廣州市黃埔區(qū)學(xué)大道攬?jiān)侣窂V州企業(yè)孵化器B座402
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1.3.2 miRNA與mRNA結(jié)合預(yù)測(cè)
miRNA是非編碼調(diào)控小分子，通過(guò)抑制基因表達(dá)發(fā)揮作用，前體pri-miRNA、pre-miRNA通過(guò)核內(nèi)的drosa酶作用，由核孔復(fù)合體進(jìn)入至胞漿中，在通過(guò)Dicer酶的剪切，形成成熟的miRNA,AGO2可介導(dǎo)miRNA結(jié)合至mRNA的3’UTR，進(jìn)而對(duì)基因的表達(dá)進(jìn)行抑制，可在mRNA、蛋白水平發(fā)生降解作用
我們對(duì)數(shù)據(jù)的整理，通過(guò)數(shù)據(jù)庫(kù)查詢分類(lèi)、數(shù)據(jù)庫(kù)功能及用途、示例結(jié)合分析、數(shù)據(jù)庫(kù)優(yōu)化等這四大項(xiàng)，進(jìn)行闡述和演示數(shù)據(jù)庫(kù)的查詢和使用，希望對(duì)您的實(shí)驗(yàn)項(xiàng)目有所幫助
數(shù)據(jù)庫(kù)查詢分類(lèi)
① microRNA.org：http://www.microrna.org/microrna/home.do
② TargetScan：http://www.targetscan.org/vert_70/
③ starbase: http://starbase.sysu.edu.cn/
④ Tarbase: http://www.tarbase.com/
⑤ deepBase： http://deepbase.sysu.edu.cn/
⑥ miRanda： http://www.microrna.org/microrna/home.do
⑦ RNAhybrid：https://bibiserv.cebitec.uni-bielefeld.de/
⑧ CoGeMiR：http://cogemir.tigem.it/
數(shù)據(jù)庫(kù)功能及用途（常用數(shù)據(jù)庫(kù)）
1. microRNA.org：
Predicted microRNA targets & target downregulation scores. Experimentally observed expression patterns
數(shù)據(jù)庫(kù)功能：
1. mirSVR predicted target site scoring method: Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites
2. microRNA target predictions: The microRNA.org resource: targets and expression.
3. miRanda application: Human MicroRNA targets.
4. miRanda algorithm: MicroRNA targets in Drosophila.
2. TargetScan：
Search for predicted microRNA targets in mammals
數(shù)據(jù)庫(kù)功能：
Search for predicted microRNA targets in mammals
3. starbase：
CLIP-Seq, Pan-Cancer. Portal, Visualize, Analyze, Discover.
數(shù)據(jù)庫(kù)功能：
1. starBase is designed for decoding Pan-Cancer and Interaction Networks of lncRNAs, miRNAs, competing endogenous RNAs(ceRNAs), RNA-binding proteins (RBPs) and mRNAs from large-scale CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) data and tumor samples (14 cancer types, >6000 samples).
2. starBase is also developed for deciphering Protein-RNA and miRNA-target interactions, such as protein-lncRNA, protein-sncRNA, protein-mRNA, protein-pseudogene, miRNA-lncRNA, miRNA-mRNA, miRNA-circRNA, miRNA-pseudogene, miRNA-sncRNA interactions and ceRNA networks from 108 CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) datasets.
3. starBase provides miRFunction and ceRNAFunction web tools to predict the function of ncRNAs (miRNAs, lncRNAs, pseduogenes) and protein-coding genes from the miRNA-mediated (ceRNA) regulatory networks
示例結(jié)合分析：
microRNA.org:
預(yù)測(cè)已知mRNA結(jié)合的miRNA:以H19為例
1. 打開(kāi)主頁(yè)面
2. 點(diǎn)擊“target mRNA”，對(duì)話框輸入h19，選擇種屬
3. 點(diǎn)擊“GO”，即可獲取得到預(yù)測(cè)結(jié)合的miRNA
已知miRNA,查詢?cè)搈iRNA調(diào)控的mRNA:以mir-9為例
1. 打開(kāi)主頁(yè)面
2. 點(diǎn)擊“miRNA”，對(duì)話框輸入miR-9，選擇種屬
3. 點(diǎn)擊“go”，即可獲取miR-9調(diào)控的mRN
數(shù)據(jù)庫(kù)優(yōu)化：
microRNA.org是一款預(yù)測(cè)可以預(yù)測(cè)miRNA的靶標(biāo)mRNA,以及引起靶標(biāo)基因下調(diào)的得分值，以及miRNA的表達(dá)情況，也可以預(yù)測(cè)mRNA結(jié)合的miRNA，無(wú)法預(yù)測(cè)得到miRNA的調(diào)控網(wǎng)絡(luò)
2. starBase：以mir-9為例
①打開(kāi)主頁(yè)面
②點(diǎn)擊“miRNA-mRNA”，點(diǎn)擊（兩種查詢：miRNA-mRNA intersections、miRNA-mRNA interactions）
③這里我們演示miRNA-mRNA interactions的示例
數(shù)據(jù)庫(kù)優(yōu)化：
Starbase可查詢miRNA、LncRNA、mRNA相互調(diào)控和結(jié)合的預(yù)測(cè)，存儲(chǔ)了大量的互作網(wǎng)絡(luò)結(jié)合的miRNA,ceRNA的競(jìng)爭(zhēng)結(jié)合，RNA蛋白結(jié)合等數(shù)據(jù)