0	-10000	0	0
DTX1	-0.003	0.12	-10000	0	-0.86	7	7
LRP6/FZD1	0	0	-10000	0	-10000	0	0
TLE1	0.008	0.063	-10000	0	-0.86	2	2
AP1	-0.16	0.27	-10000	0	-0.5	130	130
NCSTN	0.013	0	-10000	0	-10000	0	0
ADAM10	0.004	0.089	-10000	0	-0.86	4	4
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4	0.041	0.05	-10000	0	-0.34	1	1
NICD/RBPSUH	-0.008	0.079	-10000	0	-0.77	4	4
WIF1	-0.033	0.1	-10000	0	-0.3	47	47
NOTCH1	-0.008	0.081	-10000	0	-0.79	4	4
PSENEN	0.013	0	-10000	0	-10000	0	0
KREMEN2	-0.01	0.081	-10000	0	-10000	0	0
DKK1	-0.035	0.12	-10000	0	-0.32	54	54
beta catenin/beta TrCP1	0.036	0.04	-10000	0	-10000	0	0
APH1B	0.013	0	-10000	0	-10000	0	0
APH1A	0.013	0	-10000	0	-10000	0	0
AXIN1	0.002	0.028	-10000	0	-10000	0	0
CtBP/CBP/TCF1/TLE1/AES	0.003	0.035	-10000	0	-0.36	1	1
PSEN1	0.013	0	-10000	0	-10000	0	0
FOS	-0.22	0.39	-10000	0	-0.86	103	103
JUN	-0.19	0.37	-10000	0	-0.86	88	88
MAP3K7	0.011	0.003	-10000	0	-10000	0	0
CTNNB1	0.03	0.043	-10000	0	-10000	0	0
MAPK3	0.013	0	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	-0.038	0.13	-10000	0	-0.6	16	16
HNF1A	0.012	0.002	-10000	0	-10000	0	0
CTBP1	0.012	0.002	-10000	0	-10000	0	0
MYC	-0.007	0.22	-10000	0	-1.5	8	8
NKD1	-0.02	0.16	-10000	0	-0.75	16	16
FZD1	0.013	0	-10000	0	-10000	0	0
NOTCH1 precursor/Deltex homolog 1	-0.017	0.099	-10000	0	-0.58	11	11
apoptosis	-0.16	0.27	-10000	0	-0.5	130	130
Delta 1/NOTCHprecursor	-0.008	0.076	-10000	0	-0.74	4	4
DLL1	0.012	0.016	-10000	0	-0.3	1	1
PPARD	0.024	0.015	-10000	0	-10000	0	0
Gamma Secretase	0	0	-10000	0	-10000	0	0
APC	0.002	0.028	-10000	0	-10000	0	0
DVL1	0	0.001	-10000	0	-10000	0	0
CSNK2A1	0.013	0.002	-10000	0	-10000	0	0
MAP3K7IP1	-0.002	0.003	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	-0.034	0.079	-10000	0	-0.65	2	2
LRP6	0.013	0	-10000	0	-10000	0	0
CSNK1A1	0.013	0.002	-10000	0	-10000	0	0
NLK	0.014	0.007	-10000	0	-10000	0	0
CCND1	0.018	0.042	-10000	0	-10000	0	0
WNT1	0.008	0.028	-10000	0	-0.3	3	3
Axin1/APC/beta catenin	0.047	0.033	-10000	0	-10000	0	0
DKK2	-0.031	0.18	-10000	0	-0.66	25	25
NOTCH1 precursor/DVL1	-0.004	0.069	-10000	0	-0.66	4	4
GSK3B	0.013	0.001	-10000	0	-10000	0	0
FRAT1	0.012	0.001	-10000	0	-10000	0	0
NOTCH/Deltex homolog 1	-0.017	0.1	-10000	0	-0.59	11	11
PPP2R5D	0.014	0.07	0.38	13	-10000	0	13
MAPK1	0.013	0	-10000	0	-10000	0	0
WNT1/LRP6/FZD1	-0.016	0.042	-10000	0	-10000	0	0
RBPJ	0.012	0.016	-10000	0	-0.3	1	1
CREBBP	0.016	0.004	-10000	0	-10000	0	0

×

FOXM1 transcription factor network

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
NFATC3	0.034	0.35	-9999	-0.93	11	11
PLK1	0.04	0.072	-9999	-10000	0	0
BIRC5	0.018	0.13	-9999	-1.6	1	1
HSPA1B	0.033	0.35	-9999	-0.93	11	11
MAP2K1	0.03	0.037	-9999	-10000	0	0
BRCA2	0.027	0.37	-9999	-0.99	15	15
FOXM1	0.021	0.39	-9999	-1.1	13	13
XRCC1	0.034	0.35	-9999	-0.93	11	11
FOXM1B/p19	-0.1	0.31	-9999	-0.91	19	19
Cyclin D1/CDK4	0.021	0.33	-9999	-0.86	11	11
CDC2	0.026	0.37	-9999	-0.96	13	13
TGFA	0.005	0.34	-9999	-0.86	12	12
SKP2	0.031	0.36	-9999	-0.94	12	12
CCNE1	0.015	0.01	-9999	-10000	0	0
CKS1B	0.034	0.35	-9999	-0.93	11	11
RB1	-0.055	0.097	-9999	-10000	0	0
FOXM1C/SP1	0.019	0.37	-9999	-1	14	14
AURKB	-0.005	0.12	-9999	-10000	0	0
CENPF	0.027	0.36	-9999	-0.96	12	12
CDK4	0.018	0.015	-9999	-10000	0	0
MYC	0.03	0.35	-9999	-0.9	17	17
CHEK2	0.03	0.037	-9999	-10000	0	0
ONECUT1	0.017	0.35	-9999	-0.9	12	12
CDKN2A	-0.13	0.15	-9999	-10000	0	0
LAMA4	0.034	0.35	-9999	-0.93	11	11
FOXM1B/HNF6	0.009	0.37	-9999	-1	12	12
FOS	-0.21	0.66	-9999	-1.2	104	104
SP1	0.014	0.003	-9999	-10000	0	0
CDC25B	0.033	0.35	-9999	-0.92	12	12
response to radiation	0.013	0.034	-9999	-10000	0	0
CENPB	0.034	0.35	-9999	-0.93	11	11
CENPA	0.018	0.38	-9999	-0.99	16	16
NEK2	0.023	0.36	-9999	-0.96	13	13
HIST1H2BA	0.025	0.35	-9999	-0.94	11	11
CCNA2	0.007	0.053	-9999	-0.31	2	2
EP300	0.013	0	-9999	-10000	0	0
CCNB1/CDK1	0.021	0.38	-9999	-1	12	12
CCNB2	0.03	0.36	-9999	-0.97	11	11
CCNB1	0.029	0.36	-9999	-0.96	12	12
ETV5	0.032	0.35	-9999	-0.94	11	11
ESR1	-0.014	0.43	-9999	-1.1	27	27
CCND1	0.023	0.34	-9999	-0.88	11	11
GSK3A	0.029	0.03	-9999	-10000	0	0
Cyclin A-E1/CDK1-2	0.033	0.052	-9999	-10000	0	0
CDK2	0.015	0.01	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	0.016	0.041	-9999	-10000	0	0
FOXM1B/Cbp/p300	-0.13	0.23	-9999	-0.93	15	15
GAS1	-0.15	0.62	-9999	-1.2	83	83
MMP2	0.026	0.37	-9999	-1.1	13	13
RB1/FOXM1C	0.031	0.34	-9999	-0.92	11	11
CREBBP	0.013	0	-9999	-10000	0	0

×

Signaling events mediated by HDAC Class III

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
EP300	0.013	0	-9999	-10000	0	0
HDAC4	0.013	0	-9999	-10000	0	0
induction of apoptosis	0	0	-9999	-10000	0	0
regulation of S phase of mitotic cell cycle	-0.021	0.012	-9999	-10000	0	0
CDKN1A	-0.007	0.035	-9999	-10000	0	0
KAT2B	0.013	0	-9999	-10000	0	0
BAX	0.013	0	-9999	-10000	0	0
FOXO3	0	0	-9999	-10000	0	0
FOXO1	0.013	0	-9999	-10000	0	0
FOXO4	0.024	0	-9999	-10000	0	0
response to UV	0	0	-9999	-10000	0	0
XRCC6	0.013	0	-9999	-10000	0	0
TAT	0.008	0.017	-9999	-10000	0	0
mol:Lysophosphatidic acid	0	0	-9999	-10000	0	0
MYOD1	0.011	0.021	-9999	-10000	0	0
PPARGC1A	-0.36	0.43	-9999	-0.86	163	163
FHL2	-0.058	0.24	-9999	-0.86	31	31
response to nutrient levels	0	0	-9999	-10000	0	0
KU70/SIRT1	0.002	0.011	-9999	-10000	0	0
HIST2H4A	0.021	0.012	-9999	-10000	0	0
SIRT1/FOXO3a	0.001	0.008	-9999	-10000	0	0
SIRT1	0.002	0.012	-9999	-10000	0	0
response to hypoxia	0	0	-9999	-10000	0	0
SIRT1/MEF2D/HDAC4	0.002	0.011	-9999	-10000	0	0
SIRT1/Histone H1b	-0.005	0.048	-9999	-0.32	8	8
apoptosis	-0.002	0.011	-9999	-10000	0	0
SIRT1/PGC1A	-0.25	0.29	-9999	-0.58	163	163
p53/SIRT1	0.006	0.031	-9999	-10000	0	0
SIRT1/FOXO4	0.002	0.012	-9999	-10000	0	0
FOXO1/FHL2/SIRT1	-0.042	0.15	-9999	-0.53	31	31
HIST1H1E	0.014	0.059	-9999	-0.38	8	8
SIRT1/p300	0.002	0.011	-9999	-10000	0	0
muscle cell differentiation	0	0.018	-9999	-10000	0	0
TP53	0.002	0.012	-9999	-10000	0	0
KU70/SIRT1/BAX	0.002	0.011	-9999	-10000	0	0
CREBBP	0.013	0	-9999	-10000	0	0
MEF2D	0.013	0	-9999	-10000	0	0
HIV-1 Tat/SIRT1	0.001	0.014	-9999	-10000	0	0
ACSS2	0.022	0.004	-9999	-10000	0	0
SIRT1/PCAF/MYOD	0	0.018	-9999	-10000	0	0

×

IL2 signaling events mediated by STAT5

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GAB2	0.014	0	-9999	-10000	0	0
ELF1	-0.006	0.098	-9999	-0.42	17	17
CCNA2	0.005	0.05	-9999	-10000	0	0
PIK3CA	0.011	0.045	-9999	-0.86	1	1
JAK3	-0.059	0.13	-9999	-0.3	89	89
PIK3R1	0.014	0	-9999	-10000	0	0
JAK1	0.014	0	-9999	-10000	0	0
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.022	0.14	-9999	-0.59	13	13
SHC1	0.014	0	-9999	-10000	0	0
SP1	0.021	0	-9999	-10000	0	0
IL2RA	-0.03	0.23	-9999	-1	17	17
IL2RB	-0.017	0.14	-9999	-0.54	21	21
SOS1	0.014	0	-9999	-10000	0	0
IL2RG	-0.051	0.2	-9999	-0.51	47	47
G1/S transition of mitotic cell cycle	0.04	0.041	-9999	-0.62	1	1
PTPN11	0.014	0	-9999	-10000	0	0
CCND2	0.032	0	-9999	-10000	0	0
LCK	-0.011	0.11	-9999	-0.39	23	23
GRB2	0.014	0	-9999	-10000	0	0
IL2	0.005	0.006	-9999	-10000	0	0
CDK6	0.011	0.045	-9999	-0.86	1	1
CCND3	0.032	0.12	-9999	-0.67	5	5

×

Rapid glucocorticoid signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma	-0.063	0.17	-10000	0	-0.5	47	47
MAPK9	0.009	0	-10000	0	-10000	0	0
adrenocorticotropin secretion	-0.007	0.052	-10000	0	-10000	0	0
GNB1/GNG2	0	0	-10000	0	-10000	0	0
GNB1	0.013	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	-0.068	0.18	-10000	0	-0.55	47	47
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	0.015	0.04	0.12	47	-10000	0	47
GNAL	-0.095	0.29	-10000	0	-0.86	47	47
GNG2	0.013	0	-10000	0	-10000	0	0
CRH	-0.013	0.076	-10000	0	-0.3	25	25
mol:cortisol	0	0	-10000	0	-10000	0	0
MAPK8	0.006	0.035	-10000	0	-0.47	2	2
MAPK11	0.009	0	-10000	0	-10000	0	0

×

Signaling events mediated by PRL

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCNE1	0.013	0	-9999	-10000	0	0
mol:Halofuginone	0.005	0.002	-9999	-10000	0	0
ITGA1	0.001	0.099	-9999	-0.86	5	5
CDKN1A	-0.017	0.093	-9999	-10000	0	0
PRL-3/alpha Tubulin	-0.014	0.049	-9999	-10000	0	0
mol:Ca2+	-0.015	0.11	-9999	-0.68	8	8
AGT	-0.019	0.14	-9999	-0.48	25	25
CCNA2	-0.074	0.22	-9999	-0.61	5	5
TUBA1B	0.013	0	-9999	-10000	0	0
EGR1	-0.13	0.28	-9999	-0.66	84	84
CDK2/Cyclin E1	-0.034	0.062	-9999	-10000	0	0
MAPK3	0.009	0.055	-9999	-10000	0	0
PRL-2 /Rab GGTase beta	0	0	-9999	-10000	0	0
MAPK1	0.009	0.055	-9999	-10000	0	0
PTP4A1	-0.083	0.23	-9999	-0.51	84	84
PTP4A3	-0.009	0.08	-9999	-0.3	27	27
PTP4A2	0.013	0	-9999	-10000	0	0
ITGB1	0.009	0.055	-9999	-10000	0	0
SRC	0.012	0.016	-9999	-10000	0	0
RAC1	-0.019	0.095	-9999	-10000	0	0
Rab GGTase beta/Rab GGTase alpha	0	0	-9999	-10000	0	0
PRL-1/ATF-5	-0.078	0.22	-9999	-0.61	4	4
RABGGTA	0.013	0	-9999	-10000	0	0
BCAR1	0.01	0.036	-9999	-10000	0	0
RHOC	-0.019	0.095	-9999	-10000	0	0
RHOA	-0.019	0.095	-9999	-10000	0	0
cell motility	-0.018	0.1	-9999	-0.27	9	9
PRL-1/alpha Tubulin	-0.072	0.21	-9999	-10000	0	0
PRL-3/alpha1 Integrin	-0.022	0.094	-9999	-0.72	5	5
ROCK1	-0.018	0.1	-9999	-0.27	9	9
RABGGTB	0.013	0	-9999	-10000	0	0
CDK2	0.013	0	-9999	-10000	0	0
mitosis	-0.082	0.23	-9999	-0.51	84	84
ATF5	-0.001	0.064	-9999	-10000	0	0

×

Class IB PI3K non-lipid kinase events

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
cAMP biosynthetic process	0.001	0.096	0.52	10	-10000	0	10
PI3K Class IB/PDE3B	-0.001	0.096	-10000	0	-0.52	10	10
PDE3B	-0.001	0.096	-10000	0	-0.52	10	10

×

a4b1 and a4b7 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ITGB1	0.013	0	-9999	-10000	0	0
ITGB7	-0.024	0.15	-9999	-0.5	27	27
ITGA4	0.006	0.047	-9999	-0.3	9	9
alpha4/beta7 Integrin	-0.03	0.12	-9999	-0.64	11	11
alpha4/beta1 Integrin	-0.005	0.029	-9999	-10000	0	0

×

Insulin-mediated glucose transport

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Insulin responsive Vesicles	0.003	0.079	-9999	-0.37	5	5
CaM/Ca2+	0	0	-9999	-10000	0	0
AKT1	0.013	0	-9999	-10000	0	0
AKT2	0.013	0	-9999	-10000	0	0
STXBP4	0.013	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
mol:glucose	0.036	0.074	-9999	-10000	0	0
YWHAZ	0.013	0	-9999	-10000	0	0
CALM1	0.013	0	-9999	-10000	0	0
YWHAQ	0.013	0	-9999	-10000	0	0
TBC1D4	-0.056	0.22	-9999	-0.66	44	44
mol:Ca2+	0	0	-9999	-10000	0	0
YWHAH	0.013	0	-9999	-10000	0	0
YWHAB	0.013	0	-9999	-10000	0	0
SNARE/Synip	0	0	-9999	-10000	0	0
YWHAG	0.013	0	-9999	-10000	0	0
ASIP	-0.022	0.096	-9999	-10000	0	0
PRKCI	0.013	0	-9999	-10000	0	0
AS160/CaM/Ca2+	0	0	-9999	-10000	0	0
RHOQ	0.013	0	-9999	-10000	0	0
GYS1	0.034	0	-9999	-10000	0	0
PRKCZ	0.013	0	-9999	-10000	0	0
TRIP10	0.013	0	-9999	-10000	0	0
TC10/GTP/CIP4/Exocyst	0	0	-9999	-10000	0	0
AS160/14-3-3	-0.033	0.096	-9999	-10000	0	0
VAMP2	0.013	0	-9999	-10000	0	0
SLC2A4	0.037	0.078	-9999	-10000	0	0
STX4	0.013	0	-9999	-10000	0	0
GSK3B	0.027	0	-9999	-10000	0	0
SFN	-0.21	0.17	-9999	-0.32	254	254
LNPEP	-0.012	0.15	-9999	-0.86	11	11
YWHAE	0.013	0	-9999	-10000	0	0

×

IFN-gamma 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	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2	-0.058	0.15	-9999	-0.46	46	46
positive regulation of NF-kappaB transcription factor activity	0	0	-9999	-10000	0	0
CRKL	0.013	0	-9999	-10000	0	0
STAT1 (dimer)/Cbp/p300	-0.049	0.12	-9999	-10000	0	0
IFN-gammaR/JAK1/JAK1/JAK2/JAK2	-0.008	0.023	-9999	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class I	-0.024	0.06	-9999	-10000	0	0
CaM/Ca2+	-0.054	0.14	-9999	-0.42	46	46
RAP1A	0.013	0	-9999	-10000	0	0
STAT1 (dimer)/SHP2	-0.019	0.16	-9999	-0.43	46	46
AKT1	-0.002	0.14	-9999	-10000	0	0
MAP2K1	-0.004	0.15	-9999	-0.46	2	2
MAP3K11	-0.015	0.16	-9999	-0.43	46	46
IFNGR1	0.009	0.014	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKII	-0.025	0.071	-9999	-0.66	1	1
Rap1/GTP	-0.04	0.1	-9999	-10000	0	0
CRKL/C3G	0	0	-9999	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP	-0.061	0.16	-9999	-0.48	46	46
CEBPB	0.017	0.17	-9999	-0.78	2	2
STAT3	0.013	0	-9999	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1	-0.055	0.14	-9999	-10000	0	0
STAT1	-0.018	0.16	-9999	-0.42	46	46
CALM1	0.013	0	-9999	-10000	0	0
IFN-gamma (dimer)	-0.1	0.28	-9999	-0.84	47	47
PIK3CA	0.011	0.045	-9999	-0.86	1	1
STAT1 (dimer)/PIAS1	-0.045	0.14	-9999	-0.42	2	2
CEBPB/PTGES2/Cbp/p300	-0.035	0.08	-9999	-0.43	2	2
mol:Ca2+	-0.058	0.15	-9999	-0.45	46	46
MAPK3	0.01	0.14	-9999	-0.49	2	2
STAT1 (dimer)	-0.031	0.08	-9999	-10000	0	0
MAPK1	0.01	0.14	-9999	-0.49	2	2
JAK2	0.009	0.014	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
JAK1	0.009	0.014	-9999	-10000	0	0
CAMK2D	0.013	0	-9999	-10000	0	0
DAPK1	0.013	0.18	-9999	-0.66	19	19
SMAD7	0.041	0.055	-9999	-10000	0	0
CBL/CRKL/C3G	-0.048	0.12	-9999	-10000	0	0
PI3K	-0.053	0.13	-9999	-0.47	1	1
IFNG	-0.1	0.28	-9999	-0.84	47	47
apoptosis	0.011	0.13	-9999	-0.44	19	19
CAMK2G	0.013	0	-9999	-10000	0	0
STAT3 (dimer)	0.013	0	-9999	-10000	0	0
CAMK2A	-0.003	0.062	-9999	-10000	0	0
CAMK2B	0.002	0.099	-9999	-0.86	5	5
FRAP1	0.002	0.14	-9999	-10000	0	0
PRKCD	0.001	0.14	-9999	-10000	0	0
RAP1B	0.013	0	-9999	-10000	0	0
negative regulation of cell growth	-0.024	0.06	-9999	-10000	0	0
PTPN2	0.013	0	-9999	-10000	0	0
EP300	0.014	0	-9999	-10000	0	0
IRF1	0.03	0.12	-9999	-10000	0	0
STAT1 (dimer)/PIASy	-0.053	0.13	-9999	-10000	0	0
SOCS1	0.004	0.027	-9999	-10000	0	0
mol:GDP	-0.046	0.12	-9999	-10000	0	0
CASP1	0.039	0.063	-9999	-0.36	2	2
PTGES2	0.013	0	-9999	-10000	0	0
IRF9	0.041	0.057	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.051	0.13	-9999	-0.45	1	1
RAP1/GDP	-0.04	0.1	-9999	-10000	0	0
CBL	-0.016	0.15	-9999	-0.43	46	46
MAP3K1	-0.015	0.16	-9999	-0.43	46	46
PIAS1	0.013	0	-9999	-10000	0	0
PIAS4	0.013	0	-9999	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class II	-0.024	0.06	-9999	-10000	0	0
PTPN11	-0.025	0.16	-9999	-0.45	46	46
CREBBP	0.014	0	-9999	-10000	0	0
RAPGEF1	0.013	0	-9999	-10000	0	0

