Comparison of pathway and gene-level models for cancer prognosis prediction

BMC Bioinformatics

Table 1 Predictive performance results for all 33 analyzed TCGA cohorts. For each cohort, the table includes the sample size (n), death rate and average Cox concordance index values for both the gene-level (GLv CI) and pathway-level (PLv CI) models

	Full name	n	Death rate	GLv CI	PLv CI
ACC	Adrenocortical Carcinoma	79	0.37	0.77	0.77
UVM	Ocular Melanoma	80	0.29	0.74	0.70
MESO	Mesothelioma	87	0.84	0.70	0.71
KICH	Kidney Chromophobe	91	0.13	0.53	0.59
READ	Rectal Cancer	105	0.17	0.48	0.53
THYM	Thymoma	122	0.07	0.57	0.51
TGCT	Testicular Cancer	156	0.03	0.48	0.57
GBM	Glioblastoma	172	0.78	0.52	0.54
LAML	Acute Myeloid Leukemia	173	0.60	0.61	0.55
PAAD	Pancreatic Cancer	183	0.55	0.59	0.60
PCPG	Pheochromocytoma and Paraganglioma	187	0.04	0.52	0.51
ESCA	Esophageal Cancer	196	0.41	0.49	0.50
UCEC	Endometroid Cancer	201	0.16	0.50	0.48
SARC	Sarcoma	265	0.38	0.66	0.62
CESC	Cervical Cancer	308	0.23	0.65	0.67
OV	Ovarian Cancer	308	0.57	0.50	0.50
KIRP	Kidney Papillary Cell Carcinoma	323	0.17	0.79	0.77
COAD	Colon Cancer	329	0.22	0.54	0.49
LIHC	Liver Cancer	423	0.39	0.65	0.65
BLCA	Bladder Carcinoma	426	0.45	0.60	0.60
COADREAD	Colon and Rectal Cancer	434	0.21	0.53	0.55
STAD	Stomach Cancer	450	0.33	0.53	0.58
SKCM	Skin Cutaneous Melanoma	474	0.47	0.51	0.49
LGG	Lower Grade Glioma	530	0.25	0.82	0.77
PRAD	Prostate Cancer	550	0.02	0.47	0.47
LUSC	Lung Squamous Cell Carcinoma	553	0.45	0.52	0.52
HNSC	Head and Neck Cancer	566	0.45	0.57	0.59
THCA	Thyroid Cancer	572	0.03	0.51	0.56
LUAD	Lung Adenocarcinoma	576	0.34	0.61	0.63
KIRC	Kidney Clear Cell Carcinoma	606	0.36	0.68	0.66
GBMLGG	Lower grade glioma and glioblastoma	702	0.54	0.85	0.83
LUNG	Lung Cancer	1129	0.40	0.57	0.57
BRCA	Breast Cancer	1218	0.16	0.63	0.61

ISSN: 1471-2105