Institute of Bioinformatics and Applied Biotechnology (IBAB), Biotech Park, Electronic City, Bengaluru (Bangalore) 560 100, Karnataka state, India.
BMC Genomics. 2013 Dec 27;14:922. doi: 10.1186/1471-2164-14-922.
Standard 3' Affymetrix gene expression arrays have contributed a significantly higher volume of existing gene expression data than other microarray platforms. These arrays were designed to identify differentially expressed genes, but not their alternatively spliced transcript forms. No resource can currently identify expression pattern of specific mRNA forms using these microarray data, even though it is possible to do this.
We report a web server for expression profiling of alternatively spliced transcripts using microarray data sets from 31 standard 3' Affymetrix arrays for human, mouse and rat species. The tool has been experimentally validated for mRNAs transcribed or not-detected in a human disease condition (non-obstructive azoospermia, a male infertility condition). About 4000 gene expression datasets were downloaded from a public repository. 'Good probes' with complete coverage and identity to latest reference transcript sequences were first identified. Using them, 'Transcript specific probe-clusters' were derived for each platform and used to identify expression status of possible transcripts. The web server can lead the user to datasets corresponding to specific tissues, conditions via identifiers of the microarray studies or hybridizations, keywords, official gene symbols or reference transcript identifiers. It can identify, in the tissues and conditions of interest, about 40% of known transcripts as 'transcribed', 'not-detected' or 'differentially regulated'. Corresponding additional information for probes, genes, transcripts and proteins can be viewed too. We identified the expression of transcripts in a specific clinical condition and validated a few of these transcripts by experiments (using reverse transcription followed by polymerase chain reaction). The experimental observations indicated higher agreements with the web server results, than contradictions. The tool is accessible at http://resource.ibab.ac.in/TIPMaP.
The newly developed online tool forms a reliable means for identification of alternatively spliced transcript-isoforms that may be differentially expressed in various tissues, cell types or physiological conditions. Thus, by making better use of existing data, TIPMaP avoids the dependence on precious tissue-samples, in experiments with a goal to establish expression profiles of alternative splice forms--at least in some cases.
标准的 3' Affymetrix 基因表达阵列比其他微阵列平台贡献了更多现有的基因表达数据。这些阵列旨在识别差异表达的基因，但不能识别其选择性剪接的转录本形式。目前没有资源可以使用这些微阵列数据来确定特定 mRNA 形式的表达模式，尽管这是可能的。
我们报告了一个使用 31 个人类、小鼠和大鼠物种的标准 3' Affymetrix 阵列的微阵列数据集进行选择性剪接转录本表达谱分析的网络服务器。该工具已在人类疾病（非阻塞性无精子症，一种男性不育症）条件下进行了实验验证。从公共存储库中下载了大约 4000 个基因表达数据集。首先识别出具有完整覆盖度和与最新参考转录序列同一性的“好探针”。使用这些探针，为每个平台衍生出“转录本特异性探针簇”，并用于识别可能转录本的表达状态。该网络服务器可以通过微阵列研究或杂交、关键词、官方基因符号或参考转录标识符，引导用户访问特定组织、条件下的数据集。它可以识别出感兴趣的组织和条件下，约 40%的已知转录本为“转录”、“未检测到”或“差异调节”。也可以查看探针、基因、转录本和蛋白质的其他相关信息。我们在特定的临床条件下识别了转录本的表达，并通过实验（使用反转录聚合酶链反应）验证了其中的一些转录本。实验观察结果表明，与网络服务器结果的一致性高于矛盾。该工具可在 http://resource.ibab.ac.in/TIPMaP 上访问。
新开发的在线工具为鉴定在各种组织、细胞类型或生理条件下可能差异表达的选择性剪接转录本异构体提供了可靠的手段。因此，通过更好地利用现有数据，TIPMaP 避免了在以确定选择性剪接形式的表达谱为目标的实验中对珍贵组织样本的依赖——至少在某些情况下是这样。
