Max Planck Institute for Heart and Lung Research, Ludwigstr 43, 61231 Bad Nauheim, Germany.
Nucleic Acids Res. 2013 Jan 7;41(1):e20. doi: 10.1093/nar/gks877. Epub 2012 Sep 24.
Due to recent technical developments, a high number of long non-coding RNAs (lncRNAs) have been discovered in mammals. Although it has been shown that lncRNAs are regulated differently among tissues and disease statuses, functions of these transcripts are still unknown in most cases. GeneChip Exon 1.0 ST Arrays (exon arrays) from Affymetrix, Inc. have been used widely to profile genome-wide expression changes and alternative splicing of protein-coding genes. Here, we demonstrate that re-annotation of exon array probes can be used to profile expressions of tens of thousands of lncRNAs. With this annotation, a detailed inspection of lncRNAs and their isoforms is possible. To allow for a general usage to the research community, we developed a user-friendly web interface called 'noncoder'. By uploading CEL files from exon arrays and with a few mouse clicks and parameter settings, exon array data will be normalized and analysed to identify differentially expressed lncRNAs. Noncoder provides the detailed annotation information of lncRNAs and is equipped with unique features to allow for an efficient search for interesting lncRNAs to be studied further. The web interface is available at http://noncoder.mpi-bn.mpg.de.
由于最近的技术发展，哺乳动物中发现了大量的长非编码 RNA（lncRNA）。尽管已经表明 lncRNA 在组织和疾病状态之间的调控方式不同，但在大多数情况下，这些转录物的功能仍然未知。Affymetrix 公司的 GeneChip Exon 1.0 ST Arrays（exon arrays）已被广泛用于分析全基因组表达变化和蛋白编码基因的可变剪接。在这里，我们证明了重新注释 exon 芯片探针可用于分析数万种 lncRNA 的表达。通过这种注释，可以对 lncRNA 及其异构体进行详细检查。为了允许研究社区的广泛使用，我们开发了一个用户友好的网络界面，称为“noncoder”。通过从 exon 芯片上传 CEL 文件，并通过几次鼠标点击和参数设置，exon 芯片数据将被归一化和分析，以识别差异表达的 lncRNA。Noncoder 提供了 lncRNA 的详细注释信息，并配备了独特的功能，可有效地搜索有趣的 lncRNA 进行进一步研究。该网络界面可在 http://noncoder.mpi-bn.mpg.de 上访问。
