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The Classification Prediction of MADS-box Genes on Angiosperms Using SVM and the Construction of Related Websites
Oncidium Gower Ramsey
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|摘要:||在花器發育的過程中，MADS-box基因是很重要的轉錄調控因子，而MADS-box基因的分類主要是依據模式植物-阿拉伯芥的ABCDE模型為基礎來相互對應與比較。在type II MADS-box基因囊括的MIKC class，有調控花器形成的重要功能。花器的組成與調控，由外至內:萼片，被class A與E調控；花瓣，被class A、B與E調控；雄蕊，被class B、C與E調控；心皮，被class C以及E的基因調控；class D的基因則與胚珠的發育有關。ABCDE類型中，特定類型的基因組合會與花不同組織的發育有關，如果能進一步分析特定MADS-box基因屬於哪種類型，或許對其生化功能的判斷有所幫助。有別於比較序列相似程度的傳統分類方法，本研究把已知分群的MADS-box基因序列當成input，取用BLAST後的e-value做為learning set，利用SVM的學習機制來建構一個分類的模型，最後利用經實驗證實而得知MADS-box基因分群的文心蘭序列來驗證分類模型，預測結果相當一致。iMADS是一個整合性分析工具的網站，除了提供MADS-box基因的分類預測結果，也呈現其他經由實驗驗證的相關資訊供研究者參考，如:蛋白質的保留性區域與在植物中可能的表現部位，便於相關研究者快速獲得相關資訊，進行更深入的研究。|
MADS-box genes are important transcriptional factors during floral organ development. The classical classification model of MADS-box genes is constructed by Arabidopsis thaliana, whose floral tissues such as sepal is controlled by class A and E; petal is controlled by class A, B and E; stamen is controlled by class B, C and E; and carpel is controlled by class C and E. It is showed that specific classes of MADS-box genes feature in specific functions. It is showed that specific classes of MADS-box genes feature in specific functions. The traditional classification estimation of MADS-box genes relies on phylogenetic analysis or multiple sequences alignment which is needed to waste time on collecting reference sequences. Data collection is the key point to affect the evaluation of target genes. This study proposed a new prediction method of MADS-box genes classification based on similarity measure evaluated by general five programs of BLAST and constructed the classification model using Support Vector Machine which depended on 210 MADS-box genes of different plant species and validated classification model by 10 MADS-box genes of Oncidium Gower Ramsey. Furthermore, we constructed a web-based tool, iMADS, which integrates several web tools in order to shorten the wasted time and provide related information about putative class of MADS-box gene, expressed tissues in plants, conserved domain search, coiled-coil prediction and evolutionary analysis. Those contents of latter three are assayed from web tools including NCBI Conserved Domain Search, COILS and Phylodendron separately. iMADS is an information-integrated analytic tool for MADS-box genes. It may reduce costing of time and money of researchers, making a quickly-output prediction, and presenting reliable and systematic results to users. This web-based tool is publicly available at http://predictor.nchu.edu.tw/iMADS.
|Appears in Collections:||基因體暨生物資訊學研究所|
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