Mining hidden knowledge for drug safety assessment: topic modeling of LiverTox as a case study

Yu, Ke; Zhang, Jie; Chen, Minjun; Xu, Xiaowei; Suzuki, Ayako; Ilic, Katarina; Tong, Weida

doi:10.1186/1471-2105-15-S17-S6

BMC Bioinformatics

Table 2 Summary of 50 drugs implicated by ALF-Topic without apparent ALF evidence in the LiverTox database.

From: Mining hidden knowledge for drug safety assessment: topic modeling of LiverTox as a case study

Drug name	1^st topic		2^nd topic		3^rd topic
	Topic ID	Prob.	Topic ID	Prob.	Topic ID	Prob.
Atovaquone^†	37	6.2E-01	14	3.8E-01	40	5.9E-05
Buprenorphine^†	22	4.1E-01	37	3.1E-01	31	2.5E-01
Clarithromycin^†	37	5.3E-01	17	2.6E-01	3	1.8E-01
Diflunisal^†	37	3.6E-01	38	2.6E-01	29	2.2E-01
Flecainide^†	37	4.3E-01	18	2.7E-01	30	2.1E-01
Infliximab^†	37	5.4E-01	14	3.6E-01	39	9.6E-02
Methimazole^†	37	6.1E-01	7	3.9E-01	40	4.4E-05
Minocycline^†	37	8.9E-01	35	1.1E-01	40	6.9E-05
Nabumetone^†	38	4.2E-01	36	4.2E-01	37	1.5E-01
Proguanil^†	37	5.8E-01	14	4.2E-01	40	4.0E-05
Salsalate^†	38	6.4E-01	37	1.9E-01	30	1.7E-01
Ticlopidine^†	37	4.5E-01	31	2.9E-01	7	2.5E-01
Topiramate^†	35	4.9E-01	37	3.5E-01	5	1.7E-01
Chlorzoxazone^*	37	6.4E-01	17	2.2E-01	20	1.0E-01
Cocaine^*	29	4.7E-01	37	2.4E-01	23	1.7E-01
Chlorpromazine^*	13	7.0E-01	21	1.9E-01	37	1.1E-01
Greater celandine^*	37	8.2E-01	20	9.8E-02	34	5.9E-02
Hydralazine^*	37	6.7E-01	17	3.0E-01	35	3.4E-02
Jin bu huan^*	37	5.7E-01	27	2.6E-01	14	1.7E-01
Shouwupian^*	37	9.8E-01	27	2.1E-02	40	5.2E-05
Colchicine^‡§	33	4.0E-01	37	2.5E-01	9	1.9E-01
Fenofibrate^‡§	37	8.7E-01	33	1.3E-01	40	2.7E-05
Mebendazole^‡§	5	4.6E-01	2	2.5E-01	37	2.3E-01
Metformin^‡§	37	6.2E-01	10	3.5E-01	32	2.8E-02
Nifedipine^‡§	37	5.9E-01	14	2.2E-01	21	1.7E-01
Verapamil^‡§	37	5.9E-01	21	3.6E-01	9	5.1E-02
Acebutolol^‡	37	5.4E-01	5	4.6E-01	40	3.6E-05
Adefovir^‡	26	5.9E-01	37	3.1E-01	30	9.6E-02
Alfuzosin^‡	21	6.0E-01	37	2.2E-01	30	1.8E-01
Ceftriaxone^‡	37	5.3E-01	33	3.3E-01	7	8.0E-02
Gold salts^‡	37	7.0E-01	39	1.9E-01	4	1.1E-01
Linezolid^‡	6	3.9E-01	36	2.6E-01	37	2.0E-01
Montelukast^‡	31	4.3E-01	37	3.4E-01	5	2.1E-01
Olanzapine^‡	37	5.9E-01	13	1.8E-01	19	1.7E-01
Orphenadrine^‡	29	5.8E-01	37	3.7E-01	11	5.2E-02
Oxacillin^‡	37	5.8E-01	4	3.7E-01	12	4.5E-02
Phenelzine^‡	31	6.2E-01	37	3.6E-01	1	1.9E-02
Risperidone^‡	37	6.4E-01	13	3.2E-01	18	2.9E-02
Sotalol^‡	32	4.7E-01	37	4.3E-01	7	1.0E-01
Thioridazine^‡	13	8.4E-01	37	1.6E-01	40	4.0E-05
Ticarcillin/clavulanate^‡	37	4.5E-01	4	3.2E-01	3	2.3E-01
Trisalicylate^‡	38	5.4E-01	37	4.6E-01	40	4.1E-05
Clofibrate	37	4.0E-01	31	3.4E-01	33	2.6E-01
Methocarbamol	37	3.5E-01	25	3.3E-01	38	2.9E-01
Pentamidine	37	7.7E-01	29	2.3E-01	40	5.7E-05
Reserpine	37	5.3E-01	36	3.2E-01	9	9.3E-02
Aloe Vera	37	6.1E-01	9	2.8E-01	36	1.1E-01
Ba Jiao Lian	25	5.9E-01	37	4.1E-01	40	6.4E-05
Chi R Yun	25	3.2E-01	37	2.7E-01	11	2.4E-01
Shosaikoto/daisaikoto	37	7.6E-01	23	2.4E-01	40	3.8E-05

^†26% (13/50) drugs confirmed by safety concerns about ALF in the FDA-approved drug labels.
^*14% (7/50) drugs confirmed by the literature with justified ALF causality.
^‡44% (22/50) drugs confirmed by ALF case reports in the FAERS.
^§These 6 drugs were predicted as ALF positive drugs by the in vitro experiment.
Topic-37 is the ALF-Topic.
Topic ID: serial number of topics in topic model.
Prob.: conditional probability of each topic to a drug.
Topic model ranks topics in accordance to their probability to each drug.

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ISSN: 1471-2105

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