PARADIGM pathway analysis of mRNASeq expression data - Head and Neck Squamous Cell Carcinoma (Primary solid tumor)

Pathway.Name	Avg.Num.Perturbations
TCGA08_retinoblastoma	121
Syndecan-1-mediated signaling events	113
Syndecan-4-mediated signaling events	96
IL4-mediated signaling events	93
HIF-1-alpha transcription factor network	73
Osteopontin-mediated events	60
amb2 Integrin signaling	49
Glypican 2 network	43
Syndecan-2-mediated signaling events	42
IL23-mediated signaling events	41

Pathway.Name	Avg.Num.Perturbations	Total.Perturbations	Num.Entities	Min.Mean.Truth	Max.Mean.Truth	Min.Mean.Within	Max.Mean.Within	Min.Mean.Any	Max.Mean.Within.1
TCGA08_retinoblastoma	121	969	8	-0.31	0.14	1000	-1000	-0.026	-1000
Syndecan-1-mediated signaling events	113	3855	34	-0.72	0.013	1000	-1000	-0.078	-1000
Syndecan-4-mediated signaling events	96	6473	67	-0.74	0.099	1000	-1000	-0.11	-1000
IL4-mediated signaling events	93	8508	91	-1.4	1.3	1000	-1000	-0.18	-1000
HIF-1-alpha transcription factor network	73	5576	76	-1	0.022	1000	-1000	-0.2	-1000
Osteopontin-mediated events	60	2300	38	-0.45	0.013	1000	-1000	-0.14	-1000
amb2 Integrin signaling	49	4051	82	-0.61	0.013	1000	-1000	-0.11	-1000
Glypican 2 network	43	173	4	-0.12	-0.12	1000	-1000	-0.049	-1000
Syndecan-2-mediated signaling events	42	2921	69	-0.44	0.027	1000	-1000	-0.082	-1000
IL23-mediated signaling events	41	2511	60	-0.7	0.013	1000	-1000	-0.21	-1000
Endothelins	39	3770	96	-0.55	0.014	1000	-1000	-0.1	-1000
TCGA08_p53	36	257	7	-0.24	0.12	1000	-1000	-0.016	-1000
p75(NTR)-mediated signaling	27	3464	125	-0.55	0.013	1000	-1000	-0.14	-1000
Visual signal transduction: Cones	26	995	38	-0.31	0.013	1000	-1000	-0.087	-1000
PDGFR-beta signaling pathway	26	2543	97	-0.21	0.014	1000	-1000	-0.11	-1000
Visual signal transduction: Rods	26	1352	52	-0.46	0.013	1000	-1000	-0.11	-1000
FOXA2 and FOXA3 transcription factor networks	24	1149	46	-0.54	0.021	1000	-1000	-0.11	-1000
BMP receptor signaling	23	1919	81	-0.41	0.047	1000	-1000	-0.12	-1000
Effects of Botulinum toxin	23	602	26	-0.23	0.013	1000	-1000	-0.077	-1000
Glypican 1 network	22	1067	48	-0.4	0.035	1000	-1000	-0.073	-1000
Calcium signaling in the CD4+ TCR pathway	22	686	31	-0.48	0.014	1000	-1000	-0.12	-1000
Signaling events mediated by the Hedgehog family	21	1093	52	-0.43	0.071	1000	-1000	-0.1	-1000
Signaling events regulated by Ret tyrosine kinase	20	1695	82	-0.18	0.013	1000	-1000	-0.12	-1000
TCR signaling in naïve CD8+ T cells	20	1944	93	-0.33	0.17	1000	-1000	-0.11	-1000
Neurotrophic factor-mediated Trk receptor signaling	20	2439	120	-0.28	0.12	1000	-1000	-0.1	-1000
IL12-mediated signaling events	19	1657	87	-0.26	0.098	1000	-1000	-0.17	-1000
Calcineurin-regulated NFAT-dependent transcription in lymphocytes	19	1345	68	-0.52	0.025	1000	-1000	-0.17	-1000
Coregulation of Androgen receptor activity	18	1369	76	-0.52	0.042	1000	-1000	-0.063	-1000
Glucocorticoid receptor regulatory network	17	1953	114	-0.64	0.24	1000	-1000	-0.094	-1000
Ephrin B reverse signaling	17	859	48	-0.17	0.15	1000	-1000	-0.083	-1000
BCR signaling pathway	17	1707	99	-0.17	0.031	1000	-1000	-0.13	-1000
LPA4-mediated signaling events	16	196	12	-0.11	0.022	1000	-1000	-0.041	-1000
Caspase cascade in apoptosis	16	1205	74	-0.14	0.049	1000	-1000	-0.08	-1000
ErbB4 signaling events	16	1171	69	-0.38	0.091	1000	-1000	-0.12	-1000
Signaling mediated by p38-gamma and p38-delta	16	247	15	-0.14	0.024	1000	-1000	-0.036	-1000
Canonical Wnt signaling pathway	16	851	51	-0.34	0.12	1000	-1000	-0.082	-1000
Nongenotropic Androgen signaling	16	867	52	-0.11	0.044	1000	-1000	-0.079	-1000
Signaling events mediated by Stem cell factor receptor (c-Kit)	16	1281	78	-0.11	0.035	1000	-1000	-0.098	-1000
Thromboxane A2 receptor signaling	15	1591	105	-0.14	0.022	1000	-1000	-0.087	-1000
Reelin signaling pathway	15	881	56	-0.25	0.013	1000	-1000	-0.11	-1000
IL1-mediated signaling events	15	937	62	-0.24	0.073	1000	-1000	-0.13	-1000
Presenilin action in Notch and Wnt signaling	14	869	61	-0.34	0.038	1000	-1000	-0.094	-1000
Integrins in angiogenesis	14	1214	84	-0.45	0.019	1000	-1000	-0.13	-1000
EPHB forward signaling	14	1261	85	-0.3	0.12	1000	-1000	-0.12	-1000
Regulation of nuclear SMAD2/3 signaling	13	1816	136	-0.38	0.37	1000	-1000	-0.11	-1000
Nephrin/Neph1 signaling in the kidney podocyte	13	460	34	-0.063	0.013	1000	-1000	-0.082	-1000
Signaling events mediated by PTP1B	13	989	76	-0.22	0.041	1000	-1000	-0.11	-1000
Syndecan-3-mediated signaling events	13	461	35	-0.23	0.013	1000	-1000	-0.088	-1000
LPA receptor mediated events	13	1370	102	-0.61	0.016	1000	-1000	-0.12	-1000
Hypoxic and oxygen homeostasis regulation of HIF-1-alpha	13	446	33	-0.31	0.037	1000	-1000	-0.076	-1000
IL27-mediated signaling events	12	619	51	-0.16	0.025	1000	-1000	-0.11	-1000
Lissencephaly gene (LIS1) in neuronal migration and development	11	618	54	-0.34	0.028	1000	-1000	-0.13	-1000
Signaling events mediated by HDAC Class III	11	470	40	-0.21	0.091	1000	-1000	-0.055	-1000
Angiopoietin receptor Tie2-mediated signaling	11	996	88	-0.44	0.077	1000	-1000	-0.13	-1000
Regulation of Androgen receptor activity	11	778	70	-0.54	0.034	1000	-1000	-0.088	-1000
Ephrin A reverse signaling	10	70	7	-0.02	0.003	1000	-1000	-0.039	-1000
PDGFR-alpha signaling pathway	10	481	44	-0.17	0.03	1000	-1000	-0.076	-1000
Wnt signaling	10	74	7	-0.074	0.013	1000	-1000	-0.042	-1000
Regulation of Telomerase	10	1024	102	-0.18	0.046	1000	-1000	-0.13	-1000
ErbB2/ErbB3 signaling events	9	640	65	-0.38	0.026	1000	-1000	-0.09	-1000
Arf6 signaling events	9	611	62	-0.16	0.044	1000	-1000	-0.08	-1000
Signaling mediated by p38-alpha and p38-beta	9	432	44	-0.17	0.013	1000	-1000	-0.064	-1000
EGFR-dependent Endothelin signaling events	9	191	21	-0.14	0.013	1000	-1000	-0.099	-1000
Plasma membrane estrogen receptor signaling	9	801	86	-0.3	0.039	1000	-1000	-0.11	-1000
Paxillin-independent events mediated by a4b1 and a4b7	8	304	37	-0.078	0.013	1000	-1000	-0.096	-1000
S1P1 pathway	8	318	36	-0.22	0.014	1000	-1000	-0.076	-1000
Fc-epsilon receptor I signaling in mast cells	7	731	97	-0.22	0.036	1000	-1000	-0.12	-1000
Nectin adhesion pathway	7	463	63	-0.22	0.046	1000	-1000	-0.09	-1000
TRAIL signaling pathway	7	377	48	-0.084	0.017	1000	-1000	-0.096	-1000
Retinoic acid receptors-mediated signaling	7	415	58	-0.15	0.018	1000	-1000	-0.1	-1000
S1P3 pathway	7	295	42	-0.22	0.041	1000	-1000	-0.08	-1000
Rapid glucocorticoid signaling	7	141	20	-0.06	0.013	1000	-1000	-0.04	-1000
Signaling events mediated by PRL	7	264	34	-0.14	0.032	1000	-1000	-0.059	-1000
Class IB PI3K non-lipid kinase events	7	21	3	-0.004	-1000	1000	-1000	-0.024	-1000
JNK signaling in the CD4+ TCR pathway	6	112	17	-0.042	0.036	1000	-1000	-0.081	-1000
Noncanonical Wnt signaling pathway	6	177	26	-0.074	0.013	1000	-1000	-0.11	-1000
a4b1 and a4b7 Integrin signaling	6	34	5	-0.022	0.011	1000	-1000	-0.048	-1000
Cellular roles of Anthrax toxin	6	261	39	-0.049	0.019	1000	-1000	-0.04	-1000
IFN-gamma pathway	6	463	68	-0.18	0.041	1000	-1000	-0.14	-1000
RXR and RAR heterodimerization with other nuclear receptor	6	344	52	-0.24	0.03	1000	-1000	-0.082	-1000
FAS signaling pathway (CD95)	6	306	47	-0.084	0.014	1000	-1000	-0.075	-1000
IL2 signaling events mediated by PI3K	6	370	58	-0.16	0.056	1000	-1000	-0.11	-1000
Stabilization and expansion of the E-cadherin adherens junction	6	496	74	-0.37	0.084	1000	-1000	-0.12	-1000
Ras signaling in the CD4+ TCR pathway	6	116	17	-0.029	0.025	1000	-1000	-0.055	-1000
EPO signaling pathway	5	288	55	-0.054	0.04	1000	-1000	-0.12	-1000
Ceramide signaling pathway	5	385	76	-0.14	0.043	1000	-1000	-0.09	-1000
Paxillin-dependent events mediated by a4b1	5	190	36	-0.078	0.025	1000	-1000	-0.092	-1000
IL6-mediated signaling events	5	446	75	-0.1	0.067	1000	-1000	-0.13	-1000
FOXM1 transcription factor network	5	279	51	-0.32	0.14	1000	-1000	-0.2	-1000
p38 MAPK signaling pathway	5	252	44	-0.16	0.021	1000	-1000	-0.084	-1000
Class I PI3K signaling events mediated by Akt	4	273	68	-0.14	0.064	1000	-1000	-0.078	-1000
HIV-1 Nef: Negative effector of Fas and TNF-alpha	4	195	45	-0.084	0.041	1000	-1000	-0.13	-1000
IL2 signaling events mediated by STAT5	4	105	22	-0.056	0.045	1000	-1000	-0.068	-1000
Insulin Pathway	4	348	74	-0.29	0.042	1000	-1000	-0.13	-1000
Sphingosine 1-phosphate (S1P) pathway	3	109	28	-0.095	0.019	1000	-1000	-0.083	-1000
Circadian rhythm pathway	3	84	22	-0.092	0.047	1000	-1000	-0.083	-1000
Aurora A signaling	3	196	60	-0.075	0.033	1000	-1000	-0.073	-1000
HIF-2-alpha transcription factor network	3	136	43	-0.24	0.025	1000	-1000	-0.12	-1000
Regulation of p38-alpha and p38-beta	3	164	54	-0.12	0.032	1000	-1000	-0.079	-1000
VEGFR1 specific signals	3	189	56	-0.12	0.044	1000	-1000	-0.11	-1000
S1P4 pathway	3	89	25	-0.035	0.029	1000	-1000	-0.077	-1000
Aurora B signaling	3	240	67	-0.3	0.046	1000	-1000	-0.094	-1000
Signaling events activated by Hepatocyte Growth Factor Receptor (c-Met)	2	253	85	-0.092	0.066	1000	-1000	-0.1	-1000
Hedgehog signaling events mediated by Gli proteins	2	141	65	-0.089	0.068	1000	-1000	-0.086	-1000
Arf6 downstream pathway	2	95	43	-0.03	0.025	1000	-1000	-0.055	-1000
ceramide signaling pathway	2	106	49	-0.024	0.048	1000	-1000	-0.078	-1000
Role of Calcineurin-dependent NFAT signaling in lymphocytes	2	169	83	-0.069	0.067	1000	-1000	-0.1	-1000
Signaling events mediated by VEGFR1 and VEGFR2	2	292	125	-0.088	0.099	1000	-1000	-0.14	-1000
TCGA08_rtk_signaling	2	53	26	-0.031	0.048	1000	-1000	-0.03	-1000
Class I PI3K signaling events	2	177	73	-0.12	0.042	1000	-1000	-0.092	-1000
Arf6 trafficking events	2	168	71	-0.27	0.047	1000	-1000	-0.093	-1000
IGF1 pathway	2	164	57	-0.054	0.038	1000	-1000	-0.14	-1000
E-cadherin signaling events	2	10	5	-0.005	0.011	1000	-1000	-0.056	-1000
Canonical NF-kappaB pathway	1	43	39	-0.028	0.09	1000	-1000	-0.12	-1000
Signaling events mediated by HDAC Class II	1	107	75	-0.04	0.032	1000	-1000	-0.094	-1000
PLK1 signaling events	1	130	85	-0.013	0.034	1000	-1000	-0.075	-1000
S1P5 pathway	1	20	17	-0.007	0.029	1000	-1000	-0.077	-1000
E-cadherin signaling in the nascent adherens junction	1	87	76	-0.016	0.06	1000	-1000	-0.11	-1000
E-cadherin signaling in keratinocytes	1	67	43	-0.016	0.052	1000	-1000	-0.087	-1000
Regulation of cytoplasmic and nuclear SMAD2/3 signaling	0	9	23	-0.006	0.05	1000	-1000	-0.09	-1000
BARD1 signaling events	0	50	57	-0.007	0.074	1000	-1000	-0.084	-1000
PLK2 and PLK4 events	0	0	3	0.013	0.025	1000	-1000	-0.031	-1000
Aurora C signaling	0	5	7	-0.004	0.011	1000	-1000	-0.057	-1000
Insulin-mediated glucose transport	0	27	32	-0.081	0.05	1000	-1000	-0.085	-1000
mTOR signaling pathway	0	3	53	0	0.037	1000	-1000	-0.083	-1000
Signaling events mediated by HDAC Class I	0	71	104	-0.14	0.063	1000	-1000	-0.091	-1000
FoxO family signaling	0	47	64	-0.016	0.16	1000	-1000	-0.11	-1000
Atypical NF-kappaB pathway	0	18	31	-0.014	0.048	1000	-1000	-0.093	-1000
Sumoylation by RanBP2 regulates transcriptional repression	0	0	27	0	0.031	1000	-1000	-0.078	-1000
Arf1 pathway	0	7	54	-0.005	0.036	1000	-1000	-0.056	-1000
Alternative NF-kappaB pathway	0	8	13	-0.004	0.013	1000	-1000	-0.085	-1000
Total	1861	109423	7203	-29	-990	131000	-131000	-12	-131000

TCGA08_retinoblastoma

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CDKN2B	-0.1	0.24	-10000	0	-0.6	57	57
CDKN2C	0.009	0.15	-10000	0	-0.73	11	11
CDKN2A	-0.31	0.38	-10000	0	-0.77	124	124
CCND2	0.12	0.14	0.24	155	-0.15	1	156
RB1	-0.13	0.15	-10000	0	-0.26	155	155
CDK4	0.14	0.16	0.27	157	-10000	0	157
CDK6	0.14	0.16	0.27	154	-10000	0	154
G1/S progression	0.12	0.16	0.26	155	-10000	0	155

×

Syndecan-1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.011	0.047	-9999	-0.8	1	1
CCL5	-0.097	0.28	-9999	-0.8	41	41
SDCBP	0.013	0	-9999	-10000	0	0
FGFR/FGF2/Syndecan-1	-0.45	0.17	-9999	-0.54	221	221
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
RP11-540L11.1	0	0	-9999	-10000	0	0
Syndecan-1/Laminin-5	-0.42	0.17	-9999	-0.51	221	221
Syndecan-1/Syntenin	-0.42	0.17	-9999	-0.51	221	221
MAPK3	-0.38	0.16	-9999	-0.62	43	43
HGF/MET	-0.019	0.098	-9999	-0.52	11	11
TGFB1/TGF beta receptor Type II	0.011	0.047	-9999	-0.8	1	1
BSG	0.013	0	-9999	-10000	0	0
keratinocyte migration	-0.42	0.16	-9999	-0.5	221	221
Syndecan-1/RANTES	-0.48	0.23	-9999	-0.58	231	231
Syndecan-1/CD147	-0.4	0.16	-9999	-0.49	216	216
Syndecan-1/Syntenin/PIP2	-0.41	0.16	-9999	-0.5	221	221
LAMA5	0.013	0	-9999	-10000	0	0
positive regulation of cell-cell adhesion	-0.4	0.15	-9999	-0.48	221	221
MMP7	-0.13	0.3	-9999	-0.76	55	55
HGF	-0.008	0.12	-9999	-0.7	9	9
Syndecan-1/CASK	-0.43	0.17	-9999	-0.52	221	221
Syndecan-1/HGF/MET	-0.42	0.17	-9999	-0.5	225	225
regulation of cell adhesion	-0.36	0.15	-9999	-0.59	43	43
HPSE	0.009	0.053	-9999	-0.64	2	2
positive regulation of cell migration	-0.45	0.17	-9999	-0.54	221	221
SDC1	-0.46	0.18	-9999	-0.55	221	221
Syndecan-1/Collagen	-0.45	0.17	-9999	-0.54	221	221
PPIB	0.013	0	-9999	-10000	0	0
MET	0.009	0.06	-9999	-0.72	2	2
PRKACA	0.013	0	-9999	-10000	0	0
MMP9	-0.61	0.35	-9999	-0.8	230	230
MAPK1	-0.38	0.16	-9999	-0.62	43	43
homophilic cell adhesion	-0.45	0.17	-9999	-0.54	221	221
MMP1	-0.72	0.25	-9999	-0.8	271	271

×

Syndecan-4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.26	0.23	-9999	-0.46	170	170
Syndecan-4/Syndesmos	-0.42	0.25	-9999	-0.61	168	168
positive regulation of JNK cascade	-0.42	0.22	-9999	-0.57	184	184
Syndecan-4/ADAM12	-0.74	0.33	-9999	-0.94	211	211
CCL5	-0.097	0.28	-9999	-0.8	41	41
Rac1/GDP	0	0	-9999	-10000	0	0
DNM2	0.013	0	-9999	-10000	0	0
ITGA5	-0.27	0.39	-9999	-0.8	105	105
SDCBP	0.013	0	-9999	-10000	0	0
PLG	0.007	0.013	-9999	-10000	0	0
ADAM12	-0.63	0.33	-9999	-0.8	239	239
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	-0.12	0.061	-9999	-10000	0	0
Syndecan-4/Laminin alpha1	-0.61	0.34	-9999	-0.8	202	202
Syndecan-4/CXCL12/CXCR4	-0.44	0.24	-9999	-0.61	184	184
Syndecan-4/Laminin alpha3	-0.53	0.33	-9999	-0.74	188	188
MDK	-0.01	0.14	-9999	-0.78	9	9
Syndecan-4/FZD7	-0.42	0.26	-9999	-0.62	168	168
Syndecan-4/Midkine	-0.43	0.26	-9999	-0.62	172	172
FZD7	0	0.1	-9999	-0.77	5	5
Syndecan-4/FGFR1/FGF	-0.4	0.23	-9999	-0.57	176	176
THBS1	-0.02	0.16	-9999	-0.77	13	13
integrin-mediated signaling pathway	-0.47	0.3	-9999	-0.68	177	177
positive regulation of MAPKKK cascade	-0.42	0.22	-9999	-0.57	184	184
Syndecan-4/TACI	-0.47	0.28	-9999	-0.66	185	185
CXCR4	-0.019	0.16	-9999	-0.8	12	12
cell adhesion	-0.22	0.2	-9999	-0.39	168	168
Syndecan-4/Dynamin	-0.42	0.25	-9999	-0.61	168	168
Syndecan-4/TSP1	-0.43	0.27	-9999	-0.64	168	168
Syndecan-4/GIPC	-0.42	0.25	-9999	-0.61	168	168
Syndecan-4/RANTES	-0.47	0.29	-9999	-0.67	183	183
ITGB1	0.011	0.047	-9999	-0.8	1	1
LAMA1	-0.37	0.41	-9999	-0.8	143	143
LAMA3	-0.22	0.37	-9999	-0.8	87	87
RAC1	0.013	0	-9999	-10000	0	0
PRKCA	0.099	0.072	-9999	-0.77	1	1
Syndecan-4/alpha-Actinin	-0.42	0.25	-9999	-0.61	168	168
TFPI	0.009	0.06	-9999	-0.72	2	2
F2	-0.07	0.23	-9999	-0.81	26	26
alpha5/beta1 Integrin	-0.22	0.29	-9999	-0.61	106	106
positive regulation of cell adhesion	-0.68	0.36	-9999	-0.87	214	214
ACTN1	0.011	0.047	-9999	-0.8	1	1
TNC	-0.15	0.33	-9999	-0.8	61	61
Syndecan-4/CXCL12	-0.45	0.25	-9999	-0.62	181	181
FGF6	0.003	0.005	-9999	-10000	0	0
RHOA	0.013	0	-9999	-10000	0	0
CXCL12	-0.048	0.19	-9999	-0.65	28	28
TNFRSF13B	-0.093	0.27	-9999	-0.8	39	39
FGF2	-0.012	0.13	-9999	-0.68	11	11
FGFR1	0.008	0.066	-9999	-0.8	2	2
Syndecan-4/PI-4-5-P2	-0.42	0.25	-9999	-0.62	168	168
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.44	0.41	-9999	-0.8	170	170
cell migration	-0.041	0.02	-9999	-10000	0	0
PRKCD	0.026	0.012	-9999	-10000	0	0
vasculogenesis	-0.41	0.26	-9999	-0.61	168	168
SDC4	-0.45	0.27	-9999	-0.65	168	168
Syndecan-4/Tenascin C	-0.5	0.32	-9999	-0.72	177	177
Syndecan-4/PI-4-5-P2/PKC alpha	-0.097	0.048	-9999	-10000	0	0
Syndecan-4/Syntenin	-0.42	0.25	-9999	-0.61	168	168
MMP9	-0.6	0.35	-9999	-0.8	230	230
Rac1/GTP	-0.23	0.21	-9999	-0.4	168	168
cytoskeleton organization	-0.4	0.24	-9999	-0.58	168	168
GIPC1	0.013	0	-9999	-10000	0	0
Syndecan-4/TFPI	-0.42	0.25	-9999	-0.61	169	169

×

IL4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	-1.1	0.48	-10000	0	-1.4	208	208
STAT6 (cleaved dimer)	-1.2	0.51	-10000	0	-1.4	236	236
IGHG1	-0.33	0.12	-10000	0	-0.47	58	58
IGHG3	-1.1	0.46	-10000	0	-1.3	233	233
AKT1	-0.42	0.18	-10000	0	-0.74	32	32
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHP1	-0.31	0.17	-10000	0	-0.77	18	18
IL4/IL4R/JAK1/IL2R gamma/JAK3/IRS1	-0.44	0.18	-10000	0	-0.72	26	26
THY1	-1.2	0.54	-10000	0	-1.5	215	215
MYB	-0.054	0.2	-10000	0	-0.65	31	31
HMGA1	0.013	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3	-0.55	0.24	-10000	0	-0.7	142	142
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHIP	-0.44	0.18	-10000	0	-0.72	27	27
SP1	0.011	0.011	-10000	0	-10000	0	0
INPP5D	0.011	0.038	-10000	0	-0.64	1	1
SOCS5	0.036	0.01	-10000	0	-10000	0	0
STAT6 (dimer)/ETS1	-1.2	0.49	-10000	0	-1.4	230	230
SOCS1	-0.68	0.25	-10000	0	-0.83	189	189
SOCS3	-0.45	0.2	-10000	0	-0.86	24	24
FCER2	-0.79	0.35	-10000	0	-1	174	174
PARP14	0.008	0.066	-10000	0	-0.8	2	2
CCL17	-1.1	0.49	-10000	0	-1.4	215	215
GRB2	0.013	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP	-0.35	0.15	-10000	0	-0.73	15	15
T cell proliferation	-1.2	0.52	-10000	0	-1.4	216	216
IL4R/JAK1	-1.1	0.49	-10000	0	-1.4	213	213
EGR2	-1.1	0.49	-10000	0	-1.4	209	209
JAK2	-0.031	0.019	-10000	0	-10000	0	0
JAK3	-0.023	0.18	-10000	0	-0.8	16	16
PIK3R1	0.013	0	-10000	0	-10000	0	0
JAK1	0.001	0.005	-10000	0	-10000	0	0
COL1A2	-0.59	0.36	-10000	0	-0.93	155	155
CCL26	-1.2	0.5	-10000	0	-1.4	213	213
IL4R	-1.2	0.54	-10000	0	-1.5	212	212
PTPN6	0.035	0.007	-10000	0	-10000	0	0
IL13RA2	-1.2	0.51	-10000	0	-1.4	212	212
IL13RA1	-0.031	0.019	-10000	0	-10000	0	0
IRF4	-0.3	0.35	-10000	0	-0.95	59	59
ARG1	-0.49	0.53	-10000	0	-1.3	76	76
CBL	-0.51	0.22	-10000	0	-0.88	38	38
GTF3A	0.005	0.016	-10000	0	-10000	0	0
PIK3CA	0.013	0	-10000	0	-10000	0	0
IL13RA1/JAK2	-0.043	0.023	-10000	0	-10000	0	0
IRF4/BCL6	-0.28	0.32	-10000	0	-0.88	59	59
CD40LG	-0.069	0.23	-10000	0	-0.66	39	39
MAPK14	-0.51	0.22	-10000	0	-0.89	37	37
mitosis	-0.41	0.17	-10000	0	-0.7	31	31
STAT6	-1.4	0.71	-10000	0	-1.7	227	227
SPI1	-0.009	0.059	-10000	0	-0.7	1	1
RPS6KB1	-0.39	0.17	-10000	0	-0.73	18	18
STAT6 (dimer)	-1.4	0.71	-10000	0	-1.7	227	227
STAT6 (dimer)/PARP14	-1.3	0.58	-10000	0	-1.5	222	222
mast cell activation	0.022	0.007	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/DOK2	-0.42	0.19	-10000	0	-0.77	30	30
FRAP1	-0.42	0.18	-10000	0	-0.74	32	32
LTA	-1.2	0.5	-10000	0	-1.4	217	217
FES	0.013	0	-10000	0	-10000	0	0
T-helper 1 cell differentiation	1.3	0.62	1.6	227	-10000	0	227
CCL11	-1.2	0.47	-10000	0	-1.4	239	239
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES	-0.42	0.19	-10000	0	-0.75	31	31
IL2RG	-0.008	0.15	-10000	0	-0.78	11	11
IL10	-1.1	0.49	-10000	0	-1.4	211	211
IRS1	0.013	0	-10000	0	-10000	0	0
IRS2	0.009	0.053	-10000	0	-0.64	2	2
IL4	-0.21	0.069	-10000	0	-10000	0	0
IL5	-1.1	0.49	-10000	0	-1.4	211	211
IL4/IL4R/JAK1/IL13RA1/JAK2	-0.81	0.29	-10000	0	-0.97	210	210
COL1A1	-0.73	0.35	-10000	0	-0.96	206	206
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
IL4/IL4R/JAK1	-1.2	0.53	-10000	0	-1.5	206	206
IL2R gamma/JAK3	-0.031	0.2	-10000	0	-0.73	22	22
TFF3	-1.3	0.58	-10000	0	-1.6	229	229
ALOX15	-1.2	0.52	-10000	0	-1.5	224	224
MYBL1	0	0.1	-10000	0	-0.8	5	5
T-helper 2 cell differentiation	-0.84	0.31	-10000	0	-1	216	216
SHC1	0.013	0	-10000	0	-10000	0	0
CEBPB	-0.006	0.044	-10000	0	-10000	0	0
IL4/IL4R/JAK1/IL2R gamma/JAK3/FES/IRS2	-0.42	0.17	-10000	0	-0.72	24	24
mol:PI-3-4-5-P3	-0.42	0.18	-10000	0	-0.74	32	32
PI3K	-0.44	0.2	-10000	0	-0.79	32	32
DOK2	0.011	0.038	-10000	0	-0.64	1	1
ETS1	0.03	0.068	-10000	0	-0.8	2	2
IL4/IL4R/JAK1/IL2R gamma/JAK3/SHC/SHIP/GRB2	-0.33	0.15	-10000	0	-0.72	15	15
ITGB3	-1.1	0.49	-10000	0	-1.4	208	208
PIGR	-1.4	0.59	-10000	0	-1.7	237	237
IGHE	0.056	0.043	0.27	3	-10000	0	3
MAPKKK cascade	-0.32	0.14	-10000	0	-0.7	15	15
BCL6	0.013	0.002	-10000	0	-10000	0	0
OPRM1	-1.1	0.48	-10000	0	-1.4	208	208
RETNLB	-1.1	0.49	-10000	0	-1.4	213	213
SELP	-1.2	0.52	-10000	0	-1.5	212	212
AICDA	-1.1	0.47	-10000	0	-1.4	221	221

×

HIF-1-alpha transcription factor network

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
PKM2	-0.72	0.5	-9999	-1.2	105	105
HDAC7	0.014	0.001	-9999	-10000	0	0
HIF1A/ARNT/Cbp/p300/Src-1	-0.48	0.32	-9999	-0.87	52	52
SMAD4	0.013	0.037	-9999	-0.64	1	1
ID2	-0.72	0.5	-9999	-1.2	105	105
AP1	-0.076	0.17	-9999	-0.47	49	49
ABCG2	-0.73	0.5	-9999	-1.2	117	117
HIF1A	-0.083	0.056	-9999	-10000	0	0
TFF3	-0.86	0.57	-9999	-1.3	153	153
GATA2	0.01	0.066	-9999	-0.8	2	2
AKT1	-0.086	0.065	-9999	-10000	0	0
response to hypoxia	-0.11	0.068	-9999	-10000	0	0
MCL1	-0.72	0.5	-9999	-1.2	117	117
NDRG1	-0.72	0.5	-9999	-1.3	104	104
SERPINE1	-0.94	0.56	-9999	-1.4	163	163
FECH	-0.72	0.5	-9999	-1.2	117	117
FURIN	-0.72	0.5	-9999	-1.2	104	104
NCOA2	0.005	0.075	-9999	-0.64	4	4
EP300	-0.091	0.093	-9999	-0.32	7	7
HMOX1	-0.72	0.5	-9999	-1.2	117	117
BHLHE40	-0.72	0.5	-9999	-1.2	105	105
BHLHE41	-0.73	0.51	-9999	-1.2	118	118
HIF1A/ARNT/SMAD3/SMAD4/SP1	-0.068	0.061	-9999	-10000	0	0
ENG	-0.044	0.077	-9999	-10000	0	0
JUN	0.014	0.001	-9999	-10000	0	0
RORA	-0.72	0.5	-9999	-1.3	105	105
ABCB1	-0.2	0.32	-9999	-1.4	18	18
TFRC	-0.74	0.5	-9999	-1.2	128	128
CXCR4	-0.74	0.51	-9999	-1.2	120	120
TF	-0.93	0.56	-9999	-1.3	181	181
CITED2	-0.72	0.5	-9999	-1.3	104	104
HIF1A/ARNT	-0.84	0.64	-9999	-1.4	143	143
LDHA	-0.069	0.046	-9999	-10000	0	0
ETS1	-0.72	0.5	-9999	-1.2	117	117
PGK1	-0.72	0.5	-9999	-1.2	105	105
NOS2	-0.78	0.52	-9999	-1.3	128	128
ITGB2	-0.74	0.5	-9999	-1.2	125	125
ALDOA	-0.72	0.5	-9999	-1.2	117	117
Cbp/p300/CITED2	-0.7	0.51	-9999	-1.3	91	91
FOS	-0.091	0.24	-9999	-0.64	49	49
HK2	-0.72	0.5	-9999	-1.2	104	104
SP1	0.022	0.006	-9999	-10000	0	0
GCK	-0.18	0.22	-9999	-0.79	24	24
HK1	-0.72	0.5	-9999	-1.2	105	105
NPM1	-0.72	0.5	-9999	-1.2	117	117
EGLN1	-0.72	0.5	-9999	-1.2	117	117
CREB1	0.022	0	-9999	-10000	0	0
PGM1	-0.72	0.5	-9999	-1.2	117	117
SMAD3	0.013	0.037	-9999	-0.64	1	1
EDN1	-0.1	0.18	-9999	-1.3	3	3
IGFBP1	-0.75	0.51	-9999	-1.3	110	110
VEGFA	-0.4	0.3	-9999	-0.92	11	11
HIF1A/JAB1	-0.042	0.029	-9999	-10000	0	0
CP	-0.85	0.57	-9999	-1.3	153	153
CXCL12	-0.74	0.52	-9999	-1.3	109	109
COPS5	0.013	0.005	-9999	-10000	0	0
SMAD3/SMAD4	-0.003	0.038	-9999	-0.47	2	2
BNIP3	-0.72	0.5	-9999	-1.2	109	109
EGLN3	-0.74	0.52	-9999	-1.3	121	121
CA9	-1	0.51	-9999	-1.4	197	197
TERT	-0.8	0.54	-9999	-1.3	133	133
ENO1	-0.72	0.5	-9999	-1.3	94	94
PFKL	-0.72	0.5	-9999	-1.2	104	104
NCOA1	0.013	0.003	-9999	-10000	0	0
ADM	-0.72	0.5	-9999	-1.2	117	117
ARNT	-0.083	0.055	-9999	-10000	0	0
HNF4A	-0.071	0.24	-9999	-0.8	30	30
ADFP	-0.73	0.5	-9999	-1.2	139	139
SLC2A1	-0.41	0.31	-9999	-1.1	13	13
LEP	-0.77	0.54	-9999	-1.3	117	117
HIF1A/ARNT/Cbp/p300	-0.5	0.34	-9999	-0.88	66	66
EPO	-0.37	0.27	-9999	-0.97	20	20
CREBBP	-0.091	0.093	-9999	-0.32	8	8
HIF1A/ARNT/Cbp/p300/HDAC7	-0.48	0.33	-9999	-0.93	33	33
PFKFB3	-0.72	0.5	-9999	-1.2	107	107
NT5E	-0.78	0.55	-9999	-1.3	124	124

×

Osteopontin-mediated events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IKK alpha homodimer	-0.28	0.27	-9999	-0.57	91	91
NF kappa B1 p50/RelA/I kappa B alpha	-0.28	0.23	-9999	-0.57	91	91
alphaV/beta3 Integrin/Osteopontin/Src	-0.36	0.32	-9999	-0.63	172	172
AP1	-0.38	0.31	-9999	-0.83	72	72
ILK	-0.29	0.28	-9999	-0.56	105	105
bone resorption	-0.24	0.22	-9999	-0.78	9	9
PTK2B	0.013	0	-9999	-10000	0	0
PYK2/p130Cas	-0.27	0.24	-9999	-0.88	8	8
ITGAV	0.004	0.077	-9999	-0.76	3	3
mol:GTP	0	0	-9999	-10000	0	0
CD44/Rho Family GTPase/ROCK2	-0.002	0.027	-9999	-0.47	1	1
alphaV/beta3 Integrin/Osteopontin	-0.34	0.29	-9999	-0.57	176	176
MAP3K1	-0.3	0.28	-9999	-0.52	176	176
JUN	0.012	0.002	-9999	-10000	0	0
MAPK3	-0.3	0.29	-9999	-0.63	91	91
MAPK1	-0.3	0.29	-9999	-0.63	91	91
Rac1/GDP	0	0	-9999	-10000	0	0
NFKB1	0.013	0	-9999	-10000	0	0
MAPK8	-0.28	0.28	-9999	-0.56	103	103
ITGB3	-0.02	0.15	-9999	-0.77	12	12
NFKBIA	-0.3	0.28	-9999	-0.63	91	91
FOS	-0.094	0.24	-9999	-0.64	49	49
CD44	0.013	0	-9999	-10000	0	0
CHUK	0.013	0	-9999	-10000	0	0
PLAU	-0.44	0.4	-9999	-0.92	100	100
NF kappa B1 p50/RelA	-0.3	0.24	-9999	-0.61	91	91
BCAR1	0.013	0	-9999	-10000	0	0
RELA	0.013	0	-9999	-10000	0	0
alphaV beta3 Integrin	-0.03	0.13	-9999	-0.63	14	14
mol:GDP	0	0	-9999	-10000	0	0
SYK	-0.29	0.28	-9999	-0.52	176	176
VAV3	-0.29	0.28	-9999	-0.57	105	105
MAP3K14	-0.31	0.29	-9999	-0.54	176	176
ROCK2	0.011	0.038	-9999	-0.64	1	1
SPP1	-0.45	0.41	-9999	-0.81	171	171
RAC1	0.013	0	-9999	-10000	0	0
Rac1/GTP	-0.28	0.24	-9999	-0.6	49	49
MMP2	-0.34	0.34	-9999	-0.81	76	76

×

amb2 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaM/beta2 Integrin/proMMP-2	-0.18	0.31	-9999	-0.63	82	82
alphaM/beta2 Integrin/GPIbA	-0.089	0.24	-9999	-0.7	37	37
alphaM/beta2 Integrin/proMMP-9	-0.46	0.32	-9999	-0.61	231	231
PLAUR	-0.022	0.16	-9999	-0.8	13	13
HMGB1	0.01	0.017	-9999	-10000	0	0
alphaM/beta2 Integrin/Talin	-0.073	0.22	-9999	-0.69	30	30
AGER	0.005	0.067	-9999	-0.8	2	2
RAP1A	0.013	0	-9999	-10000	0	0
SELPLG	0.013	0	-9999	-10000	0	0
mol:LDL	0	0	-9999	-10000	0	0
alphaM/beta2 Integrin/RAGE/HMGB1	-0.086	0.2	-9999	-0.62	31	31
mol:GTP	0	0	-9999	-10000	0	0
MMP9	-0.61	0.35	-9999	-0.8	230	230
CYR61	0.009	0.06	-9999	-0.72	2	2
TLN1	0.011	0.047	-9999	-0.8	1	1
Rap1/GTP	-0.19	0.16	-9999	-0.51	37	37
RHOA	0.013	0	-9999	-10000	0	0
P-selectin oligomer	-0.1	0.25	-9999	-0.64	54	54
MYH2	-0.42	0.26	-9999	-0.62	165	165
MST1R	0	0.091	-9999	-0.64	6	6
leukocyte activation during inflammatory response	-0.087	0.22	-9999	-0.57	44	44
APOB	-0.01	0.13	-9999	-0.78	8	8
mol:GDP	0	0	-9999	-10000	0	0
complement component iC3b receptor activity	0	0	-9999	-10000	0	0
MMP2	-0.15	0.33	-9999	-0.8	61	61
JAM3	0.011	0.047	-9999	-0.8	1	1
GP1BA	-0.017	0.15	-9999	-0.79	11	11
alphaM/beta2 Integrin/CTGF	-0.074	0.22	-9999	-0.68	31	31
alphaM/beta2 Integrin	-0.22	0.2	-9999	-0.44	108	108
JAM3 homodimer	0.011	0.047	-9999	-0.8	1	1
ICAM2	0.009	0.053	-9999	-0.64	2	2
ICAM1	-0.032	0.19	-9999	-0.8	17	17
phagocytosis triggered by activation of immune response cell surface activating receptor	-0.22	0.2	-9999	-0.44	108	108
cell adhesion	-0.089	0.24	-9999	-0.69	37	37
NFKB1	-0.044	0.24	-9999	-0.82	15	15
THY1	-0.26	0.38	-9999	-0.8	101	101
RhoA/GDP	0	0	-9999	-10000	0	0
Lipoprotein(a)	-0.032	0.13	-9999	-0.53	18	18
alphaM/beta2 Integrin/LRP/tPA	-0.076	0.21	-9999	-0.62	36	36
IL6	-0.072	0.31	-9999	-0.8	38	38
ITGB2	-0.024	0.16	-9999	-0.79	13	13
elevation of cytosolic calcium ion concentration	-0.29	0.33	-9999	-0.57	153	153
alphaM/beta2 Integrin/JAM2/JAM3	-0.075	0.21	-9999	-0.63	33	33
JAM2	-0.004	0.1	-9999	-0.64	8	8
alphaM/beta2 Integrin/ICAM1	-0.094	0.24	-9999	-0.76	27	27
alphaM/beta2 Integrin/uPA/Plg	-0.28	0.31	-9999	-0.55	151	151
RhoA/GTP	-0.27	0.22	-9999	-0.54	95	95
positive regulation of phagocytosis	-0.17	0.19	-9999	-0.61	33	33
Ron/MSP	-0.014	0.083	-9999	-0.49	9	9
alphaM/beta2 Integrin/uPAR/uPA	-0.29	0.34	-9999	-0.57	153	153
alphaM/beta2 Integrin/uPAR	-0.092	0.25	-9999	-0.7	38	38
PLAU	-0.34	0.4	-9999	-0.8	133	133
PLAT	-0.008	0.13	-9999	-0.8	8	8
actin filament polymerization	-0.4	0.24	-9999	-0.58	165	165
MST1	0.006	0.071	-9999	-0.7	3	3
alphaM/beta2 Integrin/lipoprotein(a)	-0.089	0.22	-9999	-0.58	44	44
TNF	-0.048	0.26	-9999	-0.78	24	24
RAP1B	0.011	0.047	-9999	-0.8	1	1
alphaM/beta2 Integrin/uPA	-0.3	0.33	-9999	-0.6	151	151
fibrinolysis	-0.27	0.3	-9999	-0.55	151	151
HCK	0.004	0.084	-9999	-0.72	4	4
dendritic cell antigen processing and presentation	-0.22	0.2	-9999	-0.44	108	108
VTN	-0.059	0.23	-9999	-0.8	27	27
alphaM/beta2 Integrin/CYR61	-0.074	0.22	-9999	-0.68	31	31
LPA	-0.019	0.14	-9999	-0.8	10	10
LRP1	0.013	0	-9999	-10000	0	0
cell migration	-0.52	0.38	-9999	-0.66	236	236
FN1	-0.44	0.4	-9999	-0.8	170	170
alphaM/beta2 Integrin/Thy1	-0.24	0.35	-9999	-0.65	112	112
MPO	-0.01	0.12	-9999	-0.67	10	10
KNG1	-0.005	0.093	-9999	-0.8	4	4
RAP1/GDP	-0.002	0.031	-9999	-0.54	1	1
ROCK1	-0.24	0.21	-9999	-0.5	92	92
ELA2	0	0	-9999	-10000	0	0
PLG	0.002	0.005	-9999	-10000	0	0
CTGF	0.009	0.053	-9999	-0.64	2	2
alphaM/beta2 Integrin/Hck	-0.077	0.22	-9999	-0.68	32	32
ITGAM	-0.061	0.23	-9999	-0.79	27	27
alphaM/beta2 Integrin/P-Selectin/PSGL1	-0.13	0.23	-9999	-0.66	30	30
HP	-0.24	0.32	-9999	-0.65	116	116
leukocyte adhesion	-0.2	0.27	-9999	-0.79	34	34
SELP	-0.1	0.25	-9999	-0.64	54	54

×

Glypican 2 network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MDK	-0.01	0.14	-9999	-0.78	9	9
GPC2	-0.12	0.3	-9999	-0.8	50	50
GPC2/Midkine	-0.12	0.25	-9999	-0.63	57	57
neuron projection morphogenesis	-0.12	0.25	-9999	-0.63	57	57

×

Syndecan-2-mediated signaling events

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
Syndecan-2/Fibronectin	-0.31	0.31	-9999	-0.56	171	171
EPHB2	-0.17	0.34	-9999	-0.8	67	67
Syndecan-2/TACI	-0.072	0.21	-9999	-0.54	51	51
LAMA1	-0.37	0.41	-9999	-0.8	143	143
Syndecan-2/alpha2 ITGB1	-0.15	0.22	-9999	-0.46	97	97
HRAS	0.013	0	-9999	-10000	0	0
Syndecan-2/CASK	-0.023	0.11	-9999	-0.54	13	13
ITGA5	-0.27	0.39	-9999	-0.8	105	105
BAX	0.02	0.11	-9999	-0.79	1	1
EPB41	0.013	0	-9999	-10000	0	0
positive regulation of cell-cell adhesion	-0.021	0.098	-9999	-0.48	13	13
LAMA3	-0.22	0.37	-9999	-0.8	87	87
EZR	0.013	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
CAV2	0.009	0.06	-9999	-0.72	2	2
Syndecan-2/MMP2	-0.11	0.26	-9999	-0.59	66	66
RP11-540L11.1	0	0	-9999	-10000	0	0
alpha2 ITGB1	-0.002	0.035	-9999	-0.61	1	1
dendrite morphogenesis	-0.12	0.25	-9999	-0.55	77	77
Syndecan-2/GM-CSF	-0.28	0.3	-9999	-0.55	162	162
determination of left/right symmetry	-0.005	0.13	-9999	-0.61	13	13
Syndecan-2/PKC delta	0.003	0.11	-9999	-0.53	13	13
GNB2L1	0.013	0	-9999	-10000	0	0
MAPK3	-0.25	0.28	-9999	-0.5	162	162
MAPK1	-0.25	0.28	-9999	-0.5	162	162
Syndecan-2/RACK1	-0.019	0.092	-9999	-0.45	13	13
NF1	0.013	0	-9999	-10000	0	0
FGFR/FGF/Syndecan-2	-0.005	0.13	-9999	-0.61	13	13
ITGA2	0.013	0	-9999	-10000	0	0
MAPK8	0.011	0.12	-9999	-0.55	13	13
Syndecan-2/alpha2/beta1 Integrin	-0.23	0.25	-9999	-0.48	144	144
Syndecan-2/Kininogen	-0.019	0.13	-9999	-0.56	16	16
ITGB1	0.011	0.047	-9999	-0.8	1	1
SRC	0.02	0.094	-9999	-0.42	13	13
Syndecan-2/CASK/Protein 4.1	-0.021	0.098	-9999	-0.49	13	13
extracellular matrix organization	0.001	0.12	-9999	-0.56	13	13
actin cytoskeleton reorganization	-0.3	0.3	-9999	-0.56	171	171
Syndecan-2/Caveolin-2/Ras	-0.023	0.1	-9999	-0.48	14	14
Syndecan-2/Laminin alpha3	-0.16	0.27	-9999	-0.55	96	96
Syndecan-2/RasGAP	-0.018	0.087	-9999	-0.43	13	13
alpha5/beta1 Integrin	-0.22	0.29	-9999	-0.61	106	106
PRKCD	0.013	0	-9999	-10000	0	0
Syndecan-2 dimer	-0.12	0.25	-9999	-0.55	77	77
GO:0007205	0.004	0.001	-9999	-10000	0	0
DNA mediated transformation	0	0	-9999	-10000	0	0
Syndecan-2/RasGAP/Src	0.027	0.092	-9999	-10000	0	0
RHOA	0.013	0	-9999	-10000	0	0
SDCBP	0.013	0	-9999	-10000	0	0
TNFRSF13B	-0.093	0.27	-9999	-0.8	39	39
RASA1	0.013	0	-9999	-10000	0	0
alpha2/beta1 Integrin	-0.002	0.035	-9999	-0.61	1	1
Syndecan-2/Synbindin	0.003	0.11	-9999	-0.53	13	13
TGFB1	0.011	0.047	-9999	-0.8	1	1
CASP3	0.014	0.1	-9999	-0.48	13	13
FN1	-0.44	0.4	-9999	-0.8	170	170
Syndecan-2/IL8	-0.12	0.26	-9999	-0.56	73	73
SDC2	-0.005	0.13	-9999	-0.61	13	13
KNG1	-0.005	0.093	-9999	-0.8	4	4
Syndecan-2/Neurofibromin	0.003	0.11	-9999	-0.53	13	13
TRAPPC4	0.013	0	-9999	-10000	0	0
CSF2	-0.41	0.41	-9999	-0.8	157	157
Syndecan-2/TGFB1	0.001	0.12	-9999	-0.56	13	13
Syndecan-2/Syntenin/PI-4-5-P2	-0.021	0.098	-9999	-0.49	13	13
Syndecan-2/Ezrin	-0.02	0.097	-9999	-0.48	13	13
PRKACA	0.014	0.1	-9999	-0.48	13	13
angiogenesis	-0.11	0.26	-9999	-0.56	73	73
MMP2	-0.15	0.33	-9999	-0.8	61	61
IL8	-0.16	0.33	-9999	-0.8	65	65
calcineurin-NFAT signaling pathway	-0.071	0.21	-9999	-0.54	51	51

×

IL23-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCL2	-0.55	0.44	-10000	0	-1.2	60	60
IL23A	-0.53	0.42	-10000	0	-1.2	50	50
NF kappa B1 p50/RelA/I kappa B alpha	-0.53	0.4	-10000	0	-1.1	72	72
positive regulation of T cell mediated cytotoxicity	-0.59	0.47	-10000	0	-1.2	74	74
ITGA3	-0.53	0.42	-10000	0	-1.2	55	55
IL17F	-0.36	0.27	-10000	0	-0.76	36	36
IL12B	-0.094	0.26	-10000	0	-0.84	33	33
STAT1 (dimer)	-0.59	0.47	-10000	0	-1.2	81	81
CD4	-0.52	0.4	-10000	0	-1.1	49	49
IL23	-0.55	0.42	-10000	0	-1.2	61	61
IL23R	-0.084	0.11	-10000	0	-0.7	6	6
IL1B	-0.56	0.44	-10000	0	-1.2	60	60
T-helper cell lineage commitment	0	0	-10000	0	-10000	0	0
IL24	-0.7	0.44	-10000	0	-1.2	113	113
TYK2	-0.001	0.012	-10000	0	-10000	0	0
STAT4	-0.002	0.11	-10000	0	-0.78	6	6
STAT3	0.013	0.001	-10000	0	-10000	0	0
IL18RAP	-0.007	0.12	-10000	0	-0.71	8	8
IL12RB1	-0.088	0.26	-10000	0	-0.83	32	32
PIK3CA	0.013	0.001	-10000	0	-10000	0	0
IL12Rbeta1/TYK2	-0.073	0.2	-10000	0	-0.65	32	32
IL23R/JAK2	-0.099	0.11	-10000	0	-0.74	4	4
positive regulation of chronic inflammatory response	-0.59	0.47	-10000	0	-1.2	74	74
natural killer cell activation	0.008	0.009	0.059	6	-10000	0	6
JAK2	0.003	0.014	-10000	0	-10000	0	0
PIK3R1	0.013	0.001	-10000	0	-10000	0	0
NFKB1	0.01	0.003	-10000	0	-10000	0	0
RELA	0.01	0.003	-10000	0	-10000	0	0
positive regulation of dendritic cell antigen processing and presentation	-0.52	0.4	-10000	0	-1.1	61	61
ALOX12B	-0.62	0.46	-10000	0	-1.2	93	93
CXCL1	-0.56	0.44	-10000	0	-1.2	69	69
T cell proliferation	-0.59	0.47	-10000	0	-1.2	74	74
NFKBIA	0.01	0.003	-10000	0	-10000	0	0
IL17A	-0.28	0.22	-10000	0	-0.63	15	15
PI3K	-0.54	0.41	-10000	0	-1.1	74	74
IFNG	-0.03	0.047	0.13	5	-0.11	55	60
STAT3 (dimer)	-0.51	0.39	-10000	0	-1.1	71	71
IL18R1	0.008	0.061	-10000	0	-0.73	2	2
IL23/IL23R/JAK2/TYK2/SOCS3	-0.33	0.26	-10000	0	-0.8	32	32
IL18/IL18R	-0.004	0.12	-10000	0	-0.55	7	7
macrophage activation	-0.027	0.015	-10000	0	-0.045	17	17
TNF	-0.55	0.44	-10000	0	-1.2	51	51
STAT3/STAT4	-0.55	0.41	-10000	0	-1.1	79	79
STAT4 (dimer)	-0.57	0.45	-10000	0	-1.2	75	75
IL18	-0.009	0.12	-10000	0	-0.64	10	10
IL19	-0.66	0.52	-10000	0	-1.3	107	107
STAT5A (dimer)	-0.56	0.45	-10000	0	-1.2	74	74
STAT1	-0.048	0.22	-10000	0	-0.8	23	23
SOCS3	0.011	0.038	-10000	0	-0.64	1	1
CXCL9	-0.65	0.47	-10000	0	-1.1	111	111
MPO	-0.54	0.42	-10000	0	-1.2	60	60
positive regulation of humoral immune response	-0.59	0.47	-10000	0	-1.2	74	74
IL23/IL23R/JAK2/TYK2	-0.61	0.51	-10000	0	-1.3	74	74
IL6	-0.56	0.46	-10000	0	-1.3	58	58
STAT5A	0.013	0	-10000	0	-10000	0	0
IL2	0.005	0.047	-10000	0	-0.79	1	1
positive regulation of tyrosine phosphorylation of STAT protein	0.008	0.009	0.059	6	-10000	0	6
CD3E	-0.52	0.41	-10000	0	-1.1	72	72
keratinocyte proliferation	-0.59	0.47	-10000	0	-1.2	74	74
NOS2	-0.57	0.43	-10000	0	-1.1	74	74

×

Endothelins

Figure S11. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

Table S11. Get Full Table This table displays mean, standard deviation, and perturbation statistics for Inferred Pathway Levels (IPLs). A mean perturbation of -9999 implies that the IPLs across all the real samples did not differ enough from the IPLs generated by a background model of permuted samples (> 1 Std.Dev from the permuted sample IPLs).

