TAGmapper: A web-based tool for mapping SAGE tags

被引：7

作者：

Bala, P

Georgantas, RW

Sudhir, D

Suresh, M

Shanker, K

Vrushabendra, BM

Civin, CI

Pandey, A ^{[1
]}

机构：

[1] Johns Hopkins Univ, McKusick Nathans Inst Genet Med, Baltimore, MD 21205 USA

[2] Johns Hopkins Univ, Dept Biol Chem, Baltimore, MD 21205 USA

[3] Johns Hopkins Univ, Dept Oncol, Baltimore, MD 21205 USA

[4] Int Tech Pk, Inst Bioinformat, Bangalore 560066, Karnataka, India

[5] Johns Hopkins Univ, Sidney Kimmel Comprehens Canc Ctr, Dept Oncol, Baltimore, MD 21231 USA

[6] Johns Hopkins Univ, Sidney Kimmel Comprehens Canc Ctr, Dept Pediat, Baltimore, MD 21231 USA

来源：

GENE | 2005年 / 364卷

关键词：

expressed sequence tag; serial analysis of gene expression; annotation; bioinformatics;

D O I：

10.1016/j.gene.2005.05.044

中图分类号：

Q3 [遗传学];

学科分类号：

071007 ; 090102 ;

摘要：

Serial Analysis of Gene Expression (SAGE) is an important means of obtaining quantitative information about expression of genes in different samples. Short SAGE tags are 10 nucleotides long and often contain enough information to uniquely identify the gene(s) corresponding to the tag. We have observed, however, that the currently available resources are not adequate for accurate mapping of all SAGE tags to genes. Here, we describe development of a web-based tool called TAGmapper (http://tagmapper.ibioinformatics.org), which provides a comprehensive and accurate mapping of SAGE tags to genes. We were able to map SAGE tags accurately in several instances where two other popular resources, SAGErnap (http://www.ncbi.nlm.nih.gov/projects/SAGE/) and SAGE Genic (http://cgap.nci.nih.gov/ SAGE), provided incorrect or no assignment of tags to genes. Finally, we experimentally determined the expression of a subset of genes assigned by TAGmapper using DNA microarrays and/or quantitative PCR to confirm the reliability of the gene mappings. We anticipate that TAGmapper will be a useful toot in functional genomic approaches by providing accurate identification of genes in SAGE experiments. (C) 2005 Elsevier B.V. All rights reserved.

引用

页码：123 / 129

页数：7

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