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	HydPred: a novel method for the identification of protein hydroxylation sites that reveals new insights into human inherited disease
	Li, Shuyan1; Lu, Jun2; Li, Jiazhong3; Chen, Ximing4; Yao, Xiaojun1; Xie, Lili5
刊名	MOLECULAR BIOSYSTEMS
	2016
卷号	12期号:2页码:490-498
ISSN号	1742-206X
DOI	10.1039/c5mb00681c
通讯作者	Xie, Lili(xill@lzu.edu.cn)
英文摘要	The disruption of protein hydroxylation is highly associated with several serious diseases and consequently the identification of protein hydroxylation sites has attracted significant attention recently. Here, we report the development of an improved method, called HydPred, to identify protein hydroxylation sites (hydroxyproline and hydroxylysine) based on the synthetic minority over-sampling technique (SMOTE), the random forest (RF) algorithm and four blocks of newly composed features that are derived from the protein primary sequence. The HydPred method achieved the best prediction performance reported until now with Matthew's correlation coefficient values of 0.770 and 0.857 for hydroxyproline and hydroxylysine, respectively, according to jack-knife cross-validation. This represents an improvement of 8% for hydroxyproline and 19% for hydroxylysine compared to the best results of available predictors. The prediction performance of HydPred for the external validation of hydroxyproline and hydroxylysine was also improved compared with other published methods. We subsequently applied HydPred to study the association of disruption of hydroxylation sites with human inherited disease. The analyses suggested that the loss of hydroxylation sites is more likely to cause disease instead of the gain of hydroxylation sites and 52 different human inherited diseases were found to be highly associated with the loss of hydroxylation sites. Therefore, HydPred represents a new strategy to discover the molecular basis of pathogenesis associated with abnormal hydroxylation. HydPred is now available online as a user-friendly web server at http://lishuyan.lzu.edu.cn/hydpred/.
收录类别	SCI
WOS关键词	COLLAGEN PROLYL 3-HYDROXYLATION ; ESTROGEN HYDROXYLATION ; PROLIDASE ACTIVITY ; RANDOM FOREST ; CANCER ; PREDICTION ; SEQUENCE ; HYDROXYPROLINE ; HYDROPHOBICITY ; PARAMETERS
WOS研究方向	Biochemistry & Molecular Biology
WOS类目	Biochemistry & Molecular Biology
语种	英语
出版者	ROYAL SOC CHEMISTRY
WOS记录号	WOS:000368858900019
内容类型	期刊论文
URI标识	http://www.corc.org.cn/handle/1471x/2557092
专题	寒区旱区环境与工程研究所
通讯作者	Xie, Lili
作者单位	1.Lanzhou Univ, Coll Chem & Chem Engn, Lanzhou 730000, Peoples R China 2.Lanzhou Univ, Sch Basic Med Sci, Lanzhou 730000, Peoples R China 3.Lanzhou Univ, Sch Pharm, Lanzhou 730000, Peoples R China 4.Chinese Acad Sci, Cold & Arid Regions Environm & Engn Res Inst, Key Lab Desert & Desertificat, Lanzhou 730000, Peoples R China 5.Lanzhou Univ, Hosp 1, Dept Pharm, Lanzhou 730000, Peoples R China
推荐引用方式 GB/T 7714	Li, Shuyan,Lu, Jun,Li, Jiazhong,et al. HydPred: a novel method for the identification of protein hydroxylation sites that reveals new insights into human inherited disease[J]. MOLECULAR BIOSYSTEMS,2016,12(2):490-498.
APA	Li, Shuyan,Lu, Jun,Li, Jiazhong,Chen, Ximing,Yao, Xiaojun,&Xie, Lili.(2016).HydPred: a novel method for the identification of protein hydroxylation sites that reveals new insights into human inherited disease.MOLECULAR BIOSYSTEMS,12(2),490-498.
MLA	Li, Shuyan,et al."HydPred: a novel method for the identification of protein hydroxylation sites that reveals new insights into human inherited disease".MOLECULAR BIOSYSTEMS 12.2(2016):490-498.

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