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Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome Inra
Aubourg, S.; Martin-Magniette, M.L.; Brunaud, V.; Taconnat, L.; Bitton, F.; Balzergue, S.; Jullien, P.E.; Ingouff, M.; Thareau, V.; Schiex, T.; Lecharny, A.; Renou, J.P..
Background: Since the finishing of the sequencing of the Arabidopsis thaliana genome, the Arabidopsis community and the annotator centers have been working on the improvement of gene annotation at the structural and functional levels. In this context, we have used the large CATMA resource on the Arabidopsis transcriptome to search for genes missed by different annotation processes. Probes on the CATMA microarrays are specific gene sequence tags (GSTs) based on the CDS models predicted by the Eugene software. Among the 24 576 CATMA v2 GSTs, 677 are in regions considered as intergenic by the TAIR annotation. We analyzed the cognate transcriptome data in the CATMA resource and carried out data-mining to characterize novel genes and improve gene models....
Tipo: Journal Article Palavras-chave: ADNC; EXPRESSION DES GENES; SEQUENCE NUCLEOTIDIQUE; ARABIDOPSIS THALIANA; GENOME; MODELE; METHODE STATISTIQUE; PROTEINE; TRANSCRIPTION; ARN MESSAGER; PCR; RT-PCR CDNA MICROARRAY DATA; EXPRESSION PROFILES; SEQUENCE TAGS; ANNOTATION; THALIANA; NORMALIZATION; REGIONS; TOOLS.
Ano: 2007 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD20116115e9a4&uri=/notices/prodinra1/2011/03/
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CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform Inra
Gagnot, S.; Tamby, J.P.; Martin-Magniette, M.L.; Bitton, F.; Taconnat, L.; Balzergue, S.; Aubourg, S.; Renou, J.P.; Lecharny, A.; Brunaud, V..
CATdb is a free resource available at http://urgv.evry.inra.fr/CATdb that provides public access to a large collection of transcriptome data for Arabidopsis thaliana produced by a single Complete Arabidopsis Transcriptome Micro Array (CATMA) platform. CATMA probes consist of gene-specific sequence tags (GSTs) of 150500 bp. The v2 version of CATMA contains 24 576 GST probes representing most of the predicted A. thaliana genes, and 615 probes tiling the chloroplastic and mitochondrial genomes. Data in CATdb are entirely processed with the same standardized protocol, from microarray printing to data analyses. CATdb contains the results of 53 projects including 1724 hybridized samples distributed between 13 different organs, 49 different developmental...
Tipo: Journal Article Palavras-chave: CDNA MICROARRAY DATA; SEQUENCE TAGS; INFORMATION; GENOME; NORMALIZATION; BIOLOGY; GENE COMPONENTS ; ADNC; SEQUENCE NUCLEOTIDIQUE; NORMALISATION; BIOLOGIE; ARABIDOPSIS THALIANA; MUTATION; MITOCHONDRIE; CHLOROPLASTE; METHODE STATISTIQUE; EXPRESSION DES GENES.
Ano: 2008 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD20111a416d88&uri=/notices/prodinra1/2011/03/
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Unique genes in plants: specificities and conserved features throughout evolution Inra
Armisén, D.; Lecharny, A.; Aubourg, S..
Background: Plant genomes contain a high proportion of duplicated genes as a result of numerous whole, segmental and local duplications. These duplications lead up to the formation of gene families, which are the usual material for many evolutionary studies. However, all characterized genomes include single-copy (unique) genes that have not received much attention. Unlike gene duplication, gene loss is not an unspecific mechanism but is rather influenced by a functional selection. In this context, we have established and used stringent criteria in order to identify suitable sets of unique genes present in plant proteomes. Comparisons of unique genes in the green phylum were used to characterize the gene and protein features exhibited by both conserved and...
Tipo: Journal Article Palavras-chave: GENETIQUE; HEREDITE; MONOCOTYLEDONE; PLANTE; ANGIOSPERME; DICOTYLEDONE; EVOLUTION MOLECULAIRE; BIOLOGIE DE L'EVOLUTION; CHAMPIGNON; EUCARYOTE; VERTEBRE; EXPRESSION DES GENES; TRANSCRIPTION; GENE HOMOLOGUE; SELECTION; ORYZA SATIVA; PROTEINE; TAILLE; PROMOTEUR; INTRON EVOLUTIONARY BIOLOGY; GENETICS; HEREDITY; ARABIDOPSIS-THALIANA PROTEOME; MONOCOT-DICOT DIVERGENCE; OPEN READING FRAMES; GENOME DUPLICATION; SACCHAROMYCES-CEREVISIAE; HEMIASCOMYCETOUS YEASTS; VERTEBRATE EVOLUTION; MOLECULAR EVOLUTION; TRANSCRIPTOME DATA; BINDING SITES.
Ano: 2008 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD2010bf4c2544&uri=/notices/prodinra1/2011/01/
Registros recuperados: 3
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