Exploring relationships and mining data with the UCSC Gene Sorter
Exploring relationships and mining data with the UCSC Gene Sorter
复制标题
DOI：
10.1101/gr.3694705
复制
发表时间：
2005-05-01
期刊：
影响因子：
7
通讯作者：
Haussler, D
中科院分区：
文献类型：
--
作者：
Kent, WJ;Hsu, F;Haussler, D
在人类基因组测序和组装工作的同时，还开发了许多工具来检查人类基因集的结构和功能。加州大学圣克鲁斯分校 (UCSC) 基因分选仪是作为基于基因的 UCSC 基因组浏览器的对应产品而创建的，以促进基因功能和进化的研究。这个简单但功能强大的工具提供了相关基因的图形显示，这些基因根据油的各种标准进行分类和过滤。基因可以基于表达谱、邻近基因组、共享基因本体（GO）术语和蛋白质相似性等特征进行排序。通过过滤表达水平、基因名称或 ID、染色体位置等，将显示调用限制为满足一组特定约束的基因集。每个基因条目的默认信息集 - 基因名称、选定的表达数据、BLASTP E 值、基因组位置和描述 - 可以配置为包括许多其他类型的数据，包括扩展表达数据、相关登录号和 IN、其他物种的直向同源物、GO 术语等等。 Gene Sorter 是一个用 C 语言编写的基于 CGI 的 Web 应用程序，带有 MySQL 数据库，与 UCSC Genome Browser Suite 中的其他应用程序紧密集成。可用油在基因组浏览器中找到的基因组组件的选定子集，它进一步增强了 UCSC 工具集在交互式基因组探索和分析中的实用性。
In parallel with the human genome sequencing and assembly effort, many tools have been developed to examine the structure and function of the human gene set. The University of California Santa Cruz (UCSC) Gene Sorter has been created as a gene-based Counterpart to the chromosome-oriented UCSC Genome Browser to facilitate the Study of gene function and evolution. This simple, but powerful tool provides a graphical display of related genes that call be sorted and filtered based oil a variety of criteria. Genes may be ordered based oil Such characteristics as expression profiles, proximity ill genome, shared Gene Ontology (GO) terms, and protein similarity. The display call be restricted to a gene set meeting a specific set of constraints by filtering on expression levels, gene name or ID, chromosomal position, and so oil. The default set of information for each gene entry-gene name, selected expression data, a BLASTP E-value, genomic position, and a description-can be configured to include many other types of data, inducing expanded expression data, related accession numbers and IN, orthologs ill other species, GO terms, and much more. The Gene Sorter, a CGI-based Web application written in C with a MySQL database, is tightly integrated with the other applications in the UCSC Genome Browser Suite. Available oil a selected subset of the genome assemblies found in the Genome Browser, it further enhances the usefulness of the UCSC tool set ill interactive genomic exploration and analysis.