The Cancer Genome Anatomy Projects Genetic Annotation In

液化石油气生物信息学核心小组扮演着两个角色。第一是通过数据分析和管理，以及通过促进实验室内部的沟通，支持液化石油气的活动。第二个是提供资源，供更广泛的癌症研究社区使用。核心小组为液化石油气内的研究人员提供技术支持。Core的成员与Struewing和Lee实验室合作设计了一种癌症基因重测序微阵列，该微阵列将用于识别79个与癌症相关的基因座的新突变。他们与张团队合作，为Affymetrix人类和小鼠基因表达阵列制作了基于基因的芯片定义文件。核心集团还为Buetow实验室的肝癌和乳腺癌项目提供技术、分析和管理支持。核心小组的成员参与了国家癌症研究所的基因注释倡议(GAI)，该倡议扩大了用于癌症研究的基于基因的基因分析试剂的收集。GAI已经通过分析公开可用的表达序列标签色谱图确定了40,000多个候选人类单核苷酸多态(SNPs)。已经确定了超过16,000个候选老鼠SNPs。GAI已经通过质谱学验证了8000多个人类SNPs。生物信息学核心小组与LPG的成员合作，开发和维护各种基于网络的癌症研究工具。整合的遗传和物理SNP图谱，一个基于JAVA的工具，用于查看EST组装、试剂信息(包括聚合酶链式反应和延伸引物)中的候选SNP，以及SNP搜索引擎，请访问http://lpgws.nci.nih.gov/GAI/.在http://lpgws.nci.nih.gov/cgi-bin/GeneViewer.cgi/.上可以访问显示基因序列、开放阅读框架、蛋白质基序和三维蛋白质结构域结构背景下的多态的浏览器Affymetrix人类和小鼠基因芯片表达阵列集的注释可在http://lpgws.nci.nih.gov/cgi-bin/AffyViewer.cgi.The核心小组开发并维护一个基于网络的工具，以访问由美国国立卫生研究院弗雷德里克基因表达实验室创建的定量PCRPrimer数据库。通过这个搜索引擎，http://lpgws.nci.nih.gov/cgi-bin/PrimerViewer，的研究人员可以检索到基于聚合酶链式反应的试剂的信息，以测量人类和老鼠的基因表达。生物信息学核心小组正在与科学应用国际公司合作，定制和扩展开源的实验室信息管理系统CALIMS。LpgLIMS将包括Affymetrix基因表达和图谱微阵列的适配器，并将具有更好的安装简便性。

The LPG Bioinformatics Core Group performs two roles. The first is to support the activities of the LPG through data analysis and management, as well as by facilitating communication within the Laboratory. The second is to provide resources for use by the wider cancer research community. The Core Group provides technical support to researchers within the LPG. Members of the Core worked with the Struewing and Lee labs to design a cancer gene resequencing microarray, which will be used to identify novel mutations in 79 loci associated with cancer. They collaborated with the Zhang group to produce gene-based chip definition files for Affymetrix human and mouse gene expression arrays. The Core Group also provides technical, analytic and management support for Buetow lab liver and breast cancer projects. Members of the Core Group participate in the National Cancer Institute's Genetic Annotation Initiative (GAI), which expands the collection of gene-based genetic analysis reagents for cancer research. The GAI has identified more than 40,000 candidate human single nucleotide polymorphisms (SNPs) by analyzing publicly available expressed sequence tag chromatograms. Over 16,000 candidate mouse SNPs have been identified. The GAI has validated more than 8,000 human SNPs via mass spectrometry. The Bioinformatics Core Group works with members of the LPG to develop and maintain a variety of web-based tools for cancer research. Integrated genetic and physical SNP maps, a Java-based tool for viewing candidate SNPs in the context of EST assemblies, reagent information (including PCR primers and extension primers) and a SNP search engine are available at http://lpgws.nci.nih.gov/GAI/. A browser that displays polymorphisms in the context of mRNA sequences, open reading frames, protein motifs and three-dimensional protein domain structures is accessible at http://lpgws.nci.nih.gov/cgi-bin/GeneViewer.cgi/. Annotation for Affymetrix human and mouse GeneChip expression array sets are available at http://lpgws.nci.nih.gov/cgi-bin/AffyViewer.cgi.The Core Group developed and maintains a web-based tool for accessing the Quantitative PCR Primer Database created by the Gene Expression Laboratory at NCI-Frederick. Through this search engine, http://lpgws.nci.nih.gov/cgi-bin/PrimerViewer, researchers can retrieve information about PCR-based reagents for measuring the expression of human and mouse genes. The database includes 2055 human and 290 mouse primer sets.The Bioinformatics Core Group is working with Science Applications International Corporation to customize and extend the open source laboratory information management system caLIMS. lpgLIMS will include adaptors for Affymetrix gene expression and mapping microarrays and will feature improved ease of installation.