The DIANA-mirExTra web server: from gene expression data to microRNA function.
The DIANA-mirExTra web server: from gene expression data to microRNA function.
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DOI：
10.1371/journal.pone.0009171
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发表时间：
2010-02-11
期刊：
影响因子：
3.7
通讯作者：
Hatzigeorgiou AG
中科院分区：
文献类型：
--
作者：
Alexiou P;Maragkakis M;Papadopoulos GL;Simmosis VA;Zhang L;Hatzigeorgiou AG
高通量的基因表达实验被广泛用于确定与感兴趣的生物条件有关的基因的作用。MicroRNAs(MiRNA)是一种调节分子，在功能上与几个发育项目相关，并与包括癌症在内的各种疾病的解除调控有关。虽然在高通量实验中可能不能常规地测量miRNA的表达水平，但通过分析去调控基因3‘非翻译区(3’UTR)序列中过高表达的基序，可以计算预测和量化miRNAs参与基因表达解除调控的可能性。在这里，我们介绍了一个用户友好的网络服务器Diana-mirExtra(www.micrororna.gr/mirextra)，它允许比较不同基因集之间的miRNA相关基序的频率，这可以导致识别导致大量基因放松调控的miRNAs。为此，我们研究了不同的方法和措施，并在实验数据上进行了实际实施。在几个miRNA过表达和抑制实验的数据集上，我们提出的方法已经成功地识别了解除调控的miRNA。除了预测负责解除转录调控的miRNA外，网络服务器还提供了到Diana-mirPath的广泛链接，Diana-mirPath是一种将miRNA靶标纳入生物途径的功能分析工具。此外，如果提供了有关miRNA表达变化的信息，则可以过滤结果以仅显示感兴趣的miRNAs的分析。
High-throughput gene expression experiments are widely used to identify the role of genes involved in biological conditions of interest. MicroRNAs (miRNA) are regulatory molecules that have been functionally associated with several developmental programs and their deregulation with diverse diseases including cancer. Although miRNA expression levels may not be routinely measured in high-throughput experiments, a possible involvement of miRNAs in the deregulation of gene expression can be computationally predicted and quantified through analysis of overrepresented motifs in the deregulated genes 3′ untranslated region (3′UTR) sequences. Here, we introduce a user-friendly web-server, DIANA-mirExTra (www.microrna.gr/mirextra) that allows the comparison of frequencies of miRNA associated motifs between sets of genes that can lead to the identification of miRNAs responsible for the deregulation of large numbers of genes. To this end, we have investigated different approaches and measures, and have practically implemented them on experimental data. On several datasets of miRNA overexpression and repression experiments, our proposed approaches have successfully identified the deregulated miRNA. Beyond the prediction of miRNAs responsible for the deregulation of transcripts, the web-server provides extensive links to DIANA-mirPath, a functional analysis tool incorporating miRNA targets in biological pathways. Additionally, in case information about miRNA expression changes is provided, the results can be filtered to display the analysis for miRNAs of interest only.
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影响因子：
4.3
作者：
Elkon, Ran;Agami, Reuven
通讯作者：
Agami, Reuven
影响因子：
14.9
作者：
Flicek P;Aken BL;Beal K;Ballester B;Caccamo M;Chen Y;Clarke L;Coates G;Cunningham F;Cutts T;Down T;Dyer SC;Eyre T;Fitzgerald S;Fernandez-Banet J;Gräf S;Haider S;Hammond M;Holland R;Howe KL;Howe K;Johnson N;Jenkinson A;Kähäri A;Keefe D;Kokocinski F;Kulesha E;Lawson D;Longden I;Megy K;Meidl P;Overduin B;Parker A;Pritchard B;Prlic A;Rice S;Rios D;Schuster M;Sealy I;Slater G;Smedley D;Spudich G;Trevanion S;Vilella AJ;Vogel J;White S;Wood M;Birney E;Cox T;Curwen V;Durbin R;Fernandez-Suarez XM;Herrero J;Hubbard TJ;Kasprzyk A;Proctor G;Smith J;Ureta-Vidal A;Searle S
通讯作者：
Searle S
影响因子：
30.8
作者：
Bussemaker, HJ;Li, H;Siggia, ED
通讯作者：
Siggia, ED
DOI：
10.1073/pnas.0801615105
发表时间：
2008-05-13
影响因子：
11.1
作者：
Zhang, Lin;Volinia, Stefano;Coukos, George
通讯作者：
Coukos, George
DOI：
10.1073/pnas.0511045103
发表时间：
2006-02-21
影响因子：
11.1
作者：
Sood, P;Krek, A;Rajewsky, N
通讯作者：
Rajewsky, N