×

Ceramide signaling 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.024	0	-10000	0	-10000	0	0
MAP4K4	-0.003	0.14	-10000	0	-0.73	8	8
BAG4	0.011	0.045	-10000	0	-0.86	1	1
PKC zeta/ceramide	-0.017	0.04	-10000	0	-10000	0	0
NFKBIA	0.013	0	-10000	0	-10000	0	0
BIRC3	-0.038	0.19	-10000	0	-0.68	28	28
BAX	-0.005	0.019	-10000	0	-10000	0	0
RIPK1	0.013	0	-10000	0	-10000	0	0
AKT1	0.023	0.009	-10000	0	-10000	0	0
BAD	-0.017	0.041	-10000	0	-10000	0	0
SMPD1	-0.006	0.097	-10000	0	-0.27	43	43
RB1	-0.017	0.041	-10000	0	-10000	0	0
FADD/Caspase 8	0.009	0.14	-10000	0	-0.69	8	8
MAP2K4	-0.009	0.038	-10000	0	-10000	0	0
NSMAF	0.013	0	-10000	0	-10000	0	0
response to UV	0	0	-10000	0	-10000	0	0
RAF1	-0.01	0.049	-10000	0	-0.59	1	1
EGF	-0.11	0.3	-10000	0	-0.86	51	51
mol:ceramide	-0.028	0.043	-10000	0	-10000	0	0
MADD	0.013	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
mol:Free Fatty acid	0.022	0.035	-10000	0	-0.66	1	1
ASAH1	0.011	0.045	-10000	0	-0.86	1	1
negative regulation of cell cycle	-0.017	0.04	-10000	0	-10000	0	0
cell proliferation	-0.096	0.17	-10000	0	-0.41	81	81
BID	-0.017	0.09	-10000	0	-0.39	9	9
MAP3K1	-0.017	0.041	-10000	0	-10000	0	0
EIF2A	0	0.037	-10000	0	-10000	0	0
TRADD	0.013	0	-10000	0	-10000	0	0
CRADD	0.013	0	-10000	0	-10000	0	0
MAPK3	0.003	0.046	-10000	0	-0.54	1	1
response to heat	0	0	-10000	0	-10000	0	0
MAPK1	0.003	0.046	-10000	0	-0.54	1	1
Cathepsin D/ceramide	-0.017	0.04	-10000	0	-10000	0	0
FADD	-0.003	0.14	-10000	0	-0.73	8	8
KSR1	-0.018	0.051	-10000	0	-0.63	1	1
MAPK8	-0.005	0.046	-10000	0	-0.39	2	2
PRKRA	-0.017	0.041	-10000	0	-10000	0	0
PDGFA	0.013	0	-10000	0	-10000	0	0
TRAF2	0.013	0	-10000	0	-10000	0	0
IGF1	-0.18	0.36	-10000	0	-0.82	86	86
mol:GD3	0	0	-10000	0	-10000	0	0
ganglioside biosynthetic process	-0.028	0.043	-10000	0	-10000	0	0
CTSD	0.013	0	-10000	0	-10000	0	0
regulation of nitric oxide biosynthetic process	0	0	-10000	0	-10000	0	0
response to radiation	0	0	-10000	0	-10000	0	0
ERK1/PKC delta	-0.084	0.19	-10000	0	-0.44	81	81
PRKCD	0.013	0	-10000	0	-10000	0	0
PRKCZ	0.013	0	-10000	0	-10000	0	0
mol:GW4869	0	0	-10000	0	-10000	0	0
mol:sphingosine	0.022	0.035	-10000	0	-0.66	1	1
RelA/NF kappa B1	0	0	-10000	0	-10000	0	0
mol:glutathione	0	0	-10000	0	-10000	0	0
PAWR	0.013	0	-10000	0	-10000	0	0
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD	-0.012	0.15	-10000	0	-0.64	11	11
TNFR1A/BAG4/TNF-alpha	-0.069	0.18	-10000	0	-0.57	44	44
mol:Sphingosine-1-phosphate	0.024	0	-10000	0	-10000	0	0
MAP2K1	-0.001	0.046	-10000	0	-0.56	1	1
mol:C11AG	0	0	-10000	0	-10000	0	0
RELA	0.013	0	-10000	0	-10000	0	0
CYCS	0.001	0.05	0.18	18	-10000	0	18
TNFRSF1A	0.013	0	-10000	0	-10000	0	0
NFKB1	0.013	0	-10000	0	-10000	0	0
TNFR1A/BAG4	-0.002	0.034	-10000	0	-0.66	1	1
EIF2AK2	-0.009	0.038	-10000	0	-10000	0	0
TNF-alpha/TNFR1A/FAN	-0.067	0.18	-10000	0	-0.57	43	43
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
CASP8	0.015	0.079	-10000	0	-0.34	8	8
MAP2K2	-0.001	0.046	-10000	0	-0.56	1	1
SMPD3	-0.012	0.12	-10000	0	-0.31	47	47
TNF	-0.09	0.28	-10000	0	-0.8	48	48
PKC zeta/PAR4	0	0	-10000	0	-10000	0	0
mol:PHOSPHOCHOLINE	0.022	0.11	0.28	51	-10000	0	51
NF kappa B1/RelA/I kappa B alpha	0	0	-10000	0	-10000	0	0
AIFM1	0.001	0.05	0.18	18	-10000	0	18
BCL2	-0.038	0.2	-10000	0	-0.86	22	22

×

IL2 signaling events mediated by PI3K

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
BCL2L1	0.012	0.12	-10000	0	-0.6	8	8
UGCG	-0.03	0.15	-10000	0	-0.83	12	12
AKT1/mTOR/p70S6K/Hsp90/TERT	0.027	0.12	-10000	0	-0.41	11	11
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucosylceramide	-0.009	0.15	-10000	0	-0.81	12	12
mol:DAG	0	0.004	-10000	0	-10000	0	0
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.051	0.12	-10000	0	-0.45	21	21
FRAP1	0.013	0.18	-10000	0	-0.48	32	32
FOXO3	0.027	0.15	-10000	0	-0.62	10	10
AKT1	0.019	0.16	-10000	0	-0.54	19	19
GAB2	0.013	0.004	-10000	0	-10000	0	0
SMPD1	-0.005	0.021	-10000	0	-10000	0	0
SGMS1	-0.005	0.021	-10000	0	-10000	0	0
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	0.021	0.032	-10000	0	-0.59	1	1
CALM1	0.013	0	-10000	0	-10000	0	0
cell proliferation	0.008	0.14	-10000	0	-0.44	21	21
EIF3A	0.013	0	-10000	0	-10000	0	0
PI3K	0.022	0.036	-10000	0	-0.67	1	1
RPS6KB1	0.017	0.041	-10000	0	-10000	0	0
mol:sphingomyelin	0	0.004	-10000	0	-10000	0	0
natural killer cell activation	0	0.002	-10000	0	-0.012	5	5
JAK3	-0.058	0.13	-10000	0	-0.3	89	89
PIK3R1	0.015	0.004	-10000	0	-10000	0	0
JAK1	0.015	0.004	-10000	0	-10000	0	0
NFKB1	0.013	0	-10000	0	-10000	0	0
MYC	0.017	0.2	-10000	0	-0.92	12	12
MYB	-0.016	0.2	-10000	0	-1.4	8	8
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.014	0.16	-10000	0	-0.6	15	15
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.031	0.037	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	0.014	0.15	-10000	0	-0.58	15	15
Rac1/GDP	0.026	0.03	-10000	0	-0.54	1	1
T cell proliferation	0.023	0.14	-10000	0	-0.56	13	13
SHC1	0.013	0.004	-10000	0	-10000	0	0
RAC1	0.013	0	-10000	0	-10000	0	0
positive regulation of cyclin-dependent protein kinase activity	0.004	0.011	-10000	0	-0.053	12	12
PRKCZ	0.022	0.15	-10000	0	-0.58	13	13
NF kappa B1 p50/RelA	-0.049	0.12	-10000	0	-0.53	11	11
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K	0.002	0.13	-10000	0	-0.61	10	10
HSP90AA1	0.013	0	-10000	0	-10000	0	0
RELA	0.013	0	-10000	0	-10000	0	0
IL2RA	-0.04	0.18	-10000	0	-0.86	16	16
IL2RB	-0.015	0.14	-10000	0	-0.54	21	21
TERT	0	0.031	-10000	0	-10000	0	0
E2F1	-0.003	0.075	-10000	0	-0.45	8	8
SOS1	0.013	0.004	-10000	0	-10000	0	0
RPS6	0.013	0	-10000	0	-10000	0	0
mol:cAMP	-0.002	0.005	0.025	12	-10000	0	12
PTPN11	0.013	0.004	-10000	0	-10000	0	0
IL2RG	-0.05	0.2	-10000	0	-0.51	47	47
actin cytoskeleton organization	0.023	0.14	-10000	0	-0.56	13	13
GRB2	0.013	0.004	-10000	0	-10000	0	0
IL2	0.007	0.007	-10000	0	-10000	0	0
PIK3CA	0.013	0.045	-10000	0	-0.86	1	1
Rac1/GTP	0.032	0.03	-10000	0	-0.51	1	1
LCK	-0.01	0.11	-10000	0	-0.39	23	23
BCL2	-0.009	0.26	-10000	0	-0.84	29	29

×

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BAG4	0.011	0.045	-9999	-0.86	1	1
Caspase 8 (4 units)	-0.022	0.061	-9999	-10000	0	0
NEF	-0.012	0.053	-9999	-0.22	19	19
NFKBIA	0.009	0.029	-9999	-10000	0	0
BIRC3	-0.005	0.2	-9999	-0.86	19	19
CYCS	-0.008	0.099	-9999	-0.39	3	3
RIPK1	0.013	0	-9999	-10000	0	0
CD247	-0.043	0.2	-9999	-0.73	24	24
MAP2K7	0.023	0.08	-9999	-10000	0	0
protein ubiquitination	0.039	0.087	-9999	-10000	0	0
CRADD	0.013	0	-9999	-10000	0	0
DAXX	0.013	0	-9999	-10000	0	0
FAS	0.013	0	-9999	-10000	0	0
BID	-0.017	0.1	-9999	-0.31	21	21
NF-kappa-B/RelA/I kappa B alpha	-0.021	0.078	-9999	-0.35	19	19
TRADD	0.013	0	-9999	-10000	0	0
MAP3K5	0.011	0.045	-9999	-0.86	1	1
CFLAR	0.013	0	-9999	-10000	0	0
FADD	0.013	0	-9999	-10000	0	0
NF-kappa-B/RelA/I kappa B alpha/ubiquitin	-0.021	0.078	-9999	-0.35	19	19
MAPK8	0.028	0.083	-9999	-0.42	2	2
APAF1	0.013	0	-9999	-10000	0	0
TRAF1	0.013	0	-9999	-10000	0	0
TRAF2	0.013	0	-9999	-10000	0	0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG	0.008	0.096	-9999	-0.31	26	26
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD	0.024	0.1	-9999	-0.38	8	8
CHUK	0.039	0.092	-9999	-10000	0	0
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8	-0.001	0.025	-9999	-0.49	1	1
TCRz/NEF	-0.063	0.18	-9999	-0.53	42	42
TNF	-0.09	0.28	-9999	-0.8	48	48
FASLG	-0.073	0.29	-9999	-0.83	42	42
NFKB1	0.009	0.029	-9999	-10000	0	0
TNFR1A/BAG4/TNF-alpha	-0.069	0.18	-9999	-0.57	44	44
CASP6	-0.003	0.046	-9999	-10000	0	0
CASP7	0.028	0.17	-9999	-0.64	19	19
RELA	0.009	0.029	-9999	-10000	0	0
CASP2	0.013	0	-9999	-10000	0	0
CASP3	0.028	0.17	-9999	-0.64	19	19
TNFRSF1A	0.013	0	-9999	-10000	0	0
TNFR1A/BAG4	-0.002	0.034	-9999	-0.66	1	1
CASP8	0.013	0	-9999	-10000	0	0
CASP9	0.013	0	-9999	-10000	0	0
MAP3K14	0.032	0.099	-9999	-0.35	5	5
APAF-1/Caspase 9	-0.045	0.12	-9999	-0.54	19	19
BCL2	0.007	0.13	-9999	-0.42	23	23

×

Nectin adhesion pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	0.013	0	-9999	-10000	0	0
alphaV beta3 Integrin	-0.022	0.13	-9999	-0.71	12	12
PTK2	-0.034	0.14	-9999	-0.65	17	17
positive regulation of JNK cascade	-0.016	0.073	-9999	-0.35	17	17
CDC42/GDP	0.036	0.11	-9999	-0.48	17	17
Rac1/GDP	0.038	0.11	-9999	-0.48	17	17
RAP1B	0.013	0	-9999	-10000	0	0
RAP1A	0.013	0	-9999	-10000	0	0
CTNNB1	0.013	0	-9999	-10000	0	0
CDC42/GTP	-0.02	0.091	-9999	-0.44	17	17
nectin-3/I-afadin	-0.03	0.14	-9999	-0.66	17	17
RAPGEF1	0.03	0.13	-9999	-0.55	17	17
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.02	0.15	-9999	-0.65	17	17
PDGFB-D/PDGFRB	0.013	0	-9999	-10000	0	0
TLN1	0.021	0.075	-9999	-0.97	1	1
Rap1/GTP	-0.018	0.079	-9999	-0.38	17	17
IQGAP1	0.013	0	-9999	-10000	0	0
Rap1/GTP/I-afadin	0	0	-9999	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin	-0.03	0.14	-9999	-0.66	17	17
PVR	0.013	0	-9999	-10000	0	0
Necl-5(dimer)	0.013	0	-9999	-10000	0	0
mol:GDP	0.031	0.14	-9999	-0.61	17	17
MLLT4	0.013	0	-9999	-10000	0	0
PIK3CA	0.011	0.045	-9999	-0.86	1	1
PI3K	-0.023	0.11	-9999	-0.52	17	17
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin	-0.004	0.027	-9999	-10000	0	0
positive regulation of lamellipodium assembly	-0.017	0.077	-9999	-0.37	17	17
PVRL1	0.006	0.045	-9999	-0.3	8	8
PVRL3	-0.026	0.18	-9999	-0.86	17	17
PVRL2	0.013	0	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
CDH1	0.013	0	-9999	-10000	0	0
CLDN1	-0.25	0.16	-9999	-0.86	10	10
JAM-A/CLDN1	-0.13	0.13	-9999	-0.58	27	27
SRC	-0.035	0.16	-9999	-0.74	17	17
ITGB3	-0.015	0.15	-9999	-0.86	12	12
nectin-1(dimer)/I-afadin/I-afadin	-0.004	0.027	-9999	-10000	0	0
FARP2	0.025	0.14	-9999	-0.6	17	17
RAC1	0.013	0	-9999	-10000	0	0
CTNNA1	0.013	0	-9999	-10000	0	0
nectin-3(dimer)/I-afadin/I-afadin/Necl-5(dimer)	-0.026	0.12	-9999	-0.57	17	17
nectin-1/I-afadin	-0.004	0.027	-9999	-10000	0	0
nectin-2/I-afadin	0	0	-9999	-10000	0	0
RAC1/GTP/IQGAP1/filamentous actin	0	0	-9999	-10000	0	0
nectin-1(dimer)/I-afadin/I-afadin/nectin-3(dimer/I-afadin/I-afadin	-0.029	0.12	-9999	-0.57	17	17
CDC42/GTP/IQGAP1/filamentous actin	0	0	-9999	-10000	0	0
F11R	0.013	0	-9999	-10000	0	0
positive regulation of filopodium formation	-0.016	0.073	-9999	-0.35	17	17
alphaV/beta3 Integrin/Talin	0.018	0.14	-9999	-0.63	12	12
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0	0	-9999	-10000	0	0
nectin-2(dimer)/I-afadin/I-afadin	0	0	-9999	-10000	0	0
PIP5K1C	0.014	0.08	-9999	-0.31	17	17
VAV2	0.024	0.14	-9999	-0.61	17	17
RAP1/GDP	-0.02	0.092	-9999	-0.44	17	17
ITGAV	0.011	0.045	-9999	-0.86	1	1
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin	-0.026	0.12	-9999	-0.57	17	17
nectin-3(dimer)/I-afadin/I-afadin	-0.03	0.14	-9999	-0.66	17	17
Rac1/GTP	-0.021	0.095	-9999	-0.46	17	17
PTPRM	-0.016	0.083	-9999	-0.35	17	17
E-cadherin/beta catenin/alpha catenin	-0.002	0.013	-9999	-10000	0	0
adherens junction assembly	0	0	-9999	-10000	0	0
CDC42	0.013	0	-9999	-10000	0	0

×

S1P1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	-0.009	0.076	-9999	-0.66	5	5
PDGFRB	0.013	0.005	-9999	-10000	0	0
SPHK1	-0.008	0.022	-9999	-10000	0	0
mol:S1P	-0.01	0.027	-9999	-10000	0	0
S1P1/S1P/Gi	0.009	0.15	-9999	-0.39	41	41
GNAO1	-0.013	0.14	-9999	-0.87	10	10
PDGFB-D/PDGFRB/PLCgamma1	0.02	0.14	-9999	-0.6	7	7
PLCG1	0.016	0.14	-9999	-0.62	8	8
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.013	0.005	-9999	-10000	0	0
GNAI2	0.013	0.005	-9999	-10000	0	0
GNAI3	0.013	0.005	-9999	-10000	0	0
GNAI1	0.011	0.045	-9999	-0.86	1	1
mol:GDP	0	0	-9999	-10000	0	0
EDG1	0.01	0.068	-9999	-0.58	5	5
S1P1/S1P	-0.018	0.061	-9999	-0.44	5	5
negative regulation of cAMP metabolic process	0.01	0.15	-9999	-0.38	41	41
MAPK3	-0.001	0.21	-9999	-0.58	38	38
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	0.005	0.077	-9999	-0.86	3	3
PLCB2	0.027	0.07	-9999	-0.39	5	5
RAC1	0.013	0	-9999	-10000	0	0
RhoA/GTP	-0.015	0.051	-9999	-0.37	5	5
receptor internalization	-0.017	0.057	-9999	-0.41	5	5
PTGS2	-0.051	0.36	-9999	-1.1	38	38
Rac1/GTP	-0.015	0.051	-9999	-0.37	5	5
RHOA	0.013	0	-9999	-10000	0	0
VEGFA	0.008	0.063	-9999	-0.86	2	2
negative regulation of T cell proliferation	0.01	0.15	-9999	-0.38	41	41
GO:0007205	0	0	-9999	-10000	0	0
GNAZ	0.013	0.005	-9999	-10000	0	0
MAPK1	-0.001	0.21	-9999	-0.58	38	38
S1P1/S1P/PDGFB-D/PDGFRB	0.029	0.081	-9999	-0.44	5	5
ABCC1	0.013	0.002	-9999	-10000	0	0

×

Retinoic acid receptors-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.013	0	-10000	0	-10000	0	0
HDAC3	0.013	0	-10000	0	-10000	0	0
VDR	0.012	0.016	-10000	0	-10000	0	0
Cbp/p300/PCAF	0	0	-10000	0	-10000	0	0
EP300	0.013	0	-10000	0	-10000	0	0
RARs/AIB1/Cbp/p300/PCAF/9cRA	0.033	0.059	-10000	0	-0.33	5	5
KAT2B	0.013	0	-10000	0	-10000	0	0
MAPK14	0.013	0	-10000	0	-10000	0	0
AKT1	0.011	0.084	0.24	4	-0.42	10	14
RAR alpha/9cRA/Cyclin H	-0.025	0.094	-10000	0	-0.4	22	22
mol:9cRA	0	0	-10000	0	-10000	0	0
RARs/Src-1/Cbp/p300/PCAF/9cRA	0.029	0.066	-10000	0	-0.32	10	10
CDC2	0.001	0.001	-10000	0	-10000	0	0
response to UV	0.001	0.002	-10000	0	-10000	0	0
RAR alpha/Jnk1	-0.019	0.077	-10000	0	-0.48	4	4
NCOR2	0.013	0	-10000	0	-10000	0	0
VDR/VDR/Vit D3	-0.001	0.01	-10000	0	-10000	0	0
RXRs/RARs/NRIP1/9cRA	-0.022	0.17	-10000	0	-0.64	23	23
NCOA2	-0.04	0.21	-10000	0	-0.86	23	23
NCOA3	0.013	0	-10000	0	-10000	0	0
NCOA1	0.013	0	-10000	0	-10000	0	0
VDR/VDR/DNA	0.012	0.016	-10000	0	-10000	0	0
RARG	0.014	0.002	-10000	0	-10000	0	0
RAR gamma1/9cRA	0	0	-10000	0	-10000	0	0
MAPK3	0.013	0.002	-10000	0	-10000	0	0
MAPK1	0.013	0	-10000	0	-10000	0	0
MAPK8	0.009	0.063	-10000	0	-0.86	2	2
mol:Vit D3	0	0	-10000	0	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.041	0.16	-10000	0	-0.66	22	22
RARA	0.006	0.084	-10000	0	-0.32	24	24
negative regulation of phosphoinositide 3-kinase cascade	0	0	-10000	0	-10000	0	0
RARs/TIF2/Cbp/p300/PCAF/9cRA	0.009	0.12	-10000	0	-0.34	30	30
PRKCA	-0.034	0.2	-10000	0	-0.86	22	22
RXRs/RARs/NRIP1/9cRA/HDAC1	-0.033	0.17	-10000	0	-0.67	23	23
RXRG	-0.11	0.12	-10000	0	-0.55	24	24
RXRA	0.011	0.093	-10000	0	-0.34	24	24
RXRB	-0.002	0.11	-10000	0	-0.46	22	22
VDR/Vit D3/DNA	-0.001	0.01	-10000	0	-10000	0	0
RBP1	-0.002	0.1	-10000	0	-0.61	9	9
CRBP1/9-cic-RA	-0.011	0.079	-10000	0	-0.67	5	5
RARB	-0.008	0.14	-10000	0	-0.86	10	10
PRKCG	0.008	0.023	-10000	0	-0.3	2	2
MNAT1	0.013	0	-10000	0	-10000	0	0
RAR alpha/RXRs	-0.03	0.18	-10000	0	-0.7	23	23
RXRs/RARs/SMRT(N-CoR2)/9cRA	-0.011	0.15	-10000	0	-0.56	23	23
proteasomal ubiquitin-dependent protein catabolic process	0.028	0.081	-10000	0	-0.43	5	5
RXRs/RARs/NRIP1/9cRA/HDAC3	-0.033	0.17	-10000	0	-0.67	23	23
positive regulation of DNA binding	-0.023	0.089	-10000	0	-0.37	22	22
NRIP1	-0.028	0.16	-10000	0	-0.61	22	22
RXRs/RARs	-0.042	0.17	-10000	0	-0.66	23	23
RXRs/RXRs/DNA/9cRA	-0.052	0.16	-10000	0	-0.69	22	22
PRKACA	0.013	0	-10000	0	-10000	0	0
CDK7	0.013	0	-10000	0	-10000	0	0
TFIIH	0	0	-10000	0	-10000	0	0
RAR alpha/9cRA	-0.012	0.046	-10000	0	-10000	0	0
CCNH	0.013	0	-10000	0	-10000	0	0
CREBBP	0.013	0	-10000	0	-10000	0	0
RAR gamma2/9cRA	0	0	-10000	0	-10000	0	0

×

Stabilization and expansion of the E-cadherin adherens junction

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
adherens junction organization	0.032	0	-9999	-10000	0	0
epithelial cell differentiation	0	0	-9999	-10000	0	0
CYFIP2	0.013	0	-9999	-10000	0	0
ENAH	0.07	0.008	-9999	-10000	0	0
EGFR	0.001	0.099	-9999	-0.86	5	5
EPHA2	0.011	0.023	-9999	-0.3	2	2
MYO6	0.04	0	-9999	-10000	0	0
CTNNB1	0.013	0	-9999	-10000	0	0
ABI1/Sra1/Nap1	0	0	-9999	-10000	0	0
AQP5	-0.04	0.14	-9999	-0.61	21	21
CTNND1	0.013	0	-9999	-10000	0	0
mol:PI-4-5-P2	0.04	0	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.034	0.069	-9999	-10000	0	0
EGF	-0.11	0.3	-9999	-0.86	51	51
NCKAP1	0.013	0	-9999	-10000	0	0
AQP3	-0.075	0.2	-9999	-0.61	46	46
cortical microtubule organization	0	0	-9999	-10000	0	0
GO:0000145	0.039	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0	0	-9999	-10000	0	0
MLLT4	0.013	0	-9999	-10000	0	0
ARF6/GDP	0	0.004	-9999	-10000	0	0
ARF6	0.013	0	-9999	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	-0.001	0.009	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
VASP	0.051	0.02	-9999	-10000	0	0
PVRL2	0.013	0	-9999	-10000	0	0
ZYX	0.04	0	-9999	-10000	0	0
ARF6/GTP	-0.001	0.007	-9999	-10000	0	0
CDH1	0.013	0	-9999	-10000	0	0
EGFR/EGFR/EGF/EGF	-0.068	0.16	-9999	-0.45	56	56
RhoA/GDP	0	0	-9999	-10000	0	0
actin cytoskeleton organization	0.047	0	-9999	-10000	0	0
IGF-1R heterotetramer	0.013	0	-9999	-10000	0	0
GIT1	0.013	0	-9999	-10000	0	0
IGF1R	0.013	0	-9999	-10000	0	0
IGF1	-0.18	0.36	-9999	-0.82	86	86
DIAPH1	0	0.002	-9999	-10000	0	0
Wnt receptor signaling pathway	0	0	-9999	-10000	0	0
RHOA	0.013	0	-9999	-10000	0	0
RhoA/GTP	0	0.004	-9999	-10000	0	0
CTNNA1	0.013	0	-9999	-10000	0	0
VCL	0.047	0	-9999	-10000	0	0
EFNA1	0.013	0	-9999	-10000	0	0
LPP	0.044	0.037	-9999	-0.45	2	2
Ephrin A1/EPHA2	0	0.006	-9999	-10000	0	0
SEC6/SEC8	0	0	-9999	-10000	0	0
MGAT3	-0.034	0.07	-9999	-10000	0	0
HGF/MET	-0.099	0.17	-9999	-0.51	51	51
HGF	-0.1	0.3	-9999	-0.86	51	51
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN	0.033	0	-9999	-10000	0	0
actin cable formation	0.086	0.014	-9999	-10000	0	0
KIAA1543	0.046	0.025	-9999	-0.44	1	1
KIFC3	0.04	0	-9999	-10000	0	0
NCK1	0.013	0	-9999	-10000	0	0
EXOC3	0.013	0	-9999	-10000	0	0
ACTN1	0.04	0.007	-9999	-10000	0	0
NCK1/GIT1	0	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
EXOC4	0.013	0	-9999	-10000	0	0
STX4	0.04	0	-9999	-10000	0	0
PIP5K1C	0.04	0	-9999	-10000	0	0
LIMA1	0.013	0	-9999	-10000	0	0
ABI1	0.013	0	-9999	-10000	0	0
ROCK1	0	0.003	-9999	-10000	0	0
adherens junction assembly	0.063	0.023	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1	-0.098	0.18	-9999	-0.45	81	81
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0	0	-9999	-10000	0	0
MET	-0.11	0.15	-9999	-0.3	154	154
PLEKHA7	0.039	0.026	-9999	-0.47	1	1
mol:GTP	-0.001	0.009	-9999	-10000	0	0
establishment of epithelial cell apical/basal polarity	0.066	0	-9999	-10000	0	0
cortical actin cytoskeleton stabilization	0.032	0	-9999	-10000	0	0
regulation of cell-cell adhesion	0.047	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton	0.033	0	-9999	-10000	0	0

