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正常发育、疾病和进化过程中的基因表达的基因相互作用的复杂网络。在伯克利果蝇基因组计划(BDGP)中，我们已经建立了果蝇发育的基因表达资源，其中包含空间和时间胚胎表达模式，使用标准化的受控词汇对模式进行注释，基于解剖学本体和模式的标准化虚拟表示。我们开发了工具来识别相似、部分重叠或反相关的表达。我们的数据库目前包含超过100,000张带注释的图像，显示了利用分段整装胚胎的原位杂交产生的表达模式，这些表达模式大约是果蝇基因组中60%(8500)蛋白质编码基因的表达模式。我们建议：(1)尽可能多地获得剩余40%蛋白质编码基因的表达模式；(2)用电动显微镜和分析管道开发全自动图像采集，以加快数据收集和高通量研究的准备；(3)继续改进和改进我们的虚拟图像表示法，并创建网络工具和界面，供研究人员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中保守的调控模块的表达模式。产生RNA探针的主要来源是我们的果蝇基因收藏(DGC)，它目前包含与88%的注释基因相对应的cDNA克隆。为了捕捉没有代表性的cDNA克隆的基因的表达模式(12%)，我们使用基因特异的PCR产物来生成96孔格式的RNA探针。本研究获得的基因表达数据将为阐明果蝇13,831个蛋白质编码基因的功能提供基础信息，并有助于阐明包括人类在内的其他真核生物中同源基因的功能。全基因组关联研究已经显示了调节区和基因表达在人类疾病中的基本作用。对调控区域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发现调控相互作用网络的研究。

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.