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miRNA與mRNA、miRNA與mRNA、LncRNA與蛋白RNP相關(guān)結(jié)合預(yù)測分析

2021.09.12

本篇我們將介紹miRNA與mRNA結(jié)合預(yù)測、LncRNA與miRNA結(jié)合預(yù)測、LncRNA與蛋白RNP結(jié)合預(yù)測相關(guān)內(nèi)容

一、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(xiàng)，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(shí)驗(yàn)項(xiàng)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 & targetdownregulation scores. Experimentally observed expression patterns

數(shù)據(jù)庫功能：

1. mirSVR predicted target site scoringmethod: Comprehensive modeling of microRNA targets predicts functionalnon-conserved and non-canonical sites

2. microRNA target predictions: ThemicroRNA.org resource: targets and expression.

3. miRanda application: Human MicroRNAtargets.

4. miRanda algorithm: MicroRNA targets inDrosophila.

2. TargetScan：

Search for predicted microRNA targets inmammals

數(shù)據(jù)庫功能：

Search for predicted microRNA targets inmammals

3. starbase：

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

數(shù)據(jù)庫功能：

1. starBase is designed for decodingPan-Cancer and Interaction Networks of lncRNAs, miRNAs, competing endogenousRNAs(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 fordeciphering 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 networksfrom 108 CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) datasets.

3. starBase provides miRFunction andceRNAFunction 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(diǎn)擊“targetmRNA”，對話框輸入h19，選擇種屬

3. 點(diǎn)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(diǎn)擊“miRNA”，對話框輸入miR-9，選擇種屬

3. 點(diǎn)擊“go”，即可獲取miR-9調(diào)控的mRNA

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(diǎn)擊“miRNA-mRNA”，點(diǎn)擊（兩種查詢：miRNA-mRNA intersections、miRNA-mRNAinteractions）

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)

二、LncRNA與miRNA結(jié)合預(yù)測

長鏈非編碼RNA（Long-noncodingRNA，lncRNA）是一類轉(zhuǎn)錄本長度大于200bp的非編碼RNA，可作為人類基因組中一類重要的調(diào)控分子通過多種方式發(fā)揮其生物學(xué)功能．近年來的研究表明，lncRNA也可以作為一種競爭性內(nèi)源性RNA（competing endogenous RNA），與miRNA互作結(jié)合，形成ceRNA的競爭機(jī)制

數(shù)據(jù)庫查詢分類

①lncRNABase：http://starbase.sysu.edu.cn/mirLncRNA.php

② starbase: http://starbase.sysu.edu.cn/

③RegRNA2.0：http://regrna2.mbc.nctu.edu.tw/detection.html

數(shù)據(jù)庫功能及用途：

1. lncRNABase

數(shù)據(jù)庫功能：

View the predicted miRNA-lncRNAinteractions by scanning lncRNA sequences overlapping with CLIP-Seq peaks forpotential microRNA targets (miRanda/mirSVR) and then output the detailedinformation. Here, we list predicted miRNA-target interactions overlapped withCLIP-Seq data

2. starbase：

數(shù)據(jù)庫功能：

1. starBase is designed for decodingPan-Cancer and Interaction Networks of lncRNAs, miRNAs, competing endogenousRNAs(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 fordeciphering 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 networksfrom 108 CLIP-Seq (HITS-CLIP, PAR-CLIP, iCLIP, CLASH) datasets.

3. starBase provides miRFunction andceRNAFunction web tools to predict the function of ncRNAs (miRNAs, lncRNAs,pseduogenes) and protein-coding genes from the miRNA-mediated (ceRNA)regulatory networks

3. RegRNA2.0：

an integrated web server for identifyingfunctional RNA motifs and sites

示例結(jié)合分析：

以H19為例

lncRNABase：

1. 打開主頁面

2. 在“l(fā)ncRNAGene Symbol”對話框中輸入H19

3. 點(diǎn)擊“search”，查詢即可獲取

三、LncRNA與蛋白RNP結(jié)合預(yù)測

長鏈非編碼RNAs（longnon-coding RNAs，lncRNAs）在表觀遺傳、轉(zhuǎn)錄和轉(zhuǎn)錄后水平上調(diào)控基因表達(dá)中起著重要作用，能夠通過多種機(jī)制，包括遺傳印記、染色質(zhì)重塑、剪切調(diào)控、mRNA降解和翻譯調(diào)控確定lncRNAs的功能，探索lncRNAs的主要工具包括微陣列、RNA測序（RNA-seq）、Northern blotting、實(shí)時定量逆轉(zhuǎn)錄聚合酶鏈?zhǔn)椒磻?yīng)（qRT-PCR），熒光原位雜交（FISH）、RNA干擾（RNAi）、RNA-結(jié)合蛋白質(zhì)免疫沉淀（RIP）、通過RNA純化進(jìn)行染色質(zhì)分離（ChIRP）、交聯(lián)免疫沉淀（CLIP）和生物信息學(xué)預(yù)測等方法，LncRNA可與蛋白互作結(jié)合，調(diào)控基因的表達(dá)、轉(zhuǎn)錄、修飾等生物學(xué)過程

以下是我們對數(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(xiàng)，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(shí)驗(yàn)項(xiàng)目有所幫助

數(shù)據(jù)庫查詢分類

RPISeq ：http://pridb.gdcb.iastate.edu/RPISeq/

數(shù)據(jù)庫功能及用途：

RPISeq

數(shù)據(jù)庫功能：

Submit a protein sequence and an RNAsequence to predict the interaction probability.

實(shí)例分析：

以蛋白AGO2和LncRNA H19為例

Interaction probabilities

Prediction using RF classifier 0.55

Prediction using SVM classifier 0.54

兩者數(shù)值均>0.5,表示預(yù)測會相互結(jié)合