CORE 3: Bioinformatics

摘要核心3 生物信息学核心的目标是在 及时高效地开展工作。核心将处理和分析来自P01项目的数据 并为这些项目提供生物信息学支持和专业知识。我们提出了三个目标。这个 第一个目标将是提供数据的管理、存储和共享。我们将建立一个 数据库，允许研究人员选择针对特定问题量身定做的样本和数据。这个 数据库将作为数据分析和集成的平台。第二个目标是 为前3个研究项目提供分析支持。我们将帮助识别司机 与黑色素瘤进展相关的突变。我们还将提供全面的 扩展(上游监管机构和下游目标)对热门项目(项目1)的注释。 全基因组甲基化分析(项目2)预计将像所有其他研究项目一样， 跨多个区域生成多个命中。我们开发了强大的分析工具，使 确定其下游作用将受到阻碍的一组转录因子 异常甲基化。我们还将为基因表达分析提供生物信息学支持 (项目3)。我们将构建长时间差异表达基因的调控网络。 长期(&gt；5年)与短期(&lt；5年)不良幸存者。我们将提供全面的 以分子鉴定为目标的差异表达基因注释 与转移进展相关的通路。我们的第三个目标是提供 为数据整合提供生物信息学支持(项目4)。我们看到了两个级别的整合： 将P01的项目与所产生的数据和成果相结合 外面的如果是P01。第一级整合将基于黑色素瘤的假设 进展是由一种或几种生物功能的调节和那些 功能可以通过不同的机制来改变：生殖系和体细胞突变， 通过遗传和体细胞的多态，甲基化， 以及暴露在环境中。我们希望在结果之间找到更强的重叠 由不同的项目在生物功能水平上产生，而不是在基因水平上产生。 黑色素瘤一直是黑色素瘤研究的热点领域，与黑色素瘤相关的数据和结果很多 已经产生了进展。我们将把这个P01产生的数据和TCGA结合起来， Geo、GTEx、Oncomine、人类蛋白质图谱和其他公共来源。使用来自 外部来源将允许我们测试和完善这一P01的关键发现。

SUMMARY CORE 3 The goal of Bioinformatics core is to provide data management and bioinformatics support in a timely and efficient manner. The core will process, and analyze the data derived from P01 projects and provide bioinformatics support and expertise to the projects. We propose 3 objectives. The first objective will be to provide management, storage and sharing of the data. We will build a database to allow researchers to select samples and data tailored to specific questions. The database will be used as a platform for data analysis and integration. The second objective is to provide analytical support for the first 3 research projects. We will help to identify drivers mutations associated with melanoma progression. We will also provide a comprehensive extended (upstream regulators and downstream targets) annotation of the top hits (project 1). Whole genome methylation analysis (project 2) is expected, like all other research projects, to generate multiple hits across multiple regions. We developed powerful analytical tool that allows identification of the set of transcription factors whose downstream effects will be impeded by abnormal methylation. We will also provide bioinformatics support for gene expression analysis (project 3). We will construct regulatory network of the genes differentially expressed in long- term (>5 years) versus short-term (<5 years) bad survivors. We will provide comprehensive annotations of differentially expressed genes with the goal of the identification of molecular pathways associated with metastatic progression. Our third objective will be to provide bioinformatics support for data integration (project 4). We see two levels of integration: integration between the projects of the P01 and integration with the data and results generated outside if the P01. The first level of integration will be based on the assumption that melanoma progression is driven by a modulation of a single or a few biological functions and those functions can be modified by different mechanisms: germline and somatic mutations, modulation of the gene expression through genetic and somatic polymorphisms, methylation, and environmental exposures. We expect to find a stronger overlap between the results generated by different projects on the level of biological functions than on the gene level. Melanoma has been a hot research area and a lot of data and results related to the melanoma progression have been generated. We will combine the data generated by this P01 with TCGA, GEO, GTEx, ONCOMINE, Human Protein Atlas and other public sources. Using data from outside sources will allow us to test and refine key findings from this P01.