Transcriptome annotation using tandem SAGE tags

Eric Rivals 1 Anthony Boureux 2 Mireille Lejeune 2 Florence Ottones 2 Oscar Pecharromàn Pérez 3 Jorma Tarhio 3 Fabien Pierrat 4 Florence Ruffle 2 Thérèse Commes 2 Jacques Marti 2
1 MAB - Méthodes et Algorithmes pour la Bioinformatique
LIRMM - Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier
2 IGH - Institut de génétique humaine
3 SWT - Laboratory of Software Technology
4 Skuld-Tech - Skuld-Tech, biotechnology company
Abstract : Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial Analysis of Gene Expression (SAGE) can reveal new polyadenylated RNAs transcribed from previously unrecognized chromosomal regions. However, conventional SAGE tags are too short to identify unambiguously unique sites in large genomes. Here, we design a novel strategy with tags anchored on two different restrictions sites of cDNAs. New transcripts are then tentatively defined by the two SAGE tags in tandem and by the spanning sequence read on the genome between these tagged sites. Having developed a new algorithm to locate these tag-delimited genomic sequences, we first validated its capacity to recognize known genes and its ability to reveal new transcripts with two SAGE libraries built in parallel from a single RNA sample. Our algorithm proves fast enough to experiment this strategy at a large scale. We then collected and processed the complete sets of human SAGE tags to predict yet unknown transcripts. A crossvalidation with tiling arrays data shows that 47% of these tag-delimited genomic sequences overlap transcriptional active regions. Our method provides a new and complementary approach for complex transcriptome annotation.
Type de document :
Communication dans un congrès
Guy Perriere. Réunion satellite "Transcriptome et bioinformatique", Jul 2007, Marseille, France. Société Française de BioInformatique (SFBI), pp.8, 2007, 〈http://crfb.univ-mrs.fr/jobim2007/index.php?l=fr&c=satell〉
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https://hal-lirmm.ccsd.cnrs.fr/lirmm-00203923
Contributeur : Eric Rivals <>
Soumis le : vendredi 11 janvier 2008 - 14:27:59
Dernière modification le : jeudi 11 janvier 2018 - 06:26:12
Document(s) archivé(s) le : jeudi 27 septembre 2012 - 14:05:56

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  • HAL Id : lirmm-00203923, version 1

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MAB | LIRMM | MIPS | BS | UNIV-MONTPELLIER

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Eric Rivals, Anthony Boureux, Mireille Lejeune, Florence Ottones, Oscar Pecharromàn Pérez, et al.. Transcriptome annotation using tandem SAGE tags. Guy Perriere. Réunion satellite "Transcriptome et bioinformatique", Jul 2007, Marseille, France. Société Française de BioInformatique (SFBI), pp.8, 2007, 〈http://crfb.univ-mrs.fr/jobim2007/index.php?l=fr&c=satell〉. 〈lirmm-00203923〉

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