ArticleFEBS letters2006
Pan-genome isolation of low abundance transcripts using SAGE tag.
Article in FEBS letters, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Alternative splicing regulation of telomerase: a new paradigm?Trends in genetics : TIG · 2014Article
- Methodology optimizing SAGE library tag-to-gene mapping: application to Leishmania.BMC research notes · 2012Article
- Specific regulation of low-abundance transcript variants encoding human Acyl-CoA binding protein (ACBP) isoforms.Journal of cellular and molecular medicine · 2011Article
- The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE.BMC plant biology · 2011Article
- Developmental Regulation of Genes Encoding Universal Stress Proteins in Schistosoma mansoni.Gene regulation and systems biology · 2011Article
- hSAGEing: an improved SAGE-based software for identification of human tissue-specific or common tumor markers and suppressors.PloS one · 2010Article
- The transcriptome of human CD34+ hematopoietic stem-progenitor cells.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression.Genome biology · 2009Article
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Authors and funding
6 authors.
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Abstract
The SAGE (serial analysis of gene expression) method is sensitive at detecting the lower abundance transcripts. More than a third of human SAGE tags identified are novel representing the low abundance unknown transcripts. Using the GLGI method (generation of longer 3' EST from SAGE tag for gene identification), we converted 1009 low-copy, human X chromosome-specific SAGE tags into 10210 3' ESTs. We identified 3418 unique 3' ESTs, 46% of which are novel and originated from the lower abundance transcripts. However, nearly all 3' ESTs were mapped to various regions across the genome but not X chromosome. Detailed analysis indicates that those 3' ESTs were isolated by SAGE tag mis-priming to the non-parent transcripts. Replacing SAGE tags with non-transcribed genomic DNA tags resulted in poor amplification, indicating that the sequence similarity between different transcripts contributed to the amplification. Our study shows the prevalence of novel low abundance transcripts that can be isolated efficiently through SAGE tags mis-priming.
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