MtExpress, a Comprehensive and Curated RNAseq-based Gene Expression Atlas for the Model Legume Medicago truncatula.

Autor: Carrere S; LIPME, INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde Rouge, 31320 Auzeville-Tolosane, Castanet-Tolosan 31320, France., Verdier J; Institut Agro, INRAE, IRHS, SFR QUASAV, Université d'Angers, 42 Rue Georges Morel, 49070 Beaucouzé, Angers 49000, France., Gamas P; LIPME, INRAE, CNRS, Université de Toulouse, 24 Chemin de Borde Rouge, 31320 Auzeville-Tolosane, Castanet-Tolosan 31320, France.
Jazyk: angličtina
Zdroj: Plant & cell physiology [Plant Cell Physiol] 2021 Nov 17; Vol. 62 (9), pp. 1494-1500.
DOI: 10.1093/pcp/pcab110
Abstrakt: Although RNA sequencing (RNAseq) has been becoming the main transcriptomic approach in the model legume Medicago truncatula, there is currently no genome-wide gene expression atlas covering the whole set of RNAseq data published for this species. Nowadays, such a tool is highly valuable to provide a global view of gene expression in a wide range of conditions and tissues/organs. Here, we present MtExpress, a gene expression atlas that compiles an exhaustive set of published M. truncatula RNAseq data (https://medicago.toulouse.inrae.fr/MtExpress). MtExpress makes use of recent releases of M. truncatula genome sequence and annotation, as well as up-to-date tools to perform mapping, quality control, statistical analysis and normalization of RNAseq data. MtExpress combines semi-automated pipelines with manual re-labeling and organization of samples to produce an attractive and user-friendly interface, fully integrated with other available Medicago genomic resources. Importantly, MtExpress is highly flexible, in terms of both queries, e.g. allowing searches with gene names and orthologous gene IDs from Arabidopsis and other legume species, and outputs, to customize visualization and redirect gene study to relevant Medicago webservers. Thanks to its semi-automated pipeline, MtExpress will be frequently updated to follow the rapid pace of M. truncatula RNAseq data publications, as well as the constant improvement of genome annotation. MtExpress also hosts legacy GeneChip expression data originally stored in the Medicago Gene Expression Atlas, as a very valuable and complementary resource.
(© The Author(s) 2021. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)
Databáze: MEDLINE
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