×

Regulation of Telomerase

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Telomerase catalytic core complex	-0.024	0.09	-9999	-10000	0	0
RAD9A	0.013	0	-9999	-10000	0	0
AP1	-0.31	0.48	-9999	-0.98	120	120
IFNAR2	0.014	0.003	-9999	-10000	0	0
AKT1	-0.001	0.07	-9999	-0.3	17	17
ER alpha/Oestrogen	-0.045	0.14	-9999	-0.67	17	17
NFX1/SIN3/HDAC complex	0.048	0.019	-9999	-10000	0	0
EGF	-0.11	0.3	-9999	-0.86	51	51
SMG5	0.013	0	-9999	-10000	0	0
SMG6	0.013	0	-9999	-10000	0	0
SP3/HDAC2	0.005	0.01	-9999	-10000	0	0
TERT/c-Abl	-0.037	0.065	-9999	-10000	0	0
SAP18	0.013	0	-9999	-10000	0	0
MRN complex	0	0	-9999	-10000	0	0
WT1	-0.029	0.1	-9999	-0.3	48	48
WRN	0.013	0	-9999	-10000	0	0
SP1	0.014	0.003	-9999	-10000	0	0
SP3	0.013	0.002	-9999	-10000	0	0
TERF2IP	0.013	0	-9999	-10000	0	0
Telomerase/Nucleolin	-0.03	0.05	-9999	-10000	0	0
Mad/Max	0	0	-9999	-10000	0	0
TERT	-0.025	0.091	-9999	-10000	0	0
CCND1	-0.017	0.09	-9999	-10000	0	0
MAX	0.013	0.002	-9999	-10000	0	0
RBBP7	0.013	0	-9999	-10000	0	0
RBBP4	0.013	0	-9999	-10000	0	0
TERF2	0	0.005	-9999	-10000	0	0
PTGES3	0.013	0	-9999	-10000	0	0
SIN3A	0.013	0	-9999	-10000	0	0
Telomerase/911	0.034	0.021	-9999	-10000	0	0
CDKN1B	-0.04	0.19	-9999	-0.55	46	46
RAD1	0.013	0	-9999	-10000	0	0
XRCC5	0.013	0	-9999	-10000	0	0
XRCC6	0.013	0	-9999	-10000	0	0
SAP30	0.011	0.045	-9999	-0.86	1	1
TRF2/PARP2	0	0.005	-9999	-10000	0	0
UBE3A	0.013	0.002	-9999	-10000	0	0
JUN	-0.19	0.37	-9999	-0.86	88	88
E6	0	0.001	-9999	-10000	0	0
HPV-16 E6/E6AP	0.003	0.005	-9999	-10000	0	0
FOS	-0.22	0.39	-9999	-0.86	103	103
IFN-gamma/IRF1	-0.085	0.21	-9999	-0.64	47	47
PARP2	0.013	0	-9999	-10000	0	0
BLM	0.012	0.016	-9999	-0.3	1	1
Telomerase	0.013	0.071	-9999	-0.48	4	4
IRF1	0.017	0.016	-9999	-0.29	1	1
ESR1	-0.049	0.19	-9999	-0.51	45	45
KU/TER	0	0	-9999	-10000	0	0
ATM/TRF2	-0.002	0.03	-9999	-0.59	1	1
ubiquitin-dependent protein catabolic process	0.053	0.018	-9999	-10000	0	0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex	0.053	0.018	-9999	-10000	0	0
HDAC1	0.013	0	-9999	-10000	0	0
HDAC2	0.014	0.003	-9999	-10000	0	0
ATM	-0.002	0.03	-9999	-0.58	1	1
SMAD3	0.019	0.029	-9999	-10000	0	0
ABL1	0.013	0	-9999	-10000	0	0
MXD1	0.013	0.002	-9999	-10000	0	0
MRE11A	0.013	0	-9999	-10000	0	0
HUS1	0.013	0	-9999	-10000	0	0
RPS6KB1	0.013	0	-9999	-10000	0	0
TERT/NF kappa B1/14-3-3	-0.031	0.058	-9999	-10000	0	0
NR2F2	0.011	0.003	-9999	-10000	0	0
MAPK3	0.016	0.006	-9999	-10000	0	0
MAPK1	0.016	0.006	-9999	-10000	0	0
TGFB1/TGF beta receptor Type II	0.007	0.042	-9999	-10000	0	0
NFKB1	0.013	0	-9999	-10000	0	0
HNRNPC	0.013	0	-9999	-10000	0	0
DNA damage response signal transduction by p53 class mediator resulting in induction of apoptosis	-0.002	0.03	-9999	-0.58	1	1
NBN	0.013	0	-9999	-10000	0	0
EGFR	0.002	0.099	-9999	-0.86	5	5
mol:Oestrogen	0	0.001	-9999	-10000	0	0
EGF/EGFR	-0.1	0.23	-9999	-0.66	56	56
MYC	-0.005	0.12	-9999	-0.86	8	8
IL2	0.005	0.007	-9999	-10000	0	0
KU	0	0	-9999	-10000	0	0
RAD50	0.013	0	-9999	-10000	0	0
HSP90AA1	0.013	0	-9999	-10000	0	0
TGFB1	0.007	0.042	-9999	-10000	0	0
TRF2/BLM	0	0.01	-9999	-10000	0	0
FRAP1	0	0	-9999	-10000	0	0
KU/TERT	-0.033	0.064	-9999	-10000	0	0
SP1/HDAC2	0.007	0.012	-9999	-10000	0	0
PINX1	0.013	0	-9999	-10000	0	0
Telomerase/EST1A	-0.03	0.05	-9999	-10000	0	0
Smad3/Myc	0.006	0.091	-9999	-0.59	8	8
911 complex	0	0	-9999	-10000	0	0
IFNG	-0.1	0.28	-9999	-0.84	46	46
Telomerase/PinX1	-0.03	0.05	-9999	-10000	0	0
Telomerase/AKT1/mTOR/p70S6K	0.02	0.036	-9999	-10000	0	0
SIN3B	0.013	0	-9999	-10000	0	0
YWHAE	0.013	0	-9999	-10000	0	0
Telomerase/EST1B	-0.03	0.05	-9999	-10000	0	0
response to DNA damage stimulus	0.003	0.008	-9999	-10000	0	0
MRN complex/TRF2/Rap1	0	0.005	-9999	-10000	0	0
TRF2/WRN	0	0.005	-9999	-10000	0	0
Telomerase/hnRNP C1/C2	-0.03	0.05	-9999	-10000	0	0
E2F1	-0.084	0.14	-9999	-0.3	119	119
ZNFX1	0.013	0	-9999	-10000	0	0
PIF1	0.001	0.093	-9999	-0.62	7	7
NCL	0.013	0	-9999	-10000	0	0
DKC1	0.013	0	-9999	-10000	0	0
telomeric DNA binding	0	0	-9999	-10000	0	0

×

Caspase cascade in apoptosis

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TOP1	0.019	0.086	-10000	0	-0.43	9	9
ACTA1	0.014	0.1	-10000	0	-0.52	9	9
NUMA1	0.019	0.086	-10000	0	-0.43	9	9
SPTAN1	0.016	0.1	-10000	0	-0.56	7	7
LIMK1	0.016	0.1	-10000	0	-0.56	7	7
BIRC3	-0.038	0.19	-10000	0	-0.68	28	28
BIRC2	0.013	0	-10000	0	-10000	0	0
BAX	0.013	0	-10000	0	-10000	0	0
CASP10	0	0.12	-10000	0	-0.63	9	9
CRMA	0	0	-10000	0	-10000	0	0
XIAP	0.013	0	-10000	0	-10000	0	0
PTK2	0.019	0.086	-10000	0	-0.43	9	9
DIABLO	0.013	0	-10000	0	-10000	0	0
apoptotic nuclear changes	0.016	0.1	-10000	0	-0.55	7	7
response to UV	0	0	-10000	0	-10000	0	0
CRADD	0.013	0	-10000	0	-10000	0	0
GSN	0.016	0.1	-10000	0	-0.57	7	7
MADD	0.013	0	-10000	0	-10000	0	0
TFAP2A	-0.056	0.22	-10000	0	-0.66	45	45
BID	-0.012	0.066	-10000	0	-0.3	9	9
MAP3K1	0.014	0.04	-10000	0	-0.22	1	1
TRADD	0.013	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
APAF-1/Pro-Caspase 9	0	0	-10000	0	-10000	0	0
mol:Activated DNA	0	0	-10000	0	-10000	0	0
ARHGDIB	0.013	0.11	-10000	0	-0.54	8	8
CASP9	0.013	0	-10000	0	-10000	0	0
DNA repair	-0.016	0.05	-10000	0	-0.23	16	16
neuron apoptosis	0.023	0.015	-10000	0	-10000	0	0
mol:NAD	0	0	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	0.022	0.098	-10000	0	-0.54	7	7
APAF1	0.013	0	-10000	0	-10000	0	0
CASP6	0.021	0.064	-10000	0	-0.4	4	4
TRAF2	0.013	0	-10000	0	-10000	0	0
ICAD/CAD	0.023	0.099	-10000	0	-0.54	7	7
CASP7	0.009	0.081	0.35	19	-10000	0	19
KRT18	0.016	0.018	-10000	0	-10000	0	0
apoptosis	0.029	0.091	-10000	0	-0.47	7	7
DFFA	0.016	0.1	-10000	0	-0.56	7	7
DFFB	0.016	0.1	-10000	0	-0.56	7	7
PARP1	0.016	0.05	0.23	16	-10000	0	16
actin filament polymerization	-0.023	0.095	0.52	7	-10000	0	7
TNF	-0.09	0.28	-10000	0	-0.8	48	48
CYCS	0.005	0.044	-10000	0	-0.22	9	9
SATB1	0.029	0.061	-10000	0	-0.38	4	4
SLK	0.016	0.1	-10000	0	-0.56	7	7
p15 BID/BAX	-0.003	0.058	-10000	0	-0.34	2	2
CASP2	0.006	0.12	-10000	0	-0.47	8	8
JNK cascade	-0.014	0.04	0.22	1	-10000	0	1
CASP3	0.008	0.11	-10000	0	-0.55	9	9
LMNB2	0.02	0.078	-10000	0	-0.32	4	4
RIPK1	0.013	0	-10000	0	-10000	0	0
CASP4	0.013	0	-10000	0	-10000	0	0
Mammalian IAPs/DIABLO	-0.029	0.12	-10000	0	-0.52	19	19
negative regulation of DNA binding	-0.055	0.22	-10000	0	-0.65	45	45
stress fiber formation	0.016	0.1	-10000	0	-0.55	7	7
GZMB	-0.013	0.13	-10000	0	-0.62	13	13
CASP1	0.014	0.037	-10000	0	-0.46	2	2
LMNB1	0.02	0.078	-10000	0	-0.32	4	4
APP	0.023	0.015	-10000	0	-10000	0	0
TNFRSF1A	0.013	0	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
CASP8	0.012	0	-10000	0	-10000	0	0
VIM	0.023	0.09	-10000	0	-0.46	7	7
LMNA	0.02	0.078	-10000	0	-0.32	4	4
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD	-0.003	0.12	-10000	0	-0.31	43	43
LRDD	0.013	0	-10000	0	-10000	0	0
SREBF1	0.015	0.1	-10000	0	-0.56	7	7
APAF-1/Caspase 9	0.005	0.037	-10000	0	-10000	0	0
nuclear fragmentation during apoptosis	0.019	0.085	-10000	0	-0.43	9	9
CFL2	0.023	0.098	-10000	0	-0.53	7	7
GAS2	0.009	0.12	-10000	0	-0.55	12	12
positive regulation of apoptosis	0.022	0.08	-10000	0	-0.31	4	4
PRF1	0	0.094	-10000	0	-0.86	4	4

×

Cellular roles of Anthrax toxin

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
ANTXR1	-0.005	0.12	-10000	0	-0.86	8	8
ANTXR2	0.011	0.045	-10000	0	-0.86	1	1
negative regulation of myeloid dendritic cell antigen processing and presentation	-0.003	0.016	-10000	0	-0.1	9	9
monocyte activation	-0.045	0.16	-10000	0	-0.48	45	45
MAP2K2	-0.001	0.007	-10000	0	-10000	0	0
MAP2K1	-0.002	0.014	-10000	0	-10000	0	0
MAP2K7	-0.002	0.014	-10000	0	-10000	0	0
MAP2K6	-0.011	0.068	-10000	0	-0.54	6	6
CYAA	0.004	0.08	-10000	0	-0.51	9	9
MAP2K4	-0.002	0.014	-10000	0	-10000	0	0
IL1B	-0.023	0.13	-10000	0	-0.48	28	28
Channel	-0.013	0.082	-10000	0	-0.54	9	9
NLRP1	-0.005	0.04	-10000	0	-0.52	2	2
CALM1	0.013	0	-10000	0	-10000	0	0
negative regulation of phagocytosis	-0.003	0.019	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
regulation of endothelial cell proliferation	0.003	0.016	0.1	9	-10000	0	9
MAPK3	-0.002	0.014	-10000	0	-10000	0	0
MAPK1	-0.002	0.014	-10000	0	-10000	0	0
PGR	-0.024	0.087	-10000	0	-0.47	11	11
PA/Cellular Receptors	-0.014	0.089	-10000	0	-0.58	9	9
apoptosis	-0.003	0.016	-10000	0	-0.1	9	9
LOC728358	0	0	-10000	0	-10000	0	0
Lethal toxin (unfolded)	0.004	0.079	-10000	0	-0.5	9	9
macrophage activation	0.019	0.015	-10000	0	-10000	0	0
TNF	-0.09	0.28	-10000	0	-0.8	48	48
VCAM1	-0.045	0.17	-10000	0	-0.48	45	45
platelet activation	-0.003	0.019	-10000	0	-10000	0	0
MAPKKK cascade	-0.013	0.023	0.21	1	-10000	0	1
IL18	-0.008	0.083	-10000	0	-0.42	10	10
negative regulation of macrophage activation	-0.003	0.016	-10000	0	-0.1	9	9
LEF	-0.003	0.016	-10000	0	-0.11	9	9
CASP1	-0.004	0.022	-10000	0	-0.23	2	2
mol:cAMP	-0.003	0.019	-10000	0	-10000	0	0
necrosis	-0.003	0.016	-10000	0	-0.1	9	9
intracellular pH reduction	0	0	-10000	0	-10000	0	0
PAGA	0	0	-10000	0	-10000	0	0
Edema toxin (unfolded)	-0.012	0.078	-10000	0	-0.51	9	9
mol:Epigallocatechin-3-gallate (EGCG)	0	0	-10000	0	-10000	0	0

×

Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.013	0	-10000	0	-10000	0	0
NFATC1	0.046	0.056	-10000	0	-0.39	5	5
NFATC2	-0.009	0.082	-10000	0	-0.27	14	14
NFATC3	0.018	0.012	-10000	0	-10000	0	0
YWHAE	0.013	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/CABIN1	0.006	0.093	-10000	0	-0.3	24	24
Exportin 1/Ran/NUP214	0	0	-10000	0	-10000	0	0
mol:DAG	-0.002	0.004	-10000	0	-10000	0	0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV	-0.027	0.091	-10000	0	-0.61	4	4
BCL2/BAX	-0.038	0.16	-10000	0	-0.66	22	22
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.002	0.007	-10000	0	-10000	0	0
CaM/Ca2+	-0.002	0.007	-10000	0	-10000	0	0
BAX	0.013	0	-10000	0	-10000	0	0
MAPK14	0.009	0.006	-10000	0	-10000	0	0
BAD	0.013	0	-10000	0	-10000	0	0
CABIN1/MEF2D	0.01	0.088	-10000	0	-0.55	2	2
Calcineurin A alpha-beta B1/BCL2	-0.037	0.2	-10000	0	-0.85	22	22
FKBP8	0.013	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	-0.01	0.087	0.54	2	-10000	0	2
KPNB1	0.013	0	-10000	0	-10000	0	0
KPNA2	0.013	0	-10000	0	-10000	0	0
XPO1	0.012	0.001	-10000	0	-10000	0	0
SFN	-0.21	0.17	-10000	0	-0.32	254	254
MAP3K8	0	0.089	-10000	0	-0.86	4	4
NFAT4/CK1 alpha	0	0	-10000	0	-10000	0	0
MEF2D/NFAT1/Cbp/p300	-0.11	0.16	-10000	0	-0.48	13	13
CABIN1	0.006	0.094	-10000	0	-0.3	24	24
CALM1	0.009	0.006	-10000	0	-10000	0	0
RAN	0.012	0.001	-10000	0	-10000	0	0
MAP3K1	0.013	0	-10000	0	-10000	0	0
CAMK4	-0.004	0.1	-10000	0	-0.86	4	4
mol:Ca2+	-0.005	0.01	-10000	0	-10000	0	0
MAPK3	0.013	0	-10000	0	-10000	0	0
YWHAH	0.013	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/AKAP79/PKA	0	0	-10000	0	-10000	0	0
YWHAB	0.013	0	-10000	0	-10000	0	0
MAPK8	0.005	0.063	-10000	0	-0.86	2	2
MAPK9	0.013	0	-10000	0	-10000	0	0
YWHAG	0.013	0	-10000	0	-10000	0	0
FKBP1A	0.013	0	-10000	0	-10000	0	0
NFAT1-c-4/YWHAQ	-0.008	0.045	-10000	0	-10000	0	0
PRKCH	0.013	0	-10000	0	-10000	0	0
CABIN1/Cbp/p300	-0.003	0.005	-10000	0	-10000	0	0
CASP3	0.009	0.006	-10000	0	-10000	0	0
PIM1	0.013	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	0	0	-10000	0	-10000	0	0
apoptosis	-0.012	0.048	-10000	0	-10000	0	0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1	-0.006	0.042	-10000	0	-10000	0	0
PRKCB	-0.028	0.11	-10000	0	-0.31	48	48
PRKCE	0.006	0.077	-10000	0	-0.86	3	3
JNK2/NFAT4	0.021	0.014	-10000	0	-10000	0	0
BAD/BCL-XL	0	0	-10000	0	-10000	0	0
PRKCD	0.013	0	-10000	0	-10000	0	0
NUP214	0.012	0.001	-10000	0	-10000	0	0
PRKCZ	0.009	0.006	-10000	0	-10000	0	0
PRKCA	-0.038	0.2	-10000	0	-0.86	22	22
PRKCG	0.005	0.023	-10000	0	-0.3	2	2
PRKCQ	-0.001	0.11	-10000	0	-0.86	6	6
FKBP38/BCL2	-0.038	0.16	-10000	0	-0.66	22	22
EP300	0.009	0.007	-10000	0	-10000	0	0
PRKCB1	0	0	-10000	0	-10000	0	0
CSNK2A1	0.013	0	-10000	0	-10000	0	0
NFATc/JNK1	0.038	0.068	-10000	0	-0.42	2	2
CaM/Ca2+/FKBP38	0	0	-10000	0	-10000	0	0
FKBP12/FK506	0	0	-10000	0	-10000	0	0
CSNK1A1	0.015	0.01	-10000	0	-10000	0	0
CaM/Ca2+/CAMK IV	-0.01	0.065	-10000	0	-0.59	4	4
NFATc/ERK1	0.052	0.053	-10000	0	-10000	0	0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV	-0.026	0.089	-10000	0	-0.6	4	4
NR4A1	-0.19	0.38	-10000	0	-0.76	116	116
GSK3B	0.009	0.006	-10000	0	-10000	0	0
positive T cell selection	0.018	0.012	-10000	0	-10000	0	0
NFAT1/CK1 alpha	-0.029	0.052	-10000	0	-0.49	1	1
RCH1/ KPNB1	0	0	-10000	0	-10000	0	0
YWHAQ	0.013	0	-10000	0	-10000	0	0
PRKACA	0.009	0.006	-10000	0	-10000	0	0
AKAP5	0.013	0	-10000	0	-10000	0	0
MEF2D	0.009	0.007	-10000	0	-10000	0	0
mol:FK506	0	0	-10000	0	-10000	0	0
YWHAZ	0.013	0	-10000	0	-10000	0	0
NFATc/p38 alpha	0.04	0.059	-10000	0	-0.37	5	5
CREBBP	0.009	0.007	-10000	0	-10000	0	0
BCL2	-0.038	0.2	-10000	0	-0.86	22	22

×

Class I PI3K signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ARF5/GTP	-0.001	0.032	0.31	1	-0.55	1	2
DAPP1	-0.057	0.14	-10000	0	-0.56	6	6
Src family/SYK family/BLNK-LAT/BTK-ITK	-0.064	0.18	-10000	0	-0.58	14	14
mol:DAG	-0.008	0.096	-10000	0	-0.28	10	10
HRAS	0.013	0.016	-10000	0	-0.29	1	1
RAP1A	0.014	0.001	-10000	0	-10000	0	0
ARF5/GDP	0.025	0.035	-10000	0	-0.47	1	1
PLCG2	0.013	0	-10000	0	-10000	0	0
PLCG1	0.013	0	-10000	0	-10000	0	0
ARF5	0.013	0	-10000	0	-10000	0	0
mol:GTP	0	0.015	-10000	0	-10000	0	0
ARF1/GTP	0	0.022	0.29	1	-10000	0	1
RHOA	0.013	0	-10000	0	-10000	0	0
YES1	0.013	0	-10000	0	-10000	0	0
RAP1A/GTP	0	0.014	-10000	0	-10000	0	0
ADAP1	0	0.014	-10000	0	-10000	0	0
ARAP3	0	0.015	0.27	1	-10000	0	1
INPPL1	0.013	0	-10000	0	-10000	0	0
PREX1	0.013	0	-10000	0	-10000	0	0
ARHGEF6	0.013	0	-10000	0	-10000	0	0
ARHGEF7	0.013	0	-10000	0	-10000	0	0
ARF1	0.013	0	-10000	0	-10000	0	0
NRAS	0.014	0.001	-10000	0	-10000	0	0
FYN	0.013	0	-10000	0	-10000	0	0
ARF6	0.013	0	-10000	0	-10000	0	0
FGR	0.01	0.032	-10000	0	-10000	0	0
mol:Ca2+	0.005	0.054	-10000	0	-10000	0	0
mol:IP4	0	0	-10000	0	-10000	0	0
TIAM1	-0.16	0.16	-10000	0	-0.3	210	210
ZAP70	-0.028	0.17	-10000	0	-0.66	23	23
mol:IP3	0.002	0.072	-10000	0	-10000	0	0
LYN	0.013	0	-10000	0	-10000	0	0
ARF1/GDP	0.025	0.035	-10000	0	-0.47	1	1
RhoA/GDP	0	0.021	0.29	1	-10000	0	1
PDK1/Src/Hsp90	-0.002	0.03	-10000	0	-0.57	1	1
BLNK	0.013	0	-10000	0	-10000	0	0
actin cytoskeleton reorganization	0.041	0.037	-10000	0	-10000	0	0
SRC	0.012	0.016	-10000	0	-10000	0	0
PLEKHA2	0.018	0.046	-10000	0	-10000	0	0
RAC1	0.013	0	-10000	0	-10000	0	0
PTEN	-0.002	0.043	-10000	0	-0.83	1	1
HSP90AA1	0.013	0	-10000	0	-10000	0	0
ARF6/GTP	0.001	0.016	0.31	1	-10000	0	1
RhoA/GTP	0	0.014	-10000	0	-10000	0	0
Src family/SYK family/BLNK-LAT	-0.056	0.16	-10000	0	-0.63	10	10
BLK	-0.26	0.39	-10000	0	-0.86	113	113
PDPK1	0.011	0.045	-10000	0	-0.86	1	1
CYTH1	0	0.014	-10000	0	-10000	0	0
HCK	-0.007	0.076	-10000	0	-0.3	24	24
CYTH3	-0.001	0.032	-10000	0	-0.57	1	1
CYTH2	0	0.014	-10000	0	-10000	0	0
KRAS	0.014	0.001	-10000	0	-10000	0	0
GO:0030676	0	0	-10000	0	-10000	0	0
FOXO3	-0.011	0.086	-10000	0	-0.62	7	7
SGK1	-0.012	0.097	-10000	0	-0.69	7	7
INPP5D	-0.01	0.081	-10000	0	-0.3	28	28
mol:GDP	0.017	0.037	-10000	0	-0.5	1	1
SOS1	0.013	0	-10000	0	-10000	0	0
SYK	0.013	0	-10000	0	-10000	0	0
ARF6/GDP	0	0.021	0.3	1	-10000	0	1
mol:PI-3-4-5-P3	0.001	0.02	0.37	1	-10000	0	1
ARAP3/RAP1A/GTP	0	0.014	-10000	0	-10000	0	0
VAV1	-0.013	0.1	-10000	0	-0.86	2	2
mol:PI-3-4-P2	0.008	0.056	-10000	0	-10000	0	0
RAS family/GTP/PI3K Class I	0	0.005	-10000	0	-10000	0	0
PLEKHA1	0.018	0.046	-10000	0	-10000	0	0
Rac1/GDP	0.025	0.035	-10000	0	-0.47	1	1
LAT	0.003	0.09	-10000	0	-0.74	5	5
Rac1/GTP	-0.002	0.053	-10000	0	-0.62	1	1
ITK	-0.058	0.15	-10000	0	-0.46	45	45
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma	-0.019	0.13	-10000	0	-0.41	10	10
LCK	-0.012	0.11	-10000	0	-0.4	23	23
BTK	-0.011	0.05	-10000	0	-0.46	3	3