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
AKT1	-0.23	0.3	-10000	0	-0.7	46	46
PTK2B	0.013	0.001	-10000	0	-10000	0	0
mol:Ca2+	-0.091	0.22	-10000	0	-0.66	23	23
EDN1	-0.14	0.2	-10000	0	-0.82	3	3
EDN3	-0.31	0.32	-10000	0	-0.64	147	147
EDN2	-0.09	0.26	-10000	0	-0.71	43	43
HRAS/GDP	-0.086	0.18	-10000	0	-0.55	9	9
ETA receptor/Endothelin-1/Gq/GTP/PLC beta	-0.083	0.14	-10000	0	-0.39	20	20
ADCY4	-0.23	0.25	-10000	0	-0.61	60	60
ADCY5	-0.31	0.26	-10000	0	-0.64	87	87
ADCY6	-0.24	0.25	-10000	0	-0.63	60	60
ADCY7	-0.23	0.25	-10000	0	-0.61	60	60
ADCY1	-0.25	0.26	-10000	0	-0.64	67	67
ADCY2	-0.34	0.26	-10000	0	-0.64	104	104
ADCY3	-0.23	0.25	-10000	0	-0.61	60	60
ADCY8	-0.25	0.26	-10000	0	-0.63	68	68
ADCY9	-0.23	0.25	-10000	0	-0.61	58	58
arachidonic acid secretion	-0.12	0.23	-10000	0	-0.55	41	41
ETB receptor/Endothelin-1/Gq/GTP	-0.08	0.14	-10000	0	-0.42	20	20
GNAO1	0.009	0.06	-10000	0	-0.72	2	2
HRAS	0.012	0.005	-10000	0	-10000	0	0
ETA receptor/Endothelin-1/G12/GTP	-0.16	0.34	0.34	63	-0.67	44	107
ETA receptor/Endothelin-1/Gs/GTP	-0.2	0.33	0.32	47	-0.65	60	107
mol:GTP	0	0.005	-10000	0	-10000	0	0
COL3A1	-0.51	0.48	-10000	0	-0.86	190	190
EDNRB	-0.026	0.072	-10000	0	-0.64	3	3
response to oxidative stress	0	0	-10000	0	-10000	0	0
CYSLTR2	-0.3	0.4	-10000	0	-0.96	58	58
CYSLTR1	-0.27	0.33	-10000	0	-0.76	58	58
SLC9A1	-0.095	0.16	-10000	0	-0.33	15	15
mol:GDP	-0.098	0.18	-10000	0	-0.49	22	22
SLC9A3	-0.27	0.35	-10000	0	-0.76	82	82
RAF1	-0.12	0.2	-10000	0	-0.54	28	28
JUN	-0.069	0.17	-10000	0	-0.66	1	1
JAK2	-0.23	0.3	-10000	0	-0.71	43	43
mol:IP3	-0.1	0.16	-10000	0	-0.5	21	21
ETA receptor/Endothelin-1	-0.22	0.41	0.4	65	-0.77	50	115
PLCB1	0.009	0.038	-10000	0	-0.64	1	1
PLCB2	0.01	0.038	-10000	0	-0.64	1	1
ETA receptor/Endothelin-3	-0.3	0.27	-10000	0	-0.55	147	147
FOS	-0.18	0.37	-10000	0	-0.96	50	50
Gai/GDP	0.009	0.07	-10000	0	-0.6	2	2
CRK	0.013	0.001	-10000	0	-10000	0	0
mol:Ca ++	-0.25	0.28	-10000	0	-0.66	59	59
BCAR1	0.014	0	-10000	0	-10000	0	0
PRKCB1	-0.1	0.16	-10000	0	-0.47	22	22
GNAQ	0.013	0.007	-10000	0	-10000	0	0
GNAZ	-0.004	0.11	-10000	0	-0.73	7	7
GNAL	-0.06	0.21	-10000	0	-0.64	34	34
Gs family/GDP	-0.15	0.16	-10000	0	-0.5	33	33
ETA receptor/Endothelin-1/Gq/GTP	-0.11	0.17	-10000	0	-0.4	35	35
MAPK14	-0.048	0.12	-10000	0	-0.6	3	3
TRPC6	-0.095	0.22	-10000	0	-0.7	23	23
GNAI2	0.013	0	-10000	0	-10000	0	0
GNAI3	0.013	0	-10000	0	-10000	0	0
GNAI1	0.011	0.038	-10000	0	-0.64	1	1
ETB receptor/Endothelin-1/Gq/GTP/PLC beta	-0.06	0.12	-10000	0	-0.38	17	17
ETB receptor/Endothelin-2	-0.091	0.19	-10000	0	-0.54	46	46
ETB receptor/Endothelin-3	-0.25	0.24	-10000	0	-0.49	149	149
ETB receptor/Endothelin-1	-0.12	0.18	-10000	0	-0.58	6	6
MAPK3	-0.16	0.32	-10000	0	-0.82	50	50
MAPK1	-0.16	0.32	-10000	0	-0.82	50	50
Rac1/GDP	-0.085	0.17	-10000	0	-0.54	10	10
cAMP biosynthetic process	-0.27	0.23	-10000	0	-0.59	72	72
MAPK8	-0.088	0.19	-10000	0	-0.56	15	15
SRC	0.013	0	-10000	0	-10000	0	0
ETB receptor/Endothelin-1/Gi/GTP	-0.028	0.089	-10000	0	-0.46	1	1
p130Cas/CRK/Src/PYK2	-0.092	0.19	-10000	0	-0.57	14	14
mol:K +	0	0	-10000	0	-10000	0	0
G12/GDP	-0.088	0.18	-10000	0	-0.56	9	9
COL1A2	-0.41	0.47	-10000	0	-0.85	155	155
EntrezGene:2778	0	0	-10000	0	-10000	0	0
ETA receptor/Endothelin-2	-0.14	0.23	-10000	0	-0.61	43	43
mol:DAG	-0.1	0.16	-10000	0	-0.5	21	21
MAP2K2	-0.13	0.25	-10000	0	-0.65	38	38
MAP2K1	-0.13	0.25	-10000	0	-0.63	44	44
EDNRA	-0.12	0.18	-10000	0	-0.61	1	1
positive regulation of muscle contraction	-0.19	0.26	-10000	0	-0.63	43	43
Gq family/GDP	-0.11	0.17	-10000	0	-0.53	22	22
HRAS/GTP	-0.11	0.18	-10000	0	-0.48	29	29
PRKCH	-0.094	0.16	-10000	0	-0.48	19	19
RAC1	0.013	0	-10000	0	-10000	0	0
PRKCA	-0.096	0.16	-10000	0	-0.47	21	21
PRKCB	-0.1	0.17	-10000	0	-0.51	26	26
PRKCE	-0.094	0.16	-10000	0	-0.48	19	19
PRKCD	-0.095	0.16	-10000	0	-0.48	19	19
PRKCG	-0.14	0.21	-10000	0	-0.55	42	42
regulation of vascular smooth muscle contraction	-0.2	0.43	-10000	0	-1.1	50	50
PRKCQ	-0.1	0.17	-10000	0	-0.5	25	25
PLA2G4A	-0.13	0.24	-10000	0	-0.6	41	41
GNA14	-0.095	0.24	-10000	0	-0.64	50	50
GNA15	0.012	0.006	-10000	0	-10000	0	0
GNA12	0.008	0.066	-10000	0	-0.8	2	2
GNA11	0.012	0.006	-10000	0	-10000	0	0
Rac1/GTP	-0.16	0.34	0.34	61	-0.67	43	104
MMP1	-0.55	0.23	-10000	0	-0.63	271	271

×

TCGA08_p53

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
CDKN2A	-0.24	0.3	-10000	0	-0.59	124	124
TP53	-0.071	0.088	-10000	0	-0.41	3	3
Senescence	-0.071	0.088	-10000	0	-0.41	3	3
Apoptosis	-0.071	0.088	-10000	0	-0.41	3	3
Activated_Oncogenes	0	0	-10000	0	-10000	0	0
MDM2	0.12	0.15	0.3	124	-10000	0	124
MDM4	0.013	0	-10000	0	-10000	0	0

×

p75(NTR)-mediated signaling

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
Sortilin/TRAF6	-0.014	0.08	-9999	-0.47	9	9
Necdin/E2F1	-0.041	0.15	-9999	-0.59	21	21
proNGF (dimer)/p75(NTR)/Sortilin/NADE/14-3-3 E	-0.13	0.2	-9999	-0.78	1	1
NGF (dimer)/p75(NTR)/BEX1	-0.16	0.25	-9999	-0.54	85	85
NT-4/5 (dimer)/p75(NTR)	-0.027	0.12	-9999	-0.55	15	15
IKBKB	0.013	0	-9999	-10000	0	0
AKT1	-0.083	0.21	-9999	-10000	0	0
IKBKG	0.013	0	-9999	-10000	0	0
BDNF	-0.042	0.2	-9999	-0.72	23	23
MGDIs/NGR/p75(NTR)/LINGO1	-0.073	0.2	-9999	-0.58	38	38
FURIN	0.013	0	-9999	-10000	0	0
proBDNF (dimer)/p75(NTR)/Sortilin	-0.069	0.17	-9999	-0.47	45	45
LINGO1	-0.046	0.21	-9999	-0.8	22	22
Sortilin/TRAF6/NRIF	-0.009	0.051	-9999	-10000	0	0
proBDNF (dimer)	-0.042	0.2	-9999	-0.72	23	23
NTRK1	-0.062	0.24	-9999	-0.8	28	28
RTN4R	-0.005	0.12	-9999	-0.8	7	7
neuron apoptosis	-0.065	0.18	-9999	-0.59	12	12
IRAK1	0.013	0	-9999	-10000	0	0
SHC1	-0.12	0.24	-9999	-0.53	72	72
ARHGDIA	0.013	0	-9999	-10000	0	0
RhoA/GTP	0	0	-9999	-10000	0	0
Gamma Secretase	-0.001	0.026	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-H1	-0.14	0.22	-9999	-0.49	73	73
MAGEH1	0.011	0.047	-9999	-0.8	1	1
proNGF (dimer)/p75(NTR)/Sortilin/Necdin	-0.14	0.22	-9999	-0.5	74	74
Mammalian IAPs/DIABLO	-0.031	0.14	-9999	-0.6	16	16
proNGF (dimer)	-0.16	0.33	-9999	-0.8	66	66
MAGED1	0.011	0.038	-9999	-0.64	1	1
APP	0.013	0	-9999	-10000	0	0
NT-4/5 (dimer)	0.013	0.001	-9999	-10000	0	0
ZNF274	0.013	0	-9999	-10000	0	0
RhoA/GDP/RHOGDI	-0.12	0.19	-9999	-0.45	72	72
NGF	-0.16	0.34	-9999	-0.8	66	66
cell cycle arrest	-0.12	0.22	-9999	-0.49	72	72
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK	-0.038	0.13	-9999	-10000	0	0
NT-4/5 (dimer)/p75(NTR)/TRAF6	-0.023	0.1	-9999	-0.47	15	15
NCSTN	0.013	0	-9999	-10000	0	0
mol:GTP	-0.14	0.23	-9999	-0.53	72	72
PSENEN	0.011	0.047	-9999	-0.8	1	1
mol:ceramide	-0.11	0.22	-9999	-0.48	72	72
NGF (dimer)/p75(NTR)/TRAF6/RIP2/IRAK/p62/Atypical PKCs	-0.017	0.11	-9999	-0.6	1	1
p75(NTR)/beta APP	-0.027	0.12	-9999	-0.55	15	15
BEX1	-0.03	0.18	-9999	-0.8	15	15
mol:GDP	-0.12	0.24	-9999	-0.52	81	81
NGF (dimer)	-0.19	0.26	-9999	-0.54	96	96
MGDIs/NGR/p75(NTR)/LINGO1/RHOGDI	-0.066	0.18	-9999	-0.56	33	33
PIK3R1	0.013	0	-9999	-10000	0	0
RAC1/GTP	-0.12	0.2	-9999	-0.46	72	72
MYD88	0.013	0	-9999	-10000	0	0
CHUK	0.013	0	-9999	-10000	0	0
NGF (dimer)/p75(NTR)/PKA	-0.14	0.23	-9999	-0.53	72	72
RHOB	0.013	0	-9999	-10000	0	0
RHOA	0.013	0	-9999	-10000	0	0
MAGE-G1/E2F1	-0.034	0.14	-9999	-0.61	17	17
NT3 (dimer)	-0.18	0.3	-9999	-0.64	90	90
TP53	-0.015	0.16	-9999	-0.63	3	3
PRDM4	-0.11	0.23	-9999	-0.48	72	72
BDNF (dimer)	-0.44	0.3	-9999	-0.59	222	222
PIK3CA	0.013	0	-9999	-10000	0	0
SORT1	-0.006	0.11	-9999	-0.64	9	9
activation of caspase activity	-0.12	0.2	-9999	-0.77	1	1
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.14	0.21	-9999	-0.48	72	72
RHOC	0.013	0	-9999	-10000	0	0
XIAP	0.013	0	-9999	-10000	0	0
MAPK10	-0.07	0.19	-9999	-0.52	13	13
DIABLO	0.013	0	-9999	-10000	0	0
SMPD2	-0.11	0.23	-9999	-0.48	72	72
APH1B	0.013	0	-9999	-10000	0	0
APH1A	0.013	0	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin	-0.15	0.23	-9999	-0.53	72	72
PSEN1	0.013	0	-9999	-10000	0	0
APAF-1/Pro-Caspase 9	0	0	-9999	-10000	0	0
NT3 (dimer)/p75(NTR)	-0.17	0.24	-9999	-0.49	102	102
MAPK8	-0.06	0.19	-9999	-0.52	10	10
MAPK9	-0.058	0.19	-9999	-0.52	9	9
APAF1	0.013	0	-9999	-10000	0	0
NTF3	-0.18	0.3	-9999	-0.64	90	90
NTF4	0.013	0.001	-9999	-10000	0	0
NDN	0.005	0.075	-9999	-0.64	4	4
RAC1/GDP	0	0	-9999	-10000	0	0
RhoA-B-C/GDP	-0.11	0.18	-9999	-10000	0	0
p75 CTF/Sortilin/TRAF6/NRIF	-0.01	0.06	-9999	-10000	0	0
RhoA-B-C/GTP	-0.14	0.23	-9999	-0.52	72	72
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.058	0.14	-9999	-0.47	21	21
proBDNF (dimer)/p75(NTR)/Sortilin/TRAF6	-0.063	0.15	-9999	-0.5	21	21
PRKACB	0.013	0	-9999	-10000	0	0
proBDNF (dimer)/p75 ECD	-0.041	0.14	-9999	-0.54	23	23
ChemicalAbstracts:86-01-1	0	0	-9999	-10000	0	0
BIRC3	-0.024	0.17	-9999	-0.8	14	14
BIRC2	-0.003	0.11	-9999	-0.8	6	6
neuron projection morphogenesis	-0.11	0.21	-9999	-0.44	73	73
BAD	-0.053	0.18	-9999	-0.49	9	9
RIPK2	0.013	0	-9999	-10000	0	0
NGFR	-0.023	0.16	-9999	-0.73	15	15
CYCS	-0.095	0.22	-9999	-0.45	72	72
ADAM17	0.013	0	-9999	-10000	0	0
NGF (dimer)/p75(NTR)/TRAF6/RIP2	-0.12	0.21	-9999	-0.48	72	72
BCL2L11	-0.053	0.18	-9999	-0.49	9	9
BDNF (dimer)/p75(NTR)	-0.068	0.18	-9999	-0.54	38	38
PI3K	-0.12	0.21	-9999	-0.48	72	72
proNGF (dimer)/p75(NTR)/Sortilin/MAGE-G1	-0.14	0.21	-9999	-0.48	72	72
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)	-0.16	0.26	-9999	-0.6	81	81
ChemicalAbstracts:146-91-8	0	0	-9999	-10000	0	0
proNGF (dimer)/p75(NTR)/Sortilin/NRAGE	-0.14	0.21	-9999	-0.48	72	72
TRAF6	0.013	0	-9999	-10000	0	0
RAC1	0.013	0	-9999	-10000	0	0
PRKCZ	0.011	0.038	-9999	-0.64	1	1
PLG	0.002	0.005	-9999	-10000	0	0
oligodendrocyte cell fate commitment	0	0	-9999	-10000	0	0
CASP6	-0.11	0.22	-9999	-0.74	9	9
SQSTM1	0.013	0	-9999	-10000	0	0
NGFRAP1	0.011	0.047	-9999	-0.8	1	1
CASP3	-0.046	0.17	-9999	-0.45	9	9
E2F1	-0.032	0.19	-9999	-0.8	17	17
CASP9	0.013	0	-9999	-10000	0	0
IKK complex	-0.12	0.18	-9999	-0.7	7	7
NGF (dimer)/TRKA	-0.19	0.3	-9999	-0.64	88	88
MMP7	-0.13	0.3	-9999	-0.76	55	55
proNGF (dimer)/p75(NTR)/Sortilin/TRAF6/NRIF	-0.12	0.2	-9999	-0.45	72	72
MMP3	-0.55	0.38	-9999	-0.8	210	210
APAF-1/Caspase 9	-0.11	0.17	-9999	-0.69	8	8

×

Visual signal transduction: Cones

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
Cone Metarhodopsin II/Cone Transducin	-0.008	0.06	-9999	-0.46	4	4
RGS9BP	-0.013	0.13	-9999	-0.64	12	12
mol:GTP	0	0	-9999	-10000	0	0
GRK1	0.003	0.006	-9999	-10000	0	0
mol:Na +	-0.2	0.26	-9999	-0.54	112	112
mol:ADP	-0.059	0.2	-9999	-0.62	35	35
GNAT2	0.012	0.004	-9999	-10000	0	0
RGS9-1/Gbeta5/R9AP	-0.019	0.085	-9999	-0.4	14	14
mol:GDP	0	0	-9999	-10000	0	0
PDE6H/GNAT2/GTP	0	0	-9999	-10000	0	0
GRK7	-0.081	0.26	-9999	-0.8	35	35
CNGB3	-0.29	0.39	-9999	-0.8	112	112
Cone Metarhodopsin II/X-Arrestin	0	0	-9999	-10000	0	0
mol:Ca2+	-0.3	0.33	-9999	-0.58	162	162
Cone PDE6	-0.016	0.073	-9999	-0.46	1	1
Cone Metarhodopsin II	-0.058	0.16	-9999	-0.5	35	35
Na + (4 Units)	-0.31	0.32	-9999	-0.58	162	162
GNAT2/GDP	-0.016	0.072	-9999	-0.45	1	1
GNB5	0.013	0	-9999	-10000	0	0
mol:GMP (4 units)	0.011	0.005	-9999	-10000	0	0
Cone Transducin	-0.009	0.063	-9999	-0.49	4	4
SLC24A2	-0.21	0.36	-9999	-0.8	83	83
GNB3/GNGT2	-0.011	0.079	-9999	-0.56	6	6
GNB3	0.001	0.096	-9999	-0.74	5	5
GNAT2/GTP	0	0	-9999	-10000	0	0
CNGA3	0.01	0.006	-9999	-10000	0	0
ARR3	0.001	0.004	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
cGMP/Cone CNG Channel	-0.2	0.26	-9999	-0.54	112	112
mol:Pi	-0.019	0.085	-9999	-0.4	14	14
Cone CNG Channel	-0.16	0.22	-9999	-10000	0	0
mol:all-trans-retinal	0	0	-9999	-10000	0	0
mol:K +	-0.21	0.36	-9999	-0.8	83	83
RGS9	0.009	0.06	-9999	-0.72	2	2
PDE6C	0.002	0.005	-9999	-10000	0	0
GNGT2	0.011	0.047	-9999	-0.8	1	1
mol:cGMP (4 units)	0	0	-9999	-10000	0	0
PDE6H	0.002	0.004	-9999	-10000	0	0

×

PDGFR-beta signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
S1P1/Sphingosine-1-phosphate	-0.086	0.14	-9999	-0.37	1	1
PDGFB-D/PDGFRB/SLAP	-0.17	0.27	-9999	-0.6	86	86
PDGFB-D/PDGFRB/APS/CBL	-0.15	0.23	-9999	-0.52	86	86
AKT1	-0.047	0.18	-9999	-0.62	2	2
mol:PI-4-5-P2	-0.001	0.001	-9999	-10000	0	0
mol:Sphingosine-1-phosphate	-0.061	0.16	-9999	-10000	0	0
PIK3CA	0.013	0	-9999	-10000	0	0
FGR	-0.11	0.18	-9999	-0.41	2	2
mol:Ca2+	-0.064	0.16	-9999	-0.37	2	2
MYC	-0.023	0.12	-9999	-10000	0	0
SHC1	0.013	0	-9999	-10000	0	0
HRAS/GDP	-0.12	0.19	-9999	-0.41	85	85
LRP1/PDGFRB/PDGFB	-0.16	0.24	-9999	-0.53	89	89
GRB10	0.011	0.047	-9999	-0.8	1	1
PTPN11	0.013	0	-9999	-10000	0	0
GO:0007205	-0.066	0.16	-9999	-0.37	2	2
PTEN	0.013	0	-9999	-10000	0	0
GRB2	0.013	0	-9999	-10000	0	0
GRB7	0.003	0.089	-9999	-0.76	4	4
PDGFB-D/PDGFRB/SHP2	-0.17	0.27	-9999	-0.6	85	85
PDGFB-D/PDGFRB/GRB10	-0.17	0.27	-9999	-0.6	86	86
cell cycle arrest	-0.17	0.27	-9999	-0.6	86	86
HRAS	0.013	0	-9999	-10000	0	0
HIF1A	-0.031	0.16	-9999	-0.53	2	2
GAB1	-0.066	0.16	-9999	-0.38	11	11
mol:GTP	0	0	-9999	-10000	0	0
DNM2	-0.059	0.16	-9999	-0.43	1	1
PDGFB-D/PDGFRB	-0.14	0.24	-9999	-0.52	85	85
mol:GDP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/LMW-PTP	-0.17	0.27	-9999	-0.6	85	85
S1P1/Sphingosine-1-phosphate/PDGFB-D/PDGFRB	-0.089	0.14	-9999	-0.43	1	1
positive regulation of MAPKKK cascade	-0.17	0.27	-9999	-0.6	85	85
PIK3R1	0.013	0	-9999	-10000	0	0
mol:IP3	-0.066	0.16	-9999	-0.37	2	2
E5	-0.001	0.002	-9999	-10000	0	0
CSK	0.014	0.002	-9999	-10000	0	0
PDGFB-D/PDGFRB/GRB7	-0.18	0.28	-9999	-0.61	87	87
SHB	0.009	0.053	-9999	-0.64	2	2
BLK	-0.17	0.21	-9999	-0.44	95	95
PTPN2	0.012	0.003	-9999	-10000	0	0
PDGFB-D/PDGFRB/SNX15	-0.17	0.27	-9999	-0.6	85	85
BCAR1	0.013	0	-9999	-10000	0	0
VAV2	-0.062	0.16	-9999	-0.42	3	3
CBL	0.013	0	-9999	-10000	0	0
PDGFB-D/PDGFRB/DEP1	-0.17	0.27	-9999	-0.6	85	85
LCK	-0.12	0.18	-9999	-0.4	85	85
PDGFRB	-0.21	0.36	-9999	-0.8	85	85
ACP1	0.013	0	-9999	-10000	0	0
HCK	-0.11	0.18	-9999	-0.41	14	14
ABL1	-0.076	0.17	-9999	-0.4	12	12
PDGFB-D/PDGFRB/CBL	-0.064	0.16	-9999	-0.41	2	2
PTPN1	0.012	0.003	-9999	-10000	0	0
SNX15	0.013	0	-9999	-10000	0	0
STAT3	0.013	0	-9999	-10000	0	0
STAT1	-0.048	0.22	-9999	-0.8	23	23
cell proliferation	-0.02	0.12	-9999	-10000	0	0
SLA	0.011	0.047	-9999	-0.8	1	1
actin cytoskeleton reorganization	-0.1	0.18	-9999	-10000	0	0
SRC	-0.11	0.18	-9999	-0.39	85	85
PI3K	-0.1	0.17	-9999	-0.71	2	2
PDGFB-D/PDGFRB/GRB7/SHC	-0.15	0.24	-9999	-0.53	87	87
SH2B2	0.011	0.047	-9999	-0.8	1	1
PLCgamma1/SPHK1	-0.063	0.16	-9999	-10000	0	0
LYN	-0.11	0.18	-9999	-10000	0	0
LRP1	0.013	0	-9999	-10000	0	0
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	-0.11	0.18	-9999	-10000	0	0
SPHK1	0.002	0.08	-9999	-0.8	3	3
EDG1	-0.001	0.004	-9999	-10000	0	0
mol:DAG	-0.066	0.16	-9999	-0.37	2	2
PLCG1	-0.068	0.16	-9999	-0.38	2	2
NHERF/PDGFRB	-0.15	0.24	-9999	-0.52	86	86
YES1	-0.11	0.18	-9999	-0.39	85	85
cell migration	-0.15	0.24	-9999	-0.52	86	86
SHC/Grb2/SOS1	-0.11	0.18	-9999	-10000	0	0
SLC9A3R2	0.011	0.047	-9999	-0.8	1	1
SLC9A3R1	0.009	0.053	-9999	-0.64	2	2
NHERF1-2/PDGFRB/PTEN	-0.14	0.22	-9999	-0.48	85	85
FYN	-0.11	0.18	-9999	-0.42	12	12
DOK1	-0.1	0.23	-9999	-0.46	85	85
HRAS/GTP	0	0	-9999	-10000	0	0
PDGFB	-0.003	0.11	-9999	-0.8	6	6
RAC1	-0.045	0.15	-9999	-10000	0	0
PRKCD	-0.1	0.23	-9999	-0.47	85	85
FER	-0.1	0.23	-9999	-0.47	85	85
MAPKKK cascade	-0.11	0.18	-9999	-10000	0	0
RASA1	-0.1	0.23	-9999	-0.47	85	85
NCK1	0.013	0	-9999	-10000	0	0
NCK2	0.013	0	-9999	-10000	0	0
p62DOK/Csk	-0.11	0.2	-9999	-10000	0	0
PDGFB-D/PDGFRB/SHB	-0.17	0.27	-9999	-0.6	87	87
chemotaxis	-0.074	0.17	-9999	-0.39	12	12
STAT1-3-5/STAT1-3-5	-0.14	0.2	-9999	-0.82	6	6
Bovine Papilomavirus E5/PDGFRB	-0.17	0.28	-9999	-0.61	85	85
PTPRJ	0.013	0	-9999	-10000	0	0

×

Visual signal transduction: Rods

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:K +	0.013	0	-9999	-10000	0	0
GNAT1/GTP	0	0	-9999	-10000	0	0
Metarhodopsin II/Arrestin	-0.005	0.054	-9999	-0.55	3	3
PDE6G/GNAT1/GTP	-0.021	0.11	-9999	-0.54	12	12
mol:GTP	0	0	-9999	-10000	0	0
absorption of light	0	0	-9999	-10000	0	0
GNAT1	0.007	0.007	-9999	-10000	0	0
GRK1	0.003	0.006	-9999	-10000	0	0
CNG Channel	-0.46	0.3	-9999	-0.78	123	123
mol:Na +	-0.32	0.26	-9999	-0.79	38	38
mol:ADP	0.003	0.006	-9999	-10000	0	0
RGS9-1/Gbeta5/R9AP	-0.019	0.085	-9999	-0.4	14	14
mol:GDP	0	0	-9999	-10000	0	0
cGMP/CNG Channel	-0.33	0.27	-9999	-0.83	38	38
CNGB1	-0.45	0.4	-9999	-0.8	172	172
RDH5	0.011	0.038	-9999	-0.64	1	1
SAG	0.002	0.004	-9999	-10000	0	0
mol:Ca2+	-0.29	0.26	-9999	-0.76	38	38
Na + (4 Units)	-0.3	0.24	-9999	-0.73	38	38
RGS9	0.009	0.06	-9999	-0.72	2	2
GNB1/GNGT1	-0.1	0.23	-9999	-0.61	51	51
GNAT1/GDP	-0.016	0.072	-9999	-0.45	1	1
GUCY2D	-0.027	0.18	-9999	-0.8	15	15
GNGT1	-0.12	0.3	-9999	-0.8	51	51
GUCY2F	0	0.047	-9999	-0.8	1	1
GNB5	0.013	0	-9999	-10000	0	0
mol:GMP (4 units)	-0.21	0.23	-9999	-0.63	34	34
mol:11-cis-retinal	0.011	0.037	-9999	-0.64	1	1
mol:cGMP	-0.082	0.18	-9999	-0.49	48	48
GNB1	0.013	0	-9999	-10000	0	0
Rhodopsin	-0.008	0.066	-9999	-0.58	4	4
SLC24A1	0.013	0	-9999	-10000	0	0
CNGA1	-0.038	0.18	-9999	-0.64	24	24
Metarhodopsin II	-0.005	0.049	-9999	-0.5	3	3
mol:Ca ++	0	0	-9999	-10000	0	0
GC1/GCAP Family	-0.085	0.19	-9999	-0.52	47	47
RGS9BP	-0.013	0.13	-9999	-0.64	12	12
Metarhodopsin II/Transducin	-0.034	0.11	-9999	-0.28	13	13
GCAP Family/Ca ++	-0.062	0.16	-9999	-0.49	38	38
PDE6A/B	-0.28	0.27	-9999	-0.51	166	166
mol:Pi	-0.019	0.085	-9999	-0.4	14	14
mol:all-trans-retinal	0	0	-9999	-10000	0	0
Transducin	-0.083	0.18	-9999	-0.49	51	51
PDE6B	-0.046	0.2	-9999	-0.71	25	25
PDE6A	-0.32	0.33	-9999	-0.64	155	155
PDE6G	-0.019	0.16	-9999	-0.8	12	12
RHO	-0.004	0.08	-9999	-0.8	3	3
PDE6	-0.22	0.22	-9999	-0.68	30	30
GUCA1A	-0.079	0.26	-9999	-0.8	34	34
GC2/GCAP Family	-0.063	0.17	-9999	-0.5	35	35
GUCA1C	0	0	-9999	-10000	0	0
GUCA1B	0.003	0.083	-9999	-0.64	5	5

×

FOXA2 and FOXA3 transcription factor networks

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
ACADVL	-0.22	0.36	-9999	-1.1	26	26
PCK1	-0.54	0.64	-9999	-1.4	110	110
HNF4A	-0.27	0.43	-9999	-1.2	29	29
KCNJ11	-0.32	0.49	-9999	-1.2	57	57
AKT1	-0.076	0.14	-9999	-10000	0	0
response to starvation	-0.003	0.023	-9999	-10000	0	0
DLK1	-0.45	0.58	-9999	-1.2	103	103
NKX2-1	-0.076	0.33	-9999	-0.83	29	29
ACADM	-0.22	0.36	-9999	-1.1	26	26
TAT	-0.15	0.23	-9999	-0.82	10	10
CEBPB	0.015	0.002	-9999	-10000	0	0
CEBPA	0.01	0.053	-9999	-0.64	2	2
TTR	-0.29	0.3	-9999	-0.85	40	40
PKLR	-0.26	0.41	-9999	-1	45	45
APOA1	-0.26	0.41	-9999	-1.2	23	23
CPT1C	-0.22	0.36	-9999	-1.1	26	26
ALAS1	-0.082	0.16	-9999	-10000	0	0
TFRC	-0.22	0.31	-9999	-0.86	33	33
FOXF1	0.014	0.11	-9999	-0.7	5	5
NF1	0.021	0	-9999	-10000	0	0
HNF1A (dimer)	-0.001	0.12	-9999	-0.8	6	6
CPT1A	-0.22	0.36	-9999	-1.1	27	27
HMGCS1	-0.22	0.36	-9999	-1.1	27	27
NR3C1	0.016	0.032	-9999	-10000	0	0
CPT1B	-0.22	0.38	-9999	-1.1	26	26
chromatin remodeling	0	0	-9999	-10000	0	0
SP1	0.013	0.026	-9999	-10000	0	0
GCK	-0.25	0.38	-9999	-1	36	36
CREB1	-0.041	0.086	-9999	-10000	0	0
IGFBP1	-0.11	0.22	-9999	-0.82	16	16
PDX1	-0.11	0.22	-9999	-0.79	14	14
UCP2	-0.22	0.37	-9999	-1.1	28	28
ALDOB	-0.25	0.4	-9999	-1.1	33	33
AFP	-0.21	0.24	-9999	-0.71	30	30
BDH1	-0.22	0.36	-9999	-1.1	25	25
HADH	-0.23	0.38	-9999	-1.1	26	26
F2	-0.28	0.43	-9999	-1.3	24	24
HNF1A	-0.001	0.12	-9999	-0.8	6	6
G6PC	-0.064	0.14	-9999	-10000	0	0
SLC2A2	-0.13	0.22	-9999	-0.83	3	3
INS	-0.005	0.035	-9999	-10000	0	0
FOXA1	-0.23	0.33	-9999	-0.65	111	111
FOXA3	-0.15	0.3	-9999	-0.9	34	34
FOXA2	-0.27	0.44	-9999	-1.2	33	33
ABCC8	-0.24	0.39	-9999	-1.1	29	29
ALB	-0.25	0.3	-9999	-0.8	51	51

×

BMP receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BMP7/BMPR2/BMPR1A-1B/FS	-0.24	0.28	-9999	-0.84	29	29
SMAD6-7/SMURF1	0	0	-9999	-10000	0	0
NOG	-0.062	0.22	-9999	-0.71	31	31
SMAD9	-0.07	0.16	-9999	-0.71	15	15
SMAD4	0.011	0.038	-9999	-0.64	1	1
SMAD5	-0.053	0.16	-9999	-0.52	18	18
BMP7/USAG1	-0.17	0.27	-9999	-0.55	94	94
SMAD5/SKI	-0.043	0.15	-9999	-0.51	14	14
SMAD1	0.041	0.029	-9999	-10000	0	0
BMP2	-0.016	0.15	-9999	-0.79	11	11
SMAD1/SMAD1/SMAD4	-0.001	0.017	-9999	-10000	0	0
BMPR1A	0.013	0	-9999	-10000	0	0
BMPR1B	-0.077	0.25	-9999	-0.77	35	35
BMPR1A-1B/BAMBI	-0.074	0.18	-9999	-0.54	33	33
AHSG	-0.041	0.2	-9999	-0.8	19	19
CER1	-0.007	0.092	-9999	-0.8	4	4
BMP2-4/CER1	-0.033	0.12	-9999	-0.49	20	20
BMP2-4/BMPR2/BMPR1A-1B/RGM/ENDOFIN/GADD34/PP1CA	-0.095	0.21	-9999	-0.59	30	30
BMP2-4 (homodimer)	-0.03	0.13	-9999	-0.56	16	16
RGMB	0.013	0	-9999	-10000	0	0
BMP6/BMPR2/BMPR1A-1B	-0.057	0.15	-9999	-0.48	30	30
RGMA	-0.071	0.22	-9999	-0.64	39	39
SMURF1	0.013	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/XIAP	-0.094	0.2	-9999	-0.54	31	31
BMP2-4/USAG1	-0.14	0.22	-9999	-0.45	97	97
SMAD6/SMURF1/SMAD5	-0.043	0.15	-9999	-0.51	14	14
SOSTDC1	-0.18	0.31	-9999	-0.67	85	85
BMP7/BMPR2/BMPR1A-1B	-0.078	0.17	-9999	-0.5	30	30
SKI	0.013	0	-9999	-10000	0	0
BMP6 (homodimer)	0.006	0.076	-9999	-0.75	3	3
HFE2	-0.17	0.29	-9999	-0.64	81	81
ZFYVE16	0.013	0	-9999	-10000	0	0
MAP3K7	0.013	0	-9999	-10000	0	0
BMP2-4/CHRD	-0.042	0.14	-9999	-0.51	25	25
SMAD5/SMAD5/SMAD4	-0.044	0.15	-9999	-0.52	15	15
MAPK1	0.013	0	-9999	-10000	0	0
TAK1/TAB family	-0.097	0.15	-9999	-0.57	15	15
BMP7 (homodimer)	-0.035	0.17	-9999	-0.65	22	22
NUP214	0.013	0	-9999	-10000	0	0
BMP6/FETUA	-0.044	0.16	-9999	-0.61	22	22
SMAD1/SKI	0.047	0.028	-9999	-10000	0	0
SMAD6	0.013	0	-9999	-10000	0	0
CTDSP2	0.013	0	-9999	-10000	0	0
BMP2-4/FETUA	-0.058	0.17	-9999	-0.52	34	34
MAP3K7IP1	0	0	-9999	-10000	0	0
GREM1	-0.41	0.41	-9999	-0.8	158	158
BMPR2 (homodimer)	0.013	0	-9999	-10000	0	0
GADD34/PP1CA	0	0	-9999	-10000	0	0
BMPR1A-1B (homodimer)	-0.068	0.19	-9999	-0.58	35	35
CHRDL1	-0.3	0.33	-9999	-0.64	143	143
ENDOFIN/SMAD1	0.047	0.028	-9999	-10000	0	0
SMAD6-7/SMURF1/SMAD1	-0.001	0.004	-9999	-10000	0	0
SMAD6/SMURF1	0.013	0	-9999	-10000	0	0
BAMBI	-0.012	0.13	-9999	-0.7	11	11
SMURF2	0.013	0	-9999	-10000	0	0
BMP2-4/CHRDL1	-0.21	0.23	-9999	-0.43	147	147
BMP2-4/GREM1	-0.3	0.29	-9999	-0.55	164	164
SMAD7	0.013	0	-9999	-10000	0	0
SMAD8A/SMAD8A/SMAD4	-0.04	0.16	-9999	-0.68	15	15
SMAD1/SMAD6	0.047	0.028	-9999	-10000	0	0
TAK1/SMAD6	0	0	-9999	-10000	0	0
BMP7	-0.035	0.17	-9999	-0.65	22	22
BMP6	0.006	0.076	-9999	-0.75	3	3
MAP3K7IP2	0	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/SMAD7/SMURF1	-0.075	0.17	-9999	-0.47	31	31
PPM1A	0.013	0	-9999	-10000	0	0
SMAD1/SMURF2	0.047	0.028	-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	0.013	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM/FS	-0.18	0.25	-9999	-0.56	69	69
CHRD	-0.013	0.14	-9999	-0.79	10	10
BMPR2	0.013	0	-9999	-10000	0	0
BMP2-4/BMPR2/BMPR1A-1B/RGM	-0.1	0.2	-9999	-0.57	31	31
BMP4	0.003	0.083	-9999	-0.64	5	5
FST	-0.29	0.4	-9999	-0.8	113	113
BMP2-4/NOG	-0.071	0.17	-9999	-0.46	47	47
BMP7/BMPR2/BMPR1A-1B/SMAD6/SMURF1	-0.073	0.16	-9999	-0.73	2	2

×

Effects of Botulinum toxin

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
STX1A	0	0.089	-9999	-0.62	6	6
UniProt:P19321	0	0	-9999	-10000	0	0
RIMS1/UNC13B	-0.066	0.16	-9999	-0.47	42	42
STXBP1	0.013	0	-9999	-10000	0	0
ACh/CHRNA1	-0.16	0.25	-9999	-0.51	98	98
RAB3GAP2/RIMS1/UNC13B	-0.055	0.14	-9999	-0.47	2	2
mol:Ca2+	0	0	-9999	-10000	0	0
UniProt:P30996	0	0	-9999	-10000	0	0
UniProt:Q60393	0	0	-9999	-10000	0	0
CST086	0	0	-9999	-10000	0	0
RIMS1	-0.08	0.22	-9999	-0.64	41	41
mol:ACh	0.002	0.032	-9999	-0.12	20	20
RAB3GAP2	0.013	0	-9999	-10000	0	0
STX1A/SNAP25/VAMP2	-0.052	0.11	-9999	-0.4	4	4
UniProt:P10844	0	0	-9999	-10000	0	0
muscle contraction	-0.16	0.25	-9999	-0.51	98	98
UNC13B	0.011	0.038	-9999	-0.64	1	1
CHRNA1	-0.23	0.35	-9999	-0.73	98	98
UniProt:P10845	0	0	-9999	-10000	0	0
ACh/Synaptotagmin 1	-0.15	0.26	-9999	-0.56	84	84
SNAP25	-0.006	0.064	-9999	-0.3	14	14
VAMP2	0.007	0	-9999	-10000	0	0
SYT1	-0.21	0.36	-9999	-0.79	84	84
UniProt:Q00496	0	0	-9999	-10000	0	0
STXIA/STXBP1	0.008	0.077	-9999	-0.54	6	6
STX1A/SNAP25 fragment 1/VAMP2	-0.052	0.11	-9999	-0.4	4	4

×

Glypican 1 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GPC1/FGF2 dimer/FGFR1 dimer	-0.021	0.096	-10000	0	-0.53	6	6
fibroblast growth factor receptor signaling pathway	-0.021	0.096	-10000	0	-0.53	6	6
LAMA1	-0.37	0.41	-10000	0	-0.8	143	143
PRNP	0.011	0.047	-10000	0	-0.8	1	1
GPC1/SLIT2	-0.035	0.13	-10000	0	-0.48	22	22
SMAD2	0.035	0.029	-10000	0	-0.48	1	1
GPC1/PrPc/Cu2+	-0.004	0.043	-10000	0	-0.54	2	2
GPC1/Laminin alpha1	-0.29	0.31	-10000	0	-0.61	143	143
TDGF1	0	0.081	-10000	0	-0.8	3	3
CRIPTO/GPC1	-0.008	0.07	-10000	0	-0.61	4	4
APP/GPC1	-0.002	0.035	-10000	0	-0.61	1	1
mol:NO	0	0	-10000	0	-10000	0	0
YES1	0.019	0.063	-10000	0	-0.53	4	4
FLT1	0.013	0	-10000	0	-10000	0	0
GPC1/TGFB/TGFBR1/TGFBR2	-0.002	0.03	-10000	0	-0.53	1	1
SERPINC1	0.007	0.066	-10000	0	-0.8	2	2
FYN	0.017	0.071	-10000	0	-0.53	5	5
FGR	0.017	0.071	-10000	0	-0.53	5	5
positive regulation of MAPKKK cascade	0.001	0.12	-10000	0	-0.44	10	10
SLIT2	-0.033	0.17	-10000	0	-0.65	21	21
GPC1/NRG	-0.12	0.25	-10000	0	-0.61	62	62
NRG1	-0.15	0.32	-10000	0	-0.8	61	61
GPC1/VEGF165 homodimer/VEGFR1 homodimer	-0.003	0.043	-10000	0	-0.53	2	2
LYN	0.019	0.063	-10000	0	-0.53	4	4
mol:Spermine	0.01	0.036	-10000	0	-0.62	1	1
cell growth	-0.021	0.096	-10000	0	-0.53	6	6
BMP signaling pathway	-0.011	0.047	0.8	1	-10000	0	1
SRC	0.019	0.063	-10000	0	-0.53	4	4
TGFBR1	0.013	0	-10000	0	-10000	0	0
mol:Cu2+	0	0	-10000	0	-10000	0	0
PLA2G2A	-0.4	0.32	-10000	0	-0.64	193	193
GPC1	0.011	0.047	-10000	0	-0.8	1	1
TGFBR1 (dimer)	0.013	0	-10000	0	-10000	0	0
VEGFA	0.011	0.047	-10000	0	-0.8	1	1
BLK	-0.075	0.21	-10000	0	-0.52	56	56
HCK	0.013	0.093	-10000	0	-0.56	7	7
FGF2	-0.012	0.13	-10000	0	-0.68	11	11
FGFR1	0.008	0.066	-10000	0	-0.8	2	2
VEGFR1 homodimer	0.013	0	-10000	0	-10000	0	0
TGFBR2	0.013	0	-10000	0	-10000	0	0
cell death	-0.002	0.035	-10000	0	-0.61	1	1
ATIII/GPC1	-0.006	0.061	-10000	0	-0.61	3	3
PLA2G2A/GPC1	-0.3	0.23	-10000	0	-0.47	194	194
LCK	0.001	0.12	-10000	0	-0.53	14	14
neuron differentiation	-0.12	0.24	-10000	0	-0.61	62	62
PrPc/Cu2+	-0.002	0.036	-10000	0	-0.62	1	1
APP	0.013	0	-10000	0	-10000	0	0
TGFBR2 (dimer)	0.013	0	-10000	0	-10000	0	0

×

Calcium signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC1	-0.013	0.036	-9999	-10000	0	0
NFATC2	-0.042	0.11	-9999	-0.46	19	19
NFATC3	-0.013	0.036	-9999	-10000	0	0
CD40LG	-0.33	0.36	-9999	-0.88	66	66
PTGS2	-0.34	0.37	-9999	-0.88	72	72
JUNB	0.013	0	-9999	-10000	0	0
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.016	0.015	-9999	-10000	0	0
CaM/Ca2+	-0.016	0.015	-9999	-10000	0	0
CALM1	0.004	0.011	-9999	-10000	0	0
JUN	0.005	0.011	-9999	-10000	0	0
mol:Ca2+	-0.017	0.014	-9999	-10000	0	0
Calcineurin A alpha-beta B1/FKBP12/FK506	-0.001	0.004	-9999	-10000	0	0
FOSL1	0.005	0.081	-9999	-0.8	3	3
CREM	0.013	0.001	-9999	-10000	0	0
Jun/NFAT1-c-4/p21SNFT	-0.14	0.15	-9999	-0.66	9	9
FOS	-0.1	0.24	-9999	-0.66	49	49
IFNG	-0.36	0.38	-9999	-0.91	71	71
AP-1/NFAT1-c-4	-0.39	0.37	-9999	-1.1	49	49
FASLG	-0.31	0.34	-9999	-0.87	55	55
NFAT1-c-4/ICER1	-0.085	0.11	-9999	-0.54	8	8
IL2RA	-0.33	0.37	-9999	-0.9	65	65
FKBP12/FK506	0	0	-9999	-10000	0	0
CSF2	-0.48	0.42	-9999	-0.82	157	157
JunB/Fra1/NFAT1-c-4	-0.081	0.11	-9999	-0.52	10	10
IL4	-0.3	0.31	-9999	-0.82	49	49
IL2	-0.012	0.042	-9999	-0.67	1	1
IL3	-0.028	0.023	-9999	-10000	0	0
FKBP1A	0.013	0	-9999	-10000	0	0
BATF3	0.005	0.081	-9999	-0.8	3	3
mol:FK506	0	0	-9999	-10000	0	0
POU2F1	0.014	0.002	-9999	-10000	0	0

×

Signaling events mediated by the Hedgehog family

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB2	-0.25	0.21	-10000	0	-0.91	2	2
IHH	-0.049	0.062	-10000	0	-0.76	1	1
SHH Np/Cholesterol/GAS1	-0.044	0.14	-10000	0	-0.48	28	28
LRPAP1	0.013	0	-10000	0	-10000	0	0
dorsoventral neural tube patterning	0.044	0.14	0.48	28	-10000	0	28
SMO/beta Arrestin2	-0.13	0.13	-10000	0	-0.53	8	8
SMO	-0.14	0.14	-10000	0	-0.57	8	8
AKT1	-0.051	0.071	-10000	0	-10000	0	0
ARRB2	0.013	0	-10000	0	-10000	0	0
BOC	-0.047	0.19	-10000	0	-0.64	28	28
ADRBK1	0.013	0	-10000	0	-10000	0	0
heart looping	-0.14	0.14	-10000	0	-0.56	8	8
STIL	-0.12	0.15	-10000	0	-0.58	18	18
DHH N/PTCH2	-0.025	0.11	-10000	0	-0.51	15	15
DHH N/PTCH1	-0.13	0.13	-10000	0	-0.57	6	6
PIK3CA	0.013	0	-10000	0	-10000	0	0
DHH	-0.004	0.11	-10000	0	-0.69	7	7
PTHLH	-0.43	0.32	-10000	0	-0.63	214	214
determination of left/right symmetry	-0.14	0.14	-10000	0	-0.56	8	8
PIK3R1	0.013	0	-10000	0	-10000	0	0
skeletal system development	-0.43	0.32	-10000	0	-0.63	214	214
IHH N/Hhip	-0.057	0.17	-10000	0	-0.67	22	22
DHH N/Hhip	-0.054	0.17	-10000	0	-0.58	28	28
mol:Cholesterol	0	0	-10000	0	-10000	0	0
heart development	-0.14	0.14	-10000	0	-0.56	8	8
pancreas development	-0.045	0.2	-10000	0	-0.79	21	21
HHAT	0.013	0	-10000	0	-10000	0	0
PI3K	0	0	-10000	0	-10000	0	0
EntrezGene:84976	0	0	-10000	0	-10000	0	0
GAS1	0.004	0.084	-10000	0	-0.72	4	4
somite specification	-0.14	0.14	-10000	0	-0.56	8	8
SHH Np/Cholesterol/PTCH1	-0.13	0.16	-10000	0	-0.62	17	17
SHH Np/Cholesterol/PTCH2	-0.049	0.15	-10000	0	-0.49	30	30
SHH Np/Cholesterol/Megalin	-0.061	0.18	-10000	0	-0.54	34	34
SHH	-0.03	0.17	-10000	0	-0.62	24	24
catabolic process	-0.15	0.13	-10000	0	-0.43	1	1
SMO/Vitamin D3	-0.14	0.16	-10000	0	-0.6	17	17
SHH Np/Cholesterol/Hhip	-0.071	0.2	-10000	0	-0.57	38	38
LRP2	-0.026	0.17	-10000	0	-0.8	14	14
receptor-mediated endocytosis	-0.16	0.15	-10000	0	-0.58	20	20
SHH Np/Cholesterol/BOC	-0.072	0.16	-10000	0	-0.43	51	51
SHH Np/Cholesterol/CDO	-0.043	0.14	-10000	0	-0.47	28	28
mesenchymal cell differentiation	0.071	0.2	0.56	38	-10000	0	38
mol:Vitamin D3	-0.13	0.16	-10000	0	-0.62	17	17
IHH N/PTCH2	-0.023	0.098	-10000	0	-0.57	9	9
CDON	0.005	0.075	-10000	0	-0.64	4	4
IHH N/PTCH1	-0.15	0.13	-10000	0	-10000	0	0
Megalin/LRPAP1	-0.028	0.13	-10000	0	-0.61	14	14
PTCH2	-0.005	0.11	-10000	0	-0.68	8	8
SHH Np/Cholesterol	-0.039	0.13	-10000	0	-0.5	24	24
PTCH1	-0.15	0.13	-10000	0	-10000	0	0
HHIP	-0.045	0.2	-10000	0	-0.8	21	21

×

Signaling events regulated by Ret tyrosine kinase

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	-0.041	0.058	-9999	-10000	0	0
Crk/p130 Cas/Paxillin	-0.1	0.14	-9999	-0.46	20	20
JUN	-0.059	0.16	-9999	-0.47	21	21
HRAS	0.013	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/GRB10	-0.17	0.26	-9999	-0.62	56	56
RAP1A	0.013	0	-9999	-10000	0	0
FRS2	0.005	0.081	-9999	-0.8	3	3
RAP1A/GDP	0	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/DOK1	-0.17	0.26	-9999	-0.61	55	55
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	-0.12	0.21	-9999	-0.44	83	83
RHOA	0.013	0	-9999	-10000	0	0
RAP1A/GTP	-0.15	0.23	-9999	-0.55	55	55
GRB7	0.003	0.089	-9999	-0.76	4	4
RET51/GFRalpha1/GDNF	-0.17	0.26	-9999	-0.61	55	55
MAPKKK cascade	-0.13	0.19	-9999	-0.64	20	20
BCAR1	0.013	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/IRS1	-0.12	0.21	-9999	-0.61	26	26
lamellipodium assembly	-0.093	0.14	-9999	-0.42	20	20
RET51/GFRalpha1/GDNF/SHC	-0.17	0.26	-9999	-0.61	55	55
PIK3CA	0.013	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/SHC	-0.12	0.21	-9999	-0.52	42	42
RET9/GFRalpha1/GDNF/Shank3	-0.12	0.21	-9999	-0.61	26	26
MAPK3	-0.11	0.24	-9999	-0.72	20	20
DOK1	0.013	0	-9999	-10000	0	0
DOK6	-0.001	0.1	-9999	-0.72	6	6
PXN	0.013	0	-9999	-10000	0	0
neurite development	-0.095	0.22	-9999	-0.66	20	20
DOK5	-0.008	0.12	-9999	-0.7	9	9
GFRA1	-0.12	0.27	-9999	-0.64	64	64
MAPK8	-0.071	0.17	-9999	-0.5	21	21
HRAS/GTP	-0.15	0.22	-9999	-0.74	20	20
tube development	-0.11	0.2	-9999	-0.57	26	26
MAPK1	-0.11	0.24	-9999	-0.72	20	20
RET9/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.059	0.16	-9999	-0.54	9	9
Rac1/GDP	0	0	-9999	-10000	0	0
SRC	0.013	0	-9999	-10000	0	0
PDLIM7	0.008	0.066	-9999	-0.8	2	2
RET51/GFRalpha1/GDNF/Dok6	-0.17	0.25	-9999	-0.58	59	59
SHC1	0.013	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/Dok4	-0.17	0.26	-9999	-0.61	55	55
RET51/GFRalpha1/GDNF/Dok5	-0.18	0.26	-9999	-0.61	62	62
PRKCA	0.011	0.047	-9999	-0.8	1	1
HRAS/GDP	0	0	-9999	-10000	0	0
CREB1	-0.072	0.17	-9999	-0.53	16	16
PIK3R1	0.013	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.056	0.15	-9999	-0.54	9	9
RET51/GFRalpha1/GDNF/Grb7	-0.18	0.26	-9999	-0.62	59	59
mol:GDP	0	0	-9999	-10000	0	0
RET	-0.079	0.26	-9999	-0.79	35	35
DOK4	0.013	0	-9999	-10000	0	0
JNK cascade	-0.057	0.16	-9999	-0.46	21	21
RET9/GFRalpha1/GDNF/FRS2	-0.12	0.21	-9999	-0.44	84	84
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	-0.056	0.15	-9999	-0.55	9	9
RET51/GFRalpha1/GDNF/FRS2/SHP2/Grb2	-0.085	0.18	-9999	-0.53	21	21
RET51/GFRalpha1/GDNF/DOK/RasGAP/NCK	-0.082	0.18	-9999	-0.53	20	20
RET51/GFRalpha1/GDNF/SHC/Grb2/SOS1	-0.085	0.19	-9999	-0.58	20	20
PI3K	-0.095	0.24	-9999	-0.69	20	20
SOS1	0.013	0	-9999	-10000	0	0
RET9/GFRalpha1/GDNF/Shank3/Grb2	-0.11	0.2	-9999	-0.57	26	26
GRB10	0.011	0.047	-9999	-0.8	1	1
activation of MAPKK activity	-0.08	0.18	-9999	-0.52	21	21
RET51/GFRalpha1/GDNF/FRS2	-0.17	0.26	-9999	-0.62	57	57
GAB1	0.013	0	-9999	-10000	0	0
IRS1	0.013	0	-9999	-10000	0	0
IRS2	0.009	0.053	-9999	-0.64	2	2
RET51/GFRalpha1/GDNF/SHC/GAB1/Grb2	-0.085	0.19	-9999	-0.58	20	20
RET51/GFRalpha1/GDNF/PKC alpha	-0.17	0.26	-9999	-0.61	56	56
GRB2	0.013	0	-9999	-10000	0	0
PRKACA	0.013	0	-9999	-10000	0	0
GDNF	-0.058	0.23	-9999	-0.8	26	26
RAC1	0.013	0	-9999	-10000	0	0
RET51/GFRalpha1/GDNF/IRS1	-0.17	0.26	-9999	-0.61	55	55
Rac1/GTP	-0.11	0.16	-9999	-0.52	20	20
RET9/GFRalpha1/GDNF	-0.13	0.23	-9999	-0.49	81	81
GFRalpha1/GDNF	-0.15	0.26	-9999	-0.56	81	81

×

TCR signaling in naïve CD8+ T cells

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
GRB2/SOS1/SHC	-0.067	0.16	-10000	0	-0.58	22	22
FYN	-0.043	0.24	-10000	0	-0.71	28	28
LAT/GRAP2/SLP76	-0.052	0.2	-10000	0	-0.66	23	23
IKBKB	0.013	0	-10000	0	-10000	0	0
AKT1	-0.013	0.16	-10000	0	-0.47	25	25
B2M	0.013	0.005	-10000	0	-10000	0	0
IKBKG	-0.02	0.045	-10000	0	-0.18	3	3
MAP3K8	0.013	0	-10000	0	-10000	0	0
mol:Ca2+	-0.047	0.047	-10000	0	-0.12	28	28
integrin-mediated signaling pathway	-0.001	0.023	-10000	0	-0.4	1	1
LAT/GRAP2/SLP76/VAV1/PI3K Class IA	-0.039	0.24	-10000	0	-0.68	29	29
TRPV6	-0.33	0.33	-10000	0	-0.65	153	153
CD28	-0.032	0.18	-10000	0	-0.79	17	17
SHC1	-0.045	0.24	-10000	0	-0.71	28	28
receptor internalization	-0.042	0.25	-10000	0	-0.7	31	31
PRF1	-0.059	0.29	-10000	0	-0.86	30	30
KRAS	0.013	0	-10000	0	-10000	0	0
GRB2	0.013	0	-10000	0	-10000	0	0
COT/AKT1	0	0.13	-10000	0	-0.39	17	17
LAT	-0.051	0.26	-10000	0	-0.78	28	28
EntrezGene:6955	-0.001	0.005	-10000	0	-10000	0	0
CD3D	0.001	0.093	-10000	0	-0.71	5	5
CD3E	-0.007	0.13	-10000	0	-0.77	8	8
CD3G	-0.031	0.18	-10000	0	-0.74	18	18
RASGRP2	0.005	0.024	-10000	0	-0.12	5	5
RASGRP1	-0.008	0.18	-10000	0	-0.5	26	26
HLA-A	0.008	0.06	-10000	0	-0.72	2	2
RASSF5	0.011	0.038	-10000	0	-0.64	1	1
RAP1A/GTP/RAPL	-0.001	0.023	-10000	0	-0.4	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
mol:GDP	0.025	0.058	-10000	0	-0.13	16	16
PDK1/CARD11/BCL10/MALT1/TRAF6	-0.04	0.078	-10000	0	-0.28	10	10
PRKCA	-0.011	0.097	-10000	0	-0.3	16	16
GRAP2	-0.007	0.12	-10000	0	-0.74	8	8
mol:IP3	0.05	0.2	0.24	116	-0.49	17	133
EntrezGene:6957	0	0.005	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.039	0.24	-10000	0	-0.64	31	31
ORAI1	0.17	0.17	0.34	153	-10000	0	153
CSK	-0.048	0.25	-10000	0	-0.72	28	28
B7 family/CD28	-0.19	0.29	-10000	0	-0.78	43	43
CHUK	0.013	0	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8/LCK/ZAP-70	-0.065	0.28	-10000	0	-0.85	28	28
PTPN6	-0.053	0.25	-10000	0	-0.73	28	28
VAV1	-0.048	0.25	-10000	0	-0.72	29	29
Monovalent TCR/CD3	-0.025	0.18	-10000	0	-0.58	23	23
CBL	0.013	0	-10000	0	-10000	0	0
LCK	-0.052	0.26	-10000	0	-0.76	28	28
PAG1	-0.05	0.25	-10000	0	-0.7	30	30
RAP1A	0.013	0	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8/LCK	-0.068	0.28	-10000	0	-0.82	29	29
CD80	-0.24	0.38	-10000	0	-0.8	93	93
CD86	0.01	0.047	-10000	0	-0.8	1	1
PDK1/CARD11/BCL10/MALT1	-0.048	0.095	-10000	0	-0.32	14	14
HRAS	0.013	0	-10000	0	-10000	0	0
GO:0035030	-0.11	0.26	-10000	0	-0.62	43	43
CD8A	-0.059	0.23	-10000	0	-0.75	29	29
CD8B	-0.067	0.24	-10000	0	-0.76	32	32
PTPRC	-0.013	0.14	-10000	0	-0.74	10	10
PDK1/PKC theta	-0.015	0.2	-10000	0	-0.6	24	24
CSK/PAG1	-0.044	0.24	-10000	0	-0.71	27	27
SOS1	0.013	0	-10000	0	-10000	0	0
peptide-MHC class I	0.01	0.047	-10000	0	-0.54	2	2
GRAP2/SLP76	-0.066	0.23	-10000	0	-0.69	28	28
STIM1	0.09	0.086	-10000	0	-10000	0	0
RAS family/GTP	0.024	0.074	-10000	0	-0.19	6	6
TCR/CD3/MHC I/CD8/LCK/ZAP-70/CBL/ubiquitin	-0.049	0.28	-10000	0	-0.77	31	31
mol:DAG	-0.009	0.14	-10000	0	-0.43	20	20
RAP1A/GDP	0.012	0.025	-10000	0	-10000	0	0
PLCG1	0.013	0	-10000	0	-10000	0	0
CD247	-0.023	0.17	-10000	0	-0.78	14	14
cytotoxic T cell degranulation	-0.054	0.28	-10000	0	-0.81	30	30
RAP1A/GTP	-0.002	0.006	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	-0.025	0.2	-10000	0	-0.54	29	29
LAT/GRAP2/SLP76/VAV1/PLCgamma1	0.034	0.24	0.27	74	-0.64	20	94
NRAS	0.013	0	-10000	0	-10000	0	0
ZAP70	-0.022	0.16	-10000	0	-0.75	14	14
GRB2/SOS1	0	0	-10000	0	-10000	0	0
LAT/GRAP2/SLP76/VAV1	-0.046	0.2	-10000	0	-0.62	24	24
MALT1	0.013	0	-10000	0	-10000	0	0
TRAF6	0.013	0	-10000	0	-10000	0	0
CD8 heterodimer	-0.094	0.29	-10000	0	-0.78	42	42
CARD11	-0.047	0.21	-10000	0	-0.79	23	23
PRKCB	-0.014	0.11	-10000	0	-0.36	17	17
PRKCE	-0.009	0.096	-10000	0	-0.31	15	15
PRKCQ	-0.029	0.23	-10000	0	-0.69	25	25
LCP2	0.005	0.081	-10000	0	-0.8	3	3
BCL10	0.013	0	-10000	0	-10000	0	0
regulation of survival gene product expression	-0.007	0.14	-10000	0	-0.39	25	25
IKK complex	0.032	0.054	-10000	0	-0.13	5	5
RAS family/GDP	-0.003	0.008	-10000	0	-10000	0	0
MAP3K14	0.01	0.1	-10000	0	-0.3	12	12
PDPK1	-0.009	0.16	-10000	0	-0.46	21	21
TCR/CD3/MHC I/CD8/Fyn	-0.054	0.28	-10000	0	-0.82	29	29

×

Neurotrophic factor-mediated Trk receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.011	0.047	-10000	0	-0.8	1	1
RAS family/GTP/Tiam1	-0.092	0.11	-10000	0	-0.46	2	2
NT3 (dimer)/TRKC	-0.25	0.3	-10000	0	-0.56	133	133
NT3 (dimer)/TRKB	-0.25	0.3	-10000	0	-0.53	141	141
SHC/Grb2/SOS1/GAB1/PI3K	0.04	0	-10000	0	-10000	0	0
RAPGEF1	0.013	0	-10000	0	-10000	0	0
BDNF	-0.042	0.2	-10000	0	-0.72	23	23
PIK3CA	0.013	0	-10000	0	-10000	0	0
DYNLT1	0.013	0	-10000	0	-10000	0	0
NTRK1	-0.062	0.24	-10000	0	-0.8	28	28
NTRK2	-0.17	0.31	-10000	0	-0.68	80	80
NTRK3	-0.14	0.28	-10000	0	-0.64	73	73
NT-4/5 (dimer)/TRKB	-0.14	0.22	-10000	0	-0.45	90	90
neuron apoptosis	0.12	0.13	0.46	10	-10000	0	10
SHC 2-3/Grb2	-0.12	0.14	-10000	0	-0.51	10	10
SHC1	0.013	0	-10000	0	-10000	0	0
SHC2	-0.11	0.13	0.22	1	-0.4	31	32
SHC3	-0.12	0.14	-10000	0	-0.41	35	35
STAT3 (dimer)	0.014	0.054	-10000	0	-10000	0	0
NT3 (dimer)/TRKA	-0.19	0.25	-10000	0	-0.47	121	121
RIN/GDP	-0.053	0.11	-10000	0	-0.29	3	3
GIPC1	0.013	0	-10000	0	-10000	0	0
KRAS	0.013	0	-10000	0	-10000	0	0
DNAJA3	-0.088	0.13	0.26	1	-0.47	6	7
RIN/GTP	0	0	-10000	0	-10000	0	0
CCND1	0.014	0.12	-10000	0	-0.8	7	7
MAGED1	0.011	0.038	-10000	0	-0.64	1	1
PTPN11	0.013	0	-10000	0	-10000	0	0
RICS	0	0	-10000	0	-10000	0	0
NT-4/5 (dimer)	0.013	0.001	-10000	0	-10000	0	0
SHC/GRB2/SOS1	0	0	-10000	0	-10000	0	0
GRB2	0.013	0	-10000	0	-10000	0	0
NGF (dimer)/TRKA/MATK	-0.18	0.27	-10000	0	-0.57	92	92
TRKA/NEDD4-2	-0.057	0.18	-10000	0	-0.61	28	28
ELMO1	0.013	0	-10000	0	-10000	0	0
RhoG/GTP/ELMO1/DOCK1	0	0	-10000	0	-10000	0	0
NGF	-0.16	0.34	-10000	0	-0.8	66	66
HRAS	0.013	0	-10000	0	-10000	0	0
DOCK1	0.013	0	-10000	0	-10000	0	0
GAB2	0.009	0.053	-10000	0	-0.64	2	2
RIT2	0.001	0.003	-10000	0	-10000	0	0
RIT1	0.013	0	-10000	0	-10000	0	0
FRS2	0.005	0.081	-10000	0	-0.8	3	3
DNM1	-0.043	0.21	-10000	0	-0.8	21	21
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	-0.085	0.13	0.25	1	-0.46	6	7
mol:GDP	-0.079	0.15	-10000	0	-0.42	9	9
NGF (dimer)	-0.16	0.33	-10000	0	-0.8	66	66
RhoG/GDP	0	0	-10000	0	-10000	0	0
RIT1/GDP	-0.047	0.11	-10000	0	-0.28	3	3
TIAM1	0.007	0.065	-10000	0	-0.64	3	3
PIK3R1	0.013	0	-10000	0	-10000	0	0
BDNF (dimer)/TRKB	-0.15	0.22	-10000	0	-0.57	31	31
KIDINS220/CRKL/C3G	-0.002	0.035	-10000	0	-0.61	1	1
SHC/RasGAP	0	0	-10000	0	-10000	0	0
FRS2 family/SHP2	-0.005	0.052	-10000	0	-0.53	3	3
SHC/GRB2/SOS1/GAB1	0	0	-10000	0	-10000	0	0
RIT1/GTP	0	0	-10000	0	-10000	0	0
NT3 (dimer)	-0.18	0.3	-10000	0	-0.64	90	90
RAP1/GDP	-0.06	0.072	-10000	0	-0.37	1	1
KIDINS220/CRKL	0.011	0.047	-10000	0	-0.8	1	1
BDNF (dimer)	-0.042	0.2	-10000	0	-0.72	23	23
ubiquitin-dependent protein catabolic process	-0.16	0.26	-10000	0	-0.56	86	86
Schwann cell development	-0.051	0.038	-10000	0	-10000	0	0
EHD4	0.013	0	-10000	0	-10000	0	0
FRS2 family/GRB2/SOS1	-0.005	0.047	-10000	0	-0.48	3	3
FRS2 family/SHP2/CRK family/C3G/GAB2	0.039	0.035	-10000	0	-10000	0	0
RAP1B	0.011	0.047	-10000	0	-0.8	1	1
RAP1A	0.013	0	-10000	0	-10000	0	0
CDC42/GTP	-0.28	0.3	-10000	0	-0.7	85	85
ABL1	0.013	0	-10000	0	-10000	0	0
SH2B family/GRB2/SOS1	0	0	-10000	0	-10000	0	0
Rap1/GTP	-0.05	0.077	-10000	0	-0.57	1	1
STAT3	0.014	0.054	-10000	0	-10000	0	0
axon guidance	-0.26	0.28	-10000	0	-0.66	85	85
MAPK3	-0.13	0.26	-10000	0	-0.52	92	92
MAPK1	-0.13	0.26	-10000	0	-0.52	92	92
CDC42/GDP	-0.047	0.11	-10000	0	-0.29	2	2
NTF3	-0.18	0.3	-10000	0	-0.64	90	90
NTF4	0.013	0.001	-10000	0	-10000	0	0
NGF (dimer)/TRKA/FAIM	-0.16	0.26	-10000	0	-0.56	86	86
PI3K	0	0	-10000	0	-10000	0	0
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	-0.19	0.23	0.26	1	-0.54	70	71
SOS1	0.013	0	-10000	0	-10000	0	0
MCF2L	-0.21	0.3	-10000	0	-0.51	135	135
RGS19	0.013	0	-10000	0	-10000	0	0
CDC42	0.013	0	-10000	0	-10000	0	0
RAS family/GTP	-0.007	0.087	-10000	0	-10000	0	0
Rac1/GDP	-0.047	0.11	-10000	0	-0.28	3	3
NGF (dimer)/TRKA/GRIT	-0.16	0.27	-10000	0	-0.57	88	88
neuron projection morphogenesis	-0.051	0.13	-10000	0	-0.54	1	1
NGF (dimer)/TRKA/NEDD4-2	-0.16	0.26	-10000	0	-0.56	86	86
MAP2K1	0.043	0	-10000	0	-10000	0	0
NGFR	-0.023	0.16	-10000	0	-0.73	15	15
NGF (dimer)/TRKA/GIPC/GAIP	-0.07	0.16	-10000	0	-0.55	9	9
RAS family/GTP/PI3K	0.034	0	-10000	0	-10000	0	0
FRS2 family/SHP2/GRB2/SOS1	-0.004	0.044	-10000	0	-0.45	3	3
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	0.011	0.038	-10000	0	-0.64	1	1
MAPKKK cascade	-0.09	0.14	-10000	0	-0.48	8	8
RASA1	0.013	0	-10000	0	-10000	0	0
TRKA/c-Abl	-0.057	0.18	-10000	0	-0.61	28	28
SQSTM1	0.013	0	-10000	0	-10000	0	0
BDNF (dimer)/TRKB/GIPC	-0.13	0.2	-10000	0	-0.52	31	31
NGF (dimer)/TRKA/p62/Atypical PKCs	-0.14	0.22	-10000	0	-0.9	6	6
MATK	-0.008	0.13	-10000	0	-0.8	8	8
NEDD4L	0.013	0	-10000	0	-10000	0	0
RAS family/GDP	-0.056	0.067	-10000	0	-10000	0	0
NGF (dimer)/TRKA	-0.095	0.14	0.28	1	-0.39	21	22
Rac1/GTP	-0.13	0.13	-10000	0	-0.36	50	50
FRS2 family/SHP2/CRK family	-0.006	0.051	-10000	0	-0.45	4	4

