Table 2. Benchmarking results for 19 sets of known disease-associated genes using top seven significant associations as the threshold.

Disease	Sensitivity	Precision	F-score
Atherosclerosis (athe)	0.786±0.04	0.848±0.06	0.814±0.03
Autism (auti)	0.824±0.02	0.839±0.07	0.830±0.03
Cervical carcinoma (cerv)	0.779±0.03	0.834±0.03	0.805±0.03
Cirrhosis (cirr)	0.850±0.02	0.848±0.05	0.848±0.02
Endometrial carcinoma (enca)	0.770±0.02	0.903±0.06	0.829±0.02
Endometriosis (endo)	0.621±0.07	0.897±0.07	0.729±0.03
Epilepsy (epil)	0.744±0.02	0.777±0.08	0.759±0.03
Grave's disease (grav)	0.803±0.01	0.934±0.04	0.863±0.02
Hypercholesterolaemia (hycl)	0.875±0.00	0.893±0.03	0.884±0.02
Inflammatory bowel disease (inbd)	0.897±0.04	0.838±0.08	0.863±0.04
Ischaemic stroke (isch)	0.909±0.04	0.845±0.08	0.874±0.04
Lymphoma (lymp)	0.636±0.10	0.788±0.06	0.697±0.05
Migraine (migr)	0.712±0.03	0.812±0.10	0.755±0.03
Myocardial ischemia (myis)	0.803±0.02	0.889±0.06	0.842±0.03
Neural tube defects (neur)	0.682±0.03	0.817±0.07	0.742±0.03
Osteoarthritis (oste)	0.822±0.02	0.870±0.05	0.844±0.02
Pancreatitis (panc)	0.923±0.05	0.874±0.07	0.895±0.03
Systemic scleroderma (sysc)	0.826±0.03	0.818±0.06	0.821±0.03
Ulcerative colitis (ulco)	0.856±0.02	0.831±0.08	0.841±0.04