×

Insulin Pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CBL/APS/CAP	-0.046	0.14	-9999	-0.46	38	38
TC10/GTP	-0.003	0.033	-9999	-0.45	2	2
Insulin Receptor/Insulin/IRS1/Shp2	-0.051	0.16	-9999	-0.54	36	36
HRAS	0.012	0.016	-9999	-0.3	1	1
APS homodimer	0.012	0.016	-9999	-0.3	1	1
GRB14	-0.022	0.17	-9999	-0.86	15	15
FOXO3	-0.022	0.1	-9999	-0.72	7	7
AKT1	-0.009	0.16	-9999	-0.79	1	1
INSR	0.015	0	-9999	-10000	0	0
Insulin Receptor/Insulin	0	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
GRB10	0.013	0	-9999	-10000	0	0
SORBS1	0.008	0.063	-9999	-0.86	2	2
CRK	0.013	0	-9999	-10000	0	0
PTPN1	0.037	0	-9999	-10000	0	0
CAV1	-0.038	0.18	-9999	-0.51	47	47
CBL/APS/CAP/Crk-II/C3G	-0.003	0.036	-9999	-0.49	2	2
Insulin Receptor/Insulin/IRS1/NCK2	-0.051	0.16	-9999	-0.54	36	36
mol:GDP	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.046	0.14	-9999	-0.47	37	37
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B	0.009	0.098	-9999	-10000	0	0
RPS6KB1	0.001	0.15	-9999	-0.69	1	1
PARD6A	0.013	0	-9999	-10000	0	0
CBL	0.013	0	-9999	-10000	0	0
tumor necrosis factor-mediated signaling pathway	0	0	-9999	-10000	0	0
DOK1	0	0	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/Shc	-0.052	0.13	-9999	-0.68	1	1
HRAS/GTP	-0.044	0.12	-9999	-0.52	1	1
Insulin Receptor	0.015	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC	-0.048	0.15	-9999	-0.5	36	36
PRKCI	-0.014	0.034	-9999	-10000	0	0
Insulin Receptor/Insulin/GRB14/PDK1	-0.061	0.15	-9999	-0.88	1	1
SHC1	0.013	0	-9999	-10000	0	0
negative regulation of MAPKKK cascade	0	0	-9999	-10000	0	0
PI3K	-0.047	0.14	-9999	-0.48	37	37
NCK2	0.013	0	-9999	-10000	0	0
RHOQ	0.013	0	-9999	-10000	0	0
mol:H2O2	0	0	-9999	-10000	0	0
HRAS/GDP	-0.001	0.01	-9999	-10000	0	0
AKT2	-0.009	0.16	-9999	-0.79	1	1
PRKCZ	-0.014	0.034	-9999	-10000	0	0
SH2B2	0.012	0.016	-9999	-0.3	1	1
SHC/SHIP	-0.024	0.15	-9999	-0.48	36	36
F2RL2	-0.076	0.14	-9999	-0.86	1	1
TRIP10	0.013	0	-9999	-10000	0	0
Insulin Receptor/Insulin/Shc	0	0	-9999	-10000	0	0
TC10/GTP/CIP4/Exocyst	0	0	-9999	-10000	0	0
Insulin Receptor/Insulin/SHC/GRB2/Sos1	0	0	-9999	-10000	0	0
RAPGEF1	0.013	0	-9999	-10000	0	0
RASA1	0.013	0	-9999	-10000	0	0
NCK1	0.013	0	-9999	-10000	0	0
CBL/APS/CAP/Crk-II	-0.003	0.038	-9999	-0.52	2	2
TC10/GDP	0	0	-9999	-10000	0	0
Insulin Receptor/Insulin/SHC/GRB10	0	0	-9999	-10000	0	0
INPP5D	-0.033	0.16	-9999	-0.51	36	36
SOS1	0.013	0	-9999	-10000	0	0
SGK1	-0.023	0.14	-9999	-1.1	7	7
mol:cAMP	0	0	-9999	-10000	0	0
PTPN11	0.013	0	-9999	-10000	0	0
IRS1	-0.07	0.26	-9999	-0.86	36	36
p62DOK/RasGAP	0	0	-9999	-10000	0	0
INS	0.003	0	-9999	-10000	0	0
mol:PI-3-4-P2	-0.033	0.16	-9999	-0.5	36	36
GRB2	0.013	0	-9999	-10000	0	0
EIF4EBP1	0	0.15	-9999	-0.55	3	3
PTPRA	0.015	0	-9999	-10000	0	0
PIK3CA	0.011	0.045	-9999	-0.86	1	1
TC10/GTP/CIP4	0	0	-9999	-10000	0	0
PDPK1	0.011	0.045	-9999	-0.86	1	1
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos	-0.001	0.11	-9999	-0.34	36	36
Insulin Receptor/Insulin/IRS1	-0.052	0.16	-9999	-0.55	36	36
Insulin Receptor/Insulin/IRS3	0	0	-9999	-10000	0	0
Par3/Par6	-0.033	0.056	-9999	-0.5	1	1

×

BARD1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BARD1/CSTF1	-0.028	0.13	-10000	0	-0.66	16	16
ATM	0.011	0.045	-10000	0	-0.86	1	1
UBE2D3	0.013	0	-10000	0	-10000	0	0
PRKDC	0.013	0	-10000	0	-10000	0	0
ATR	0.013	0	-10000	0	-10000	0	0
UBE2L3	0.013	0	-10000	0	-10000	0	0
FANCD2	0.026	0.025	-10000	0	-0.45	1	1
protein ubiquitination	-0.022	0.1	-10000	0	-0.48	17	17
XRCC5	0.013	0	-10000	0	-10000	0	0
XRCC6	0.013	0	-10000	0	-10000	0	0
M/R/N Complex	0	0	-10000	0	-10000	0	0
MRE11A	0.013	0	-10000	0	-10000	0	0
DNA-PK	0	0	-10000	0	-10000	0	0
FA complex/FANCD2/Ubiquitin	-0.002	0.011	-10000	0	-10000	0	0
FANCF	0.013	0	-10000	0	-10000	0	0
BRCA1	0.013	0	-10000	0	-10000	0	0
CCNE1	0.013	0	-10000	0	-10000	0	0
CDK2/Cyclin E1	0	0	-10000	0	-10000	0	0
FANCG	0.013	0	-10000	0	-10000	0	0
BRCA1/BACH1/BARD1	-0.028	0.13	-10000	0	-0.66	16	16
FANCE	0.013	0	-10000	0	-10000	0	0
FANCC	0.013	0	-10000	0	-10000	0	0
NBN	0.013	0	-10000	0	-10000	0	0
FANCA	-0.003	0.068	-10000	0	-10000	0	0
DNA repair	0.055	0.096	-10000	0	-10000	0	0
BRCA1/BARD1/ubiquitin	-0.028	0.13	-10000	0	-0.66	16	16
BARD1/DNA-PK	-0.022	0.1	-10000	0	-0.52	16	16
FANCL	0.013	0	-10000	0	-10000	0	0
mRNA polyadenylation	0.028	0.13	0.66	16	-10000	0	16
BRCA1/BARD1/CTIP/M/R/N Complex	0.025	0.082	-10000	0	-0.35	17	17
BRCA1/BACH1/BARD1/TopBP1	-0.024	0.12	-10000	0	-0.57	16	16
BRCA1/BARD1/P53	-0.022	0.1	-10000	0	-0.52	16	16
BARD1/CSTF1/BRCA1	-0.024	0.12	-10000	0	-0.57	16	16
BRCA1/BACH1	0.013	0	-10000	0	-10000	0	0
BARD1	-0.024	0.18	-10000	0	-0.86	16	16
PCNA	0.013	0	-10000	0	-10000	0	0
BRCA1/BARD1/UbcH5C	-0.024	0.12	-10000	0	-0.57	16	16
BRCA1/BARD1/UbcH7	-0.024	0.12	-10000	0	-0.57	16	16
BRCA1/BARD1/RAD51/PCNA	-0.023	0.11	-10000	0	-0.52	16	16
BARD1/DNA-PK/P53	-0.021	0.098	-10000	0	-0.49	16	16
BRCA1/BARD1/Ubiquitin	-0.028	0.13	-10000	0	-0.66	16	16
BRCA1/BARD1/CTIP	-0.023	0.11	-10000	0	-0.52	17	17
FA complex	0.038	0.02	-10000	0	-10000	0	0
BARD1/EWS	-0.028	0.13	-10000	0	-0.66	16	16
RBBP8	0.022	0.035	-10000	0	-0.66	1	1
TP53	0.013	0	-10000	0	-10000	0	0
TOPBP1	0.013	0	-10000	0	-10000	0	0
G1/S transition of mitotic cell cycle	0.022	0.1	0.52	16	-10000	0	16
BRCA1/BARD1	-0.022	0.1	-10000	0	-0.49	17	17
CSTF1	0.013	0	-10000	0	-10000	0	0
BARD1/EWS-Fli1	-0.028	0.14	-10000	0	-0.67	16	16
CDK2	0.013	0	-10000	0	-10000	0	0
UniProt:Q9BZD1	0	0	-10000	0	-10000	0	0
RAD51	0.01	0.032	-10000	0	-0.3	4	4
RAD50	0.013	0	-10000	0	-10000	0	0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme	-0.028	0.13	-10000	0	-0.66	16	16
EWSR1	0.013	0	-10000	0	-10000	0	0

×

Sphingosine 1-phosphate (S1P) pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPHK2	0.013	0	-9999	-10000	0	0
SPHK1	0.006	0.045	-9999	-0.3	8	8
GNAI2	0.013	0	-9999	-10000	0	0
mol:S1P	0.022	0.015	-9999	-10000	0	0
GNAO1	-0.013	0.14	-9999	-0.86	10	10
mol:Sphinganine-1-P	0.019	0.031	-9999	-10000	0	0
growth factor activity	0	0	-9999	-10000	0	0
S1P/S1P2/G12/G13	-0.001	0.007	-9999	-10000	0	0
GNAI3	0.013	0	-9999	-10000	0	0
G12/G13	0	0	-9999	-10000	0	0
S1PR3	0.013	0	-9999	-10000	0	0
S1PR2	0.012	0.016	-9999	-0.3	1	1
EDG1	0	0	-9999	-10000	0	0
S1P1/S1P	-0.001	0.01	-9999	-10000	0	0
S1PR5	0.01	0.032	-9999	-0.3	4	4
S1PR4	0.009	0.035	-9999	-0.3	5	5
GNAI1	0.011	0.045	-9999	-0.86	1	1
S1P/S1P5/G12	-0.002	0.015	-9999	-10000	0	0
S1P/S1P3/Gq	-0.051	0.15	-9999	-0.38	17	17
S1P/S1P4/Gi	0.032	0.063	-9999	-0.33	10	10
GNAQ	0.013	0	-9999	-10000	0	0
GNAZ	0.013	0	-9999	-10000	0	0
GNA14	-0.2	0.37	-9999	-0.86	91	91
GNA15	-0.017	0.099	-9999	-0.31	35	35
GNA12	0.013	0	-9999	-10000	0	0
GNA13	0.013	0	-9999	-10000	0	0
GNA11	0.006	0.077	-9999	-0.86	3	3
ABCC1	0.013	0	-9999	-10000	0	0

×

Class I PI3K signaling events mediated by Akt

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
BCL2L1	0.024	0	-10000	0	-10000	0	0
BAD/BCL-XL/YWHAZ	0	0	-10000	0	-10000	0	0
CDKN1B	0.039	0.01	-10000	0	-10000	0	0
CDKN1A	0.034	0.027	-10000	0	-10000	0	0
FRAP1	0	0	-10000	0	-10000	0	0
PRKDC	0.013	0	-10000	0	-10000	0	0
FOXO3	0.039	0.01	-10000	0	-10000	0	0
AKT1	0	0.008	-10000	0	-10000	0	0
BAD	0.013	0	-10000	0	-10000	0	0
AKT3	0.017	0.025	-10000	0	-0.46	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
FOXO4	0.039	0.01	-10000	0	-10000	0	0
AKT1/ASK1	-0.002	0.024	-10000	0	-0.46	1	1
BAD/YWHAZ	0	0	-10000	0	-10000	0	0
RICTOR	0.013	0	-10000	0	-10000	0	0
RAF1	0.013	0	-10000	0	-10000	0	0
JNK cascade	0.002	0.024	0.44	1	-10000	0	1
TSC1	0.039	0.01	-10000	0	-10000	0	0
YWHAZ	0.013	0	-10000	0	-10000	0	0
AKT1/RAF1	0.038	0.01	-10000	0	-10000	0	0
EP300	0.013	0	-10000	0	-10000	0	0
mol:GDP	0	0.008	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	0	0	-10000	0	-10000	0	0
TSC2	0.039	0.01	-10000	0	-10000	0	0
YWHAQ	0.013	0	-10000	0	-10000	0	0
TBC1D4	-0.044	0.19	-10000	0	-0.58	44	44
MAP3K5	0.011	0.045	-10000	0	-0.86	1	1
MAPKAP1	0.013	0	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.012	0.032	-10000	0	-10000	0	0
YWHAH	0.013	0	-10000	0	-10000	0	0
AKT1S1	0.039	0.01	-10000	0	-10000	0	0
CASP9	0.039	0.01	-10000	0	-10000	0	0
YWHAB	0.013	0	-10000	0	-10000	0	0
p27Kip1/KPNA1	0.045	0.009	-10000	0	-10000	0	0
GBL	0	0	-10000	0	-10000	0	0
PDK1/Src/Hsp90	-0.002	0.03	-10000	0	-0.57	1	1
YWHAE	0.013	0	-10000	0	-10000	0	0
SRC	0.012	0.016	-10000	0	-10000	0	0
AKT2/p21CIP1	-0.004	0.024	-10000	0	-10000	0	0
KIAA1303	0	0	-10000	0	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL	0.019	0.003	-10000	0	-10000	0	0
CHUK	0.039	0.01	-10000	0	-10000	0	0
BAD/BCL-XL	0.051	0.009	-10000	0	-10000	0	0
mTORC2	0	0	-10000	0	-10000	0	0
AKT2	0.017	0.025	-10000	0	-0.46	1	1
FOXO1-3a-4/14-3-3 family	0.025	0.037	-10000	0	-10000	0	0
PDPK1	0.011	0.045	-10000	0	-0.86	1	1
MDM2	0.039	0.01	-10000	0	-10000	0	0
MAPKKK cascade	-0.037	0.009	-10000	0	-10000	0	0
MDM2/Cbp/p300	0	0.006	-10000	0	-10000	0	0
TSC1/TSC2	0.046	0.009	-10000	0	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0	0.006	-10000	0	-10000	0	0
glucose import	-0.054	0.21	-10000	0	-0.56	55	55
mTOR/RHEB/GDP/Raptor/GBL/PRAS40	0.033	0.006	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
SLC2A4	-0.055	0.22	-10000	0	-0.56	55	55
GSK3A	0.039	0.01	-10000	0	-10000	0	0
FOXO1	0.039	0.01	-10000	0	-10000	0	0
GSK3B	0.039	0.01	-10000	0	-10000	0	0
SFN	-0.21	0.17	-10000	0	-0.32	254	254
G1/S transition of mitotic cell cycle	0.046	0.009	-10000	0	-10000	0	0
p27Kip1/14-3-3 family	0	0.047	-10000	0	-10000	0	0
PRKACA	0.013	0	-10000	0	-10000	0	0
KPNA1	0.013	0	-10000	0	-10000	0	0
HSP90AA1	0.013	0	-10000	0	-10000	0	0
YWHAG	0.013	0	-10000	0	-10000	0	0
RHEB	0.013	0	-10000	0	-10000	0	0
CREBBP	0.013	0	-10000	0	-10000	0	0

×

S1P3 pathway

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
PDGFRB	0.013	0	-9999	-10000	0	0
mol:S1P	0.002	0	-9999	-10000	0	0
S1P1/S1P/Gi	0.027	0.055	-9999	-0.29	11	11
GNAO1	-0.011	0.14	-9999	-0.85	10	10
S1P/S1P3/G12/G13	0	0	-9999	-10000	0	0
AKT1	-0.003	0.018	-9999	-10000	0	0
AKT3	0.049	0.041	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.013	0	-9999	-10000	0	0
GNAI2	0.015	0	-9999	-10000	0	0
GNAI3	0.015	0	-9999	-10000	0	0
GNAI1	0.012	0.045	-9999	-0.86	1	1
mol:GDP	0	0	-9999	-10000	0	0
S1PR3	0.015	0	-9999	-10000	0	0
S1PR2	0.012	0.016	-9999	-0.3	1	1
EDG1	0	0	-9999	-10000	0	0
mol:Ca2+	0.037	0.063	-9999	-0.33	10	10
MAPK3	0.043	0.06	-9999	-10000	0	0
MAPK1	0.043	0.06	-9999	-10000	0	0
JAK2	0.046	0.06	-9999	-10000	0	0
CXCR4	0.042	0.062	-9999	-10000	0	0
FLT1	0.016	0	-9999	-10000	0	0
RhoA/GDP	0	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
SRC	0.043	0.06	-9999	-10000	0	0
S1P/S1P3/Gi	0.037	0.063	-9999	-0.33	10	10
RAC1	0.013	0	-9999	-10000	0	0
RhoA/GTP	-0.009	0.049	-9999	-0.29	10	10
VEGFA	0.012	0.063	-9999	-0.86	2	2
S1P/S1P2/Gi	0.032	0.064	-9999	-0.33	11	11
VEGFR1 homodimer/VEGFA homodimer	0.025	0.05	-9999	-0.66	2	2
RHOA	0.013	0	-9999	-10000	0	0
S1P/S1P3/Gq	-0.069	0.17	-9999	-0.36	94	94
GNAQ	0.013	0	-9999	-10000	0	0
GNAZ	0.015	0	-9999	-10000	0	0
G12/G13	0	0	-9999	-10000	0	0
GNA14	-0.2	0.37	-9999	-0.86	91	91
GNA15	-0.017	0.099	-9999	-0.31	35	35
GNA12	0.013	0	-9999	-10000	0	0
GNA13	0.013	0	-9999	-10000	0	0
GNA11	0.006	0.077	-9999	-0.86	3	3
Rac1/GTP	-0.009	0.049	-9999	-10000	0	0

×

Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A	-0.18	0.36	-9999	-0.86	84	84
oxygen homeostasis	0	0	-9999	-10000	0	0
TCEB2	0.013	0	-9999	-10000	0	0
TCEB1	0.013	0	-9999	-10000	0	0
HIF1A/p53	0.029	0.022	-9999	-10000	0	0
HIF1A	0.022	0.023	-9999	-10000	0	0
COPS5	0.013	0	-9999	-10000	0	0
VHL/Elongin B/Elongin C/RBX1/CUL2	-0.003	0.035	-9999	-0.49	2	2
FIH (dimer)	0.013	0	-9999	-10000	0	0
CDKN2A	-0.12	0.15	-9999	-10000	0	0
ARNT/IPAS	-0.15	0.28	-9999	-0.66	84	84
HIF1AN	0.013	0	-9999	-10000	0	0
GNB2L1	0.013	0	-9999	-10000	0	0
HIF1A/ARNT	0.029	0.022	-9999	-10000	0	0
CUL2	0.013	0	-9999	-10000	0	0
OS9	0.013	0	-9999	-10000	0	0
RACK1/Elongin B/Elongin C	0	0	-9999	-10000	0	0
response to hypoxia	0	0	-9999	-10000	0	0
HIF1A/Hsp90	0.029	0.022	-9999	-10000	0	0
PHD1-3/OS9	-0.016	0.079	-9999	-0.52	8	8
HIF1A/RACK1/Elongin B/Elongin C	-0.002	0.012	-9999	-10000	0	0
VHL	0.008	0.063	-9999	-0.86	2	2
HSP90AA1	0.013	0	-9999	-10000	0	0
HIF1A/JAB1	0.029	0.022	-9999	-10000	0	0
EGLN3	-0.019	0.14	-9999	-0.48	25	25
EGLN2	0.013	0	-9999	-10000	0	0
EGLN1	0.013	0	-9999	-10000	0	0
TP53	0.013	0	-9999	-10000	0	0
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A	0.035	0.046	-9999	-0.59	2	2
ARNT	0.013	0	-9999	-10000	0	0
ARD1A	0	0	-9999	-10000	0	0
RBX1	0.013	0	-9999	-10000	0	0
HIF1A/p19ARF	-0.03	0.069	-9999	-10000	0	0

×

mTOR signaling pathway

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
GBL	0	0	-10000	0	-10000	0	0
MKNK1	0.013	0	-10000	0	-10000	0	0
mol:PIP3	-0.034	0.11	0.34	1	-0.36	37	38
FRAP1	0.009	0.023	-10000	0	-10000	0	0
AKT1	-0.028	0.091	0.25	1	-0.68	1	2
INSR	0.013	0	-10000	0	-10000	0	0
Insulin Receptor/Insulin	0	0	-10000	0	-10000	0	0
mol:GTP	-0.022	0.068	-10000	0	-0.54	1	1
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit	-0.006	0.02	-10000	0	-10000	0	0
TSC2	0.013	0	-10000	0	-10000	0	0
RHEB/GDP	-0.018	0.058	-10000	0	-0.49	1	1
TSC1	0.013	0	-10000	0	-10000	0	0
Insulin Receptor/IRS1	-0.026	0.13	-10000	0	-0.43	36	36
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA	-0.007	0.024	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
EIF3A	0.013	0	-10000	0	-10000	0	0
RPS6KB1	0.013	0.054	-10000	0	-0.38	1	1
MAP3K5	0.01	0.024	-10000	0	-0.46	1	1
PIK3R1	0.013	0	-10000	0	-10000	0	0
apoptosis	0.01	0.024	-10000	0	-0.46	1	1
mol:LY294002	0	0.001	0.001	1	-0.002	36	37
EIF4B	0.021	0.049	-10000	0	-0.32	1	1
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	-0.011	0.034	-10000	0	-0.3	1	1
eIF4E/eIF4G1/eIF4A1	-0.001	0.006	-10000	0	-10000	0	0
KIAA1303	0	0	-10000	0	-10000	0	0
PI3K	-0.016	0.12	-10000	0	-0.39	37	37
mTOR/RHEB/GTP/Raptor/GBL	0.023	0.036	0.18	1	-0.27	1	2
FKBP1A	0.013	0.001	-10000	0	-10000	0	0
RHEB/GTP	-0.018	0.057	-10000	0	-0.48	1	1
mol:Amino Acids	0	0.001	0.001	1	-0.002	36	37
FKBP12/Rapamycin	0	0.001	-10000	0	-10000	0	0
PDPK1	-0.032	0.1	0.26	1	-0.89	1	2
EIF4E	0.013	0	-10000	0	-10000	0	0
ASK1/PP5C	0.016	0.037	-10000	0	-0.63	1	1
mTOR/RHEB/GTP/Raptor/GBL/eIF4E	0.018	0.001	-10000	0	-10000	0	0
TSC1/TSC2	-0.023	0.073	-10000	0	-0.59	1	1
tumor necrosis factor receptor activity	0	0.001	0.002	36	-0.001	1	37
RPS6	0.013	0	-10000	0	-10000	0	0
PPP5C	0.013	0	-10000	0	-10000	0	0
EIF4G1	0.013	0	-10000	0	-10000	0	0
IRS1	-0.036	0.14	-10000	0	-0.47	36	36
INS	0	0	-10000	0	-10000	0	0
PTEN	0.01	0.044	-10000	0	-0.85	1	1
PDK2	-0.031	0.097	0.26	1	-0.32	37	38
EIF4EBP1	0.012	0.009	-10000	0	-10000	0	0
PIK3CA	0.011	0.045	-10000	0	-0.86	1	1
PPP2R5D	0.017	0.022	-10000	0	-10000	0	0
peptide biosynthetic process	0.018	0	-10000	0	-10000	0	0
RHEB	0.013	0	-10000	0	-10000	0	0
EIF4A1	0.013	0	-10000	0	-10000	0	0
mol:Rapamycin	0	0	0.004	1	-0.004	1	2
EEF2	0.018	0	-10000	0	-10000	0	0
eIF4E/4E-BP1	0.018	0.008	-10000	0	-10000	0	0

