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1.3.2 miRNA與mRNA結(jié)合預(yù)測

miRNA是非編碼調(diào)控小分子，通過抑制基因表達(dá)發(fā)揮作用，前體pri-miRNA、pre-miRNA通過核內(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

我們對數(shù)據(jù)的整理，通過數(shù)據(jù)庫查詢分類、數(shù)據(jù)庫功能及用途、示例結(jié)合分析、數(shù)據(jù)庫優(yōu)化等這四大項，進(jìn)行闡述和演示數(shù)據(jù)庫的查詢和使用，希望對您的實驗項目有所幫助

數(shù)據(jù)庫查詢分類

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)庫功能及用途（常用數(shù)據(jù)庫）

1. microRNA.org：

Predicted microRNA targets & target downregulation scores. Experimentally observed expression patterns

數(shù)據(jù)庫功能：

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)庫功能：

Search for predicted microRNA targets in mammals 

3. starbase：

CLIP-Seq, Pan-Cancer. Portal, Visualize, Analyze, Discover.

數(shù)據(jù)庫功能：

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)測已知mRNA結(jié)合的miRNA:以H19為例

1. 打開主頁面

2. 點擊“target mRNA”，對話框輸入h19，選擇種屬

3. 點擊“GO”，即可獲取得到預(yù)測結(jié)合的miRNA

已知miRNA,查詢該miRNA調(diào)控的mRNA:以mir-9為例

1. 打開主頁面

2. 點擊“miRNA”，對話框輸入miR-9，選擇種屬

3. 點擊“go”，即可獲取miR-9調(diào)控的mRN

數(shù)據(jù)庫優(yōu)化：

microRNA.org是一款預(yù)測可以預(yù)測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mRNA結(jié)合的miRNA，無法預(yù)測得到miRNA的調(diào)控網(wǎng)絡(luò)

2. starBase：以mir-9為例

①打開主頁面

②點擊“miRNA-mRNA”，點擊（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)庫優(yōu)化：

Starbase可查詢miRNA、LncRNA、mRNA相互調(diào)控和結(jié)合的預(yù)測，存儲了大量的互作網(wǎng)絡(luò)結(jié)合的miRNA,ceRNA的競爭結(jié)合，RNA蛋白結(jié)合等數(shù)據(jù)

• 1 . 生物信息學(xué)概述
• 2 . 生物信息學(xué)相關(guān)數(shù)據(jù)庫
• 3 . 轉(zhuǎn)錄因子相關(guān)數(shù)據(jù)庫
• 4 . miRNA與mRNA結(jié)合預(yù)測
• 5 . LncRNA與miRNA結(jié)合預(yù)測
• 6 . LncRNA與蛋白RNP結(jié)合預(yù)測