×

IL12-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IL12/IL12R/TYK2/JAK2/SOCS1	-0.099	0.24	-10000	0	-0.6	39	39
TBX21	-0.13	0.45	-10000	0	-1.3	29	29
B2M	0.011	0.01	-10000	0	-10000	0	0
TYK2	0.018	0.02	-10000	0	-10000	0	0
IL12RB1	-0.068	0.26	-10000	0	-0.82	32	32
GADD45B	-0.047	0.29	-10000	0	-0.85	12	12
IL12RB2	-0.15	0.33	-10000	0	-0.79	63	63
GADD45G	-0.063	0.32	-10000	0	-0.94	17	17
natural killer cell activation	0.008	0.024	-10000	0	-10000	0	0
RELB	0.008	0.066	-10000	0	-0.8	2	2
RELA	0.013	0	-10000	0	-10000	0	0
IL18	-0.005	0.12	-10000	0	-0.64	10	10
IL2RA	-0.086	0.27	-10000	0	-0.8	37	37
IFNG	-0.15	0.32	-10000	0	-0.8	59	59
STAT3 (dimer)	-0.073	0.32	-10000	0	-0.82	29	29
HLA-DRB5	-0.015	0.14	-10000	0	-0.75	11	11
FASLG	-0.13	0.46	-10000	0	-1.2	33	33
NF kappa B2 p52/RelB	-0.19	0.35	-10000	0	-1	34	34
CD4	0.007	0.06	-10000	0	-0.72	2	2
SOCS1	-0.054	0.22	-10000	0	-0.8	25	25
EntrezGene:6955	-0.006	0.017	-10000	0	-10000	0	0
CD3D	-0.002	0.093	-10000	0	-0.71	5	5
CD3E	-0.011	0.13	-10000	0	-0.77	8	8
CD3G	-0.035	0.18	-10000	0	-0.74	18	18
IL12Rbeta2/JAK2	-0.099	0.26	-10000	0	-0.6	63	63
CCL3	-0.12	0.43	-10000	0	-1.2	31	31
CCL4	-0.12	0.43	-10000	0	-1.2	29	29
HLA-A	0.006	0.06	-10000	0	-0.72	2	2
IL18/IL18R	0.03	0.13	-10000	0	-0.49	13	13
NOS2	-0.13	0.43	-10000	0	-1.1	34	34
IL12/IL12R/TYK2/JAK2/SPHK2	-0.075	0.22	-10000	0	-0.59	30	30
IL1R1	-0.1	0.4	-10000	0	-1.1	26	26
IL4	-0.006	0.024	-10000	0	-10000	0	0
JAK2	0.018	0.02	-10000	0	-10000	0	0
EntrezGene:6957	-0.006	0.016	-10000	0	-10000	0	0
TCR/CD3/MHC I/CD8	-0.11	0.35	-10000	0	-0.83	44	44
RAB7A	-0.026	0.27	-10000	0	-0.75	8	8
lysosomal transport	-0.022	0.26	-10000	0	-0.71	8	8
FOS	-0.21	0.52	-10000	0	-1.2	56	56
STAT4 (dimer)	-0.071	0.35	-10000	0	-0.91	27	27
STAT5A (dimer)	-0.26	0.41	-10000	0	-1.1	49	49
GZMA	-0.14	0.48	-10000	0	-1.3	37	37
GZMB	-0.15	0.47	-10000	0	-1.2	41	41
HLX	0.008	0.066	-10000	0	-0.8	2	2
LCK	-0.14	0.46	-10000	0	-1.2	34	34
TCR/CD3/MHC II/CD4	-0.044	0.21	-10000	0	-0.67	19	19
IL2/IL2R	-0.086	0.22	-10000	0	-0.57	45	45
MAPK14	-0.048	0.31	-10000	0	-0.83	17	17
CCR5	-0.07	0.35	-10000	0	-1.1	17	17
IL1B	-0.059	0.24	-10000	0	-0.79	29	29
STAT6	-0.007	0.12	-10000	0	-10000	0	0
STAT4	-0.002	0.11	-10000	0	-0.78	6	6
STAT3	0.013	0	-10000	0	-10000	0	0
STAT1	-0.048	0.22	-10000	0	-0.8	23	23
NFKB1	0.013	0	-10000	0	-10000	0	0
NFKB2	0.013	0	-10000	0	-10000	0	0
IL12B	-0.07	0.26	-10000	0	-0.81	33	33
CD8A	-0.062	0.23	-10000	0	-0.76	29	29
CD8B	-0.071	0.24	-10000	0	-0.77	32	32
T-helper 1 cell differentiation	0	0	-10000	0	-10000	0	0
natural killer cell mediated cytotoxicity	0.098	0.24	0.59	39	-10000	0	39
IL2RB	-0.003	0.11	-10000	0	-0.8	6	6
proteasomal ubiquitin-dependent protein catabolic process	-0.06	0.32	-10000	0	-0.82	27	27
IL2RG	-0.016	0.15	-10000	0	-0.79	11	11
IL12	-0.055	0.22	-10000	0	-0.59	43	43
STAT5A	0.013	0	-10000	0	-10000	0	0
CD247	-0.026	0.17	-10000	0	-0.78	14	14
IL2	0.002	0.047	-10000	0	-0.8	1	1
SPHK2	0.013	0	-10000	0	-10000	0	0
FRAP1	0	0	-10000	0	-10000	0	0
IL12A	-0.004	0.12	-10000	0	-0.64	10	10
IL12/IL12R/TYK2/JAK2	-0.15	0.51	-10000	0	-1.3	34	34
MAP2K3	-0.049	0.3	-10000	0	-0.81	18	18
RIPK2	0.013	0	-10000	0	-10000	0	0
MAP2K6	-0.059	0.32	-10000	0	-0.84	20	20
regulation of dendritic cell antigen processing and presentation	0	0	-10000	0	-10000	0	0
HLA-DRA	0.008	0.053	-10000	0	-0.64	2	2
IL18RAP	-0.002	0.12	-10000	0	-0.71	8	8
IL12Rbeta1/TYK2	-0.041	0.21	-10000	0	-0.63	32	32
EOMES	-0.098	0.27	-10000	0	-0.65	53	53
STAT1 (dimer)	-0.13	0.38	-10000	0	-0.9	39	39
T cell proliferation	-0.018	0.26	0.48	1	-0.65	17	18
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
IL18R1	0.012	0.062	-10000	0	-0.74	2	2
CD8-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.14	0.22	-10000	0	-0.73	18	18
ATF2	-0.036	0.29	-10000	0	-0.8	13	13

×

Calcineurin-regulated NFAT-dependent transcription in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
FOXP3	-0.14	0.35	-10000	0	-0.92	50	50
NFATC2	-0.011	0.21	-10000	0	-0.88	11	11
NFATC3	-0.011	0.06	-10000	0	-10000	0	0
CD40LG	-0.36	0.44	-10000	0	-1.1	44	44
ITCH	0.015	0.098	-10000	0	-10000	0	0
CBLB	0.015	0.098	-10000	0	-10000	0	0
CD4-positive CD25-positive alpha-beta regulatory T cell lineage commitment	-0.33	0.46	-10000	0	-1.2	57	57
JUNB	0.013	0	-10000	0	-10000	0	0
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.039	0.1	-10000	0	-10000	0	0
T cell anergy	-0.004	0.16	-10000	0	-0.46	10	10
TLE4	0.011	0.17	-10000	0	-0.79	8	8
Jun/NFAT1-c-4/p21SNFT	-0.15	0.24	-10000	0	-1	11	11
AP-1/NFAT1-c-4	-0.38	0.44	-10000	0	-1.2	46	46
IKZF1	-0.001	0.21	-10000	0	-0.89	12	12
T-helper 2 cell differentiation	-0.04	0.21	-10000	0	-0.83	13	13
AP-1/NFAT1	-0.14	0.2	-10000	0	-0.67	22	22
CALM1	0.005	0.063	-10000	0	-10000	0	0
EGR2	-0.048	0.32	-10000	0	-1.5	10	10
EGR3	-0.03	0.25	-10000	0	-1.2	8	8
NFAT1/FOXP3	-0.14	0.36	-10000	0	-0.82	57	57
EGR1	-0.01	0.12	-10000	0	-0.64	11	11
JUN	-0.018	0.035	-10000	0	-10000	0	0
EGR4	-0.08	0.26	-10000	0	-0.79	35	35
mol:Ca2+	-0.01	0.068	-10000	0	-10000	0	0
GBP3	-0.016	0.23	-10000	0	-0.8	20	20
FOSL1	0.005	0.081	-10000	0	-0.8	3	3
NFAT1-c-4/MAF/IRF4	-0.12	0.27	-10000	0	-1.1	11	11
DGKA	0.012	0.16	-10000	0	-0.74	8	8
CREM	0.013	0.001	-10000	0	-10000	0	0
NFAT1-c-4/PPARG	-0.22	0.3	-10000	0	-1.1	16	16
CTLA4	-0.16	0.42	-10000	0	-1.1	44	44
NFAT1-c-4 (dimer)/EGR1	-0.097	0.25	-10000	0	-1	13	13
NFAT1-c-4 (dimer)/EGR4	-0.14	0.28	-10000	0	-1	14	14
FOS	-0.13	0.24	-10000	0	-0.67	49	49
IFNG	-0.19	0.32	-10000	0	-0.87	37	37
T cell activation	-0.094	0.21	-10000	0	-0.84	6	6
MAF	0.009	0.053	-10000	0	-0.64	2	2
T-helper 2 cell lineage commitment	0	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	0.025	0.16	0.74	6	-10000	0	6
TNF	-0.11	0.31	-10000	0	-1	16	16
FASLG	-0.096	0.37	-10000	0	-1.3	18	18
TBX21	-0.042	0.19	-10000	0	-0.8	17	17
BATF3	0.005	0.081	-10000	0	-0.8	3	3
PRKCQ	-0.001	0.1	-10000	0	-0.72	6	6
PTPN1	0.012	0.16	-10000	0	-0.74	8	8
NFAT1-c-4/ICER1	-0.084	0.23	-10000	0	-1.1	9	9
GATA3	-0.012	0.14	-10000	0	-0.77	10	10
T-helper 1 cell differentiation	-0.18	0.33	-10000	0	-0.85	37	37
IL2RA	-0.3	0.4	-10000	0	-1	58	58
T-helper 1 cell lineage commitment	0	0	-10000	0	-10000	0	0
CASP3	0.012	0.16	-10000	0	-0.74	8	8
E2F1	-0.025	0.19	-10000	0	-0.8	17	17
PPARG	-0.24	0.32	-10000	0	-0.64	116	116
SLC3A2	0.012	0.16	-10000	0	-0.74	8	8
IRF4	-0.059	0.23	-10000	0	-0.77	28	28
PTGS2	-0.37	0.46	-10000	0	-1.2	52	52
CSF2	-0.52	0.51	-10000	0	-1.1	109	109
JunB/Fra1/NFAT1-c-4	-0.078	0.22	-10000	0	-1.1	8	8
IL4	-0.043	0.22	-10000	0	-0.88	13	13
IL5	-0.33	0.39	-10000	0	-1.1	35	35
IL2	-0.096	0.21	-10000	0	-0.86	6	6
IL3	-0.062	0.051	-10000	0	-10000	0	0
RNF128	-0.048	0.26	-10000	0	-0.7	40	40
NFATC1	-0.025	0.16	-10000	0	-0.76	5	5
CDK4	0.008	0.15	0.67	2	-10000	0	2
PTPRK	0.012	0.16	-10000	0	-0.74	8	8
IL8	-0.4	0.47	-10000	0	-1.1	74	74
POU2F1	0.014	0.002	-10000	0	-10000	0	0

×

Coregulation of Androgen receptor activity

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NRIP1	-0.001	0.046	-9999	-0.64	1	1
SVIL	0.002	0.024	-9999	-10000	0	0
ZNF318	0.04	0.064	-9999	-10000	0	0
JMJD2C	0.006	0.027	-9999	-0.12	11	11
T-DHT/AR/Ubc9	-0.1	0.18	-9999	-0.46	57	57
CARM1	0.012	0.004	-9999	-10000	0	0
PRDX1	0.015	0.004	-9999	-10000	0	0
PELP1	0.018	0.01	-9999	-10000	0	0
CTNNB1	0.003	0.042	-9999	-0.64	1	1
AKT1	0.022	0.018	-9999	-10000	0	0
PTK2B	0.006	0.016	-9999	-10000	0	0
MED1	0.02	0.051	-9999	-0.8	1	1
MAK	0.028	0.11	-9999	-0.67	5	5
response to oxidative stress	0.002	0.005	-9999	-10000	0	0
HIP1	0.002	0.024	-9999	-10000	0	0
GSN	0.001	0.027	-9999	-10000	0	0
NCOA2	0.003	0.075	-9999	-0.64	4	4
NCOA6	0.003	0.023	-9999	-10000	0	0
DNA-PK	0.033	0.068	-9999	-10000	0	0
NCOA4	0.011	0.005	-9999	-10000	0	0
PIAS3	0.005	0.019	-9999	-10000	0	0
cell proliferation	-0.011	0.12	-9999	-0.77	5	5
XRCC5	0.02	0.014	-9999	-10000	0	0
UBE3A	-0.004	0.039	-9999	-10000	0	0
T-DHT/AR/SNURF	-0.11	0.2	-9999	-0.48	63	63
FHL2	-0.024	0.12	-9999	-1	2	2
RANBP9	0.003	0.023	-9999	-10000	0	0
JMJD1A	-0.06	0.077	-9999	-0.14	147	147
CDK6	0.001	0.1	-9999	-0.8	5	5
TGFB1I1	-0.019	0.13	-9999	-0.81	8	8
T-DHT/AR/CyclinD1	-0.12	0.2	-9999	-0.49	61	61
XRCC6	0.02	0.014	-9999	-10000	0	0
T-DHT/AR	-0.12	0.21	-9999	-0.5	57	57
CTDSP1	0.011	0.005	-9999	-10000	0	0
CTDSP2	0.033	0.043	-9999	-10000	0	0
BRCA1	0.002	0.024	-9999	-10000	0	0
TCF4	0.028	0.031	-9999	-10000	0	0
CDKN2A	-0.3	0.39	-9999	-0.76	124	124
SRF	0.03	0.024	-9999	-10000	0	0
NKX3-1	-0.13	0.14	-9999	-0.82	2	2
KLK3	-0.25	0.57	-9999	-1.4	57	57
TMF1	0.011	0.005	-9999	-10000	0	0
HNRNPA1	0.025	0.026	-9999	-10000	0	0
AOF2	-0.013	0.028	-9999	-0.071	55	55
APPL1	0.042	0.038	-9999	-10000	0	0
T-DHT/AR/Caspase 8	-0.094	0.18	-9999	-0.46	57	57
AR	-0.14	0.27	-9999	-0.68	57	57
UBA3	0.011	0.005	-9999	-10000	0	0
PATZ1	0.025	0.026	-9999	-10000	0	0
PAWR	0.011	0.005	-9999	-10000	0	0
PRKDC	0.02	0.014	-9999	-10000	0	0
PA2G4	0.026	0.029	-9999	-10000	0	0
UBE2I	0.013	0	-9999	-10000	0	0
T-DHT/AR/Cyclin D3/CDK11 p58	-0.081	0.17	-9999	-0.42	57	57
RPS6KA3	0.001	0.027	-9999	-10000	0	0
T-DHT/AR/ARA70	-0.1	0.18	-9999	-0.46	57	57
LATS2	0.024	0.023	-9999	-10000	0	0
T-DHT/AR/PRX1	-0.077	0.17	-9999	-0.42	54	54
Cyclin D3/CDK11 p58	0	0	-9999	-10000	0	0
VAV3	-0.041	0.17	-9999	-0.65	21	21
KLK2	-0.08	0.19	-9999	-0.97	11	11
CASP8	0.017	0.008	-9999	-10000	0	0
T-DHT/AR/TIF2/CARM1	-0.093	0.18	-9999	-0.47	40	40
TMPRSS2	-0.52	0.52	-9999	-1.1	145	145
CCND1	-0.007	0.11	-9999	-0.72	7	7
PIAS1	-0.004	0.039	-9999	-10000	0	0
mol:T-DHT	-0.026	0.037	-9999	-0.069	116	116
CDC2L1	0.001	0.002	-9999	-10000	0	0
PIAS4	-0.014	0.059	-9999	-10000	0	0
T-DHT/AR/CDK6	-0.11	0.19	-9999	-0.47	61	61
CMTM2	-0.014	0.15	-9999	-0.8	11	11
SNURF	-0.007	0.11	-9999	-0.64	9	9
ZMIZ1	-0.007	0.031	-9999	-10000	0	0
CCND3	0.014	0.002	-9999	-10000	0	0
TGIF1	0.025	0.026	-9999	-10000	0	0
FKBP4	0.003	0.023	-9999	-10000	0	0

×

Glucocorticoid receptor regulatory network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PCK2	0.013	0.061	0.34	1	-10000	0	1
SMARCC2	0.015	0.003	-10000	0	-10000	0	0
SMARCC1	0.015	0.003	-10000	0	-10000	0	0
TBX21	-0.089	0.23	-10000	0	-0.84	21	21
SUMO2	0.014	0.007	-10000	0	-10000	0	0
STAT1 (dimer)	-0.039	0.21	-10000	0	-0.78	23	23
FKBP4	0.013	0	-10000	0	-10000	0	0
FKBP5	0.009	0.053	-10000	0	-0.64	2	2
GR alpha/HSP90/FKBP51/HSP90	0.091	0.095	0.37	5	-10000	0	5
PRL	-0.089	0.17	-10000	0	-0.76	6	6
cortisol/GR alpha (dimer)/TIF2	0.2	0.22	0.58	38	-10000	0	38
RELA	-0.007	0.089	-10000	0	-10000	0	0
FGG	0.12	0.24	0.58	11	-0.66	15	26
GR beta/TIF2	0.09	0.11	0.4	7	-0.42	2	9
IFNG	-0.35	0.31	-10000	0	-0.87	66	66
apoptosis	0.025	0.16	0.5	4	-0.71	1	5
CREB1	0.017	0.019	-10000	0	-10000	0	0
histone acetylation	0.006	0.12	0.45	3	-0.39	5	8
BGLAP	-0.039	0.11	-10000	0	-0.56	1	1
GR/PKAc	0.09	0.09	0.36	4	-10000	0	4
NF kappa B1 p50/RelA	-0.019	0.16	-10000	0	-0.47	4	4
SMARCD1	0.015	0.003	-10000	0	-10000	0	0
MDM2	0.078	0.08	0.32	8	-10000	0	8
GATA3	-0.008	0.14	-10000	0	-0.76	10	10
AKT1	0	0	-10000	0	-10000	0	0
CSF2	-0.29	0.28	-10000	0	-0.55	148	148
GSK3B	0.014	0.007	-10000	0	-10000	0	0
NR1I3	0.058	0.16	0.5	2	-0.76	2	4
CSN2	0.12	0.14	0.46	8	-0.49	1	9
BRG1/BAF155/BAF170/BAF60A	0.022	0.024	-10000	0	-10000	0	0
NFATC1	0.014	0.003	-10000	0	-10000	0	0
POU2F1	0.015	0.015	-10000	0	-10000	0	0
CDKN1A	0.03	0.042	-10000	0	-10000	0	0
response to stress	0	0	-10000	0	-10000	0	0
response to UV	0.001	0.007	-10000	0	-10000	0	0
SFN	0.011	0.038	-10000	0	-0.64	1	1
GR alpha/HSP90/FKBP51/HSP90/14-3-3	0.092	0.092	0.38	3	-10000	0	3
prolactin receptor activity	0	0	-10000	0	-10000	0	0
EGR1	0.038	0.21	0.48	2	-0.86	11	13
JUN	-0.2	0.16	-10000	0	-0.66	15	15
IL4	-0.063	0.11	-10000	0	-0.5	4	4
CDK5R1	0.011	0.047	-10000	0	-0.8	1	1
PRKACA	0.013	0	-10000	0	-10000	0	0
cortisol/GR alpha (monomer)/AP-1	-0.15	0.31	-10000	0	-0.62	51	51
GR alpha/HSP90/FKBP51/HSP90/PP5C	0.094	0.091	0.37	4	-10000	0	4
cortisol/GR alpha (monomer)	0.23	0.26	0.68	42	-10000	0	42
NCOA2	0.005	0.075	-10000	0	-0.64	4	4
response to hypoxia	0	0	-10000	0	-10000	0	0
FOS	-0.17	0.24	-10000	0	-0.71	49	49
AP-1/NFAT1-c-4	-0.41	0.25	-10000	0	-0.81	52	52
AFP	-0.14	0.19	-10000	0	-0.84	15	15
SUV420H1	0.013	0	-10000	0	-10000	0	0
IRF1	0.1	0.17	0.51	7	-0.48	1	8
TP53	0.031	0.065	-10000	0	-0.62	3	3
PPP5C	0.013	0	-10000	0	-10000	0	0
KRT17	-0.38	0.37	-10000	0	-0.94	81	81
KRT14	-0.22	0.38	-10000	0	-1.1	37	37
TBP	0.024	0	-10000	0	-10000	0	0
CREBBP	0.066	0.087	0.33	12	-10000	0	12
HDAC1	0.012	0.012	-10000	0	-10000	0	0
HDAC2	0.042	0.031	-10000	0	-10000	0	0
AP-1	-0.41	0.25	-10000	0	-0.81	55	55
MAPK14	0.014	0.007	-10000	0	-10000	0	0
MAPK10	-0.017	0.14	-10000	0	-0.65	14	14
MAPK11	0.014	0.007	-10000	0	-10000	0	0
KRT5	-0.26	0.21	-10000	0	-0.72	25	25
interleukin-1 receptor activity	0.029	0.031	-10000	0	-10000	0	0
NCOA1	0.017	0.001	-10000	0	-10000	0	0
STAT1	-0.039	0.21	-10000	0	-0.78	23	23
CGA	-0.055	0.13	-10000	0	-0.69	4	4
NF kappa B1 p50/RelA/Cbp/cortisol/GR alpha (monomer)/HDAC2	0.24	0.2	0.41	152	-10000	0	152
MAPK3	0.014	0.007	-10000	0	-10000	0	0
MAPK1	0.014	0.007	-10000	0	-10000	0	0
ICAM1	-0.14	0.25	-10000	0	-0.76	27	27
NFKB1	-0.007	0.089	-10000	0	-10000	0	0
MAPK8	-0.16	0.15	-10000	0	-0.62	13	13
MAPK9	0.014	0.007	-10000	0	-10000	0	0
cortisol/GR alpha (dimer)	0.017	0.16	0.5	4	-0.76	1	5
BAX	0.03	0.042	-10000	0	-10000	0	0
POMC	-0.16	0.31	-10000	0	-0.91	31	31
EP300	0.068	0.088	0.32	16	-10000	0	16
cortisol/GR alpha (dimer)/p53	0.22	0.22	0.59	42	-0.58	1	43
proteasomal ubiquitin-dependent protein catabolic process	0.054	0.062	0.28	1	-10000	0	1
SGK1	0.12	0.13	-10000	0	-1.4	1	1
IL13	-0.21	0.18	-10000	0	-0.79	11	11
IL6	-0.18	0.36	-10000	0	-1.1	32	32
PRKACG	0.001	0.047	-10000	0	-0.8	1	1
IL5	-0.19	0.16	-10000	0	-0.77	8	8
IL2	-0.26	0.19	-10000	0	-0.79	12	12
CDK5	0.013	0.005	-10000	0	-10000	0	0
PRKACB	0.013	0	-10000	0	-10000	0	0
HSP90AA1	0.013	0	-10000	0	-10000	0	0
IL8	-0.22	0.34	-10000	0	-0.76	69	69
CDK5R1/CDK5	0.002	0.038	-10000	0	-0.61	1	1
NF kappa B1 p50/RelA/PKAc	0.01	0.12	-10000	0	-10000	0	0
cortisol/GR alpha (dimer)/Hsp90/FKBP52/HSP90	0.2	0.2	0.57	33	-10000	0	33
SMARCA4	0.015	0.003	-10000	0	-10000	0	0
chromatin remodeling	0.14	0.13	0.46	12	-10000	0	12
NF kappa B1 p50/RelA/Cbp	0.065	0.16	0.42	9	-10000	0	9
JUN (dimer)	-0.2	0.16	-10000	0	-0.66	15	15
YWHAH	0.013	0	-10000	0	-10000	0	0
VIPR1	-0.076	0.2	-10000	0	-0.89	13	13
NR3C1	0.14	0.15	0.49	22	-10000	0	22
NR4A1	-0.022	0.13	-10000	0	-0.57	10	10
TIF2/SUV420H1	-0.006	0.054	-10000	0	-0.47	4	4
MAPKKK cascade	0.025	0.16	0.5	4	-0.71	1	5
cortisol/GR alpha (dimer)/Src-1	0.21	0.22	0.59	39	-10000	0	39
PBX1	-0.082	0.23	-10000	0	-0.64	45	45
POU1F1	0.003	0.016	-10000	0	-10000	0	0
SELE	-0.23	0.42	-10000	0	-1.1	49	49
cortisol/GR alpha/BRG1/BAF155/BAF170/BAF60A	0.14	0.13	0.46	12	-10000	0	12
cortisol/GR alpha (monomer)/Hsp90/FKBP52/HSP90	0.2	0.2	0.57	33	-10000	0	33
mol:cortisol	0.12	0.16	0.4	44	-10000	0	44
MMP1	-0.64	0.21	-10000	0	-0.71	271	271

×

Ephrin B reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EFNB2	0.013	0	-10000	0	-10000	0	0
EPHB2	-0.17	0.34	-10000	0	-0.8	67	67
EFNB1	-0.021	0.16	-10000	0	-0.62	21	21
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	-0.15	0.22	-10000	0	-0.71	14	14
Ephrin B2/EPHB1-2	-0.14	0.22	-10000	0	-0.48	87	87
neuron projection morphogenesis	-0.14	0.21	-10000	0	-0.65	15	15
Ephrin B1/EPHB1-2/Tiam1	-0.15	0.24	-10000	0	-0.49	92	92
DNM1	-0.044	0.21	-10000	0	-0.8	21	21
cell-cell signaling	0	0.002	-10000	0	-10000	0	0
MAP2K4	0.014	0.065	-10000	0	-0.62	3	3
YES1	-0.007	0.086	-10000	0	-0.86	3	3
Ephrin B1/EPHB1-2/NCK2	-0.15	0.24	-10000	0	-0.63	24	24
PI3K	0.014	0.065	-10000	0	-0.63	3	3
mol:GDP	-0.16	0.24	-10000	0	-0.48	92	92
ITGA2B	-0.04	0.2	-10000	0	-0.8	20	20
endothelial cell proliferation	0	0	-10000	0	-10000	0	0
FYN	-0.007	0.086	-10000	0	-0.86	3	3
MAP3K7	-0.006	0.066	-10000	0	-0.66	3	3
FGR	-0.007	0.085	-10000	0	-0.85	3	3
TIAM1	0.007	0.065	-10000	0	-0.64	3	3
PIK3R1	0.013	0	-10000	0	-10000	0	0
RGS3	0.013	0	-10000	0	-10000	0	0
cell adhesion	-0.017	0.15	-10000	0	-0.64	4	4
LYN	-0.007	0.086	-10000	0	-0.86	3	3
Ephrin B1/EPHB1-2/Src Family Kinases	-0.01	0.08	-10000	0	-0.8	3	3
Ephrin B1/EPHB1-2	-0.012	0.071	-10000	0	-0.72	3	3
SRC	-0.007	0.085	-10000	0	-0.85	3	3
ITGB3	-0.017	0.15	-10000	0	-0.76	12	12
EPHB1	-0.038	0.19	-10000	0	-0.75	20	20
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	-0.063	0.19	-10000	0	-0.62	31	31
BLK	-0.027	0.095	-10000	0	-0.86	3	3
HCK	-0.008	0.087	-10000	0	-0.86	3	3
regulation of stress fiber formation	0.15	0.24	0.54	43	-10000	0	43
MAPK8	0.02	0.068	-10000	0	-0.58	3	3
Ephrin B1/EPHB1-2/RGS3	-0.15	0.24	-10000	0	-0.49	92	92
endothelial cell migration	-0.001	0.057	-10000	0	-0.56	3	3
NCK2	0.013	0	-10000	0	-10000	0	0
PTPN13	0.004	0.076	-10000	0	-0.75	3	3
regulation of focal adhesion formation	0.15	0.24	0.54	43	-10000	0	43
chemotaxis	0.15	0.24	0.48	92	-10000	0	92
PIK3CA	0.013	0	-10000	0	-10000	0	0
Rac1/GTP	-0.14	0.22	-10000	0	-0.68	15	15
angiogenesis	-0.012	0.071	-10000	0	-0.72	3	3
LCK	-0.01	0.086	-10000	0	-0.85	3	3

×

BCR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
JUN	-0.037	0.16	-10000	0	-0.45	18	18
IKBKB	-0.015	0.082	-10000	0	-0.28	1	1
AKT1	-0.035	0.12	-10000	0	-0.29	28	28
IKBKG	-0.014	0.086	-10000	0	-0.29	3	3
CALM1	-0.052	0.13	-10000	0	-0.41	22	22
PIK3CA	0.013	0	-10000	0	-10000	0	0
MAP3K1	-0.069	0.22	-10000	0	-0.65	21	21
MAP3K7	0.013	0	-10000	0	-10000	0	0
mol:Ca2+	-0.064	0.13	-10000	0	-0.44	22	22
DOK1	0.013	0	-10000	0	-10000	0	0
AP-1	-0.033	0.1	0.18	1	-0.27	8	9
LYN	0.013	0	-10000	0	-10000	0	0
BLNK	-0.056	0.2	-10000	0	-0.64	32	32
SHC1	0.013	0	-10000	0	-10000	0	0
BCR complex	-0.16	0.31	-10000	0	-0.67	71	71
CD22	-0.14	0.29	-10000	0	-0.86	34	34
CAMK2G	-0.041	0.12	-10000	0	-0.42	9	9
CSNK2A1	0.013	0	-10000	0	-10000	0	0
INPP5D	0.011	0.038	-10000	0	-0.64	1	1
SHC/GRB2/SOS1	-0.13	0.22	-10000	0	-0.72	22	22
GO:0007205	-0.064	0.14	-10000	0	-0.45	22	22
SYK	0.011	0.038	-10000	0	-0.64	1	1
ELK1	-0.055	0.13	-10000	0	-0.42	23	23
NFATC1	-0.082	0.21	-10000	0	-0.48	50	50
B-cell antigen/BCR complex	-0.16	0.31	-10000	0	-0.67	71	71
PAG1/CSK	-0.004	0.05	-10000	0	-0.61	2	2
NFKBIB	0.006	0.031	0.083	1	-10000	0	1
HRAS	-0.058	0.14	-10000	0	-0.46	22	22
NFKBIA	0.006	0.031	-10000	0	-10000	0	0
NF-kappa-B/RelA/I kappa B beta	0.012	0.026	-10000	0	-10000	0	0
RasGAP/Csk	-0.12	0.24	-10000	0	-0.86	18	18
mol:GDP	-0.062	0.13	-10000	0	-0.42	22	22
PTEN	0.013	0	-10000	0	-10000	0	0
CD79B	-0.029	0.18	-10000	0	-0.78	16	16
NF-kappa-B/RelA/I kappa B alpha	0.013	0.025	-10000	0	-10000	0	0
GRB2	0.013	0	-10000	0	-10000	0	0
PI3K/BCAP/CD19	-0.11	0.24	-10000	0	-0.55	55	55
PIK3R1	0.013	0	-10000	0	-10000	0	0
mol:IP3	-0.073	0.13	-10000	0	-0.45	22	22
CSK	0.013	0	-10000	0	-10000	0	0
FOS	-0.095	0.18	-10000	0	-0.5	25	25
CHUK	-0.014	0.086	-10000	0	-0.3	2	2
IBTK	0.013	0	-10000	0	-10000	0	0
CARD11/BCL10/MALT1/TAK1	-0.08	0.14	-10000	0	-0.57	10	10
PTPN6	-0.13	0.27	-10000	0	-0.85	30	30
RELA	0.013	0	-10000	0	-10000	0	0
BCL2A1	0.007	0.038	-10000	0	-0.12	18	18
VAV2	-0.17	0.29	-10000	0	-0.76	51	51
ubiquitin-dependent protein catabolic process	0.01	0.03	0.086	1	-10000	0	1
BTK	-0.004	0.03	0.38	1	-10000	0	1
CD19	-0.17	0.33	-10000	0	-0.81	55	55
MAP4K1	-0.012	0.14	-10000	0	-0.75	10	10
CD72	-0.083	0.26	-10000	0	-0.8	36	36
PAG1	0.008	0.066	-10000	0	-0.8	2	2
MAPK14	-0.048	0.19	-10000	0	-0.54	20	20
SH3BP5	0.011	0.038	-10000	0	-0.64	1	1
PIK3AP1	-0.073	0.16	-10000	0	-0.47	33	33
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2/CD72	-0.099	0.22	-10000	0	-0.66	25	25
RAF1	-0.047	0.14	-10000	0	-0.42	22	22
RasGAP/p62DOK/SHIP	-0.12	0.23	-10000	0	-0.81	19	19
CD79A	-0.16	0.32	-10000	0	-0.75	70	70
re-entry into mitotic cell cycle	-0.034	0.1	0.18	1	-0.27	8	9
RASA1	0.013	0	-10000	0	-10000	0	0
MAPK3	-0.024	0.12	-10000	0	-0.51	1	1
MAPK1	-0.024	0.12	-10000	0	-0.45	2	2
CD72/SHP1	-0.12	0.32	-10000	0	-0.89	33	33
NFKB1	0.013	0	-10000	0	-10000	0	0
MAPK8	-0.05	0.19	-10000	0	-0.54	20	20
actin cytoskeleton organization	-0.11	0.26	-10000	0	-0.62	50	50
NF-kappa-B/RelA	0.031	0.048	-10000	0	-10000	0	0
Calcineurin	-0.053	0.095	-10000	0	-0.55	1	1
PI3K	-0.14	0.23	-10000	0	-0.62	50	50
B-cell antigen/BCR complex/Btk/LYN/SYK/BLNK/PLCgamma2	-0.077	0.14	-10000	0	-0.48	22	22
SOS1	0.013	0	-10000	0	-10000	0	0
Bam32/HPK1	-0.067	0.23	-10000	0	-0.76	22	22
DAPP1	-0.094	0.21	-10000	0	-0.73	21	21
cytokine secretion	-0.075	0.19	-10000	0	-0.45	50	50
mol:DAG	-0.073	0.13	-10000	0	-0.45	22	22
PLCG2	0.013	0	-10000	0	-10000	0	0
MAP2K1	-0.035	0.13	-10000	0	-0.48	3	3
B-cell antigen/BCR complex/FcgammaRIIB	-0.14	0.28	-10000	0	-0.6	73	73
mol:PI-3-4-5-P3	-0.099	0.16	-10000	0	-0.41	47	47
ETS1	-0.033	0.12	-10000	0	-0.43	4	4
B-cell antigen/BCR complex/LYN/SYK/BLNK	-0.15	0.25	-10000	0	-0.83	22	22
B-cell antigen/BCR complex/LYN	-0.1	0.22	-10000	0	-0.78	19	19
MALT1	0.013	0	-10000	0	-10000	0	0
TRAF6	0.013	0	-10000	0	-10000	0	0
RAC1	-0.12	0.28	-10000	0	-0.68	50	50
B-cell antigen/BCR complex/LYN/SYK	-0.14	0.29	-10000	0	-0.92	29	29
CARD11	-0.086	0.18	-10000	0	-0.48	41	41
FCGR2B	0	0.091	-10000	0	-0.64	6	6
PPP3CA	0.013	0	-10000	0	-10000	0	0
BCL10	0.013	0	-10000	0	-10000	0	0
IKK complex	0.004	0.04	-10000	0	-10000	0	0
PTPRC	-0.011	0.14	-10000	0	-0.74	10	10
PDPK1	-0.034	0.12	-10000	0	-0.29	27	27
PPP3CB	0.013	0	-10000	0	-10000	0	0
PPP3CC	0.013	0	-10000	0	-10000	0	0
POU2F2	0.006	0.044	-10000	0	-0.14	24	24

×

LPA4-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ADCY4	0.022	0	-9999	-10000	0	0
ADCY5	-0.072	0.18	-9999	-0.42	65	65
ADCY6	0.009	0.072	-9999	-0.4	9	9
ADCY7	0.022	0	-9999	-10000	0	0
ADCY1	-0.002	0.11	-9999	-0.54	13	13
ADCY2	-0.11	0.2	-9999	-0.41	95	95
ADCY3	0.022	0	-9999	-10000	0	0
ADCY8	-0.002	0.094	-9999	-0.54	9	9
PRKCE	0.012	0	-9999	-10000	0	0
ADCY9	0.022	0	-9999	-10000	0	0
mol:DAG	0	0	-9999	-10000	0	0
cAMP biosynthetic process	-0.048	0.11	-9999	-0.43	5	5

×

Caspase cascade in apoptosis

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
TOP1	-0.038	0.18	-10000	0	-0.42	49	49
ACTA1	-0.14	0.24	-10000	0	-0.62	52	52
NUMA1	-0.039	0.18	-10000	0	-0.53	25	25
SPTAN1	-0.063	0.24	-10000	0	-0.56	49	49
LIMK1	-0.063	0.24	-10000	0	-0.56	49	49
BIRC3	-0.024	0.17	-10000	0	-0.8	14	14
BIRC2	-0.003	0.11	-10000	0	-0.8	6	6
BAX	0.013	0	-10000	0	-10000	0	0
CASP10	-0.097	0.3	-10000	0	-0.72	52	52
CRMA	0	0	-10000	0	-10000	0	0
XIAP	0.013	0	-10000	0	-10000	0	0
PTK2	-0.038	0.18	-10000	0	-0.53	25	25
DIABLO	0.013	0	-10000	0	-10000	0	0
apoptotic nuclear changes	-0.061	0.23	-10000	0	-0.55	49	49
response to UV	0	0	-10000	0	-10000	0	0
CRADD	0.013	0	-10000	0	-10000	0	0
GSN	-0.063	0.24	-10000	0	-0.56	49	49
MADD	0.013	0	-10000	0	-10000	0	0
TFAP2A	-0.001	0.1	-10000	0	-0.6	5	5
BID	-0.027	0.12	-10000	0	-0.35	23	23
MAP3K1	-0.011	0.075	-10000	0	-10000	0	0
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	-0.063	0.24	-10000	0	-0.56	49	49
CASP9	0.013	0.002	-10000	0	-10000	0	0
DNA repair	0.006	0.063	-10000	0	-0.2	6	6
neuron apoptosis	0.018	0.024	-10000	0	-10000	0	0
mol:NAD	0	0	-10000	0	-10000	0	0
DNA fragmentation during apoptosis	-0.053	0.23	-10000	0	-0.72	23	23
APAF1	0.013	0	-10000	0	-10000	0	0
CASP6	-0.002	0.1	-10000	0	-0.47	1	1
TRAF2	0.008	0.066	-10000	0	-0.8	2	2
ICAD/CAD	-0.053	0.23	-10000	0	-0.74	22	22
CASP7	0.007	0.065	0.31	10	-10000	0	10
KRT18	0.004	0.065	-10000	0	-0.48	4	4
apoptosis	-0.042	0.21	-10000	0	-0.66	22	22
DFFA	-0.063	0.24	-10000	0	-0.56	49	49
DFFB	-0.063	0.24	-10000	0	-0.56	49	49
PARP1	-0.006	0.063	0.2	6	-10000	0	6
actin filament polymerization	0.049	0.22	0.68	23	-10000	0	23
TNF	-0.025	0.17	-10000	0	-0.76	15	15
CYCS	-0.017	0.094	-10000	0	-0.27	22	22
SATB1	-0.006	0.12	-10000	0	-0.47	3	3
SLK	-0.063	0.24	-10000	0	-0.56	49	49
p15 BID/BAX	-0.018	0.11	-10000	0	-0.32	22	22
CASP2	0.034	0.071	-10000	0	-10000	0	0
JNK cascade	0.011	0.075	-10000	0	-10000	0	0
CASP3	-0.075	0.25	-10000	0	-0.6	49	49
LMNB2	0.028	0.06	-10000	0	-0.37	1	1
RIPK1	0.013	0	-10000	0	-10000	0	0
CASP4	0.011	0.038	-10000	0	-0.64	1	1
Mammalian IAPs/DIABLO	-0.031	0.14	-10000	0	-0.59	16	16
negative regulation of DNA binding	-0.001	0.099	-10000	0	-0.6	5	5
stress fiber formation	-0.061	0.23	-10000	0	-0.55	49	49
GZMB	-0.12	0.34	-10000	0	-0.82	52	52
CASP1	0.016	0.032	-10000	0	-0.37	2	2
LMNB1	0.028	0.06	-10000	0	-0.37	1	1
APP	0.018	0.024	-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	-0.045	0.2	-10000	0	-0.63	23	23
LMNA	0.028	0.06	-10000	0	-0.37	1	1
TNF-alpha/TNFR1A/TRADD/MADD/cIAP2/RIP1/TRAF2/RAIDD/PIDD	0.027	0.075	-10000	0	-0.37	4	4
LRDD	0.011	0.047	-10000	0	-0.8	1	1
SREBF1	-0.063	0.24	-10000	0	-0.56	49	49
APAF-1/Caspase 9	-0.001	0.075	0.48	5	-10000	0	5
nuclear fragmentation during apoptosis	-0.038	0.18	-10000	0	-0.52	25	25
CFL2	-0.051	0.22	-10000	0	-0.7	23	23
GAS2	-0.12	0.26	-10000	0	-0.62	49	49
positive regulation of apoptosis	0.032	0.06	-10000	0	-0.37	1	1
PRF1	-0.051	0.22	-10000	0	-0.8	24	24

×

ErbB4 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ErbB4/ErbB4/HBEGF/HBEGF	-0.017	0.082	-10000	0	-10000	0	0
epithelial cell differentiation	-0.087	0.14	-10000	0	-0.6	2	2
ITCH	0.028	0.02	-10000	0	-10000	0	0
WWP1	-0.012	0.076	-10000	0	-10000	0	0
FYN	0.011	0.047	-10000	0	-0.8	1	1
EGFR	-0.014	0.15	-10000	0	-0.8	10	10
PRL	-0.003	0.08	-10000	0	-0.8	3	3
neuron projection morphogenesis	-0.046	0.18	-10000	0	-10000	0	0
PTPRZ1	0.003	0.083	-10000	0	-0.64	5	5
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/GRB2/SHC	-0.1	0.17	-10000	0	-10000	0	0
ErbB4 CYT2/ErbB4 CYT2/neuregulin 1 beta/neuregulin 1 beta	-0.1	0.22	-10000	0	-0.52	60	60
ADAM17	0.028	0.02	-10000	0	-10000	0	0
ErbB4/ErbB4	-0.027	0.098	-10000	0	-10000	0	0
ErbB4/ErbB4/neuregulin 3/neuregulin 3	-0.051	0.12	-10000	0	-0.52	7	7
NCOR1	0.013	0	-10000	0	-10000	0	0
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta/Fyn	-0.12	0.19	-10000	0	-0.56	25	25
GRIN2B	-0.088	0.2	-10000	0	-0.53	25	25
ErbB4/ErbB2/betacellulin	-0.13	0.17	-10000	0	-0.67	2	2
STAT1	-0.048	0.22	-10000	0	-0.8	23	23
HBEGF	0.013	0	-10000	0	-10000	0	0
PRLR	-0.13	0.27	-10000	0	-0.65	64	64
E4ICDs/ETO2	-0.017	0.082	-10000	0	-10000	0	0
axon guidance	-0.026	0.091	-10000	0	-0.41	2	2
NEDD4	0.028	0.02	-10000	0	-10000	0	0
Prolactin receptor/Prolactin receptor/Prolactin	-0.11	0.21	-10000	0	-0.49	66	66
CBFA2T3	0.013	0	-10000	0	-10000	0	0
ErbB4/ErbB2/HBEGF	-0.028	0.053	-10000	0	-0.56	1	1
MAPK3	-0.056	0.18	-10000	0	-10000	0	0
STAT1 (dimer)	-0.056	0.16	-10000	0	-0.56	22	22
MAPK1	-0.056	0.18	-10000	0	-10000	0	0
JAK2	0.013	0	-10000	0	-10000	0	0
ErbB4/ErbB2/neuregulin 1 beta	-0.11	0.2	-10000	0	-0.51	42	42
NRG1	-0.096	0.26	-10000	0	-0.61	61	61
NRG3	-0.029	0.15	-10000	0	-0.64	17	17
NRG2	-0.38	0.32	-10000	0	-0.64	184	184
NRG4	-0.07	0.22	-10000	0	-0.64	38	38
heart development	-0.026	0.091	-10000	0	-0.41	2	2
neural crest cell migration	-0.11	0.2	-10000	0	-0.51	42	42
ERBB2	0.03	0.054	-10000	0	-0.62	2	2
WWOX/E4ICDs	-0.017	0.082	-10000	0	-10000	0	0
SHC1	0.013	0	-10000	0	-10000	0	0
ErbB4/EGFR/neuregulin 4	-0.097	0.16	-10000	0	-0.49	31	31
apoptosis	0.091	0.14	0.66	10	-10000	0	10
ErbB4/ErbB4/neuregulin 2 beta/neuregulin 2 beta	-0.26	0.21	-10000	0	-0.52	66	66
ErbB4/ErbB2/epiregulin	-0.12	0.16	-10000	0	-0.63	3	3
ErbB4/ErbB4/betacellulin/betacellulin	-0.14	0.2	-10000	0	-0.52	36	36
ErbB4/ErbB4/HBEGF/HBEGF/Prolactin receptor/Prolactin receptor/Prolactin/JAK2	-0.1	0.15	-10000	0	-0.65	3	3
MDM2	-0.013	0.084	-10000	0	-10000	0	0
ErbB4 JM-B/ErbB4 JM-B/neuregulin 1 beta/neuregulin 1 beta	-0.11	0.19	-10000	0	-0.49	59	59
STAT5A	-0.016	0.086	-10000	0	-10000	0	0
ErbB4/EGFR/neuregulin 1 beta	-0.13	0.21	-10000	0	-0.59	28	28
DLG4	0.011	0.038	-10000	0	-0.64	1	1
GRB2/SHC	0	0	-10000	0	-10000	0	0
E4ICDs/TAB2/NCoR1	-0.04	0.058	-10000	0	-10000	0	0
STAT5A (dimer)	-0.092	0.14	-10000	0	-0.66	2	2
MAP3K7IP2	0	0	-10000	0	-10000	0	0
STAT5B (dimer)	-0.017	0.085	-10000	0	-10000	0	0
LRIG1	0	0.091	-10000	0	-0.64	6	6
EREG	-0.17	0.3	-10000	0	-0.64	84	84
BTC	-0.19	0.3	-10000	0	-0.64	94	94
ErbB4/ErbB4/neuregulin 1 beta/neuregulin 1 beta	-0.026	0.092	-10000	0	-0.42	2	2
ERBB4	-0.027	0.098	-10000	0	-10000	0	0
STAT5B	0.013	0	-10000	0	-10000	0	0
YAP1	-0.02	0.053	-10000	0	-0.37	6	6
GRB2	0.013	0	-10000	0	-10000	0	0
ErbB4/ErbB2/neuregulin 4	-0.071	0.13	-10000	0	-0.56	1	1
glial cell differentiation	0.04	0.057	-10000	0	-10000	0	0
WWOX	0.013	0	-10000	0	-10000	0	0
cell proliferation	-0.17	0.25	-10000	0	-0.69	33	33

×

Signaling mediated by p38-gamma and p38-delta

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
EEF2K	0.026	0.054	-9999	-0.39	5	5
SNTA1	0.013	0	-9999	-10000	0	0
response to hypoxia	0	0	-9999	-10000	0	0
STMN1	0.024	0.063	-9999	-0.42	6	6
MAPK12	-0.011	0.14	-9999	-0.44	27	27
CCND1	-0.002	0.086	-9999	-0.38	9	9
p38 gamma/SNTA1	-0.003	0.13	-9999	-0.49	14	14
MAP2K3	0.011	0.038	-9999	-0.64	1	1
PKN1	0.008	0.066	-9999	-0.8	2	2
G2/M transition checkpoint	-0.01	0.14	-9999	-0.44	27	27
MAP2K6	0.004	0.093	-9999	-0.38	17	17
MAPT	-0.14	0.19	-9999	-0.35	131	131
MAPK13	0.017	0.063	-9999	-0.47	5	5
hyperosmotic response	0	0	-9999	-10000	0	0
ZAK	0.015	0.037	-9999	-0.36	3	3

×

Canonical Wnt signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.003	0.016	-10000	0	-10000	0	0
AES	0.002	0.014	-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	-0.01	0.078	-10000	0	-0.61	5	5
SMAD4	0.011	0.038	-10000	0	-0.64	1	1
DKK2	-0.012	0.14	-10000	0	-0.74	10	10
TLE1	0.002	0.014	-10000	0	-10000	0	0
MACF1	0.014	0.001	-10000	0	-10000	0	0
CTNNB1	0.047	0.12	-10000	0	-0.41	1	1
WIF1	-0.31	0.33	-10000	0	-0.65	145	145
beta catenin/RanBP3	-0.013	0.082	0.37	7	-10000	0	7
KREMEN2	-0.27	0.39	-10000	0	-0.8	106	106
DKK1	-0.23	0.37	-10000	0	-0.78	93	93
beta catenin/beta TrCP1	0.053	0.11	-10000	0	-10000	0	0
FZD1	0	0.1	-10000	0	-0.8	5	5
AXIN2	0.004	0.16	-10000	0	-1.5	3	3
AXIN1	0.014	0.001	-10000	0	-10000	0	0
RAN	0.013	0	-10000	0	-10000	0	0
Axin1/APC/GSK3/beta catenin	0.006	0.025	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES/SMAD4	0.088	0.065	-10000	0	-10000	0	0
Axin1/APC/GSK3	0.005	0.041	-10000	0	-10000	0	0
Axin1/APC/GSK3/beta catenin/Macf1	0.058	0.072	-10000	0	-10000	0	0
HNF1A	-0.014	0.11	-10000	0	-0.8	6	6
CTBP1	0.002	0.015	-10000	0	-10000	0	0
MYC	0.016	0.045	-10000	0	-0.53	1	1
RANBP3	0.013	0	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	-0.2	0.26	-10000	0	-0.53	114	114
NKD1	-0.015	0.14	-10000	0	-0.76	11	11
TCF4	0.002	0.015	-10000	0	-10000	0	0
TCF3	0.002	0.015	-10000	0	-10000	0	0
WNT1/LRP6/FZD1/Axin1	-0.011	0.072	-10000	0	-0.48	7	7
Ran/GTP	0	0.002	-10000	0	-10000	0	0
CtBP/CBP/TCF/TLE1/AES	0.008	0.084	0.53	5	-10000	0	5
LEF1	-0.003	0.067	-10000	0	-0.81	2	2
DVL1	0.066	0.06	-10000	0	-10000	0	0
CSNK2A1	0.014	0	-10000	0	-10000	0	0
beta catenin/TCF/CtBP/CBP/TLE1/AES	0.1	0.072	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	-0.34	0.34	-10000	0	-0.62	164	164
LRP6	0.014	0.001	-10000	0	-10000	0	0
CSNK1A1	0.003	0.016	-10000	0	-10000	0	0
NLK	0.014	0.003	-10000	0	-10000	0	0
CCND1	-0.006	0.19	-10000	0	-1.1	7	7
WNT1	0.006	0.066	-10000	0	-0.8	2	2
GSK3A	0.014	0.001	-10000	0	-10000	0	0
GSK3B	0.013	0.001	-10000	0	-10000	0	0
FRAT1	0.013	0.001	-10000	0	-10000	0	0
PPP2R5D	0.052	0.066	0.36	11	-10000	0	11
APC	0.031	0.073	-10000	0	-10000	0	0
WNT1/LRP6/FZD1	0.12	0.13	0.25	145	-10000	0	145
CREBBP	0.002	0.015	-10000	0	-10000	0	0

×

Nongenotropic Androgen signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.012	0	-10000	0	-10000	0	0
GNB1/GNG2	-0.071	0.15	-10000	0	-0.37	58	58
regulation of S phase of mitotic cell cycle	-0.025	0.12	-10000	0	-10000	0	0
GNAO1	0.008	0.06	-10000	0	-0.72	2	2
HRAS	0.013	0.001	-10000	0	-10000	0	0
SHBG/T-DHT	0	0	-10000	0	-10000	0	0
PELP1	0.013	0.001	-10000	0	-10000	0	0
AKT1	0.012	0	-10000	0	-10000	0	0
MAP2K1	-0.029	0.14	-10000	0	-0.5	2	2
T-DHT/AR	-0.092	0.19	-10000	0	-0.49	57	57
G-protein coupled receptor activity	0	0	-10000	0	-10000	0	0
mol:GTP	-0.001	0.003	-10000	0	-0.007	49	49
GNAI2	0.013	0	-10000	0	-10000	0	0
GNAI3	0.013	0	-10000	0	-10000	0	0
GNAI1	0.011	0.038	-10000	0	-0.64	1	1
mol:GDP	-0.09	0.19	-10000	0	-0.48	57	57
cell proliferation	-0.046	0.2	-10000	0	-0.61	13	13
PIK3CA	0.013	0	-10000	0	-10000	0	0
FOS	-0.1	0.33	-10000	0	-0.84	49	49
mol:Ca2+	-0.011	0.02	-10000	0	-0.092	4	4
MAPK3	-0.036	0.17	-10000	0	-0.53	13	13
MAPK1	-0.016	0.099	-10000	0	-0.28	13	13
PIK3R1	0.013	0	-10000	0	-10000	0	0
mol:IP3	0	0.002	-10000	0	-0.005	49	49
cAMP biosynthetic process	0.01	0.02	-10000	0	-10000	0	0
GNG2	0.011	0.047	-10000	0	-0.8	1	1
potassium channel inhibitor activity	0	0.002	-10000	0	-0.005	49	49
HRAS/GTP	-0.066	0.13	-10000	0	-0.46	4	4
actin cytoskeleton reorganization	0	0	-10000	0	-10000	0	0
SRC	0.013	0.001	-10000	0	-10000	0	0
voltage-gated calcium channel activity	0	0.002	-10000	0	-0.005	49	49
PI3K	0	0	-10000	0	-10000	0	0
apoptosis	0.044	0.19	0.42	49	-10000	0	49
T-DHT/AR/PELP1	-0.077	0.16	-10000	0	-0.42	57	57
HRAS/GDP	-0.083	0.18	-10000	0	-0.45	57	57
CREB1	-0.049	0.2	-10000	0	-0.46	49	49
RAC1-CDC42/GTP	0	0	-10000	0	-10000	0	0
AR	-0.11	0.26	-10000	0	-0.65	57	57
GNB1	0.013	0	-10000	0	-10000	0	0
RAF1	-0.034	0.14	-10000	0	-0.5	2	2
RAC1-CDC42/GDP	-0.08	0.17	-10000	0	-0.43	53	53
T-DHT/AR/PELP1/Src	-0.07	0.15	-10000	0	-0.42	15	15
MAP2K2	-0.029	0.14	-10000	0	-0.5	2	2
T-DHT/AR/PELP1/Src/PI3K	-0.025	0.12	-10000	0	-10000	0	0
GNAZ	-0.004	0.11	-10000	0	-0.73	7	7
SHBG	0.013	0.003	-10000	0	-10000	0	0
Gi family/GNB1/GNG2/GDP	0.022	0.066	-10000	0	-0.44	1	1
mol:T-DHT	0	0.001	-10000	0	-0.003	36	36
RAC1	0.013	0	-10000	0	-10000	0	0
GNRH1	-0.004	0.099	-10000	0	-0.61	8	8
Gi family/GTP	-0.035	0.076	-10000	0	-0.4	4	4
CDC42	0.013	0	-10000	0	-10000	0	0

×

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

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
MAP4K1	-0.015	0.15	-10000	0	-0.46	2	2
CRKL	-0.011	0.14	-10000	0	-0.4	30	30
HRAS	-0.007	0.15	-10000	0	-0.53	5	5
mol:PIP3	-0.025	0.13	-10000	0	-0.4	29	29
SPRED1	0.013	0	-10000	0	-10000	0	0
SPRED2	0.013	0	-10000	0	-10000	0	0
GAB1	-0.019	0.14	-10000	0	-0.43	29	29
FOXO3	-0.003	0.13	-10000	0	-0.37	25	25
AKT1	-0.013	0.14	-10000	0	-0.4	29	29
BAD	-0.003	0.13	-10000	0	-0.4	3	3
megakaryocyte differentiation	-0.033	0.16	-10000	0	-0.43	39	39
GSK3B	-0.003	0.13	-10000	0	-0.37	25	25
RAF1	0.006	0.13	-10000	0	-0.49	1	1
SHC1	0.013	0	-10000	0	-10000	0	0
STAT3	-0.019	0.14	-10000	0	-0.43	29	29
STAT1	-0.086	0.35	-10000	0	-1.1	29	29
HRAS/SPRED1	-0.049	0.097	-10000	0	-0.42	5	5
cell proliferation	-0.02	0.15	-10000	0	-0.43	29	29
PIK3CA	0.013	0	-10000	0	-10000	0	0
TEC	-0.023	0.15	-10000	0	-0.64	17	17
RPS6KB1	-0.019	0.14	-10000	0	-0.43	29	29
HRAS/SPRED2	-0.049	0.097	-10000	0	-0.42	5	5
LYN/TEC/p62DOK	-0.063	0.14	-10000	0	-0.66	6	6
MAPK3	0.02	0.096	-10000	0	-0.33	1	1
STAP1	-0.056	0.18	-10000	0	-0.44	53	53
GRAP2	-0.007	0.12	-10000	0	-0.74	8	8
JAK2	-0.11	0.25	-10000	0	-0.84	29	29
STAT1 (dimer)	-0.083	0.34	-10000	0	-1	29	29
mol:Gleevec	0	0.006	-10000	0	-10000	0	0
GRB2/SOCS1/VAV1	-0.084	0.17	-10000	0	-0.58	10	10
actin filament polymerization	-0.019	0.15	-10000	0	-0.44	29	29
LYN	0.013	0	-10000	0	-10000	0	0
STAP1/STAT5A (dimer)	-0.059	0.22	-10000	0	-0.59	32	32
PIK3R1	0.013	0	-10000	0	-10000	0	0
CBL/CRKL/GRB2	-0.042	0.11	-10000	0	-10000	0	0
PI3K	-0.047	0.12	-10000	0	-0.4	25	25
PTEN	0.013	0	-10000	0	-10000	0	0
SCF/KIT/EPO/EPOR	-0.11	0.42	-10000	0	-1.3	29	29
MAPK8	-0.021	0.15	-10000	0	-0.44	29	29
STAT3 (dimer)	-0.018	0.14	-10000	0	-0.42	29	29
positive regulation of transcription	0.022	0.083	-10000	0	-10000	0	0
mol:GDP	-0.071	0.14	-10000	0	-0.6	6	6
PIK3C2B	-0.02	0.15	-10000	0	-0.44	29	29
CBL/CRKL	-0.002	0.13	-10000	0	-0.4	2	2
FER	-0.019	0.14	-10000	0	-0.43	29	29
SH2B3	-0.02	0.15	-10000	0	-0.43	30	30
PDPK1	-0.015	0.12	-10000	0	-0.36	29	29
SNAI2	-0.025	0.16	-10000	0	-0.44	32	32
positive regulation of cell proliferation	-0.046	0.25	-10000	0	-0.74	29	29
KITLG	0.015	0.009	-10000	0	-10000	0	0
cell motility	-0.046	0.25	-10000	0	-0.74	29	29
PTPN6	0.007	0.012	-10000	0	-10000	0	0
EPOR	0.002	0.14	-10000	0	-0.65	7	7
STAT5A (dimer)	-0.03	0.2	-10000	0	-0.6	29	29
SOCS1	-0.054	0.22	-10000	0	-0.8	25	25
cell migration	0.03	0.16	0.43	36	-10000	0	36
SOS1	0.013	0	-10000	0	-10000	0	0
EPO	-0.055	0.22	-10000	0	-0.8	25	25
VAV1	0.003	0.083	-10000	0	-0.64	5	5
GRB10	-0.02	0.15	-10000	0	-0.43	30	30
PTPN11	0.006	0.01	-10000	0	-10000	0	0
SCF/KIT	-0.054	0.14	-10000	0	-0.46	29	29
GO:0007205	0.001	0.009	-10000	0	-10000	0	0
MAP2K1	0.017	0.1	-10000	0	-0.36	1	1
CBL	0.013	0	-10000	0	-10000	0	0
KIT	-0.093	0.41	-10000	0	-1.3	30	30
MAP2K2	0.017	0.1	-10000	0	-0.36	1	1
SHC/Grb2/SOS1	-0.046	0.12	-10000	0	-0.43	2	2
STAT5A	-0.032	0.21	-10000	0	-0.62	29	29
GRB2	0.013	0	-10000	0	-10000	0	0
response to radiation	-0.024	0.15	-10000	0	-0.44	32	32
SHC/GRAP2	-0.015	0.09	-10000	0	-0.56	8	8
PTPRO	-0.034	0.16	-10000	0	-0.44	39	39
SH2B2	-0.02	0.15	-10000	0	-0.44	29	29
DOK1	0.013	0	-10000	0	-10000	0	0
MATK	-0.031	0.16	-10000	0	-0.44	36	36
CREBBP	0.035	0.014	-10000	0	-10000	0	0
BCL2	0.002	0.17	-10000	0	-1.2	4	4

