基于计算机文本挖掘的白内障氧化应激相关基因功能富集及药物治疗分析

Text mining-based in silico gene functional enrichment and drug discovery analysis in oxidative stress related cataract

目的利用计算机工具和已知的数据库进行挖掘和分析进而确定与白内障和抗氧化应激相关的基因集及信号通路,并进行白内障可能的有效治疗药物的预测和探索。方法利用文本挖掘工具pubmed2ensembl对白内障和抗氧化应激均相关的基因进行初步筛选,得到的基因集利用GeneC odis工具进行基因功能的富集分析和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes,KEGG)通路分析,富集的结果则应用STRING工具进行进一步蛋白质-蛋白质相互作用分析,选取相互作用紧密的基因,最后使用DGIdb工具得到基因-药物相互作用的结果,然后对药物进行筛选,确定可能有效的白内障治疗药物。结果通过文本挖掘得到103个与白内障和抗氧化应激均相关的基因集,通过对这些基因的生物学过程的功能富集分析,筛选出22个基因,KEGG工具的进一步筛选确定了11个基因,通过蛋白质-蛋白质相互作用分析得到9个紧密联系的基因,与之对应的基因-药物相互作用分析筛选出了31种药物。结论利用文本挖掘和基因功能富集等生物信息学工具可以进一步探索白内障的发病机制,并且能够很方便地预测可能有效的治疗药物,为白内障的临床治疗提供了新的线索。

Objective To determine genes and signal pathways associated with cataract and anti-oxidative stress using computational tools and publicly available data and to explore the potentially effective drugs for cataract.M ethods Text mining tools pubmed2 ensembl was used for screening cataract and anti-oxidant stress related genes in preliminary screening,the intersection of the two gene sets was selected for gene enrichment and KEGG( Kyoto Encyclopedia of Genes and Genomes) pathway analysis using GeneCodis.Protein interaction network analysis was performed by STRING to identify genes that were closely related to each other,then DGIdb was used to checked the druggene interaction database to find the potentially drugs for cataract.Results Through text mining,a set of genes contained 103 genes which was associated with cataract and anti-oxidative stress was identified.Gene enrichment analysis yielded 22 genes and further screening of KEGG identified 11 genes.Nine closely linked genes were got by protein interaction analysis.At last,a total of 31 drugs were screened by gene-drug interaction analysis.Conclusion The use of bioinformatics tools such as text mining and enrichment of gene function can be further used to explore the pathogeneses of cataract and can facilitate the prediction of the effective drug treatment.These all can provide new clues for the clinical treatment of cataract.