×

TRAIL signaling pathway

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
TNFSF10	0.01	0.047	-9999	-0.58	2	2
positive regulation of NF-kappaB transcription factor activity	-0.002	0.035	-9999	-0.66	1	1
MAP2K4	0.048	0.021	-9999	-10000	0	0
IKBKB	0.013	0	-9999	-10000	0	0
TNFRSF10B	0.013	0	-9999	-10000	0	0
TNFRSF10A	0.011	0.045	-9999	-0.86	1	1
SMPD1	-0.001	0.016	-9999	-0.3	1	1
IKBKG	0.013	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
TNFRSF10D	0.013	0	-9999	-10000	0	0
TRAIL/TRAILR2	-0.002	0.035	-9999	-0.66	1	1
TRAIL/TRAILR3	-0.059	0.093	-9999	-0.66	1	1
TRAIL/TRAILR1	-0.004	0.049	-9999	-0.66	2	2
TRAIL/TRAILR4	-0.002	0.035	-9999	-0.66	1	1
TRAIL/TRAILR1/DAP3/GTP	-0.003	0.039	-9999	-0.53	2	2
IKK complex	-0.001	0.012	-9999	-10000	0	0
RIPK1	0.013	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
DAP3/GTP	0	0	-9999	-10000	0	0
MAPK3	0.022	0.037	-9999	-0.66	1	1
MAP3K1	-0.001	0.019	-9999	-0.33	1	1
TRAILR4 (trimer)	0.013	0	-9999	-10000	0	0
TRADD	0.013	0	-9999	-10000	0	0
TRAILR1 (trimer)	0.011	0.044	-9999	-0.85	1	1
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2	0.037	0.028	-9999	-0.34	2	2
CFLAR	0.013	0	-9999	-10000	0	0
MAPK1	0.022	0.037	-9999	-0.66	1	1
TRAIL/TRAILR1/FADD/TRADD/RIP	-0.003	0.036	-9999	-0.49	2	2
mol:ceramide	-0.001	0.016	-9999	-0.3	1	1
FADD	0.013	0	-9999	-10000	0	0
MAPK8	0.052	0.042	-9999	-0.45	2	2
TRAF2	0.013	0	-9999	-10000	0	0
TRAILR3 (trimer)	-0.08	0.14	-9999	-0.3	114	114
CHUK	0.013	0	-9999	-10000	0	0
TRAIL/TRAILR1/FADD	-0.003	0.042	-9999	-0.57	2	2
DAP3	0.013	0	-9999	-10000	0	0
CASP10	-0.002	0.032	-9999	-0.55	1	1
JNK cascade	-0.002	0.035	-9999	-0.66	1	1
TRAIL (trimer)	0.01	0.047	-9999	-0.58	2	2
TNFRSF10C	-0.081	0.14	-9999	-0.3	114	114
TRAIL/TRAILR1/DAP3/GTP/FADD	-0.003	0.036	-9999	-0.5	2	2
TRAIL/TRAILR2/FADD	-0.002	0.03	-9999	-0.57	1	1
cell death	-0.001	0.016	-9999	-0.3	1	1
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2	0.038	0.02	-9999	-0.34	1	1
TRAILR2 (trimer)	0.013	0	-9999	-10000	0	0
CASP8	0	0.009	-9999	-10000	0	0
negative regulation of caspase activity	0	0	-9999	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP	-0.002	0.026	-9999	-0.49	1	1

×

ceramide signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAP4K4	0.004	0.13	-10000	0	-0.5	11	11
BAG4	0.011	0.045	-10000	0	-0.86	1	1
BAD	0.018	0.046	-10000	0	-10000	0	0
NFKBIA	0.013	0	-10000	0	-10000	0	0
BIRC3	-0.038	0.19	-10000	0	-0.68	28	28
BAX	0.018	0.046	-10000	0	-10000	0	0
EnzymeConsortium:3.1.4.12	0.004	0.034	-10000	0	-0.12	8	8
IKBKB	0.013	0.12	-10000	0	-0.53	8	8
MAP2K2	0.028	0.055	-10000	0	-0.39	1	1
MAP2K1	0.028	0.055	-10000	0	-0.39	1	1
SMPD1	0.01	0.034	-10000	0	-10000	0	0
GO:0005551	0	0	-10000	0	-10000	0	0
FADD/Caspase 8	0.013	0.13	-10000	0	-0.55	8	8
MAP2K4	0.024	0.047	-10000	0	-10000	0	0
protein ubiquitination	0.014	0.13	-10000	0	-0.54	8	8
EnzymeConsortium:2.7.1.37	0.031	0.06	-10000	0	-0.39	1	1
response to UV	0	0.001	-10000	0	-0.003	1	1
RAF1	0.022	0.055	-10000	0	-0.42	1	1
CRADD	0.013	0	-10000	0	-10000	0	0
mol:ceramide	0.01	0.048	-10000	0	-0.17	8	8
I-kappa-B-alpha/RELA/p50/ubiquitin	0	0	-10000	0	-10000	0	0
MADD	0.013	0	-10000	0	-10000	0	0
MAP3K1	0.017	0.047	-10000	0	-10000	0	0
TRADD	0.013	0	-10000	0	-10000	0	0
RELA/p50	0.013	0	-10000	0	-10000	0	0
MAPK3	0.03	0.054	-10000	0	-0.38	1	1
MAPK1	0.03	0.054	-10000	0	-0.38	1	1
p50/RELA/I-kappa-B-alpha	0	0	-10000	0	-10000	0	0
FADD	0.004	0.13	-10000	0	-0.57	8	8
KSR1	0.016	0.054	-10000	0	-0.45	1	1
MAPK8	0.028	0.056	-10000	0	-0.45	2	2
TRAF2	0.013	0	-10000	0	-10000	0	0
response to radiation	0	0	-10000	0	-10000	0	0
CHUK	0.013	0.12	-10000	0	-0.53	8	8
TNF R/SODD	-0.002	0.034	-10000	0	-0.66	1	1
TNF	-0.09	0.28	-10000	0	-0.8	48	48
CYCS	0.026	0.054	0.16	18	-10000	0	18
IKBKG	0.013	0.12	-10000	0	-0.53	8	8
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD	-0.004	0.14	-10000	0	-0.45	19	19
RELA	0.013	0	-10000	0	-10000	0	0
RIPK1	0.013	0	-10000	0	-10000	0	0
AIFM1	0.026	0.054	0.16	18	-10000	0	18
TNF/TNF R/SODD	-0.068	0.18	-10000	0	-0.57	44	44
TNFRSF1A	0.013	0	-10000	0	-10000	0	0
response to heat	0	0	-10000	0	-10000	0	0
CASP8	0.019	0.033	-10000	0	-10000	0	0
NSMAF	0.005	0.13	-10000	0	-0.56	8	8
response to hydrogen peroxide	0	0.001	-10000	0	-0.003	1	1
BCL2	-0.038	0.2	-10000	0	-0.86	22	22

×

Canonical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FBXW11	0.017	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.069	0.057	-9999	-10000	0	0
ERC1	0.013	0	-9999	-10000	0	0
RIP2/NOD2	-0.026	0.072	-9999	-0.66	1	1
NFKBIA	0.049	0	-9999	-10000	0	0
BIRC2	0.013	0	-9999	-10000	0	0
IKBKB	0.013	0	-9999	-10000	0	0
RIPK2	0.013	0	-9999	-10000	0	0
IKBKG	-0.004	0.017	-9999	-10000	0	0
IKK complex/A20	-0.049	0.13	-9999	-0.42	43	43
NEMO/A20/RIP2	0.013	0	-9999	-10000	0	0
XPO1	0.013	0	-9999	-10000	0	0
NEMO/ATM	0.042	0.038	-9999	-0.45	1	1
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
RAN	0.013	0	-9999	-10000	0	0
Exportin 1/RanGTP	0	0	-9999	-10000	0	0
IKK complex/ELKS	0	0.012	-9999	-10000	0	0
BCL10/MALT1/TRAF6	-0.002	0.029	-9999	-0.57	1	1
NOD2	-0.03	0.11	-9999	-0.86	1	1
NFKB1	0.017	0	-9999	-10000	0	0
RELA	0.017	0	-9999	-10000	0	0
MALT1	0.013	0	-9999	-10000	0	0
cIAP1/UbcH5C	0	0	-9999	-10000	0	0
ATM	0.011	0.045	-9999	-0.86	1	1
TNF/TNFR1A	-0.078	0.21	-9999	-0.66	43	43
TRAF6	0.011	0.045	-9999	-0.86	1	1
PRKCA	-0.038	0.2	-9999	-0.86	22	22
CHUK	0.013	0	-9999	-10000	0	0
UBE2D3	0.013	0	-9999	-10000	0	0
TNF	-0.09	0.28	-9999	-0.8	48	48
NF kappa B1 p50/RelA	0	0	-9999	-10000	0	0
BCL10	0.013	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.049	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.016	0	-9999	-10000	0	0
TNFRSF1A	0.013	0	-9999	-10000	0	0
IKK complex	-0.002	0.013	-9999	-10000	0	0
CYLD	0.013	0	-9999	-10000	0	0
IKK complex/PKC alpha	-0.024	0.097	-9999	-0.41	22	22

×

Arf6 downstream pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLAUR	-0.057	0.12	-10000	0	-10000	0	0
regulation of axonogenesis	-0.012	0.029	-10000	0	-10000	0	0
myoblast fusion	0.03	0.045	-10000	0	-10000	0	0
mol:GTP	-0.026	0.038	-10000	0	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	0.086	0.1	0.55	1	-10000	0	1
ARF1/GTP	-0.015	0.021	-10000	0	-10000	0	0
mol:GM1	-0.011	0.032	-10000	0	-10000	0	0
mol:Choline	0.012	0.028	-10000	0	-10000	0	0
lamellipodium assembly	-0.003	0.061	-10000	0	-10000	0	0
MAPK3	-0.016	0.062	-10000	0	-10000	0	0
ARF6/GTP/NME1/Tiam1	-0.086	0.1	-10000	0	-0.55	1	1
ARF1	0.013	0	-10000	0	-10000	0	0
ARF6/GDP	-0.03	0.045	-10000	0	-10000	0	0
ARF1/GDP	0.004	0.056	-10000	0	-10000	0	0
ARF6	-0.002	0.021	-10000	0	-10000	0	0
RAB11A	0.013	0	-10000	0	-10000	0	0
TIAM1	-0.16	0.16	-10000	0	-0.3	210	210
fibronectin binding	0	0	-10000	0	-10000	0	0
MAPK1	-0.016	0.062	-10000	0	-10000	0	0
actin filament bundle formation	0.024	0.036	-10000	0	-10000	0	0
KALRN	-0.006	0.049	-10000	0	-10000	0	0
RAB11FIP3/RAB11A	0	0	-10000	0	-10000	0	0
RhoA/GDP	-0.024	0.036	-10000	0	-10000	0	0
NME1	0.01	0.007	-10000	0	-10000	0	0
Rac1/GDP	-0.024	0.036	-10000	0	-10000	0	0
substrate adhesion-dependent cell spreading	-0.026	0.037	-10000	0	-10000	0	0
cortical actin cytoskeleton organization	-0.003	0.061	-10000	0	-10000	0	0
RAC1	0.013	0	-10000	0	-10000	0	0
liver development	-0.026	0.037	-10000	0	-10000	0	0
ARF6/GTP	-0.026	0.038	-10000	0	-10000	0	0
RhoA/GTP	-0.015	0.021	-10000	0	-10000	0	0
mol:GDP	-0.011	0.062	-10000	0	-10000	0	0
ARF6/GTP/RAB11FIP3/RAB11A	-0.009	0.013	-10000	0	-10000	0	0
RHOA	0.013	0	-10000	0	-10000	0	0
PLD1	0.001	0.032	-10000	0	-10000	0	0
RAB11FIP3	0.013	0	-10000	0	-10000	0	0
tube morphogenesis	-0.003	0.061	-10000	0	-10000	0	0
ruffle organization	0.012	0.029	-10000	0	-10000	0	0
regulation of epithelial cell migration	-0.026	0.037	-10000	0	-10000	0	0
PLD2	0.001	0.032	-10000	0	-10000	0	0
PIP5K1A	0.012	0.029	-10000	0	-10000	0	0
mol:Phosphatidic acid	0.012	0.028	-10000	0	-10000	0	0
Rac1/GTP	-0.003	0.062	-10000	0	-10000	0	0

×

Signaling events mediated by HDAC Class I

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
NF kappa B/RelA	-0.061	0.17	-9999	-0.53	43	43
Ran/GTP/Exportin 1/HDAC1	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	-0.05	0.14	-9999	-0.43	43	43
SUMO1	0.013	0	-9999	-10000	0	0
ZFPM1	0.013	0	-9999	-10000	0	0
NPC/RanGAP1/SUMO1/Ubc9	0.023	0	-9999	-10000	0	0
FKBP3	0.013	0	-9999	-10000	0	0
Histones	-0.025	0.068	-9999	-10000	0	0
YY1/LSF	0.027	0.052	-9999	-0.56	3	3
SMG5	0.013	0	-9999	-10000	0	0
RAN	0.013	0	-9999	-10000	0	0
I kappa B alpha/HDAC3	-0.044	0.12	-9999	-0.38	43	43
I kappa B alpha/HDAC1	-0.028	0.082	-9999	-10000	0	0
SAP18	0.013	0	-9999	-10000	0	0
RELA	-0.003	0.12	-9999	-0.33	43	43
HDAC1/Smad7	0	0	-9999	-10000	0	0
RANGAP1	0.013	0	-9999	-10000	0	0
HDAC3/TR2	-0.028	0.082	-9999	-10000	0	0
NuRD/MBD3 Complex	0.05	0	-9999	-10000	0	0
NF kappa B1 p50/RelA	0.003	0.11	-9999	-0.3	43	43
EntrezGene:23225	0	0	-9999	-10000	0	0
GATA2	0.012	0.016	-9999	-0.3	1	1
GATA1	0.009	0.006	-9999	-10000	0	0
Mad/Max	0	0	-9999	-10000	0	0
NuRD/MBD3 Complex/GATA1/Fog1	0.06	0.002	-9999	-10000	0	0
RBBP7	0.013	0	-9999	-10000	0	0
NPC	0	0	-9999	-10000	0	0
RBBP4	0.013	0	-9999	-10000	0	0
MAX	0.013	0	-9999	-10000	0	0
EntrezGene:9972	0	0	-9999	-10000	0	0
FBXW11	0.013	0	-9999	-10000	0	0
NFKBIA	-0.008	0.1	-9999	-0.29	43	43
KAT2B	0.013	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
SIN3/HDAC complex	0.045	0.016	-9999	-10000	0	0
SIN3 complex	-0.001	0.027	-9999	-0.52	1	1
SMURF1	0.013	0	-9999	-10000	0	0
CHD3	0.013	0	-9999	-10000	0	0
SAP30	0.011	0.045	-9999	-0.86	1	1
EntrezGene:23636	0	0	-9999	-10000	0	0
NCOR1	0.013	0	-9999	-10000	0	0
YY1/HDAC3	-0.024	0.072	-9999	-10000	0	0
YY1/HDAC2	0.032	0	-9999	-10000	0	0
YY1/HDAC1	0.032	0	-9999	-10000	0	0
NuRD/MBD2 Complex (MeCP1)	0.05	0	-9999	-10000	0	0
PPARG	-0.06	0.16	-9999	-0.47	47	47
HDAC8/hEST1B	0	0	-9999	-10000	0	0
UBE2I	0.013	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.013	0	-9999	-10000	0	0
TNFRSF1A	0.013	0	-9999	-10000	0	0
HDAC3/SMRT (N-CoR2)	-0.028	0.082	-9999	-10000	0	0
MBD3L2	0	0	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
CREBBP	0.013	0	-9999	-10000	0	0
NuRD/MBD3/MBD3L2 Complex	0.053	0	-9999	-10000	0	0
HDAC1	0.013	0	-9999	-10000	0	0
HDAC3	-0.008	0.1	-9999	-10000	0	0
HDAC2	0.013	0	-9999	-10000	0	0
YY1	0.032	0	-9999	-10000	0	0
HDAC8	0.013	0	-9999	-10000	0	0
SMAD7	0.013	0	-9999	-10000	0	0
NCOR2	0.013	0	-9999	-10000	0	0
MXD1	0.013	0	-9999	-10000	0	0
STAT3	0.027	0	-9999	-10000	0	0
NFKB1	0.013	0	-9999	-10000	0	0
EntrezGene:8021	0	0	-9999	-10000	0	0
RANBP2	0.013	0	-9999	-10000	0	0
YY1/LSF/HDAC1	-0.004	0.045	-9999	-0.51	3	3
YY1/SAP30/HDAC1	-0.001	0.026	-9999	-0.51	1	1
EP300	0.013	0	-9999	-10000	0	0
STAT3 (dimer non-phopshorylated)	0.027	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	-0.008	0.1	-9999	-0.29	43	43
histone deacetylation	0.05	0	-9999	-10000	0	0
STAT3 (dimer non-phopshorylated)/HDAC3	-0.025	0.073	-9999	-10000	0	0
nuclear export	0	0	-9999	-10000	0	0
PRKACA	0.013	0	-9999	-10000	0	0
GATAD2B	0.013	0	-9999	-10000	0	0
GATAD2A	0.013	0	-9999	-10000	0	0
GATA2/HDAC3	-0.029	0.082	-9999	-10000	0	0
GATA1/HDAC1	0	0	-9999	-10000	0	0
GATA1/HDAC3	-0.03	0.083	-9999	-10000	0	0
CHD4	0.013	0	-9999	-10000	0	0
TNF-alpha/TNFR1A	-0.078	0.21	-9999	-0.66	43	43
SIN3/HDAC complex/Mad/Max	0.049	0.013	-9999	-10000	0	0
NuRD Complex	0.059	0	-9999	-10000	0	0
positive regulation of chromatin silencing	-0.024	0.067	-9999	-10000	0	0
SIN3B	0.013	0	-9999	-10000	0	0
MTA2	0.013	0	-9999	-10000	0	0
SIN3A	0.013	0	-9999	-10000	0	0
XPO1	0.013	0	-9999	-10000	0	0
SUMO1/HDAC1	0	0	-9999	-10000	0	0
HDAC complex	0	0	-9999	-10000	0	0
GATA1/Fog1	0	0	-9999	-10000	0	0
FKBP25/HDAC1/HDAC2	0	0	-9999	-10000	0	0
TNF	-0.09	0.28	-9999	-0.8	48	48
negative regulation of cell growth	0.049	0.013	-9999	-10000	0	0
NuRD/MBD2/PRMT5 Complex	0.05	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0	0	-9999	-10000	0	0
NF kappa B/RelA/I kappa B alpha	-0.052	0.14	-9999	-0.46	43	43
SIN3/HDAC complex/NCoR1	0.047	0.013	-9999	-10000	0	0
TFCP2	0.006	0.077	-9999	-0.86	3	3
NR2C1	0.013	0	-9999	-10000	0	0
MBD3	0.013	0	-9999	-10000	0	0
MBD2	0.013	0	-9999	-10000	0	0

×

FoxO family signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G6PC	0.039	0.016	-9999	-10000	0	0
PLK1	0.11	0.094	-9999	-10000	0	0
CDKN1B	0.15	0.033	-9999	-10000	0	0
FOXO3	0.11	0.094	-9999	-10000	0	0
KAT2B	0.025	0.009	-9999	-10000	0	0
FOXO1/SIRT1	0.011	0.026	-9999	-10000	0	0
CAT	0.11	0.087	-9999	-10000	0	0
CTNNB1	0.013	0	-9999	-10000	0	0
AKT1	0.028	0.01	-9999	-10000	0	0
FOXO1	0.042	0.011	-9999	-10000	0	0
MAPK10	0.044	0.006	-9999	-10000	0	0
mol:GTP	0.002	0.001	-9999	-10000	0	0
FOXO4	0.11	0.038	-9999	-0.47	1	1
response to oxidative stress	0.015	0.012	-9999	-10000	0	0
FOXO3A/SIRT1	0.015	0.058	-9999	-10000	0	0
XPO1	0.014	0	-9999	-10000	0	0
EP300	0.015	0.001	-9999	-10000	0	0
BCL2L11	0.041	0.026	-9999	-10000	0	0
FOXO1/SKP2	0.042	0.029	-9999	-0.49	1	1
mol:GDP	0.015	0.012	-9999	-10000	0	0
RAN	0.015	0.001	-9999	-10000	0	0
GADD45A	0.13	0.034	-9999	-10000	0	0
YWHAQ	0.013	0	-9999	-10000	0	0
FOXO1/14-3-3 family	0.041	0.037	-9999	-10000	0	0
MST1	0.022	0.048	-9999	-0.84	1	1
CSNK1D	0.013	0	-9999	-10000	0	0
CSNK1E	0.013	0	-9999	-10000	0	0
FOXO4/14-3-3 family	0.013	0.058	-9999	-10000	0	0
YWHAB	0.013	0	-9999	-10000	0	0
MAPK8	0.042	0.041	-9999	-0.52	2	2
MAPK9	0.044	0.006	-9999	-10000	0	0
YWHAG	0.013	0	-9999	-10000	0	0
YWHAE	0.013	0	-9999	-10000	0	0
YWHAZ	0.013	0	-9999	-10000	0	0
SIRT1	0.007	0.02	-9999	-10000	0	0
SOD2	0.16	0.046	-9999	-10000	0	0
RBL2	0.12	0.098	-9999	-1.2	1	1
RAL/GDP	0.033	0.012	-9999	-10000	0	0
CHUK	0.025	0.009	-9999	-10000	0	0
Ran/GTP	0.015	0.001	-9999	-10000	0	0
CSNK1G2	0.013	0	-9999	-10000	0	0
RAL/GTP	0.042	0.009	-9999	-10000	0	0
CSNK1G1	0.013	0	-9999	-10000	0	0
FASLG	-0.069	0.4	-9999	-1.5	25	25
SKP2	0.011	0.045	-9999	-0.86	1	1
USP7	0.015	0.001	-9999	-10000	0	0
IKBKB	0.025	0.009	-9999	-10000	0	0
CCNB1	0.11	0.087	-9999	-10000	0	0
FOXO1-3a-4/beta catenin	-0.004	0.033	-9999	-0.41	2	2
proteasomal ubiquitin-dependent protein catabolic process	0.042	0.029	-9999	-0.49	1	1
CSNK1A1	0.013	0	-9999	-10000	0	0
SGK1	0.009	0.12	-9999	-0.84	7	7
CSNK1G3	0.013	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.025	0.002	-9999	-10000	0	0
ZFAND5	0.11	0.033	-9999	-10000	0	0
SFN	-0.21	0.17	-9999	-0.32	254	254
CDK2	0.013	0.002	-9999	-10000	0	0
FOXO3A/14-3-3	0.016	0.059	-9999	-10000	0	0
CREBBP	0.013	0.002	-9999	-10000	0	0
FBXO32	0.11	0.089	-9999	-10000	0	0
BCL6	0.12	0.097	-9999	-1.2	1	1
RALB	0.014	0	-9999	-10000	0	0
RALA	0.014	0	-9999	-10000	0	0
YWHAH	0.013	0	-9999	-10000	0	0