×

Thromboxane A2 receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGM2	-0.049	0.21	-10000	0	-0.8	22	22
GNB1/GNG2	-0.057	0.077	-10000	0	-0.21	20	20
AKT1	-0.002	0.12	-10000	0	-0.26	1	1
EGF	-0.14	0.27	-10000	0	-0.64	69	69
mol:TXA2	0	0.001	-10000	0	-10000	0	0
FGR	-0.018	0.1	-10000	0	-0.51	4	4
mol:Ca2+	-0.029	0.16	-10000	0	-0.32	31	31
LYN	-0.016	0.1	-10000	0	-0.51	4	4
RhoA/GTP	-0.034	0.051	-10000	0	-10000	0	0
mol:PGI2	0	0	-10000	0	-10000	0	0
SYK	-0.033	0.18	-10000	0	-0.36	22	22
GNG2	0.011	0.047	-10000	0	-0.8	1	1
ARRB2	0.013	0	-10000	0	-10000	0	0
TP alpha/Gq family/GDP/G beta5/gamma2	0.007	0.067	-10000	0	-10000	0	0
G beta5/gamma2	-0.074	0.1	-10000	0	-0.3	19	19
PRKCH	-0.038	0.18	-10000	0	-0.38	25	25
DNM1	-0.043	0.21	-10000	0	-0.8	21	21
TXA2/TP beta/beta Arrestin3	-0.023	0.065	-10000	0	-0.26	18	18
mol:GTP	0	0.001	-10000	0	-10000	0	0
PTGDR	0.006	0.076	-10000	0	-0.75	3	3
G12 family/GTP	-0.084	0.12	-10000	0	-0.33	23	23
ADRBK1	0.013	0	-10000	0	-10000	0	0
ADRBK2	0.011	0.047	-10000	0	-0.8	1	1
RhoA/GTP/ROCK1	0	0	-10000	0	-10000	0	0
mol:GDP	0.015	0.12	0.36	14	-10000	0	14
mol:NADP	0	0.1	-10000	0	-0.8	5	5
RAB11A	0.013	0	-10000	0	-10000	0	0
PRKG1	-0.008	0.12	-10000	0	-0.71	9	9
mol:IP3	-0.045	0.2	-10000	0	-0.4	32	32
cell morphogenesis	0	0	-10000	0	-10000	0	0
PLCB2	-0.074	0.26	-10000	0	-0.51	58	58
mol:cGMP	0	0.001	-10000	0	-10000	0	0
BLK	-0.079	0.17	-10000	0	-0.57	13	13
mol:PDG2	0	0	-10000	0	-10000	0	0
HCK	-0.021	0.11	-10000	0	-0.51	4	4
RHOA	0.013	0	-10000	0	-10000	0	0
PTGIR	-0.008	0.13	-10000	0	-0.8	8	8
PRKCB1	-0.046	0.2	-10000	0	-0.38	58	58
GNAQ	0.013	0	-10000	0	-10000	0	0
mol:L-citrulline	0	0.1	-10000	0	-0.8	5	5
TXA2/TXA2-R family	-0.075	0.26	-10000	0	-0.52	59	59
LCK	-0.029	0.12	-10000	0	-0.53	6	6
TXA2/TP beta/beta Arrestin3/RAB11/GDP	-0.038	0.13	-10000	0	-0.46	22	22
TXA2-R family/G12 family/GDP/G beta/gamma	0.022	0.046	-10000	0	-0.38	1	1
TXA2/TP beta/beta Arrestin2/RAB11/GDP	-0.037	0.12	-10000	0	-0.45	22	22
MAPK14	-0.008	0.13	-10000	0	-10000	0	0
TGM2/GTP	-0.058	0.22	-10000	0	-0.49	28	28
MAPK11	-0.008	0.13	-10000	0	-10000	0	0
ARHGEF1	-0.007	0.1	-10000	0	-0.23	1	1
GNAI2	0.013	0	-10000	0	-10000	0	0
JNK cascade	-0.045	0.2	-10000	0	-0.38	59	59
RAB11/GDP	0.013	0.002	-10000	0	-10000	0	0
ICAM1	-0.03	0.16	-10000	0	-0.34	30	30
cAMP biosynthetic process	-0.044	0.19	-10000	0	-0.39	27	27
Gq family/GTP/EBP50	-0.008	0.088	-10000	0	-0.36	2	2
actin cytoskeleton reorganization	0	0	-10000	0	-10000	0	0
SRC	-0.016	0.1	-10000	0	-0.51	4	4
GNB5	0.013	0	-10000	0	-10000	0	0
GNB1	0.013	0	-10000	0	-10000	0	0
EGF/EGFR	-0.013	0.12	-10000	0	-0.37	4	4
VCAM1	-0.04	0.18	-10000	0	-0.36	46	46
TP beta/Gq family/GDP/G beta5/gamma2	0.007	0.067	-10000	0	-10000	0	0
platelet activation	-0.014	0.17	-10000	0	-0.32	17	17
PGI2/IP	-0.016	0.1	-10000	0	-0.62	8	8
PRKACA	0.009	0.067	-10000	0	-0.34	10	10
Gq family/GDP/G beta5/gamma2	0.011	0.067	-10000	0	-10000	0	0
TXA2/TP beta/beta Arrestin2	-0.028	0.09	-10000	0	-0.35	21	21
positive regulation of NF-kappaB transcription factor activity	0	0	-10000	0	-10000	0	0
TBXA2R	-0.015	0.15	-10000	0	-0.52	22	22
mol:DAG	-0.054	0.22	-10000	0	-0.42	58	58
EGFR	-0.014	0.15	-10000	0	-0.8	10	10
TXA2/TP alpha	-0.066	0.24	-10000	0	-0.53	28	28
Gq family/GTP	-0.038	0.094	-10000	0	-0.25	50	50
YES1	-0.016	0.1	-10000	0	-0.51	4	4
GNAI2/GTP	-0.035	0.11	-10000	0	-0.62	4	4
PGD2/DP	-0.006	0.057	-10000	0	-0.57	3	3
SLC9A3R1	0.009	0.053	-10000	0	-0.64	2	2
FYN	-0.017	0.11	-10000	0	-0.54	5	5
mol:NO	0	0.1	-10000	0	-0.8	5	5
GNA15	0.013	0	-10000	0	-10000	0	0
PGK/cGMP	-0.023	0.1	-10000	0	-0.49	14	14
RhoA/GDP	0.013	0.002	-10000	0	-10000	0	0
TP alpha/TGM2/GDP/G beta/gamma	-0.067	0.18	-10000	0	-0.79	9	9
NOS3	0	0.1	-10000	0	-0.8	5	5
RAC1	0.013	0	-10000	0	-10000	0	0
PRKCA	-0.039	0.18	-10000	0	-0.38	26	26
PRKCB	-0.044	0.19	-10000	0	-0.4	31	31
PRKCE	-0.037	0.19	-10000	0	-0.38	24	24
PRKCD	-0.043	0.2	-10000	0	-0.38	54	54
PRKCG	-0.064	0.22	-10000	0	-0.45	46	46
muscle contraction	-0.063	0.25	-10000	0	-0.48	59	59
PRKCZ	-0.032	0.18	-10000	0	-0.37	22	22
ARR3	0.001	0.004	-10000	0	-10000	0	0
TXA2/TP beta	-0.039	0.13	-10000	0	-0.45	23	23
PRKCQ	-0.043	0.19	-10000	0	-0.4	29	29
MAPKKK cascade	-0.059	0.23	-10000	0	-0.47	34	34
SELE	-0.045	0.19	-10000	0	-0.4	52	52
TP beta/GNAI2/GDP/G beta/gamma	-0.038	0.12	-10000	0	-0.7	4	4
ROCK1	0.013	0	-10000	0	-10000	0	0
GNA14	-0.095	0.24	-10000	0	-0.64	50	50
chemotaxis	-0.09	0.3	-10000	0	-0.6	59	59
GNA12	0.008	0.066	-10000	0	-0.8	2	2
GNA13	0.013	0	-10000	0	-10000	0	0
GNA11	0.013	0	-10000	0	-10000	0	0
Rac1/GTP	0	0	-10000	0	-10000	0	0

×

Reelin signaling pathway

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
CDK5R1/CDK5	-0.002	0.035	-9999	-0.61	1	1
VLDLR	0.003	0.083	-9999	-0.64	5	5
CRKL	0.011	0.047	-9999	-0.8	1	1
LRPAP1	0.013	0	-9999	-10000	0	0
FYN	0.011	0.047	-9999	-0.8	1	1
ITGA3	-0.026	0.18	-9999	-0.79	15	15
RELN/VLDLR/Fyn	-0.083	0.16	-9999	-0.4	63	63
MAPK8IP1/MKK7/MAP3K11/JNK1	-0.004	0.037	-9999	-10000	0	0
AKT1	-0.031	0.13	-9999	-0.54	4	4
MAP2K7	0.013	0	-9999	-10000	0	0
RAPGEF1	0.013	0	-9999	-10000	0	0
DAB1	-0.022	0.16	-9999	-0.8	12	12
RELN/LRP8/DAB1	-0.1	0.19	-9999	-0.42	72	72
LRPAP1/LRP8	-0.016	0.098	-9999	-0.61	8	8
RELN/LRP8/DAB1/Fyn	-0.095	0.18	-9999	-0.54	21	21
DAB1/alpha3/beta1 Integrin	-0.11	0.18	-9999	-0.72	7	7
long-term memory	-0.16	0.23	-9999	-0.77	18	18
DAB1/LIS1	-0.09	0.17	-9999	-0.75	6	6
DAB1/CRLK/C3G	-0.088	0.16	-9999	-0.72	7	7
PIK3CA	0.013	0	-9999	-10000	0	0
DAB1/NCK2	-0.091	0.17	-9999	-0.75	6	6
ARHGEF2	0.013	0	-9999	-10000	0	0
mol:Src family inhibitors PP1 and PP2	0	0	-9999	-10000	0	0
GRIN2A	-0.12	0.29	-9999	-0.72	56	56
CDK5R1	0.011	0.047	-9999	-0.8	1	1
RELN	-0.11	0.26	-9999	-0.64	57	57
PIK3R1	0.013	0	-9999	-10000	0	0
RELN/LRP8/Fyn	-0.09	0.18	-9999	-0.42	64	64
GRIN2A/RELN/LRP8/DAB1/Fyn	-0.16	0.23	-9999	-0.56	54	54
MAPK8	0.009	0.053	-9999	-0.64	2	2
RELN/VLDLR/DAB1	-0.093	0.18	-9999	-0.4	70	70
ITGB1	0.011	0.047	-9999	-0.8	1	1
MAP1B	-0.08	0.22	-9999	-0.64	19	19
RELN/LRP8	-0.088	0.18	-9999	-0.42	63	63
GRIN2B/RELN/LRP8/DAB1/Fyn	-0.098	0.19	-9999	-0.54	23	23
PI3K	0	0	-9999	-10000	0	0
mol:PP2	0	0	-9999	-10000	0	0
alpha3/beta1 Integrin	-0.032	0.14	-9999	-0.6	16	16
RAP1A	-0.036	0.18	-9999	-0.67	7	7
PAFAH1B1	0.013	0	-9999	-10000	0	0
MAPK8IP1	0.011	0.047	-9999	-0.8	1	1
CRLK/C3G	-0.002	0.035	-9999	-0.61	1	1
GRIN2B	-0.003	0.08	-9999	-0.8	3	3
NCK2	0.013	0	-9999	-10000	0	0
neuron differentiation	-0.012	0.11	-9999	-0.42	7	7
neuron adhesion	-0.041	0.19	-9999	-0.63	8	8
LRP8	-0.008	0.13	-9999	-0.8	8	8
GSK3B	-0.021	0.13	-9999	-0.5	4	4
RELN/VLDLR/DAB1/Fyn	-0.088	0.17	-9999	-0.56	13	13
MAP3K11	0.013	0	-9999	-10000	0	0
RELN/VLDLR/DAB1/P13K	-0.042	0.14	-9999	-0.57	4	4
CDK5	0.013	0	-9999	-10000	0	0
MAPT	-0.25	0.3	-9999	-0.6	131	131
neuron migration	-0.025	0.18	-9999	-0.56	6	6
RELN/LRP8/DAB1/Fyn/MAPK8IP1/MKK7/MAP3K11/JNK1	-0.012	0.11	-9999	-0.42	7	7
RELN/VLDLR	-0.085	0.16	-9999	-0.56	8	8

×

IL1-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
UBC13/UEV1A	0	0	-10000	0	-10000	0	0
PRKCZ	0.011	0.038	-10000	0	-0.64	1	1
MAP3K7IP2	0	0	-10000	0	-10000	0	0
ERC1	0.013	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4	-0.021	0.062	-10000	0	-10000	0	0
IRAK/TOLLIP	0.034	0.003	-10000	0	-10000	0	0
IKBKB	0.013	0	-10000	0	-10000	0	0
IKBKG	0.013	0	-10000	0	-10000	0	0
IL1 alpha/IL1R2	-0.24	0.3	-10000	0	-0.58	128	128
IL1A	-0.18	0.34	-10000	0	-0.8	72	72
IL1B	-0.037	0.19	-10000	0	-0.6	30	30
IRAK/TRAF6/p62/Atypical PKCs	-0.001	0.016	-10000	0	-10000	0	0
IL1R2	-0.13	0.27	-10000	0	-0.65	64	64
IL1R1	0.013	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.011	0.056	0.22	2	-10000	0	2
TOLLIP	0.013	0	-10000	0	-10000	0	0
TICAM2	0.013	0	-10000	0	-10000	0	0
MAP3K3	0.013	0	-10000	0	-10000	0	0
TAK1/TAB1/TAB2	0	0	-10000	0	-10000	0	0
IKK complex/ELKS	0.073	0.007	-10000	0	-10000	0	0
JUN	0.036	0.07	-10000	0	-10000	0	0
MAP3K7	0.013	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/PI3K	-0.042	0.12	-10000	0	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88	-0.11	0.2	-10000	0	-0.48	70	70
PIK3R1	0.013	0	-10000	0	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4	-0.11	0.19	-10000	0	-0.45	70	70
IL1 beta fragment/IL1R1/IL1RAP	-0.048	0.14	-10000	0	-0.48	28	28
NFKB1	0.013	0	-10000	0	-10000	0	0
MAPK8	0.029	0.074	-10000	0	-10000	0	0
IRAK1	0.029	0.004	-10000	0	-10000	0	0
IL1RN/IL1R1	-0.14	0.22	-10000	0	-0.47	90	90
IRAK4	0.013	0	-10000	0	-10000	0	0
PRKCI	0.013	0	-10000	0	-10000	0	0
TRAF6	0.013	0	-10000	0	-10000	0	0
PI3K	0	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	0.017	0.079	-10000	0	-10000	0	0
CHUK	0.013	0	-10000	0	-10000	0	0
IL1 beta fragment/IL1R1/IL1RAP/MYD88s	-0.048	0.14	-10000	0	-0.48	28	28
IL1 beta/IL1R2	-0.14	0.22	-10000	0	-0.56	35	35
IRAK/TRAF6/TAK1/TAB1/TAB2	0	0	-10000	0	-10000	0	0
NF kappa B1 p50/RelA	-0.037	0.11	-10000	0	-10000	0	0
IRAK3	-0.004	0.12	-10000	0	-0.76	7	7
IL1 beta fragment/IL1R1/IL1RAP/TICAM2/IRAK4	-0.042	0.12	-10000	0	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/TOLLIP	-0.03	0.12	-10000	0	-10000	0	0
IL1 alpha/IL1R1/IL1RAP	-0.13	0.22	-10000	0	-0.52	73	73
RELA	0.013	0	-10000	0	-10000	0	0
MAP3K7IP1	0	0	-10000	0	-10000	0	0
SQSTM1	0.013	0	-10000	0	-10000	0	0
MYD88	0.013	0	-10000	0	-10000	0	0
IRAK/TRAF6/MEKK3	0	0	-10000	0	-10000	0	0
IL1RAP	0.011	0.047	-10000	0	-0.8	1	1
UBE2N	0.013	0	-10000	0	-10000	0	0
IRAK/TRAF6	-0.034	0.1	-10000	0	-10000	0	0
CASP1	0.011	0.038	-10000	0	-0.64	1	1
IL1RN/IL1R2	-0.23	0.31	-10000	0	-0.59	119	119
IL1 beta fragment/IL1R1/IL1RAP/MYD88	-0.044	0.13	-10000	0	-0.45	28	28
TMEM189-UBE2V1	0.011	0.005	-10000	0	-10000	0	0
IL1 alpha/IL1R1/IL1RAP/MYD88/IRAK4/IRAK/TOLLIP	-0.036	0.078	-10000	0	-10000	0	0
PIK3CA	0.013	0	-10000	0	-10000	0	0
IL1RN	-0.18	0.3	-10000	0	-0.64	90	90
TRAF6/TAK1/TAB1/TAB2	0	0	-10000	0	-10000	0	0
MAP2K6	0.023	0.072	-10000	0	-10000	0	0

×

Presenilin action in Notch and Wnt signaling

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
Delta 1/NOTCH/NOTCH(cleaved)	-0.008	0.061	-10000	0	-0.62	2	2
HDAC1	0.001	0.007	-10000	0	-10000	0	0
AES	0.012	0.001	-10000	0	-10000	0	0
FBXW11	0.013	0	-10000	0	-10000	0	0
DTX1	0.011	0.038	-10000	0	-0.64	1	1
LRP6/FZD1	-0.01	0.078	-10000	0	-0.61	5	5
TLE1	0.013	0.001	-10000	0	-10000	0	0
AP1	-0.037	0.14	-10000	0	-0.32	51	51
NCSTN	0.013	0	-10000	0	-10000	0	0
ADAM10	0.013	0	-10000	0	-10000	0	0
Beta Catenin/TCF1/CtBP/CBP/TLE1/AES/SMAD4	0.038	0.048	-10000	0	-10000	0	0
NICD/RBPSUH	-0.004	0.05	-10000	0	-0.61	2	2
WIF1	-0.31	0.33	-10000	0	-0.65	145	145
NOTCH1	-0.005	0.053	-10000	0	-0.65	2	2
PSENEN	0.011	0.047	-10000	0	-0.8	1	1
KREMEN2	-0.27	0.39	-10000	0	-0.8	106	106
DKK1	-0.23	0.37	-10000	0	-0.78	93	93
beta catenin/beta TrCP1	0.017	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	0.024	-10000	0	-0.27	1	1
CtBP/CBP/TCF1/TLE1/AES	-0.002	0.044	-10000	0	-10000	0	0
PSEN1	0.013	0	-10000	0	-10000	0	0
FOS	-0.092	0.24	-10000	0	-0.64	49	49
JUN	0.013	0	-10000	0	-10000	0	0
MAP3K7	0.012	0.003	-10000	0	-10000	0	0
CTNNB1	0.01	0.043	-10000	0	-10000	0	0
MAPK3	0.013	0	-10000	0	-10000	0	0
DKK2/LRP6/Kremen 2	-0.2	0.26	-10000	0	-0.53	114	114
HNF1A	-0.004	0.11	-10000	0	-0.8	6	6
CTBP1	0.012	0.001	-10000	0	-10000	0	0
MYC	0.025	0.014	-10000	0	-10000	0	0
NKD1	-0.015	0.14	-10000	0	-0.76	11	11
FZD1	0	0.1	-10000	0	-0.8	5	5
NOTCH1 precursor/Deltex homolog 1	-0.005	0.064	-10000	0	-0.78	2	2
apoptosis	-0.037	0.14	-10000	0	-0.31	51	51
Delta 1/NOTCHprecursor	-0.008	0.061	-10000	0	-0.61	2	2
DLL1	0.005	0.075	-10000	0	-0.64	4	4
PPARD	0.025	0.014	-10000	0	-10000	0	0
Gamma Secretase	-0.001	0.026	-10000	0	-0.45	1	1
APC	0.002	0.024	-10000	0	-0.27	1	1
DVL1	-0.026	0.026	-10000	0	-10000	0	0
CSNK2A1	0.014	0.002	-10000	0	-10000	0	0
MAP3K7IP1	-0.002	0.003	-10000	0	-10000	0	0
DKK1/LRP6/Kremen 2	-0.34	0.34	-10000	0	-0.62	164	164
LRP6	0.013	0	-10000	0	-10000	0	0
CSNK1A1	0.014	0.002	-10000	0	-10000	0	0
NLK	0.014	0.006	-10000	0	-10000	0	0
CCND1	0.001	0.18	-10000	0	-1.1	7	7
WNT1	0.005	0.066	-10000	0	-0.8	2	2
Axin1/APC/beta catenin	0.023	0.04	-10000	0	-0.35	1	1
DKK2	-0.011	0.14	-10000	0	-0.74	10	10
NOTCH1 precursor/DVL1	-0.011	0.049	-10000	0	-0.61	2	2
GSK3B	0.013	0.001	-10000	0	-10000	0	0
FRAT1	0.013	0.001	-10000	0	-10000	0	0
NOTCH/Deltex homolog 1	-0.005	0.064	-10000	0	-0.78	2	2
PPP2R5D	-0.001	0.063	0.31	11	-10000	0	11
MAPK1	0.013	0	-10000	0	-10000	0	0
WNT1/LRP6/FZD1	-0.18	0.18	-10000	0	-0.48	15	15
RBPJ	0.013	0	-10000	0	-10000	0	0
CREBBP	0.017	0.003	-10000	0	-10000	0	0

×

Integrins in angiogenesis

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	-0.004	0.05	-9999	-0.61	2	2
alphaV beta3 Integrin	-0.04	0.14	-9999	-0.52	23	23
PTK2	-0.002	0.15	-9999	-0.64	4	4
IGF1R	0.013	0	-9999	-10000	0	0
PI4KB	0.013	0	-9999	-10000	0	0
MFGE8	0.013	0	-9999	-10000	0	0
SRC	0.013	0	-9999	-10000	0	0
CDKN1B	-0.047	0.12	-9999	-0.4	27	27
VEGFA	0.011	0.047	-9999	-0.8	1	1
ILK	-0.047	0.12	-9999	-0.4	27	27
ROCK1	0.013	0	-9999	-10000	0	0
AKT1	-0.042	0.11	-9999	-0.49	3	3
PTK2B	0.018	0.11	-9999	-0.66	1	1
alphaV/beta3 Integrin/JAM-A	-0.073	0.18	-9999	-0.5	40	40
CBL	0.013	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
alphaV beta3 Integrin/ANGPTL3	-0.028	0.12	-9999	-0.53	16	16
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.037	0.11	-9999	-0.48	5	5
VEGF/Rho/ROCK/alphaV/beta3 Integrin	0.013	0.089	-9999	-0.42	3	3
alphaV/beta3 Integrin/Syndecan-1	-0.024	0.11	-9999	-0.53	14	14
PI4KA	0.013	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.29	0.25	-9999	-0.82	26	26
PI4 Kinase	0	0	-9999	-10000	0	0
PIK3CA	0.013	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Osteopontin	-0.32	0.28	-9999	-0.55	178	178
RPS6KB1	-0.24	0.26	-9999	-0.75	26	26
TLN1	0.011	0.047	-9999	-0.8	1	1
MAPK3	-0.12	0.16	-9999	-0.72	11	11
GPR124	0.008	0.066	-9999	-0.8	2	2
MAPK1	-0.12	0.16	-9999	-0.7	12	12
PXN	0.013	0	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Tumstatin	-0.086	0.2	-9999	-0.53	49	49
cell adhesion	-0.023	0.1	-9999	-0.46	12	12
ANGPTL3	-0.001	0.066	-9999	-0.8	2	2
VEGFR2 homodimer/VEGFA homodimer/Src	-0.003	0.043	-9999	-0.53	2	2
IGF-1R heterotetramer	0.013	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
TGFBR2	0.013	0	-9999	-10000	0	0
ITGB3	-0.017	0.15	-9999	-0.76	12	12
IGF1	-0.054	0.2	-9999	-0.67	30	30
RAC1	0.013	0	-9999	-10000	0	0
regulation of cell-matrix adhesion	-0.027	0.12	-9999	-0.56	15	15
apoptosis	0.006	0.076	-9999	-0.75	3	3
CD47	0.013	0	-9999	-10000	0	0
alphaV/beta3 Integrin/CD47	-0.024	0.11	-9999	-0.53	14	14
VCL	0.013	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Del1	-0.075	0.2	-9999	-0.56	41	41
CSF1	0.009	0.053	-9999	-0.64	2	2
PIK3C2A	-0.047	0.12	-9999	-0.4	27	27
PI4 Kinase/Pyk2	-0.063	0.15	-9999	-0.74	5	5
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	-0.025	0.11	-9999	-0.5	14	14
FAK1/Vinculin	0.009	0.12	-9999	-0.51	3	3
alphaV beta3/Integrin/ppsTEM5	-0.028	0.12	-9999	-0.56	15	15
RHOA	0.013	0	-9999	-10000	0	0
VTN	-0.059	0.23	-9999	-0.8	27	27
BCAR1	0.013	0	-9999	-10000	0	0
FGF2	-0.012	0.13	-9999	-0.68	11	11
F11R	0.005	0.1	-9999	-0.51	11	11
alphaV/beta3 Integrin/Lactadherin	-0.024	0.11	-9999	-0.53	14	14
alphaV/beta3 Integrin/TGFBR2	-0.024	0.11	-9999	-0.53	14	14
alphaV/beta3 Integrin/c-FMS/Cbl/Cas	-0.007	0.052	-9999	-0.48	2	2
HSP90AA1	0.013	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Talin	-0.024	0.11	-9999	-0.49	15	15
mol:GDP	0	0	-9999	-10000	0	0
FN1	-0.44	0.4	-9999	-0.8	170	170
alphaV/beta3 Integrin/Pyk2	-0.023	0.1	-9999	-0.67	1	1
SDC1	0.013	0	-9999	-10000	0	0
VAV3	0.011	0.11	-9999	-10000	0	0
PTPN11	0.013	0	-9999	-10000	0	0
IRS1	0.013	0	-9999	-10000	0	0
FAK1/Paxillin	0.009	0.12	-9999	-0.51	3	3
cell migration	0.019	0.12	-9999	-0.45	3	3
ITGAV	0.006	0.076	-9999	-0.75	3	3
PI3K	-0.065	0.16	-9999	-0.79	5	5
SPP1	-0.45	0.4	-9999	-0.8	171	171
KDR	0.011	0.047	-9999	-0.8	1	1
mol:PI-4-5-P2	0	0	-9999	-10000	0	0
alphaV/beta3 Integrin/Caspase 8	0.006	0.076	-9999	-0.75	3	3
COL4A3	-0.084	0.26	-9999	-0.76	38	38
angiogenesis	-0.094	0.18	-9999	-0.77	9	9
Rac1/GTP	-0.026	0.085	-9999	-10000	0	0
EDIL3	-0.067	0.24	-9999	-0.77	31	31
cell proliferation	-0.024	0.11	-9999	-0.52	14	14

×

EPHB forward signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Ephrin A5/EPHB2	-0.13	0.24	-10000	0	-0.54	75	75
cell-cell adhesion	0.12	0.16	0.56	3	-10000	0	3
Ephrin B/EPHB2/RasGAP	-0.12	0.19	-10000	0	-0.45	67	67
ITSN1	0.013	0	-10000	0	-10000	0	0
PIK3CA	0.013	0	-10000	0	-10000	0	0
SHC1	0.013	0	-10000	0	-10000	0	0
Ephrin B1/EPHB3	-0.012	0.069	-10000	0	-0.4	9	9
Ephrin B1/EPHB1	-0.033	0.12	-10000	0	-0.5	20	20
HRAS/GDP	-0.057	0.11	-10000	0	-0.57	2	2
Ephrin B/EPHB1/GRB7	-0.052	0.14	-10000	0	-0.47	19	19
Endophilin/SYNJ1	-0.081	0.2	-10000	0	-0.42	67	67
KRAS	0.013	0	-10000	0	-10000	0	0
Ephrin B/EPHB1/Src	-0.046	0.13	-10000	0	-0.47	16	16
endothelial cell migration	0	0	-10000	0	-10000	0	0
GRB2	0.013	0	-10000	0	-10000	0	0
GRB7	0.003	0.089	-10000	0	-0.76	4	4
PAK1	-0.096	0.22	-10000	0	-0.68	8	8
HRAS	0.013	0	-10000	0	-10000	0	0
RRAS	-0.082	0.2	-10000	0	-0.43	67	67
DNM1	-0.043	0.21	-10000	0	-0.8	21	21
cell-cell signaling	0	0	-10000	0	-10000	0	0
CRK	-0.007	0.14	-10000	0	-0.45	16	16
lamellipodium assembly	-0.12	0.16	-10000	0	-0.56	3	3
Ephrin B/EPHB1/Src/p52 SHC/GRB2	0.009	0.097	-10000	0	-0.5	2	2
PIK3R1	0.013	0	-10000	0	-10000	0	0
EPHB2	-0.17	0.34	-10000	0	-0.8	67	67
EPHB3	-0.006	0.11	-10000	0	-0.64	9	9
EPHB1	-0.037	0.19	-10000	0	-0.75	20	20
EPHB4	0.013	0	-10000	0	-10000	0	0
mol:GDP	-0.054	0.11	-10000	0	-0.52	3	3
Ephrin B/EPHB2	-0.12	0.2	-10000	0	-0.46	67	67
Ephrin B/EPHB3	-0.03	0.099	-10000	0	-0.68	1	1
JNK cascade	-0.093	0.22	-10000	0	-0.44	81	81
Ephrin B/EPHB1	-0.047	0.13	-10000	0	-0.48	16	16
RAP1/GDP	-0.045	0.096	-10000	0	-0.48	2	2
EFNB2	0.013	0	-10000	0	-10000	0	0
EFNB3	-0.025	0.16	-10000	0	-0.64	18	18
EFNB1	0.013	0	-10000	0	-10000	0	0
Ephrin B2/EPHB1-2	-0.14	0.22	-10000	0	-0.48	87	87
RAP1B	0.011	0.047	-10000	0	-0.8	1	1
RAP1A	0.013	0	-10000	0	-10000	0	0
CDC42/GTP	-0.12	0.17	-10000	0	-0.62	3	3
Rap1/GTP	-0.12	0.16	-10000	0	-0.57	3	3
axon guidance	-0.13	0.23	-10000	0	-0.53	75	75
MAPK3	0.026	0.088	-10000	0	-0.44	2	2
MAPK1	0.026	0.088	-10000	0	-0.44	2	2
Rac1/GDP	-0.012	0.12	-10000	0	-0.47	3	3
actin cytoskeleton reorganization	-0.091	0.13	-10000	0	-0.44	3	3
CDC42/GDP	-0.012	0.12	-10000	0	-0.5	2	2
PI3K	0	0	-10000	0	-10000	0	0
EFNA5	-0.01	0.12	-10000	0	-0.64	11	11
Ephrin B2/EPHB4	0	0	-10000	0	-10000	0	0
Ephrin B/EPHB2/Intersectin/N-WASP	-0.042	0.13	-10000	0	-0.54	1	1
CDC42	0.013	0	-10000	0	-10000	0	0
RAS family/GTP	-0.11	0.16	-10000	0	-0.55	3	3
PTK2	0.029	0.046	-10000	0	-10000	0	0
MAP4K4	-0.094	0.22	-10000	0	-0.44	81	81
SRC	0.013	0	-10000	0	-10000	0	0
KALRN	-0.025	0.16	-10000	0	-0.64	18	18
Intersectin/N-WASP	0	0	-10000	0	-10000	0	0
neuron projection morphogenesis	-0.047	0.17	-10000	0	-0.49	5	5
MAP2K1	0.018	0.092	-10000	0	-0.47	2	2
WASL	0.013	0	-10000	0	-10000	0	0
Ephrin B1/EPHB1-2/NCK1	-0.14	0.21	-10000	0	-0.48	81	81
cell migration	0.022	0.1	-10000	0	-0.54	2	2
NRAS	0.013	0	-10000	0	-10000	0	0
SYNJ1	-0.082	0.2	-10000	0	-0.74	1	1
PXN	0.013	0	-10000	0	-10000	0	0
TF	-0.3	0.25	-10000	0	-0.7	62	62
HRAS/GTP	-0.12	0.18	-10000	0	-0.61	3	3
Ephrin B1/EPHB1-2	-0.14	0.22	-10000	0	-0.48	87	87
cell adhesion mediated by integrin	0.014	0.087	0.41	2	-10000	0	2
RAC1	0.013	0	-10000	0	-10000	0	0
mol:GTP	-0.13	0.19	-10000	0	-0.66	3	3
RAC1-CDC42/GTP	-0.12	0.17	-10000	0	-0.58	6	6
RASA1	0.013	0	-10000	0	-10000	0	0
RAC1-CDC42/GDP	-0.043	0.094	-10000	0	-0.48	2	2
ruffle organization	-0.068	0.2	-10000	0	-0.57	3	3
NCK1	0.013	0	-10000	0	-10000	0	0
receptor internalization	-0.1	0.24	-10000	0	-0.82	11	11
Ephrin B/EPHB2/KALRN	-0.14	0.21	-10000	0	-0.7	7	7
ROCK1	0.016	0.066	-10000	0	-10000	0	0
RAS family/GDP	-0.088	0.13	-10000	0	-0.5	1	1
Rac1/GTP	-0.12	0.17	-10000	0	-0.6	3	3
Ephrin B/EPHB1/Src/Paxillin	0.003	0.1	-10000	0	-0.55	2	2

×

Regulation of nuclear SMAD2/3 signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EP300	0.007	0.011	-10000	0	-10000	0	0
HSPA8	0.016	0.005	-10000	0	-10000	0	0
SMAD3/SMAD4/ER alpha	0.053	0.17	-10000	0	-0.54	12	12
AKT1	0.002	0.031	-10000	0	-10000	0	0
GSC	-0.017	0.18	-10000	0	-0.63	23	23
NKX2-5	-0.2	0.35	-10000	0	-0.79	80	80
muscle cell differentiation	0.15	0.22	0.68	27	-10000	0	27
SMAD2-3/SMAD4/SP1	-0.059	0.1	-10000	0	-10000	0	0
SMAD4	-0.001	0.054	-10000	0	-0.61	1	1
CBFB	0.013	0	-10000	0	-10000	0	0
SAP18	0.014	0.002	-10000	0	-10000	0	0
Cbp/p300/MSG1	0.001	0.048	-10000	0	-0.53	2	2
SMAD3/SMAD4/VDR	0.005	0.039	-10000	0	-10000	0	0
MYC	0.025	0.032	-10000	0	-10000	0	0
CDKN2B	-0.22	0.56	-10000	0	-1.4	57	57
AP1	-0.02	0.13	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/SnoN/SIN3/HDAC complex/NCoR1	0.057	0.038	-10000	0	-10000	0	0
SMAD2-3/SMAD4/FOXO1-3a-4/FOXG1	-0.054	0.16	-10000	0	-0.59	7	7
SP3	0.016	0.001	-10000	0	-10000	0	0
CREB1	0.013	0	-10000	0	-10000	0	0
FOXH1	-0.08	0.26	-10000	0	-0.79	34	34
SMAD3/SMAD4/GR	0.035	0.073	-10000	0	-10000	0	0
GATA3	-0.013	0.14	-10000	0	-0.76	10	10
SKI/SIN3/HDAC complex/NCoR1	0.058	0.017	-10000	0	-10000	0	0
MEF2C/TIF2	-0.16	0.25	-10000	0	-0.78	20	20
endothelial cell migration	0.37	0.32	0.64	181	-10000	0	181
MAX	0.035	0.02	-10000	0	-10000	0	0
RBBP7	0.014	0.002	-10000	0	-10000	0	0
RBBP4	0.014	0.002	-10000	0	-10000	0	0
RUNX2	0.011	0.038	-10000	0	-0.64	1	1
RUNX3	0.005	0.081	-10000	0	-0.8	3	3
RUNX1	0.013	0	-10000	0	-10000	0	0
CTBP1	0.013	0	-10000	0	-10000	0	0
NR3C1	0.035	0.02	-10000	0	-10000	0	0
VDR	0.013	0	-10000	0	-10000	0	0
CDKN1A	-0.001	0.095	-10000	0	-10000	0	0
KAT2B	-0.019	0.13	-10000	0	-0.65	13	13
SMAD2/SMAD2/SMAD4/FOXH1	-0.06	0.18	-10000	0	-0.54	34	34
DCP1A	0.013	0	-10000	0	-10000	0	0
SKI	0.014	0.002	-10000	0	-10000	0	0
SERPINE1	-0.37	0.33	-10000	0	-0.64	181	181
SMAD3/SMAD4/ATF2	0.009	0.054	-10000	0	-10000	0	0
SMAD3/SMAD4/ATF3	0.002	0.084	-10000	0	-0.52	4	4
SAP30	0.014	0.002	-10000	0	-10000	0	0
Cbp/p300/PIAS3	0.002	0.028	-10000	0	-10000	0	0
JUN	-0.005	0.13	-10000	0	-10000	0	0
SMAD3/SMAD4/IRF7	-0.001	0.1	-10000	0	-0.63	4	4
TFE3	0	0.017	-10000	0	-10000	0	0
COL1A2	-0.34	0.35	-10000	0	-0.68	155	155
mesenchymal cell differentiation	-0.008	0.059	-10000	0	-10000	0	0
DLX1	-0.38	0.41	-10000	0	-0.8	146	146
TCF3	0.013	0	-10000	0	-10000	0	0
FOS	-0.087	0.24	-10000	0	-0.63	49	49
SMAD3/SMAD4/Max	0.035	0.073	-10000	0	-10000	0	0
Cbp/p300/SNIP1	0.002	0.01	-10000	0	-10000	0	0
ZBTB17	0.023	0.025	-10000	0	-10000	0	0
LAMC1	0.005	0.048	-10000	0	-10000	0	0
TGIF2/HDAC complex/SMAD3/SMAD4	0.007	0.066	-10000	0	-0.64	1	1
IRF7	0	0.1	-10000	0	-0.8	5	5
ESR1	-0.009	0.18	-10000	0	-0.74	17	17
HNF4A	-0.07	0.24	-10000	0	-0.8	30	30
MEF2C	-0.15	0.28	-10000	0	-0.77	23	23
SMAD2-3/SMAD4	-0.003	0.067	-10000	0	-10000	0	0
Cbp/p300/Src-1	0.005	0.018	-10000	0	-10000	0	0
IGHV3OR16-13	-0.002	0.012	-10000	0	-10000	0	0
TGIF2/HDAC complex	0.011	0.047	-10000	0	-0.8	1	1
CREBBP	0.007	0.01	-10000	0	-10000	0	0
SKIL	0.013	0	-10000	0	-10000	0	0
HDAC1	0.014	0.002	-10000	0	-10000	0	0
HDAC2	0.014	0.002	-10000	0	-10000	0	0
SNIP1	0.015	0.005	-10000	0	-10000	0	0
GCN5L2	-0.009	0.013	-10000	0	-10000	0	0
SMAD3/SMAD4/TFE3	-0.009	0.05	-10000	0	-10000	0	0
MSG1/HSC70	0.014	0.053	-10000	0	-0.61	2	2
SMAD2	0.002	0.036	-10000	0	-10000	0	0
SMAD3	0.004	0.051	-10000	0	-0.59	1	1
SMAD3/E2F4-5/DP1/p107/SMAD4	0.023	0.043	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4	-0.025	0.084	-10000	0	-0.39	14	14
NCOR1	0.014	0.002	-10000	0	-10000	0	0
NCOA2	0.005	0.075	-10000	0	-0.64	4	4
NCOA1	0.013	0	-10000	0	-10000	0	0
MYOD/E2A	-0.088	0.19	-10000	0	-0.48	56	56
SMAD2-3/SMAD4/SP1/MIZ-1	-0.048	0.098	-10000	0	-10000	0	0
IFNB1	0.01	0.13	-10000	0	-0.85	4	4
SMAD3/SMAD4/MEF2C	-0.14	0.27	-10000	0	-0.81	17	17
CITED1	0.008	0.066	-10000	0	-0.8	2	2
SMAD2-3/SMAD4/ARC105	0.004	0.068	-10000	0	-0.54	1	1
RBL1	0.013	0	-10000	0	-10000	0	0
SMAD2-3/SMAD4/FOXO1-3a-4/CEBPB	-0.054	0.22	-10000	0	-0.5	56	56
RUNX1-3/PEBPB2	-0.005	0.052	-10000	0	-0.53	3	3
SMAD7	-0.042	0.13	-10000	0	-10000	0	0
MYC/MIZ-1	0.03	0.063	-10000	0	-10000	0	0
SMAD3/SMAD4	-0.13	0.15	0.35	4	-0.4	4	8
IL10	0	0.17	-10000	0	-0.69	12	12
PIASy/HDAC complex	0.023	0.012	-10000	0	-10000	0	0
PIAS3	0.006	0.008	-10000	0	-10000	0	0
CDK2	0.007	0.009	-10000	0	-10000	0	0
IL5	0.002	0.14	-10000	0	-0.71	5	5
CDK4	0.007	0.01	-10000	0	-10000	0	0
PIAS4	0.023	0.012	-10000	0	-10000	0	0
ATF3	0.002	0.092	-10000	0	-0.71	5	5
SMAD3/SMAD4/SP1	-0.077	0.087	-10000	0	-10000	0	0
FOXG1	-0.1	0.26	-10000	0	-0.72	44	44
FOXO3	0.01	0.042	-10000	0	-10000	0	0
FOXO1	0.01	0.042	-10000	0	-10000	0	0
FOXO4	0.007	0.057	-10000	0	-0.47	2	2
heart looping	-0.14	0.28	-10000	0	-0.76	23	23
CEBPB	0.008	0.015	-10000	0	-10000	0	0
SMAD3/SMAD4/DLX1	-0.27	0.29	-10000	0	-0.57	146	146
MYOD1	-0.11	0.26	-10000	0	-0.65	56	56
SMAD3/SMAD4/HNF4	-0.049	0.18	-10000	0	-0.56	30	30
SMAD3/SMAD4/GATA3	-0.012	0.13	-10000	0	-0.57	8	8
SnoN/SIN3/HDAC complex/NCoR1	0.013	0	-10000	0	-10000	0	0
SMAD3/SMAD4/RUNX1-3/PEBPB2	0.013	0.068	-10000	0	-0.47	3	3
SMAD3/SMAD4/SP1-3	-0.056	0.07	-10000	0	-10000	0	0
MED15	0.011	0.047	-10000	0	-0.8	1	1
SP1	-0.053	0.075	-10000	0	-10000	0	0
SIN3B	0.014	0.002	-10000	0	-10000	0	0
SIN3A	0.014	0.002	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/NKX2-5	-0.18	0.28	-10000	0	-0.58	70	70
ITGB5	-0.012	0.093	-10000	0	-10000	0	0
TGIF/SIN3/HDAC complex/CtBP	0.054	0.01	-10000	0	-10000	0	0
SMAD3/SMAD4/AR	-0.069	0.18	-10000	0	-0.52	16	16
AR	-0.11	0.26	-10000	0	-0.65	57	57
negative regulation of cell growth	0.025	0.056	-10000	0	-10000	0	0
SMAD3/SMAD4/MYOD	-0.075	0.18	-10000	0	-0.46	37	37
E2F5	0.013	0	-10000	0	-10000	0	0
E2F4	0.013	0	-10000	0	-10000	0	0
SMAD2/SMAD2/SMAD4/FOXH1/SMIF	-0.054	0.15	-10000	0	-0.5	10	10
SMAD2-3/SMAD4/FOXO1-3a-4	-0.026	0.15	-10000	0	-10000	0	0
TFDP1	0.011	0.047	-10000	0	-0.8	1	1
SMAD3/SMAD4/AP1	-0.012	0.14	-10000	0	-10000	0	0
SMAD3/SMAD4/RUNX2	0.008	0.059	-10000	0	-10000	0	0
TGIF2	0.011	0.047	-10000	0	-0.8	1	1
TGIF1	0.013	0	-10000	0	-10000	0	0
ATF2	0.013	0	-10000	0	-10000	0	0

×

Nephrin/Neph1 signaling in the kidney podocyte

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
positive regulation of NF-kappaB transcription factor activity	0.046	0.16	0.62	22	-10000	0	22
KIRREL	0.006	0.042	-10000	0	-0.64	1	1
Nephrin/NEPH1Par3/Par6/Atypical PKCs	-0.047	0.16	-10000	0	-0.62	22	22
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	-0.046	0.16	-10000	0	-0.55	25	25
ChemicalAbstracts:57-88-5	0	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/NCK1-2/N-WASP	0.002	0.1	-10000	0	-0.56	5	5
FYN	-0.025	0.15	-10000	0	-0.49	26	26
mol:Ca2+	-0.046	0.16	-10000	0	-0.54	25	25
mol:DAG	-0.046	0.16	-10000	0	-0.54	25	25
NPHS2	-0.025	0.14	-10000	0	-0.84	9	9
mol:IP3	-0.046	0.16	-10000	0	-0.54	25	25
regulation of endocytosis	-0.04	0.14	-10000	0	-0.72	6	6
Nephrin/NEPH1/podocin/Cholesterol	-0.047	0.16	-10000	0	-0.55	26	26
establishment of cell polarity	-0.046	0.16	-10000	0	-0.62	22	22
Nephrin/NEPH1/podocin/NCK1-2	-0.042	0.15	-10000	0	-0.52	20	20
Nephrin/NEPH1/beta Arrestin2	-0.041	0.14	-10000	0	-0.73	6	6
NPHS1	-0.05	0.21	-10000	0	-0.81	21	21
Nephrin/NEPH1/podocin	-0.044	0.15	-10000	0	-0.5	26	26
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	-0.046	0.16	-10000	0	-0.55	25	25
CD2AP	0.013	0	-10000	0	-10000	0	0
Nephrin/NEPH1/podocin/GRB2	-0.046	0.16	-10000	0	-0.55	25	25
GRB2	0.013	0	-10000	0	-10000	0	0
homophilic cell adhesion	0	0	-10000	0	-10000	0	0
TRPC6	-0.063	0.21	-10000	0	-0.51	49	49
cytoskeleton organization	0	0.14	-10000	0	-0.75	5	5
Nephrin/NEPH1	-0.035	0.12	-10000	0	-0.47	22	22
Nephrin/NEPH1/ZO-1	-0.038	0.13	-10000	0	-0.51	22	22

×

Signaling events mediated by PTP1B

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
PDGFRB	-0.22	0.37	-10000	0	-0.8	85	85
Jak2/Leptin Receptor	-0.074	0.1	-10000	0	-0.38	6	6
PTP1B/AKT1	-0.029	0.078	0.23	1	-0.31	1	2
FYN	0.011	0.047	-10000	0	-0.8	1	1
p210 bcr-abl/PTP1B	-0.041	0.087	0.26	1	-0.32	2	3
EGFR	-0.017	0.14	-10000	0	-0.8	10	10
EGF/EGFR	-0.13	0.16	-10000	0	-0.45	30	30
CSF1	0.009	0.053	-10000	0	-0.64	2	2
AKT1	0.013	0.001	-10000	0	-10000	0	0
INSR	0.013	0.001	-10000	0	-10000	0	0
PTP1B/N-cadherin	-0.12	0.21	0.23	1	-0.53	55	56
Insulin Receptor/Insulin	-0.033	0.043	-10000	0	-10000	0	0
HCK	0.004	0.084	-10000	0	-0.72	4	4
CRK	0.013	0	-10000	0	-10000	0	0
TYK2	-0.031	0.083	0.25	1	-0.33	1	2
EGF	-0.14	0.28	-10000	0	-0.65	69	69
YES1	0.013	0	-10000	0	-10000	0	0
CAV1	-0.062	0.11	0.25	1	-0.36	11	12
TXN	0.01	0.006	-10000	0	-10000	0	0
PTP1B/IRS1/GRB2	-0.036	0.067	-10000	0	-10000	0	0
cell migration	0.041	0.087	0.32	2	-0.26	1	3
STAT3	0.013	0.001	-10000	0	-10000	0	0
PRLR	-0.13	0.27	-10000	0	-0.65	64	64
ITGA2B	-0.041	0.2	-10000	0	-0.8	20	20
CSF1R	0.009	0.053	-10000	0	-0.64	2	2
Prolactin Receptor/Prolactin	-0.1	0.21	-10000	0	-0.49	66	66
FGR	0.011	0.047	-10000	0	-0.8	1	1
PTP1B/p130 Cas	-0.032	0.082	-10000	0	-10000	0	0
Crk/p130 Cas	-0.036	0.067	-10000	0	-10000	0	0
DOK1	-0.079	0.15	0.25	1	-0.4	12	13
JAK2	-0.07	0.12	-10000	0	-0.35	20	20
Jak2/Leptin Receptor/Leptin	-0.086	0.12	-10000	0	-0.49	1	1
PIK3R1	0.013	0	-10000	0	-10000	0	0
PTPN1	-0.042	0.088	0.26	1	-0.32	2	3
LYN	0.013	0	-10000	0	-10000	0	0
CDH2	-0.13	0.31	-10000	0	-0.79	55	55
SRC	0	0.037	-10000	0	-10000	0	0
ITGB3	-0.018	0.15	-10000	0	-0.76	12	12
CAT1/PTP1B	-0.14	0.16	0.26	1	-0.45	18	19
CAPN1	0.011	0.005	-10000	0	-10000	0	0
CSK	0.013	0	-10000	0	-10000	0	0
PI3K	-0.022	0.037	-10000	0	-10000	0	0
mol:H2O2	0	0.006	-10000	0	-10000	0	0
STAT3 (dimer)	-0.076	0.11	-10000	0	-0.46	1	1
negative regulation of transcription	-0.069	0.12	-10000	0	-0.35	20	20
FCGR2A	-0.046	0.21	-10000	0	-0.8	22	22
FER	0.01	0.006	-10000	0	-10000	0	0
alphaIIb/beta3 Integrin	-0.063	0.19	-10000	0	-0.62	31	31
BLK	-0.12	0.3	-10000	0	-0.77	53	53
Insulin Receptor/Insulin/Shc	0	0.002	-10000	0	-10000	0	0
RHOA	0.011	0.005	-10000	0	-10000	0	0
LEPR	0.013	0.001	-10000	0	-10000	0	0
BCAR1	0.013	0	-10000	0	-10000	0	0
p210 bcr-abl/Grb2	0.013	0	-10000	0	-10000	0	0
mol:NADPH	-0.002	0.004	-10000	0	-10000	0	0
TRPV6	-0.13	0.16	-10000	0	-0.46	33	33
PRL	-0.004	0.08	-10000	0	-0.8	3	3
SOCS3	0.018	0.082	-10000	0	-1.4	1	1
SPRY2	0.004	0.075	-10000	0	-0.65	4	4
Insulin Receptor/Insulin/IRS1	0	0.002	-10000	0	-10000	0	0
CSF1/CSF1R	-0.041	0.074	-10000	0	-0.39	1	1
Ras protein signal transduction	0.03	0.028	-10000	0	-10000	0	0
IRS1	0.013	0	-10000	0	-10000	0	0
INS	0	0.001	-10000	0	-10000	0	0
LEP	-0.11	0.26	-10000	0	-0.7	50	50
STAT5B	-0.048	0.085	0.21	1	-0.29	4	5
STAT5A	-0.048	0.085	0.21	1	-0.29	4	5
GRB2	0.013	0	-10000	0	-10000	0	0
PDGFB-D/PDGFRB	-0.16	0.26	0.23	1	-0.56	85	86
CSN2	-0.025	0.09	-10000	0	-0.66	1	1
PIK3CA	0.013	0	-10000	0	-10000	0	0
LAT	-0.027	0.093	-10000	0	-0.31	19	19
YBX1	0.02	0.002	-10000	0	-10000	0	0
LCK	-0.014	0.15	-10000	0	-0.8	10	10
SHC1	0.013	0	-10000	0	-10000	0	0
NOX4	-0.21	0.36	-10000	0	-0.8	83	83

×

Syndecan-3-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
CTTN	-0.005	0.12	-9999	-0.8	7	7
Syndecan-3/Src/Cortactin	-0.12	0.16	-9999	-0.59	7	7
Syndecan-3/Neurocan	-0.012	0.07	-9999	-0.44	8	8
POMC	-0.067	0.24	-9999	-0.77	31	31
EGFR	-0.014	0.15	-9999	-0.8	10	10
Syndecan-3/EGFR	-0.016	0.082	-9999	-0.44	11	11
AGRP	0.005	0.006	-9999	-10000	0	0
NCSTN	0.013	0	-9999	-10000	0	0
PSENEN	0.011	0.047	-9999	-0.8	1	1
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	-0.009	0.12	-9999	-0.8	7	7
long-term memory	-0.012	0.069	-9999	-0.42	8	8
Syndecan-3/IL8	-0.097	0.18	-9999	-0.45	65	65
PSEN1	0.013	0	-9999	-10000	0	0
Src/Cortactin	-0.014	0.092	-9999	-0.61	7	7
FYN	0.011	0.047	-9999	-0.8	1	1
limb bud formation	-0.001	0.021	-9999	-0.36	1	1
MC4R	0.006	0.007	-9999	-10000	0	0
SRC	0.013	0	-9999	-10000	0	0
PTN	-0.23	0.32	-9999	-0.64	111	111
FGFR/FGF/Syndecan-3	-0.001	0.022	-9999	-0.37	1	1
neuron projection morphogenesis	-0.12	0.16	-9999	-0.69	5	5
Syndecan-3/AgRP	-0.001	0.021	-9999	-0.35	1	1
Syndecan-3/AgRP/MC4R	-0.001	0.019	-9999	-10000	0	0
Fyn/Cortactin	-0.016	0.098	-9999	-0.61	8	8
SDC3	-0.002	0.022	-9999	-0.37	1	1
GO:0007205	0	0	-9999	-10000	0	0
positive regulation of leukocyte migration	-0.096	0.18	-9999	-0.44	65	65
IL8	-0.16	0.33	-9999	-0.8	65	65
Syndecan-3/Fyn/Cortactin	-0.013	0.071	-9999	-0.43	8	8
Syndecan-3/CASK	-0.001	0.021	-9999	-0.35	1	1
alpha-MSH/MC4R	-0.06	0.18	-9999	-0.59	31	31
Gamma Secretase	-0.001	0.026	-9999	-10000	0	0

×

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	-0.057	0.12	-9999	-0.47	7	7
NF kappa B1 p50/RelA/I kappa B alpha	-0.022	0.048	-9999	-10000	0	0
AP1	-0.097	0.14	-9999	-0.55	8	8
mol:PIP3	-0.055	0.1	-9999	-0.63	1	1
AKT1	-0.034	0.071	-9999	-0.5	2	2
PTK2B	-0.008	0.079	-9999	-0.29	1	1
RHOA	0.003	0.063	-9999	-10000	0	0
PIK3CB	0.013	0.001	-9999	-10000	0	0
mol:Ca2+	0.008	0.07	-9999	-0.46	2	2
MAGI3	0.013	0	-9999	-10000	0	0
RELA	0.013	0	-9999	-10000	0	0
apoptosis	-0.031	0.12	-9999	-0.34	10	10
HRAS/GDP	0	0	-9999	-10000	0	0
positive regulation of microtubule depolymerization	-0.13	0.17	-9999	-0.45	24	24
NF kappa B1 p50/RelA	-0.039	0.088	-9999	-0.56	2	2
endothelial cell migration	-0.13	0.31	-9999	-0.75	61	61
ADCY4	-0.015	0.13	-9999	-0.48	8	8
ADCY5	-0.059	0.15	-9999	-0.59	10	10
ADCY6	-0.022	0.14	-9999	-0.57	9	9
ADCY7	-0.015	0.13	-9999	-0.48	8	8
ADCY1	-0.023	0.13	-9999	-0.48	8	8
ADCY2	-0.08	0.15	-9999	-0.56	11	11
ADCY3	-0.015	0.13	-9999	-0.48	8	8
ADCY8	-0.023	0.13	-9999	-0.49	8	8
ADCY9	-0.015	0.13	-9999	-0.48	8	8
GSK3B	0	0.076	-9999	-10000	0	0
arachidonic acid secretion	-0.008	0.12	-9999	-0.46	7	7
GNG2	0.011	0.047	-9999	-0.8	1	1
TRIP6	0.015	0.025	-9999	-10000	0	0
GNAO1	-0.043	0.14	-9999	-0.47	8	8
HRAS	0.013	0	-9999	-10000	0	0
NFKBIA	0.011	0.082	-9999	-0.45	1	1
GAB1	0.013	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
lamellipodium assembly	-0.004	0.09	-9999	-0.9	3	3
JUN	0.013	0	-9999	-10000	0	0
LPA/LPA2/NHERF2	-0.019	0.049	-9999	-0.62	1	1
TIAM1	-0.007	0.11	-9999	-1.1	3	3
PIK3R1	0.013	0.001	-9999	-10000	0	0
mol:IP3	0.008	0.071	-9999	-0.47	2	2
PLCB3	0.01	0.051	-9999	-0.57	1	1
FOS	-0.092	0.24	-9999	-0.64	49	49
positive regulation of mitosis	-0.008	0.12	-9999	-0.46	7	7
LPA/LPA1-2-3	-0.06	0.12	-9999	-0.81	1	1
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	-0.004	0.093	-9999	-0.43	1	1
GNAZ	-0.051	0.16	-9999	-0.53	12	12
EGFR/PI3K-beta/Gab1	-0.057	0.1	-9999	-0.67	1	1
positive regulation of dendritic cell cytokine production	-0.06	0.12	-9999	-0.8	1	1
LPA/LPA2/MAGI-3	-0.017	0.034	-9999	-10000	0	0
ARHGEF1	-0.02	0.12	-9999	-0.62	3	3
GNAI2	-0.039	0.14	-9999	-0.47	6	6
GNAI3	-0.039	0.14	-9999	-0.47	6	6
GNAI1	-0.041	0.14	-9999	-0.46	7	7
LPA/LPA3	-0.03	0.07	-9999	-0.48	4	4
LPA/LPA2	-0.024	0.048	-9999	-10000	0	0
LPA/LPA1	-0.077	0.15	-9999	-0.36	66	66
HB-EGF/EGFR	-0.41	0.25	-9999	-0.54	232	232
HBEGF	-0.46	0.27	-9999	-0.61	230	230
mol:DAG	0.008	0.071	-9999	-0.47	2	2
cAMP biosynthetic process	-0.028	0.13	-9999	-0.56	7	7
NFKB1	0.013	0	-9999	-10000	0	0
SRC	0.013	0	-9999	-10000	0	0
GNB1	0.013	0.001	-9999	-10000	0	0
LYN	0.011	0.082	-9999	-0.45	1	1
GNAQ	0.001	0.055	-9999	-0.33	4	4
LPAR2	0.013	0	-9999	-10000	0	0
LPAR3	0.005	0.075	-9999	-0.64	4	4
LPAR1	-0.034	0.12	-9999	-0.69	6	6
IL8	-0.24	0.18	-9999	-0.49	58	58
PTK2	-0.021	0.12	-9999	-0.76	1	1
Rac1/GDP	0	0	-9999	-10000	0	0
CASP3	-0.031	0.12	-9999	-0.35	10	10
EGFR	-0.014	0.15	-9999	-0.8	10	10
PLCG1	-0.01	0.074	-9999	-0.38	4	4
PLD2	-0.021	0.12	-9999	-0.76	1	1
G12/G13	-0.059	0.12	-9999	-0.67	3	3
PI3K-beta	-0.04	0.083	-9999	-0.59	2	2
cell migration	-0.012	0.045	-9999	-10000	0	0
SLC9A3R2	0.011	0.047	-9999	-0.8	1	1
PXN	-0.005	0.094	-9999	-0.44	1	1
HRAS/GTP	-0.009	0.12	-9999	-0.47	7	7
RAC1	0.013	0	-9999	-10000	0	0
MMP9	-0.61	0.35	-9999	-0.8	230	230
PRKCE	0.013	0.001	-9999	-10000	0	0
PRKCD	0.016	0.068	-9999	-0.46	1	1
Gi(beta/gamma)	-0.012	0.12	-9999	-0.45	9	9
mol:LPA	-0.037	0.082	-9999	-10000	0	0
TRIP6/p130 Cas/FAK1/Paxillin	-0.033	0.086	-9999	-0.6	1	1
MAPKKK cascade	-0.008	0.12	-9999	-0.46	7	7
contractile ring contraction involved in cytokinesis	0.003	0.063	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
GNA14	-0.057	0.14	-9999	-0.34	53	53
GNA15	0.001	0.055	-9999	-0.33	4	4
GNA12	0.008	0.066	-9999	-0.8	2	2
GNA13	0.013	0	-9999	-10000	0	0
MAPT	-0.14	0.18	-9999	-0.46	24	24
GNA11	0.001	0.055	-9999	-0.33	4	4
Rac1/GTP	-0.004	0.096	-9999	-0.96	3	3
MMP2	-0.13	0.32	-9999	-0.75	61	61

×

Hypoxic and oxygen homeostasis regulation of HIF-1-alpha

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
HIF3A	-0.17	0.3	-9999	-0.65	85	85
oxygen homeostasis	0	0	-9999	-10000	0	0
TCEB2	0.013	0	-9999	-10000	0	0
TCEB1	0.011	0.047	-9999	-0.8	1	1
HIF1A/p53	0.022	0.047	-9999	-10000	0	0
HIF1A	0.018	0.035	-9999	-10000	0	0
COPS5	0.013	0	-9999	-10000	0	0
VHL/Elongin B/Elongin C/RBX1/CUL2	-0.001	0.026	-9999	-0.45	1	1
FIH (dimer)	0.013	0	-9999	-10000	0	0
CDKN2A	-0.31	0.39	-9999	-0.77	124	124
ARNT/IPAS	-0.13	0.22	-9999	-0.48	85	85
HIF1AN	0.013	0	-9999	-10000	0	0
GNB2L1	0.013	0	-9999	-10000	0	0
HIF1A/ARNT	0.025	0.034	-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	-0.002	0.03	-9999	-0.53	1	1
response to hypoxia	0	0	-9999	-10000	0	0
HIF1A/Hsp90	0.025	0.034	-9999	-10000	0	0
PHD1-3/OS9	-0.036	0.13	-9999	-0.48	22	22
HIF1A/RACK1/Elongin B/Elongin C	-0.007	0.029	-9999	-0.38	1	1
VHL	0.013	0	-9999	-10000	0	0
HSP90AA1	0.013	0	-9999	-10000	0	0
HIF1A/JAB1	0.025	0.034	-9999	-10000	0	0
EGLN3	-0.048	0.22	-9999	-0.8	23	23
EGLN2	0.013	0	-9999	-10000	0	0
EGLN1	0.013	0	-9999	-10000	0	0
TP53	0.007	0.065	-9999	-0.64	3	3
VHL/Elongin B/Elongin C/RBX1/CUL2/HIF1A	0.037	0.018	-9999	-10000	0	0
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	-0.15	0.22	-9999	-0.43	100	100

×

IL27-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TGFB1	0.012	0.06	-10000	0	-0.79	1	1
CD4-positive alpha-beta T cell lineage commitment	0	0	-10000	0	-10000	0	0
cytokine production during immune response	0.025	0.14	0.57	7	-10000	0	7
IL27/IL27R/JAK1	-0.073	0.17	-10000	0	-0.71	9	9
TBX21	-0.084	0.26	-10000	0	-0.72	24	24
IL12B	-0.079	0.26	-10000	0	-0.81	33	33
IL12A	-0.006	0.088	-10000	0	-0.48	10	10
IL6ST	-0.004	0.099	-10000	0	-0.65	7	7
IL27RA/JAK1	-0.004	0.1	-10000	0	-0.57	9	9
IL27	-0.027	0.17	-10000	0	-0.82	13	13
TYK2	0.013	0.007	-10000	0	-10000	0	0
T-helper cell lineage commitment	-0.023	0.13	-10000	0	-0.63	6	6
T-helper 2 cell differentiation	0.025	0.14	0.57	7	-10000	0	7
T cell proliferation during immune response	0.025	0.14	0.57	7	-10000	0	7
MAPKKK cascade	-0.025	0.14	-10000	0	-0.57	7	7
STAT3	0.013	0	-10000	0	-10000	0	0
STAT2	0.013	0	-10000	0	-10000	0	0
STAT1	-0.049	0.22	-10000	0	-0.8	23	23
IL12RB1	-0.073	0.25	-10000	0	-0.8	32	32
positive regulation of tyrosine phosphorylation of STAT protein	0	0	-10000	0	-10000	0	0
IL12RB2	-0.14	0.33	-10000	0	-0.68	67	67
IL27/IL27R/JAK2/TYK2	-0.026	0.14	-10000	0	-0.57	7	7
positive regulation of T cell mediated cytotoxicity	-0.025	0.14	-10000	0	-0.57	7	7
STAT1 (dimer)	-0.16	0.29	0.52	1	-0.89	27	28
JAK2	0.012	0.007	-10000	0	-10000	0	0
JAK1	0.013	0.003	-10000	0	-10000	0	0
STAT2 (dimer)	-0.018	0.14	-10000	0	-0.75	2	2
T cell proliferation	-0.05	0.18	-10000	0	-0.61	12	12
IL12/IL12R/TYK2/JAK2	-0.066	0.2	-10000	0	-0.61	24	24
IL17A	-0.024	0.13	-10000	0	-0.63	6	6
mast cell activation	0.025	0.14	0.57	7	-10000	0	7
IFNG	-0.013	0.048	-10000	0	-0.11	59	59
T cell differentiation	-0.006	0.009	-10000	0	-0.025	28	28
STAT3 (dimer)	-0.018	0.14	-10000	0	-0.54	7	7
STAT5A (dimer)	-0.018	0.14	-10000	0	-0.54	7	7
STAT4 (dimer)	-0.027	0.15	-10000	0	-0.58	8	8
STAT4	-0.002	0.11	-10000	0	-0.78	6	6
T cell activation	-0.006	0.018	0.092	9	-10000	0	9
IL27R/JAK2/TYK2	-0.031	0.11	-10000	0	-0.6	6	6
GATA3	-0.005	0.15	-10000	0	-0.75	9	9
IL18	-0.004	0.088	-10000	0	-0.48	10	10
positive regulation of mast cell cytokine production	-0.017	0.13	-10000	0	-0.53	7	7
IL27/EBI3	-0.03	0.16	-10000	0	-0.61	20	20
IL27RA	-0.013	0.11	-10000	0	-0.62	9	9
IL6	-0.048	0.2	-10000	0	-0.66	28	28
STAT5A	0.013	0	-10000	0	-10000	0	0
monocyte differentiation	-0.001	0.002	-10000	0	-10000	0	0
IL2	0.013	0.062	-10000	0	-10000	0	0
IL1B	-0.048	0.18	-10000	0	-0.61	29	29
EBI3	-0.007	0.11	-10000	0	-0.74	7	7
TNF	-0.018	0.13	-10000	0	-0.58	15	15

