Cancer Genome Anatomy Project's Genetic Annotation Init.

作为国家癌症研究所癌症基因组解剖项目(CGAP)的一部分，基因注释倡议(GAI)寻求扩大用于癌症研究的基于基因的遗传分析试剂的集合。 我们通过使用一套序列分析工具分析公开可用的表达序列标签色谱图，继续鉴定并现已鉴定出40,000多个高概率候选单核苷酸多态(SNPs)。这种方法还被应用于在老鼠身上识别超过16,000个候选SNP。使用92个无关个体的混合DNA和MALDI-TOF质谱仪，我们现在已经验证了8000多个人类SNPs。 我们已经将我们的SNP发现工作与其他工作人员的工作相结合，以全面了解基于基因的SNP。我们提供了一个浏览器，它显示了mRNA序列中的多态位置，并指出了变异是否会导致氨基酸替换。浏览器中还显示了Pfam数据库中的编码区和保守的蛋白质基序。如果SNP改变了保守蛋白质结构域中的氨基酸，我们评估氨基酸替代如何影响蛋白质对基序模型的适合性。SNP在适当的时候被投射到已知的三维结构上，因此有可能评估它们在分子间相互作用中的作用。 整合的MAP，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)的候选SNP，以及SNP搜索引擎，可在我们的网站上获得：http://lpgws.nci.nih.gov/GAI/.我们为非商业用途提供对我们的SNP检测软件的访问。 我们还开发了基于网络的工具，用于访问由NCI-Frederick的基因表达实验室维护的定量PCR引物数据库。通过我们的搜索引擎，http://lpgws.nci.nih.gov/cgi-bin/PrimerViewer，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。该数据库目前包括1938套人类和290套小鼠引物。 此外，GAI还为Affymetrix U95和U133人，以及M74和MOE430小鼠基因芯片表达阵列集提供了注释。在当前的Unigene构建中，已经将来自表达阵列的寡核苷酸序列与完整的一组mRNA和EST序列进行了映射。这些数据使用户能够确定由微阵列探针组分析的基因的当前名称和描述，可视化探针在转录本中的位置，并验证探针是否针对其目标。有关注记工具，请访问http://lpgws.nci.nih.gov/cgi-bin/AffyViewer.cgi.

As part of the National Cancer Institute's Cancer Genome Anatomy Project (CGAP), the Genetic Annotation Initiative (GAI) seeks to expand the collection of gene-based genetic analysis reagents for cancer research. We continue to identify and have now identified more than 40,000 high-probability candidate single nucleotide polymorphisms (SNPs) by analyzing publicly available expressed sequence tag chromatograms with a set of sequence analysis tools. This approach has also been applied to identify more than 16,000 candidate SNPs in the mouse. Using pooled DNA from 92 unrelated individuals and MALDI-TOF mass spectrometry, we have now validated more than 8,000 human SNPs. We have integrated our SNP discovery efforts with those from other workers to give a comprehensive view of gene-based SNPs. We provide a browser that shows the location of polymorphisms in mRNA sequences, and indicates whether variants cause amino acid substitutions. Coding regions and conserved protein motifs from the Pfam database are also displayed in the browser. If a SNP alters an amino acid in a conserved protein domain, we assess how the amino acid substitution affects the fit of the protein to the motif model. SNPs are projected onto known three-dimensional structures, when appropriate, so it is possible to assess their role in intermolecular interactions. The integrated 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 our website: http://lpgws.nci.nih.gov/GAI/. We provide access to our SNP detection software for non-commercial use. We also have developed web-based tools for accessing the Quantitative PCR Primer Database maintained by the Gene Expression Laboratory at NCI-Frederick. Through our 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 currently includes 1938 human and 290 mouse primer sets. In addition, the GAI provides annotation for the Affymetrix U95 and U133 human, and M74 and MOE430 mouse GeneChip expression array sets. Oligonucleotide sequences from the expression arrays have been mapped against the complete set of mRNA and EST sequences in the current UniGene build. This data enables users to determine the current name and description of a gene assayed by a microarray probe set, visualize the position of probes within a transcript and verify whether probe is specific for its target. Annotation tools are available at http://lpgws.nci.nih.gov/cgi-bin/AffyViewer.cgi.