Whole transcriptome analysis for neurobiology

描述（由申请人提供）：像大脑这样复杂的器官的发育依赖于数千种信号蛋白的复杂相互作用，由一个相互作用的调节因子网络精心策划。最近的ENCODE数据显示，内含子内和基因间的大量所谓的“垃圾”DNA实际上是活跃转录的。这些数以百万计的非编码转录本的功能实际上是未知的，尽管其中一个小的同类——微rna——作为调控rna正受到密切关注。一个可能由非编码转录本控制的过程是外显子的交替使用——这一机制显著增加了细胞蛋白质的多样性（特别是在中枢神经系统中），目前对其调控知之甚少。产生全转录组数据的最新进展为系统地探索这两个因素提供了手段。然而，生物信息学方面的挑战是巨大的，缺乏全面的、设计良好的、易于使用的软件来管理、可视化、分析和解释数据，这可能是这一研究领域的限制因素。我们建议开发一个生物信息学工具包，专门集成来自两种不同技术的全转录组数据，Affymetrix All外显子微阵列，其中包含140万个不同的转录物测量，以及RNASeq，它提供了整个转录组的“数字”表达分析。该工具包还将整合表观基因组数据，这将是必不可少的转录调控的理解。该软件的设计和开发将由从事大脑研究的杰出科学家指导，并将应用于来自神经组织的样本数据集，以确保该程序包含与该领域相关的功能和注释。

DESCRIPTION (provided by applicant): Development of an organ as complex as the brain depends on an intricate interplay of thousands of signaling proteins, orchestrated by an interacting web of regulatory factors. Recent ENCODE data reveal that the large tracts of so-called 'junk' DNA in introns and between genes is, in fact, actively transcribed. The functions of these non-coding transcripts, which number in the millions, are virtually unknown, although one small sib-class - the microRNAs - is receiving close attention as regulatory RNAs. One process that may be controlled by the non-coding transcripts is alternate exon use - a mechanism that adds significantly to the diversity of cellular proteins (particularly in the CNS), the regulation of which is little understood at this time. Recent advances that generate whole-transcriptome data have provided the means to systematically explore both these factors. However, the bioinformatic challenges are substantial, and the lack of comprehensive, well designed, and easily used software to manage, visualize, analyze and interpret the data will likely be the limiting factor in this field of research. We propose to develop a bioinformatics toolkit specifically to integrate whole-transcriptome data from two different technologies, the Affymetrix All Exon microarray which 1.4 million distinct transcript measurements, and RNASeq, which provides for 'digital' expression analysis of the whole transcriptome. The toolkit will also integrate epigenomic data that will be essential in the understanding of regulation of transcription. The design and development of the software will be guided by prominent scientists engaged in the study of the brain, and will be applied to sample datasets derived from neurological tissues, to ensure that the program incorporates functions and annotations relevant to this field. PUBLIC HEALTH RELEVANCE: While the large-scale array technologies have provided an unprecedented capability to model cellular processes in the brain, both in normal functioning and disease states, this capability is utterly dependent on the availability of complex data management, computational, statistical and informatics software tools. The utility of the next generation of arrays and sequencing technologies- which focus on critical regulation and control functions of the cell - will be stymied by an initial lack of suitable bioinformatic tools. This proposal initiates an accelerated development of an integrated software package intended to empower biologists in the application and analysis of these powerful new technologies, with broadly reaching impact at all levels of biological and clinical research, and across every discipline.