PBHMDA: Path-Based Human Microbe-Disease Association Prediction

doi:10.3389/fmicb.2017.00233

CSpace > 应用数学研究所

	PBHMDA: Path-Based Human Microbe-Disease Association Prediction
	Huang, Zhi-An 1; Chen, Xing 2; Zhu, Zexuan 1; Liu, Hongsheng 3,4; Yan, Gui-Ying5 ; You, Zhu-Hong 6; Wen, Zhenkun 1
	2017-02-22
发表期刊	FRONTIERS IN MICROBIOLOGY
ISSN	1664-302X
卷号	8 页码:10
摘要	With the advance of sequencing technology and microbiology, the microorganismshave been found to be closely related to various important human diseases. The increasing identification of human microbe-disease associations offers important in sights into the underlying disease mechanism understanding from the perspective of humanmicrobes, which are greatly helpful for investigating pathogenesis, promoting early diagnosis and improving precision medicine. However, the current knowledge in this domain is still limited and far from complete. Here, we present the computational modelof Path-Based Human Microbe-Disease Association prediction (PBHMDA) based on the integration of known microbe-disease associations and the Gaussian interactionprofile kernel similarity for microbes and diseases. A special depth-first search algorithm was implemented to traverse all possible paths between microbes and diseases for inferring the most possible disease-related microbes. As a result, PBHMDA obtained a reliable prediction performance with AUCs (The area under ROC curve) of 0.9169 and 0.8767 in the frameworks of both global and local leave-one-out cross validations,respectively. Based on 5-fold cross validation, average AUCs of 0.9082 +/- 0.0061 further demonstrated the efficiency of the proposed model. For the case studies of liver cirrhosis, type 1 diabetes, and asthma, 9, 7, and 9 out of predicted microbes in the top 10 have been confirmed by previously published experimental literatures,respectively. We have publicly released the prioritized microbe-disease associations,which may help to select the most potential pairs for further guiding the experimental confirmation. In conclusion, PBHMDA may have potential to boost the discovery of novelmicrobe-disease associations and aid future research efforts toward microbe involvement in human disease mechanism. The code and data of PBHMDA is freely available at http://www.escience.cn/system/file?fileId=85214.
关键词	microbes diseases path-based measure computational prediction model association network
DOI	10.3389/fmicb.2017.00233
语种	英语
资助项目	National Natural Science Foundation of China[11301517] ; National Natural Science Foundation of China[11631014] ; National Natural Science Foundation of China[61471246] ; National Natural Science Foundation of China[31570160] ; National Natural Science Foundation of China[11371355] ; National Natural Science Foundation of China[61572506] ; National Natural Science Foundation of China[61572328] ; Guangdong Foundation of Outstanding Young Teachers in Higher Education Institutions[Yq2013141] ; Guangdong Special Support Program of Top-notch Young Professionals[2014TQ01X273] ; Innovation Team Project from the Education Department of Liaoning Province[LT2015011] ; Pioneer Hundred Talents Program of Chinese Academy of Sciences ; China-UK Visual Information Processing Lab
WOS研究方向	Microbiology
WOS类目	Microbiology
WOS记录号	WOS:000394543000001
出版者	FRONTIERS MEDIA SA
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/24809
专题	应用数学研究所
通讯作者	Chen, Xing; Zhu, Zexuan
作者单位	1.Shenzhen Univ, Coll Comp Sci & Software Engn, Shenzhen, Peoples R China 2.China Univ Min & Technol, Sch Informat & Control Engn, Xuzhou, Peoples R China 3.Liaoning Univ, Sch Life Sci, Shenyang, Peoples R China 4.Res Ctr Comp Simulating & Informat Proc Biomacrom, Shenyang, Peoples R China 5.Chinese Acad Sci, Acad Math & Syst Sci, Beijing, Peoples R China 6.Chinese Acad Sci, Xinjiang Tech Inst Phys & Chem, Urumqi, Peoples R China
推荐引用方式 GB/T 7714	Huang, Zhi-An,Chen, Xing,Zhu, Zexuan,et al. PBHMDA: Path-Based Human Microbe-Disease Association Prediction[J]. FRONTIERS IN MICROBIOLOGY,2017,8:10.
APA	Huang, Zhi-An.,Chen, Xing.,Zhu, Zexuan.,Liu, Hongsheng.,Yan, Gui-Ying.,...&Wen, Zhenkun.(2017).PBHMDA: Path-Based Human Microbe-Disease Association Prediction.FRONTIERS IN MICROBIOLOGY,8,10.
MLA	Huang, Zhi-An,et al."PBHMDA: Path-Based Human Microbe-Disease Association Prediction".FRONTIERS IN MICROBIOLOGY 8(2017):10.