×

Canonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.006	0.021	-10000	0	-10000	0	0
AES	0.005	0.018	-10000	0	-10000	0	0
FBXW11	0.013	0	-10000	0	-10000	0	0
mol:GTP	0	0.001	-10000	0	-10000	0	0
LRP6/FZD1	0	0	-10000	0	-10000	0	0
SMAD4	0.013	0	-10000	0	-10000	0	0
DKK2	-0.031	0.18	-10000	0	-0.66	25	25
TLE1	0	0.063	-10000	0	-0.83	2	2
MACF1	0.013	0	-10000	0	-10000	0	0
CTNNB1	0.047	0.042	-10000	0	-10000	0	0
WIF1	-0.033	0.1	-10000	0	-0.3	47	47
beta catenin/RanBP3	0.02	0.089	0.37	19	-10000	0	19
KREMEN2	-0.01	0.081	-10000	0	-10000	0	0
DKK1	-0.034	0.12	-10000	0	-0.32	54	54
beta catenin/beta TrCP1	0.052	0.04	-10000	0	-10000	0	0
FZD1	0.013	0.001	-10000	0	-10000	0	0
AXIN2	-0.047	0.31	-10000	0	-1.6	14	14
AXIN1	0.013	0	-10000	0	-10000	0	0
RAN	0.013	0.001	-10000	0	-10000	0	0
Axin1/APC/GSK3/beta catenin	0.005	0.018	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4	0.063	0.038	-10000	0	-10000	0	0
Axin1/APC/GSK3	0.007	0.033	-10000	0	-10000	0	0
Axin1/APC/GSK3/beta catenin/Macf1	0.058	0.018	-10000	0	-10000	0	0
HNF1A	0.005	0.019	-10000	0	-10000	0	0
CTBP1	0.005	0.02	-10000	0	-10000	0	0
MYC	-0.024	0.24	-10000	0	-1.6	8	8
RANBP3	0.013	0.001	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	-0.038	0.13	-10000	0	-0.6	16	16
NKD1	-0.02	0.16	-10000	0	-0.75	16	16
TCF4	0.005	0.019	-10000	0	-10000	0	0
TCF3	0.005	0.019	-10000	0	-10000	0	0
WNT1/LRP6/FZD1/Axin1	-0.001	0.011	-10000	0	-10000	0	0
Ran/GTP	0.001	0.004	-10000	0	-10000	0	0
CtBP/CBP/TCF/TLE1/AES	0.028	0.11	0.46	21	-10000	0	21
LEF1	0	0.045	-10000	0	-0.3	7	7
DVL1	0.014	0.026	-10000	0	-10000	0	0
CSNK2A1	0.013	0	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES	0.069	0.065	-10000	0	-0.53	2	2
DKK1/LRP6/Kremen 2	-0.034	0.079	-10000	0	-0.65	2	2
LRP6	0.013	0	-10000	0	-10000	0	0
CSNK1A1	0.006	0.021	-10000	0	-10000	0	0
NLK	0.013	0.004	-10000	0	-10000	0	0
CCND1	0	0.069	-10000	0	-0.46	2	2
WNT1	0.008	0.028	-10000	0	-0.3	3	3
GSK3A	0.013	0	-10000	0	-10000	0	0
GSK3B	0.013	0.001	-10000	0	-10000	0	0
FRAT1	0.013	0	-10000	0	-10000	0	0
PPP2R5D	0.032	0.066	0.37	13	-10000	0	13
APC	0.038	0.015	-10000	0	-10000	0	0
WNT1/LRP6/FZD1	0.034	0.035	-10000	0	-10000	0	0
CREBBP	0.005	0.019	-10000	0	-10000	0	0

×

Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.011	0.081	-9999	-0.44	10	10
CRKL	0.013	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
DOCK1	0.011	0.045	-9999	-0.86	1	1
ITGA4	0.006	0.047	-9999	-0.3	9	9
alpha4/beta7 Integrin/MAdCAM1	-0.032	0.094	-9999	-0.52	10	10
EPO	0.006	0.017	-9999	-0.3	1	1
alpha4/beta7 Integrin	-0.03	0.12	-9999	-0.64	11	11
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.013	0	-9999	-10000	0	0
alpha4/beta1 Integrin	-0.005	0.029	-9999	-10000	0	0
EPO/EPOR (dimer)	-0.003	0.022	-9999	-10000	0	0
lamellipodium assembly	0	0.028	-9999	-0.52	1	1
PIK3CA	0.011	0.045	-9999	-0.86	1	1
PI3K	-0.002	0.034	-9999	-0.66	1	1
ARF6	0.013	0	-9999	-10000	0	0
JAK2	-0.003	0.014	-9999	-10000	0	0
PXN	0.013	0	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
MADCAM1	-0.014	0.082	-9999	-0.3	29	29
cell adhesion	-0.032	0.093	-9999	-0.52	10	10
CRKL/CBL	0	0	-9999	-10000	0	0
ITGB1	0.013	0	-9999	-10000	0	0
SRC	0.024	0.06	-9999	-0.52	3	3
ITGB7	-0.024	0.15	-9999	-0.5	27	27
RAC1	0.013	0	-9999	-10000	0	0
alpha4/beta1 Integrin/VCAM1	-0.01	0.06	-9999	-0.57	3	3
p130Cas/Crk/Dock1	-0.008	0.049	-9999	-0.44	4	4
VCAM1	0.001	0.086	-9999	-0.48	9	9
RHOA	0.013	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/GIT1	-0.003	0.018	-9999	-10000	0	0
BCAR1	0.033	0.057	-9999	-0.48	3	3
EPOR	0.01	0.032	-9999	-0.3	4	4
mol:GDP	0	0	-9999	-10000	0	0
CBL	0.013	0	-9999	-10000	0	0
GIT1	0.013	0	-9999	-10000	0	0
Rac1/GTP	0	0.029	-9999	-0.54	1	1

×

S1P5 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	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	0.009	0.05	0.3	10	-10000	0	10
GNAI2	0.013	0	-10000	0	-10000	0	0
S1P/S1P5/G12	-0.002	0.016	-10000	0	-10000	0	0
mol:GDP	0	0	-10000	0	-10000	0	0
GNAO1	-0.013	0.14	-10000	0	-0.86	10	10
RhoA/GTP	-0.01	0.05	-10000	0	-0.3	10	10
negative regulation of cAMP metabolic process	0.024	0.063	-10000	0	-0.33	11	11
GNAZ	0.013	0	-10000	0	-10000	0	0
GNAI3	0.013	0	-10000	0	-10000	0	0
GNA12	0.013	0	-10000	0	-10000	0	0
S1PR5	0.01	0.032	-10000	0	-0.3	4	4
mol:GTP	0	0	-10000	0	-10000	0	0
S1P/S1P5/Gi	0.024	0.064	-10000	0	-0.34	11	11
RhoA/GDP	0	0	-10000	0	-10000	0	0
RHOA	0.013	0	-10000	0	-10000	0	0
GNAI1	0.011	0.045	-10000	0	-0.86	1	1

×

Signaling events mediated by VEGFR1 and VEGFR2

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
alphaV beta3 Integrin	-0.022	0.13	-9999	-0.71	12	12
AKT1	0.083	0.084	-9999	-0.61	4	4
PTK2B	0.034	0.14	-9999	-0.92	5	5
VEGFR2 homodimer/Frs2	-0.009	0.089	-9999	-0.85	4	4
CAV1	-0.012	0.15	-9999	-0.86	11	11
CALM1	0.013	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2	-0.011	0.09	-9999	-0.69	6	6
endothelial cell proliferation	0.071	0.1	-9999	-0.63	3	3
mol:Ca2+	0.05	0.088	-9999	-0.79	3	3
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac	-0.01	0.085	-9999	-0.84	3	3
RP11-342D11.1	0.041	0.088	-9999	-0.63	6	6
CDH5	0.013	0	-9999	-10000	0	0
VEGFA homodimer	-0.005	0.053	-9999	-0.52	4	4
SHC1	0.013	0	-9999	-10000	0	0
SHC2	0.008	0.063	-9999	-0.86	2	2
HRAS/GDP	-0.008	0.068	-9999	-0.68	3	3
SH2D2A	-0.039	0.19	-9999	-0.86	19	19
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS	-0.008	0.064	-9999	-0.62	3	3
VEGFR2 homodimer/VEGFA homodimer/TsAd	-0.039	0.15	-9999	-0.58	24	24
VEGFR1 homodimer	0.013	0	-9999	-10000	0	0
SHC/GRB2/SOS1	-0.009	0.077	-9999	-0.76	3	3
GRB10	0.05	0.088	-9999	-0.79	3	3
PTPN11	0.013	0	-9999	-10000	0	0
GRB2	0.013	0	-9999	-10000	0	0
PAK1	0.013	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin	-0.01	0.081	-9999	-0.81	3	3
HRAS	0.012	0.016	-9999	-0.3	1	1
VEGF/Rho/ROCK1/Integrin Complex	0.039	0.082	-9999	-0.51	5	5
HIF1A	0.013	0	-9999	-10000	0	0
FRS2	0.013	0	-9999	-10000	0	0
oxygen and reactive oxygen species metabolic process	-0.01	0.084	-9999	-0.82	3	3
mol:GTP	0	0	-9999	-10000	0	0
FLT4	0.004	0.089	-9999	-0.86	4	4
Nck/Pak	0	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Fyn	-0.011	0.09	-9999	-0.69	6	6
mol:GDP	-0.009	0.074	-9999	-0.73	3	3
mol:NADP	0.075	0.064	-9999	-0.51	3	3
eNOS/Hsp90	0.078	0.061	-9999	-0.48	3	3
PIK3R1	0.013	0	-9999	-10000	0	0
mol:IP3	0.05	0.089	-9999	-0.81	3	3
HIF1A/ARNT	0	0	-9999	-10000	0	0
SHB	0.013	0	-9999	-10000	0	0
VEGFA	0.011	0.063	-9999	-0.85	2	2
VEGFC	0.011	0.045	-9999	-0.86	1	1
FAK1/Vinculin	0.056	0.12	-9999	-0.78	5	5
mol:Ca ++	0	0	-9999	-10000	0	0
RHOA	0.013	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	-0.027	0.14	-9999	-0.98	5	5
PTPN6	0.013	0	-9999	-10000	0	0
EPAS1	0.018	0.057	-9999	-0.5	4	4
mol:L-citrulline	0.075	0.064	-9999	-0.51	3	3
ITGAV	0.011	0.045	-9999	-0.86	1	1
PIK3CA	0.011	0.045	-9999	-0.86	1	1
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2	-0.01	0.085	-9999	-0.69	5	5
VEGFR2 homodimer/VEGFA homodimer	-0.011	0.089	-9999	-0.69	6	6
VEGFR2/3 heterodimer	-0.015	0.12	-9999	-0.8	7	7
VEGFB	0.013	0	-9999	-10000	0	0
MAPK11	0.053	0.092	-9999	-0.68	5	5
VEGFR2 homodimer	0.028	0.1	-9999	-0.95	4	4
FLT1	0.013	0	-9999	-10000	0	0
NEDD4	0.015	0	-9999	-10000	0	0
MAPK3	0.04	0.096	-9999	-0.7	4	4
MAPK1	0.04	0.096	-9999	-0.7	4	4
VEGFA145/NRP2	-0.022	0.072	-9999	-0.66	2	2
VEGFR1/2 heterodimer	-0.009	0.089	-9999	-0.85	4	4
KDR	0.028	0.1	-9999	-0.95	4	4
VEGFA165/NRP1/VEGFR2 homodimer	-0.018	0.087	-9999	-0.85	3	3
SRC	0.012	0.016	-9999	-10000	0	0
platelet activating factor biosynthetic process	0.043	0.097	-9999	-0.72	4	4
PI3K	-0.011	0.081	-9999	-0.77	3	3
VEGFR2 homodimer/VEGFA homodimer/NCK1	-0.011	0.09	-9999	-0.69	6	6
FES	0.05	0.091	-9999	-0.82	3	3
GAB1	-0.01	0.082	-9999	-0.79	3	3
VEGFR2 homodimer/VEGFA homodimer/Src	-0.011	0.09	-9999	-0.69	6	6
CTNNB1	0.013	0	-9999	-10000	0	0
SOS1	0.013	0	-9999	-10000	0	0
ARNT	0.013	0	-9999	-10000	0	0
eNOS/Caveolin-1	0.066	0.097	-9999	-0.57	3	3
VEGFR2 homodimer/VEGFA homodimer/Yes	-0.011	0.09	-9999	-0.69	6	6
PI3K/GAB1	0.084	0.082	-9999	-0.64	3	3
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak	-0.01	0.081	-9999	-0.81	3	3
PRKACA	0.013	0	-9999	-10000	0	0
VEGFR2/3 heterodimer/VEGFC homodimer	-0.015	0.12	-9999	-0.81	7	7
HSP90AA1	0.013	0	-9999	-10000	0	0
CDC42	0.05	0.091	-9999	-0.82	3	3
actin cytoskeleton reorganization	-0.039	0.14	-9999	-0.57	24	24
PTK2	0.05	0.13	-9999	-0.76	7	7
EDG1	0.041	0.088	-9999	-0.63	6	6
mol:DAG	0.05	0.089	-9999	-0.81	3	3
CaM/Ca2+	-0.009	0.075	-9999	-0.74	3	3
MAP2K3	0.052	0.1	-9999	-0.78	3	3
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4	-0.01	0.084	-9999	-0.84	3	3
PLCG1	0.05	0.091	-9999	-0.82	3	3
VEGFR2 homodimer/VEGFA homodimer/Src/Shb	-0.011	0.085	-9999	-0.84	3	3
IQGAP1	0.013	0	-9999	-10000	0	0
YES1	0.013	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/SHP2	-0.011	0.09	-9999	-0.69	6	6
VEGFR2 homodimer/VEGFA homodimer/SHP1	-0.011	0.09	-9999	-0.69	6	6
cell migration	0.08	0.1	-9999	-0.67	4	4
mol:PI-3-4-5-P3	-0.01	0.074	-9999	-0.69	3	3
FYN	0.013	0	-9999	-10000	0	0
VEGFB/NRP1	-0.009	0.077	-9999	-0.75	3	3
mol:NO	0.075	0.064	-9999	-0.51	3	3
PXN	0.013	0	-9999	-10000	0	0
HRAS/GTP	-0.008	0.068	-9999	-0.68	3	3
VEGFR2 homodimer/VEGFA homodimer/GRB10	-0.01	0.085	-9999	-0.84	3	3
VHL	0.008	0.063	-9999	-0.86	2	2
ITGB3	-0.015	0.15	-9999	-0.86	12	12
NOS3	0.077	0.072	-9999	-0.59	3	3
VEGFR2 homodimer/VEGFA homodimer/Sck	-0.014	0.097	-9999	-0.65	8	8
RAC1	0.013	0	-9999	-10000	0	0
PRKCA	0.027	0.15	-9999	-0.9	3	3
PRKCB	0.038	0.1	-9999	-0.73	4	4
VCL	0.013	0	-9999	-10000	0	0
VEGFA165/NRP1	0.04	0.088	-9999	-0.64	6	6
VEGFR1/2 heterodimer/VEGFA homodimer	-0.011	0.09	-9999	-0.69	6	6
VEGFA165/NRP2	-0.022	0.072	-9999	-0.66	2	2
MAPKKK cascade	-0.008	0.068	-9999	-0.68	3	3
NRP2	-0.017	0.092	-9999	-10000	0	0
VEGFC homodimer	0.011	0.044	-9999	-0.85	1	1
NCK1	0.013	0	-9999	-10000	0	0
ROCK1	0.013	0	-9999	-10000	0	0
FAK1/Paxillin	0.056	0.12	-9999	-0.78	5	5
MAP3K13	0.044	0.1	-9999	-0.82	3	3
PDPK1	0.075	0.084	-9999	-0.63	4	4

×

E-cadherin signaling in the nascent adherens junction

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CTTN	0.044	0.007	-9999	-10000	0	0
KLHL20	-0.008	0.022	-9999	-10000	0	0
CYFIP2	0.013	0	-9999	-10000	0	0
Rac1/GDP	0.072	0.009	-9999	-10000	0	0
ENAH	0.044	0.007	-9999	-10000	0	0
AP1M1	0.013	0	-9999	-10000	0	0
RAP1B	0.013	0	-9999	-10000	0	0
RAP1A	0.013	0	-9999	-10000	0	0
CTNNB1	0.013	0	-9999	-10000	0	0
CDC42/GTP	0	0.002	-9999	-10000	0	0
ABI1/Sra1/Nap1	-0.003	0.015	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin	-0.019	0.087	-9999	-0.52	10	10
RAPGEF1	0.057	0.006	-9999	-10000	0	0
CTNND1	0.013	0	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	0	0	-9999	-10000	0	0
CRK	0.051	0.007	-9999	-10000	0	0
E-cadherin/gamma catenin/alpha catenin	0	0	-9999	-10000	0	0
alphaE/beta7 Integrin	-0.026	0.11	-9999	-0.66	10	10
IQGAP1	0.013	0	-9999	-10000	0	0
NCKAP1	0.013	0	-9999	-10000	0	0
Rap1/GTP/I-afadin	0	0	-9999	-10000	0	0
DLG1	0.044	0.007	-9999	-10000	0	0
ChemicalAbstracts:7440-70-2	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.001	0.011	-9999	-10000	0	0
MLLT4	0.013	0	-9999	-10000	0	0
ARF6/GTP/NME1/Tiam1	-0.073	0.069	-9999	-0.53	1	1
PI3K	-0.001	0.014	-9999	-10000	0	0
ARF6	0.013	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
E-cadherin/gamma catenin	0	0	-9999	-10000	0	0
TIAM1	-0.16	0.16	-9999	-0.3	210	210
E-cadherin(dimer)/Ca2+	0	0	-9999	-10000	0	0
AKT1	0	0.008	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
CDH1	0.013	0	-9999	-10000	0	0
RhoA/GDP	0.072	0.009	-9999	-10000	0	0
actin cytoskeleton organization	-0.006	0.016	-9999	-10000	0	0
CDC42/GDP	0.072	0.009	-9999	-10000	0	0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin	0.026	0	-9999	-10000	0	0
ITGB7	-0.024	0.15	-9999	-0.5	27	27
RAC1	0.013	0	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/p120 catenin	0	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin	0	0	-9999	-10000	0	0
mol:GDP	0.071	0.01	-9999	-10000	0	0
CDC42/GTP/IQGAP1	0	0	-9999	-10000	0	0
JUP	0.013	0	-9999	-10000	0	0
p120 catenin/RhoA/GDP	0	0.002	-9999	-10000	0	0
RAC1/GTP/IQGAP1	0	0	-9999	-10000	0	0
PIP5K1C/AP1M1	0	0	-9999	-10000	0	0
RHOA	0.013	0	-9999	-10000	0	0
CDC42	0.013	0	-9999	-10000	0	0
CTNNA1	0.013	0	-9999	-10000	0	0
positive regulation of S phase of mitotic cell cycle	0.015	0.032	-9999	-0.14	10	10
NME1	0.013	0	-9999	-10000	0	0
clathrin coat assembly	0	0	-9999	-10000	0	0
TJP1	0.044	0.007	-9999	-10000	0	0
regulation of cell-cell adhesion	0	0.002	-9999	-10000	0	0
WASF2	0.002	0.009	-9999	-10000	0	0
Rap1/GTP	0	0.003	-9999	-10000	0	0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin	-0.018	0.081	-9999	-0.49	10	10
CCND1	0.017	0.038	-9999	-0.17	10	10
VAV2	0.055	0.007	-9999	-10000	0	0
RAP1/GDP	0	0.002	-9999	-10000	0	0
adherens junction assembly	0.044	0.001	-9999	-10000	0	0
homophilic cell adhesion	0	0	-9999	-10000	0	0
ABI1	0.013	0	-9999	-10000	0	0
PIP5K1C	0.013	0	-9999	-10000	0	0
regulation of heterotypic cell-cell adhesion	-0.016	0.076	-9999	-0.46	10	10
E-cadherin/beta catenin	0	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
SRC	0.043	0.01	-9999	-10000	0	0
PIK3CA	0.011	0.045	-9999	-0.86	1	1
Rac1/GTP	0.004	0.038	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin	0	0	-9999	-10000	0	0
ITGAE	0.013	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0	0	-9999	-10000	0	0

×

S1P4 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
mol:S1P	0	0	-9999	-10000	0	0
GNAO1	-0.013	0.14	-9999	-0.86	10	10
CDC42/GTP	-0.01	0.05	-9999	-0.3	10	10
PLCG1	0.031	0.06	-9999	-0.32	10	10
mol:GTP	0	0	-9999	-10000	0	0
GNAI2	0.013	0	-9999	-10000	0	0
GNAI3	0.013	0	-9999	-10000	0	0
G12/G13	0	0	-9999	-10000	0	0
cell migration	-0.009	0.05	-9999	-0.3	10	10
S1PR5	0.01	0.032	-9999	-0.3	4	4
S1PR4	0.009	0.035	-9999	-0.3	5	5
MAPK3	0.031	0.06	-9999	-0.32	10	10
MAPK1	0.031	0.06	-9999	-0.32	10	10
S1P/S1P5/Gi	0.024	0.064	-9999	-0.34	11	11
GNAI1	0.011	0.045	-9999	-0.86	1	1
CDC42/GDP	0	0	-9999	-10000	0	0
S1P/S1P5/G12	-0.002	0.016	-9999	-10000	0	0
RHOA	0.032	0.017	-9999	-10000	0	0
S1P/S1P4/Gi	0.024	0.064	-9999	-0.34	11	11
mol:GDP	0	0	-9999	-10000	0	0
GNAZ	0.013	0	-9999	-10000	0	0
S1P/S1P4/G12/G13	-0.002	0.015	-9999	-10000	0	0
GNA12	0.013	0	-9999	-10000	0	0
GNA13	0.013	0	-9999	-10000	0	0
CDC42	0.013	0	-9999	-10000	0	0

×

Circadian rhythm 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
chromatin modification	-0.021	0.035	-9999	-10000	0	0
CLOCK	-0.014	0.15	-9999	-0.86	11	11
TIMELESS/CRY2	-0.001	0.06	-9999	-10000	0	0
DEC1/BMAL1	-0.027	0.068	-9999	-10000	0	0
ATR	0.013	0	-9999	-10000	0	0
NR1D1	-0.05	0.12	-9999	-10000	0	0
ARNTL	-0.029	0.1	-9999	-0.32	15	15
TIMELESS	-0.008	0.068	-9999	-10000	0	0
NPAS2	0.007	0.05	-9999	-0.48	3	3
CRY2	0.013	0	-9999	-10000	0	0
mol:CO	0.006	0.029	-9999	-10000	0	0
CHEK1	0.013	0	-9999	-10000	0	0
mol:HEME	-0.006	0.029	-9999	-10000	0	0
PER1	0.013	0	-9999	-10000	0	0
BMAL/CLOCK/NPAS2	-0.018	0.13	-9999	-0.61	12	12
BMAL1/CLOCK	-0.039	0.13	-9999	-0.64	6	6
S phase of mitotic cell cycle	-0.021	0.035	-9999	-10000	0	0
TIMELESS/CHEK1/ATR	-0.021	0.036	-9999	-10000	0	0
mol:NADPH	-0.006	0.029	-9999	-10000	0	0
PER1/TIMELESS	-0.001	0.06	-9999	-10000	0	0
PER1-2 / CRY1-2	0	0	-9999	-10000	0	0
DEC1	0	0.016	-9999	-0.3	1	1

