miR靶位点预常用软件

miRNA

的分布与靶基因组织分布的 相关性也是在做靶基因预测时要考虑

的重要因素。

miRNA

靶基因预测的软件种类较多，包括

miRanda, EMBL, PicTar,

TargetScan(S), DIANA-microT 3.0, PITA, ElMMo, rna22, GenMiR++, TarBase, miRBase,

miRGen-Targets

等。软件侧重点不同，预测能力 可谓各有千秋。选择靶基因预测软件时可

以重点选取两个，辅助添加一两个。一般而言， 不同软件的预测交集具有更好的特异性。

下面列出几个较常用软件及其出处，应用软件可 登陆相应网站，了解其特性及其细节，可

参看相应文献：

预测软件

miRBase

，为最常用

miRNA

数据库，其靶基因预测功能现在已交

microCosm(EBI),

关于

miRBase

请参考：

Griffiths-Jones S, Grocock RJ, van Dongen S, Bateman A, Enright AJ. 2006. miRBase:

microRNA sequences, targets and gene nomenclature. Nucleic Acids Res. 34:D140-4.

Abstract: The miRBase database aims to provide integrated interfaces to comprehensive

microRNA sequence data, annotation and predicted gene targets. miRBase takes over

functionality from the microRNA Registry and fulfils three main roles: the miRBase Registry acts

as an independent arbiter of microRNA gene nomenclature, assigning names prior to publication

of novel miRNA sequences. miRBase Sequences is the primary online repository for miRNA

sequence data and annotation. miRBase Targets is a comprehensive new database of predicted

miRNA target genes. miRBase is available at /.

TargetScan

由

Lewis

等人开发，请参考：

Lewis, B.P., Shih, I.H., Jones-Rhoades, M.W., Bartel, D.P., Burge, C.B. 2003. Prediction of

mammalian microRNA targets. Cell. 115, 787-798.

Abstract: MicroRNAs (miRNAs) can play important gene regulatory roles in nematodes, insects,

and plants by base-pairing to mRNAs to specify posttranscriptional repression of these messages.

However, the mRNAs regulated by vertebrate miRNAs are all unknown. Here we predict more

than 400 regulatory target genes for the conserved vertebrate miRNAs by identifying mRNAs

with conserved pairing to the 5’ region of the miRNA and evaluating the number and quality of

these complementary sites. Rigorous tests using shuffled miRNA controls supported a majority of

these predictions, with the fraction of false positives estimated at 31% for targets identified in

human, mouse, and rat and 22% for targets identified in pufferfish as well as mammals. Eleven

predicted targets (out of 15 tested) were supported experimentally using a HeLa cell reporter

system. The predicted regulatory targets of mammalian miRNAs were enriched for genes involved

in transcriptional regulation but also encompassed an unexpectedly broad range of other functions.

由

Krek

等人开发，有关

PicTar

情况请参考：

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