TY - JOUR
T1 - TAGmapper
T2 - A web-based tool for mapping SAGE tags
AU - Bala, P.
AU - Georgantas, Robert W.
AU - Sudhir, D.
AU - Suresh, M.
AU - Shanker, K.
AU - Vrushabendra, B. M.
AU - Civin, Curt I.
AU - Pandey, Akhilesh
PY - 2005/12/30
Y1 - 2005/12/30
N2 - 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, SAGEmap (http://www.ncbi.nlm.nih.gov/projects/SAGE/) and SAGE Genie (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 tool in functional genomic approaches by providing accurate identification of genes in SAGE experiments.
AB - 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, SAGEmap (http://www.ncbi.nlm.nih.gov/projects/SAGE/) and SAGE Genie (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 tool in functional genomic approaches by providing accurate identification of genes in SAGE experiments.
KW - Annotation
KW - Bioinformatics
KW - Expressed sequence tag: Serial Analysis of Gene Expression
UR - http://www.scopus.com/inward/record.url?scp=28844471129&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=28844471129&partnerID=8YFLogxK
U2 - 10.1016/j.gene.2005.05.044
DO - 10.1016/j.gene.2005.05.044
M3 - Article
C2 - 16112519
AN - SCOPUS:28844471129
SN - 0378-1119
VL - 364
SP - 123
EP - 129
JO - Gene
JF - Gene
IS - 1-2
ER -