×

Aurora A signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Aurora A/GADD45A	0.007	0.015	-9999	-10000	0	0
BIRC5	-0.021	0.1	-9999	-0.31	39	39
NFKBIA	0.032	0.009	-9999	-10000	0	0
CPEB1	-0.051	0.23	-9999	-0.86	28	28
AKT1	0.032	0.009	-9999	-10000	0	0
NDEL1	0.013	0	-9999	-10000	0	0
Aurora A/BRCA1	0.003	0.012	-9999	-10000	0	0
NDEL1/TACC3	0.003	0.014	-9999	-10000	0	0
GADD45A	0.013	0	-9999	-10000	0	0
GSK3B	0.012	0.005	-9999	-10000	0	0
PAK1/Aurora A	0.007	0.015	-9999	-10000	0	0
MDM2	0.013	0	-9999	-10000	0	0
JUB	0.008	0.063	-9999	-0.86	2	2
TPX2	-0.003	0.071	-9999	-10000	0	0
TP53	0.008	0.015	-9999	-10000	0	0
DLG7	0.021	0.009	-9999	-10000	0	0
AURKAIP1	0.013	0	-9999	-10000	0	0
ARHGEF7	0.013	0	-9999	-10000	0	0
G2 phase of mitotic cell cycle	0	0	-9999	-10000	0	0
Aurora A/NDEL1/TACC3	0.003	0.015	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	0.003	0.012	-9999	-10000	0	0
AURKA	0.026	0.012	-9999	-10000	0	0
AURKB	-0.013	0.026	-9999	-10000	0	0
CDC25B	0.006	0.021	-9999	-10000	0	0
G2/M transition checkpoint	0	0.04	-9999	-0.53	2	2
mRNA polyadenylation	-0.036	0.14	-9999	-0.53	28	28
Aurora A/CPEB	-0.037	0.14	-9999	-0.53	28	28
Aurora A/TACC1/TRAP/chTOG	0.004	0.015	-9999	-10000	0	0
BRCA1	0.013	0	-9999	-10000	0	0
centrosome duplication	0.007	0.015	-9999	-10000	0	0
regulation of centrosome cycle	0	0.006	-9999	-10000	0	0
spindle assembly	0	0	-9999	-10000	0	0
TDRD7	0.013	0	-9999	-10000	0	0
Aurora A/RasGAP/Survivin	-0.011	0.038	-9999	-0.47	1	1
CENPA	-0.009	0.027	-9999	-0.26	3	3
Aurora A/PP2A	0.007	0.015	-9999	-10000	0	0
meiosis	0	0	-9999	-10000	0	0
protein catabolic process	0.038	0.008	-9999	-10000	0	0
negative regulation of DNA binding	0.031	0.007	-9999	-10000	0	0
prophase	0	0	-9999	-10000	0	0
GIT1/beta-PIX	0	0	-9999	-10000	0	0
RASA1	0.013	0	-9999	-10000	0	0
Ajuba/Aurora A	0	0.04	-9999	-0.53	2	2
mitotic prometaphase	0.005	0.01	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.026	0.012	-9999	-10000	0	0
TACC1	0.013	0	-9999	-10000	0	0
TACC3	0.012	0.016	-9999	-0.3	1	1
Aurora A/Antizyme1	0.004	0.014	-9999	-10000	0	0
Aurora A/RasGAP	0.007	0.015	-9999	-10000	0	0
OAZ1	0.013	0	-9999	-10000	0	0
RAN	0.013	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
PRKACA	0.012	0.005	-9999	-10000	0	0
GIT1	0.013	0	-9999	-10000	0	0
GIT1/beta-PIX/PAK1	0	0	-9999	-10000	0	0
Importin alpha/Importin beta/TPX2	-0.003	0.071	-9999	-10000	0	0
PPP2R5D	0.013	0	-9999	-10000	0	0
Aurora A/TPX2	0.016	0.053	-9999	-10000	0	0
PAK1	0.013	0	-9999	-10000	0	0
CKAP5	0.013	0	-9999	-10000	0	0

×

EPO signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.059	0.092	-9999	-10000	0	0
CRKL	0.043	0.03	-9999	-10000	0	0
mol:DAG	0.046	0.039	-9999	-10000	0	0
HRAS	0.066	0.028	-9999	-10000	0	0
MAPK8	0.031	0.047	-9999	-0.55	2	2
RAP1A	0.043	0.03	-9999	-10000	0	0
GAB1	0.043	0.03	-9999	-10000	0	0
MAPK14	0.034	0.019	-9999	-10000	0	0
EPO	0.009	0.017	-9999	-10000	0	0
PLCG1	0.023	0.044	-9999	-10000	0	0
EPOR/TRPC2/IP3 Receptors	0.012	0.032	-9999	-0.3	4	4
RAPGEF1	0.013	0	-9999	-10000	0	0
EPO/EPOR (dimer)/SOCS3	-0.045	0.15	-9999	-0.6	27	27
GAB1/SHC/GRB2/SOS1	-0.003	0.011	-9999	-10000	0	0
EPO/EPOR (dimer)	0.018	0.025	-9999	-10000	0	0
IRS2	0.043	0.03	-9999	-10000	0	0
STAT1	0.048	0.066	-9999	-10000	0	0
STAT5B	0.048	0.054	-9999	-10000	0	0
cell proliferation	0.038	0.044	-9999	-0.51	2	2
GAB1/SHIP/PIK3R1/SHP2/SHC	-0.006	0.016	-9999	-10000	0	0
TEC	0.043	0.03	-9999	-10000	0	0
SOCS3	-0.05	0.22	-9999	-0.84	28	28
STAT1 (dimer)	0.047	0.066	-9999	-10000	0	0
JAK2	0.014	0.004	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
EPO/EPOR (dimer)/JAK2	0.047	0.035	-9999	-10000	0	0
EPO/EPOR	0.018	0.025	-9999	-10000	0	0
LYN	0.014	0.004	-9999	-10000	0	0
TEC/VAV2	0.051	0.029	-9999	-10000	0	0
elevation of cytosolic calcium ion concentration	0.012	0.032	-9999	-0.3	4	4
SHC1	0.013	0	-9999	-10000	0	0
EPO/EPOR (dimer)/LYN	0.032	0.023	-9999	-10000	0	0
mol:IP3	0.046	0.039	-9999	-10000	0	0
PI3K regualtory subunit polypeptide 1/IRS2/SHIP	-0.008	0.021	-9999	-10000	0	0
SH2B3	0.014	0.004	-9999	-10000	0	0
NFKB1	0.034	0.019	-9999	-10000	0	0
EPO/EPOR (dimer)/JAK2/SOCS3	-0.021	0.075	-9999	-0.29	27	27
PTPN6	0.036	0.031	-9999	-10000	0	0
TEC/VAV2/GRB2	0.025	0.035	-9999	-10000	0	0
EPOR	0.012	0.032	-9999	-0.3	4	4
INPP5D	-0.01	0.081	-9999	-0.3	28	28
mol:GDP	-0.003	0.011	-9999	-10000	0	0
SOS1	0.013	0	-9999	-10000	0	0
PLCG2	0.013	0	-9999	-10000	0	0
CRKL/CBL/C3G	0.025	0.035	-9999	-10000	0	0
VAV2	0.043	0.03	-9999	-10000	0	0
CBL	0.043	0.03	-9999	-10000	0	0
SHC/Grb2/SOS1	-0.003	0.013	-9999	-10000	0	0
STAT5A	0.048	0.054	-9999	-10000	0	0
GRB2	0.013	0	-9999	-10000	0	0
STAT5 (dimer)	0.06	0.085	-9999	-10000	0	0
LYN/PLCgamma2	0	0	-9999	-10000	0	0
PTPN11	0.013	0	-9999	-10000	0	0
BTK	0.028	0.065	-9999	-0.46	3	3
BCL2	0.019	0.25	-9999	-0.99	22	22

×

Signaling mediated by p38-gamma and p38-delta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EEF2K	0.032	0	-9999	-10000	0	0
SNTA1	0.013	0	-9999	-10000	0	0
response to hypoxia	0	0	-9999	-10000	0	0
STMN1	0.031	0.009	-9999	-10000	0	0
MAPK12	0.022	0.07	-9999	-0.52	6	6
CCND1	0.018	0.03	-9999	-0.2	6	6
p38 gamma/SNTA1	0.028	0.066	-9999	-0.48	6	6
MAP2K3	0.013	0	-9999	-10000	0	0
PKN1	0.013	0	-9999	-10000	0	0
G2/M transition checkpoint	0.022	0.07	-9999	-0.52	6	6
MAP2K6	0.016	0.075	-9999	-0.57	6	6
MAPT	0.025	0.042	-9999	-0.41	2	2
MAPK13	0.024	0	-9999	-10000	0	0
hyperosmotic response	0	0	-9999	-10000	0	0
ZAK	0.018	0	-9999	-10000	0	0

×

Paxillin-dependent events mediated by a4b1

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
CRKL	0.013	0	-9999	-10000	0	0
Rac1/GDP	0.001	0.005	-9999	-10000	0	0
DOCK1	0.011	0.045	-9999	-0.86	1	1
ITGA4	0.006	0.047	-9999	-0.3	9	9
RAC1	0.013	0	-9999	-10000	0	0
alpha4/beta7 Integrin	-0.03	0.12	-9999	-0.64	11	11
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.013	0	-9999	-10000	0	0
alpha4/beta1 Integrin	-0.003	0.022	-9999	-10000	0	0
alpha4/beta7 Integrin/Paxillin	-0.022	0.089	-9999	-0.52	10	10
lamellipodium assembly	-0.001	0.039	-9999	-0.75	1	1
PIK3CA	0.011	0.045	-9999	-0.86	1	1
PI3K	-0.002	0.034	-9999	-0.66	1	1
ARF6	0.013	0	-9999	-10000	0	0
TLN1	0.013	0	-9999	-10000	0	0
PXN	0.024	0	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
ARF6/GTP	-0.002	0.013	-9999	-10000	0	0
cell adhesion	-0.002	0.016	-9999	-10000	0	0
CRKL/CBL	0	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin	-0.003	0.018	-9999	-10000	0	0
ITGB1	0.013	0	-9999	-10000	0	0
ITGB7	-0.024	0.15	-9999	-0.5	27	27
ARF6/GDP	0.001	0.005	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/VCAM1	-0.008	0.05	-9999	-0.49	3	3
p130Cas/Crk/Dock1	-0.002	0.029	-9999	-0.57	1	1
VCAM1	0.001	0.086	-9999	-0.48	9	9
alpha4/beta1 Integrin/Paxillin/Talin	-0.002	0.016	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/GIT1	-0.002	0.016	-9999	-10000	0	0
BCAR1	0.013	0	-9999	-10000	0	0
mol:GDP	0.002	0.016	-9999	-10000	0	0
CBL	0.013	0	-9999	-10000	0	0
PRKACA	0.013	0	-9999	-10000	0	0
GIT1	0.013	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton	-0.002	0.016	-9999	-10000	0	0
Rac1/GTP	-0.001	0.047	-9999	-0.9	1	1

×

Atypical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL3/RelA	-0.001	0.01	-9999	-10000	0	0
FBXW11	0.013	0	-9999	-10000	0	0
NF kappa B1 p50/c-Rel	0.002	0.12	-9999	-0.57	16	16
NF kappa B1 p50/RelA/I kappa B alpha	0.044	0.032	-9999	-10000	0	0
NFKBIA	0.024	0.036	-9999	-0.28	4	4
MAPK14	0.013	0	-9999	-10000	0	0
NF kappa B1 p105/p50	0.027	0	-9999	-10000	0	0
ARRB2	0.018	0	-9999	-10000	0	0
REL	-0.024	0.18	-9999	-0.86	16	16
response to oxidative stress	0	0	-9999	-10000	0	0
BCL3/NF kappa B1 p50	0.027	0.009	-9999	-10000	0	0
response to UV	0	0	-9999	-10000	0	0
NF kappa B1 p105/RelA	0.027	0	-9999	-10000	0	0
PIK3CA	0.011	0.045	-9999	-0.86	1	1
NF kappa B1 p50 dimer	0.021	0	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
NFKB1	0.024	0	-9999	-10000	0	0
RELA	0.013	0	-9999	-10000	0	0
positive regulation of anti-apoptosis	0.031	0.036	-9999	-0.28	4	4
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2	0.047	0.031	-9999	-10000	0	0
SRC	0.012	0.016	-9999	-10000	0	0
PI3K	-0.002	0.034	-9999	-0.66	1	1
NF kappa B1 p50/RelA	0.031	0.036	-9999	-0.28	4	4
IKBKB	0.013	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.013	0	-9999	-10000	0	0
SYK	0.013	0	-9999	-10000	0	0
I kappa B alpha/PIK3R1	0.029	0.034	-9999	-10000	0	0
cell death	-0.003	0.022	-9999	-10000	0	0
NF kappa B1 p105/c-Rel	0.002	0.12	-9999	-0.57	16	16
LCK	-0.012	0.11	-9999	-0.4	23	23
BCL3	0.012	0.016	-9999	-0.3	1	1

×

PDGFR-beta signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate	0.001	0.019	-9999	-10000	0	0
PDGFB-D/PDGFRB/SLAP	-0.001	0.01	-9999	-10000	0	0
PDGFB-D/PDGFRB/APS/CBL	0	0.008	-9999	-10000	0	0
AKT1	0.06	0.033	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
mol:Sphingosine-1-phosphate	0.025	0.033	-9999	-10000	0	0
PIK3CA	0.011	0.045	-9999	-0.86	1	1
FGR	0.004	0.012	-9999	-10000	0	0
mol:Ca2+	0.021	0.029	-9999	-10000	0	0
MYC	0.023	0.14	-9999	-0.87	8	8
SHC1	0.013	0	-9999	-10000	0	0
HRAS/GDP	0.011	0.018	-9999	-10000	0	0
LRP1/PDGFRB/PDGFB	-0.002	0.03	-9999	-0.58	1	1
GRB10	0.013	0	-9999	-10000	0	0
PTPN11	0.013	0	-9999	-10000	0	0
GO:0007205	0.021	0.029	-9999	-10000	0	0
PTEN	0.011	0.045	-9999	-0.86	1	1
GRB2	0.013	0	-9999	-10000	0	0
GRB7	-0.033	0.11	-9999	-0.3	56	56
PDGFB-D/PDGFRB/SHP2	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/GRB10	0	0	-9999	-10000	0	0
cell cycle arrest	-0.001	0.01	-9999	-10000	0	0
HRAS	0.012	0.016	-9999	-0.3	1	1
HIF1A	0.066	0.03	-9999	-10000	0	0
GAB1	0.014	0.048	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
DNM2	0.02	0.045	-9999	-10000	0	0
PDGFB-D/PDGFRB	0.012	0.016	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/LMW-PTP	0	0	-9999	-10000	0	0
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB	0.004	0.028	-9999	-10000	0	0
positive regulation of MAPKKK cascade	0	0	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
mol:IP3	0.021	0.029	-9999	-10000	0	0
E5	0	0.001	-9999	-10000	0	0
CSK	0.012	0.001	-9999	-10000	0	0
PDGFB-D/PDGFRB/GRB7	-0.028	0.068	-9999	-10000	0	0
SHB	0.013	0	-9999	-10000	0	0
BLK	-0.19	0.28	-9999	-0.62	113	113
PTPN2	0.013	0.002	-9999	-10000	0	0
PDGFB-D/PDGFRB/SNX15	0	0	-9999	-10000	0	0
BCAR1	0.013	0	-9999	-10000	0	0
VAV2	0.018	0.054	-9999	-10000	0	0
CBL	0.013	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/DEP1	0	0	-9999	-10000	0	0
LCK	-0.006	0.066	-9999	-0.62	4	4
PDGFRB	0.014	0.002	-9999	-10000	0	0
ACP1	0.013	0	-9999	-10000	0	0
HCK	0.007	0.023	-9999	-10000	0	0
ABL1	0.01	0.047	-9999	-10000	0	0
PDGFB-D/PDGFRB/CBL	0.01	0.05	-9999	-10000	0	0
PTPN1	0.013	0.002	-9999	-10000	0	0
SNX15	0.013	0	-9999	-10000	0	0
STAT3	0.013	0	-9999	-10000	0	0
STAT1	0.005	0.05	-9999	-0.3	10	10
cell proliferation	0.024	0.12	-9999	-0.75	8	8
SLA	0.012	0.016	-9999	-10000	0	0
actin cytoskeleton reorganization	0.021	0.026	-9999	-10000	0	0
SRC	0.007	0.012	-9999	-10000	0	0
PI3K	-0.003	0.031	-9999	-10000	0	0
PDGFB-D/PDGFRB/GRB7/SHC	-0.022	0.052	-9999	-10000	0	0
SH2B2	0.012	0.016	-9999	-0.3	1	1
PLCgamma1/SPHK1	0.025	0.033	-9999	-10000	0	0
LYN	0.007	0.013	-9999	-10000	0	0
LRP1	0.011	0.045	-9999	-0.86	1	1
SOS1	0.013	0	-9999	-10000	0	0
STAT5B	0.013	0	-9999	-10000	0	0
STAT5A	0.013	0	-9999	-10000	0	0
NCK1-2/p130 Cas	0.001	0.006	-9999	-10000	0	0
SPHK1	0.007	0.045	-9999	-0.3	8	8
EDG1	0.001	0.001	-9999	-10000	0	0
mol:DAG	0.021	0.029	-9999	-10000	0	0
PLCG1	0.021	0.029	-9999	-10000	0	0
NHERF/PDGFRB	-0.001	0.011	-9999	-10000	0	0
YES1	0.005	0.01	-9999	-10000	0	0
cell migration	-0.001	0.011	-9999	-10000	0	0
SHC/Grb2/SOS1	0.001	0.006	-9999	-10000	0	0
SLC9A3R2	0.013	0	-9999	-10000	0	0
SLC9A3R1	0.011	0.023	-9999	-0.3	2	2
NHERF1-2/PDGFRB/PTEN	-0.002	0.028	-9999	-0.53	1	1
FYN	0.007	0.012	-9999	-10000	0	0
DOK1	0.034	0.005	-9999	-10000	0	0
HRAS/GTP	-0.001	0.01	-9999	-10000	0	0
PDGFB	0.013	0	-9999	-10000	0	0
RAC1	0.031	0.073	-9999	-10000	0	0
PRKCD	0.035	0.006	-9999	-10000	0	0
FER	0.032	0.041	-9999	-0.53	2	2
MAPKKK cascade	0	0.005	-9999	-10000	0	0
RASA1	0.035	0.006	-9999	-10000	0	0
NCK1	0.013	0	-9999	-10000	0	0
NCK2	0.013	0	-9999	-10000	0	0
p62DOK/Csk	0.016	0.02	-9999	-10000	0	0
PDGFB-D/PDGFRB/SHB	0	0	-9999	-10000	0	0
chemotaxis	0.01	0.046	-9999	-10000	0	0
STAT1-3-5/STAT1-3-5	-0.002	0.013	-9999	-10000	0	0
Bovine Papilomavirus E5/PDGFRB	0.003	0.004	-9999	-10000	0	0
PTPRJ	0.013	0	-9999	-10000	0	0

×

p38 MAPK signaling 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
TRAF6/ASK1	-0.002	0.032	-9999	-0.43	2	2
TRAF2/ASK1	-0.002	0.03	-9999	-0.58	1	1
ATM	0.011	0.045	-9999	-0.86	1	1
MAP2K3	0.028	0.058	-9999	-0.54	2	2
response to stress	0	0	-9999	-10000	0	0
MAP2K6	0.028	0.076	-9999	-0.43	5	5
hyperosmotic response	0	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
GADD45G	0	0.1	-9999	-0.7	7	7
TXN	0.009	0.006	-9999	-10000	0	0
CALM1	0.013	0	-9999	-10000	0	0
GADD45A	0.013	0	-9999	-10000	0	0
GADD45B	-0.021	0.17	-9999	-0.86	15	15
MAP3K1	0.013	0	-9999	-10000	0	0
MAP3K6	0.013	0	-9999	-10000	0	0
MAP3K7	0.013	0	-9999	-10000	0	0
MAP3K4	0.013	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
ASK1/ASK2	-0.002	0.034	-9999	-0.66	1	1
TAK1/TAB family	-0.001	0.011	-9999	-0.22	1	1
RAC1/OSM/MEKK3	0	0	-9999	-10000	0	0
TRAF2	0.013	0	-9999	-10000	0	0
RAC1/OSM/MEKK3/MKK3	-0.007	0.034	-9999	-0.48	1	1
TRAF6	0.008	0.025	-9999	-0.47	1	1
RAC1	0.013	0	-9999	-10000	0	0
mol:LPS	0	0	-9999	-10000	0	0
CAMK2B	0.001	0.099	-9999	-0.86	5	5
CCM2	0.013	0	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB	-0.008	0.066	-9999	-0.58	5	5
MAPK11	0.013	0	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB/ASK1	-0.008	0.076	-9999	-0.63	5	5
OSM/MEKK3	0	0	-9999	-10000	0	0
TAOK1	-0.027	0.15	-9999	-0.48	34	34
TAOK2	0.017	0.025	-9999	-0.46	1	1
TAOK3	0.017	0.025	-9999	-0.46	1	1
MAP3K7IP1	0	0	-9999	-10000	0	0
MAPK14	0.013	0	-9999	-10000	0	0
MAP3K7IP2	0	0	-9999	-10000	0	0
MAP3K5	0.011	0.045	-9999	-0.86	1	1
MAP3K10	0.013	0	-9999	-10000	0	0
MAP3K3	0.013	0	-9999	-10000	0	0
TRX/ASK1	0.014	0.031	-9999	-0.57	1	1
GADD45/MTK1/MTK1	-0.027	0.12	-9999	-0.52	19	19

×

Regulation of cytoplasmic and nuclear SMAD2/3 signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SMAD4	0.013	0	-9999	-10000	0	0
SMAD2	0.015	0	-9999	-10000	0	0
SMAD3	0.044	0	-9999	-10000	0	0
SMAD3/SMAD4	0.049	0	-9999	-10000	0	0
SMAD4/Ubc9/PIASy	0	0	-9999	-10000	0	0
SMAD2/SMAD2/SMAD4	0	0	-9999	-10000	0	0
PPM1A	0.013	0	-9999	-10000	0	0
CALM1	0.013	0	-9999	-10000	0	0
SMAD2/SMAD4	0.021	0	-9999	-10000	0	0
MAP3K1	0.013	0	-9999	-10000	0	0
TRAP-1/SMAD4	-0.028	0.13	-9999	-0.66	16	16
MAPK3	0.013	0	-9999	-10000	0	0
MAPK1	0.013	0	-9999	-10000	0	0
NUP214	0.013	0	-9999	-10000	0	0
CTDSP1	0.013	0	-9999	-10000	0	0
CTDSP2	0.013	0	-9999	-10000	0	0
CTDSPL	0.013	0	-9999	-10000	0	0
KPNB1	0.013	0	-9999	-10000	0	0
TGFBRAP1	-0.024	0.18	-9999	-0.86	16	16
UBE2I	0.013	0	-9999	-10000	0	0
NUP153	0.013	0	-9999	-10000	0	0
KPNA2	0.013	0	-9999	-10000	0	0
PIAS4	0.013	0	-9999	-10000	0	0