×

Lissencephaly gene (LIS1) in neuronal migration and development

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
DYNC1H1	0.013	0	-9999	-10000	0	0
VLDLR	0.003	0.083	-9999	-0.64	5	5
LRPAP1	0.013	0	-9999	-10000	0	0
NUDC	0.013	0	-9999	-10000	0	0
RELN/LRP8	-0.088	0.18	-9999	-0.42	63	63
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	-0.05	0.17	-9999	-0.56	8	8
IQGAP1/CaM	0	0	-9999	-10000	0	0
DAB1	-0.022	0.16	-9999	-0.8	12	12
IQGAP1	0.013	0	-9999	-10000	0	0
PLA2G7	-0.34	0.4	-9999	-0.8	132	132
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	-0.016	0.098	-9999	-0.61	8	8
UniProt:Q4QZ09	0	0	-9999	-10000	0	0
CLIP1	0.013	0	-9999	-10000	0	0
CDK5R1	0.011	0.047	-9999	-0.8	1	1
LIS1/Poliovirus Protein 3A	0	0	-9999	-10000	0	0
CDK5R2	-0.095	0.27	-9999	-0.8	39	39
mol:PP1	0	0	-9999	-10000	0	0
RELN/VLDLR/DAB1	-0.1	0.19	-9999	-0.44	70	70
YWHAE	0.013	0	-9999	-10000	0	0
NDEL1/14-3-3 E	-0.043	0.17	-9999	-0.59	9	9
MAP1B	-0.01	0.054	-9999	-0.3	10	10
RAC1	0	0	-9999	-10000	0	0
p35/CDK5	-0.029	0.16	-9999	-0.72	2	2
RELN	-0.11	0.26	-9999	-0.64	57	57
PAFAH/LIS1	-0.21	0.28	-9999	-0.53	132	132
LIS1/CLIP170	0.028	0	-9999	-10000	0	0
LIS1/NDEL1/Katanin 60/Dynein Light chain/Dynein heavy chain	-0.064	0.11	-9999	-0.55	2	2
RELN/VLDLR/DAB1/LIS1/PAFAH1B2/PAFAH1B3	-0.031	0.14	-9999	-0.61	4	4
GO:0005869	0	0	-9999	-10000	0	0
NDEL1	-0.054	0.18	-9999	-0.64	9	9
LIS1/IQGAP1	0.028	0	-9999	-10000	0	0
RHOA	0	0	-9999	-10000	0	0
PAFAH1B1	0.025	0	-9999	-10000	0	0
PAFAH1B3	0.013	0	-9999	-10000	0	0
PAFAH1B2	0.013	0	-9999	-10000	0	0
MAP1B/LIS1/Dynein heavy chain	0.02	0.039	-9999	-10000	0	0
NDEL1/Katanin 60/Dynein heavy chain	-0.081	0.13	-9999	-0.56	9	9
LRP8	-0.008	0.13	-9999	-0.8	8	8
NDEL1/Katanin 60	-0.043	0.17	-9999	-0.59	9	9
P39/CDK5	-0.09	0.22	-9999	-0.82	9	9
LIS1/NudC/Dynein intermediate chain/microtubule organizing center	0.028	0	-9999	-10000	0	0
CDK5	-0.037	0.16	-9999	-0.52	8	8
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	-0.085	0.16	-9999	-0.78	4	4
RELN/VLDLR	-0.085	0.16	-9999	-0.56	8	8
CDC42	0	0	-9999	-10000	0	0

×

Signaling events mediated by HDAC Class III

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
EP300	0.013	0	-10000	0	-10000	0	0
HDAC4	0.013	0	-10000	0	-10000	0	0
induction of apoptosis	0	0	-10000	0	-10000	0	0
regulation of S phase of mitotic cell cycle	0.012	0.14	0.61	16	-10000	0	16
CDKN1A	0.001	0.012	-10000	0	-10000	0	0
KAT2B	-0.015	0.13	-10000	0	-0.64	13	13
BAX	0.013	0	-10000	0	-10000	0	0
FOXO3	0	0	-10000	0	-10000	0	0
FOXO1	0.013	0	-10000	0	-10000	0	0
FOXO4	0.023	0.027	-10000	0	-0.31	2	2
response to UV	0	0	-10000	0	-10000	0	0
XRCC6	0.013	0	-10000	0	-10000	0	0
TAT	0.005	0.047	-10000	0	-0.8	1	1
mol:Lysophosphatidic acid	0	0	-10000	0	-10000	0	0
MYOD1	-0.093	0.22	-10000	0	-0.5	66	66
PPARGC1A	-0.21	0.31	-10000	0	-0.64	102	102
FHL2	0.009	0.053	-10000	0	-0.64	2	2
response to nutrient levels	0	0	-10000	0	-10000	0	0
KU70/SIRT1	0	0	-10000	0	-10000	0	0
HIST2H4A	-0.012	0.14	-10000	0	-0.62	16	16
SIRT1/FOXO3a	0	0	-10000	0	-10000	0	0
SIRT1	0	0.001	-10000	0	-10000	0	0
response to hypoxia	0	0	-10000	0	-10000	0	0
SIRT1/MEF2D/HDAC4	0	0	-10000	0	-10000	0	0
SIRT1/Histone H1b	-0.007	0.04	-10000	0	-10000	0	0
apoptosis	0	0	-10000	0	-10000	0	0
SIRT1/PGC1A	-0.14	0.19	-10000	0	-0.4	102	102
p53/SIRT1	-0.005	0.047	-10000	0	-0.47	3	3
SIRT1/FOXO4	-0.001	0.021	-10000	0	-10000	0	0
FOXO1/FHL2/SIRT1	-0.002	0.029	-10000	0	-0.36	2	2
HIST1H1E	0.016	0.052	-10000	0	-0.28	9	9
SIRT1/p300	0	0	-10000	0	-10000	0	0
muscle cell differentiation	0.091	0.18	0.42	66	-10000	0	66
TP53	-0.006	0.064	-10000	0	-0.64	3	3
KU70/SIRT1/BAX	0	0	-10000	0	-10000	0	0
CREBBP	0.013	0	-10000	0	-10000	0	0
MEF2D	0.013	0	-10000	0	-10000	0	0
HIV-1 Tat/SIRT1	-0.002	0.035	-10000	0	-0.61	1	1
ACSS2	0.022	0	-10000	0	-10000	0	0
SIRT1/PCAF/MYOD	-0.091	0.18	-10000	0	-0.42	66	66

×

Angiopoietin receptor Tie2-mediated 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
AKT1	0.065	0.2	-10000	0	-0.88	8	8
NCK1/PAK1/Dok-R	-0.022	0.076	-10000	0	-0.42	8	8
NCK1/Dok-R	-0.035	0.19	-10000	0	-1.1	8	8
PIK3CA	0.012	0.004	-10000	0	-10000	0	0
mol:beta2-estradiol	-0.007	0.036	0.24	5	-10000	0	5
RELA	0.013	0	-10000	0	-10000	0	0
SHC1	0.013	0.004	-10000	0	-10000	0	0
Rac/GDP	0	0	-10000	0	-10000	0	0
F2	-0.072	0.23	-10000	0	-0.83	26	26
TNIP2	0.013	0	-10000	0	-10000	0	0
NF kappa B/RelA	-0.031	0.17	-10000	0	-1	8	8
FN1	-0.44	0.4	-10000	0	-0.8	170	170
PLD2	0.048	0.21	-10000	0	-1.2	8	8
PTPN11	0.013	0	-10000	0	-10000	0	0
GRB14	-0.058	0.21	-10000	0	-0.66	32	32
ELK1	0.061	0.19	-10000	0	-1	8	8
GRB7	0.003	0.089	-10000	0	-0.76	4	4
PAK1	0.011	0.047	-10000	0	-0.8	1	1
Tie2/Ang1/alpha5/beta1 Integrin	-0.37	0.34	-10000	0	-0.82	91	91
CDKN1A	0.067	0.18	-10000	0	-0.66	3	3
ITGA5	-0.27	0.39	-10000	0	-0.8	105	105
mol:GTP	0	0	-10000	0	-10000	0	0
RasGAP/Dok-R	-0.035	0.19	-10000	0	-1.1	8	8
CRK	0.013	0	-10000	0	-10000	0	0
mol:NO	0.068	0.16	-10000	0	-0.64	8	8
PLG	0.042	0.21	-10000	0	-1.2	8	8
mol:GDP	0	0	-10000	0	-10000	0	0
chemokinesis	0.048	0.18	-10000	0	-0.86	8	8
GRB2	0.013	0	-10000	0	-10000	0	0
PIK3R1	0.013	0.004	-10000	0	-10000	0	0
ANGPT2	0.014	0.2	-10000	0	-0.6	19	19
BMX	0.013	0.25	-10000	0	-1.3	8	8
ANGPT1	0.022	0.21	-10000	0	-1.2	7	7
tube development	0.06	0.19	-10000	0	-0.72	5	5
ANGPT4	0.009	0.007	-10000	0	-10000	0	0
response to hypoxia	0.003	0.013	-10000	0	-10000	0	0
Tie2/Ang1/GRB14	0.004	0.24	-10000	0	-1.2	8	8
alpha5/beta1 Integrin	-0.22	0.29	-10000	0	-0.61	106	106
FGF2	-0.013	0.13	-10000	0	-0.68	11	11
STAT5A (dimer)	0.064	0.21	-10000	0	-0.81	4	4
mol:L-citrulline	0.068	0.16	-10000	0	-0.64	8	8
AGTR1	-0.047	0.19	-10000	0	-0.66	27	27
MAPK14	0.051	0.21	-10000	0	-1.1	8	8
Tie2/SHP2	-0.017	0.12	-10000	0	-1.2	3	3
TEK	0.03	0.15	-10000	0	-1.4	3	3
RPS6KB1	0.069	0.19	-10000	0	-0.85	8	8
Angiotensin II/AT1	-0.035	0.14	-10000	0	-0.5	27	27
Tie2/Ang1/GRB2	0.044	0.22	-10000	0	-1.2	8	8
MAPK3	0.056	0.19	-10000	0	-1	8	8
MAPK1	0.056	0.19	-10000	0	-1	8	8
Tie2/Ang1/GRB7	0.038	0.22	-10000	0	-1.2	8	8
NFKB1	0.013	0	-10000	0	-10000	0	0
MAPK8	0.046	0.22	-10000	0	-1.2	8	8
PI3K	0.06	0.21	-10000	0	-1	8	8
FES	0.051	0.21	-10000	0	-1.1	8	8
Crk/Dok-R	-0.035	0.19	-10000	0	-1.1	8	8
Tie2/Ang1/ABIN2	0.044	0.22	-10000	0	-1.2	8	8
blood circulation	0	0	-10000	0	-10000	0	0
negative regulation of caspase activity	0.067	0.18	-10000	0	-0.78	8	8
STAT5A	0.014	0	-10000	0	-10000	0	0
mol:ROS	0	0	-10000	0	-10000	0	0
PTK2	0.069	0.19	-10000	0	-0.85	8	8
Tie2/Ang2	0.048	0.23	-10000	0	-0.83	8	8
Tie2/Ang1	0.042	0.23	-10000	0	-1.3	8	8
FOXO1	0.068	0.19	-10000	0	-0.79	8	8
ELF1	0.023	0.011	-10000	0	-10000	0	0
ELF2	0.045	0.21	-10000	0	-1.1	8	8
mol:Choline	0.05	0.2	-10000	0	-1.1	8	8
cell migration	-0.1	0.084	-10000	0	-10000	0	0
FYN	0.057	0.21	-10000	0	-0.82	5	5
DOK2	0.011	0.038	-10000	0	-0.64	1	1
negative regulation of cell cycle	0.068	0.17	-10000	0	-0.59	3	3
ETS1	0.015	0.073	-10000	0	-0.78	2	2
PXN	0.077	0.16	-10000	0	-0.69	8	8
ITGB1	0.011	0.047	-10000	0	-0.8	1	1
NOS3	0.067	0.18	-10000	0	-0.74	8	8
RAC1	0.013	0	-10000	0	-10000	0	0
TNF	-0.017	0.17	-10000	0	-0.76	15	15
MAPKKK cascade	0.05	0.2	-10000	0	-1.1	8	8
RASA1	0.013	0	-10000	0	-10000	0	0
Tie2/Ang1/Shc	0.045	0.22	-10000	0	-1.2	8	8
NCK1	0.013	0	-10000	0	-10000	0	0
vasculogenesis	0.069	0.15	-10000	0	-0.58	8	8
mol:Phosphatidic acid	0.05	0.2	-10000	0	-1.1	8	8
mol:Angiotensin II	0	0.007	-10000	0	-10000	0	0
mol:NADP	0.068	0.16	-10000	0	-0.64	8	8
Rac1/GTP	-0.038	0.14	-10000	0	-0.79	8	8
MMP2	-0.047	0.28	-10000	0	-1.2	8	8

×

Regulation of Androgen receptor activity

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
HDAC1	0.023	0.004	-9999	-10000	0	0
SMARCC1	0.01	0.011	-9999	-10000	0	0
REL	0.016	0.007	-9999	-10000	0	0
HDAC7	-0.061	0.17	-9999	-0.63	11	11
JUN	0.011	0.005	-9999	-10000	0	0
EP300	0.013	0.001	-9999	-10000	0	0
KAT2B	-0.016	0.13	-9999	-0.64	13	13
KAT5	0.014	0.001	-9999	-10000	0	0
MAPK14	-0.009	0.11	-9999	-0.5	14	14
FOXO1	0.013	0.001	-9999	-10000	0	0
T-DHT/AR	-0.077	0.17	-9999	-0.64	14	14
MAP2K6	-0.023	0.14	-9999	-0.66	14	14
BRM/BAF57	-0.001	0.002	-9999	-10000	0	0
MAP2K4	0.008	0.008	-9999	-10000	0	0
SMARCA2	0.011	0.005	-9999	-10000	0	0
PDE9A	-0.093	0.21	-9999	-1.3	8	8
NCOA2	0.004	0.075	-9999	-0.64	4	4
CEBPA	0.01	0.053	-9999	-0.64	2	2
EHMT2	0.011	0.005	-9999	-10000	0	0
cell proliferation	-0.048	0.16	-9999	-0.53	6	6
NR0B1	-0.038	0.18	-9999	-0.8	16	16
EGR1	-0.013	0.12	-9999	-0.64	11	11
RXRs/9cRA	-0.053	0.13	-9999	-0.41	19	19
AR/RACK1/Src	-0.029	0.12	-9999	-0.52	10	10
AR/GR	-0.044	0.15	-9999	-0.59	10	10
GNB2L1	0.013	0.003	-9999	-10000	0	0
PKN1	0.007	0.066	-9999	-0.8	2	2
RCHY1	0.013	0	-9999	-10000	0	0
epidermal growth factor receptor activity	0	0.002	-9999	-10000	0	0
MAPK8	0.011	0.045	-9999	-0.5	2	2
T-DHT/AR/TIF2/CARM1	-0.028	0.14	-9999	-0.58	11	11
SRC	0	0.096	-9999	-10000	0	0
NR3C1	0.013	0	-9999	-10000	0	0
KLK3	-0.31	0.47	-9999	-1.2	58	58
APPBP2	0.008	0.008	-9999	-10000	0	0
TRIM24	0.009	0.038	-9999	-0.64	1	1
T-DHT/AR/TIP60	-0.029	0.13	-9999	-0.55	11	11
TMPRSS2	-0.54	0.57	-9999	-1.1	145	145
RXRG	-0.082	0.23	-9999	-0.66	42	42
mol:9cRA	-0.001	0.003	-9999	-10000	0	0
RXRA	0.013	0.001	-9999	-10000	0	0
RXRB	0.013	0.001	-9999	-10000	0	0
CARM1	0.013	0.003	-9999	-10000	0	0
NR2C2	0.011	0.038	-9999	-0.64	1	1
KLK2	-0.022	0.17	-9999	-0.65	13	13
AR	-0.058	0.17	-9999	-0.43	36	36
SENP1	0.013	0.001	-9999	-10000	0	0
HSP90AA1	0.013	0	-9999	-10000	0	0
MDM2	0.018	0.012	-9999	-10000	0	0
SRY	-0.043	0.18	-9999	-0.65	25	25
GATA2	0.008	0.066	-9999	-0.8	2	2
MYST2	0.014	0.001	-9999	-10000	0	0
HOXB13	-0.28	0.39	-9999	-0.81	105	105
T-DHT/AR/RACK1/Src	-0.02	0.13	-9999	-0.53	10	10
positive regulation of transcription	0.008	0.066	-9999	-0.8	2	2
DNAJA1	0.008	0.008	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.034	0.004	-9999	-10000	0	0
NCOA1	0.017	0.008	-9999	-10000	0	0
SPDEF	-0.24	0.32	-9999	-0.65	117	117
T-DHT/AR/TIF2	-0.01	0.11	-9999	-0.5	5	5
T-DHT/AR/Hsp90	-0.03	0.13	-9999	-0.55	11	11
GSK3B	0.008	0.007	-9999	-10000	0	0
NR2C1	0.015	0.003	-9999	-10000	0	0
mol:T-DHT	-0.011	0.1	-9999	-0.43	8	8
SIRT1	0.013	0.001	-9999	-10000	0	0
ZMIZ2	0.018	0.012	-9999	-10000	0	0
POU2F1	0.017	0.017	-9999	-10000	0	0
T-DHT/AR/DAX-1	-0.073	0.15	-9999	-0.54	19	19
CREBBP	0.013	0.003	-9999	-10000	0	0
SMARCE1	0.011	0.005	-9999	-10000	0	0

×

Ephrin A reverse signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MAPKKK cascade	-0.02	0.092	-9999	-0.44	14	14
EFNA5	-0.01	0.12	-9999	-0.64	11	11
FYN	0.003	0.1	-9999	-0.42	14	14
neuron projection morphogenesis	-0.02	0.092	-9999	-0.44	14	14
cell-cell signaling	0	0	-9999	-10000	0	0
Ephrin A5/EPHA5	-0.02	0.092	-9999	-0.44	14	14
EPHA5	0	0.081	-9999	-0.8	3	3

×

PDGFR-alpha signaling pathway

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
PDGFRA	-0.007	0.11	-9999	-0.69	7	7
PDGF/PDGFRA/CRKL	-0.014	0.083	-9999	-0.52	8	8
positive regulation of JUN kinase activity	-0.009	0.056	-9999	-0.45	2	2
CRKL	0.011	0.047	-9999	-0.8	1	1
PDGF/PDGFRA/Caveolin-3	-0.12	0.22	-9999	-0.5	75	75
AP1	-0.17	0.37	-9999	-1	49	49
mol:IP3	0.006	0.084	-9999	-0.52	7	7
PLCG1	0.006	0.084	-9999	-0.52	7	7
PDGF/PDGFRA/alphaV Integrin	-0.017	0.1	-9999	-0.63	8	8
RAPGEF1	0.013	0	-9999	-10000	0	0
CRK	0.013	0	-9999	-10000	0	0
mol:Ca2+	0.006	0.084	-9999	-0.51	7	7
CAV3	-0.14	0.28	-9999	-0.66	69	69
CAV1	-0.065	0.24	-9999	-0.8	29	29
SHC/Grb2/SOS1	-0.009	0.056	-9999	-0.45	2	2
PDGF/PDGFRA/Shf	-0.022	0.11	-9999	-0.56	12	12
FOS	-0.12	0.39	-9999	-0.99	49	49
JUN	-0.01	0.022	-9999	-10000	0	0
oligodendrocyte development	-0.017	0.1	-9999	-0.63	8	8
GRB2	0.013	0	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
mol:DAG	0.006	0.084	-9999	-0.52	7	7
PDGF/PDGFRA	-0.007	0.11	-9999	-0.69	7	7
actin cytoskeleton reorganization	-0.015	0.084	-9999	-0.49	9	9
SRF	0.026	0.01	-9999	-10000	0	0
SHC1	0.013	0	-9999	-10000	0	0
PI3K	-0.01	0.063	-9999	-0.47	3	3
PDGF/PDGFRA/Crk/C3G	-0.01	0.063	-9999	-0.42	7	7
JAK1	0.01	0.079	-9999	-0.5	7	7
ELK1/SRF	0.03	0.068	-9999	-0.49	1	1
SHB	0.009	0.053	-9999	-0.64	2	2
SHF	-0.002	0.098	-9999	-0.64	7	7
CSNK2A1	0.01	0.022	-9999	-10000	0	0
GO:0007205	0.006	0.085	-9999	-0.52	7	7
SOS1	0.013	0	-9999	-10000	0	0
Ras protein signal transduction	-0.009	0.056	-9999	-0.45	2	2
PDGF/PDGFRA/SHB	-0.015	0.084	-9999	-0.49	9	9
PDGF/PDGFRA/Caveolin-1	-0.072	0.2	-9999	-0.6	36	36
ITGAV	0.006	0.076	-9999	-0.75	3	3
ELK1	0.008	0.089	-9999	-0.47	8	8
PIK3CA	0.013	0	-9999	-10000	0	0
PDGF/PDGFRA/Crk	-0.012	0.076	-9999	-0.5	7	7
JAK-STAT cascade	0.01	0.079	-9999	-0.5	7	7
cell proliferation	-0.022	0.11	-9999	-0.56	12	12

×

Wnt signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Noncanonical Wnts/FZD	-0.028	0.14	-9999	-0.65	5	5
FZD6	0.013	0	-9999	-10000	0	0
WNT6	-0.03	0.18	-9999	-0.76	17	17
WNT4	-0.01	0.13	-9999	-0.69	10	10
FZD3	0.005	0.075	-9999	-0.64	4	4
WNT5A	0.004	0.08	-9999	-0.68	4	4
WNT11	-0.074	0.25	-9999	-0.76	34	34

×

Regulation of Telomerase

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Telomerase catalytic core complex	-0.14	0.29	-9999	-0.67	66	66
RAD9A	0.013	0	-9999	-10000	0	0
AP1	-0.076	0.17	-9999	-0.47	49	49
IFNAR2	0.012	0.007	-9999	-10000	0	0
AKT1	-0.002	0.071	-9999	-0.36	2	2
ER alpha/Oestrogen	-0.032	0.13	-9999	-0.58	17	17
NFX1/SIN3/HDAC complex	0.041	0.023	-9999	-10000	0	0
EGF	-0.14	0.27	-9999	-0.64	69	69
SMG5	0.013	0	-9999	-10000	0	0
SMG6	0.013	0	-9999	-10000	0	0
SP3/HDAC2	0.015	0.012	-9999	-10000	0	0
TERT/c-Abl	-0.15	0.26	-9999	-0.65	52	52
SAP18	0.011	0.006	-9999	-10000	0	0
MRN complex	0	0	-9999	-10000	0	0
WT1	-0.18	0.34	-9999	-0.8	71	71
WRN	0.013	0	-9999	-10000	0	0
SP1	0.013	0.007	-9999	-10000	0	0
SP3	0.011	0.006	-9999	-10000	0	0
TERF2IP	0.013	0	-9999	-10000	0	0
Telomerase/Nucleolin	-0.14	0.23	-9999	-0.64	29	29
Mad/Max	-0.002	0.027	-9999	-0.47	1	1
TERT	-0.15	0.3	-9999	-0.68	66	66
CCND1	-0.13	0.29	-9999	-0.73	32	32
MAX	0.011	0.006	-9999	-10000	0	0
RBBP7	0.011	0.006	-9999	-10000	0	0
RBBP4	0.011	0.006	-9999	-10000	0	0
TERF2	0	0	-9999	-10000	0	0
PTGES3	0.013	0	-9999	-10000	0	0
SIN3A	0.011	0.006	-9999	-10000	0	0
Telomerase/911	0.022	0.044	-9999	-10000	0	0
CDKN1B	-0.072	0.22	-9999	-0.51	59	59
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	0.006	-9999	-10000	0	0
TRF2/PARP2	0	0	-9999	-10000	0	0
UBE3A	0.011	0.006	-9999	-10000	0	0
JUN	0.012	0.006	-9999	-10000	0	0
E6	-0.001	0.005	-9999	-10000	0	0
HPV-16 E6/E6AP	0.009	0.006	-9999	-10000	0	0
FOS	-0.094	0.24	-9999	-0.64	49	49
IFN-gamma/IRF1	-0.12	0.24	-9999	-0.6	59	59
PARP2	0.013	0	-9999	-10000	0	0
BLM	0.011	0.047	-9999	-0.8	1	1
Telomerase	0.002	0.086	-9999	-0.42	3	3
IRF1	0.015	0.008	-9999	-10000	0	0
ESR1	-0.031	0.18	-9999	-0.75	17	17
KU/TER	0	0	-9999	-10000	0	0
ATM/TRF2	0	0	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	0.045	0.025	-9999	-10000	0	0
HPV-16 E6/E6AP/NFX1/SIN3/HDAC complex	0.046	0.025	-9999	-10000	0	0
HDAC1	0.011	0.006	-9999	-10000	0	0
HDAC2	0.013	0.007	-9999	-10000	0	0
ATM	0	0	-9999	-10000	0	0
SMAD3	0.023	0.047	-9999	-0.54	2	2
ABL1	0.013	0	-9999	-10000	0	0
MXD1	0.009	0.038	-9999	-0.64	1	1
MRE11A	0.013	0	-9999	-10000	0	0
HUS1	0.011	0.047	-9999	-0.8	1	1
RPS6KB1	0.013	0	-9999	-10000	0	0
TERT/NF kappa B1/14-3-3	-0.14	0.25	-9999	-0.69	30	30
NR2F2	0.016	0.01	-9999	-10000	0	0
MAPK3	0.012	0.039	-9999	-0.64	1	1
MAPK1	0.012	0.039	-9999	-0.64	1	1
TGFB1/TGF beta receptor Type II	0.011	0.047	-9999	-0.8	1	1
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	0	-9999	-10000	0	0
NBN	0.013	0	-9999	-10000	0	0
EGFR	-0.015	0.15	-9999	-0.81	10	10
mol:Oestrogen	-0.001	0.003	-9999	-10000	0	0
EGF/EGFR	-0.13	0.22	-9999	-0.5	78	78
MYC	0.011	0.006	-9999	-10000	0	0
IL2	0	0.05	-9999	-0.84	1	1
KU	0	0	-9999	-10000	0	0
RAD50	0.013	0	-9999	-10000	0	0
HSP90AA1	0.013	0	-9999	-10000	0	0
TGFB1	0.011	0.047	-9999	-0.8	1	1
TRF2/BLM	-0.002	0.033	-9999	-0.57	1	1
FRAP1	0	0	-9999	-10000	0	0
KU/TERT	-0.15	0.26	-9999	-0.66	48	48
SP1/HDAC2	0.019	0.014	-9999	-10000	0	0
PINX1	0.013	0	-9999	-10000	0	0
Telomerase/EST1A	-0.14	0.23	-9999	-0.64	29	29
Smad3/Myc	0.018	0.042	-9999	-0.46	2	2
911 complex	-0.002	0.03	-9999	-0.53	1	1
IFNG	-0.14	0.32	-9999	-0.8	59	59
Telomerase/PinX1	-0.14	0.23	-9999	-0.64	29	29
Telomerase/AKT1/mTOR/p70S6K	-0.001	0.08	-9999	-0.48	1	1
SIN3B	0.011	0.006	-9999	-10000	0	0
YWHAE	0.013	0	-9999	-10000	0	0
Telomerase/EST1B	-0.14	0.23	-9999	-0.64	29	29
response to DNA damage stimulus	0.004	0	-9999	-10000	0	0
MRN complex/TRF2/Rap1	0	0	-9999	-10000	0	0
TRF2/WRN	0	0	-9999	-10000	0	0
Telomerase/hnRNP C1/C2	-0.14	0.23	-9999	-0.64	29	29
E2F1	-0.034	0.19	-9999	-0.81	17	17
ZNFX1	0.011	0.006	-9999	-10000	0	0
PIF1	-0.014	0.15	-9999	-0.8	10	10
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

×

ErbB2/ErbB3 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
USP8	0.02	0.006	-9999	-10000	0	0
RAS family/GTP	-0.054	0.098	-9999	-0.63	1	1
NFATC4	-0.026	0.13	-9999	-0.5	2	2
ERBB2IP	0.014	0.003	-9999	-10000	0	0
HSP90 (dimer)	0.013	0	-9999	-10000	0	0
mammary gland morphogenesis	-0.074	0.14	-9999	-0.62	1	1
JUN	0.005	0.075	-9999	-0.28	1	1
HRAS	0.013	0.001	-9999	-10000	0	0
DOCK7	-0.045	0.15	-9999	-0.59	1	1
ErbB2/ErbB3/neuregulin 1 beta/SHC	-0.099	0.19	-9999	-0.46	61	61
AKT1	0.011	0.003	-9999	-10000	0	0
BAD	0.021	0.003	-9999	-10000	0	0
MAPK10	-0.045	0.081	-9999	-0.33	6	6
mol:GTP	-0.001	0.002	-9999	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta	-0.057	0.17	-9999	-0.7	1	1
RAF1	-0.024	0.12	-9999	-0.61	1	1
ErbB2/ErbB3/neuregulin 2	-0.23	0.18	-9999	-0.4	40	40
STAT3	0.001	0.003	-9999	-10000	0	0
cell migration	0.002	0.091	-9999	-0.26	4	4
mol:PI-3-4-5-P3	-0.001	0.003	-9999	-10000	0	0
cell proliferation	-0.15	0.28	-9999	-0.6	51	51
FOS	-0.12	0.24	-9999	-0.48	60	60
NRAS	0.013	0.001	-9999	-10000	0	0
mol:Ca2+	-0.074	0.14	-9999	-0.62	1	1
MAPK3	-0.11	0.23	-9999	-0.58	14	14
MAPK1	-0.11	0.23	-9999	-0.58	14	14
JAK2	-0.045	0.15	-9999	-0.59	1	1
NF2	-0.003	0.005	-9999	-10000	0	0
ErbB2/ErbB3/neuregulin 1 beta/SHC/GRB2/SOS1	-0.038	0.13	-9999	-0.7	1	1
NRG1	-0.15	0.32	-9999	-0.8	61	61
GRB2/SOS1	0	0	-9999	-10000	0	0
MAPK8	-0.024	0.11	-9999	-0.43	1	1
MAPK9	-0.035	0.067	-9999	-0.27	1	1
ERBB2	-0.004	0.051	-9999	-0.63	2	2
ERBB3	0.001	0.075	-9999	-0.64	4	4
SHC1	0.012	0.003	-9999	-10000	0	0
RAC1	0.013	0	-9999	-10000	0	0
apoptosis	0.011	0.011	-9999	-10000	0	0
STAT3 (dimer)	0.001	0.003	-9999	-10000	0	0
RNF41	0.026	0.009	-9999	-10000	0	0
FRAP1	0.01	0.003	-9999	-10000	0	0
RAC1-CDC42/GTP	-0.05	0.095	-9999	-0.39	1	1
ErbB2/ErbB2/HSP90 (dimer)	-0.004	0.043	-9999	-0.54	2	2
CHRNA1	-0.16	0.29	-9999	-0.54	98	98
myelination	-0.017	0.13	-9999	-0.46	2	2
PPP3CB	-0.042	0.14	-9999	-0.54	1	1
KRAS	0.013	0.001	-9999	-10000	0	0
RAC1-CDC42/GDP	-0.05	0.099	-9999	-0.61	1	1
NRG2	-0.38	0.32	-9999	-0.64	184	184
mol:GDP	-0.038	0.13	-9999	-0.69	1	1
SOS1	0.013	0.001	-9999	-10000	0	0
MAP2K2	-0.029	0.13	-9999	-0.59	1	1
SRC	0.013	0	-9999	-10000	0	0
mol:cAMP	-0.001	0.002	-9999	-10000	0	0
PTPN11	-0.046	0.15	-9999	-0.58	1	1
MAP2K1	-0.097	0.2	-9999	-0.53	14	14
heart morphogenesis	-0.074	0.14	-9999	-0.62	1	1
RAS family/GDP	-0.049	0.097	-9999	-0.61	1	1
GRB2	0.013	0.001	-9999	-10000	0	0
PRKACA	-0.005	0.009	-9999	-10000	0	0
CHRNE	0.012	0.022	-9999	-0.22	1	1
HSP90AA1	0.013	0	-9999	-10000	0	0
activation of caspase activity	-0.011	0.003	-9999	-10000	0	0
nervous system development	-0.074	0.14	-9999	-0.62	1	1
CDC42	0.013	0	-9999	-10000	0	0

×

Arf6 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CENTA1/KIF3B	-0.009	0.061	-9999	-0.4	7	7
ARNO/beta Arrestin1-2	-0.025	0.088	-9999	-0.58	2	2
EGFR	-0.014	0.15	-9999	-0.8	10	10
EPHA2	0.005	0.075	-9999	-0.64	4	4
USP6	0.013	0	-9999	-10000	0	0
IQSEC1	0.013	0	-9999	-10000	0	0
EGFR/EGFR/EGF/EGF	-0.13	0.22	-9999	-0.49	78	78
ARRB2	0.011	0.003	-9999	-10000	0	0
mol:GTP	0.021	0.018	-9999	-10000	0	0
ARRB1	0.009	0.053	-9999	-0.64	2	2
FBXO8	0.013	0	-9999	-10000	0	0
TSHR	-0.005	0.11	-9999	-0.8	6	6
EGF	-0.14	0.27	-9999	-0.64	69	69
somatostatin receptor activity	0	0	-9999	-0.001	7	7
ARAP2	0.009	0.053	-9999	-0.64	2	2
mol:GDP	-0.011	0.076	-9999	-0.32	7	7
mol:PI-3-4-5-P3	0	0	-9999	-0.001	5	5
ITGA2B	-0.04	0.2	-9999	-0.8	20	20
ARF6	0.013	0	-9999	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	-0.006	0.049	-9999	-0.48	1	1
ADAP1	0.013	0	-9999	-10000	0	0
KIF13B	-0.002	0.098	-9999	-0.64	7	7
HGF/MET	-0.019	0.099	-9999	-0.52	11	11
PXN	0.013	0	-9999	-10000	0	0
ARF6/GTP	-0.028	0.11	-9999	-0.33	8	8
EGFR/EGFR/EGF/EGF/ARFGEP100	-0.11	0.18	-9999	-0.56	10	10
ADRB2	-0.038	0.18	-9999	-0.64	24	24
receptor agonist activity	0	0	-9999	0	7	7
actin filament binding	0	0	-9999	-0.001	7	7
SRC	0.013	0	-9999	-10000	0	0
ITGB3	-0.017	0.15	-9999	-0.76	12	12
GNAQ	0.013	0	-9999	-10000	0	0
EFA6/PI-4-5-P2	0	0	-9999	-0.001	5	5
ARF6/GDP	0.044	0.057	-9999	-10000	0	0
ARF6/GDP/GULP/ACAP1	-0.11	0.17	-9999	-0.44	33	33
alphaIIb/beta3 Integrin/paxillin/GIT1	-0.049	0.15	-9999	-0.5	28	28
ACAP1	-0.003	0.11	-9999	-0.8	6	6
ACAP2	0.013	0	-9999	-10000	0	0
LHCGR/beta Arrestin2	0	0	-9999	-10000	0	0
EFNA1	0.011	0.047	-9999	-0.8	1	1
HGF	-0.008	0.12	-9999	-0.7	9	9
CYTH3	0.012	0	-9999	-10000	0	0
CYTH2	0.009	0.002	-9999	-10000	0	0
NCK1	0.013	0	-9999	-10000	0	0
fibronectin binding	0	0	-9999	-0.001	7	7
endosomal lumen acidification	0	0	-9999	-0.001	8	8
microtubule-based process	0	0	-9999	-10000	0	0
GULP1	-0.16	0.29	-9999	-0.64	81	81
GNAQ/ARNO	0.014	0.008	-9999	-10000	0	0
mol:Phosphatidic acid	0	0	-9999	-10000	0	0
PIP3-E	0	0	-9999	0	1	1
MET	0.009	0.06	-9999	-0.72	2	2
GNA14	-0.095	0.24	-9999	-0.64	50	50
GNA15	0.013	0	-9999	-10000	0	0
GIT1	0.013	0	-9999	-10000	0	0
mol:PI-4-5-P2	0	0	-9999	-0.001	6	6
GNA11	0.013	0	-9999	-10000	0	0
LHCGR	0.002	0.005	-9999	-10000	0	0
AGTR1	-0.048	0.19	-9999	-0.66	27	27
desensitization of G-protein coupled receptor protein signaling pathway	0	0	-9999	-10000	0	0
IPCEF1/ARNO	-0.078	0.15	-9999	-0.44	10	10
alphaIIb/beta3 Integrin	-0.063	0.19	-9999	-0.62	31	31

×

Signaling mediated by p38-alpha and p38-beta

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
PTGS2	-0.099	0.28	-9999	-0.71	47	47
MKNK1	0.013	0	-9999	-10000	0	0
MAPK14	-0.04	0.12	-9999	-0.4	7	7
ATF2/c-Jun	-0.007	0.094	-9999	-10000	0	0
MAPK11	-0.04	0.12	-9999	-0.4	7	7
MITF	-0.041	0.16	-9999	-0.56	11	11
MAPKAPK5	-0.033	0.14	-9999	-0.49	7	7
KRT8	-0.1	0.22	-9999	-0.67	20	20
MAPKAPK3	0.013	0	-9999	-10000	0	0
MAPKAPK2	0.013	0	-9999	-10000	0	0
p38alpha-beta/CK2	-0.059	0.18	-9999	-0.52	16	16
CEBPB	-0.033	0.14	-9999	-0.49	7	7
SLC9A1	-0.033	0.14	-9999	-0.49	7	7
mol:GDP	0	0	-9999	-10000	0	0
ATF2	-0.027	0.14	-9999	-0.48	7	7
p38alpha-beta/MNK1	-0.033	0.15	-9999	-0.53	7	7
JUN	-0.006	0.093	-9999	-10000	0	0
PPARGC1A	-0.17	0.27	-9999	-0.73	39	39
USF1	-0.033	0.14	-9999	-0.49	7	7
RAB5/GDP/GDI1	-0.049	0.084	-9999	-0.36	7	7
NOS2	-0.11	0.31	-9999	-0.78	46	46
DDIT3	-0.041	0.16	-9999	-0.53	10	10
RAB5A	0.013	0	-9999	-10000	0	0
HSPB1	-0.016	0.12	-9999	-0.4	7	7
p38alpha-beta/HBP1	-0.033	0.15	-9999	-0.53	7	7
CREB1	-0.029	0.15	-9999	-0.4	16	16
RAB5/GDP	0	0	-9999	-10000	0	0
EIF4E	-0.02	0.13	-9999	-0.47	7	7
RPS6KA4	-0.033	0.14	-9999	-0.49	7	7
PLA2G4A	-0.037	0.15	-9999	-0.52	9	9
GDI1	-0.033	0.14	-9999	-0.49	7	7
TP53	-0.048	0.18	-9999	-0.64	9	9
RPS6KA5	-0.034	0.15	-9999	-0.49	7	7
ESR1	-0.055	0.18	-9999	-0.57	14	14
HBP1	0.013	0	-9999	-10000	0	0
MEF2C	-0.041	0.16	-9999	-0.54	9	9
MEF2A	-0.033	0.14	-9999	-0.49	7	7
EIF4EBP1	-0.03	0.15	-9999	-0.48	7	7
KRT19	-0.16	0.23	-9999	-0.68	23	23
ELK4	-0.033	0.14	-9999	-0.49	7	7
ATF6	-0.033	0.14	-9999	-0.49	7	7
ATF1	-0.029	0.15	-9999	-0.4	16	16
p38alpha-beta/MAPKAPK2	-0.033	0.15	-9999	-0.53	7	7
p38alpha-beta/MAPKAPK3	-0.033	0.15	-9999	-0.53	7	7

×

EGFR-dependent Endothelin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HRAS	0.013	0	-9999	-10000	0	0
EGFR	-0.014	0.15	-9999	-0.8	10	10
EGF/EGFR	-0.091	0.16	-9999	-0.49	11	11
EGF/EGFR dimer/SHC/GRB2/SOS1	-0.089	0.15	-9999	-0.78	1	1
mol:GTP	0	0	-9999	-10000	0	0
EDNRA	0.011	0.038	-9999	-0.64	1	1
response to oxidative stress	0	0	-9999	-10000	0	0
EGF	-0.14	0.27	-9999	-0.64	69	69
EGF/EGFR dimer/SHC	-0.11	0.18	-9999	-0.56	10	10
mol:GDP	-0.088	0.15	-9999	-0.77	1	1
mol:Ca2+	0	0	-9999	-10000	0	0
EDN1	0.007	0.065	-9999	-0.64	3	3
GRB2/SOS1	0	0	-9999	-10000	0	0
HRAS/GTP	-0.08	0.14	-9999	-0.72	1	1
SHC1	0.013	0	-9999	-10000	0	0
HRAS/GDP	-0.081	0.14	-9999	-0.72	1	1
FRAP1	-0.054	0.16	-9999	-0.75	1	1
EGF/EGFR dimer	-0.13	0.22	-9999	-0.49	78	78
SOS1	0.013	0	-9999	-10000	0	0
GRB2	0.013	0	-9999	-10000	0	0
ETA receptor/Endothelin-1	-0.006	0.054	-9999	-0.47	4	4

×

Plasma membrane estrogen receptor signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GNB1/GNG2	-0.035	0.12	-10000	0	-0.47	18	18
ER alpha/Gai/GDP/Gbeta gamma	0.024	0.094	-10000	0	-0.5	2	2
AKT1	0.015	0.13	-10000	0	-0.78	6	6
PIK3CA	0.013	0	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/PI3K	0.011	0.13	-10000	0	-0.79	6	6
mol:Ca2+	-0.034	0.17	-10000	0	-0.4	50	50
IGF1R	0.013	0	-10000	0	-10000	0	0
E2/ER alpha (dimer)/Striatin	-0.029	0.12	-10000	0	-0.48	18	18
SHC1	0.013	0	-10000	0	-10000	0	0
apoptosis	-0.016	0.12	0.74	6	-10000	0	6
RhoA/GTP	-0.02	0.083	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/p130 Cas	-0.024	0.086	-10000	0	-0.59	1	1
regulation of stress fiber formation	-0.038	0.078	-10000	0	-10000	0	0
E2/ERA-ERB (dimer)	-0.039	0.14	-10000	0	-0.52	23	23
KRAS	0.013	0	-10000	0	-10000	0	0
G13/GTP	-0.025	0.1	-10000	0	-0.45	17	17
pseudopodium formation	0.038	0.078	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1	-0.027	0.11	-10000	0	-0.49	17	17
GRB2	0.013	0	-10000	0	-10000	0	0
GNG2	0.011	0.047	-10000	0	-0.8	1	1
GNAO1	0.009	0.06	-10000	0	-0.72	2	2
HRAS	0.013	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
mol:NO	0.025	0.11	-10000	0	-0.51	7	7
E2/ER beta (dimer)	-0.014	0.091	-10000	0	-0.6	7	7
mol:GDP	-0.03	0.11	-10000	0	-0.42	17	17
mol:NADP	0.025	0.11	-10000	0	-0.51	7	7
PIK3R1	0.013	0	-10000	0	-10000	0	0
mol:IP3	-0.037	0.18	-10000	0	-0.68	5	5
IGF-1R heterotetramer	0.013	0	-10000	0	-10000	0	0
PLCB1	-0.045	0.18	-10000	0	-0.43	50	50
PLCB2	-0.045	0.18	-10000	0	-0.43	50	50
IGF1	-0.054	0.2	-10000	0	-0.67	30	30
mol:L-citrulline	0.025	0.11	-10000	0	-0.51	7	7
RHOA	0.013	0	-10000	0	-10000	0	0
Gai/GDP	-0.01	0.058	-10000	0	-0.57	2	2
JNK cascade	-0.014	0.09	-10000	0	-0.6	7	7
BCAR1	0.013	0	-10000	0	-10000	0	0
ESR2	-0.005	0.12	-10000	0	-0.78	7	7
GNAQ	0.013	0	-10000	0	-10000	0	0
ESR1	-0.029	0.18	-10000	0	-0.75	17	17
Gq family/GDP/Gbeta gamma	-0.002	0.1	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC/GRB2/SOS1	0.029	0.064	-10000	0	-10000	0	0
E2/ER alpha (dimer)/PELP1/Src/p52 SHC	-0.024	0.086	-10000	0	-0.52	2	2
GNAZ	-0.004	0.11	-10000	0	-0.73	7	7
E2/ER alpha (dimer)	-0.032	0.13	-10000	0	-0.57	17	17
STRN	0.011	0.038	-10000	0	-0.64	1	1
GNAL	-0.06	0.21	-10000	0	-0.64	34	34
PELP1	0.013	0	-10000	0	-10000	0	0
MAPK11	0.008	0.081	-10000	0	-0.52	7	7
GNAI2	0.013	0	-10000	0	-10000	0	0
GNAI3	0.013	0	-10000	0	-10000	0	0
GNAI1	0.011	0.038	-10000	0	-0.64	1	1
HBEGF	-0.18	0.17	-10000	0	-0.45	62	62
cAMP biosynthetic process	-0.068	0.15	-10000	0	-0.38	55	55
SRC	0.031	0.09	-10000	0	-0.55	1	1
PI3K	0	0	-10000	0	-10000	0	0
GNB1	0.013	0	-10000	0	-10000	0	0
G13/GDP/Gbeta gamma	-0.028	0.097	-10000	0	-0.73	1	1
SOS1	0.013	0	-10000	0	-10000	0	0
IGF-1R heterotetramer/IGF1	-0.042	0.1	-10000	0	-0.6	2	2
Gs family/GTP	-0.069	0.15	-10000	0	-0.38	55	55
EntrezGene:2778	0	0	-10000	0	-10000	0	0
RAS family/GTP	0	0	-10000	0	-10000	0	0
vasodilation	0.026	0.1	-10000	0	-0.49	7	7
mol:DAG	-0.037	0.18	-10000	0	-0.68	5	5
Gs family/GDP/Gbeta gamma	-0.053	0.12	-10000	0	-0.62	3	3
MSN	0.039	0.083	-10000	0	-10000	0	0
Gq family/GTP	-0.084	0.17	-10000	0	-0.46	50	50
mol:PI-3-4-5-P3	0.012	0.12	-10000	0	-0.76	6	6
NRAS	0.013	0	-10000	0	-10000	0	0
mol:E2	0	0	-10000	0	-10000	0	0
cell adhesion	-0.026	0.1	0.49	7	-10000	0	7
GRB2/SOS1	0	0	-10000	0	-10000	0	0
RhoA/GDP	-0.028	0.1	-10000	0	-0.46	6	6
NOS3	0.025	0.11	-10000	0	-0.54	7	7
GNA11	0.013	0	-10000	0	-10000	0	0
MAPKKK cascade	0.037	0.11	-10000	0	-0.58	6	6
E2/ER alpha (dimer)/PELP1/Src	-0.026	0.091	-10000	0	-0.48	6	6
ruffle organization	0.038	0.078	-10000	0	-10000	0	0
ROCK2	0.031	0.09	-10000	0	-10000	0	0
GNA14	-0.095	0.24	-10000	0	-0.64	50	50
GNA15	0.013	0	-10000	0	-10000	0	0
GNA13	0.013	0	-10000	0	-10000	0	0
MMP9	-0.3	0.2	-10000	0	-0.64	20	20
MMP2	-0.052	0.19	-10000	0	-0.55	3	3

×

Paxillin-independent events mediated by a4b1 and a4b7

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PTK2	0.015	0.094	-9999	-0.47	10	10
CRKL	0.011	0.047	-9999	-0.8	1	1
Rac1/GDP	0	0	-9999	-10000	0	0
DOCK1	0.013	0	-9999	-10000	0	0
ITGA4	-0.014	0.15	-9999	-0.8	10	10
alpha4/beta7 Integrin/MAdCAM1	-0.038	0.13	-9999	-0.48	23	23
EPO	-0.056	0.22	-9999	-0.8	25	25
alpha4/beta7 Integrin	-0.022	0.11	-9999	-0.6	11	11
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.013	0	-9999	-10000	0	0
alpha4/beta1 Integrin	-0.022	0.12	-9999	-0.61	11	11
EPO/EPOR (dimer)	-0.065	0.19	-9999	-0.61	32	32
lamellipodium assembly	0.002	0.015	-9999	-10000	0	0
PIK3CA	0.013	0	-9999	-10000	0	0
PI3K	0	0	-9999	-10000	0	0
ARF6	0.013	0	-9999	-10000	0	0
JAK2	-0.039	0.11	-9999	-0.59	2	2
PXN	0.013	0	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
MADCAM1	-0.025	0.16	-9999	-0.8	13	13
cell adhesion	-0.037	0.13	-9999	-0.48	23	23
CRKL/CBL	-0.002	0.035	-9999	-0.61	1	1
ITGB1	0.011	0.047	-9999	-0.8	1	1
SRC	-0.039	0.19	-9999	-0.5	39	39
ITGB7	0.011	0.038	-9999	-0.64	1	1
RAC1	0.013	0	-9999	-10000	0	0
alpha4/beta1 Integrin/VCAM1	-0.078	0.19	-9999	-0.54	44	44
p130Cas/Crk/Dock1	-0.058	0.14	-9999	-0.79	2	2
VCAM1	-0.078	0.25	-9999	-0.78	35	35
RHOA	0.013	0	-9999	-10000	0	0
alpha4/beta1 Integrin/Paxillin/GIT1	-0.017	0.09	-9999	-0.48	11	11
BCAR1	-0.027	0.18	-9999	-0.88	2	2
EPOR	-0.005	0.12	-9999	-0.8	7	7
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	0.002	0.015	-9999	-10000	0	0

×

S1P1 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
VEGFR2 homodimer/VEGFA homodimer	-0.004	0.05	-9999	-0.62	2	2
PDGFRB	-0.22	0.36	-9999	-0.8	85	85
SPHK1	-0.022	0.037	-9999	-0.37	1	1
mol:S1P	-0.029	0.058	-9999	-0.44	4	4
S1P1/S1P/Gi	-0.015	0.13	-9999	-0.46	7	7
GNAO1	0.007	0.061	-9999	-0.73	2	2
PDGFB-D/PDGFRB/PLCgamma1	-0.098	0.21	-9999	-0.58	11	11
PLCG1	-0.017	0.13	-9999	-0.46	5	5
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	-0.22	0.36	-9999	-0.8	85	85
GNAI2	0.011	0.005	-9999	-10000	0	0
GNAI3	0.009	0.007	-9999	-10000	0	0
GNAI1	0.007	0.039	-9999	-0.65	1	1
mol:GDP	0	0	-9999	-10000	0	0
EDG1	0.014	0.046	-9999	-0.54	2	2
S1P1/S1P	-0.038	0.068	-9999	-0.48	3	3
negative regulation of cAMP metabolic process	-0.015	0.12	-9999	-0.45	7	7
MAPK3	-0.022	0.16	-9999	-0.56	7	7
calcium-dependent phospholipase C activity	-0.002	0.003	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
RhoA/GDP	0	0	-9999	-10000	0	0
KDR	0.009	0.047	-9999	-0.8	1	1
PLCB2	-0.001	0.081	-9999	-0.42	3	3
RAC1	0.013	0	-9999	-10000	0	0
RhoA/GTP	-0.031	0.057	-9999	-0.4	3	3
receptor internalization	-0.036	0.064	-9999	-0.44	3	3
PTGS2	-0.05	0.24	-9999	-0.6	47	47
Rac1/GTP	-0.031	0.057	-9999	-0.4	3	3
RHOA	0.013	0	-9999	-10000	0	0
VEGFA	0.009	0.048	-9999	-0.82	1	1
negative regulation of T cell proliferation	-0.015	0.12	-9999	-0.45	7	7
GO:0007205	0	0	-9999	-10000	0	0
GNAZ	-0.008	0.11	-9999	-0.74	7	7
MAPK1	-0.022	0.16	-9999	-0.56	7	7
S1P1/S1P/PDGFB-D/PDGFRB	-0.09	0.2	-9999	-0.54	11	11
ABCC1	0.004	0.081	-9999	-0.8	3	3

×

Fc-epsilon receptor I signaling in mast cells

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
PPAP2A	0.013	0	-9999	-10000	0	0
LAT2	-0.05	0.13	-9999	-0.48	6	6
AP1	-0.1	0.13	-9999	-0.44	24	24
mol:PIP3	-0.073	0.19	-9999	-0.56	10	10
IKBKB	-0.027	0.12	-9999	-0.38	2	2
AKT1	-0.06	0.17	-9999	-0.63	4	4
IKBKG	-0.027	0.12	-9999	-0.38	2	2
MS4A2	-0.01	0.12	-9999	-0.7	9	9
mol:Sphingosine-1-phosphate	0	0	-9999	-10000	0	0
PIK3CA	0.013	0.001	-9999	-10000	0	0
MAP3K1	-0.013	0.12	-9999	-0.44	2	2
mol:Ca2+	-0.052	0.15	-9999	-0.4	10	10
LYN	0.014	0.004	-9999	-10000	0	0
CBLB	-0.049	0.13	-9999	-0.48	6	6
SHC1	0.013	0	-9999	-10000	0	0
RasGAP/p62DOK	-0.03	0.099	-9999	-10000	0	0
positive regulation of cell migration	0	0	-9999	-10000	0	0
INPP5D	0.011	0.038	-9999	-0.64	1	1
PLD2	-0.099	0.19	-9999	-0.72	6	6
PTPN13	-0.042	0.13	-9999	-0.48	4	4
PTPN11	0.01	0.008	-9999	-10000	0	0
GO:0007205	0	0	-9999	-10000	0	0
regulation of mast cell degranulation	-0.024	0.14	-9999	-10000	0	0
SYK	0.011	0.038	-9999	-0.65	1	1
GRB2	0.013	0.001	-9999	-10000	0	0
LAT/PLCgamma1/GRB2/SLP76/GADs	-0.12	0.16	-9999	-0.57	12	12
LAT	-0.061	0.15	-9999	-0.51	14	14
PAK2	-0.024	0.12	-9999	-0.46	4	4
NFATC2	-0.087	0.18	-9999	-0.71	19	19
HRAS	-0.035	0.13	-9999	-0.45	9	9
GAB2	0.009	0.053	-9999	-0.64	2	2
PLA2G1B	0.036	0.019	-9999	-10000	0	0
Fc epsilon R1	-0.16	0.22	-9999	-0.43	112	112
Antigen/IgE/Fc epsilon R1	-0.15	0.2	-9999	-0.55	16	16
mol:GDP	-0.042	0.14	-9999	-0.48	8	8
JUN	0.013	0	-9999	-10000	0	0
mol:Ca++	0	0	-9999	-10000	0	0
PIK3R1	0.013	0.001	-9999	-10000	0	0
FOS	-0.092	0.24	-9999	-0.64	49	49
Antigen/IgE/Fc epsilon R1/LYN/SYK	-0.086	0.12	-9999	-0.46	9	9
CHUK	-0.027	0.12	-9999	-0.38	2	2
KLRG1	-0.057	0.14	-9999	-0.49	9	9
VAV1	-0.055	0.14	-9999	-0.51	9	9
calcium-dependent protein kinase C activity	0	0	-9999	-10000	0	0
CBL	-0.049	0.13	-9999	-0.46	7	7
negative regulation of mast cell degranulation	-0.047	0.13	-9999	-0.45	9	9
BTK	-0.076	0.11	-9999	-0.45	7	7
Fc epsilon R1/FcgammaRIIB/SHIP/RasGAP/p62DOK	-0.087	0.18	-9999	-0.66	10	10
GAB2/PI3K/SHP2	-0.11	0.15	-9999	-0.65	6	6
Antigen/IgE/Fc epsilon R1/LYN/SYK/WIP	-0.071	0.15	-9999	-0.63	6	6
RAF1	0.024	0.023	-9999	-10000	0	0
Fc epsilon R1/FcgammaRIIB/SHIP	-0.14	0.19	-9999	-0.64	14	14
FCER1G	-0.002	0.1	-9999	-0.81	5	5
FCER1A	-0.22	0.32	-9999	-0.65	106	106
Antigen/IgE/Fc epsilon R1/Fyn	-0.14	0.19	-9999	-0.64	10	10
MAPK3	0.035	0.02	-9999	-10000	0	0
MAPK1	0.035	0.02	-9999	-10000	0	0
NFKB1	0.013	0	-9999	-10000	0	0
MAPK8	0.006	0.065	-9999	-0.6	2	2
DUSP1	-0.041	0.18	-9999	-0.64	25	25
NF-kappa-B/RelA	-0.039	0.049	-9999	-10000	0	0
actin cytoskeleton reorganization	-0.048	0.13	-9999	-0.45	6	6
mol:Glucocorticoid Dexamethasone	0	0	-9999	-10000	0	0
PI3K	-0.068	0.099	-9999	-0.5	4	4
FER	-0.049	0.13	-9999	-0.48	6	6
RELA	0.013	0	-9999	-10000	0	0
ITK	-0.035	0.085	-9999	-0.42	12	12
SOS1	0.013	0	-9999	-10000	0	0
PLCG1	-0.042	0.14	-9999	-0.48	9	9
cytokine secretion	-0.028	0.036	-9999	-10000	0	0
SPHK1	-0.053	0.14	-9999	-0.51	9	9
PTK2	-0.05	0.13	-9999	-0.47	6	6
NTAL/PLCgamma1/GRB2/SLP76/GADs	-0.12	0.16	-9999	-0.58	9	9
EDG1	0	0	-9999	-10000	0	0
mol:DAG	-0.063	0.18	-9999	-0.54	7	7
MAP2K2	0.031	0.02	-9999	-10000	0	0
MAP2K1	0.031	0.02	-9999	-10000	0	0
MAP2K7	0.013	0	-9999	-10000	0	0
KLRG1/SHP2	-0.081	0.11	-9999	-0.47	9	9
MAP2K4	0.019	0.009	-9999	-10000	0	0
Fc epsilon R1/FcgammaRIIB	-0.15	0.2	-9999	-0.68	14	14
mol:Choline	-0.098	0.19	-9999	-0.71	6	6
SHC/Grb2/SOS1	-0.069	0.097	-9999	-0.49	1	1
FYN	0.011	0.047	-9999	-0.8	1	1
DOK1	0.013	0	-9999	-10000	0	0
PXN	-0.039	0.12	-9999	-0.48	3	3
HCLS1	-0.053	0.14	-9999	-0.49	9	9
PRKCB	-0.051	0.15	-9999	-0.44	7	7
FCGR2B	0	0.091	-9999	-0.64	6	6
IGHE	-0.001	0.006	-9999	-10000	0	0
KLRG1/SHIP	-0.047	0.13	-9999	-0.46	9	9
LCP2	0.005	0.081	-9999	-0.8	3	3
PLA2G4A	-0.063	0.16	-9999	-0.53	16	16
RASA1	0.013	0	-9999	-10000	0	0
mol:Phosphatidic acid	-0.098	0.19	-9999	-0.71	6	6
IKK complex	-0.004	0.095	-9999	-0.28	1	1
WIPF1	0.003	0.093	-9999	-0.8	4	4

×

Nectin adhesion pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	-0.22	0.37	-9999	-0.8	85	85
alphaV beta3 Integrin	-0.028	0.13	-9999	-0.61	14	14
PTK2	-0.023	0.081	-9999	-0.5	3	3
positive regulation of JNK cascade	-0.009	0.041	-9999	-0.32	3	3
CDC42/GDP	0.044	0.069	-9999	-0.43	3	3
Rac1/GDP	0.046	0.069	-9999	-0.42	3	3
RAP1B	0.011	0.047	-9999	-0.8	1	1
RAP1A	0.013	0	-9999	-10000	0	0
CTNNB1	0.011	0.038	-9999	-0.64	1	1
CDC42/GTP	-0.011	0.05	-9999	-0.39	3	3
nectin-3/I-afadin	-0.023	0.11	-9999	-0.58	12	12
RAPGEF1	0.043	0.075	-9999	-0.48	3	3
mol:GTP	0	0	-9999	-10000	0	0
CRK	0.036	0.084	-9999	-0.56	3	3
PDGFB-D/PDGFRB	-0.22	0.37	-9999	-0.8	85	85
TLN1	0.025	0.057	-9999	-0.45	1	1
Rap1/GTP	-0.01	0.046	-9999	-0.39	1	1
IQGAP1	0.013	0	-9999	-10000	0	0
Rap1/GTP/I-afadin	-0.002	0.028	-9999	-0.49	1	1
nectin-3(dimer)/I-afadin/I-afadin/nectin-3(dimer)/I-afadin/I-afadin	-0.023	0.11	-9999	-0.58	12	12
PVR	0.011	0.047	-9999	-0.8	1	1
Necl-5(dimer)	0.011	0.047	-9999	-0.8	1	1
mol:GDP	0.043	0.081	-9999	-0.53	3	3
MLLT4	0.013	0	-9999	-10000	0	0
PIK3CA	0.013	0	-9999	-10000	0	0
PI3K	-0.14	0.21	-9999	-0.46	92	92
nectin-1(dimer)/I-afadin/I-afadin/nectin-1(dimer)/I-afadin/I-afadin	-0.002	0.027	-9999	-0.47	1	1
positive regulation of lamellipodium assembly	-0.015	0.049	-9999	-0.33	3	3
PVRL1	0.011	0.038	-9999	-0.64	1	1
PVRL3	-0.017	0.15	-9999	-0.76	12	12
PVRL2	0.013	0	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
CDH1	0.009	0.053	-9999	-0.64	2	2
CLDN1	-0.012	0.13	-9999	-0.7	11	11
JAM-A/CLDN1	-0.032	0.11	-9999	-0.48	13	13
SRC	-0.018	0.079	-9999	-0.63	3	3
ITGB3	-0.017	0.15	-9999	-0.76	12	12
nectin-1(dimer)/I-afadin/I-afadin	-0.002	0.027	-9999	-0.47	1	1
FARP2	0.04	0.078	-9999	-0.52	3	3
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)	-0.021	0.1	-9999	-0.5	13	13
nectin-1/I-afadin	-0.002	0.027	-9999	-0.47	1	1
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	-0.021	0.1	-9999	-0.49	13	13
CDC42/GTP/IQGAP1/filamentous actin	0	0	-9999	-10000	0	0
F11R	0.013	0	-9999	-10000	0	0
positive regulation of filopodium formation	-0.009	0.041	-9999	-0.32	3	3
alphaV/beta3 Integrin/Talin	0.017	0.11	-9999	-0.58	3	3
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	0.019	0.053	-9999	-0.39	1	1
VAV2	0.029	0.091	-9999	-0.53	3	3
RAP1/GDP	-0.011	0.052	-9999	-0.46	1	1
ITGAV	0.006	0.076	-9999	-0.75	3	3
nectin-3(dimer)/I-afadin/I-afadin/nectin-2(dimer)/I-afadin/I-afadin	-0.02	0.097	-9999	-0.5	12	12
nectin-3(dimer)/I-afadin/I-afadin	-0.023	0.11	-9999	-0.58	12	12
Rac1/GTP	-0.017	0.058	-9999	-0.41	3	3
PTPRM	-0.011	0.054	-9999	-0.43	1	1
E-cadherin/beta catenin/alpha catenin	-0.004	0.044	-9999	-0.64	1	1
adherens junction assembly	0	0	-9999	-10000	0	0
CDC42	0.013	0	-9999	-10000	0	0

