SigReannot-mart: a query environment for expression microarray probe re-annotations.

François Moreews (1, 2) , Gaelle Rauffet (2) , Patrice Dehais (2, 3) , Christophe C. Klopp (2, 4)

1 SYMBIOSE - Biological systems and models, bioinformatics and sequences
2 SIGENAE - Système d'Information des GENomes des Animaux d'Elevage
3 LGC - Laboratoire de Génétique Cellulaire
4 UBIA - Unité de Biométrie et Intelligence Artificielle (ancêtre de MIAT)

Expression microarrays are commonly used to study transcriptomes. Most of the arrays are now based on oligo-nucleotide probes. Probe design being a tedious task, it often takes place once at the beginning of the project. The oligo set is then used for several years. During this time period, the knowledge gathered by the community on the genome and the transcriptome increases and gets more precise. Therefore re-annotating the set is essential to supply the biologists with up-to-date annotations. SigReannot-mart is a query environment populated with regularly updated annotations for different oligo sets. It stores the results of the SigReannot pipeline that has mainly been used on farm and aquaculture species. It permits easy extraction in different formats using filters. It is used to compare probe sets on different criteria, to choose the set for a given experiment to mix probe sets in order to create a new one.

Mots clés: microarray; annotation; database interoperability; biomart

Domaines: Bio-informatique [q-bio.QM]; Bio-Informatique, Biologie Systémique [q-bio.QM]; Génétique animale

François Moreews, Gaelle Rauffet, Patrice Dehais, Christophe C. Klopp. SigReannot-mart: a query environment for expression microarray probe re-annotations.. Database - The journal of Biological Databases and Curation, 2011, 2011, pp.bar025. ⟨10.1093/database/bar025⟩. ⟨inria-00638684⟩