×

Signaling events mediated by HDAC Class II

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G beta1gamma2/HDAC5	0	0	-9999	-10000	0	0
HDAC3	0.013	0	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC4	0	0	-9999	-10000	0	0
GATA1/HDAC4	0	0	-9999	-10000	0	0
GATA1/HDAC5	0	0	-9999	-10000	0	0
GATA2/HDAC5	-0.001	0.01	-9999	-10000	0	0
HDAC5/BCL6/BCoR	-0.002	0.029	-9999	-0.57	1	1
HDAC9	-0.022	0.098	-9999	-0.3	42	42
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	0.023	0	-9999	-10000	0	0
GATA2	0.012	0.016	-9999	-0.3	1	1
HDAC4/RFXANK	0	0	-9999	-10000	0	0
BCOR	0.013	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
HDAC10	0.013	0	-9999	-10000	0	0
HDAC5	0.013	0	-9999	-10000	0	0
GNB1/GNG2	0	0	-9999	-10000	0	0
Histones	0.034	0.024	-9999	-10000	0	0
ADRBK1	0.013	0	-9999	-10000	0	0
HDAC4	0.013	0	-9999	-10000	0	0
XPO1	0.013	0	-9999	-10000	0	0
HDAC5/ANKRA2	0	0	-9999	-10000	0	0
HDAC4/Ubc9	0	0	-9999	-10000	0	0
HDAC7	0.013	0	-9999	-10000	0	0
HDAC5/14-3-3 E	0	0	-9999	-10000	0	0
TUBA1B	0.013	0	-9999	-10000	0	0
HDAC6	0.013	0	-9999	-10000	0	0
HDAC5/RFXANK	0	0	-9999	-10000	0	0
CAMK4	-0.004	0.1	-9999	-0.86	4	4
Tubulin/HDAC6	-0.006	0.059	-9999	-0.57	4	4
SUMO1	0.013	0	-9999	-10000	0	0
EntrezGene:9972	0	0	-9999	-10000	0	0
YWHAB	0.013	0	-9999	-10000	0	0
GATA1	0.009	0.006	-9999	-10000	0	0
EntrezGene:8021	0	0	-9999	-10000	0	0
YWHAE	0.013	0	-9999	-10000	0	0
NR3C1	0.013	0	-9999	-10000	0	0
SUMO1/HDAC4	0	0	-9999	-10000	0	0
SRF	0.013	0	-9999	-10000	0	0
HDAC4/YWHAB	0	0	-9999	-10000	0	0
Tubulin	-0.007	0.068	-9999	-0.66	4	4
HDAC4/14-3-3 E	0	0	-9999	-10000	0	0
GNB1	0.013	0	-9999	-10000	0	0
RANGAP1	0.013	0	-9999	-10000	0	0
BCL6/BCoR	-0.002	0.034	-9999	-0.66	1	1
HDAC4/HDAC3/SMRT (N-CoR2)	0	0	-9999	-10000	0	0
HDAC4/SRF	-0.01	0.062	-9999	-0.57	4	4
HDAC4/ER alpha	-0.044	0.14	-9999	-0.66	17	17
EntrezGene:23225	0	0	-9999	-10000	0	0
positive regulation of chromatin silencing	0.034	0.023	-9999	-10000	0	0
cell motility	-0.006	0.058	-9999	-0.57	4	4
EntrezGene:23636	0	0	-9999	-10000	0	0
UBE2I	0.013	0	-9999	-10000	0	0
HDAC7/HDAC3	0	0	-9999	-10000	0	0
BCL6	0.011	0.045	-9999	-0.86	1	1
HDAC4/CaMK II delta B	0.013	0	-9999	-10000	0	0
Hsp90/HDAC6	0	0	-9999	-10000	0	0
ESR1	-0.049	0.19	-9999	-0.51	45	45
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	0.013	0	-9999	-10000	0	0
RAN	0.013	0	-9999	-10000	0	0
HDAC4/MEF2C	0	0	-9999	-10000	0	0
GNG2	0.013	0	-9999	-10000	0	0
NCOR2	0.013	0	-9999	-10000	0	0
TUBB2A	0.004	0.089	-9999	-0.86	4	4
HDAC11	0.013	0	-9999	-10000	0	0
HSP90AA1	0.013	0	-9999	-10000	0	0
RANBP2	0.013	0	-9999	-10000	0	0
ANKRA2	0.013	0	-9999	-10000	0	0
RFXANK	0.013	0	-9999	-10000	0	0
nuclear import	0	0	-9999	-10000	0	0

×

PLK2 and PLK4 events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLK2	0.009	0.035	-9999	-0.3	5	5
PLK4	0.013	0	-9999	-10000	0	0
regulation of centriole replication	0.021	0.024	-9999	-10000	0	0

×

PLK1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
regulation of centriole-centriole cohesion	-0.009	0.019	-9999	-10000	0	0
BUB1B	0.016	0.028	-9999	-10000	0	0
PLK1	0.017	0.01	-9999	-0.1	1	1
PLK1S1	0.015	0.006	-9999	-10000	0	0
KIF2A	0.024	0.009	-9999	-10000	0	0
regulation of mitotic centrosome separation	0.017	0.01	-9999	-0.1	1	1
GOLGA2	0.013	0	-9999	-10000	0	0
Hec1/SPC24	-0.007	0.078	-9999	-10000	0	0
WEE1	0.022	0.01	-9999	-10000	0	0
cytokinesis	0.005	0.06	-9999	-0.32	1	1
PP2A-alpha B56	-0.014	0.018	-9999	-10000	0	0
AURKA	0.016	0.007	-9999	-10000	0	0
PICH/PLK1	0.007	0.016	-9999	-10000	0	0
CENPE	0.02	0.038	-9999	-0.52	1	1
RhoA/GTP	0	0	-9999	-10000	0	0
positive regulation of microtubule depolymerization	0.024	0.009	-9999	-10000	0	0
PPP2CA	0.013	0	-9999	-10000	0	0
FZR1	0.013	0	-9999	-10000	0	0
TPX2	0.008	0.022	-9999	-10000	0	0
PAK1	0.013	0	-9999	-10000	0	0
SPC24	-0.009	0.078	-9999	-10000	0	0
FBXW11	0.013	0	-9999	-10000	0	0
CLSPN	0.005	0.027	-9999	-10000	0	0
GORASP1	0.013	0	-9999	-10000	0	0
metaphase	0.001	0.001	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
NLP	0.009	0.006	-9999	-0.069	1	1
G2 phase of mitotic cell cycle	0	0	-9999	-10000	0	0
STAG2	0.013	0	-9999	-10000	0	0
GRASP65/GM130/RAB1/GTP	0.001	0.003	-9999	-10000	0	0
spindle elongation	0.017	0.01	-9999	-0.1	1	1
ODF2	0.013	0.001	-9999	-10000	0	0
BUB1	-0.022	0.028	-9999	-10000	0	0
TPT1	0.015	0.006	-9999	-10000	0	0
CDC25C	0.01	0.024	-9999	-10000	0	0
CDC25B	0.011	0.027	-9999	-0.3	3	3
SGOL1	0.009	0.019	-9999	-10000	0	0
RHOA	0.013	0	-9999	-10000	0	0
CCNB1/CDK1	0.006	0.014	-9999	-10000	0	0
CDC14B	0.005	0.071	-9999	-0.68	4	4
CDC20	0.009	0.035	-9999	-10000	0	0
PLK1/PBIP1	0.003	0.022	-9999	-10000	0	0
mitosis	0	0.001	-9999	-0.023	1	1
FBXO5	0.021	0.008	-9999	-10000	0	0
CDC2	0.001	0.001	-9999	-10000	0	0
NDC80	-0.044	0.12	-9999	-10000	0	0
metaphase plate congression	0.015	0.006	-9999	-10000	0	0
ERCC6L	0.008	0.016	-9999	-10000	0	0
NLP/gamma Tubulin	0.013	0.007	-9999	-10000	0	0
microtubule cytoskeleton organization	0.015	0.006	-9999	-10000	0	0
G2/M transition DNA damage checkpoint	0	0.001	-9999	-0.011	1	1
PPP1R12A	0.013	0	-9999	-10000	0	0
interphase	0	0.001	-9999	-0.011	1	1
PLK1/PRC1-2	0.002	0.06	-9999	-10000	0	0
GRASP65/GM130/RAB1/GTP/PLK1	0	0.003	-9999	-10000	0	0
RAB1A	0.013	0	-9999	-10000	0	0
prophase	0	0	-9999	-10000	0	0
Aurora A/BORA	0.02	0.027	-9999	-0.5	1	1
mitotic prometaphase	0	0.001	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.01	0.036	-9999	-0.33	2	2
microtubule-based process	-0.007	0.064	-9999	-10000	0	0
Golgi organization	0.017	0.01	-9999	-0.1	1	1
Cohesin/SA2	0	0.004	-9999	-10000	0	0
PPP1CB/MYPT1	0	0	-9999	-10000	0	0
KIF20A	-0.048	0.12	-9999	-0.3	74	74
APC/C/CDC20	0.021	0.022	-9999	-10000	0	0
PPP2R1A	0.013	0	-9999	-10000	0	0
chromosome segregation	0.003	0.021	-9999	-10000	0	0
PRC1	0.013	0	-9999	-10000	0	0
ECT2	0.024	0.009	-9999	-10000	0	0
C13orf34	0.02	0.028	-9999	-0.51	1	1
NUDC	0.015	0.006	-9999	-10000	0	0
regulation of attachment of spindle microtubules to kinetochore	0.016	0.028	-9999	-10000	0	0
spindle assembly	0.017	0.009	-9999	-0.096	1	1
spindle stabilization	0.015	0.006	-9999	-10000	0	0
APC/C/HCDH1	0.012	0.062	-9999	-0.59	4	4
MKLP2/PLK1	-0.007	0.064	-9999	-10000	0	0
CCNB1	0.013	0.001	-9999	-10000	0	0
PPP1CB	0.013	0	-9999	-10000	0	0
BTRC	0.013	0	-9999	-10000	0	0
ROCK2	0.012	0.08	-9999	-0.53	8	8
TUBG1	0.015	0.006	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	-0.001	0.009	-9999	-10000	0	0
MLF1IP	0.008	0.031	-9999	-10000	0	0
INCENP	0.012	0.001	-9999	-10000	0	0

×

HIF-2-alpha transcription factor network

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
MMP14	-0.001	0.022	-9999	-10000	0	0
oxygen homeostasis	0.016	0.011	-9999	-10000	0	0
TCEB2	0.013	0	-9999	-10000	0	0
TCEB1	0.013	0	-9999	-10000	0	0
VHL/Elongin B/Elongin C/HIF2A	-0.009	0.045	-9999	-0.52	1	1
EPO	0.19	0.12	-9999	-10000	0	0
FIH (dimer)	0.028	0.011	-9999	-10000	0	0
APEX1	0.026	0.011	-9999	-10000	0	0
SERPINE1	0.18	0.15	-9999	-0.66	1	1
FLT1	0.001	0.017	-9999	-10000	0	0
ADORA2A	0.19	0.13	-9999	-10000	0	0
germ cell development	0.19	0.13	-9999	-10000	0	0
SLC11A2	0.19	0.13	-9999	-10000	0	0
BHLHE40	0.18	0.15	-9999	-10000	0	0
HIF1AN	0.028	0.011	-9999	-10000	0	0
HIF2A/ARNT/SIRT1	0	0.046	-9999	-10000	0	0
ETS1	0.029	0.003	-9999	-10000	0	0
CITED2	-0.081	0.3	-9999	-1.2	26	26
KDR	-0.009	0.12	-9999	-1.4	3	3
PGK1	0.19	0.13	-9999	-10000	0	0
SIRT1	0.013	0	-9999	-10000	0	0
response to hypoxia	0	0.001	-9999	-10000	0	0
HIF2A/ARNT	0.21	0.14	-9999	-10000	0	0
EPAS1	0.11	0.089	-9999	-10000	0	0
SP1	0.021	0.002	-9999	-10000	0	0
ABCG2	0.19	0.15	-9999	-0.82	3	3
EFNA1	0.19	0.13	-9999	-10000	0	0
FXN	0.19	0.13	-9999	-10000	0	0
POU5F1	0.19	0.13	-9999	-10000	0	0
neuron apoptosis	-0.2	0.14	-9999	-10000	0	0
EP300	0.013	0	-9999	-10000	0	0
EGLN3	-0.004	0.14	-9999	-0.53	19	19
EGLN2	0.028	0.011	-9999	-10000	0	0
EGLN1	0.028	0.011	-9999	-10000	0	0
VHL/Elongin B/Elongin C	-0.003	0.042	-9999	-0.57	2	2
VHL	0.008	0.063	-9999	-0.86	2	2
ARNT	0.026	0.011	-9999	-10000	0	0
SLC2A1	0.19	0.13	-9999	-10000	0	0
TWIST1	0.18	0.16	-9999	-0.63	5	5
ELK1	0.015	0.025	-9999	-10000	0	0
HIF2A/ARNT/Cbp/p300	0.001	0.045	-9999	-10000	0	0
VEGFA	0.19	0.14	-9999	-0.69	2	2
CREBBP	0.013	0	-9999	-10000	0	0

×

E-cadherin signaling in keratinocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
keratinocyte differentiation	0.052	0.026	-10000	0	-0.46	1	1
adherens junction organization	0.043	0.032	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.051	0.057	-10000	0	-10000	0	0
FMN1	0.03	0.091	-10000	0	-0.47	12	12
mol:IP3	-0.001	0.022	-10000	0	-0.43	1	1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.04	0.008	-10000	0	-10000	0	0
CTNNB1	0.012	0	-10000	0	-10000	0	0
AKT1	0.05	0.024	-10000	0	-0.42	1	1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.045	0.006	-10000	0	-10000	0	0
CTNND1	0.014	0.001	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.046	0.008	-10000	0	-10000	0	0
VASP	0.046	0.008	-10000	0	-10000	0	0
ZYX	0.046	0.008	-10000	0	-10000	0	0
JUB	0.044	0.038	-10000	0	-0.46	2	2
EGFR(dimer)	0.038	0.058	-10000	0	-0.46	5	5
E-cadherin/beta catenin-gamma catenin	0	0.002	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	-0.001	0.023	-10000	0	-0.45	1	1
PIK3CA	0.012	0.045	-10000	0	-0.86	1	1
PI3K	-0.001	0.024	-10000	0	-0.46	1	1
FYN	0.051	0.026	-10000	0	-10000	0	0
mol:Ca2+	-0.001	0.022	-10000	0	-0.42	1	1
JUP	0.012	0	-10000	0	-10000	0	0
PIK3R1	0.014	0.001	-10000	0	-10000	0	0
mol:DAG	-0.001	0.022	-10000	0	-0.43	1	1
CDH1	0.012	0	-10000	0	-10000	0	0
RhoA/GDP	0.051	0.057	-10000	0	-0.4	6	6
establishment of polarity of embryonic epithelium	0.046	0.008	-10000	0	-10000	0	0
SRC	0.012	0.016	-10000	0	-10000	0	0
RAC1	0.013	0	-10000	0	-10000	0	0
RHOA	0.013	0	-10000	0	-10000	0	0
EGFR	0.001	0.099	-10000	0	-0.86	5	5
CASR	0.043	0.029	-10000	0	-0.4	1	1
RhoA/GTP	-0.001	0.02	-10000	0	-0.38	1	1
AKT2	0.05	0.024	-10000	0	-0.42	1	1
actin cable formation	0.038	0.089	-10000	0	-0.45	12	12
apoptosis	0.001	0.022	0.44	1	-10000	0	1
CTNNA1	0.014	0.001	-10000	0	-10000	0	0
mol:GDP	0.045	0.061	-10000	0	-0.43	6	6
PIP5K1A	0.046	0.008	-10000	0	-10000	0	0
PLCG1	-0.001	0.023	-10000	0	-0.44	1	1
Rac1/GTP	-0.006	0.048	-10000	0	-0.42	5	5
homophilic cell adhesion	0.001	0.001	-10000	0	-10000	0	0

×

TCGA08_p53

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations
CDKN2A	-0.081	0.11	-9999	-9999
TP53	-0.027	0.031	-9999	-9999
Senescence	-0.027	0.031	-9999	-9999
Apoptosis	-0.027	0.031	-9999	-9999
Activated_Oncogenes	0	0	-9999	-9999
MDM2	0.052	0.059	-9999	-9999
MDM4	0.013	0	-9999	-9999

×

Sumoylation by RanBP2 regulates transcriptional repression

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	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations
HDAC1	0.013	-9999	-9999
Ran/GTP/Exportin 1/HDAC4	0	-9999	-9999
MDM2/SUMO1	0	-9999	-9999
HDAC4	0.013	-9999	-9999
Ran/GTP/Exportin 1/HDAC1	0	-9999	-9999
SUMO1	0.013	-9999	-9999
NPC/RanGAP1/SUMO1	0.018	-9999	-9999
mol:GTP	0	-9999	-9999
XPO1	0.03	-9999	-9999
EntrezGene:23636	0	-9999	-9999
RAN	0.013	-9999	-9999
EntrezGene:8021	0	-9999	-9999
RANBP2	0.013	-9999	-9999
SUMO1/HDAC4	0	-9999	-9999
SUMO1/HDAC1	0	-9999	-9999
RANGAP1	0.013	-9999	-9999
MDM2/SUMO1/SUMO1	0	-9999	-9999
NPC/RanGAP1/SUMO1/RanBP2/Ubc9	0.023	-9999	-9999
Ran/GTP	0	-9999	-9999
EntrezGene:23225	0	-9999	-9999
MDM2	0.013	-9999	-9999
UBE2I	0.013	-9999	-9999
Ran/GTP/Exportin 1	0	-9999	-9999
NPC	0	-9999	-9999
PIAS2	0.013	-9999	-9999
PIAS1	0.013	-9999	-9999
EntrezGene:9972	0	-9999	-9999

×

Arf6 trafficking events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SLC2A4	-0.024	0.17	-10000	0	-0.76	18	18
CLTC	0.034	0	-10000	0	-10000	0	0
calcium ion-dependent exocytosis	0.028	0	-10000	0	-10000	0	0
Dynamin 2/GTP	0	0	-10000	0	-10000	0	0
EXOC4	0.013	0	-10000	0	-10000	0	0
CD59	0.031	0	-10000	0	-10000	0	0
CPE	0.008	0.081	-10000	0	-0.58	7	7
CTNNB1	0.013	0	-10000	0	-10000	0	0
membrane fusion	0	0	-10000	0	-10000	0	0
CTNND1	0.034	0	-10000	0	-10000	0	0
DNM2	0.013	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.035	0	-10000	0	-10000	0	0
TSHR	0.016	0.044	-10000	0	-0.58	2	2
INS	0.013	0	-10000	0	-10000	0	0
BIN1	0.013	0	-10000	0	-10000	0	0
mol:Choline	0	0	-10000	0	-10000	0	0
growth hormone secretagogue receptor activity	0	0	-10000	0	-10000	0	0
mol:GDP	0.02	0	-10000	0	-10000	0	0
membrane depolarization	0	0	-10000	0	-10000	0	0
ARF6	0.013	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
JUP	0.031	0	-10000	0	-10000	0	0
ASAP2/amphiphysin II	-0.001	0.027	-10000	0	-0.53	1	1
ARF6/GTP	0	0	-10000	0	-10000	0	0
CDH1	0.031	0	-10000	0	-10000	0	0
clathrin-independent pinocytosis	0	0	-10000	0	-10000	0	0
MAPK8IP3	0.013	0	-10000	0	-10000	0	0
positive regulation of endocytosis	0	0	-10000	0	-10000	0	0
EXOC2	0.013	0	-10000	0	-10000	0	0
substrate adhesion-dependent cell spreading	0.045	0	-10000	0	-10000	0	0
insulin receptor binding	0	0	-10000	0	-10000	0	0
SPAG9	0.013	0	-10000	0	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	0	0	-10000	0	-10000	0	0
positive regulation of phagocytosis	0.02	0	-10000	0	-10000	0	0
ARF6/GTP/JIP3	0	0	-10000	0	-10000	0	0
ACAP1	0.026	0.01	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
CHRM2	0.025	0.001	-10000	0	-10000	0	0
clathrin heavy chain/ACAP1	0.04	0.003	-10000	0	-10000	0	0
JIP4/KLC1	0	0	-10000	0	-10000	0	0
EXOC1	0.013	0	-10000	0	-10000	0	0
exocyst	0.045	0	-10000	0	-10000	0	0
RALA/GTP	0	0	-10000	0	-10000	0	0
ARF6/GTP/ARF6/GTP/JIP4/Dynactin Complex	0	0	-10000	0	-10000	0	0
receptor recycling	0	0	-10000	0	-10000	0	0
CTNNA1	0.034	0	-10000	0	-10000	0	0
NME1	0.02	0	-10000	0	-10000	0	0
clathrin coat assembly	0.034	0	-10000	0	-10000	0	0
IL2RA	0.013	0.064	-10000	0	-10000	0	0
VAMP3	0.02	0	-10000	0	-10000	0	0
GLUT4/clathrin heavy chain/ACAP1	-0.018	0.084	-10000	0	-0.43	15	15
EXOC6	0.013	0	-10000	0	-10000	0	0
PLD1	0	0	-10000	0	-10000	0	0
PLD2	0	0	-10000	0	-10000	0	0
EXOC5	0.013	0	-10000	0	-10000	0	0
PIP5K1C	0.035	0	-10000	0	-10000	0	0
SDC1	0.03	0.007	-10000	0	-10000	0	0
ARF6/GDP	0.019	0	-10000	0	-10000	0	0
EXOC7	0.013	0	-10000	0	-10000	0	0
E-cadherin/beta catenin	0	0	-10000	0	-10000	0	0
mol:Phosphatidic acid	0	0	-10000	0	-10000	0	0
endocytosis	0.001	0.027	0.53	1	-10000	0	1
SCAMP2	0.013	0	-10000	0	-10000	0	0
ADRB2	0.027	0.081	-10000	0	-0.46	10	10
EXOC3	0.013	0	-10000	0	-10000	0	0
ASAP2	0.011	0.045	-10000	0	-0.86	1	1
Dynamin 2/GDP	0.026	0	-10000	0	-10000	0	0
KLC1	0.013	0	-10000	0	-10000	0	0
AVPR2	0.029	0.073	-10000	0	-0.46	8	8
RALA	0.013	0	-10000	0	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	0	0	-10000	0	-10000	0	0

×

E-cadherin signaling events

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

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

Entity	Mean	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations
E-cadherin/beta catenin-gamma catenin	0	-9999	-9999
E-cadherin/beta catenin	0	-9999	-9999
CTNNB1	0.013	-9999	-9999
JUP	0.013	-9999	-9999
CDH1	0.013	-9999	-9999

×

Arf1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
coatomer protein complex	0	0	-9999	-10000	0	0
EntrezGene:79658	0	0	-9999	-10000	0	0
ARF1/GDP/Membrin/GBF1/p115/Brefeldin A	0.022	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	0.013	0	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ER cargo protein	0.027	0	-9999	-10000	0	0
CD4	0.003	0.054	-9999	-0.3	12	12
CLTA	0.013	0	-9999	-10000	0	0
mol:GTP	0.002	0	-9999	-10000	0	0
ARFGAP1	0.012	0	-9999	-10000	0	0
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	-9999	-10000	0	0
mol:Choline	0	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
ARF1	0.013	0	-9999	-10000	0	0
DDEF1	0	0	-9999	-10000	0	0
ARF1/GDP	0	0	-9999	-10000	0	0
AP2M1	0.013	0	-9999	-10000	0	0
EntrezGene:1313	0	0	-9999	-10000	0	0
actin filament polymerization	0	0	-9999	-10000	0	0
Rac/GTP	0	0	-9999	-10000	0	0
ARF1/GTP/GGA3/ARF-GAP1	0	0	-9999	-10000	0	0
ARFIP2	0	0	-9999	-10000	0	0
COPA	0.013	0	-9999	-10000	0	0
RAC1	0.013	0	-9999	-10000	0	0
ARF1/GTP/coatomer protein complex	0.027	0	-9999	-10000	0	0
ARF1/GTP/ARHGAP10	0	0	-9999	-10000	0	0
GGA3	0.013	0	-9999	-10000	0	0
ARF1/GTP/Membrin	0	0	-9999	-10000	0	0
AP2A1	0.013	0	-9999	-10000	0	0
coatomer protein complex/ARF1/GTP/ARF-GAP1	0.029	0	-9999	-10000	0	0
ARF1/GDP/Membrin	0	0	-9999	-10000	0	0
Arfaptin 2/Rac/GDP	0	0	-9999	-10000	0	0
CYTH2	0.013	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	0.035	0.013	-9999	-10000	0	0
PLD2	0	0	-9999	-10000	0	0
ARF-GAP1/v-SNARE	0.012	0	-9999	-10000	0	0
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	0.012	0	-9999	-10000	0	0
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	-0.005	0.026	-9999	-10000	0	0

×

Alternative NF-kappaB pathway

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

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

Entity	Mean	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations
IKK alpha homodimer	0	-9999	-9999
FBXW11	0.013	-9999	-9999
proteasomal ubiquitin-dependent protein catabolic process	0	-9999	-9999
beta TrCP1/SCF ubiquitin ligase complex	0.013	-9999	-9999
CHUK	0.013	-9999	-9999
NF kappa B2 p100/RelB	0	-9999	-9999
NFKB1	0.013	-9999	-9999
MAP3K14	0.013	-9999	-9999
NF kappa B1 p50/RelB	0	-9999	-9999
RELB	0.013	-9999	-9999
NFKB2	0.013	-9999	-9999
NF kappa B2 p52/RelB	0	-9999	-9999
regulation of B cell activation	0	-9999	-9999

pid_entity	TCGA.J8.A3YH	TCGA.J8.A3YG	TCGA.J8.A3YE	TCGA.J8.A3YD
109_MAP3K5	-0.013	-0.013	-0.22	0.057
47_PPARGC1A	-0.86	-0.86	0.013	0.013
105_BMP4	0.013	0.013	-0.86	0.013
105_BMP6	0.013	0.013	0.013	0.013
105_BMP7	0.013	0.013	0.013	0.013
105_BMP2	0.013	0.013	0.013	0.013
131_RELN/VLDLR	-0.52	-0.52	-0.52	0
30_TGFB1/TGF beta receptor Type II	0.013	0.013	0.013	0.013
84_STAT5B	0.0047	0.0023	-0.068	0.11
84_STAT5A	0.0047	0.0023	-0.068	0.11