Patterned Gene Expression in Drosophila Development

描述（由申请人提供）：我们的长期目标是了解控制基因表达的遗传相互作用的复杂网络，这些基因表达是正常发育、疾病和进化过程的基础。在伯克利果蝇基因组计划（BDGP），我们已经建立了一个基因表达资源果蝇的发展，包含空间和时间的胚胎表达模式，注释的模式使用标准化，控制词汇，基于解剖本体和标准化的虚拟表示的模式。我们创建了一些工具来识别相似的、部分重叠的或反相关的表达。我们的数据库目前包含超过100，000个注释图像，这些图像显示了果蝇基因组中约60%（8500）的蛋白质编码基因的表达模式。我们建议：（1）获得尽可能多的剩余40%的蛋白质编码基因的表达模式，（2）开发具有电动显微镜和分析管道的全自动图像采集，以加速数据收集并为高通量研究做准备，（3）继续改进和完善我们的虚拟图像表示，并创建Web-工具和接口，供研究界使用我们的数据集和上传的图像进行分析，以及（4）表征和分析转录因子保守调控模块的表达模式。用于产生RNA探针的主要资源是我们的果蝇基因收集（DGC），其目前包含对应于88%的注释基因的cDNA克隆。为了捕获不具有代表性cDNA克隆（12%）的基因的表达模式，我们使用基因特异性PCR产物以96孔格式产生RNA探针。我们的研究产生的基因表达数据将为阐明果蝇中13，831个蛋白质编码基因的功能提供基础信息，并将有助于阐明其他真核生物（包括人类）中同源基因的功能。全基因组关联研究已经显示了调节区域和基因表达在人类疾病中的基本作用。调控区的功能分析将为转录因子的发育作用提供新的见解。此外，基因表达数据与调控和基因序列的整合将促进研究发现调控相互作用的网络。

DESCRIPTION (provided by applicant): Our long-term objective is to understand the complex network of genetic interactions that control gene expression underlying the processes of normal development, disease and evolution. At the Berkeley Drosophila Genome Project (BDGP), we have established a gene expression resource for Drosophila development that contains spatial and temporal embryonic expression patterns, annotations of the patterns using a standardized, controlled vocabulary, based on an anatomical ontology and a standardized virtual representation of the patterns. We created tools to identify similar, partially overlapping or anti-correlated expression. Our database currently contains over 100,000 annotated images showing expression patterns generated using in-situ hybridization of staged whole-mounted embryos for approximately 60% (8500) of the protein-coding genes in the Drosophila genome. We propose to: (1) obtain expression patterns for as many of the remaining 40% of the protein-coding genes as possible, (2) develop fully automatic image acquisition with a motorized microscope and analysis pipeline to accelerate data collection and in preparation for high-throughput studies, (3) continue advancements and refinements to our virtual image representation and create web-tools and interfaces for the research community to conduct analysis with our dataset and uploaded images and (4) characterize and analyze expression patterns of conserved regulatory modules from transcription factors. The primary resource for generation of RNA probes is our Drosophila Gene Collection (DGC), which currently contains cDNA clones corresponding to 88% of the annotated genes. To capture expression patterns for genes that do not have a representative cDNA clone (12%), we used gene-specific PCR products to generate RNA probes in 96- well format. The gene expression data produced by our study will provide fundamental information for elaborating the function of the 13,831 protein-coding genes in Drosophila and will aid in elucidating the function of the homologous genes in other eukaryotes, including humans. Genome wide association studies have shown fundamental roles for regulatory regions and gene expression in human diseases. The functional analysis of regulatory regions will provide novel insights into the developmental roles of transcription factors. In addition, the integration of the gene expression data with regulatory and gene sequences will promote research to discover networks of regulatory interactions.