ArticleBMC bioinformatics2004
Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries.
Article in BMC bioinformatics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 21 citations in OpenAlex.
- Gill transcriptome response to changes in environmental calcium in the green spotted puffer fish.BMC genomics · 2010Article
- In-depth global analysis of transcript abundance levels in porcine alveolar macrophages following infection with porcine reproductive and respiratory syndrome virus.Advances in virology · 2010Article
- An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation.Genome biology · 2010Article
- Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus.BMC genomics · 2009Article
- A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling.BMC bioinformatics · 2009Article
- SQUAT: A web tool to mine human, murine and avian SAGE data.BMC bioinformatics · 2008Article
- Clustering-based approaches to SAGE data mining.BioData mining · 2008Article
- Article
- SAGExplore: a web server for unambiguous tag mapping in serial analysis of gene expression oriented to gene discovery and annotation.Nucleic acids research · 2007Article
- Unexpected observations after mapping LongSAGE tags to the human genome.BMC bioinformatics · 2007Article
- SAGE2Splice: unmapped SAGE tags reveal novel splice junctions.PLoS computational biology · 2006Article
- Global transcription analysis of immature avian erythrocytic progenitors: from self-renewal to differentiation.Oncogene · 2004Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSerial Analysis of Gene Expression (SAGE) is a method of large-scale gene expression analysis that has the potential to generate the full list of mRNAs present within a cell population at a given time and their frequency. An essential step in SAGE library analysis is the unambiguous assignment of each 14 bp tag to the transcript from which it was derived. This process, called tag-to-gene mapping, represents a step that has to be improved in the analysis of SAGE libraries. Indeed, the existing web sites providing correspondence between tags and transcripts do not concern all species for which numerous EST and cDNA have already been sequenced.
resultsThis is the reason why we designed and implemented a freely available tool called Identitag for tag identification that can be used in any species for which transcript sequences are available. Identitag is based on a relational database structure in order to allow rapid and easy storage and updating of data and, most importantly, in order to be able to precisely define identification parameters. This structure can be seen like three interconnected modules : the first one stores virtual tags extracted from a given list of transcript sequences, the second stores experimental tags observed in SAGE experiments, and the third allows the annotation of the transcript sequences used for virtual tag extraction. It therefore connects an observed tag to a virtual tag and to the sequence it comes from, and then to its functional annotation when available. Databases made from different species can be connected according to orthology relationship thus allowing the comparison of SAGE libraries between species. We successfully used Identitag to identify tags from our chicken SAGE libraries and for chicken to human SAGE tags interspecies comparison. Identitag sources are freely available on http://pbil.univ-lyon1.fr/software/identitag/ web site.
conclusionsIdentitag is a flexible and powerful tool for tag identification in any single species and for interspecies comparison of SAGE libraries. It opens the way to comparative transcriptomic analysis, an emerging branch of biology.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.