×

TRAIL signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TNFSF10	-0.005	0.12	-10000	0	-0.78	7	7
positive regulation of NF-kappaB transcription factor activity	-0.037	0.14	-10000	0	-0.59	19	19
MAP2K4	0.011	0.099	-10000	0	-0.5	1	1
IKBKB	0.013	0	-10000	0	-10000	0	0
TNFRSF10B	0.013	0	-10000	0	-10000	0	0
TNFRSF10A	0.013	0	-10000	0	-10000	0	0
SMPD1	-0.006	0.037	-10000	0	-10000	0	0
IKBKG	0.013	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
TNFRSF10D	-0.018	0.15	-10000	0	-0.78	12	12
TRAIL/TRAILR2	-0.014	0.089	-10000	0	-0.59	7	7
TRAIL/TRAILR3	-0.027	0.12	-10000	0	-0.59	14	14
TRAIL/TRAILR1	-0.014	0.089	-10000	0	-0.59	7	7
TRAIL/TRAILR4	-0.037	0.14	-10000	0	-0.59	19	19
TRAIL/TRAILR1/DAP3/GTP	-0.011	0.071	-10000	0	-0.49	6	6
IKK complex	-0.025	0.062	-10000	0	-10000	0	0
RIPK1	0.013	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
DAP3/GTP	0	0	-10000	0	-10000	0	0
MAPK3	0.011	0.093	-10000	0	-0.59	7	7
MAP3K1	-0.036	0.089	-10000	0	-0.54	1	1
TRAILR4 (trimer)	-0.018	0.15	-10000	0	-0.77	12	12
TRADD	0.013	0	-10000	0	-10000	0	0
TRAILR1 (trimer)	0.013	0	-10000	0	-10000	0	0
TRAIL/TRAILR1/FADD/TRADD/RIP/TRAF2	-0.003	0.11	-10000	0	-0.54	1	1
CFLAR	0.013	0	-10000	0	-10000	0	0
MAPK1	0.011	0.093	-10000	0	-0.59	7	7
TRAIL/TRAILR1/FADD/TRADD/RIP	-0.063	0.16	-10000	0	-0.78	1	1
mol:ceramide	-0.006	0.037	-10000	0	-10000	0	0
FADD	-0.084	0.26	-10000	0	-0.8	36	36
MAPK8	0.017	0.1	-10000	0	-0.5	2	2
TRAF2	0.008	0.066	-10000	0	-0.8	2	2
TRAILR3 (trimer)	-0.005	0.12	-10000	0	-0.78	7	7
CHUK	0.013	0	-10000	0	-10000	0	0
TRAIL/TRAILR1/FADD	-0.074	0.19	-10000	0	-0.54	42	42
DAP3	0.013	0	-10000	0	-10000	0	0
CASP10	-0.051	0.16	0.28	9	-0.44	39	48
JNK cascade	-0.037	0.14	-10000	0	-0.59	19	19
TRAIL (trimer)	-0.005	0.12	-10000	0	-0.78	7	7
TNFRSF10C	-0.005	0.12	-10000	0	-0.78	7	7
TRAIL/TRAILR1/DAP3/GTP/FADD	-0.064	0.16	-10000	0	-0.46	42	42
TRAIL/TRAILR2/FADD	-0.074	0.19	-10000	0	-0.54	42	42
cell death	-0.006	0.037	-10000	0	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP/TRAF2	-0.003	0.11	-10000	0	-0.54	1	1
TRAILR2 (trimer)	0.013	0	-10000	0	-10000	0	0
CASP8	0	0.023	-10000	0	-10000	0	0
negative regulation of caspase activity	0	0	-10000	0	-10000	0	0
TRAIL/TRAILR2/FADD/TRADD/RIP	-0.063	0.16	-10000	0	-0.78	1	1

×

Retinoic acid receptors-mediated signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
HDAC1	0.013	0	-9999	-10000	0	0
HDAC3	0.013	0	-9999	-10000	0	0
VDR	0.013	0	-9999	-10000	0	0
Cbp/p300/PCAF	-0.017	0.08	-9999	-0.4	13	13
EP300	0.013	0	-9999	-10000	0	0
RARs/AIB1/Cbp/p300/PCAF/9cRA	0.005	0.1	-9999	-0.49	6	6
KAT2B	-0.015	0.13	-9999	-0.64	13	13
MAPK14	0.013	0	-9999	-10000	0	0
AKT1	0.018	0.12	-9999	-0.28	25	25
RAR alpha/9cRA/Cyclin H	-0.018	0.053	-9999	-10000	0	0
mol:9cRA	0	0	-9999	-10000	0	0
RARs/Src-1/Cbp/p300/PCAF/9cRA	-0.001	0.11	-9999	-0.43	8	8
CDC2	0.001	0.001	-9999	-10000	0	0
response to UV	0.001	0.002	-9999	-10000	0	0
RAR alpha/Jnk1	-0.021	0.068	-9999	-0.52	2	2
NCOR2	0.013	0	-9999	-10000	0	0
VDR/VDR/Vit D3	0	0	-9999	-10000	0	0
RXRs/RARs/NRIP1/9cRA	-0.004	0.14	-9999	-0.52	3	3
NCOA2	0.005	0.075	-9999	-0.64	4	4
NCOA3	0.013	0	-9999	-10000	0	0
NCOA1	0.013	0	-9999	-10000	0	0
VDR/VDR/DNA	0.013	0	-9999	-10000	0	0
RARG	0.014	0.001	-9999	-10000	0	0
RAR gamma1/9cRA	0	0	-9999	-10000	0	0
MAPK3	0.014	0.001	-9999	-10000	0	0
MAPK1	0.013	0	-9999	-10000	0	0
MAPK8	0.01	0.053	-9999	-0.64	2	2
mol:Vit D3	0	0	-9999	-10000	0	0
RXRs/VDR/DNA/Vit D3	-0.042	0.099	-9999	-0.41	8	8
RARA	0.004	0.079	-9999	-0.27	1	1
negative regulation of phosphoinositide 3-kinase cascade	0	0	-9999	-10000	0	0
RARs/TIF2/Cbp/p300/PCAF/9cRA	-0.006	0.13	-9999	-0.51	10	10
PRKCA	0.014	0.047	-9999	-0.8	1	1
RXRs/RARs/NRIP1/9cRA/HDAC1	-0.019	0.14	-9999	-0.53	3	3
RXRG	-0.063	0.19	-9999	-0.41	64	64
RXRA	0.014	0.075	-9999	-10000	0	0
RXRB	-0.008	0.11	-9999	-0.34	30	30
VDR/Vit D3/DNA	0	0	-9999	-10000	0	0
RBP1	-0.15	0.33	-9999	-0.8	61	61
CRBP1/9-cic-RA	-0.12	0.25	-9999	-0.62	61	61
RARB	-0.058	0.21	-9999	-0.64	34	34
PRKCG	-0.065	0.24	-9999	-0.8	29	29
MNAT1	0.013	0	-9999	-10000	0	0
RAR alpha/RXRs	0.01	0.14	-9999	-0.51	2	2
RXRs/RARs/SMRT(N-CoR2)/9cRA	0.002	0.13	-9999	-0.5	2	2
proteasomal ubiquitin-dependent protein catabolic process	0.001	0.11	-9999	-0.44	9	9
RXRs/RARs/NRIP1/9cRA/HDAC3	-0.019	0.14	-9999	-0.53	3	3
positive regulation of DNA binding	-0.018	0.051	-9999	-10000	0	0
NRIP1	-0.017	0.14	-9999	-1.2	1	1
RXRs/RARs	-0.025	0.14	-9999	-0.43	12	12
RXRs/RXRs/DNA/9cRA	-0.045	0.1	-9999	-0.43	8	8
PRKACA	0.013	0	-9999	-10000	0	0
CDK7	0.013	0	-9999	-10000	0	0
TFIIH	0	0	-9999	-10000	0	0
RAR alpha/9cRA	-0.013	0.037	-9999	-10000	0	0
CCNH	0.013	0	-9999	-10000	0	0
CREBBP	0.013	0	-9999	-10000	0	0
RAR gamma2/9cRA	0	0	-9999	-10000	0	0

×

S1P3 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PDGFRB	-0.22	0.37	-9999	-0.8	85	85
mol:S1P	0.001	0.004	-9999	-10000	0	0
S1P1/S1P/Gi	0.027	0.059	-9999	-0.56	1	1
GNAO1	0.01	0.061	-9999	-0.73	2	2
S1P/S1P3/G12/G13	-0.007	0.057	-9999	-0.5	3	3
AKT1	-0.07	0.11	-9999	-0.36	5	5
AKT3	0.039	0.11	-9999	-0.67	6	6
mol:GTP	0	0	-9999	-10000	0	0
PDGFB-D/PDGFRB	-0.22	0.37	-9999	-0.8	85	85
GNAI2	0.015	0.002	-9999	-10000	0	0
GNAI3	0.015	0.002	-9999	-10000	0	0
GNAI1	0.013	0.038	-9999	-0.64	1	1
mol:GDP	0	0	-9999	-10000	0	0
S1PR3	0.008	0.072	-9999	-0.71	3	3
S1PR2	0.013	0	-9999	-10000	0	0
EDG1	0	0	-9999	-10000	0	0
mol:Ca2+	0.034	0.081	-9999	-0.62	3	3
MAPK3	0.041	0.078	-9999	-0.59	3	3
MAPK1	0.041	0.078	-9999	-0.59	3	3
JAK2	0.036	0.1	-9999	-0.64	4	4
CXCR4	0.022	0.14	-9999	-0.55	13	13
FLT1	0.016	0.002	-9999	-10000	0	0
RhoA/GDP	0	0	-9999	-10000	0	0
Rac1/GDP	0	0	-9999	-10000	0	0
SRC	0.041	0.078	-9999	-0.59	3	3
S1P/S1P3/Gi	0.034	0.082	-9999	-0.63	3	3
RAC1	0.013	0	-9999	-10000	0	0
RhoA/GTP	-0.012	0.066	-9999	-0.57	3	3
VEGFA	0.014	0.047	-9999	-0.8	1	1
S1P/S1P2/Gi	0.035	0.056	-9999	-0.58	1	1
VEGFR1 homodimer/VEGFA homodimer	0.026	0.037	-9999	-0.61	1	1
RHOA	0.013	0	-9999	-10000	0	0
S1P/S1P3/Gq	-0.019	0.12	-9999	-0.42	2	2
GNAQ	0.013	0	-9999	-10000	0	0
GNAZ	-0.002	0.11	-9999	-0.73	7	7
G12/G13	-0.004	0.05	-9999	-0.61	2	2
GNA14	-0.095	0.24	-9999	-0.64	50	50
GNA15	0.013	0	-9999	-10000	0	0
GNA12	0.008	0.066	-9999	-0.8	2	2
GNA13	0.013	0	-9999	-10000	0	0
GNA11	0.013	0	-9999	-10000	0	0
Rac1/GTP	-0.012	0.066	-9999	-0.57	3	3

×

Rapid glucocorticoid signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Gs family/GDP/Gbeta gamma	-0.04	0.11	-10000	0	-0.34	35	35
MAPK9	0.009	0	-10000	0	-10000	0	0
adrenocorticotropin secretion	0.001	0.003	-10000	0	-10000	0	0
GNB1/GNG2	-0.002	0.031	-10000	0	-0.54	1	1
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	-0.042	0.12	-10000	0	-0.38	34	34
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	0.011	0.03	0.094	34	-10000	0	34
GNAL	-0.06	0.21	-10000	0	-0.64	34	34
GNG2	0.011	0.047	-10000	0	-0.8	1	1
CRH	0.001	0.003	-10000	0	-10000	0	0
mol:cortisol	0	0	-10000	0	-10000	0	0
MAPK8	0.007	0.032	-10000	0	-0.38	2	2
MAPK11	0.009	0	-10000	0	-10000	0	0

×

Signaling events mediated by PRL

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CCNE1	0.011	0.047	-10000	0	-0.8	1	1
mol:Halofuginone	0.006	0.001	-10000	0	-10000	0	0
ITGA1	-0.14	0.32	-10000	0	-0.8	58	58
CDKN1A	0.03	0.032	-10000	0	-10000	0	0
PRL-3/alpha Tubulin	-0.008	0.07	-10000	0	-0.61	4	4
mol:Ca2+	-0.074	0.18	0.37	3	-0.49	48	51
AGT	-0.091	0.24	-10000	0	-0.65	48	48
CCNA2	0.032	0.079	-10000	0	-0.78	1	1
TUBA1B	0.013	0	-10000	0	-10000	0	0
EGR1	0.009	0.092	-10000	0	-0.46	11	11
CDK2/Cyclin E1	-0.005	0.031	-10000	0	-0.43	1	1
MAPK3	0.016	0.073	-10000	0	-0.61	4	4
PRL-2 /Rab GGTase beta	0	0	-10000	0	-10000	0	0
MAPK1	0.016	0.073	-10000	0	-0.61	4	4
PTP4A1	0.027	0.072	-10000	0	-10000	0	0
PTP4A3	0.003	0.093	-10000	0	-0.8	4	4
PTP4A2	0.013	0	-10000	0	-10000	0	0
ITGB1	0.014	0.081	-10000	0	-0.61	5	5
SRC	0.013	0	-10000	0	-10000	0	0
RAC1	0.027	0.043	-10000	0	-10000	0	0
Rab GGTase beta/Rab GGTase alpha	0	0	-10000	0	-10000	0	0
PRL-1/ATF-5	0.022	0.094	-10000	0	-10000	0	0
RABGGTA	0.013	0	-10000	0	-10000	0	0
BCAR1	0.005	0.042	0.37	4	-10000	0	4
RHOC	0.027	0.043	-10000	0	-10000	0	0
RHOA	0.027	0.043	-10000	0	-10000	0	0
cell motility	0.032	0.045	-10000	0	-10000	0	0
PRL-1/alpha Tubulin	0.032	0.067	-10000	0	-10000	0	0
PRL-3/alpha1 Integrin	-0.12	0.25	-10000	0	-0.61	62	62
ROCK1	0.032	0.046	-10000	0	-10000	0	0
RABGGTB	0.013	0	-10000	0	-10000	0	0
CDK2	0.013	0	-10000	0	-10000	0	0
mitosis	0.027	0.071	-10000	0	-10000	0	0
ATF5	-0.003	0.11	-10000	0	-0.8	6	6

×

Class IB PI3K non-lipid kinase events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
cAMP biosynthetic process	0.004	0.12	0.75	7	-10000	0	7
PI3K Class IB/PDE3B	-0.004	0.12	-10000	0	-0.76	7	7
PDE3B	-0.004	0.12	-10000	0	-0.76	7	7

×

JNK signaling in the CD4+ TCR pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
LAT/GRAP2/SLP76/HPK1	-0.042	0.21	-9999	-1	12	12
MAP4K1	-0.012	0.14	-9999	-0.75	10	10
MAP3K8	0.013	0	-9999	-10000	0	0
PRKCB	-0.005	0.12	-9999	-0.78	7	7
DBNL	0.013	0	-9999	-10000	0	0
CRKL	0.011	0.047	-9999	-0.8	1	1
MAP3K1	0.026	0.12	-9999	-0.56	10	10
JUN	0.026	0.086	-9999	-0.57	4	4
MAP3K7	0.026	0.12	-9999	-0.56	10	10
GRAP2	-0.007	0.12	-9999	-0.74	8	8
CRK	0.013	0	-9999	-10000	0	0
MAP2K4	0.036	0.11	-9999	-0.53	10	10
LAT	-0.008	0.13	-9999	-0.8	8	8
LCP2	0.005	0.081	-9999	-0.8	3	3
MAPK8	0.019	0.091	-9999	-0.51	7	7
LAT/GRAP2/SLP76/HPK1/HIP-55/CRK family	0.018	0.12	-9999	-0.6	10	10
LAT/GRAP2/SLP76/HPK1/HIP-55	-0.04	0.2	-9999	-0.95	12	12

×

Noncanonical Wnt signaling pathway

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
NFATC2	-0.028	0.16	-9999	-0.65	19	19
GNB1/GNG2	-0.052	0.11	-9999	-0.55	6	6
mol:DAG	-0.001	0.12	-9999	-0.52	5	5
PLCG1	-0.001	0.13	-9999	-0.54	5	5
YES1	-0.017	0.14	-9999	-0.61	5	5
FZD3	0.005	0.075	-9999	-0.64	4	4
FZD6	0.013	0	-9999	-10000	0	0
G protein	-0.049	0.1	-9999	-0.55	5	5
MAP3K7	-0.048	0.17	-9999	-0.51	10	10
mol:Ca2+	0	0.12	-9999	-0.5	5	5
mol:IP3	-0.001	0.12	-9999	-0.52	5	5
NLK	-0.005	0.008	-9999	-10000	0	0
GNB1	0.013	0	-9999	-10000	0	0
CAMK2A	-0.06	0.18	-9999	-0.54	15	15
MAP3K7IP1	0	0	-9999	-10000	0	0
Noncanonical Wnts/FZD	-0.028	0.14	-9999	-0.65	5	5
CSNK1A1	0.013	0	-9999	-10000	0	0
GNAS	-0.017	0.14	-9999	-0.61	5	5
GO:0007205	0	0.12	-9999	-0.51	5	5
WNT6	-0.03	0.18	-9999	-0.76	17	17
WNT4	-0.01	0.13	-9999	-0.69	10	10
NFAT1/CK1 alpha	-0.063	0.13	-9999	-0.64	7	7
GNG2	0.011	0.047	-9999	-0.8	1	1
WNT5A	0.004	0.08	-9999	-0.68	4	4
WNT11	-0.074	0.25	-9999	-0.76	34	34
CDC42	-0.007	0.13	-9999	-0.57	5	5

×

a4b1 and a4b7 Integrin signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ITGB1	0.011	0.047	-9999	-0.8	1	1
ITGB7	0.011	0.038	-9999	-0.64	1	1
ITGA4	-0.014	0.15	-9999	-0.8	10	10
alpha4/beta7 Integrin	-0.022	0.11	-9999	-0.6	11	11
alpha4/beta1 Integrin	-0.022	0.12	-9999	-0.61	11	11

×

Cellular roles of Anthrax toxin

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
ANTXR1	0.005	0.081	-10000	0	-0.8	3	3
ANTXR2	-0.008	0.13	-10000	0	-0.8	8	8
negative regulation of myeloid dendritic cell antigen processing and presentation	-0.003	0.018	-10000	0	-0.096	11	11
monocyte activation	-0.032	0.12	-10000	0	-0.43	11	11
MAP2K2	-0.001	0.007	-10000	0	-10000	0	0
MAP2K1	-0.003	0.015	-10000	0	-10000	0	0
MAP2K7	-0.003	0.015	-10000	0	-10000	0	0
MAP2K6	-0.019	0.075	-10000	0	-0.36	14	14
CYAA	-0.001	0.091	-10000	0	-0.47	11	11
MAP2K4	-0.003	0.015	-10000	0	-10000	0	0
IL1B	-0.029	0.14	-10000	0	-0.45	29	29
Channel	-0.018	0.093	-10000	0	-0.5	11	11
NLRP1	-0.004	0.031	-10000	0	-0.48	1	1
CALM1	0.013	0	-10000	0	-10000	0	0
negative regulation of phagocytosis	-0.004	0.022	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
regulation of endothelial cell proliferation	0.003	0.018	0.096	11	-10000	0	11
MAPK3	-0.003	0.015	-10000	0	-10000	0	0
MAPK1	-0.003	0.015	-10000	0	-10000	0	0
PGR	-0.049	0.12	-10000	0	-0.38	37	37
PA/Cellular Receptors	-0.019	0.1	-10000	0	-0.54	11	11
apoptosis	-0.003	0.018	-10000	0	-0.096	11	11
LOC728358	0	0	-10000	0	-10000	0	0
Lethal toxin (unfolded)	0	0.087	-10000	0	-0.45	11	11
macrophage activation	0.019	0.017	-10000	0	-10000	0	0
TNF	-0.025	0.17	-10000	0	-0.76	15	15
VCAM1	-0.032	0.12	-10000	0	-0.43	11	11
platelet activation	-0.004	0.022	-10000	0	-10000	0	0
MAPKKK cascade	-0.011	0.026	-10000	0	-10000	0	0
IL18	0.004	0.069	-10000	0	-0.35	10	10
negative regulation of macrophage activation	-0.003	0.018	-10000	0	-0.096	11	11
LEF	-0.004	0.018	-10000	0	-0.097	11	11
CASP1	-0.004	0.02	-10000	0	-0.22	1	1
mol:cAMP	-0.004	0.022	-10000	0	-10000	0	0
necrosis	-0.003	0.018	-10000	0	-0.096	11	11
intracellular pH reduction	0	0	-10000	0	-10000	0	0
PAGA	0	0	-10000	0	-10000	0	0
Edema toxin (unfolded)	-0.017	0.088	-10000	0	-0.47	11	11
mol:Epigallocatechin-3-gallate (EGCG)	0	0	-10000	0	-10000	0	0

×

IFN-gamma pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2	-0.076	0.16	-9999	-10000	0	0
positive regulation of NF-kappaB transcription factor activity	0	0.002	-9999	-10000	0	0
CRKL	0.011	0.047	-9999	-0.8	1	1
STAT1 (dimer)/Cbp/p300	-0.091	0.19	-9999	-0.71	15	15
IFN-gammaR/JAK1/JAK1/JAK2/JAK2	-0.012	0.024	-9999	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class I	-0.07	0.094	-9999	-0.37	4	4
CaM/Ca2+	-0.07	0.14	-9999	-10000	0	0
RAP1A	0.013	0	-9999	-10000	0	0
STAT1 (dimer)/SHP2	-0.061	0.23	-9999	-0.81	15	15
AKT1	-0.015	0.15	-9999	-10000	0	0
MAP2K1	-0.016	0.16	-9999	-10000	0	0
MAP3K11	-0.029	0.17	-9999	-10000	0	0
IFNGR1	0.008	0.015	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKII	-0.18	0.24	-9999	-0.65	42	42
Rap1/GTP	-0.054	0.11	-9999	-10000	0	0
CRKL/C3G	-0.002	0.035	-9999	-0.61	1	1
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2 /TC-PTP	-0.083	0.17	-9999	-10000	0	0
CEBPB	0.02	0.15	-9999	-10000	0	0
STAT3	0.013	0	-9999	-10000	0	0
IFN-gamma/IFN-gammaR/JAK1/JAK1/JAK2/JAK2/SOCS1	-0.11	0.22	-9999	-0.9	10	10
STAT1	-0.06	0.23	-9999	-0.81	15	15
CALM1	0.014	0	-9999	-10000	0	0
IFN-gamma (dimer)	-0.14	0.32	-9999	-0.79	59	59
PIK3CA	0.013	0	-9999	-10000	0	0
STAT1 (dimer)/PIAS1	-0.087	0.2	-9999	-0.75	15	15
CEBPB/PTGES2/Cbp/p300	-0.034	0.066	-9999	-10000	0	0
mol:Ca2+	-0.075	0.15	-9999	-10000	0	0
MAPK3	0.002	0.14	-9999	-10000	0	0
STAT1 (dimer)	-0.094	0.13	-9999	-0.56	4	4
MAPK1	0.002	0.14	-9999	-10000	0	0
JAK2	0.008	0.015	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
JAK1	0.008	0.015	-9999	-10000	0	0
CAMK2D	0.013	0	-9999	-10000	0	0
DAPK1	0.03	0.12	-9999	-0.63	4	4
SMAD7	0.001	0.076	-9999	-10000	0	0
CBL/CRKL/C3G	-0.065	0.13	-9999	-10000	0	0
PI3K	-0.068	0.14	-9999	-10000	0	0
IFNG	-0.14	0.32	-9999	-0.79	59	59
apoptosis	0.013	0.1	-9999	-0.44	4	4
CAMK2G	0.014	0	-9999	-10000	0	0
STAT3 (dimer)	0.013	0	-9999	-10000	0	0
CAMK2A	-0.12	0.27	-9999	-0.65	62	62
CAMK2B	-0.16	0.29	-9999	-0.65	79	79
FRAP1	-0.008	0.14	-9999	-10000	0	0
PRKCD	-0.01	0.15	-9999	-10000	0	0
RAP1B	0.011	0.047	-9999	-0.8	1	1
negative regulation of cell growth	-0.07	0.094	-9999	-0.37	4	4
PTPN2	0.013	0	-9999	-10000	0	0
EP300	0.014	0.001	-9999	-10000	0	0
IRF1	-0.02	0.19	-9999	-0.52	24	24
STAT1 (dimer)/PIASy	-0.086	0.2	-9999	-0.75	15	15
SOCS1	-0.046	0.18	-9999	-0.65	25	25
mol:GDP	-0.062	0.12	-9999	-10000	0	0
CASP1	0.001	0.078	-9999	-0.38	1	1
PTGES2	0.013	0	-9999	-10000	0	0
IRF9	0.041	0.055	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.066	0.13	-9999	-10000	0	0
RAP1/GDP	-0.055	0.11	-9999	-10000	0	0
CBL	-0.03	0.16	-9999	-10000	0	0
MAP3K1	-0.028	0.17	-9999	-10000	0	0
PIAS1	0.013	0	-9999	-10000	0	0
PIAS4	0.014	0.002	-9999	-10000	0	0
antigen processing and presentation of peptide antigen via MHC class II	-0.07	0.094	-9999	-0.37	4	4
PTPN11	-0.04	0.17	-9999	-10000	0	0
CREBBP	0.014	0.001	-9999	-10000	0	0
RAPGEF1	0.013	0	-9999	-10000	0	0

×

RXR and RAR heterodimerization with other nuclear receptor

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
TGFB1	0.009	0.044	-9999	-0.65	1	1
VDR	0.013	0	-9999	-10000	0	0
FAM120B	0.013	0	-9999	-10000	0	0
RXRs/LXRs/DNA/9cRA	0.011	0.12	-9999	-0.45	2	2
RXRs/LXRs/DNA/Oxysterols	0.021	0.12	-9999	-0.52	2	2
MED1	0.011	0.047	-9999	-0.8	1	1
mol:9cRA	0.005	0.012	-9999	-10000	0	0
RARs/THRs/DNA/Src-1	-0.012	0.12	-9999	-0.55	4	4
RXRs/NUR77	-0.017	0.15	-9999	-0.45	7	7
RXRs/PPAR	-0.11	0.18	-9999	-0.54	18	18
NCOR2	0.013	0	-9999	-10000	0	0
VDR/VDR/Vit D3	0	0	-9999	-10000	0	0
RARs/VDR/DNA/Vit D3	-0.037	0.1	-9999	-10000	0	0
RARA	0.013	0	-9999	-10000	0	0
NCOA1	0.013	0	-9999	-10000	0	0
VDR/VDR/DNA	0.013	0	-9999	-10000	0	0
RARs/RARs/DNA/9cRA	-0.038	0.11	-9999	-0.34	34	34
RARG	0.013	0	-9999	-10000	0	0
RPS6KB1	0.016	0.041	-9999	-10000	0	0
RARs/THRs/DNA/SMRT	-0.012	0.12	-9999	-0.55	4	4
THRA	0.013	0	-9999	-10000	0	0
mol:Bile acids	0	0	-9999	-10000	0	0
VDR/Vit D3/DNA	0	0	-9999	-10000	0	0
RXRs/PPAR/9cRA/PGJ2/DNA	-0.014	0.14	-9999	-0.46	7	7
NR1H4	0.004	0.006	-9999	-10000	0	0
RXRs/LXRs/DNA	0.007	0.14	-9999	-10000	0	0
NR1H2	0.019	0.008	-9999	-10000	0	0
NR1H3	0.014	0.066	-9999	-0.79	2	2
RXRs/VDR/DNA/Vit D3	-0.009	0.13	-9999	-0.44	5	5
NR4A1	0	0.091	-9999	-0.64	6	6
mol:ATRA	0	0	-9999	-10000	0	0
RXRs/FXR/9cRA/MED1	-0.001	0.095	-9999	-0.54	1	1
RXRG	-0.076	0.23	-9999	-0.66	42	42
RXR alpha/CCPG	0.003	0.008	-9999	-10000	0	0
RXRA	0.019	0.008	-9999	-10000	0	0
RXRB	0.019	0.009	-9999	-10000	0	0
THRB	-0.028	0.16	-9999	-0.64	19	19
PPARG	-0.24	0.32	-9999	-0.64	116	116
PPARD	0.013	0	-9999	-10000	0	0
TNF	0.007	0.2	-9999	-0.75	15	15
mol:Oxysterols	0.005	0.01	-9999	-10000	0	0
cholesterol transport	0.021	0.12	-9999	-0.51	2	2
PPARA	0.013	0	-9999	-10000	0	0
mol:Vit D3	0	0	-9999	-10000	0	0
RARB	-0.06	0.21	-9999	-0.64	34	34
RXRs/NUR77/BCL2	-0.017	0.11	-9999	-10000	0	0
SREBF1	0.03	0.11	-9999	-10000	0	0
RXRs/RXRs/DNA/9cRA	-0.014	0.14	-9999	-0.46	7	7
ABCA1	0.026	0.13	-9999	-0.84	2	2
RARs/THRs	-0.057	0.14	-9999	-0.67	4	4
RXRs/FXR	-0.015	0.14	-9999	-0.46	5	5
BCL2	0.004	0.08	-9999	-0.68	4	4

×

FAS signaling pathway (CD95)

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SPTAN1	0.006	0.036	0.26	2	-10000	0	2
RFC1	0.006	0.036	0.26	4	-10000	0	4
PRKDC	0.006	0.036	0.26	4	-10000	0	4
RIPK1	0.013	0.003	-10000	0	-10000	0	0
CASP7	-0.011	0.041	0.23	3	-10000	0	3
FASLG/FAS/FADD/FAF1	-0.05	0.12	-10000	0	-0.39	9	9
MAP2K4	0	0.12	-10000	0	-0.44	7	7
mol:ceramide	-0.019	0.14	-10000	0	-0.48	8	8
GSN	0.006	0.036	0.26	4	-10000	0	4
FASLG/FAS/FADD/FAF1/Caspase 8	-0.019	0.12	-10000	0	-0.46	6	6
FAS	0.013	0.004	-10000	0	-10000	0	0
BID	0.003	0.045	-10000	0	-0.54	1	1
MAP3K1	0.012	0.077	-10000	0	-10000	0	0
MAP3K7	0.013	0.004	-10000	0	-10000	0	0
RB1	0.005	0.042	0.26	4	-0.39	1	5
CFLAR	0.013	0.003	-10000	0	-10000	0	0
HGF/MET	-0.02	0.092	-10000	0	-0.43	14	14
ARHGDIB	0.006	0.036	0.26	4	-10000	0	4
FADD	-0.084	0.26	-10000	0	-0.8	36	36
actin filament polymerization	-0.006	0.036	-10000	0	-0.26	4	4
NFKB1	-0.029	0.063	-10000	0	-10000	0	0
MAPK8	-0.005	0.16	-10000	0	-0.59	7	7
DFFA	0.006	0.036	0.26	4	-10000	0	4
DNA fragmentation during apoptosis	0.006	0.036	0.26	4	-10000	0	4
FAS/FADD/MET	-0.066	0.18	-10000	0	-0.54	36	36
CFLAR/RIP1	0	0	-10000	0	-10000	0	0
FAIM3	-0.003	0.11	-10000	0	-0.8	6	6
FAF1	0.014	0.004	-10000	0	-10000	0	0
PARP1	0.006	0.036	0.26	4	-10000	0	4
DFFB	0.006	0.036	0.26	4	-10000	0	4
CHUK	-0.024	0.054	-10000	0	-10000	0	0
FASLG	-0.039	0.2	-10000	0	-0.75	21	21
FAS/FADD	-0.073	0.2	-10000	0	-0.61	36	36
HGF	-0.008	0.12	-10000	0	-0.7	9	9
LMNA	0.006	0.033	-10000	0	-10000	0	0
CASP6	0.006	0.036	0.26	4	-10000	0	4
CASP10	0.013	0.004	-10000	0	-10000	0	0
CASP3	0.008	0.042	0.3	4	-10000	0	4
PTPN13	0.007	0.065	-10000	0	-0.64	3	3
CASP8	0.007	0.052	0.37	6	-10000	0	6
IL6	-0.082	0.36	-10000	0	-1.2	28	28
MET	0.009	0.06	-10000	0	-0.72	2	2
ICAD/CAD	0.006	0.034	-10000	0	-10000	0	0
FASLG/FAS/FADD/FAF1/Caspase 10	-0.02	0.14	-10000	0	-0.49	8	8
activation of caspase activity by cytochrome c	0.003	0.045	-10000	0	-0.54	1	1
PAK2	0.006	0.035	0.25	4	-10000	0	4
BCL2	0.004	0.08	-10000	0	-0.68	4	4

×

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	0.036	0.12	-10000	0	-0.69	4	4
UGCG	-0.007	0.037	-10000	0	-0.59	1	1
AKT1/mTOR/p70S6K/Hsp90/TERT	0.011	0.13	-10000	0	-0.43	13	13
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucosylceramide	0.019	0.044	-10000	0	-0.58	1	1
mol:DAG	-0.001	0.003	-10000	0	-10000	0	0
CaM/Ca2+/Calcineurin A alpha-beta B1	-0.025	0.083	-10000	0	-0.45	8	8
FRAP1	0.047	0.13	-10000	0	-0.52	8	8
FOXO3	0.055	0.12	-10000	0	-0.55	4	4
AKT1	0.048	0.12	-10000	0	-0.57	5	5
GAB2	0.01	0.053	-10000	0	-0.64	2	2
SMPD1	-0.005	0.015	-10000	0	-10000	0	0
SGMS1	-0.005	0.015	-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	0.024	0.003	-10000	0	-10000	0	0
CALM1	0.013	0	-10000	0	-10000	0	0
cell proliferation	0.038	0.056	-10000	0	-10000	0	0
EIF3A	0.013	0	-10000	0	-10000	0	0
PI3K	0.024	0.009	-10000	0	-10000	0	0
RPS6KB1	0.006	0.069	-10000	0	-10000	0	0
mol:sphingomyelin	-0.001	0.003	-10000	0	-10000	0	0
natural killer cell activation	0.001	0.001	-10000	0	-10000	0	0
JAK3	-0.026	0.18	-10000	0	-0.8	16	16
PIK3R1	0.017	0.002	-10000	0	-10000	0	0
JAK1	0.017	0.002	-10000	0	-10000	0	0
NFKB1	0.013	0	-10000	0	-10000	0	0
MYC	0.056	0.11	-10000	0	-0.53	2	2
MYB	-0.11	0.39	-10000	0	-1.2	31	31
IL2/IL2R alpha/beta/gamma/JAK1/LCK/JAK3/SHC/GAB2/GRB2/SOS1/SHP2/PI3K	0.033	0.13	-10000	0	-0.55	10	10
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0.021	0.063	-10000	0	-10000	0	0
mol:PI-3-4-5-P3	0.033	0.13	-10000	0	-0.54	10	10
Rac1/GDP	0.028	0.01	-10000	0	-10000	0	0
T cell proliferation	0.043	0.12	-10000	0	-0.63	4	4
SHC1	0.014	0.002	-10000	0	-10000	0	0
RAC1	0.014	0	-10000	0	-10000	0	0
positive regulation of cyclin-dependent protein kinase activity	-0.001	0.022	-10000	0	-0.066	31	31
PRKCZ	0.042	0.13	-10000	0	-0.66	4	4
NF kappa B1 p50/RelA	-0.023	0.082	-10000	0	-0.49	3	3
IL2/IL2R beta/gamma/JAK1/LCK/JAK3/PI3K	0.029	0.13	-10000	0	-0.59	9	9
HSP90AA1	0.013	0	-10000	0	-10000	0	0
RELA	0.013	0	-10000	0	-10000	0	0
IL2RA	-0.085	0.27	-10000	0	-0.8	37	37
IL2RB	0	0.11	-10000	0	-0.8	6	6
TERT	-0.16	0.34	-10000	0	-0.8	66	66
E2F1	-0.029	0.15	-10000	0	-0.42	33	33
SOS1	0.014	0.002	-10000	0	-10000	0	0
RPS6	0.013	0	-10000	0	-10000	0	0
mol:cAMP	0	0.011	0.032	31	-10000	0	31
PTPN11	0.014	0.002	-10000	0	-10000	0	0
IL2RG	-0.012	0.15	-10000	0	-0.78	11	11
actin cytoskeleton organization	0.043	0.12	-10000	0	-0.63	4	4
GRB2	0.014	0.002	-10000	0	-10000	0	0
IL2	0.005	0.047	-10000	0	-0.8	1	1
PIK3CA	0.017	0.002	-10000	0	-10000	0	0
Rac1/GTP	0.035	0.012	-10000	0	-10000	0	0
LCK	-0.01	0.15	-10000	0	-0.8	10	10
BCL2	0.049	0.14	-10000	0	-0.78	5	5

×

Stabilization and expansion of the E-cadherin adherens junction

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
adherens junction organization	0.031	0.03	-9999	-10000	0	0
epithelial cell differentiation	-0.003	0.033	-9999	-10000	0	0
CYFIP2	0.009	0.053	-9999	-0.64	2	2
ENAH	0.066	0.042	-9999	-10000	0	0
EGFR	-0.014	0.15	-9999	-0.8	10	10
EPHA2	0.005	0.075	-9999	-0.64	4	4
MYO6	0.037	0.04	-9999	-10000	0	0
CTNNB1	0.011	0.038	-9999	-0.64	1	1
ABI1/Sra1/Nap1	-0.003	0.032	-9999	-0.4	2	2
AQP5	-0.37	0.21	-9999	-0.49	228	228
CTNND1	0.013	0	-9999	-10000	0	0
mol:PI-4-5-P2	0.038	0.034	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	0.005	0.12	-9999	-0.42	17	17
EGF	-0.14	0.27	-9999	-0.64	69	69
NCKAP1	0.013	0	-9999	-10000	0	0
AQP3	-0.14	0.22	-9999	-0.49	87	87
cortical microtubule organization	-0.003	0.033	-9999	-10000	0	0
GO:0000145	0.037	0.033	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.003	0.033	-9999	-10000	0	0
MLLT4	0.013	0	-9999	-10000	0	0
ARF6/GDP	-0.007	0.042	-9999	-10000	0	0
ARF6	0.013	0	-9999	-10000	0	0
Ephrin A1/EPHA2/NCK1/GIT1	-0.006	0.049	-9999	-0.48	1	1
mol:Ca2+	0	0	-9999	-10000	0	0
VASP	0.05	0.036	-9999	-10000	0	0
PVRL2	0.013	0	-9999	-10000	0	0
ZYX	0.038	0.035	-9999	-10000	0	0
ARF6/GTP	-0.006	0.044	-9999	-10000	0	0
CDH1	0.009	0.053	-9999	-0.64	2	2
EGFR/EGFR/EGF/EGF	-0.084	0.14	-9999	-0.67	2	2
RhoA/GDP	-0.003	0.03	-9999	-10000	0	0
actin cytoskeleton organization	0.044	0.038	-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	-0.054	0.2	-9999	-0.67	30	30
DIAPH1	-0.004	0.048	-9999	-0.6	2	2
Wnt receptor signaling pathway	0.003	0.033	-9999	-10000	0	0
RHOA	0.013	0	-9999	-10000	0	0
RhoA/GTP	-0.007	0.042	-9999	-10000	0	0
CTNNA1	0.013	0	-9999	-10000	0	0
VCL	0.044	0.039	-9999	-10000	0	0
EFNA1	0.011	0.047	-9999	-0.8	1	1
LPP	0.044	0.042	-9999	-10000	0	0
Ephrin A1/EPHA2	-0.008	0.05	-9999	-10000	0	0
SEC6/SEC8	-0.003	0.026	-9999	-10000	0	0
MGAT3	0.005	0.12	-9999	-0.43	17	17
HGF/MET	-0.015	0.076	-9999	-0.73	1	1
HGF	-0.008	0.12	-9999	-0.7	9	9
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN	0.031	0.03	-9999	-10000	0	0
actin cable formation	0.084	0.038	-9999	-10000	0	0
KIAA1543	0.019	0.11	-9999	-0.72	3	3
KIFC3	0.038	0.035	-9999	-10000	0	0
NCK1	0.013	0	-9999	-10000	0	0
EXOC3	0.013	0	-9999	-10000	0	0
ACTN1	0.037	0.044	-9999	-0.43	1	1
NCK1/GIT1	0	0	-9999	-10000	0	0
mol:GDP	-0.003	0.033	-9999	-10000	0	0
EXOC4	0.013	0	-9999	-10000	0	0
STX4	0.038	0.035	-9999	-10000	0	0
PIP5K1C	0.038	0.035	-9999	-10000	0	0
LIMA1	0.013	0	-9999	-10000	0	0
ABI1	0.013	0	-9999	-10000	0	0
ROCK1	-0.006	0.036	-9999	-10000	0	0
adherens junction assembly	0.037	0.11	-9999	-0.67	3	3
IGF-1R heterotetramer/IGF1	-0.034	0.098	-9999	-10000	0	0
nectin-2(dimer)/I-afadin/I-afadin/nectin-2(dimer/I-afadin/I-afadin	0	0	-9999	-10000	0	0
MET	0.009	0.06	-9999	-0.72	2	2
PLEKHA7	0.021	0.088	-9999	-0.64	1	1
mol:GTP	-0.006	0.048	-9999	-0.48	1	1
establishment of epithelial cell apical/basal polarity	0.065	0.031	-9999	-10000	0	0
cortical actin cytoskeleton stabilization	0.031	0.03	-9999	-10000	0	0
regulation of cell-cell adhesion	0.044	0.038	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin/EPLIN/cortical actin cytoskeleton	0.031	0.03	-9999	-10000	0	0

×

Ras signaling in the CD4+ TCR 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
ERK1-2/ELK1	-0.018	0.18	-9999	-0.56	10	10
MAP3K8	0.012	0.005	-9999	-10000	0	0
FOS	0	0.12	-9999	-0.46	9	9
PRKCA	0.01	0.047	-9999	-0.8	1	1
PTPN7	-0.029	0.18	-9999	-0.8	16	16
HRAS	0.013	0.001	-9999	-10000	0	0
PRKCB	-0.006	0.12	-9999	-0.79	7	7
NRAS	0.013	0.001	-9999	-10000	0	0
RAS family/GTP	0	0	-9999	-10000	0	0
MAPK3	0.006	0.086	-9999	-0.38	7	7
MAP2K1	0.025	0.072	-9999	-0.43	3	3
ELK1	0.008	0.049	-9999	-0.84	1	1
BRAF	-0.013	0.059	-9999	-0.42	3	3
mol:GTP	-0.001	0.002	-9999	-0.006	49	49
MAPK1	0.006	0.086	-9999	-0.38	7	7
RAF1	-0.013	0.059	-9999	-0.42	3	3
KRAS	0.013	0.001	-9999	-10000	0	0

×

EPO signaling 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	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.031	0.12	-10000	0	-0.57	1	1
CRKL	0.006	0.13	-10000	0	-0.48	1	1
mol:DAG	0.018	0.12	-10000	0	-0.47	1	1
HRAS	0.037	0.12	-10000	0	-10000	0	0
MAPK8	-0.012	0.15	-10000	0	-0.46	3	3
RAP1A	0.008	0.13	-10000	0	-0.48	1	1
GAB1	0.008	0.13	-10000	0	-0.48	1	1
MAPK14	-0.01	0.15	-10000	0	-0.44	32	32
EPO	-0.053	0.22	-10000	0	-0.8	25	25
PLCG1	0.017	0.12	-10000	0	-0.49	1	1
EPOR/TRPC2/IP3 Receptors	-0.005	0.12	-10000	0	-0.79	7	7
RAPGEF1	0.013	0	-10000	0	-10000	0	0
EPO/EPOR (dimer)/SOCS3	-0.054	0.16	-10000	0	-0.5	33	33
GAB1/SHC/GRB2/SOS1	-0.034	0.097	-10000	0	-10000	0	0
EPO/EPOR (dimer)	-0.043	0.19	-10000	0	-0.6	32	32
IRS2	0.005	0.13	-10000	0	-0.48	1	1
STAT1	-0.003	0.16	-10000	0	-0.63	2	2
STAT5B	0.022	0.12	-10000	0	-0.54	1	1
cell proliferation	-0.002	0.14	-10000	0	-10000	0	0
GAB1/SHIP/PIK3R1/SHP2/SHC	-0.033	0.096	-10000	0	-0.66	1	1
TEC	-0.012	0.16	-10000	0	-0.72	4	4
SOCS3	0.011	0.038	-10000	0	-0.64	1	1
STAT1 (dimer)	-0.002	0.16	-10000	0	-0.62	2	2
JAK2	0.012	0.012	-10000	0	-10000	0	0
PIK3R1	0.013	0	-10000	0	-10000	0	0
EPO/EPOR (dimer)/JAK2	0.01	0.14	-10000	0	-0.51	1	1
EPO/EPOR	-0.043	0.19	-10000	0	-0.6	32	32
LYN	0.015	0.002	-10000	0	-10000	0	0
TEC/VAV2	-0.019	0.18	-10000	0	-0.79	5	5
elevation of cytosolic calcium ion concentration	-0.005	0.12	-10000	0	-0.79	7	7
SHC1	0.013	0	-10000	0	-10000	0	0
EPO/EPOR (dimer)/LYN	-0.017	0.17	-10000	0	-0.5	32	32
mol:IP3	0.018	0.12	-10000	0	-0.47	1	1
PI3K regualtory subunit polypeptide 1/IRS2/SHIP	-0.039	0.11	-10000	0	-0.74	1	1
SH2B3	0.009	0.048	-10000	0	-0.79	1	1
NFKB1	-0.01	0.15	-10000	0	-0.44	32	32
EPO/EPOR (dimer)/JAK2/SOCS3	-0.027	0.083	0.27	1	-10000	0	1
PTPN6	-0.001	0.14	-10000	0	-0.51	1	1
TEC/VAV2/GRB2	-0.054	0.16	-10000	0	-0.76	5	5
EPOR	-0.005	0.12	-10000	0	-0.79	7	7
INPP5D	0.011	0.038	-10000	0	-0.64	1	1
mol:GDP	-0.035	0.099	-10000	0	-10000	0	0
SOS1	0.013	0	-10000	0	-10000	0	0
PLCG2	0.013	0	-10000	0	-10000	0	0
CRKL/CBL/C3G	-0.025	0.11	-10000	0	-10000	0	0
VAV2	-0.009	0.16	-10000	0	-0.7	3	3
CBL	0.008	0.13	-10000	0	-0.48	1	1
SHC/Grb2/SOS1	-0.037	0.1	-10000	0	-10000	0	0
STAT5A	0.022	0.12	-10000	0	-0.54	1	1
GRB2	0.013	0	-10000	0	-10000	0	0
STAT5 (dimer)	0.04	0.13	-10000	0	-0.65	1	1
LYN/PLCgamma2	0	0	-10000	0	-10000	0	0
PTPN11	0.013	0	-10000	0	-10000	0	0
BTK	0.006	0.13	-10000	0	-0.48	1	1
BCL2	0.025	0.15	-10000	0	-0.85	4	4

×

Ceramide signaling pathway

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
SPHK2	0.012	0.089	-10000	0	-0.61	6	6
MAP4K4	0.03	0.077	-10000	0	-0.46	2	2
BAG4	0.013	0	-10000	0	-10000	0	0
PKC zeta/ceramide	-0.018	0.053	0.21	1	-0.41	1	2
NFKBIA	0.013	0	-10000	0	-10000	0	0
BIRC3	-0.024	0.17	-10000	0	-0.8	14	14
BAX	-0.004	0.025	-10000	0	-10000	0	0
RIPK1	0.013	0	-10000	0	-10000	0	0
AKT1	0.024	0.011	-10000	0	-10000	0	0
BAD	-0.016	0.049	0.23	1	-10000	0	1
SMPD1	0.019	0.053	-10000	0	-0.26	2	2
RB1	-0.017	0.053	0.21	5	-0.36	1	6
FADD/Caspase 8	-0.012	0.17	-10000	0	-0.6	6	6
MAP2K4	-0.007	0.046	-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	-0.007	0.046	-10000	0	-10000	0	0
EGF	-0.14	0.27	-10000	0	-0.64	69	69
mol:ceramide	-0.027	0.053	0.22	5	-10000	0	5
MADD	0.013	0	-10000	0	-10000	0	0
response to oxidative stress	0	0	-10000	0	-10000	0	0
mol:Free Fatty acid	0.012	0.089	-10000	0	-0.61	6	6
ASAH1	0.013	0	-10000	0	-10000	0	0
negative regulation of cell cycle	-0.017	0.053	0.21	5	-0.36	1	6
cell proliferation	-0.038	0.087	-10000	0	-0.36	5	5
BID	0.019	0.055	-10000	0	-10000	0	0
MAP3K1	-0.016	0.049	0.21	5	-10000	0	5
EIF2A	-0.001	0.057	-10000	0	-0.43	2	2
TRADD	0.013	0	-10000	0	-10000	0	0
CRADD	0.013	0	-10000	0	-10000	0	0
MAPK3	0.006	0.044	-10000	0	-10000	0	0
response to heat	0	0	-10000	0	-10000	0	0
MAPK1	0.006	0.044	-10000	0	-10000	0	0
Cathepsin D/ceramide	-0.016	0.048	0.21	1	-10000	0	1
FADD	-0.027	0.18	-10000	0	-0.46	38	38
KSR1	-0.016	0.049	0.21	5	-10000	0	5
MAPK8	-0.004	0.052	0.22	1	-0.27	2	3
PRKRA	-0.016	0.049	0.23	1	-10000	0	1
PDGFA	-0.003	0.11	-10000	0	-0.8	6	6
TRAF2	0.008	0.066	-10000	0	-0.8	2	2
IGF1	-0.054	0.2	-10000	0	-0.67	30	30
mol:GD3	0	0	-10000	0	-10000	0	0
ganglioside biosynthetic process	-0.027	0.052	0.22	5	-10000	0	5
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	-0.019	0.1	-10000	0	-10000	0	0
PRKCD	0.013	0	-10000	0	-10000	0	0
PRKCZ	0.011	0.038	-10000	0	-0.64	1	1
mol:GW4869	0	0	-10000	0	-10000	0	0
mol:sphingosine	0.012	0.089	-10000	0	-0.61	6	6
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	0.023	0.081	-10000	0	-0.46	3	3
TNFR1A/BAG4/TNF-alpha	-0.024	0.11	-10000	0	-0.49	15	15
mol:Sphingosine-1-phosphate	0.012	0.089	-10000	0	-0.61	6	6
MAP2K1	0.002	0.044	-10000	0	-10000	0	0
mol:C11AG	0	0	-10000	0	-10000	0	0
RELA	0.013	0	-10000	0	-10000	0	0
CYCS	-0.006	0.041	0.33	1	-10000	0	1
TNFRSF1A	0.013	0	-10000	0	-10000	0	0
NFKB1	0.013	0	-10000	0	-10000	0	0
TNFR1A/BAG4	0	0	-10000	0	-10000	0	0
EIF2AK2	-0.01	0.059	-10000	0	-0.46	2	2
TNF-alpha/TNFR1A/FAN	-0.024	0.11	-10000	0	-0.49	15	15
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
CASP8	0.035	0.046	-10000	0	-10000	0	0
MAP2K2	0.002	0.044	-10000	0	-10000	0	0
SMPD3	-0.006	0.11	-10000	0	-0.34	25	25
TNF	-0.025	0.17	-10000	0	-0.76	15	15
PKC zeta/PAR4	-0.002	0.027	-10000	0	-0.47	1	1
mol:PHOSPHOCHOLINE	0.043	0.11	0.24	62	-10000	0	62
NF kappa B1/RelA/I kappa B alpha	-0.001	0.019	-10000	0	-10000	0	0
AIFM1	-0.006	0.041	0.33	1	-10000	0	1
BCL2	0.004	0.08	-10000	0	-0.68	4	4

×

Paxillin-dependent events mediated by a4b1

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CRKL	0.011	0.047	-10000	0	-0.8	1	1
Rac1/GDP	0.002	0.013	-10000	0	-10000	0	0
DOCK1	0.013	0	-10000	0	-10000	0	0
ITGA4	-0.014	0.15	-10000	0	-0.8	10	10
RAC1	0.013	0	-10000	0	-10000	0	0
alpha4/beta7 Integrin	-0.022	0.11	-10000	0	-0.6	11	11
mol:GTP	0	0	-10000	0	-10000	0	0
CRK	0.013	0	-10000	0	-10000	0	0
alpha4/beta1 Integrin	-0.019	0.099	-10000	0	-0.53	11	11
alpha4/beta7 Integrin/Paxillin	-0.017	0.088	-10000	0	-0.48	10	10
lamellipodium assembly	0.002	0.014	-10000	0	-10000	0	0
PIK3CA	0.013	0	-10000	0	-10000	0	0
PI3K	0	0	-10000	0	-10000	0	0
ARF6	0.013	0	-10000	0	-10000	0	0
TLN1	0.011	0.047	-10000	0	-0.8	1	1
PXN	0.025	0	-10000	0	-10000	0	0
PIK3R1	0.013	0	-10000	0	-10000	0	0
ARF6/GTP	-0.015	0.076	-10000	0	-10000	0	0
cell adhesion	-0.017	0.086	-10000	0	-0.44	12	12
CRKL/CBL	-0.002	0.035	-10000	0	-0.61	1	1
alpha4/beta1 Integrin/Paxillin	-0.017	0.09	-10000	0	-0.48	11	11
ITGB1	0.011	0.047	-10000	0	-0.8	1	1
ITGB7	0.011	0.038	-10000	0	-0.64	1	1
ARF6/GDP	0.002	0.013	-10000	0	-10000	0	0
alpha4/beta1 Integrin/Paxillin/VCAM1	-0.066	0.16	-10000	0	-0.47	39	39
p130Cas/Crk/Dock1	0	0	-10000	0	-10000	0	0
VCAM1	-0.078	0.25	-10000	0	-0.78	35	35
alpha4/beta1 Integrin/Paxillin/Talin	-0.018	0.087	-10000	0	-0.45	12	12
alpha4/beta1 Integrin/Paxillin/GIT1	-0.016	0.084	-10000	0	-0.45	11	11
BCAR1	0.013	0	-10000	0	-10000	0	0
mol:GDP	0.016	0.083	0.44	11	-10000	0	11
CBL	0.013	0	-10000	0	-10000	0	0
PRKACA	0.013	0	-10000	0	-10000	0	0
GIT1	0.013	0	-10000	0	-10000	0	0
alpha4/beta1 Integrin/Paxillin/Talin/Actin Cytoskeleton	-0.018	0.087	-10000	0	-0.45	12	12
Rac1/GTP	0.002	0.015	-10000	0	-10000	0	0

×

IL6-mediated signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.001	0.22	-9999	-0.66	2	2
CRP	-0.031	0.27	-9999	-0.76	18	18
cell cycle arrest	-0.013	0.24	-9999	-0.71	8	8
TIMP1	0.01	0.2	-9999	-0.64	1	1
IL6ST	0	0.099	-9999	-0.64	7	7
Rac1/GDP	0.013	0.14	-9999	-0.58	7	7
AP1	-0.002	0.14	-9999	-0.65	2	2
GAB2	0.009	0.053	-9999	-0.64	2	2
TNFSF11	-0.078	0.32	-9999	-0.76	15	15
HSP90B1	0.035	0.052	-9999	-10000	0	0
GAB1	0.014	0.001	-9999	-10000	0	0
MAPK14	0.011	0.14	-9999	-0.63	6	6
AKT1	0.058	0.03	-9999	-10000	0	0
FOXO1	0.067	0.026	-9999	-10000	0	0
MAP2K6	-0.003	0.15	-9999	-0.64	6	6
mol:GTP	0	0.003	-9999	-10000	0	0
MAP2K4	0.02	0.16	-9999	-0.56	6	6
MITF	0.004	0.15	-9999	-0.68	6	6
positive regulation of NF-kappaB transcription factor activity	0	0	-9999	-10000	0	0
TYK2	0.013	0	-9999	-10000	0	0
A2M	0.02	0.039	-9999	-0.65	1	1
CEBPB	0.02	0.007	-9999	-10000	0	0
GRB2/SOS1/GAB family/SHP2	0.025	0.07	-9999	-0.39	2	2
STAT3	-0.015	0.25	-9999	-0.74	8	8
STAT1	-0.027	0.098	-9999	-0.35	23	23
CEBPD	0.001	0.22	-9999	-0.66	3	3
PIK3CA	0.015	0	-9999	-10000	0	0
PI3K	0	0.002	-9999	-10000	0	0
JUN	0.013	0.001	-9999	-10000	0	0
PIAS3/MITF	0.01	0.14	-9999	-0.64	6	6
MAPK11	0.011	0.14	-9999	-0.63	6	6
STAT3 (dimer)/FOXO1	0.045	0.21	-9999	-10000	0	0
GRB2/SOS1/GAB family	-0.031	0.093	-9999	-0.58	4	4
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/HCK	0.001	0.13	-9999	-0.64	5	5
GRB2	0.014	0.001	-9999	-10000	0	0
JAK2	0.013	0	-9999	-10000	0	0
LBP	-0.1	0.38	-9999	-0.9	47	47
PIK3R1	0.015	0	-9999	-10000	0	0
JAK1	0.015	0.005	-9999	-10000	0	0
MYC	0.001	0.22	-9999	-0.66	3	3
FGG	-0.024	0.26	-9999	-0.77	14	14
macrophage differentiation	-0.013	0.24	-9999	-0.71	8	8
IL6/IL6RA/gp130 (dimer)/JAK2/JAK2/LMO4	-0.04	0.13	-9999	-0.57	8	8
JUNB	0	0.21	-9999	-10000	0	0
FOS	-0.093	0.24	-9999	-0.64	49	49
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4	0.002	0.14	-9999	-0.54	9	9
STAT1/PIAS1	-0.002	0.14	-9999	-0.54	7	7
GRB2/SOS1/GAB family/SHP2/PI3K	0.041	0.035	-9999	-10000	0	0
STAT3 (dimer)	-0.015	0.25	-9999	-0.74	8	8
PRKCD	0.026	0.18	-9999	-0.66	2	2
IL6R	0.013	0.038	-9999	-0.65	1	1
SOCS3	0.016	0.14	-9999	-0.78	4	4
gp130 (dimer)/JAK1/JAK1/LMO4	0.02	0.069	-9999	-0.4	7	7
Rac1/GTP	-0.051	0.11	-9999	-0.58	7	7
HCK	0.003	0.084	-9999	-0.72	4	4
MAPKKK cascade	0.039	0.07	-9999	-0.56	2	2
bone resorption	-0.072	0.31	-9999	-0.72	15	15
IRF1	0.001	0.22	-9999	-0.66	3	3
mol:GDP	0.006	0.15	-9999	-0.59	8	8
SOS1	0.012	0.005	-9999	-10000	0	0
VAV1	0.006	0.15	-9999	-0.6	8	8
IL6/IL6RA/gp130 (dimer)/JAK1/JAK1/LMO4/SOCS3	0.011	0.13	-9999	-0.69	5	5
PTPN11	-0.001	0.016	-9999	-10000	0	0
IL6/IL6RA	-0.029	0.16	-9999	-0.51	28	28
gp130 (dimer)/TYK2/TYK2/LMO4	0.015	0.067	-9999	-0.4	7	7
gp130 (dimer)/JAK2/JAK2/LMO4	0.015	0.067	-9999	-0.4	4	4
IL6	-0.048	0.2	-9999	-0.67	28	28
PIAS3	0.013	0	-9999	-10000	0	0
PTPRE	0.011	0.013	-9999	-10000	0	0
PIAS1	0.013	0	-9999	-10000	0	0
RAC1	0.014	0.002	-9999	-10000	0	0
IL6/IL6RA/gp130 (dimer)/TYK2/TYK2/LMO4	-0.007	0.13	-9999	-0.5	9	9
LMO4	0.015	0.011	-9999	-10000	0	0
STAT3 (dimer)/PIAS3	-0.1	0.17	-9999	-0.71	7	7
MCL1	0.066	0.025	-9999	-10000	0	0

×

FOXM1 transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NFATC3	0.14	0.31	-9999	-1.3	1	1
PLK1	0.08	0.082	-9999	-0.69	1	1
BIRC5	0.073	0.11	-9999	-0.68	4	4
HSPA1B	0.14	0.31	-9999	-1.3	1	1
MAP2K1	0.043	0.037	-9999	-10000	0	0
BRCA2	0.14	0.32	-9999	-1.3	2	2
FOXM1	0.13	0.35	-9999	-2.1	1	1
XRCC1	0.14	0.31	-9999	-1.3	1	1
FOXM1B/p19	-0.18	0.26	-9999	-0.99	12	12
Cyclin D1/CDK4	0.082	0.36	-9999	-1	5	5
CDC2	0.14	0.32	-9999	-1.4	1	1
TGFA	0.095	0.36	-9999	-1.1	3	3
SKP2	0.14	0.31	-9999	-1.3	1	1
CCNE1	0.016	0.047	-9999	-0.78	1	1
CKS1B	0.14	0.31	-9999	-1.5	1	1
RB1	-0.049	0.1	-9999	-0.67	2	2
FOXM1C/SP1	0.13	0.31	-9999	-1.7	1	1
AURKB	0.08	0.082	-9999	-0.72	1	1
CENPF	0.14	0.31	-9999	-1.3	1	1
CDK4	0.023	0.017	-9999	-10000	0	0
MYC	0.14	0.28	-9999	-1.1	1	1
CHEK2	0.041	0.057	-9999	-0.71	1	1
ONECUT1	0.081	0.38	-9999	-1.1	6	6
CDKN2A	-0.32	0.38	-9999	-0.78	124	124
LAMA4	0.12	0.35	-9999	-1.1	4	4
FOXM1B/HNF6	0.076	0.4	-9999	-1.2	7	7
FOS	0.006	0.54	-9999	-1.1	49	49
SP1	0.015	0.001	-9999	-10000	0	0
CDC25B	0.13	0.32	-9999	-1.3	1	1
response to radiation	0.025	0.035	-9999	-10000	0	0
CENPB	0.14	0.31	-9999	-1.3	1	1
CENPA	0.14	0.32	-9999	-1.2	2	2
NEK2	0.14	0.32	-9999	-1.3	2	2
HIST1H2BA	0.13	0.31	-9999	-1.3	1	1
CCNA2	0.016	0.049	-9999	-0.82	1	1
EP300	0.013	0	-9999	-10000	0	0
CCNB1/CDK1	0.14	0.33	-9999	-1.7	1	1
CCNB2	0.14	0.31	-9999	-1.5	1	1
CCNB1	0.14	0.32	-9999	-1.4	1	1
ETV5	0.14	0.32	-9999	-1.3	1	1
ESR1	0.11	0.36	-9999	-1	10	10
CCND1	0.086	0.38	-9999	-0.99	8	8
GSK3A	0.039	0.033	-9999	-10000	0	0
Cyclin A-E1/CDK1-2	0.045	0.064	-9999	-0.52	2	2
CDK2	0.019	0.01	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	0.03	0.04	-9999	-10000	0	0
FOXM1B/Cbp/p300	-0.072	0.18	-9999	-1.1	3	3
GAS1	0.14	0.33	-9999	-1.2	4	4
MMP2	0.072	0.38	-9999	-1	6	6
RB1/FOXM1C	0.1	0.35	-9999	-1.1	2	2
CREBBP	0.013	0	-9999	-10000	0	0

