Toolkit for Whole Transcriptome Analysis of Neural Tissues

描述（由申请人提供）：像大脑这样复杂的器官的发育必须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，尽管一个非常小的兄弟类- microrna -作为调控rna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。最近的技术进步产生了全转录组数据，为系统地探索这两个因素——非编码转录物的作用以及剪接变异的发生和控制提供了手段。然而，这些技术带来的生物信息学挑战是巨大的，缺乏全面的、设计良好的、易于使用的软件来管理、可视化、分析和解释这些数据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，专门用于从两种根本不同的技术中挖掘全转录组数据，Affymetrix All外显子微阵列提供超过140万个不同转录本的测量，以及Solexa超高通量测序仪，提供整个转录组的“数字”表达分析。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。公共卫生相关性：虽然大规模阵列技术提供了前所未有的能力来模拟大脑中正常功能和疾病状态下的细胞过程，但这种能力完全依赖于复杂数据管理、计算、统计和信息软件工具的可用性。下一代阵列的应用——聚焦于细胞的关键调控功能——将由于最初缺乏合适的生物信息学工具而受到阻碍。该提案启动了一个集成软件包的加速开发，旨在使生物学家能够应用和分析这些强大的新技术，并在生物学和临床研究的各个层面以及各个学科中产生广泛的影响。

DESCRIPTION (provided by applicant): Development of an organ as complex as the brain must depend 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 very 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 technological advances that generate whole-transcriptome data have provided the means to systematically explore both these factors - the role non-coding transcripts, and the occurrence and control of splice variation. However, the bioinformatic challenges posed by these technologies are substantial, and the lack of comprehensive, well designed, and easily used software to manage, visualize, analyze and interpret these data will likely be the limiting factor in this field of research. We propose to develop a bioinformatics toolkit specifically to mine whole-transcriptome data from two fundamentally different technologies, the Affymetrix All Exon microarray which provides measures of over 1.4 million distinct transcripts, and the Solexa ultra high throughput sequencer, which provides for `digital' expression analysis of the whole transcriptome. 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 data set derived from neurological tissue, to ensure that the progra 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 informatic software tools. The utility of the next generation of arrays - 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.