本文選題：功能基因組學(xué) + 生物信息學(xué)��； 參考：《山東農(nóng)業(yè)大學(xué)》2017年碩士論文

【摘要】：功能基因組學(xué)利用結(jié)構(gòu)基因組學(xué)的信息,系統(tǒng)的研究生物體內(nèi)多個(gè)基因和蛋白質(zhì),闡述DNA序列的功能,它代表了基因組分析的新階段。轉(zhuǎn)錄組的研究可以揭示生物體的基因表達(dá)、研究結(jié)構(gòu)變異及發(fā)現(xiàn)新基因等,轉(zhuǎn)錄組測(cè)序技術(shù)(RNA-seq)利用下一代測(cè)序技術(shù),為轉(zhuǎn)錄組的研究提供了一種新的研究手段。數(shù)量性狀與其他生物性狀一樣,受染色體上基因的控制,從基因水平上研究畜禽的數(shù)量性狀已經(jīng)成為動(dòng)物研究領(lǐng)域的熱點(diǎn)。單核苷酸多態(tài)性(SNP)是基因組中發(fā)生頻率最高的變異種類,研究SNP對(duì)探究基因組結(jié)構(gòu),基因進(jìn)化歷史及疾病發(fā)生根源具有很重要的指導(dǎo)作用。功能基因組學(xué)、控制數(shù)量性狀的QTL定位分析以及SNP分析,在闡述基因序列的功能方面,提高畜禽產(chǎn)品經(jīng)濟(jì)價(jià)值,探索與生物進(jìn)化及疾病相關(guān)的基因方面具有重大的意義。在他們不斷發(fā)展前提下,產(chǎn)生大量生物學(xué)數(shù)據(jù),需要進(jìn)行采集、歸類及分析,目前為止,沒有一款工具將這幾類數(shù)據(jù)有效的整合在一起。在本研究中,我們采用開發(fā)R包的方式,將RNA-seq數(shù)據(jù)、QTL數(shù)據(jù)、SNP數(shù)據(jù)快速的整合起來,實(shí)現(xiàn)相互查詢的功能,以及輔助功能。本研究的AnimalGene2QTL包運(yùn)行在RStudio或R中,可以查看Vignette文檔和示例文檔。通過測(cè)試查詢10000行數(shù)據(jù)量的用時(shí),結(jié)果顯示用時(shí)為47.90秒,結(jié)果說明本研究的R包操作非常簡(jiǎn)便、快速。在結(jié)果準(zhǔn)確上,我們對(duì)本研究的R包與ensembl、Animalgenome網(wǎng)站兩種查詢方式進(jìn)行比對(duì),分別查詢100個(gè)ensembl基因?qū)?yīng)的QTL,通過統(tǒng)計(jì)查看,結(jié)果顯示查詢的QTL沒有任何差別,R包與網(wǎng)站的查詢結(jié)果完全一樣,結(jié)果顯示本研究的R包查詢結(jié)果非常準(zhǔn)確,具有很高的有效性。在應(yīng)用方面,本研究中,我們用AnimalGene2QTL包分別對(duì)家禽的腸炎沙門氏菌感染相關(guān)基因和空腸彎曲桿菌感染相關(guān)基因進(jìn)行QTL查詢,腸炎沙門氏菌感染相關(guān)的數(shù)據(jù)為10000個(gè)高質(zhì)量靶基因,通過對(duì)查詢得到的35942個(gè)QTL統(tǒng)計(jì)篩選直接相關(guān)性狀,再對(duì)直接相關(guān)性狀篩選,確定了 369個(gè)與試驗(yàn)數(shù)據(jù)研究相關(guān)的QTL,通過統(tǒng)計(jì)369個(gè)QTL對(duì)應(yīng)的基因,最終我們確定了與腸炎沙門氏菌感染直接相關(guān)的基因359個(gè)。空腸彎曲桿菌感染的數(shù)據(jù)為101個(gè)ensembl基因,通過對(duì)查詢得到的1437個(gè)QTL進(jìn)行統(tǒng)計(jì)篩選直接相關(guān)性狀,在對(duì)直接相關(guān)性狀篩選,最終確定了直接相關(guān)的基因39個(gè)。我們可以結(jié)合原基因數(shù)據(jù)對(duì)這些基因進(jìn)行GO、pathway預(yù)測(cè)功能分析,不僅可以在結(jié)果上更加精確,同時(shí)可以增加對(duì)結(jié)果的可靠性。
[Abstract]:Functional genomics makes use of the information of structural genomics to systematically study many genes and proteins in organisms and explain the function of DNA sequence which represents a new stage of genome analysis. Transcriptome research can reveal gene expression, study structural variation and find new genes, etc. RNA-seq) provides a new research method for transcriptome research using next generation sequencing technology. Quantitative traits, like other biological traits, are controlled by genes on chromosomes, so the study of quantitative traits of livestock and poultry at the gene level has become a hot spot in animal research field. Single nucleotide polymorphisms (SNPs) are the most frequent mutations in genomes. The study of SNP plays an important role in exploring the genome structure, gene evolution history and the origin of disease. Functional genomics, QTL mapping and SNP analysis for quantitative traits are of great significance in explaining the function of gene sequences, improving the economic value of livestock and poultry products, and exploring genes related to biological evolution and disease. Under the premise of their continuous development, a large number of biological data need to be collected, classified and analyzed. So far, there is no tool to effectively integrate these kinds of data together. In this study, we use R package to integrate RNA-seq data quickly, and realize the function of mutual query and auxiliary function. The AnimalGene2QTL package in this study runs in RStudio or R, and you can view Vignette documents and sample documents. The test results show that the time of 10000 rows of data is 47.90 seconds. The results show that the R packet operation is very simple and fast. As to the accuracy of the results, we compared the R package of this study with the two query methods of the Animalgenome website, and queried the QTLs corresponding to 100 ensembl genes respectively, and checked the QTLs by statistical analysis. The results show that there is no difference between the QTL of the query and the query results of the website. The results show that the R packet query results of this study are very accurate and highly effective. In the aspect of application, in this study, we used AnimalGene2QTL bag to inquire the genes related to Salmonella enteritidis infection in poultry and Campylobacter jejuni infection genes respectively. The data of salmonella enteritidis infection was 10 000 high quality target genes. Three hundred and thirty-nine hundred and ninety-two QTLs related to the experimental data were identified by the 35942 QTL statistical screening and then the direct correlation traits were screened, and the corresponding genes of 369 QTL were counted. Finally, we identified 359 genes directly associated with Salmonella enteritis infection. The data of Campylobacter jejuni infection was 101 ensembl genes. Through the statistical screening of 1 437 QTL obtained from the query, 39 directly related genes were identified in the screening of the direct correlation traits of Campylobacter jejuni (Campylobacter jejuni). We can analyze the prediction function of these genes by combining proto gene data, which can not only improve the accuracy of the results, but also increase the reliability of the results.
【學(xué)位授予單位】：山東農(nóng)業(yè)大學(xué)
【學(xué)位級(jí)別】：碩士
【學(xué)位授予年份】：2017
【分類號(hào)】：Q811.4;S852.61

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本文編號(hào)：1961084