SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies
SpliceCenter: A suite of web-based bioinformatic applications for evaluating the impact of alternative splicing on RT-PCR, RNAi, microarray, and peptide-based studies
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DOI：
10.1186/1471-2105-9-313
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发表时间：
2008-07-18
影响因子：
3
通讯作者：
Weinstein, John N.
中科院分区：
文献类型：
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作者：
Ryan, Michael C.;Zeeberg, Barry R.;Weinstein, John N.
背景：脊椎动物中超过60%的蛋白质编码基因所表达的信使核糖核酸（mRNAs）会经历可变剪接。由此产生的转录异构体集合对当代生物学检测构成了重大挑战。例如，如果两种技术针对不同的剪接变体，基因表达微阵列结果的逆转录聚合酶链反应（RT - PCR）验证可能会不成功。有效使用基于序列的技术需要了解所针对的特定剪接变体。此外，可变剪接形式在生物学功能和疾病中的关键作用表明，如果在针对的剪接变体背景下进行分析，检测结果可能会提供更多信息。
结果：许多当代技术被用于分析转录本或蛋白质。为了能够研究剪接变异对从这些技术获得的数据的解释的影响，我们开发了SpliceCenter。SpliceCenter是一套用户友好的、基于网络的应用程序，包括用于分析RT - PCR引物/探针组、RNA干扰（RNAi）效应物、微阵列和蛋白质靶向技术的程序。提供了这些工具的交互式和高通量实现方式。SpliceCenter工具的交互式版本提供基因的可变转录本和探针靶向位置的可视化，使用户能够确定哪些剪接变体被靶向，哪些没有被靶向。高通量批量版本接受用户查询文件，并以表格形式提供结果。例如，当我们使用SpliceCenter的批量siRNA - Check来处理癌症基因组解剖计划（Cancer Genome Anatomy Project）的大规模短发夹核糖核酸（shRNA）文库时，我们发现文库中50766个shRNAs只有59%针对目标基因的所有已知剪接变体，32%针对部分但不是所有变体，9%不针对任何当前已注释的转录本。
结论：SpliceCenter（http://discover.nci.nih.gov/splicecenter）为评估转录本变异对RT - PCR、RNAi、基因表达微阵列、基于抗体的检测以及质谱蛋白质组学的设计和解释的影响提供了独特的、用户友好的应用程序。这些工具可供实验室生物学家以及生物信息学家使用。
Background: Over 60% of protein-coding genes in vertebrates express mRNAs that undergo alternative splicing. The resulting collection of transcript isoforms poses significant challenges for contemporary biological assays. For example, RT-PCR validation of gene expression microarray results may be unsuccessful if the two technologies target different splice variants. Effective use of sequence-based technologies requires knowledge of the specific splice variant(s) that are targeted. In addition, the critical roles of alternative splice forms in biological function and in disease suggest that assay results may be more informative if analyzed in the context of the targeted splice variant.Results: A number of contemporary technologies are used for analyzing transcripts or proteins. To enable investigation of the impact of splice variation on the interpretation of data derived from those technologies, we have developed SpliceCenter. SpliceCenter is a suite of user-friendly, web-based applications that includes programs for analysis of RT-PCR primer/probe sets, effectors of RNAi, microarrays, and protein-targeting technologies. Both interactive and high-throughput implementations of the tools are provided. The interactive versions of SpliceCenter tools provide visualizations of a gene's alternative transcripts and probe target positions, enabling the user to identify which splice variants are or are not targeted. The high-throughput batch versions accept user query files and provide results in tabular form. When, for example, we used SpliceCenter's batch siRNA-Check to process the Cancer Genome Anatomy Project's large-scale shRNA library, we found that only 59% of the 50,766 shRNAs in the library target all known splice variants of the target gene, 32% target some but not all, and 9% do not target any currently annotated transcript.Conclusion: SpliceCenter http://discover.nci.nih.gov/splicecenter provides unique, user-friendly applications for assessing the impact of transcript variation on the design and interpretation of RTPCR, RNAi, gene expression microarrays, antibody-based detection, and mass spectrometry proteomics. The tools are intended for use by bench biologists as well as bioinformaticists.