Articles
An interactive gene expression atlas for mango
Article number
1415_29
Pages
241 – 248
Language
English
Abstract
Mango (Mangifera indica L.) is a fruit of high nutritional value and great economic importance, which is widely distributed around the world.
However, despite the wide variety of omics analyses published in mango, no platform for gene expression data was available.
Here, we present a gene expression atlas for mango with 12 data sets and a total of 80 experiments.
These experiments include gene expression data of fruits in different ripening stages of several cultivars, cold stress, hot water treatment, and infection by pathogens.
Furthermore, one data set provides a representation of the main tissues of the plant such as root, bark, leaf, flower, and seed.
The mango expression atlas analyses are based on a high-quality genome reference to easily identify in which tissues, stages, and experimental conditions are genes expressed, which is of great utility for experimental design and results discussion.
Multiple interactive tools allow users to visualize and compare the gene expression data of multiple genes simultaneously and download them in different formats.
Other features allow the visualization of gene expression values together with pictures of the plant phenotype, check the replicates of each gene, or compare the gene expression of samples from any data set, allowing relative normalization based on a reference gene.
The expression atlas is integrated into MangoBase (https://mangobase.org), a genomic portal dedicated to mango, with multiple interactive bioinformatic tools, and its results are connected with the different tools of MangoBase and functional annotations from multiple databases.
However, despite the wide variety of omics analyses published in mango, no platform for gene expression data was available.
Here, we present a gene expression atlas for mango with 12 data sets and a total of 80 experiments.
These experiments include gene expression data of fruits in different ripening stages of several cultivars, cold stress, hot water treatment, and infection by pathogens.
Furthermore, one data set provides a representation of the main tissues of the plant such as root, bark, leaf, flower, and seed.
The mango expression atlas analyses are based on a high-quality genome reference to easily identify in which tissues, stages, and experimental conditions are genes expressed, which is of great utility for experimental design and results discussion.
Multiple interactive tools allow users to visualize and compare the gene expression data of multiple genes simultaneously and download them in different formats.
Other features allow the visualization of gene expression values together with pictures of the plant phenotype, check the replicates of each gene, or compare the gene expression of samples from any data set, allowing relative normalization based on a reference gene.
The expression atlas is integrated into MangoBase (https://mangobase.org), a genomic portal dedicated to mango, with multiple interactive bioinformatic tools, and its results are connected with the different tools of MangoBase and functional annotations from multiple databases.
Publication
Authors
A. Gómez-Ollé, A. Bullones, J.I. Hormaza, L.A. Mueller, N. Fernandez-Pozo
Keywords
Mangifera indica, bioinformatics, omics, RNA-seq, database, bioinformatics tools, fruit ripening
Groups involved
Online Articles (38)