OrangeExpDB: an integrative gene expression database for Citrus spp.

Publisher: BioMed Central Country of Publication: England NLM ID: 100965258 Publication Model: Electronic Cited Medium: Internet ISSN: 1471-2164 (Electronic) Linking ISSN: 14712164 NLM ISO Abbreviation: BMC Genomics Subsets: MEDLINE

Original Publication: London : BioMed Central, [2000-

Citrus*/genetics ; Databases, Genetic*; Transcriptome ; Gene Expression Profiling/methods ; Computational Biology/methods ; Gene Expression Regulation, Plant

Background: Citrus is a major fruit crop, and RNA-sequencing (RNA-seq) data can be utilized to investigate its gene functions, heredity, evolution, development, and the detection of genes linked to essential traits or resistance to pathogens. However, it is challenging to use the public RNA-seq datasets for researchers without bioinformatics training, and expertise.
Results: OrangeExpDB is a web-based database that integrates transcriptome data of various Citrus spp., including C. limon (L.) Burm., C. maxima (Burm.) Merr., C. reticulata Blanco, C. sinensis (L.) Osbeck, and Poncirus trifoliata (L.) Raf., downloaded from the NCBI SRA database. It features a blast tool for browsing and searching, enabling quick download of expression matrices for different transcriptome samples. Expression of genes of interest can be easily generated by searching gene IDs or sequence similarity. Expression data in text format can be downloaded and presented as a heatmap, with additional sample information provided at the bottom of the webpage.
Conclusions: Researchers can utilize OrangeExpDB to facilitate functional genomic analysis and identify key candidate genes, leveraging publicly available citrus RNA-seq datasets. OrangeExpDB can be accessed at http://www.orangeexpdb.com/ .
(© 2024. The Author(s).)

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GJJ201432 Foundation of Jiangxi Province Educational Committee; 20194ABC28007 Major Science and Technology R& D Program of Jiangxi Province; 32260659 National Natural Science Foundation of China

Keywords: Citrus; Database; Expression; OrangeExpDB; RNA-sequencing

Date Created: 20240527 Date Completed: 20240528 Latest Revision: 20240530

20240530

PMC11129468

10.1186/s12864-024-10445-5

38802746