ArticleGenome research2003
Assessment of SAGE in transcript identification.
Article in Genome research, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- HT-SuperSAGE of the gut tissue of a Vip3Aa-resistant Heliothis virescens (Lepidoptera: Noctuidae) strain provides insights into the basis of resistance.Insect science · 2019Article
- Digital gene expression approach over multiple RNA-Seq data sets to detect neoblast transcriptional changes in Schmidtea mediterranea.BMC genomics · 2015Article
- A SAGE based approach to human glomerular endothelium: defining the transcriptome, finding a novel molecule and highlighting endothelial diversity.BMC genomics · 2014Article
- Identification of differential expression genes associated with host selection and adaptation between two sibling insect species by transcriptional profile analysis.BMC genomics · 2013Article
- Methodology optimizing SAGE library tag-to-gene mapping: application to Leishmania.BMC research notes · 2012Article
- A novel mutation in β integrin reveals an integrin-mediated interaction between the extracellular matrix and cki-1/p27KIP1.PloS one · 2012Article
- Identifying novel genes in C. elegans using SAGE tags.BMC molecular biology · 2010Article
- High-throughput SuperSAGE for digital gene expression analysis of multiple samples using next generation sequencing.PloS one · 2010Article
- Deep SAGE analysis of the Caenorhabditis elegans transcriptome.Nucleic acids research · 2010Article
- A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling.BMC bioinformatics · 2009Article
- Identification of novel transcripts with differential dorso-ventral expression in Xenopus gastrula using serial analysis of gene expression.Genome biology · 2009Article
- Differential SAGE analysis in Arabidopsis uncovers increased transcriptome complexity in response to low temperature.BMC genomics · 2008Article
- Transcriptome analysis for Caenorhabditis elegans based on novel expressed sequence tags.BMC biology · 2008Article
- Serial Analysis of Gene Expression in Plasmodium berghei salivary gland sporozoites.BMC genomics · 2007Article
- Using LongSAGE to Detect Biomarkers of Cervical Cancer Potentially Amenable to Optical Contrast Agent Labelling.Biomarker insights · 2007Article
- Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data.BMC genomics · 2007Article
- Identification and analysis of internal promoters in Caenorhabditis elegans operons.Genome research · 2007Article
- Differential gene expression in an elite hybrid rice cultivar (Oryza sativa, L) and its parental lines based on SAGE data.BMC plant biology · 2007Article
- Genes that may modulate longevity in C. elegans in both dauer larvae and long-lived daf-2 adults.Experimental gerontology · 2007Article
- Unexpected observations after mapping LongSAGE tags to the human genome.BMC bioinformatics · 2007Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
An essential step in Serial Analysis of Gene Expression (SAGE) is tag mapping, which refers to the unambiguous determination of the gene represented by a SAGE tag. Current resources for tag mapping are incomplete, and thus do not allow assessment of the efficacy of SAGE in transcript identification. A method of tag mapping is described here and applied to the Drosophila melanogaster and Caenorhabditis elegans genomes, which permits detailed SAGE assessment and provides tag-mapping resources that were unavailable previously for these organisms. In our method, a conceptual transcriptome is constructed using genomic sequence and annotation by extending predicted coding regions to include UTRs on the basis of EST and cDNA alignments, UTR length distributions, and polyadenylation signals. Analysis of extracted tags suggests that, using the standard SAGE procedure, expression of 8% of D. melanogaster and 15% of C. elegans genes cannot be detected unambiguously by SAGE due to shared sequence or lack of NlaIII-anchoring enzyme sites. Both increasing tag length by 2-3 bp and using Sau3A instead of NlaIII as the anchoring enzyme increases potential for transcript detection. This work identifies and quantifies genes not amenable to SAGE analysis, in addition to providing tag-to-gene mappings for two model organisms.
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