The Cancer Genome Anatomy Projects Genetic Annotation Initiative

癌症基因组解剖计划遗传注释计划

• 批准号: 7733713
• 负责人: Kenneth H Buetow
• 金额: $ 24.26万
• 依托单位: DIVISION OF CANCER EPIDEMIOLOGY AND GENETICS
• 依托单位国家: 美国
• 资助国家: 美国
• 起止时间: 至
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/7733713
• 关键词: Address; Amino Acids; Antibodies; Bioinformatics; Cancer Genome Anatomy Project; Cancer cell line; Characteristics; Communication; Computer Assisted; Data; Data Analyses; Data Set; Databases; Development; Ensure; Frameshift Mutation; Gene Expression; Genes; Genetic Annotation Initiative; Genomics; Genotype; Informatics; Investigation; Laboratories; Link; Malignant Neoplasms; Malignant neoplasm of esophagus; Malignant neoplasm of liver; Management Information Systems; Molecular; Molecular Profiling; Numbers; Play; Proteins; Protocols documentation; Research; Research Personnel; Role; Score; Structure; TAF1 gene; TAF7 gene; Tissue Microarray; Transforming Growth Factor beta; Work; analytical tool; cancer Biomedical Informatics Grid; cancer genome; data management; genome wide association study; malignant breast neoplasm; open source; population genetics laboratory; programs; protein expression; protein structure; research study; tool

One focus of the Bioinformatics Core has been to expand the functionality of existing display tools. The Protein Structure Viewer has two components: one displays amino acid alterations on the global structure of a protein; the second displays these alterations on three-dimensional protein structures. This application has been modified to display nonsense and frameshift mutations, and has been integrated with the Cancer Genome WorkBench. The LPGImage application (http://lpgimage.nci.nih.gov/LPGimage/) serves to display tissue microarray (TMA) data generated by Dr. Jin Jens laboratory. The Core has modified the application to display new data: computer assisted protein expression scoring. The number of antibodies in the TMA database has been increased to 81. In addition, the Bioinformatics Core is playing a leading role in the development of caLIMS2, a open-source, caBIG-compliant laboratory information management system (http://gforge.nci.nih.gov/projects/calims2/). caLIMS2 will function both as an information management system and a link between caBIG-compliant data repositories and analytical tools. The version 0.5 milestone 1 release has been completed. Finally, the Core provides informatics support to laboratories in the LPG and their collaborators. Projects supported by the Bioinformatics Core include a genomewide association study of liver cancer (Buetow Lab), identification of gene expression profiles in the NCI60 cancer cell lines (Buetow and Monks Labs), the identification of TGF-beta responsive genes in breast cancer (Lee and Wakefield Labs), the identification of TAF1 and TAF7 targets (Buetow, Lee and Singer Labs) and the investigation of genomic alterations in esophageal cancer (Lee and Taylor Labs).

生物信息学核心的一个重点是扩大现有显示工具的功能。蛋白质结构查看器有两个组成部分：一个分量显示了蛋白质的整体结构的氨基酸改变。第二个在三维蛋白质结构上显示了这些改变。该应用已被修改以显示废话和移码突变，并已与癌症基因组工作台进行了整合。 LPGIMAGE应用程序（http://lpgimage.nci.nih.gov/lpgimage/）用于显示由Jin Jens Laboratory生成的组织微阵列（TMA）数据。核心已修改了显示新数据的应用程序：计算机辅助蛋白表达评分。 TMA数据库中的抗体数量已增加到81。此外，生物信息学核心在开放源，CABIG-COMPLEIANT实验室信息管理系统（http://gforge.nci.nci.nih.gov/protoject/protojects/calims2/calims2/calims2/）中发挥了领先作用。 Calims2既可以用作信息管理系统，又可以在符合Cabig的数据存储库和分析工具之间发挥联系。版本0.5里程碑1版本已完成。最后，核心为LPG及其合作者的实验室提供了信息学支持。 Projects supported by the Bioinformatics Core include a genomewide association study of liver cancer (Buetow Lab), identification of gene expression profiles in the NCI60 cancer cell lines (Buetow and Monks Labs), the identification of TGF-beta responsive genes in breast cancer (Lee and Wakefield Labs), the identification of TAF1 and TAF7 targets (Buetow, Lee and Singer Labs) and the investigation of食管癌（Lee和Taylor Labs）的基因组改变。