SAGE2Splice: unmapped SAGE tags reveal novel splice junctions.

Serial analysis of gene expression (SAGE) not only is a method for profiling the global expression of genes, but also offers the opportunity for the discovery of novel transcripts. SAGE tags are mapped to known transcripts to determine the gene of origin. Tags that map neither to a known transcript...

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Autores principales:	Byron Yu-Lin Kuo, Ying Chen, Slavita Bohacec, Ojvind Johansson, Wyeth W Wasserman, Elizabeth M Simpson
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2006
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/1e37d59f178347f38c8e7805011bd15d
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id	oai:doaj.org-article:1e37d59f178347f38c8e7805011bd15d
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spelling	oai:doaj.org-article:1e37d59f178347f38c8e7805011bd15d2021-11-25T05:41:07ZSAGE2Splice: unmapped SAGE tags reveal novel splice junctions.1553-734X1553-735810.1371/journal.pcbi.0020034https://doaj.org/article/1e37d59f178347f38c8e7805011bd15d2006-04-01T00:00:00Zhttps://doi.org/10.1371/journal.pcbi.0020034https://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Serial analysis of gene expression (SAGE) not only is a method for profiling the global expression of genes, but also offers the opportunity for the discovery of novel transcripts. SAGE tags are mapped to known transcripts to determine the gene of origin. Tags that map neither to a known transcript nor to the genome were hypothesized to span a splice junction, for which the exon combination or exon(s) are unknown. To test this hypothesis, we have developed an algorithm, SAGE2Splice, to efficiently map SAGE tags to potential splice junctions in a genome. The algorithm consists of three search levels. A scoring scheme was designed based on position weight matrices to assess the quality of candidates. Using optimized parameters for SAGE2Splice analysis and two sets of SAGE data, candidate junctions were discovered for 5%-6% of unmapped tags. Candidates were classified into three categories, reflecting the previous annotations of the putative splice junctions. Analysis of predicted tags extracted from EST sequences demonstrated that candidate junctions having the splice junction located closer to the center of the tags are more reliable. Nine of these 12 candidates were validated by RT-PCR and sequencing, and among these, four revealed previously uncharacterized exons. Thus, SAGE2Splice provides a new functionality for the identification of novel transcripts and exons. SAGE2Splice is available online at http://www.cisreg.ca.Byron Yu-Lin KuoYing ChenSlavita BohacecOjvind JohanssonWyeth W WassermanElizabeth M SimpsonPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 2, Iss 4, p e34 (2006)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Byron Yu-Lin Kuo Ying Chen Slavita Bohacec Ojvind Johansson Wyeth W Wasserman Elizabeth M Simpson SAGE2Splice: unmapped SAGE tags reveal novel splice junctions.
description	Serial analysis of gene expression (SAGE) not only is a method for profiling the global expression of genes, but also offers the opportunity for the discovery of novel transcripts. SAGE tags are mapped to known transcripts to determine the gene of origin. Tags that map neither to a known transcript nor to the genome were hypothesized to span a splice junction, for which the exon combination or exon(s) are unknown. To test this hypothesis, we have developed an algorithm, SAGE2Splice, to efficiently map SAGE tags to potential splice junctions in a genome. The algorithm consists of three search levels. A scoring scheme was designed based on position weight matrices to assess the quality of candidates. Using optimized parameters for SAGE2Splice analysis and two sets of SAGE data, candidate junctions were discovered for 5%-6% of unmapped tags. Candidates were classified into three categories, reflecting the previous annotations of the putative splice junctions. Analysis of predicted tags extracted from EST sequences demonstrated that candidate junctions having the splice junction located closer to the center of the tags are more reliable. Nine of these 12 candidates were validated by RT-PCR and sequencing, and among these, four revealed previously uncharacterized exons. Thus, SAGE2Splice provides a new functionality for the identification of novel transcripts and exons. SAGE2Splice is available online at http://www.cisreg.ca.
format	article
author	Byron Yu-Lin Kuo Ying Chen Slavita Bohacec Ojvind Johansson Wyeth W Wasserman Elizabeth M Simpson
author_facet	Byron Yu-Lin Kuo Ying Chen Slavita Bohacec Ojvind Johansson Wyeth W Wasserman Elizabeth M Simpson
author_sort	Byron Yu-Lin Kuo
title	SAGE2Splice: unmapped SAGE tags reveal novel splice junctions.
title_short	SAGE2Splice: unmapped SAGE tags reveal novel splice junctions.
title_full	SAGE2Splice: unmapped SAGE tags reveal novel splice junctions.
title_fullStr	SAGE2Splice: unmapped SAGE tags reveal novel splice junctions.
title_full_unstemmed	SAGE2Splice: unmapped SAGE tags reveal novel splice junctions.
title_sort	sage2splice: unmapped sage tags reveal novel splice junctions.
publisher	Public Library of Science (PLoS)
publishDate	2006
url	https://doaj.org/article/1e37d59f178347f38c8e7805011bd15d
work_keys_str_mv	AT byronyulinkuo sage2spliceunmappedsagetagsrevealnovelsplicejunctions AT yingchen sage2spliceunmappedsagetagsrevealnovelsplicejunctions AT slavitabohacec sage2spliceunmappedsagetagsrevealnovelsplicejunctions AT ojvindjohansson sage2spliceunmappedsagetagsrevealnovelsplicejunctions AT wyethwwasserman sage2spliceunmappedsagetagsrevealnovelsplicejunctions AT elizabethmsimpson sage2spliceunmappedsagetagsrevealnovelsplicejunctions
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SAGE2Splice: unmapped SAGE tags reveal novel splice junctions.

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