Contribution To The Annotations Of The Chicken 20K Oligo Microarray Of ARK-Genomics

Abstract : The chicken 20K oligo array provided by ARK-Genomics represents a very usefull tool for transcriptome analyses in the chicken. Because the 20460 70-mer oligo set was defined in 2004-2005 from heterogeneous data sources (http://www.ark-genomics.org), we checked the quality of the oligonucleotides, comparing them with the chromosomes of the 2.1 Washington University assembly of the Chicken Genome. This comparison was made using NCBI Blast 2 with a 75% similarity threshold over 50 base pairs. So we performed the annotation extraction only on the oligonucleotides found in a unique gene (even if it spanned on 2 exons). These annotations (Ensembl gene name, GO terms, orthologs, symbols corresponding to the human ortholog) were extracted from Ensembl using the blast HSP coordinates. Symbols for the human orthologs were validated with the HUGO gene nomenclature database using the GOret and HUGO_my_genes online tools (http://ouestgenopuces.univ-rennes1.fr/methodes_en.php). Other informations such as EC numbers and KEGG pathways IDs were extracted from bfind outputs and KEGG web pages. As results, among the 20460 gene-oligo, 13057 (64%) correspond to an unique coding region in a chicken genome sequence. From this oligo sub-set, only 32% presents an Ensembl gene name and/or a GO-biological process term. In contrast, 9360 (81%) presents a reliable human ortholog from which 1311 (14%) genes code enzymes. Among the 9360 genes, 7419 genes have a validated HUGO abbreviation, from which more GO terms could be extracted using different softwares (GOTM, Hugo-my-Genes) All bioinformatics procedures were developed by SIGENAE (INRA) and the results are available on site web: http://www.sigenae.org/
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Communication dans un congrès
International Plant & Animal Genomes XVI Conference, Jan 2008, San Diego, United States. 2008
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https://hal.inria.fr/inria-00329915
Contributeur : Francois Moreews <>
Soumis le : lundi 13 octobre 2008 - 16:02:59
Dernière modification le : mercredi 11 avril 2018 - 01:52:53

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  • HAL Id : inria-00329915, version 1

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Christophe Klopp, Francois Moreews, Marc Aubry, Sandrine Lagarrigue. Contribution To The Annotations Of The Chicken 20K Oligo Microarray Of ARK-Genomics. International Plant & Animal Genomes XVI Conference, Jan 2008, San Diego, United States. 2008. 〈inria-00329915〉

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