猪基因表达调控数据库(GereDB)的构建

Construction of pig gene expression and regulation database(GereDB)

【目的】构建猪基因表达调控数据库(GereDB),为从基因水平解释猪的生长发育规律、遗传育种和疾病防控等提供科学依据。【方法】从NCBI下载小鼠和猪的RNA序列原始数据进行序列比对,根据序列同源性将小鼠的基因表达调控信息转移给猪,并建立猪基因表达调控信息网络,整理加工后根据区域结构,以Linux为操作系统、Apache为Web服务器、MySQL为数据库、Python为服务器端脚本解释器构建猪GereDB数据库。【结果】从NCBI下载的Fast数据共包含291182条猪核苷酸序列,通过序列比对和手工整理,注释筛选出67000多条猪核苷酸序列;将小鼠的基因表达调控信息转移给猪,获得的猪基因表达调控关系链接有67027条,构建了猪GereDB数据库(http://www.thua45.cn/geredb-wp/),并开发GEREA生物信息学分析工具以发现猪基因表达调控因子。在猪GereDB数据库中有116个调控因子可调控100多个基因,说明其在猪转录组调控中发挥重要作用。GEREA生物信息学分析工具在已发表的猪乳腺组织数据集上进行测试,结果显示,与母猪分娩前14 d相比,分娩后1 d母猪乳腺中26个调控因子的靶基因显著差异表达(FDR<0.05),其中FGF2调控因子在母猪泌乳方面发挥重要作用。【结论】猪GereDB数据库能提供猪基因表达和调控间关系的信息,且能使用GEREA生物信息学分析工具发掘猪基因表达调控数据,有助于揭示调控因子对高通量测序差异表达基因的调控机制,为从基因水平探究猪的生长发育及疾病防控提供数据信息。

【Objective】To construct the pig gene expression and regulation database(GereDB)for providing a scientific basis to explain the growth and development,genetic breeding and disease treatment of pigs at the gene level.【Method】Original RNA sequence data of mouse and pig were downloaded for sequence alignment from NCBI and transferred gene expression and regulation information from mouse to pig according to the sequence homology,analyzed pig gene expression and regulation data to establish the pig gene expression and regulation information network.According to the regional structure after processing,GereDB database of pig was established with Linux operating system,ApacheWeb server,MySQL database management system,Python for server-side script interpreter.【Result】A total of 291182 pig nucleotide sequences were contained in Fast data downloaded form NCBI.The mouse gene expression regulation information was transferred to pig,67027 relationship links in regulating gene expression of pig were obtained,and the pig GereDB database(http://www.thua45.cn/geredb-wp/)was built,GEREA bioinformatics analysis tools were developed to find gene expression regulators of pig.There were 116 regulators could regulate more than 100 genes in pig GereDB database,indicating that they played an important role in the transcriptome regulation of pig.The GEREA bioinformatics analysis tool was tested on a published data set of pig breast tissue and the result showed that 26 target genes of regulatory factors appeared significantly differential expression(FDR<0.05)on the sow 1 d after delivery compared with the 14 d before delivery.Moreover,FGF2 was as an vital regulatory factor for the milking of sows.【Conclusion】Pig GereDB database can provide relationships between pig gene expression and regulation,and GEREA bioinformatics tool can explore pig gene expression regulation data.The database is useful for exploring how differentially expressed genes detected by high throughput experiments are regulated by certain regulator genes and can provide valid data to explore the growth and development,disease control and prevention at gene level.