×

p38 MAPK signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
TRAF6/ASK1	0	0	-9999	-10000	0	0
TRAF2/ASK1	-0.004	0.043	-9999	-0.54	2	2
ATM	0.013	0	-9999	-10000	0	0
MAP2K3	0.018	0.044	-9999	-10000	0	0
response to stress	0	0	-9999	-10000	0	0
MAP2K6	0.021	0.063	-9999	-10000	0	0
hyperosmotic response	0	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
GADD45G	0.003	0.083	-9999	-0.64	5	5
TXN	0.009	0	-9999	-10000	0	0
CALM1	0.013	0	-9999	-10000	0	0
GADD45A	0.011	0.047	-9999	-0.8	1	1
GADD45B	0.013	0	-9999	-10000	0	0
MAP3K1	0.013	0	-9999	-10000	0	0
MAP3K6	0.011	0.038	-9999	-0.64	1	1
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	0.027	-9999	-0.47	1	1
TAK1/TAB family	0	0	-9999	-10000	0	0
RAC1/OSM/MEKK3	0	0	-9999	-10000	0	0
TRAF2	0.008	0.066	-9999	-0.8	2	2
RAC1/OSM/MEKK3/MKK3	-0.006	0.012	-9999	-10000	0	0
TRAF6	0.009	0	-9999	-10000	0	0
RAC1	0.013	0	-9999	-10000	0	0
mol:LPS	0	0	-9999	-10000	0	0
CAMK2B	-0.16	0.29	-9999	-0.65	79	79
CCM2	0.013	0	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB	-0.11	0.18	-9999	-0.41	79	79
MAPK11	0.013	0	-9999	-10000	0	0
response to DNA damage stimulus	0	0	-9999	-10000	0	0
CaM/Ca2+/CAMKIIB/ASK1	-0.096	0.16	-9999	-0.37	79	79
OSM/MEKK3	0	0	-9999	-10000	0	0
TAOK1	0.017	0.023	-9999	-0.37	1	1
TAOK2	0.019	0	-9999	-10000	0	0
TAOK3	0.019	0	-9999	-10000	0	0
MAP3K7IP1	0	0	-9999	-10000	0	0
MAPK14	0.013	0	-9999	-10000	0	0
MAP3K7IP2	0	0	-9999	-10000	0	0
MAP3K5	0.013	0	-9999	-10000	0	0
MAP3K10	0.011	0.047	-9999	-0.8	1	1
MAP3K3	0.013	0	-9999	-10000	0	0
TRX/ASK1	0.017	0	-9999	-10000	0	0
GADD45/MTK1/MTK1	-0.007	0.05	-9999	-0.46	1	1

×

Class I PI3K signaling events mediated by Akt

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.025	0	-9999	-10000	0	0
BAD/BCL-XL/YWHAZ	0	0	-9999	-10000	0	0
CDKN1B	0.041	0	-9999	-10000	0	0
CDKN1A	0.041	0	-9999	-10000	0	0
FRAP1	0	0	-9999	-10000	0	0
PRKDC	0.013	0	-9999	-10000	0	0
FOXO3	0.041	0	-9999	-10000	0	0
AKT1	0	0	-9999	-10000	0	0
BAD	0.013	0	-9999	-10000	0	0
AKT3	0.011	0.052	-9999	-0.36	6	6
mol:GTP	0	0	-9999	-10000	0	0
FOXO4	0.039	0.028	-9999	-10000	0	0
AKT1/ASK1	0	0	-9999	-10000	0	0
BAD/YWHAZ	0	0	-9999	-10000	0	0
RICTOR	0.013	0	-9999	-10000	0	0
RAF1	0.013	0	-9999	-10000	0	0
JNK cascade	0	0	-9999	-10000	0	0
TSC1	0.041	0	-9999	-10000	0	0
YWHAZ	0.013	0	-9999	-10000	0	0
AKT1/RAF1	0.04	0	-9999	-10000	0	0
EP300	0.013	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	0	0	-9999	-10000	0	0
TSC2	0.041	0	-9999	-10000	0	0
YWHAQ	0.013	0	-9999	-10000	0	0
TBC1D4	0.027	0	-9999	-10000	0	0
MAP3K5	0.013	0	-9999	-10000	0	0
MAPKAP1	0.013	0	-9999	-10000	0	0
negative regulation of cell cycle	-0.048	0.009	-9999	-10000	0	0
YWHAH	0.013	0	-9999	-10000	0	0
AKT1S1	0.041	0	-9999	-10000	0	0
CASP9	0.041	0	-9999	-10000	0	0
YWHAB	0.013	0	-9999	-10000	0	0
p27Kip1/KPNA1	0.047	0	-9999	-10000	0	0
GBL	0	0	-9999	-10000	0	0
PDK1/Src/Hsp90	0	0	-9999	-10000	0	0
YWHAE	0.013	0	-9999	-10000	0	0
SRC	0.013	0	-9999	-10000	0	0
AKT2/p21CIP1	0	0	-9999	-10000	0	0
KIAA1303	0	0	-9999	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL	0.02	0	-9999	-10000	0	0
CHUK	0.041	0	-9999	-10000	0	0
BAD/BCL-XL	0.054	0	-9999	-10000	0	0
mTORC2	0	0	-9999	-10000	0	0
AKT2	0.019	0	-9999	-10000	0	0
FOXO1-3a-4/14-3-3 family	0.064	0.014	-9999	-10000	0	0
PDPK1	0.013	0	-9999	-10000	0	0
MDM2	0.041	0	-9999	-10000	0	0
MAPKKK cascade	-0.039	0	-9999	-10000	0	0
MDM2/Cbp/p300	0	0	-9999	-10000	0	0
TSC1/TSC2	0.048	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
glucose import	-0.14	0.19	-9999	-0.35	133	133
mTOR/RHEB/GDP/Raptor/GBL/PRAS40	0.035	0	-9999	-10000	0	0
response to stress	0	0	-9999	-10000	0	0
SLC2A4	-0.14	0.19	-9999	-0.35	133	133
GSK3A	0.041	0	-9999	-10000	0	0
FOXO1	0.041	0	-9999	-10000	0	0
GSK3B	0.041	0	-9999	-10000	0	0
SFN	0.011	0.038	-9999	-0.64	1	1
G1/S transition of mitotic cell cycle	0.048	0	-9999	-10000	0	0
p27Kip1/14-3-3 family	0.052	0.014	-9999	-10000	0	0
PRKACA	0.013	0	-9999	-10000	0	0
KPNA1	0.013	0	-9999	-10000	0	0
HSP90AA1	0.013	0	-9999	-10000	0	0
YWHAG	0.013	0	-9999	-10000	0	0
RHEB	0.013	0	-9999	-10000	0	0
CREBBP	0.013	0	-9999	-10000	0	0

×

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BAG4	0.013	0	-9999	-10000	0	0
Caspase 8 (4 units)	-0.033	0.075	-9999	-0.5	2	2
NEF	-0.006	0.045	-9999	-10000	0	0
NFKBIA	0.012	0.026	-9999	-10000	0	0
BIRC3	0.013	0.16	-9999	-0.74	14	14
CYCS	0.01	0.11	-9999	-0.53	3	3
RIPK1	0.013	0	-9999	-10000	0	0
CD247	-0.031	0.19	-9999	-0.86	14	14
MAP2K7	0.012	0.094	-9999	-0.43	2	2
protein ubiquitination	0.031	0.096	-9999	-0.42	1	1
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	0.002	0.11	-9999	-0.56	3	3
NF-kappa-B/RelA/I kappa B alpha	-0.015	0.067	-9999	-10000	0	0
TRADD	0.013	0	-9999	-10000	0	0
MAP3K5	0.013	0	-9999	-10000	0	0
CFLAR	0.013	0	-9999	-10000	0	0
FADD	-0.084	0.26	-9999	-0.8	36	36
NF-kappa-B/RelA/I kappa B alpha/ubiquitin	-0.015	0.067	-9999	-10000	0	0
MAPK8	0.018	0.096	-9999	-0.44	2	2
APAF1	0.013	0	-9999	-10000	0	0
TRAF1	-0.008	0.13	-9999	-0.8	8	8
TRAF2	0.008	0.066	-9999	-0.8	2	2
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8/FASLG	-0.006	0.11	-9999	-0.49	4	4
TNFR1A/Caspase 2/TNF-alpha/FADD/TRADD/RIP1/cIAP2/TRAF1/TRAF2/Ask1/RAIDD	0.014	0.12	-9999	-0.52	2	2
CHUK	0.031	0.1	-9999	-0.46	1	1
FAS/FADD/DAXX/Ask1/Caspase 8/Caspase 8	-0.053	0.14	-9999	-10000	0	0
TCRz/NEF	-0.05	0.17	-9999	-0.54	28	28
TNF	-0.025	0.17	-9999	-0.76	15	15
FASLG	-0.045	0.25	-9999	-0.81	27	27
NFKB1	0.012	0.026	-9999	-10000	0	0
TNFR1A/BAG4/TNF-alpha	-0.024	0.11	-9999	-0.49	15	15
CASP6	-0.02	0.046	-9999	-10000	0	0
CASP7	0.041	0.13	-9999	-0.5	4	4
RELA	0.012	0.026	-9999	-10000	0	0
CASP2	0.013	0	-9999	-10000	0	0
CASP3	0.041	0.13	-9999	-0.5	4	4
TNFRSF1A	0.013	0	-9999	-10000	0	0
TNFR1A/BAG4	0	0	-9999	-10000	0	0
CASP8	0.013	0	-9999	-10000	0	0
CASP9	0.013	0	-9999	-10000	0	0
MAP3K14	0.023	0.11	-9999	-0.53	1	1
APAF-1/Caspase 9	-0.039	0.1	-9999	-0.51	4	4
BCL2	0.021	0.1	-9999	-0.44	3	3

×

IL2 signaling events mediated by STAT5

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
GAB2	0.01	0.053	-9999	-0.64	2	2
ELF1	-0.019	0.11	-9999	-10000	0	0
CCNA2	0.011	0.047	-9999	-0.8	1	1
PIK3CA	0.014	0	-9999	-10000	0	0
JAK3	-0.029	0.18	-9999	-0.8	16	16
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	0.035	0.13	-9999	-0.57	9	9
SHC1	0.014	0	-9999	-10000	0	0
SP1	0.02	0.029	-9999	-10000	0	0
IL2RA	-0.056	0.24	-9999	-0.7	37	37
IL2RB	-0.002	0.11	-9999	-0.8	6	6
SOS1	0.014	0	-9999	-10000	0	0
IL2RG	-0.015	0.15	-9999	-0.79	11	11
G1/S transition of mitotic cell cycle	0.037	0.073	-9999	-0.67	1	1
PTPN11	0.014	0	-9999	-10000	0	0
CCND2	0.028	0.067	-9999	-0.78	2	2
LCK	-0.013	0.15	-9999	-0.8	10	10
GRB2	0.014	0	-9999	-10000	0	0
IL2	0.003	0.047	-9999	-0.8	1	1
CDK6	0	0.1	-9999	-0.8	5	5
CCND3	0.045	0.12	-9999	-0.59	4	4

×

Insulin Pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
CBL/APS/CAP	-0.05	0.12	-9999	-0.74	1	1
TC10/GTP	-0.048	0.11	-9999	-0.72	1	1
Insulin Receptor/Insulin/IRS1/Shp2	0	0	-9999	-10000	0	0
HRAS	0.013	0	-9999	-10000	0	0
APS homodimer	0.011	0.047	-9999	-0.8	1	1
GRB14	-0.058	0.21	-9999	-0.66	32	32
FOXO3	-0.007	0.046	-9999	-0.77	1	1
AKT1	0.021	0.1	-9999	-10000	0	0
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	0.011	0.047	-9999	-0.8	1	1
SORBS1	-0.092	0.24	-9999	-0.64	49	49
CRK	0.013	0	-9999	-10000	0	0
PTPN1	0.039	0	-9999	-10000	0	0
CAV1	-0.018	0.15	-9999	-0.47	29	29
CBL/APS/CAP/Crk-II/C3G	-0.054	0.13	-9999	-0.78	1	1
Insulin Receptor/Insulin/IRS1/NCK2	0	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	0	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/PTP1B	0.042	0	-9999	-10000	0	0
RPS6KB1	0.029	0.097	-9999	-10000	0	0
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	0.007	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/Shc	-0.025	0.074	-9999	-10000	0	0
HRAS/GTP	-0.001	0.015	-9999	-10000	0	0
Insulin Receptor	0.015	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC	0	0	-9999	-10000	0	0
PRKCI	-0.007	0.021	-9999	-10000	0	0
Insulin Receptor/Insulin/GRB14/PDK1	-0.032	0.093	-9999	-10000	0	0
SHC1	0.013	0	-9999	-10000	0	0
negative regulation of MAPKKK cascade	0	0.006	-9999	-10000	0	0
PI3K	0	0	-9999	-10000	0	0
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	0	-9999	-10000	0	0
AKT2	0.021	0.1	-9999	-10000	0	0
PRKCZ	-0.009	0.036	-9999	-0.52	1	1
SH2B2	0.011	0.047	-9999	-0.8	1	1
SHC/SHIP	0.035	0.02	-9999	-10000	0	0
F2RL2	-0.29	0.4	-9999	-0.8	114	114
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	-0.059	0.14	-9999	-0.83	1	1
TC10/GDP	0	0	-9999	-10000	0	0
Insulin Receptor/Insulin/SHC/GRB10	-0.002	0.028	-9999	-0.5	1	1
INPP5D	0.028	0.021	-9999	-10000	0	0
SOS1	0.013	0	-9999	-10000	0	0
SGK1	-0.005	0.059	-9999	-1	1	1
mol:cAMP	0	0	-9999	-10000	0	0
PTPN11	0.013	0	-9999	-10000	0	0
IRS1	0.013	0	-9999	-10000	0	0
p62DOK/RasGAP	0	0.006	-9999	-10000	0	0
INS	0.003	0	-9999	-10000	0	0
mol:PI-3-4-P2	0.028	0.021	-9999	-10000	0	0
GRB2	0.013	0	-9999	-10000	0	0
EIF4EBP1	0.025	0.1	-9999	-10000	0	0
PTPRA	0.015	0	-9999	-10000	0	0
PIK3CA	0.013	0	-9999	-10000	0	0
TC10/GTP/CIP4	0	0	-9999	-10000	0	0
PDPK1	0.013	0	-9999	-10000	0	0
Insulin Receptor/Insuli/IRS1/GRB2/SHC/Sos	0.037	0	-9999	-10000	0	0
Insulin Receptor/Insulin/IRS1	0	0	-9999	-10000	0	0
Insulin Receptor/Insulin/IRS3	0	0	-9999	-10000	0	0
Par3/Par6	-0.17	0.22	-9999	-0.46	113	113

×

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	0.005	0.081	-9999	-0.8	3	3
GNAI2	0.013	0	-9999	-10000	0	0
mol:S1P	0.019	0.043	-9999	-0.28	6	6
GNAO1	0.009	0.06	-9999	-0.72	2	2
mol:Sphinganine-1-P	0.019	0.063	-9999	-0.61	3	3
growth factor activity	0	0	-9999	-10000	0	0
S1P/S1P2/G12/G13	-0.007	0.044	-9999	-0.44	2	2
GNAI3	0.013	0	-9999	-10000	0	0
G12/G13	-0.004	0.05	-9999	-0.61	2	2
S1PR3	0.006	0.071	-9999	-0.7	3	3
S1PR2	0.013	0	-9999	-10000	0	0
EDG1	0	0	-9999	-10000	0	0
S1P1/S1P	-0.005	0.034	-9999	-10000	0	0
S1PR5	0.011	0.038	-9999	-0.64	1	1
S1PR4	-0.035	0.19	-9999	-0.8	18	18
GNAI1	0.011	0.038	-9999	-0.64	1	1
S1P/S1P5/G12	-0.008	0.051	-9999	-0.47	2	2
S1P/S1P3/Gq	-0.011	0.12	-9999	-0.49	2	2
S1P/S1P4/Gi	0.019	0.088	-9999	-0.54	2	2
GNAQ	0.013	0	-9999	-10000	0	0
GNAZ	-0.004	0.11	-9999	-0.73	7	7
GNA14	-0.095	0.24	-9999	-0.64	50	50
GNA15	0.013	0	-9999	-10000	0	0
GNA12	0.008	0.066	-9999	-0.8	2	2
GNA13	0.013	0	-9999	-10000	0	0
GNA11	0.013	0	-9999	-10000	0	0
ABCC1	0.005	0.081	-9999	-0.8	3	3

×

Circadian rhythm pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
chromatin modification	0	0.003	-9999	-10000	0	0
CLOCK	0.017	0	-9999	-10000	0	0
TIMELESS/CRY2	0.047	0.01	-9999	-10000	0	0
DEC1/BMAL1	-0.077	0.2	-9999	-0.61	38	38
ATR	0.013	0	-9999	-10000	0	0
NR1D1	0.046	0.012	-9999	-10000	0	0
ARNTL	0.017	0	-9999	-10000	0	0
TIMELESS	0.046	0.012	-9999	-10000	0	0
NPAS2	0.009	0.075	-9999	-0.64	4	4
CRY2	0.013	0	-9999	-10000	0	0
mol:CO	-0.015	0	-9999	-10000	0	0
CHEK1	0.013	0	-9999	-10000	0	0
mol:HEME	0.015	0	-9999	-10000	0	0
PER1	0.013	0	-9999	-10000	0	0
BMAL/CLOCK/NPAS2	0.041	0.049	-9999	-0.38	4	4
BMAL1/CLOCK	0.027	0.085	-9999	-10000	0	0
S phase of mitotic cell cycle	0	0.003	-9999	-10000	0	0
TIMELESS/CHEK1/ATR	0	0.003	-9999	-10000	0	0
mol:NADPH	0.015	0	-9999	-10000	0	0
PER1/TIMELESS	0.047	0.01	-9999	-10000	0	0
PER1-2 / CRY1-2	0	0	-9999	-10000	0	0
DEC1	-0.092	0.27	-9999	-0.8	38	38

×

Aurora A signaling

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Aurora A/GADD45A	-0.005	0.046	-9999	-0.53	1	1
BIRC5	0.003	0.093	-9999	-0.8	4	4
NFKBIA	0.028	0.039	-9999	-10000	0	0
CPEB1	-0.075	0.23	-9999	-0.67	39	39
AKT1	0.028	0.039	-9999	-0.29	3	3
NDEL1	0.013	0	-9999	-10000	0	0
Aurora A/BRCA1	-0.003	0.032	-9999	-10000	0	0
NDEL1/TACC3	-0.006	0.047	-9999	-0.46	2	2
GADD45A	0.011	0.047	-9999	-0.8	1	1
GSK3B	0.013	0.004	-9999	-10000	0	0
PAK1/Aurora A	-0.005	0.046	-9999	-0.53	1	1
MDM2	0.013	0	-9999	-10000	0	0
JUB	0.013	0	-9999	-10000	0	0
TPX2	0.012	0.089	-9999	-0.62	6	6
TP53	-0.005	0.039	-9999	-0.32	3	3
DLG7	0.017	0.039	-9999	-0.28	5	5
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	-0.006	0.05	-9999	-0.48	2	2
G2/M transition of mitotic cell cycle	-0.003	0.032	-9999	-10000	0	0
AURKA	0.02	0.046	-9999	-0.33	5	5
AURKB	-0.003	0.026	-9999	-0.28	2	2
CDC25B	-0.013	0.065	-9999	-0.32	10	10
G2/M transition checkpoint	-0.003	0.032	-9999	-10000	0	0
mRNA polyadenylation	-0.053	0.13	-9999	-0.39	39	39
Aurora A/CPEB	-0.053	0.13	-9999	-0.39	39	39
Aurora A/TACC1/TRAP/chTOG	-0.004	0.034	-9999	-10000	0	0
BRCA1	0.013	0	-9999	-10000	0	0
centrosome duplication	-0.005	0.046	-9999	-0.53	1	1
regulation of centrosome cycle	-0.006	0.046	-9999	-0.45	2	2
spindle assembly	-0.004	0.034	-9999	-10000	0	0
TDRD7	0.013	0	-9999	-10000	0	0
Aurora A/RasGAP/Survivin	-0.008	0.067	-9999	-0.55	4	4
CENPA	-0.005	0.034	-9999	-0.36	2	2
Aurora A/PP2A	-0.004	0.035	-9999	-10000	0	0
meiosis	0	0	-9999	-10000	0	0
protein catabolic process	0.033	0.035	-9999	-10000	0	0
negative regulation of DNA binding	0.025	0.043	-9999	-0.32	3	3
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	-0.003	0.032	-9999	-10000	0	0
mitotic prometaphase	0	0.003	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.02	0.046	-9999	-0.33	5	5
TACC1	0.011	0.038	-9999	-0.64	1	1
TACC3	0.008	0.066	-9999	-0.8	2	2
Aurora A/Antizyme1	-0.003	0.031	-9999	-10000	0	0
Aurora A/RasGAP	-0.004	0.035	-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	0.013	0.004	-9999	-10000	0	0
GIT1	0.013	0	-9999	-10000	0	0
GIT1/beta-PIX/PAK1	-0.002	0.03	-9999	-0.53	1	1
Importin alpha/Importin beta/TPX2	0.012	0.089	-9999	-0.61	6	6
PPP2R5D	0.013	0	-9999	-10000	0	0
Aurora A/TPX2	0.022	0.079	-9999	-0.48	6	6
PAK1	0.011	0.047	-9999	-0.8	1	1
CKAP5	0.013	0	-9999	-10000	0	0

×

HIF-2-alpha transcription factor network

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MMP14	-0.003	0.089	-10000	0	-0.67	5	5
oxygen homeostasis	0	0.017	-10000	0	-10000	0	0
TCEB2	0.013	0	-10000	0	-10000	0	0
TCEB1	0.011	0.047	-10000	0	-0.8	1	1
VHL/Elongin B/Elongin C/HIF2A	-0.02	0.075	-10000	0	-0.43	1	1
EPO	-0.015	0.26	-10000	0	-0.7	16	16
FIH (dimer)	0.012	0.017	-10000	0	-10000	0	0
APEX1	0.015	0.014	-10000	0	-10000	0	0
SERPINE1	-0.24	0.38	-10000	0	-0.79	29	29
FLT1	0.009	0.036	-10000	0	-10000	0	0
ADORA2A	0	0.22	-10000	0	-0.86	2	2
germ cell development	-0.004	0.23	-10000	0	-0.81	4	4
SLC11A2	0.003	0.22	-10000	0	-1	1	1
BHLHE40	0.003	0.22	-10000	0	-1	1	1
HIF1AN	0.012	0.017	-10000	0	-10000	0	0
HIF2A/ARNT/SIRT1	-0.054	0.098	-10000	0	-0.5	4	4
ETS1	0.025	0.066	-10000	0	-0.79	2	2
CITED2	-0.005	0.11	-10000	0	-1	3	3
KDR	0.007	0.052	-10000	0	-0.65	1	1
PGK1	0.003	0.22	-10000	0	-1	1	1
SIRT1	0.013	0.002	-10000	0	-10000	0	0
response to hypoxia	-0.001	0.004	-10000	0	-10000	0	0
HIF2A/ARNT	-0.007	0.25	-10000	0	-0.88	4	4
EPAS1	0.012	0.13	-10000	0	-0.43	5	5
SP1	0.022	0.003	-10000	0	-10000	0	0
ABCG2	-0.005	0.23	-10000	0	-0.88	3	3
EFNA1	0.002	0.23	-10000	0	-1.3	1	1
FXN	0.002	0.22	-10000	0	-0.99	1	1
POU5F1	-0.006	0.24	-10000	0	-0.86	4	4
neuron apoptosis	0.006	0.24	0.84	4	-10000	0	4
EP300	0.013	0	-10000	0	-10000	0	0
EGLN3	-0.049	0.22	-10000	0	-0.8	23	23
EGLN2	0.012	0.017	-10000	0	-10000	0	0
EGLN1	0.012	0.017	-10000	0	-10000	0	0
VHL/Elongin B/Elongin C	-0.002	0.03	-10000	0	-0.53	1	1
VHL	0.013	0	-10000	0	-10000	0	0
ARNT	0.015	0.014	-10000	0	-10000	0	0
SLC2A1	-0.007	0.24	-10000	0	-0.87	8	8
TWIST1	-0.007	0.24	-10000	0	-0.83	7	7
ELK1	0.019	0.047	-10000	0	-0.8	1	1
HIF2A/ARNT/Cbp/p300	-0.045	0.09	-10000	0	-0.61	1	1
VEGFA	0.002	0.23	-10000	0	-0.99	2	2
CREBBP	0.013	0	-10000	0	-10000	0	0

×

Regulation of p38-alpha and p38-beta

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
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	-0.017	0.14	-9999	-0.64	14	14
mol:GTP	0	0	-9999	-10000	0	0
MAP2K4	0.013	0	-9999	-10000	0	0
RAC1-CDC42/GTP/PAK family	0.018	0.05	-9999	-10000	0	0
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	0.011	0.047	-9999	-0.8	1	1
MAP3K12	0.013	0	-9999	-10000	0	0
FGR	0.011	0.047	-9999	-0.8	1	1
p38 alpha/TAB1	-0.02	0.045	-9999	-10000	0	0
PRKG1	-0.008	0.12	-9999	-0.71	9	9
DUSP8	0.013	0	-9999	-10000	0	0
PGK/cGMP/p38 alpha	-0.028	0.07	-9999	-0.42	5	5
apoptosis	-0.02	0.043	-9999	-10000	0	0
RAL/GTP	0	0	-9999	-10000	0	0
LYN	0.013	0	-9999	-10000	0	0
DUSP1	-0.041	0.18	-9999	-0.64	25	25
PAK1	0.011	0.047	-9999	-0.8	1	1
SRC	0.013	0	-9999	-10000	0	0
RAC1/OSM/MEKK3/MKK3	-0.001	0.02	-9999	-10000	0	0
TRAF6	0.013	0	-9999	-10000	0	0
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	0.019	0.1	-9999	-0.39	5	5
BLK	-0.12	0.3	-9999	-0.77	53	53
HCK	0.004	0.084	-9999	-0.72	4	4
MAP2K3	0.011	0.038	-9999	-0.64	1	1
DUSP16	0.013	0	-9999	-10000	0	0
DUSP10	0.011	0.047	-9999	-0.8	1	1
TRAF6/MEKK3	0	0	-9999	-10000	0	0
MAP3K7IP1	0	0	-9999	-10000	0	0
MAPK14	0.028	0.073	-9999	-10000	0	0
positive regulation of innate immune response	0.027	0.11	-9999	-0.4	5	5
LCK	-0.014	0.15	-9999	-0.8	10	10
p38alpha-beta/MKP7	0.032	0.1	-9999	-0.4	1	1
p38alpha-beta/MKP5	0.031	0.11	-9999	-0.4	1	1
PGK/cGMP	-0.016	0.093	-9999	-0.54	9	9
PAK2	0.013	0	-9999	-10000	0	0
p38alpha-beta/MKP1	0.007	0.14	-9999	-0.51	5	5
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	-0.023	0.16	-9999	-0.78	13	13

×

VEGFR1 specific signals

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
VEGFR1 homodimer/VEGFB homodimer	0.035	0	-9999	-10000	0	0
VEGFR1 homodimer/NRP1	0	0	-9999	-10000	0	0
mol:DAG	-0.039	0.19	-9999	-10000	0	0
VEGFR1 homodimer/NRP1/VEGFR 121	-0.002	0.028	-9999	-0.48	1	1
CaM/Ca2+	-0.03	0.18	-9999	-10000	0	0
HIF1A	0.022	0	-9999	-10000	0	0
GAB1	0.013	0	-9999	-10000	0	0
AKT1	-0.004	0.16	-9999	-10000	0	0
PLCG1	-0.039	0.19	-9999	-10000	0	0
NOS3	-0.002	0.16	-9999	-10000	0	0
CBL	0.013	0	-9999	-10000	0	0
mol:NO	-0.001	0.15	-9999	-10000	0	0
FLT1	0.033	0	-9999	-10000	0	0
PGF	-0.12	0.3	-9999	-0.8	49	49
VEGFR1 homodimer/NRP2/VEGFR121	-0.003	0.038	-9999	-10000	0	0
CALM1	0.013	0	-9999	-10000	0	0
PIK3CA	0.013	0	-9999	-10000	0	0
eNOS/Hsp90	0.006	0.15	-9999	-10000	0	0
endothelial cell proliferation	-0.019	0.16	-9999	-10000	0	0
mol:Ca2+	-0.039	0.19	-9999	-10000	0	0
MAPK3	-0.019	0.17	-9999	-10000	0	0
MAPK1	-0.019	0.17	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
PLGF homodimer	-0.12	0.3	-9999	-0.8	49	49
PRKACA	0.013	0	-9999	-10000	0	0
RP11-342D11.1	0	0	-9999	-10000	0	0
CAV1	-0.065	0.24	-9999	-0.8	29	29
VEGFA homodimer	0.011	0.047	-9999	-0.8	1	1
VEGFR1 homodimer/VEGFA homodimer	0.033	0.032	-9999	-0.52	1	1
platelet activating factor biosynthetic process	-0.01	0.16	-9999	-10000	0	0
PI3K	-0.071	0.16	-9999	-10000	0	0
PRKCA	-0.029	0.18	-9999	-10000	0	0
PRKCB	-0.038	0.19	-9999	-10000	0	0
VEGFR1 homodimer/PLGF homodimer	-0.055	0.2	-9999	-0.52	49	49
VEGFA	0.011	0.047	-9999	-0.8	1	1
VEGFB	0.013	0	-9999	-10000	0	0
mol:IP3	-0.039	0.19	-9999	-10000	0	0
RASA1	0.044	0	-9999	-10000	0	0
NRP2	0.011	0.047	-9999	-0.8	1	1
VEGFR1 homodimer	0.033	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	-0.035	0.2	-9999	-0.73	7	7
PTPN11	0.013	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.07	0.16	-9999	-10000	0	0
mol:L-citrulline	-0.001	0.15	-9999	-10000	0	0
VEGFR1 homodimer/VEGFA homodimer/CBL/CD2AP	-0.001	0.025	-9999	-10000	0	0
VEGFR1 homodimer/VEGFA homodimer/NCK1	-0.002	0.027	-9999	-10000	0	0
CD2AP	0.013	0	-9999	-10000	0	0
PI3K/GAB1	-0.066	0.15	-9999	-10000	0	0
PDPK1	-0.019	0.17	-9999	-10000	0	0
VEGFR1 homodimer/VEGFA homodimer/SHP2	-0.002	0.027	-9999	-10000	0	0
mol:NADP	-0.001	0.15	-9999	-10000	0	0
HSP90AA1	0.013	0	-9999	-10000	0	0
ubiquitin-dependent protein catabolic process	-0.001	0.025	-9999	-10000	0	0
VEGFR1 homodimer/NRP2	0.033	0.032	-9999	-0.52	1	1

×

S1P4 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-9999	-10000	0	0
GNAO1	0.009	0.06	-9999	-0.72	2	2
CDC42/GTP	-0.02	0.07	-9999	-0.51	2	2
PLCG1	0.02	0.084	-9999	-0.53	2	2
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	-0.004	0.05	-9999	-0.61	2	2
cell migration	-0.02	0.069	-9999	-0.5	2	2
S1PR5	0.011	0.038	-9999	-0.64	1	1
S1PR4	-0.035	0.19	-9999	-0.8	18	18
MAPK3	0.02	0.084	-9999	-0.53	2	2
MAPK1	0.02	0.084	-9999	-0.53	2	2
S1P/S1P5/Gi	0.029	0.053	-9999	-0.47	1	1
GNAI1	0.011	0.038	-9999	-0.64	1	1
CDC42/GDP	0	0	-9999	-10000	0	0
S1P/S1P5/G12	-0.005	0.049	-9999	-0.49	3	3
RHOA	0.003	0.12	-9999	-0.45	20	20
S1P/S1P4/Gi	0.012	0.089	-9999	-0.56	2	2
mol:GDP	0	0	-9999	-10000	0	0
GNAZ	-0.004	0.11	-9999	-0.73	7	7
S1P/S1P4/G12/G13	-0.032	0.12	-9999	-0.49	20	20
GNA12	0.008	0.066	-9999	-0.8	2	2
GNA13	0.013	0	-9999	-10000	0	0
CDC42	0.013	0	-9999	-10000	0	0

×

Aurora B signaling

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
Condensin I complex	0.033	0.043	-9999	-10000	0	0
STMN1	0.024	0.052	-9999	-0.62	2	2
Aurora B/RasGAP/Survivin	0.017	0.082	-9999	-0.63	4	4
Chromosomal passenger complex/Cul3 protein complex	0.035	0.046	-9999	-0.4	2	2
BIRC5	0.005	0.094	-9999	-0.81	4	4
DES	-0.3	0.26	-9999	-0.55	154	154
Aurora C/Aurora B/INCENP	0.019	0.051	-9999	-0.49	2	2
Aurora B/TACC1	0.013	0.042	-9999	-0.47	2	2
Aurora B/PP2A	0.016	0.039	-9999	-0.61	1	1
mol:GTP	0	0	-9999	-10000	0	0
CBX5	0.018	0.01	-9999	-10000	0	0
mitotic metaphase/anaphase transition	-0.001	0.001	-9999	-10000	0	0
NDC80	0.018	0.083	-9999	-0.62	5	5
Cul3 protein complex	-0.004	0.039	-9999	-10000	0	0
KIF2C	0.01	0.034	-9999	-0.28	3	3
PEBP1	0.014	0.002	-9999	-10000	0	0
KIF20A	0.012	0.002	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
Aurora B/RasGAP	0.016	0.039	-9999	-0.61	1	1
SEPT1	0	0.1	-9999	-0.8	5	5
SMC2	0.013	0	-9999	-10000	0	0
SMC4	0.013	0	-9999	-10000	0	0
NSUN2/NPM1/Nucleolin	0.033	0.027	-9999	-0.38	1	1
PSMA3	0.013	0	-9999	-10000	0	0
G2/M transition of mitotic cell cycle	0	0.002	-9999	-10000	0	0
H3F3B	0.021	0.022	-9999	-0.36	1	1
AURKB	0.019	0.049	-9999	-0.81	1	1
AURKC	0.009	0.06	-9999	-0.72	2	2
CDCA8	0.013	0.047	-9999	-0.81	1	1
cytokinesis	-0.019	0.05	-9999	-0.56	2	2
Aurora B/Septin1	0.019	0.082	-9999	-0.46	7	7
AURKA	-0.001	0.1	-9999	-0.8	5	5
INCENP	0.015	0.002	-9999	-10000	0	0
KLHL13	0.011	0.038	-9999	-0.64	1	1
BUB1	0.012	0.002	-9999	-10000	0	0
hSgo1/Aurora B/Survivin	0.017	0.077	-9999	-0.59	4	4
EVI5	0.015	0.001	-9999	-10000	0	0
RhoA/GTP	-0.004	0.037	-9999	-0.49	1	1
SGOL1	0.013	0	-9999	-10000	0	0
CENPA	0.025	0.063	-9999	-0.51	3	3
NCAPG	0.013	0	-9999	-10000	0	0
Aurora B/HC8 Proteasome	0.016	0.039	-9999	-0.61	1	1
NCAPD2	0.005	0.081	-9999	-0.8	3	3
Aurora B/PP1-gamma	0.016	0.039	-9999	-0.61	1	1
RHOA	0.013	0	-9999	-10000	0	0
NCAPH	0.005	0.081	-9999	-0.8	3	3
NPM1	0.011	0.027	-9999	-0.42	1	1
RASA1	0.013	0	-9999	-10000	0	0
KLHL9	0.009	0.053	-9999	-0.64	2	2
mitotic prometaphase	0.001	0.002	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.016	0.039	-9999	-0.61	1	1
PPP1CC	0.013	0	-9999	-10000	0	0
Centraspindlin	-0.004	0.041	-9999	-0.48	2	2
RhoA/GDP	0	0	-9999	-10000	0	0
NSUN2	0.011	0.027	-9999	-0.42	1	1
MYLK	0.017	0.043	-9999	-0.36	4	4
KIF23	0.014	0.001	-9999	-10000	0	0
VIM	0.026	0.037	-9999	-0.61	1	1
RACGAP1	0.014	0.001	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
NCL	0.011	0.027	-9999	-0.42	1	1
Chromosomal passenger complex	0.036	0.05	-9999	-0.51	2	2
Chromosomal passenger complex/EVI5	0.046	0.097	-9999	-0.88	2	2
TACC1	0.011	0.038	-9999	-0.64	1	1
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

×

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

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
MET/RANBP9	-0.004	0.044	-9999	-0.54	2	2
CRKL	0.033	0.054	-9999	-0.42	1	1
mol:PIP3	-0.024	0.003	-9999	-10000	0	0
AKT1	0	0.002	-9999	-10000	0	0
PTK2B	0.013	0	-9999	-10000	0	0
RAPGEF1	0.04	0.052	-9999	-0.4	1	1
RANBP10	0.013	0	-9999	-10000	0	0
PIK3CA	0.013	0	-9999	-10000	0	0
HGF/MET/SHIP2	-0.016	0.084	-9999	-0.44	11	11
MAP3K5	0.043	0.059	-9999	-10000	0	0
HGF/MET/CIN85/CBL/ENDOPHILINS	-0.014	0.075	-9999	-0.48	4	4
AP1	-0.067	0.15	-9999	-0.41	49	49
mol:SU11274	0	0	-9999	-10000	0	0
SHC1	0.013	0	-9999	-10000	0	0
apoptosis	-0.092	0.26	-9999	-0.69	49	49
STAT3 (dimer)	0.036	0.054	-9999	-10000	0	0
GAB1/CRKL/SHP2/PI3K	-0.007	0.038	-9999	-10000	0	0
INPP5D	0.011	0.038	-9999	-0.64	1	1
CBL/CRK	0.041	0.045	-9999	-10000	0	0
PTPN11	0.013	0	-9999	-10000	0	0
GO:0007205	0	0	-9999	-10000	0	0
PLCG1	0.013	0	-9999	-10000	0	0
PTEN	0.013	0	-9999	-10000	0	0
ELK1	0.001	0.022	-9999	-0.25	2	2
mol:SU5416	0	0	-9999	-10000	0	0
SHP2/GRB2/SOS1GAB1	-0.005	0.027	-9999	-10000	0	0
PAK1	0.007	0.027	-9999	-0.47	1	1
HGF/MET/RANBP10	-0.016	0.084	-9999	-0.44	11	11
HRAS	0.029	0.073	-9999	-0.64	1	1
DOCK1	0.04	0.052	-9999	-0.4	1	1
GAB1	0.028	0.049	-9999	-0.29	1	1
CRK	0.035	0.047	-9999	-10000	0	0
mol:PHA665752	0	0	-9999	-10000	0	0
mol:GDP	-0.016	0.083	-9999	-0.5	7	7
JUN	0.013	0	-9999	-10000	0	0
EntrezGene:200958	0	0	-9999	-10000	0	0
HGF/MET	-0.008	0.043	-9999	-0.29	2	2
PIK3R1	0.013	0	-9999	-10000	0	0
cell morphogenesis	0.066	0.059	-9999	-10000	0	0
GRB2/SHC	-0.006	0.035	-9999	-10000	0	0
FOS	-0.092	0.24	-9999	-0.64	49	49
GLMN	0	0	-9999	-10000	0	0
cell motility	0.001	0.022	-9999	-0.25	2	2
HGF/MET/MUC20	-0.016	0.085	-9999	-0.45	11	11
cell migration	-0.007	0.034	-9999	-10000	0	0
GRB2	0.013	0	-9999	-10000	0	0
CBL	0.013	0	-9999	-10000	0	0
MET/RANBP10	-0.004	0.044	-9999	-0.54	2	2
HGF/MET/Paxillin/FAK1/FAK12/RasGAP	0.03	0.056	-9999	-10000	0	0
MET/MUC20	-0.004	0.045	-9999	-0.55	2	2
RAP1B	0.046	0.055	-9999	-0.39	1	1
RAP1A	0.047	0.049	-9999	-10000	0	0
HGF/MET/RANBP9	-0.016	0.084	-9999	-0.44	11	11
RAF1	0.037	0.069	-9999	-0.6	1	1
STAT3	0.037	0.054	-9999	-10000	0	0
cell proliferation	0.048	0.071	-9999	-10000	0	0
RPS6KB1	0.012	0.018	-9999	-10000	0	0
MAPK3	-0.005	0.019	-9999	-0.26	1	1
MAPK1	-0.005	0.019	-9999	-0.26	1	1
RANBP9	0.013	0	-9999	-10000	0	0
MAPK8	0.057	0.067	-9999	-0.5	2	2
SRC	0.037	0.053	-9999	-10000	0	0
PI3K	-0.006	0.035	-9999	-10000	0	0
MET/Glomulin	0.009	0.041	-9999	-0.49	2	2
SOS1	0.013	0	-9999	-10000	0	0
MAP2K1	0.044	0.065	-9999	-0.54	1	1
MET	0.009	0.06	-9999	-0.72	2	2
MAP4K1	0.036	0.062	-9999	-10000	0	0
PTK2	0.013	0	-9999	-10000	0	0
MAP2K2	0.044	0.065	-9999	-0.54	1	1
BAD	0.008	0.002	-9999	-10000	0	0
MAP2K4	0.05	0.056	-9999	-10000	0	0
SHP2/GRB2/SOS1/GAB1	-0.007	0.04	-9999	-10000	0	0
INPPL1	0.013	0	-9999	-10000	0	0
PXN	0.013	0	-9999	-10000	0	0
SH3KBP1	0.013	0	-9999	-10000	0	0
HGS	0.017	0.043	-9999	-10000	0	0
PLCgamma1/PKC	0	0	-9999	-10000	0	0
HGF	-0.008	0.12	-9999	-0.7	9	9
RASA1	0.013	0	-9999	-10000	0	0
NCK1	0.013	0	-9999	-10000	0	0
PTPRJ	0.013	0	-9999	-10000	0	0
NCK/PLCgamma1	0.025	0.044	-9999	-10000	0	0
PDPK1	-0.01	0.002	-9999	-10000	0	0
HGF/MET/SHIP	-0.017	0.092	-9999	-0.48	11	11

×

Hedgehog signaling events mediated by Gli proteins

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
HDAC1	0.013	0.001	-9999	-10000	0	0
HDAC2	0.013	0.001	-9999	-10000	0	0
GNB1/GNG2	-0.013	0.073	-9999	-0.41	10	10
forebrain development	-0.008	0.14	-9999	-0.46	7	7
GNAO1	0.008	0.06	-9999	-0.72	2	2
SMO/beta Arrestin2	0.003	0.084	-9999	-0.47	9	9
SMO	-0.006	0.11	-9999	-0.64	9	9
ARRB2	0.013	0.005	-9999	-10000	0	0
GLI3/SPOP	0.055	0.033	-9999	-10000	0	0
mol:GTP	0	0.002	-9999	-10000	0	0
GSK3B	0.013	0	-9999	-10000	0	0
GNAI2	0.012	0.005	-9999	-10000	0	0
SIN3/HDAC complex	0.005	0.013	-9999	-10000	0	0
GNAI1	0.01	0.038	-9999	-0.64	1	1
XPO1	0.015	0.006	-9999	-10000	0	0
GLI1/Su(fu)	-0.051	0.097	-9999	-0.5	2	2
SAP30	0.013	0.001	-9999	-10000	0	0
mol:GDP	-0.006	0.11	-9999	-0.64	9	9
MIM/GLI2A	0.011	0.026	-9999	-10000	0	0
IFT88	0.013	0	-9999	-10000	0	0
GNAI3	0.012	0.005	-9999	-10000	0	0
GLI2	0.031	0.059	-9999	-10000	0	0
GLI3	0.05	0.036	-9999	-10000	0	0
CSNK1D	0.013	0	-9999	-10000	0	0
CSNK1E	0.013	0	-9999	-10000	0	0
SAP18	0.013	0.001	-9999	-10000	0	0
embryonic digit morphogenesis	0.013	0	-9999	-10000	0	0
GNG2	0.011	0.047	-9999	-0.8	1	1
Gi family/GTP	0.021	0.079	-9999	-0.49	3	3
SIN3B	0.013	0.001	-9999	-10000	0	0
SIN3A	0.013	0.001	-9999	-10000	0	0
GLI3/Su(fu)	0.058	0.038	-9999	-10000	0	0
GLI2/Su(fu)	0.038	0.065	-9999	-10000	0	0
FOXA2	-0.089	0.22	-9999	-0.64	41	41
neural tube patterning	-0.008	0.14	-9999	-0.46	7	7
SPOP	0.013	0	-9999	-10000	0	0
Su(fu)/PIAS1	0.024	0.047	-9999	-0.4	1	1
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	0.011	0.026	-9999	-10000	0	0
embryonic limb morphogenesis	-0.008	0.14	-9999	-0.46	7	7
SUFU	0.02	0.052	-9999	-0.44	1	1
LGALS3	0.013	0	-9999	-10000	0	0
catabolic process	0.068	0.05	-9999	-10000	0	0
GLI3A/CBP	-0.019	0.11	-9999	-0.35	1	1
KIF3A	0.013	0	-9999	-10000	0	0
GLI1	-0.009	0.14	-9999	-0.48	7	7
RAB23	0.008	0.066	-9999	-0.8	2	2
CSNK1A1	0.013	0	-9999	-10000	0	0
IFT172	0.013	0	-9999	-10000	0	0
RBBP7	0.013	0.001	-9999	-10000	0	0
Su(fu)/Galectin3	0.024	0.047	-9999	-0.4	1	1
GNAZ	-0.005	0.11	-9999	-0.73	7	7
RBBP4	0.013	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	0.035	0.055	-9999	-10000	0	0
STK36	0.015	0.006	-9999	-10000	0	0
Gi family/GNB1/GNG2/GDP	0.028	0.072	-9999	-0.44	3	3
PTCH1	0.002	0.13	-9999	-10000	0	0
MIM/GLI1	-0.024	0.19	-9999	-0.64	9	9
CREBBP	-0.019	0.11	-9999	-0.35	1	1
Su(fu)/SIN3/HDAC complex	0.052	0.014	-9999	-10000	0	0

×

Arf6 downstream pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
PLAUR	0.017	0.14	-10000	0	-0.64	13	13
regulation of axonogenesis	-0.025	0.029	-10000	0	-10000	0	0
myoblast fusion	0.02	0.069	0.32	13	-10000	0	13
mol:GTP	-0.01	0.039	-10000	0	-0.26	1	1
regulation of calcium-dependent cell-cell adhesion	-0.021	0.064	0.41	4	-10000	0	4
ARF1/GTP	-0.007	0.027	-10000	0	-10000	0	0
mol:GM1	0.003	0.032	-10000	0	-10000	0	0
mol:Choline	0.024	0.028	-10000	0	-10000	0	0
lamellipodium assembly	-0.019	0.07	-10000	0	-0.46	1	1
MAPK3	0.018	0.059	-10000	0	-10000	0	0
ARF6/GTP/NME1/Tiam1	0.022	0.065	-10000	0	-0.41	4	4
ARF1	0.013	0	-10000	0	-10000	0	0
ARF6/GDP	-0.02	0.069	-10000	0	-0.32	13	13
ARF1/GDP	0.01	0.07	-10000	0	-0.51	1	1
ARF6	0.007	0.022	-10000	0	-10000	0	0
RAB11A	0.013	0	-10000	0	-10000	0	0
TIAM1	0.008	0.065	-10000	0	-0.64	3	3
fibronectin binding	0	0	-10000	0	-10000	0	0
MAPK1	0.018	0.059	-10000	0	-10000	0	0
actin filament bundle formation	0.017	0.061	0.51	1	-10000	0	1
KALRN	-0.03	0.099	-10000	0	-0.37	18	18
RAB11FIP3/RAB11A	0	0	-10000	0	-10000	0	0
RhoA/GDP	-0.017	0.062	-10000	0	-0.51	1	1
NME1	0.012	0.047	-10000	0	-0.8	1	1
Rac1/GDP	-0.017	0.062	-10000	0	-0.51	1	1
substrate adhesion-dependent cell spreading	-0.01	0.039	-10000	0	-0.26	1	1
cortical actin cytoskeleton organization	-0.019	0.071	-10000	0	-0.47	1	1
RAC1	0.013	0	-10000	0	-10000	0	0
liver development	-0.01	0.039	-10000	0	-0.26	1	1
ARF6/GTP	-0.01	0.039	-10000	0	-0.26	1	1
RhoA/GTP	-0.007	0.027	-10000	0	-10000	0	0
mol:GDP	-0.019	0.071	-10000	0	-0.32	13	13
ARF6/GTP/RAB11FIP3/RAB11A	-0.004	0.021	-10000	0	-10000	0	0
RHOA	0.013	0	-10000	0	-10000	0	0
PLD1	0.015	0.032	-10000	0	-10000	0	0
RAB11FIP3	0.013	0	-10000	0	-10000	0	0
tube morphogenesis	-0.019	0.07	-10000	0	-0.46	1	1
ruffle organization	0.025	0.029	-10000	0	-10000	0	0
regulation of epithelial cell migration	-0.01	0.039	-10000	0	-0.26	1	1
PLD2	0.015	0.032	-10000	0	-10000	0	0
PIP5K1A	0.025	0.029	-10000	0	-10000	0	0
mol:Phosphatidic acid	0.024	0.028	-10000	0	-10000	0	0
Rac1/GTP	-0.019	0.071	-10000	0	-0.47	1	1

×

ceramide 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
MAP4K4	0.036	0.075	-10000	0	-10000	0	0
BAG4	0.013	0	-10000	0	-10000	0	0
BAD	0.03	0.028	-10000	0	-10000	0	0
NFKBIA	0.013	0	-10000	0	-10000	0	0
BIRC3	-0.024	0.17	-10000	0	-0.8	14	14
BAX	0.03	0.028	-10000	0	-10000	0	0
EnzymeConsortium:3.1.4.12	0.013	0.021	-10000	0	-0.095	3	3
IKBKB	0.043	0.072	-10000	0	-10000	0	0
MAP2K2	0.043	0.03	-10000	0	-10000	0	0
MAP2K1	0.043	0.03	-10000	0	-10000	0	0
SMPD1	0.019	0.021	-10000	0	-10000	0	0
GO:0005551	0	0	-10000	0	-10000	0	0
FADD/Caspase 8	-0.009	0.16	-10000	0	-0.62	5	5
MAP2K4	0.037	0.028	-10000	0	-10000	0	0
protein ubiquitination	0.045	0.073	-10000	0	-10000	0	0
EnzymeConsortium:2.7.1.37	0.048	0.033	-10000	0	-10000	0	0
response to UV	0	0	-10000	0	-10000	0	0
RAF1	0.037	0.03	-10000	0	-10000	0	0
CRADD	0.014	0	-10000	0	-10000	0	0
mol:ceramide	0.022	0.03	-10000	0	-10000	0	0
I-kappa-B-alpha/RELA/p50/ubiquitin	0	0	-10000	0	-10000	0	0
MADD	0.014	0	-10000	0	-10000	0	0
MAP3K1	0.03	0.029	-10000	0	-10000	0	0
TRADD	0.014	0	-10000	0	-10000	0	0
RELA/p50	0.013	0	-10000	0	-10000	0	0
MAPK3	0.045	0.03	-10000	0	-10000	0	0
MAPK1	0.045	0.03	-10000	0	-10000	0	0
p50/RELA/I-kappa-B-alpha	0	0	-10000	0	-10000	0	0
FADD	-0.018	0.17	-10000	0	-0.44	38	38
KSR1	0.03	0.03	-10000	0	-10000	0	0
MAPK8	0.041	0.039	-10000	0	-0.35	1	1
TRAF2	0.008	0.066	-10000	0	-0.8	2	2
response to radiation	0	0	-10000	0	-10000	0	0
CHUK	0.043	0.072	-10000	0	-10000	0	0
TNF R/SODD	0	0	-10000	0	-10000	0	0
TNF	-0.024	0.17	-10000	0	-0.76	15	15
CYCS	0.032	0.029	0.15	2	-10000	0	2
IKBKG	0.043	0.072	-10000	0	-10000	0	0
TNF/TNF R/TRADD/MADD/cIAP/RIP/TRAF2/RAIDD	0.029	0.078	-10000	0	-0.42	3	3
RELA	0.013	0	-10000	0	-10000	0	0
RIPK1	0.013	0	-10000	0	-10000	0	0
AIFM1	0.032	0.029	0.15	2	-10000	0	2
TNF/TNF R/SODD	-0.024	0.11	-10000	0	-0.49	15	15
TNFRSF1A	0.013	0	-10000	0	-10000	0	0
response to heat	0	0	-10000	0	-10000	0	0
CASP8	0.028	0.021	-10000	0	-10000	0	0
NSMAF	0.036	0.074	-10000	0	-0.4	2	2
response to hydrogen peroxide	0	0	-10000	0	-10000	0	0
BCL2	0.004	0.08	-10000	0	-0.68	4	4

×

Role of Calcineurin-dependent NFAT signaling in lymphocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL2L1	0.013	0	-10000	0	-10000	0	0
NFATC1	0.062	0.018	-10000	0	-10000	0	0
NFATC2	0.034	0.047	-10000	0	-0.3	1	1
NFATC3	0.024	0.026	-10000	0	-0.43	1	1
YWHAE	0.013	0	-10000	0	-10000	0	0
Calcineurin A alpha-beta B1/CABIN1	0.015	0.076	-10000	0	-0.47	2	2
Exportin 1/Ran/NUP214	0	0	-10000	0	-10000	0	0
mol:DAG	0	0.001	-10000	0	-10000	0	0
CABIN1/MEF2D/CaM/Ca2+/CAMK IV	-0.042	0.11	-10000	0	-0.55	7	7
BCL2/BAX	-0.007	0.058	-10000	0	-0.51	4	4
CaM/Ca2+/Calcineurin A alpha-beta B1	0.001	0.003	-10000	0	-10000	0	0
CaM/Ca2+	0.001	0.003	-10000	0	-10000	0	0
BAX	0.013	0	-10000	0	-10000	0	0
MAPK14	0.014	0.002	-10000	0	-10000	0	0
BAD	0.013	0	-10000	0	-10000	0	0
CABIN1/MEF2D	0.021	0.072	-10000	0	-0.55	1	1
Calcineurin A alpha-beta B1/BCL2	0.004	0.08	-10000	0	-0.68	4	4
FKBP8	0.013	0	-10000	0	-10000	0	0
activation-induced cell death of T cells	-0.021	0.071	0.54	1	-10000	0	1
KPNB1	0.013	0	-10000	0	-10000	0	0
KPNA2	0.013	0	-10000	0	-10000	0	0
XPO1	0.014	0	-10000	0	-10000	0	0
SFN	0.011	0.038	-10000	0	-0.64	1	1
MAP3K8	0.014	0.002	-10000	0	-10000	0	0
NFAT4/CK1 alpha	-0.001	0.014	-10000	0	-10000	0	0
MEF2D/NFAT1/Cbp/p300	-0.01	0.048	-10000	0	-10000	0	0
CABIN1	0.015	0.077	-10000	0	-0.48	2	2
CALM1	0.014	0.002	-10000	0	-10000	0	0
RAN	0.014	0	-10000	0	-10000	0	0
MAP3K1	0.013	0	-10000	0	-10000	0	0
CAMK4	-0.04	0.2	-10000	0	-0.8	20	20
mol:Ca2+	0.001	0.003	-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	-0.036	0.14	-10000	0	-0.61	18	18
YWHAB	0.013	0	-10000	0	-10000	0	0
MAPK8	0.01	0.053	-10000	0	-0.64	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	0.019	-10000	0	-10000	0	0
PRKCH	0.013	0	-10000	0	-10000	0	0
CABIN1/Cbp/p300	0	0.001	-10000	0	-10000	0	0
CASP3	0.014	0.002	-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	-0.002	0.018	-10000	0	-10000	0	0
14-3-3 family/BAD/CaM/Ca2+/Calcineurin A alpha-beta B1	0.046	0.013	-10000	0	-10000	0	0
PRKCB	-0.005	0.12	-10000	0	-0.78	7	7
PRKCE	0.013	0	-10000	0	-10000	0	0
JNK2/NFAT4	0.029	0.024	-10000	0	-0.38	1	1
BAD/BCL-XL	0	0	-10000	0	-10000	0	0
PRKCD	0.013	0	-10000	0	-10000	0	0
NUP214	0.014	0	-10000	0	-10000	0	0
PRKCZ	0.012	0.038	-10000	0	-0.64	1	1
PRKCA	0.011	0.047	-10000	0	-0.8	1	1
PRKCG	-0.069	0.24	-10000	0	-0.8	29	29
PRKCQ	-0.001	0.1	-10000	0	-0.72	6	6
FKBP38/BCL2	-0.007	0.058	-10000	0	-0.51	4	4
EP300	0.014	0.002	-10000	0	-10000	0	0
PRKCB1	0	0	-10000	0	-10000	0	0
CSNK2A1	0.013	0	-10000	0	-10000	0	0
NFATc/JNK1	0.064	0.033	-10000	0	-10000	0	0
CaM/Ca2+/FKBP38	0	0	-10000	0	-10000	0	0
FKBP12/FK506	0	0	-10000	0	-10000	0	0
CSNK1A1	0.022	0.003	-10000	0	-10000	0	0
CaM/Ca2+/CAMK IV	-0.035	0.13	-10000	0	-0.53	20	20
NFATc/ERK1	0.067	0.017	-10000	0	-10000	0	0
CABIN1/YWHAQ/CaM/Ca2+/CAMK IV	-0.042	0.12	-10000	0	-0.55	7	7
NR4A1	0.056	0.1	-10000	0	-0.61	6	6
GSK3B	0.014	0.002	-10000	0	-10000	0	0
positive T cell selection	0.024	0.026	-10000	0	-0.43	1	1
NFAT1/CK1 alpha	-0.007	0.026	-10000	0	-10000	0	0
RCH1/ KPNB1	0	0	-10000	0	-10000	0	0
YWHAQ	0.013	0	-10000	0	-10000	0	0
PRKACA	0.014	0.002	-10000	0	-10000	0	0
AKAP5	-0.035	0.19	-10000	0	-0.8	18	18
MEF2D	0.014	0.002	-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	0.066	0.019	-10000	0	-10000	0	0
CREBBP	0.014	0.002	-10000	0	-10000	0	0
BCL2	0.004	0.08	-10000	0	-0.68	4	4

×

Signaling events mediated by VEGFR1 and VEGFR2

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
alphaV beta3 Integrin	-0.028	0.13	-9999	-0.61	14	14
AKT1	0.093	0.038	-9999	-10000	0	0
PTK2B	0.038	0.11	-9999	-0.62	1	1
VEGFR2 homodimer/Frs2	0.031	0.066	-9999	-0.54	4	4
CAV1	-0.065	0.24	-9999	-0.8	29	29
CALM1	0.013	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2	-0.008	0.062	-9999	-0.48	5	5
endothelial cell proliferation	0.099	0.054	-9999	-10000	0	0
mol:Ca2+	0.058	0.046	-9999	-0.49	1	1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Rac	-0.004	0.039	-9999	-0.52	1	1
RP11-342D11.1	0.049	0.046	-9999	-0.5	1	1
CDH5	0.011	0.047	-9999	-0.8	1	1
VEGFA homodimer	-0.002	0.027	-9999	-0.48	1	1
SHC1	0.013	0	-9999	-10000	0	0
SHC2	0.009	0.06	-9999	-0.72	2	2
HRAS/GDP	-0.003	0.033	-9999	-10000	0	0
SH2D2A	-0.086	0.27	-9999	-0.8	37	37
VEGFR2 homodimer/VEGFA homodimer/SHP1/eNOS	-0.005	0.035	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/TsAd	-0.061	0.16	-9999	-0.59	2	2
VEGFR1 homodimer	0.013	0	-9999	-10000	0	0
SHC/GRB2/SOS1	-0.004	0.037	-9999	-10000	0	0
GRB10	0.057	0.061	-9999	-0.71	1	1
PTPN11	0.013	0	-9999	-10000	0	0
GRB2	0.013	0	-9999	-10000	0	0
PAK1	0.011	0.047	-9999	-0.8	1	1
VEGFR2 homodimer/VEGFA homodimer/IQGAP1/Cadherin/beta catenin	-0.006	0.047	-9999	-10000	0	0
HRAS	0.013	0	-9999	-10000	0	0
VEGF/Rho/ROCK1/Integrin Complex	0.043	0.06	-9999	-0.48	1	1
HIF1A	0.013	0	-9999	-10000	0	0
FRS2	0.005	0.081	-9999	-0.8	3	3
oxygen and reactive oxygen species metabolic process	-0.003	0.039	-9999	-0.51	1	1
mol:GTP	0	0	-9999	-10000	0	0
FLT4	0	0.1	-9999	-0.8	5	5
Nck/Pak	-0.002	0.035	-9999	-0.61	1	1
VEGFR2 homodimer/VEGFA homodimer/Fyn	-0.005	0.05	-9999	-0.55	1	1
mol:GDP	-0.003	0.036	-9999	-10000	0	0
mol:NADP	0.079	0.047	-9999	-10000	0	0
eNOS/Hsp90	0.081	0.045	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
mol:IP3	0.059	0.046	-9999	-0.5	1	1
HIF1A/ARNT	0	0	-9999	-10000	0	0
SHB	0.009	0.053	-9999	-0.64	2	2
VEGFA	0.013	0.047	-9999	-0.8	1	1
VEGFC	-0.088	0.27	-9999	-0.8	38	38
FAK1/Vinculin	0.064	0.073	-9999	-10000	0	0
mol:Ca ++	0	0	-9999	-10000	0	0
RHOA	0.013	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/alphaV beta3 Integrin	-0.023	0.099	-9999	-0.59	2	2
PTPN6	0.013	0	-9999	-10000	0	0
EPAS1	0.023	0.02	-9999	-0.31	1	1
mol:L-citrulline	0.079	0.047	-9999	-10000	0	0
ITGAV	0.006	0.076	-9999	-0.75	3	3
PIK3CA	0.013	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2/GRB2	-0.008	0.058	-9999	-0.52	1	1
VEGFR2 homodimer/VEGFA homodimer	-0.004	0.044	-9999	-0.55	1	1
VEGFR2/3 heterodimer	0.028	0.09	-9999	-0.63	5	5
VEGFB	0.013	0	-9999	-10000	0	0
MAPK11	0.062	0.047	-9999	-0.49	1	1
VEGFR2 homodimer	0.037	0.043	-9999	-0.7	1	1
FLT1	0.013	0	-9999	-10000	0	0
NEDD4	0.016	0.004	-9999	-10000	0	0
MAPK3	0.062	0.049	-9999	-10000	0	0
MAPK1	0.062	0.049	-9999	-10000	0	0
VEGFA145/NRP2	-0.004	0.049	-9999	-0.61	2	2
VEGFR1/2 heterodimer	0.037	0.037	-9999	-0.61	1	1
KDR	0.037	0.043	-9999	-0.7	1	1
VEGFA165/NRP1/VEGFR2 homodimer	-0.005	0.046	-9999	-0.49	1	1
SRC	0.013	0	-9999	-10000	0	0
platelet activating factor biosynthetic process	0.064	0.049	-9999	-10000	0	0
PI3K	-0.004	0.034	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/NCK1	-0.004	0.042	-9999	-0.51	2	2
FES	0.059	0.047	-9999	-0.51	1	1
GAB1	-0.003	0.032	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Src	-0.004	0.042	-9999	-0.55	1	1
CTNNB1	0.011	0.038	-9999	-0.64	1	1
SOS1	0.013	0	-9999	-10000	0	0
ARNT	0.013	0	-9999	-10000	0	0
eNOS/Caveolin-1	0.043	0.12	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Yes	-0.004	0.042	-9999	-0.55	1	1
PI3K/GAB1	0.094	0.039	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Frs2/Nck/Pak	-0.009	0.059	-9999	-10000	0	0
PRKACA	0.013	0	-9999	-10000	0	0
VEGFR2/3 heterodimer/VEGFC homodimer	-0.068	0.18	-9999	-0.49	41	41
HSP90AA1	0.013	0	-9999	-10000	0	0
CDC42	0.059	0.047	-9999	-0.51	1	1
actin cytoskeleton reorganization	-0.06	0.16	-9999	-0.59	2	2
PTK2	0.059	0.077	-9999	-10000	0	0
EDG1	0.049	0.046	-9999	-0.5	1	1
mol:DAG	0.059	0.046	-9999	-0.5	1	1
CaM/Ca2+	-0.004	0.037	-9999	-10000	0	0
MAP2K3	0.063	0.057	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/GRB10/NEDD4	-0.005	0.056	-9999	-0.72	1	1
PLCG1	0.059	0.047	-9999	-0.51	1	1
VEGFR2 homodimer/VEGFA homodimer/Src/Shb	-0.006	0.046	-9999	-0.52	1	1
IQGAP1	0.013	0	-9999	-10000	0	0
YES1	0.013	0	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/SHP2	-0.004	0.042	-9999	-0.55	1	1
VEGFR2 homodimer/VEGFA homodimer/SHP1	-0.004	0.042	-9999	-0.55	1	1
cell migration	0.087	0.066	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.004	0.032	-9999	-10000	0	0
FYN	0.011	0.047	-9999	-0.8	1	1
VEGFB/NRP1	-0.004	0.038	-9999	-10000	0	0
mol:NO	0.079	0.047	-9999	-10000	0	0
PXN	0.013	0	-9999	-10000	0	0
HRAS/GTP	-0.003	0.033	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/GRB10	0.056	0.062	-9999	-0.71	1	1
VHL	0.013	0	-9999	-10000	0	0
ITGB3	-0.017	0.15	-9999	-0.76	12	12
NOS3	0.081	0.051	-9999	-10000	0	0
VEGFR2 homodimer/VEGFA homodimer/Sck	-0.007	0.058	-9999	-0.59	2	2
RAC1	0.013	0	-9999	-10000	0	0
PRKCA	0.064	0.052	-9999	-10000	0	0
PRKCB	0.055	0.082	-9999	-10000	0	0
VCL	0.013	0	-9999	-10000	0	0
VEGFA165/NRP1	0.048	0.046	-9999	-0.5	1	1
VEGFR1/2 heterodimer/VEGFA homodimer	-0.004	0.042	-9999	-0.55	1	1
VEGFA165/NRP2	-0.004	0.049	-9999	-0.61	2	2
MAPKKK cascade	-0.004	0.045	-9999	-0.58	1	1
NRP2	0.011	0.047	-9999	-0.8	1	1
VEGFC homodimer	-0.088	0.27	-9999	-0.8	38	38
NCK1	0.013	0	-9999	-10000	0	0
ROCK1	0.013	0	-9999	-10000	0	0
FAK1/Paxillin	0.064	0.073	-9999	-10000	0	0
MAP3K13	0.056	0.056	-9999	-10000	0	0
PDPK1	0.085	0.039	-9999	-10000	0	0

×

TCGA08_rtk_signaling

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
PDGFRA	-0.003	0.11	-9999	-0.69	7	7
HRAS	0.013	0	-9999	-10000	0	0
EGFR	-0.014	0.15	-9999	-0.8	10	10
AKT	0.037	0.051	-9999	-0.3	6	6
FOXO3	0.013	0	-9999	-10000	0	0
AKT1	0.013	0	-9999	-10000	0	0
FOXO1	0.013	0	-9999	-10000	0	0
AKT3	-0.003	0.11	-9999	-0.8	6	6
FOXO4	0.009	0.053	-9999	-0.64	2	2
MET	0.009	0.06	-9999	-0.72	2	2
PIK3CA	0.013	0	-9999	-10000	0	0
PIK3CB	0.013	0	-9999	-10000	0	0
NRAS	0.013	0	-9999	-10000	0	0
PIK3CG	-0.025	0.17	-9999	-0.77	15	15
PIK3R3	0.011	0.038	-9999	-0.64	1	1
PIK3R2	0.013	0	-9999	-10000	0	0
NF1	0.013	0	-9999	-10000	0	0
RAS	0.019	0.043	-9999	-10000	0	0
ERBB2	0.008	0.066	-9999	-0.8	2	2
proliferation/survival/translation	-0.031	0.027	-9999	-10000	0	0
PI3K	0.025	0.052	-9999	-0.23	2	2
PIK3R1	0.013	0	-9999	-10000	0	0
KRAS	0.013	0	-9999	-10000	0	0
FOXO	0.048	0.03	-9999	-10000	0	0
AKT2	0.013	0	-9999	-10000	0	0
PTEN	0.013	0	-9999	-10000	0	0

×

Class I PI3K signaling events

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
ARF5/GTP	0	0	-9999	-10000	0	0
DAPP1	0.008	0.098	-9999	-0.39	2	2
Src family/SYK family/BLNK-LAT/BTK-ITK	-0.01	0.17	-9999	-0.75	9	9
mol:DAG	0.026	0.09	-9999	-0.31	8	8
HRAS	0.014	0	-9999	-10000	0	0
RAP1A	0.014	0	-9999	-10000	0	0
ARF5/GDP	0.042	0.036	-9999	-10000	0	0
PLCG2	0.013	0	-9999	-10000	0	0
PLCG1	0.013	0	-9999	-10000	0	0
ARF5	0.013	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
ARF1/GTP	0	0	-9999	-10000	0	0
RHOA	0.013	0	-9999	-10000	0	0
YES1	0.013	0	-9999	-10000	0	0
RAP1A/GTP	0	0	-9999	-10000	0	0
ADAP1	0	0	-9999	-10000	0	0
ARAP3	0	0	-9999	-10000	0	0
INPPL1	0.013	0	-9999	-10000	0	0
PREX1	0.013	0	-9999	-10000	0	0
ARHGEF6	0.009	0.053	-9999	-0.64	2	2
ARHGEF7	0.013	0	-9999	-10000	0	0
ARF1	0.013	0	-9999	-10000	0	0
NRAS	0.014	0	-9999	-10000	0	0
FYN	0.011	0.047	-9999	-0.8	1	1
ARF6	0.013	0	-9999	-10000	0	0
FGR	0.011	0.047	-9999	-0.8	1	1
mol:Ca2+	0.026	0.049	-9999	-10000	0	0
mol:IP4	0	0	-9999	-10000	0	0
TIAM1	0.007	0.065	-9999	-0.64	3	3
ZAP70	-0.022	0.16	-9999	-0.74	14	14
mol:IP3	0.029	0.066	-9999	-10000	0	0
LYN	0.013	0	-9999	-10000	0	0
ARF1/GDP	0.042	0.036	-9999	-10000	0	0
RhoA/GDP	-0.001	0.007	-9999	-10000	0	0
PDK1/Src/Hsp90	0	0	-9999	-10000	0	0
BLNK	-0.056	0.2	-9999	-0.64	32	32
actin cytoskeleton reorganization	0.067	0.031	-9999	-10000	0	0
SRC	0.013	0	-9999	-10000	0	0
PLEKHA2	0.031	0.024	-9999	-0.39	1	1
RAC1	0.013	0	-9999	-10000	0	0
PTEN	0	0	-9999	-10000	0	0
HSP90AA1	0.013	0	-9999	-10000	0	0
ARF6/GTP	0	0	-9999	-10000	0	0
RhoA/GTP	0	0	-9999	-10000	0	0
Src family/SYK family/BLNK-LAT	-0.029	0.18	-9999	-0.79	9	9
BLK	-0.12	0.3	-9999	-0.77	53	53
PDPK1	0.013	0	-9999	-10000	0	0
CYTH1	0	0	-9999	-10000	0	0
HCK	0.004	0.084	-9999	-0.72	4	4
CYTH3	0	0	-9999	-10000	0	0
CYTH2	0	0	-9999	-10000	0	0
KRAS	0.014	0	-9999	-10000	0	0
GO:0030676	0	0	-9999	-10000	0	0
FOXO3	-0.002	0.027	-9999	-0.47	1	1
SGK1	-0.002	0.029	-9999	-0.51	1	1
INPP5D	0.011	0.038	-9999	-0.64	1	1
mol:GDP	0.036	0.038	-9999	-10000	0	0
SOS1	0.013	0	-9999	-10000	0	0
SYK	0.011	0.038	-9999	-0.64	1	1
ARF6/GDP	-0.001	0.007	-9999	-10000	0	0
mol:PI-3-4-5-P3	0	0	-9999	-10000	0	0
ARAP3/RAP1A/GTP	0	0	-9999	-10000	0	0
VAV1	0.003	0.083	-9999	-0.64	5	5
mol:PI-3-4-P2	0.023	0.028	-9999	-0.47	1	1
RAS family/GTP/PI3K Class I	0	0	-9999	-10000	0	0
PLEKHA1	0.031	0.024	-9999	-0.39	1	1
Rac1/GDP	0.042	0.036	-9999	-10000	0	0
LAT	-0.008	0.13	-9999	-0.8	8	8
Rac1/GTP	0.037	0.052	-9999	-10000	0	0
ITK	-0.015	0.073	-9999	-10000	0	0
Src family/SYK family/BLNK-LAT/BTK-ITK/PLC-gamma	0.024	0.12	-9999	-0.44	9	9
LCK	-0.014	0.15	-9999	-0.8	10	10
BTK	-0.001	0.024	-9999	-10000	0	0

×

Arf6 trafficking events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
SLC2A4	-0.27	0.32	-10000	0	-0.64	133	133
CLTC	0.034	0.017	-10000	0	-10000	0	0
calcium ion-dependent exocytosis	0.029	0.001	-10000	0	-10000	0	0
Dynamin 2/GTP	-0.002	0.028	-10000	0	-0.49	1	1
EXOC4	0.013	0	-10000	0	-10000	0	0
CD59	0.03	0.018	-10000	0	-10000	0	0
CPE	0.015	0.055	-10000	0	-0.54	3	3
CTNNB1	0.011	0.038	-10000	0	-0.64	1	1
membrane fusion	0	0	-10000	0	-10000	0	0
CTNND1	0.033	0.028	-10000	0	-0.45	1	1
DNM2	0.013	0	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.035	0.007	-10000	0	-10000	0	0
TSHR	0.008	0.078	-10000	0	-0.54	6	6
INS	0.013	0.002	-10000	0	-10000	0	0
BIN1	0	0.1	-10000	0	-0.8	5	5
mol:Choline	0	0	-10000	0	-10000	0	0
growth hormone secretagogue receptor activity	0	0	-10000	0	-10000	0	0
mol:GDP	0.018	0.032	-10000	0	-0.54	1	1
membrane depolarization	0	0	-10000	0	-10000	0	0
ARF6	0.013	0	-10000	0	-10000	0	0
mol:Ca2+	-0.002	0.028	-10000	0	-0.48	1	1
JUP	0.03	0.018	-10000	0	-10000	0	0
ASAP2/amphiphysin II	-0.008	0.062	-10000	0	-0.49	5	5
ARF6/GTP	0	0	-10000	0	-10000	0	0
CDH1	0.029	0.023	-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	0.047	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	0.003	0.029	-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	0.027	0.01	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
CHRM2	0.026	0.011	-10000	0	-10000	0	0
clathrin heavy chain/ACAP1	0.04	0.015	-10000	0	-10000	0	0
JIP4/KLC1	0	0	-10000	0	-10000	0	0
EXOC1	0.013	0	-10000	0	-10000	0	0
exocyst	0.047	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	0.033	0.028	-10000	0	-0.45	1	1
NME1	0.019	0.032	-10000	0	-0.54	1	1
clathrin coat assembly	0.034	0.017	-10000	0	-10000	0	0
IL2RA	0.001	0.082	-10000	0	-10000	0	0
VAMP3	0.02	0	-10000	0	-10000	0	0
GLUT4/clathrin heavy chain/ACAP1	-0.12	0.14	-10000	0	-0.51	1	1
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	0.036	0.007	-10000	0	-10000	0	0
SDC1	0.031	0.011	-10000	0	-10000	0	0
ARF6/GDP	0.017	0.032	-10000	0	-0.54	1	1
EXOC7	0.013	0	-10000	0	-10000	0	0
E-cadherin/beta catenin	-0.003	0.03	-10000	0	-10000	0	0
mol:Phosphatidic acid	0	0	-10000	0	-10000	0	0
endocytosis	0.008	0.062	0.48	5	-10000	0	5
SCAMP2	0.013	0	-10000	0	-10000	0	0
ADRB2	0.013	0.098	-10000	0	-0.58	1	1
EXOC3	0.013	0	-10000	0	-10000	0	0
ASAP2	0.013	0	-10000	0	-10000	0	0
Dynamin 2/GDP	0.025	0.029	-10000	0	-0.48	1	1
KLC1	0.013	0	-10000	0	-10000	0	0
AVPR2	0.024	0.077	-10000	0	-10000	0	0
RALA	0.013	0	-10000	0	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.003	0.027	-10000	0	-10000	0	0

×

IGF1 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
NCK2	0.013	0	-9999	-10000	0	0
PTK2	0.013	0	-9999	-10000	0	0
CRKL	-0.007	0.11	-9999	-0.48	1	1
GRB2/SOS1/SHC	0	0	-9999	-10000	0	0
HRAS	0.013	0	-9999	-10000	0	0
IRS1/Crk	-0.006	0.11	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/PTP1B	-0.038	0.12	-9999	-0.47	5	5
AKT1	0.02	0.093	-9999	-10000	0	0
BAD	0.028	0.088	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
CRK	-0.006	0.11	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1/Shp2	-0.032	0.098	-9999	-10000	0	0
RAF1	0.032	0.085	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos	-0.03	0.091	-9999	-10000	0	0
YWHAZ	0.013	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1	-0.036	0.11	-9999	-0.36	30	30
PIK3CA	0.013	0	-9999	-10000	0	0
RPS6KB1	0.02	0.093	-9999	-10000	0	0
GNB2L1	0.013	0	-9999	-10000	0	0
positive regulation of MAPKKK cascade	0.027	0.076	-9999	-10000	0	0
PXN	0.013	0	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
cell adhesion	0	0	-9999	-10000	0	0
GRB2/SOS1	0	0	-9999	-10000	0	0
HRAS/GTP	-0.026	0.078	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/GRB2/Sos/Shc	-0.029	0.089	-9999	-10000	0	0
IGF-1R heterotetramer	0.006	0.025	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS/Nck	-0.032	0.098	-9999	-10000	0	0
Crk/p130 Cas/Paxillin	-0.028	0.085	-9999	-10000	0	0
IGF1R	0.006	0.025	-9999	-10000	0	0
IGF1	-0.054	0.21	-9999	-0.67	30	30
IRS2/Crk	0.001	0.1	-9999	-10000	0	0
PI3K	-0.03	0.09	-9999	-10000	0	0
apoptosis	-0.033	0.079	-9999	-10000	0	0
HRAS/GDP	0	0	-9999	-10000	0	0
PRKCD	0.004	0.13	-9999	-10000	0	0
RAF1/14-3-3 E	0.038	0.077	-9999	-10000	0	0
BAD/14-3-3	0.034	0.083	-9999	-10000	0	0
PRKCZ	0.019	0.094	-9999	-10000	0	0
Crk/p130 Cas/Paxillin/FAK1	-0.021	0.062	-9999	-10000	0	0
PTPN1	0.013	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/IRS1/GRB2/Sos/Shc/RACK1	-0.004	0.13	-9999	-0.42	25	25
BCAR1	0.013	0	-9999	-10000	0	0
IGF-1R heterotetramer/IGF1/SHC/GRB10	-0.034	0.1	-9999	-0.51	1	1
mol:GDP	0	0	-9999	-10000	0	0
SOS1	0.013	0	-9999	-10000	0	0
IRS1/NCK2	-0.006	0.11	-9999	-10000	0	0
GRB10	0.011	0.047	-9999	-0.8	1	1
PTPN11	-0.006	0.11	-9999	-10000	0	0
IRS1	-0.016	0.11	-9999	-0.36	30	30
IRS2	-0.008	0.11	-9999	-0.37	5	5
IGF-1R heterotetramer/IGF1	-0.05	0.15	-9999	-0.5	30	30
GRB2	0.013	0	-9999	-10000	0	0
PDPK1	0.011	0.097	-9999	-10000	0	0
YWHAE	0.013	0	-9999	-10000	0	0
PRKD1	-0.004	0.14	-9999	-0.53	6	6
SHC1	0.013	0	-9999	-10000	0	0

×

E-cadherin signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
E-cadherin/beta catenin-gamma catenin	-0.005	0.054	-9999	-0.52	3	3
E-cadherin/beta catenin	-0.005	0.046	-9999	-0.47	3	3
CTNNB1	0.011	0.038	-9999	-0.64	1	1
JUP	0.011	0.038	-9999	-0.64	1	1
CDH1	0.009	0.053	-9999	-0.64	2	2

×

Canonical NF-kappaB 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
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	0.09	0.024	-9999	-10000	0	0
ERC1	0.013	0	-9999	-10000	0	0
RIP2/NOD2	0	0	-9999	-10000	0	0
NFKBIA	0.051	0	-9999	-10000	0	0
BIRC2	-0.003	0.11	-9999	-0.8	6	6
IKBKB	0.013	0	-9999	-10000	0	0
RIPK2	0.013	0	-9999	-10000	0	0
IKBKG	-0.004	0.026	-9999	-10000	0	0
IKK complex/A20	-0.02	0.077	-9999	-10000	0	0
NEMO/A20/RIP2	0.013	0	-9999	-10000	0	0
XPO1	0.013	0	-9999	-10000	0	0
NEMO/ATM	0.051	0.031	-9999	-10000	0	0
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	-0.003	0.019	-9999	-10000	0	0
BCL10/MALT1/TRAF6	0	0	-9999	-10000	0	0
NOD2	0.013	0	-9999	-10000	0	0
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	-0.012	0.085	-9999	-0.61	6	6
ATM	0.013	0	-9999	-10000	0	0
TNF/TNFR1A	-0.028	0.12	-9999	-0.57	15	15
TRAF6	0.013	0	-9999	-10000	0	0
PRKCA	0.011	0.047	-9999	-0.8	1	1
CHUK	0.013	0	-9999	-10000	0	0
UBE2D3	0.013	0	-9999	-10000	0	0
TNF	-0.025	0.17	-9999	-0.76	15	15
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	0.051	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.017	0	-9999	-10000	0	0
TNFRSF1A	0.013	0	-9999	-10000	0	0
IKK complex	-0.003	0.022	-9999	-10000	0	0
CYLD	0.013	0	-9999	-10000	0	0
IKK complex/PKC alpha	-0.004	0.029	-9999	-10000	0	0

×

Signaling events mediated by HDAC Class II

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
G beta1gamma2/HDAC5	-0.002	0.027	-9999	-0.48	1	1
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	-0.004	0.05	-9999	-0.61	2	2
HDAC5/BCL6/BCoR	0	0	-9999	-10000	0	0
HDAC9	-0.024	0.17	-9999	-0.79	14	14
Glucocorticoid receptor/Hsp90/HDAC6	0	0	-9999	-10000	0	0
HDAC4/ANKRA2	0	0	-9999	-10000	0	0
HDAC5/YWHAB	0	0	-9999	-10000	0	0
NPC/RanGAP1/SUMO1/Ubc9	0.024	0	-9999	-10000	0	0
GATA2	0.008	0.066	-9999	-0.8	2	2
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	-0.002	0.035	-9999	-0.61	1	1
Histones	0.032	0.052	-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	-0.04	0.2	-9999	-0.8	20	20
Tubulin/HDAC6	-0.002	0.03	-9999	-0.53	1	1
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	0.011	0.005	-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	-0.002	0.035	-9999	-0.61	1	1
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	0	-9999	-10000	0	0
HDAC4/HDAC3/SMRT (N-CoR2)	0	0	-9999	-10000	0	0
HDAC4/SRF	-0.034	0.13	-9999	-0.52	20	20
HDAC4/ER alpha	-0.032	0.13	-9999	-0.56	17	17
EntrezGene:23225	0	0	-9999	-10000	0	0
positive regulation of chromatin silencing	0.032	0.052	-9999	-10000	0	0
cell motility	-0.002	0.03	-9999	-0.53	1	1
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	0.013	0	-9999	-10000	0	0
HDAC4/CaMK II delta B	0.013	0	-9999	-10000	0	0
Hsp90/HDAC6	0	0	-9999	-10000	0	0
ESR1	-0.029	0.18	-9999	-0.75	17	17
HDAC6/HDAC11	-0.002	0.027	-9999	-0.47	1	1
Ran/GTP/Exportin 1	0	0	-9999	-10000	0	0
NPC	0	0	-9999	-10000	0	0
MEF2C	-0.002	0.11	-9999	-0.75	6	6
RAN	0.013	0	-9999	-10000	0	0
HDAC4/MEF2C	-0.008	0.057	-9999	-10000	0	0
GNG2	0.011	0.047	-9999	-0.8	1	1
NCOR2	0.013	0	-9999	-10000	0	0
TUBB2A	0.011	0.047	-9999	-0.8	1	1
HDAC11	0.011	0.038	-9999	-0.64	1	1
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

×

PLK1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
regulation of centriole-centriole cohesion	-0.012	0.007	-10000	0	-10000	0	0
BUB1B	0.023	0.023	-10000	0	-10000	0	0
PLK1	0.018	0.02	-10000	0	-0.16	1	1
PLK1S1	0.015	0.018	-10000	0	-0.17	2	2
KIF2A	0.026	0.018	-10000	0	-10000	0	0
regulation of mitotic centrosome separation	0.018	0.02	-10000	0	-0.16	1	1
GOLGA2	0.013	0	-10000	0	-10000	0	0
Hec1/SPC24	0.015	0.091	-10000	0	-0.47	10	10
WEE1	0.023	0.024	-10000	0	-10000	0	0
cytokinesis	0.034	0.021	-10000	0	-10000	0	0
PP2A-alpha B56	0	0.007	-10000	0	-10000	0	0
AURKA	0.014	0.028	-10000	0	-0.19	5	5
PICH/PLK1	0.027	0.076	-10000	0	-0.44	1	1
CENPE	0.026	0.018	-10000	0	-10000	0	0
RhoA/GTP	0	0	-10000	0	-10000	0	0
positive regulation of microtubule depolymerization	0.026	0.018	-10000	0	-10000	0	0
PPP2CA	0.013	0	-10000	0	-10000	0	0
FZR1	0.013	0	-10000	0	-10000	0	0
TPX2	0.012	0.029	-10000	0	-0.18	6	6
PAK1	0.01	0.047	-10000	0	-0.8	1	1
SPC24	-0.003	0.11	-10000	0	-0.8	6	6
FBXW11	0.013	0	-10000	0	-10000	0	0
CLSPN	0.012	0.034	-10000	0	-0.2	7	7
GORASP1	0.013	0	-10000	0	-10000	0	0
metaphase	0	0.001	-10000	0	-0.017	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
NLP	0.01	0.01	-10000	0	-0.07	1	1
G2 phase of mitotic cell cycle	0	0.002	-10000	0	-0.013	5	5
STAG2	0.013	0	-10000	0	-10000	0	0
GRASP65/GM130/RAB1/GTP	0	0.007	-10000	0	-10000	0	0
spindle elongation	0.018	0.02	-10000	0	-0.16	1	1
ODF2	0.013	0.002	-10000	0	-10000	0	0
BUB1	-0.001	0.009	-10000	0	-10000	0	0
TPT1	0.016	0.01	-10000	0	-10000	0	0
CDC25C	0.015	0.028	-10000	0	-0.24	3	3
CDC25B	-0.013	0.14	-10000	0	-0.8	10	10
SGOL1	0.012	0.007	-10000	0	-10000	0	0
RHOA	0.013	0	-10000	0	-10000	0	0
CCNB1/CDK1	-0.013	0.069	-10000	0	-0.39	10	10
CDC14B	0.011	0.029	-10000	0	-0.49	1	1
CDC20	0.003	0.093	-10000	0	-0.8	4	4
PLK1/PBIP1	-0.005	0.04	-10000	0	-0.48	2	2
mitosis	0	0.005	0.04	5	-0.021	2	7
FBXO5	0.022	0.018	-10000	0	-10000	0	0
CDC2	0.001	0.003	-10000	0	-0.016	10	10
NDC80	0.003	0.093	-10000	0	-0.8	4	4
metaphase plate congression	0.017	0.012	-10000	0	-10000	0	0
ERCC6L	-0.012	0.065	-10000	0	-0.41	1	1
NLP/gamma Tubulin	0.015	0.011	-10000	0	-10000	0	0
microtubule cytoskeleton organization	0.016	0.01	-10000	0	-10000	0	0
G2/M transition DNA damage checkpoint	0	0.001	-10000	0	-10000	0	0
PPP1R12A	0.013	0.001	-10000	0	-10000	0	0
interphase	0	0.001	-10000	0	-10000	0	0
PLK1/PRC1-2	0.031	0.017	-10000	0	-10000	0	0
GRASP65/GM130/RAB1/GTP/PLK1	-0.001	0.009	-10000	0	-10000	0	0
RAB1A	0.013	0	-10000	0	-10000	0	0
prophase	0	0	-10000	0	-10000	0	0
Aurora A/BORA	0.018	0.044	-10000	0	-0.46	2	2
mitotic prometaphase	0	0.001	-10000	0	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	-0.002	0.019	-10000	0	-10000	0	0
microtubule-based process	0.024	0.018	-10000	0	-10000	0	0
Golgi organization	0.018	0.02	-10000	0	-0.16	1	1
Cohesin/SA2	-0.002	0.012	-10000	0	-10000	0	0
PPP1CB/MYPT1	0	0	-10000	0	-10000	0	0
KIF20A	0.013	0	-10000	0	-10000	0	0
APC/C/CDC20	0.017	0.064	-10000	0	-0.52	4	4
PPP2R1A	0.013	0	-10000	0	-10000	0	0
chromosome segregation	-0.005	0.04	-10000	0	-0.47	2	2
PRC1	0.013	0	-10000	0	-10000	0	0
ECT2	0.021	0.053	-10000	0	-0.48	3	3
C13orf34	0.019	0.043	-10000	0	-0.46	2	2
NUDC	0.017	0.012	-10000	0	-10000	0	0
regulation of attachment of spindle microtubules to kinetochore	0.023	0.022	-10000	0	-10000	0	0
spindle assembly	0.018	0.016	-10000	0	-10000	0	0
spindle stabilization	0.015	0.018	-10000	0	-0.17	2	2
APC/C/HCDH1	0.017	0.025	-10000	0	-0.41	1	1
MKLP2/PLK1	0.024	0.018	-10000	0	-10000	0	0
CCNB1	0.014	0.003	-10000	0	-10000	0	0
PPP1CB	0.013	0.001	-10000	0	-10000	0	0
BTRC	0.013	0	-10000	0	-10000	0	0
ROCK2	0.024	0.03	-10000	0	-0.44	1	1
TUBG1	0.016	0.01	-10000	0	-10000	0	0
G2/M transition of mitotic cell cycle	-0.013	0.068	-10000	0	-0.38	10	10
MLF1IP	0.009	0.052	-10000	0	-0.63	2	2
INCENP	0.013	0.001	-10000	0	-10000	0	0

×

S1P5 pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
mol:S1P	0	0	-10000	0	-10000	0	0
telencephalon oligodendrocyte cell migration	0.007	0.04	0.42	1	-10000	0	1
GNAI2	0.013	0	-10000	0	-10000	0	0
S1P/S1P5/G12	-0.005	0.049	-10000	0	-0.49	3	3
mol:GDP	0	0	-10000	0	-10000	0	0
GNAO1	0.009	0.06	-10000	0	-0.72	2	2
RhoA/GTP	-0.007	0.041	-10000	0	-0.43	1	1
negative regulation of cAMP metabolic process	0.029	0.053	-10000	0	-0.47	1	1
GNAZ	-0.004	0.11	-10000	0	-0.73	7	7
GNAI3	0.013	0	-10000	0	-10000	0	0
GNA12	0.008	0.066	-10000	0	-0.8	2	2
S1PR5	0.011	0.038	-10000	0	-0.64	1	1
mol:GTP	0	0	-10000	0	-10000	0	0
S1P/S1P5/Gi	0.029	0.053	-10000	0	-0.47	1	1
RhoA/GDP	0	0	-10000	0	-10000	0	0
RHOA	0.013	0	-10000	0	-10000	0	0
GNAI1	0.011	0.038	-10000	0	-0.64	1	1

×

E-cadherin signaling in the nascent adherens junction

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
CTTN	0.029	0.086	-9999	-0.43	10	10
KLHL20	-0.01	0.037	-9999	-0.29	1	1
CYFIP2	0.009	0.053	-9999	-0.64	2	2
Rac1/GDP	0.06	0.038	-9999	-10000	0	0
ENAH	0.04	0.053	-9999	-0.48	3	3
AP1M1	0.013	0	-9999	-10000	0	0
RAP1B	0.011	0.047	-9999	-0.8	1	1
RAP1A	0.013	0	-9999	-10000	0	0
CTNNB1	0.011	0.038	-9999	-0.64	1	1
CDC42/GTP	-0.003	0.026	-9999	-10000	0	0
ABI1/Sra1/Nap1	-0.007	0.026	-9999	-0.19	1	1
E-cadherin/beta catenin/alpha catenin/beta7/alphaE Integrin	-0.005	0.04	-9999	-10000	0	0
RAPGEF1	0.054	0.046	-9999	-10000	0	0
CTNND1	0.013	0	-9999	-10000	0	0
regulation of calcium-dependent cell-cell adhesion	-0.005	0.05	-9999	-0.5	3	3
CRK	0.048	0.05	-9999	-0.44	3	3
E-cadherin/gamma catenin/alpha catenin	-0.004	0.049	-9999	-0.58	2	2
alphaE/beta7 Integrin	-0.002	0.027	-9999	-0.47	1	1
IQGAP1	0.013	0	-9999	-10000	0	0
NCKAP1	0.013	0	-9999	-10000	0	0
Rap1/GTP/I-afadin	-0.002	0.028	-9999	-0.49	1	1
DLG1	0.04	0.053	-9999	-0.48	3	3
ChemicalAbstracts:7440-70-2	0	0	-9999	-10000	0	0
mol:PI-3-4-5-P3	-0.002	0.018	-9999	-10000	0	0
MLLT4	0.013	0	-9999	-10000	0	0
ARF6/GTP/NME1/Tiam1	-0.005	0.045	-9999	-0.39	4	4
PI3K	-0.003	0.023	-9999	-10000	0	0
ARF6	0.013	0	-9999	-10000	0	0
mol:Ca2+	0	0	-9999	-10000	0	0
E-cadherin/gamma catenin	-0.004	0.056	-9999	-0.67	2	2
TIAM1	0.007	0.065	-9999	-0.64	3	3
E-cadherin(dimer)/Ca2+	-0.003	0.033	-9999	-10000	0	0
AKT1	-0.002	0.013	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
CDH1	0.009	0.053	-9999	-0.64	2	2
RhoA/GDP	0.06	0.038	-9999	-10000	0	0
actin cytoskeleton organization	-0.007	0.028	-9999	-0.2	1	1
CDC42/GDP	0.06	0.038	-9999	-10000	0	0
E-cadherin/Ca2+/gamma catenin/alpha catenin/p120 catenin	0.024	0.038	-9999	-0.42	2	2
ITGB7	0.011	0.038	-9999	-0.64	1	1
RAC1	0.013	0	-9999	-10000	0	0
E-cadherin/beta catenin/alpha catenin/p120 catenin	-0.003	0.035	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin	-0.003	0.034	-9999	-0.34	3	3
mol:GDP	0.057	0.043	-9999	-10000	0	0
CDC42/GTP/IQGAP1	0	0	-9999	-10000	0	0
JUP	0.011	0.038	-9999	-0.64	1	1
p120 catenin/RhoA/GDP	-0.003	0.028	-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	0.03	0.047	-9999	-0.24	7	7
NME1	0.011	0.047	-9999	-0.8	1	1
clathrin coat assembly	0	0	-9999	-10000	0	0
TJP1	0.04	0.053	-9999	-0.48	3	3
regulation of cell-cell adhesion	-0.003	0.023	-9999	-10000	0	0
WASF2	-0.004	0.013	-9999	-10000	0	0
Rap1/GTP	-0.003	0.03	-9999	-10000	0	0
E-cadherin/gamma catenin/alpha catenin/beta7/alphaE Integrin	-0.004	0.046	-9999	-0.67	1	1
CCND1	0.034	0.058	-9999	-0.31	7	7
VAV2	0.041	0.075	-9999	-10000	0	0
RAP1/GDP	-0.001	0.032	-9999	-10000	0	0
adherens junction assembly	0.04	0.051	-9999	-0.46	3	3
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	-0.005	0.047	-9999	-0.64	1	1
E-cadherin/beta catenin	-0.003	0.034	-9999	-0.41	2	2
mol:GTP	0	0	-9999	-10000	0	0
SRC	0.04	0.053	-9999	-0.48	3	3
PIK3CA	0.013	0	-9999	-10000	0	0
Rac1/GTP	-0.016	0.06	-9999	-0.43	2	2
E-cadherin/beta catenin/alpha catenin	-0.004	0.039	-9999	-0.4	3	3
ITGAE	0.013	0	-9999	-10000	0	0
E-cadherin/Ca2+/beta catenin/alpha catenin/p120 catenin	-0.005	0.051	-9999	-0.51	3	3

×

E-cadherin signaling in keratinocytes

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
keratinocyte differentiation	0.052	0.03	-10000	0	-0.41	1	1
adherens junction organization	0.043	0.052	-10000	0	-0.5	2	2
mol:GTP	0	0	-10000	0	-10000	0	0
Rac1/GDP	0.044	0.081	-10000	0	-10000	0	0
FMN1	0.034	0.078	-10000	0	-0.6	2	2
mol:IP3	-0.002	0.027	-10000	0	-0.43	1	1
E-cadherin/Ca2+/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.037	0.047	-10000	0	-0.66	1	1
CTNNB1	0.011	0.037	-10000	0	-0.64	1	1
AKT1	0.05	0.034	-10000	0	-0.46	1	1
E-cadherin/beta catenin-gamma catenin/alpha catenin/p120 catenin	0.042	0.059	-10000	0	-0.52	3	3
CTNND1	0.015	0.001	-10000	0	-10000	0	0
mol:PI-4-5-P2	0.044	0.044	-10000	0	-0.6	1	1
VASP	0.044	0.045	-10000	0	-0.62	1	1
ZYX	0.044	0.045	-10000	0	-0.62	1	1
JUB	0.044	0.045	-10000	0	-0.62	1	1
EGFR(dimer)	0.028	0.094	-10000	0	-0.44	11	11
E-cadherin/beta catenin-gamma catenin	-0.005	0.052	-10000	0	-0.49	3	3
mol:PI-3-4-5-P3	-0.003	0.031	-10000	0	-0.49	1	1
PIK3CA	0.014	0.001	-10000	0	-10000	0	0
PI3K	-0.003	0.032	-10000	0	-0.5	1	1
FYN	0.052	0.053	-10000	0	-0.6	1	1
mol:Ca2+	-0.002	0.026	-10000	0	-0.42	1	1
JUP	0.011	0.037	-10000	0	-0.64	1	1
PIK3R1	0.014	0.001	-10000	0	-10000	0	0
mol:DAG	-0.002	0.027	-10000	0	-0.43	1	1
CDH1	0.009	0.053	-10000	0	-0.64	2	2
RhoA/GDP	0.044	0.081	-10000	0	-10000	0	0
establishment of polarity of embryonic epithelium	0.044	0.044	-10000	0	-0.6	1	1
SRC	0.013	0	-10000	0	-10000	0	0
RAC1	0.013	0	-10000	0	-10000	0	0
RHOA	0.013	0	-10000	0	-10000	0	0
EGFR	-0.014	0.15	-10000	0	-0.8	10	10
CASR	0.044	0.053	-10000	0	-10000	0	0
RhoA/GTP	-0.002	0.023	-10000	0	-10000	0	0
AKT2	0.05	0.034	-10000	0	-0.46	1	1
actin cable formation	0.041	0.076	-10000	0	-0.57	2	2
apoptosis	0.002	0.028	0.44	1	-10000	0	1
CTNNA1	0.015	0.001	-10000	0	-10000	0	0
mol:GDP	0.037	0.086	-10000	0	-0.43	1	1
PIP5K1A	0.044	0.045	-10000	0	-0.62	1	1
PLCG1	-0.002	0.027	-10000	0	-0.44	1	1
Rac1/GTP	-0.016	0.076	-10000	0	-0.4	11	11
homophilic cell adhesion	0.001	0.001	-10000	0	-10000	0	0

×

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	0.011	0.038	-9999	-0.64	1	1
SMAD2	0.015	0	-9999	-10000	0	0
SMAD3	0.045	0.015	-9999	-10000	0	0
SMAD3/SMAD4	0.05	0.017	-9999	-10000	0	0
SMAD4/Ubc9/PIASy	-0.001	0.023	-9999	-10000	0	0
SMAD2/SMAD2/SMAD4	-0.001	0.017	-9999	-10000	0	0
PPM1A	0.013	0	-9999	-10000	0	0
CALM1	0.013	0	-9999	-10000	0	0
SMAD2/SMAD4	0.021	0.022	-9999	-0.35	1	1
MAP3K1	0.013	0	-9999	-10000	0	0
TRAP-1/SMAD4	-0.006	0.054	-9999	-0.47	4	4
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	0.007	0.065	-9999	-0.64	3	3
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

×

BARD1 signaling events

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BARD1/CSTF1	-0.005	0.046	-10000	0	-0.47	3	3
ATM	0.013	0	-10000	0	-10000	0	0
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	0.028	0	-10000	0	-10000	0	0
protein ubiquitination	-0.005	0.04	-10000	0	-0.44	1	1
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	-0.004	0.038	-10000	0	-0.56	1	1
FANCF	0.009	0.053	-10000	0	-0.64	2	2
BRCA1	0.013	0	-10000	0	-10000	0	0
CCNE1	0.011	0.047	-10000	0	-0.8	1	1
CDK2/Cyclin E1	-0.002	0.035	-10000	0	-0.61	1	1
FANCG	0.008	0.066	-10000	0	-0.8	2	2
BRCA1/BACH1/BARD1	-0.005	0.046	-10000	0	-0.47	3	3
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	0.011	0.047	-10000	0	-0.8	1	1
DNA repair	0.074	0.056	-10000	0	-0.49	1	1
BRCA1/BARD1/ubiquitin	-0.005	0.046	-10000	0	-0.47	3	3
BARD1/DNA-PK	-0.003	0.035	-10000	0	-10000	0	0
FANCL	0.013	0	-10000	0	-10000	0	0
mRNA polyadenylation	0.005	0.046	0.47	3	-10000	0	3
BRCA1/BARD1/CTIP/M/R/N Complex	0.041	0.03	-10000	0	-10000	0	0
BRCA1/BACH1/BARD1/TopBP1	-0.004	0.039	-10000	0	-0.4	3	3
BRCA1/BARD1/P53	-0.007	0.049	-10000	0	-10000	0	0
BARD1/CSTF1/BRCA1	-0.004	0.039	-10000	0	-10000	0	0
BRCA1/BACH1	0.013	0	-10000	0	-10000	0	0
BARD1	0.007	0.065	-10000	0	-0.64	3	3
PCNA	0.013	0	-10000	0	-10000	0	0
BRCA1/BARD1/UbcH5C	-0.004	0.039	-10000	0	-10000	0	0
BRCA1/BARD1/UbcH7	-0.004	0.039	-10000	0	-0.4	3	3
BRCA1/BARD1/RAD51/PCNA	-0.005	0.044	-10000	0	-0.48	1	1
BARD1/DNA-PK/P53	-0.006	0.045	-10000	0	-10000	0	0
BRCA1/BARD1/Ubiquitin	-0.005	0.046	-10000	0	-0.47	3	3
BRCA1/BARD1/CTIP	-0.003	0.035	-10000	0	-10000	0	0
FA complex	0.039	0.041	-10000	0	-0.5	1	1
BARD1/EWS	-0.005	0.046	-10000	0	-0.47	3	3
RBBP8	0.025	0	-10000	0	-10000	0	0
TP53	0.007	0.065	-10000	0	-0.64	3	3
TOPBP1	0.013	0	-10000	0	-10000	0	0
G1/S transition of mitotic cell cycle	0.007	0.049	-10000	0	-10000	0	0
BRCA1/BARD1	-0.005	0.041	-10000	0	-0.44	1	1
CSTF1	0.013	0	-10000	0	-10000	0	0
BARD1/EWS-Fli1	-0.005	0.047	-10000	0	-0.48	3	3
CDK2	0.013	0	-10000	0	-10000	0	0
UniProt:Q9BZD1	0	0	-10000	0	-10000	0	0
RAD51	0.011	0.047	-10000	0	-0.8	1	1
RAD50	0.013	0	-10000	0	-10000	0	0
BRCA1/BARD1/DNA-directed RNA polymerase II holoenzyme	-0.005	0.046	-10000	0	-0.47	3	3
EWSR1	0.013	0	-10000	0	-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	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations
PLK2	0.013	-9999	-9999
PLK4	0.013	-9999	-9999
regulation of centriole replication	0.025	-9999	-9999

×

Aurora C signaling

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
INCENP	0.013	0	-9999	-10000	0	0
Aurora C/Aurora B/INCENP	-0.004	0.044	-9999	-0.49	2	2
metaphase	0	0	-9999	-10000	0	0
mitosis	0	0	-9999	-10000	0	0
H3F3B	-0.001	0.012	-9999	-10000	0	0
AURKB	0.011	0.047	-9999	-0.8	1	1
AURKC	0.009	0.06	-9999	-0.72	2	2

×

Insulin-mediated glucose transport

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Number.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
Insulin responsive Vesicles	-0.081	0.094	-10000	0	-0.41	1	1
CaM/Ca2+	0	0	-10000	0	-10000	0	0
AKT1	0.013	0	-10000	0	-10000	0	0
AKT2	0.013	0	-10000	0	-10000	0	0
STXBP4	0.013	0	-10000	0	-10000	0	0
mol:GTP	0	0	-10000	0	-10000	0	0
mol:glucose	-0.057	0.14	0.3	6	-0.45	1	7
YWHAZ	0.013	0	-10000	0	-10000	0	0
CALM1	0.013	0	-10000	0	-10000	0	0
YWHAQ	0.013	0	-10000	0	-10000	0	0
TBC1D4	0.025	0	-10000	0	-10000	0	0
mol:Ca2+	0	0	-10000	0	-10000	0	0
YWHAH	0.013	0	-10000	0	-10000	0	0
YWHAB	0.013	0	-10000	0	-10000	0	0
SNARE/Synip	0	0	-10000	0	-10000	0	0
YWHAG	0.013	0	-10000	0	-10000	0	0
ASIP	-0.018	0.14	-10000	0	-0.8	10	10
PRKCI	0.013	0	-10000	0	-10000	0	0
AS160/CaM/Ca2+	0	0	-10000	0	-10000	0	0
RHOQ	0.013	0	-10000	0	-10000	0	0
GYS1	0.035	0	-10000	0	-10000	0	0
PRKCZ	0.011	0.038	-10000	0	-0.64	1	1
TRIP10	0.013	0	-10000	0	-10000	0	0
TC10/GTP/CIP4/Exocyst	0	0	-10000	0	-10000	0	0
AS160/14-3-3	0.05	0.014	-10000	0	-10000	0	0
VAMP2	0.013	0	-10000	0	-10000	0	0
SLC2A4	-0.064	0.15	0.3	6	-0.51	1	7
STX4	0.013	0	-10000	0	-10000	0	0
GSK3B	0.028	0	-10000	0	-10000	0	0
SFN	0.011	0.038	-10000	0	-0.64	1	1
LNPEP	0.013	0	-10000	0	-10000	0	0
YWHAE	0.013	0	-10000	0	-10000	0	0

×

mTOR signaling pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
GBL	0	0	-9999	-10000	0	0
MKNK1	0.013	0	-9999	-10000	0	0
mol:PIP3	0	0	-9999	-10000	0	0
FRAP1	0.017	0	-9999	-10000	0	0
AKT1	0	0	-9999	-10000	0	0
INSR	0.013	0	-9999	-10000	0	0
Insulin Receptor/Insulin	0	0	-9999	-10000	0	0
mol:GTP	0	0	-9999	-10000	0	0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA/eIF3/40s Ribosomal subunit	0	0	-9999	-10000	0	0
TSC2	0.013	0	-9999	-10000	0	0
RHEB/GDP	0	0	-9999	-10000	0	0
TSC1	0.014	0	-9999	-10000	0	0
Insulin Receptor/IRS1	0.017	0	-9999	-10000	0	0
eIF4E/eIF4G1/eIF4A1/eIF4B/RNA	0	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
EIF3A	0.013	0	-9999	-10000	0	0
RPS6KB1	0.031	0	-9999	-10000	0	0
MAP3K5	0.011	0	-9999	-10000	0	0
PIK3R1	0.014	0	-9999	-10000	0	0
apoptosis	0.011	0	-9999	-10000	0	0
mol:LY294002	0	0	-9999	-10000	0	0
EIF4B	0.037	0	-9999	-10000	0	0
40S S6 ribosomal protein /40s Ribosomal subunit/eIF3	0	0	-9999	-10000	0	0
eIF4E/eIF4G1/eIF4A1	0	0	-9999	-10000	0	0
KIAA1303	0	0	-9999	-10000	0	0
PI3K	0.026	0	-9999	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL	0.035	0	-9999	-10000	0	0
FKBP1A	0.014	0	-9999	-10000	0	0
RHEB/GTP	0	0	-9999	-10000	0	0
mol:Amino Acids	0	0	-9999	-10000	0	0
FKBP12/Rapamycin	0	0	-9999	-10000	0	0
PDPK1	0	0	-9999	-10000	0	0
EIF4E	0.013	0	-9999	-10000	0	0
ASK1/PP5C	0.023	0	-9999	-10000	0	0
mTOR/RHEB/GTP/Raptor/GBL/eIF4E	0.019	0	-9999	-10000	0	0
TSC1/TSC2	0	0	-9999	-10000	0	0
tumor necrosis factor receptor activity	0	0	-9999	-10000	0	0
RPS6	0.013	0	-9999	-10000	0	0
PPP5C	0.013	0	-9999	-10000	0	0
EIF4G1	0.013	0	-9999	-10000	0	0
IRS1	0.009	0	-9999	-10000	0	0
INS	0	0	-9999	-10000	0	0
PTEN	0.013	0	-9999	-10000	0	0
PDK2	0	0	-9999	-10000	0	0
EIF4EBP1	0.009	0.039	-9999	-0.38	3	3
PIK3CA	0.014	0	-9999	-10000	0	0
PPP2R5D	0.024	0	-9999	-10000	0	0
peptide biosynthetic process	0.019	0	-9999	-10000	0	0
RHEB	0.014	0	-9999	-10000	0	0
EIF4A1	0.013	0	-9999	-10000	0	0
mol:Rapamycin	0	0	-9999	-10000	0	0
EEF2	0.019	0	-9999	-10000	0	0
eIF4E/4E-BP1	0.016	0.034	-9999	-10000	0	0

×

Signaling events mediated by HDAC Class I

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
NF kappa B/RelA	-0.019	0.085	-9999	-10000	0	0
Ran/GTP/Exportin 1/HDAC1	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	-0.015	0.065	-9999	-10000	0	0
SUMO1	0.013	0	-9999	-10000	0	0
ZFPM1	0.013	0	-9999	-10000	0	0
NPC/RanGAP1/SUMO1/Ubc9	0.024	0	-9999	-10000	0	0
FKBP3	0.013	0	-9999	-10000	0	0
Histones	-0.008	0.037	-9999	-10000	0	0
YY1/LSF	0.021	0.057	-9999	-10000	0	0
SMG5	0.013	0	-9999	-10000	0	0
RAN	0.013	0	-9999	-10000	0	0
I kappa B alpha/HDAC3	-0.015	0.064	-9999	-10000	0	0
I kappa B alpha/HDAC1	-0.01	0.045	-9999	-10000	0	0
SAP18	0.013	0	-9999	-10000	0	0
RELA	0.028	0.063	-9999	-10000	0	0
HDAC1/Smad7	0	0	-9999	-10000	0	0
RANGAP1	0.013	0	-9999	-10000	0	0
HDAC3/TR2	-0.01	0.045	-9999	-10000	0	0
NuRD/MBD3 Complex	0.052	0	-9999	-10000	0	0
NF kappa B1 p50/RelA	0.031	0.057	-9999	-10000	0	0
EntrezGene:23225	0	0	-9999	-10000	0	0
GATA2	0.008	0.066	-9999	-0.8	2	2
GATA1	0.011	0.005	-9999	-10000	0	0
Mad/Max	-0.002	0.027	-9999	-0.47	1	1
NuRD/MBD3 Complex/GATA1/Fog1	0.063	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	0.018	0.058	-9999	-10000	0	0
KAT2B	-0.015	0.13	-9999	-0.64	13	13
mol:GTP	0	0	-9999	-10000	0	0
SIN3/HDAC complex	0.047	0	-9999	-10000	0	0
SIN3 complex	0	0	-9999	-10000	0	0
SMURF1	0.013	0	-9999	-10000	0	0
CHD3	0.013	0	-9999	-10000	0	0
SAP30	0.013	0	-9999	-10000	0	0
EntrezGene:23636	0	0	-9999	-10000	0	0
NCOR1	0.013	0	-9999	-10000	0	0
YY1/HDAC3	-0.017	0.054	-9999	-10000	0	0
YY1/HDAC2	0.021	0.057	-9999	-10000	0	0
YY1/HDAC1	0.021	0.057	-9999	-10000	0	0
NuRD/MBD2 Complex (MeCP1)	0.052	0	-9999	-10000	0	0
PPARG	-0.14	0.17	-9999	-0.56	8	8
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)	-0.01	0.045	-9999	-10000	0	0
MBD3L2	-0.002	0.046	-9999	-0.8	1	1
ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
CREBBP	0.013	0	-9999	-10000	0	0
NuRD/MBD3/MBD3L2 Complex	0.055	0.012	-9999	-10000	0	0
HDAC1	0.013	0	-9999	-10000	0	0
HDAC3	0.018	0.058	-9999	-10000	0	0
HDAC2	0.013	0	-9999	-10000	0	0
YY1	0.019	0.068	-9999	-0.3	13	13
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	0.011	0.038	-9999	-0.64	1	1
STAT3	0.028	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	-0.009	0.044	-9999	-10000	0	0
YY1/SAP30/HDAC1	-0.009	0.044	-9999	-10000	0	0
EP300	0.013	0	-9999	-10000	0	0
STAT3 (dimer non-phopshorylated)	0.028	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.018	0.058	-9999	-10000	0	0
histone deacetylation	0.052	0	-9999	-10000	0	0
STAT3 (dimer non-phopshorylated)/HDAC3	-0.009	0.039	-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	-0.013	0.064	-9999	-0.58	2	2
GATA1/HDAC1	0	0	-9999	-10000	0	0
GATA1/HDAC3	-0.01	0.045	-9999	-10000	0	0
CHD4	0.013	0	-9999	-10000	0	0
TNF-alpha/TNFR1A	-0.028	0.12	-9999	-0.57	15	15
SIN3/HDAC complex/Mad/Max	0.051	0.013	-9999	-10000	0	0
NuRD Complex	0.061	0	-9999	-10000	0	0
positive regulation of chromatin silencing	-0.008	0.036	-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	-0.025	0.17	-9999	-0.76	15	15
negative regulation of cell growth	0.051	0.013	-9999	-10000	0	0
NuRD/MBD2/PRMT5 Complex	0.052	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0	0	-9999	-10000	0	0
NF kappa B/RelA/I kappa B alpha	-0.016	0.069	-9999	-10000	0	0
SIN3/HDAC complex/NCoR1	0.05	0	-9999	-10000	0	0
TFCP2	0.013	0	-9999	-10000	0	0
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 S127. Get High-res Image This plot shows pathway concept perturbations across all samples against a permutation model. The concepts along the x-axis are sorted by lowest to highest mean activity for the real patient samples. Mean inferred activities are plotted along the y-axis as a colored band showing the average level and one standard deviation range. Real samples are shown in red and permuted samples in black.

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
G6PC	0.043	0.012	-9999	-10000	0	0
PLK1	0.12	0.1	-9999	-0.74	1	1
CDKN1B	0.15	0.046	-9999	-10000	0	0
FOXO3	0.12	0.1	-9999	-10000	0	0
KAT2B	-0.001	0.13	-9999	-0.63	13	13
FOXO1/SIRT1	0.009	0.024	-9999	-10000	0	0
CAT	0.11	0.12	-9999	-1.2	1	1
CTNNB1	0.011	0.038	-9999	-0.64	1	1
AKT1	0.03	0.01	-9999	-10000	0	0
FOXO1	0.046	0.009	-9999	-10000	0	0
MAPK10	0.028	0.08	-9999	-0.45	1	1
mol:GTP	0.003	0.001	-9999	-10000	0	0
FOXO4	0.11	0.049	-9999	-10000	0	0
response to oxidative stress	0.018	0.01	-9999	-10000	0	0
FOXO3A/SIRT1	0.003	0.069	-9999	-0.54	1	1
XPO1	0.014	0	-9999	-10000	0	0
EP300	0.016	0.001	-9999	-10000	0	0
BCL2L11	0.044	0.024	-9999	-10000	0	0
FOXO1/SKP2	0.047	0.007	-9999	-10000	0	0
mol:GDP	0.018	0.01	-9999	-10000	0	0
RAN	0.015	0	-9999	-10000	0	0
GADD45A	0.13	0.055	-9999	-0.48	1	1
YWHAQ	0.013	0	-9999	-10000	0	0
FOXO1/14-3-3 family	0.083	0.011	-9999	-10000	0	0
MST1	0.02	0.071	-9999	-0.68	3	3
CSNK1D	0.013	0	-9999	-10000	0	0
CSNK1E	0.013	0	-9999	-10000	0	0
FOXO4/14-3-3 family	0.064	0.019	-9999	-10000	0	0
YWHAB	0.013	0	-9999	-10000	0	0
MAPK8	0.044	0.031	-9999	-10000	0	0
MAPK9	0.046	0.005	-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	0.005	0.017	-9999	-10000	0	0
SOD2	0.16	0.054	-9999	-10000	0	0
RBL2	0.12	0.072	-9999	-10000	0	0
RAL/GDP	0.035	0.011	-9999	-10000	0	0
CHUK	0.027	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	0.045	0.008	-9999	-10000	0	0
CSNK1G1	0.013	0	-9999	-10000	0	0
FASLG	-0.016	0.26	-9999	-0.89	21	21
SKP2	0.013	0	-9999	-10000	0	0
USP7	0.015	0.001	-9999	-10000	0	0
IKBKB	0.027	0.009	-9999	-10000	0	0
CCNB1	0.12	0.094	-9999	-10000	0	0
FOXO1-3a-4/beta catenin	0.006	0.03	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0.046	0.007	-9999	-10000	0	0
CSNK1A1	0.013	0	-9999	-10000	0	0
SGK1	0.025	0.038	-9999	-0.63	1	1
CSNK1G3	0.013	0	-9999	-10000	0	0
Ran/GTP/Exportin 1	0.026	0.002	-9999	-10000	0	0
ZFAND5	0.11	0.044	-9999	-10000	0	0
SFN	0.011	0.038	-9999	-0.64	1	1
CDK2	0.014	0.002	-9999	-10000	0	0
FOXO3A/14-3-3	0.078	0.031	-9999	-10000	0	0
CREBBP	0.014	0.002	-9999	-10000	0	0
FBXO32	0.11	0.14	-9999	-1.3	2	2
BCL6	0.12	0.072	-9999	-10000	0	0
RALB	0.015	0	-9999	-10000	0	0
RALA	0.015	0	-9999	-10000	0	0
YWHAH	0.013	0	-9999	-10000	0	0

×

Atypical NF-kappaB pathway

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

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

Entity	Mean	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
BCL3/RelA	0	0	-9999	-10000	0	0
FBXW11	0.013	0	-9999	-10000	0	0
NF kappa B1 p50/c-Rel	0.028	0	-9999	-10000	0	0
NF kappa B1 p50/RelA/I kappa B alpha	0.044	0.046	-9999	-0.46	1	1
NFKBIA	0.023	0.052	-9999	-0.54	1	1
MAPK14	0.013	0	-9999	-10000	0	0
NF kappa B1 p105/p50	0.028	0	-9999	-10000	0	0
ARRB2	0.019	0	-9999	-10000	0	0
REL	0.013	0	-9999	-10000	0	0
response to oxidative stress	0	0	-9999	-10000	0	0
BCL3/NF kappa B1 p50	0.028	0	-9999	-10000	0	0
response to UV	0	0	-9999	-10000	0	0
NF kappa B1 p105/RelA	0.028	0	-9999	-10000	0	0
PIK3CA	0.013	0	-9999	-10000	0	0
NF kappa B1 p50 dimer	0.022	0	-9999	-10000	0	0
PIK3R1	0.013	0	-9999	-10000	0	0
NFKB1	0.025	0	-9999	-10000	0	0
RELA	0.013	0	-9999	-10000	0	0
positive regulation of anti-apoptosis	0.031	0.047	-9999	-0.43	1	1
NF kappa B1 p50/RelA/I kappa B alpha/beta Arrestin2	0.048	0.045	-9999	-0.45	1	1
SRC	0.013	0	-9999	-10000	0	0
PI3K	0	0	-9999	-10000	0	0
NF kappa B1 p50/RelA	0.031	0.047	-9999	-0.43	1	1
IKBKB	0.013	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.013	0	-9999	-10000	0	0
SYK	0.011	0.038	-9999	-0.64	1	1
I kappa B alpha/PIK3R1	0.029	0.049	-9999	-0.51	1	1
cell death	-0.006	0.034	-9999	-0.43	1	1
NF kappa B1 p105/c-Rel	0.028	0	-9999	-10000	0	0
LCK	-0.014	0.15	-9999	-0.8	10	10
BCL3	0.013	0	-9999	-10000	0	0

×

Sumoylation by RanBP2 regulates transcriptional repression

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
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	0.019	-9999	-9999
mol:GTP	0	-9999	-9999
XPO1	0.031	-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	0.024	-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

×

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	-0.002	0.035	-9999	-0.61	1	1
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	0.028	0	-9999	-10000	0	0
CD4	0.009	0.06	-9999	-0.72	2	2
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	0.03	0	-9999	-10000	0	0
mol:Choline	0	0	-9999	-10000	0	0
mol:GDP	0	0	-9999	-10000	0	0
ARF1	0.014	0	-9999	-10000	0	0
DDEF1	0	0	-9999	-10000	0	0
ARF1/GDP	0	0	-9999	-10000	0	0
AP2M1	0.011	0.047	-9999	-0.8	1	1
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	0.028	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	0.03	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	0.014	0	-9999	-10000	0	0
ARF1/GTP/GGA3	0	0	-9999	-10000	0	0
mol:ATP	0	0	-9999	-10000	0	0
Rac/GDP	0	0	-9999	-10000	0	0
mol:Brefeldin A	0	0	-9999	-10000	0	0
CD4/HIV Nef/AP2/vacuolar proton-transporting V-type ATPase complex/Coatomer protein complex/ARF1/GTP	0.036	0.024	-9999	-10000	0	0
PLD2	0	0	-9999	-10000	0	0
ARF-GAP1/v-SNARE	0.012	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	0.048	-9999	-0.48	3	3

×

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	Std.Dev	Mean.of.Up.Perturbations	Mean.of.Down.Perturbations	Number.of.Down.Perturbations	Number.of.Total.Perturbations
IKK alpha homodimer	0	0	-9999	-10000	0	0
FBXW11	0.013	0	-9999	-10000	0	0
proteasomal ubiquitin-dependent protein catabolic process	0	0	-9999	-10000	0	0
beta TrCP1/SCF ubiquitin ligase complex	0.013	0	-9999	-10000	0	0
CHUK	0.013	0	-9999	-10000	0	0
NF kappa B2 p100/RelB	-0.003	0.036	-9999	-10000	0	0
NFKB1	0.013	0	-9999	-10000	0	0
MAP3K14	0.013	0	-9999	-10000	0	0
NF kappa B1 p50/RelB	-0.004	0.05	-9999	-0.61	2	2
RELB	0.008	0.066	-9999	-0.8	2	2
NFKB2	0.013	0	-9999	-10000	0	0
NF kappa B2 p52/RelB	-0.004	0.043	-9999	-0.54	2	2
regulation of B cell activation	-0.004	0.043	-9999	-0.53	2	2

pid_entity	TCGA.IQ.7632	TCGA.IQ.7631	TCGA.IQ.7630	TCGA.HD.7917
109_MAP3K5	0.06	0.06	0.06	0.06
47_PPARGC1A	0.013	0.013	0.013	0.013
105_BMP4	0.013	0.013	0.013	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	-0.35	-0.35	-0.35	-0.35
30_TGFB1/TGF beta receptor Type II	0.013	0.013	0.019	0.019
84_STAT5B	-0.071	-0.22	-0.031	0.049
84_STAT5A	-0.071	-0.22	-0.031	0.049