BarleyExpDB: an integrative gene expression database for barley

Abstract

Background RNA-sequencing (RNA-seq) has been widely used to study the dynamic expression patterns of transcribed genes, which can lead to new biological insights. However, processing and analyzing these huge amounts of histological data remains a great challenge for wet labs and field researchers who lack bioinformatics experience and computational resources. Results We present BarleyExpDB, an easy-to-operate, free, and web-accessible database that integrates transcriptional profiles of barley at different growth and developmental stages, tissues, and stress conditions, as well as differential expression of mutants and populations to build a platform for barley expression and visualization. The expression of a gene of interest can be easily queried by searching by known gene ID or sequence similarity. Expression data can be displayed as a heat map, along with functional descriptions as well as Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Proteins Families Database, and Simple Modular Architecture Research Tool annotations. Conclusions BarleyExpDB will serve as a valuable resource for the barley research community to leverage the vast publicly available RNA-seq datasets for functional genomics research and crop molecular breeding.

Genome-wide identification and expression profiling of PIN-PILS family genes in barley reveal potential role in spikelet abortion and abiotic stress tolerance

“…The Barley Expression Database (BarleyExpDB) (Li et al 2023) was used to get the expression data of HvPIN-PILSs corresponding to various conditions and developmental stages were obtained, including 16 developmental stages (Table S1) (PRJEB14349), apical spikelet abortion (PRJEB51523), heat stress (PRJNA324116), cold stress (PRJNA767196), salinity stress (PRJNA781996), heavy metals stress (PRJNA382490), low nitrogen (PRJNA566107), and drought stress (PRJEB12540). The normalized log2(FPKM) values were used to generate heatmaps of HvPIN-PILSs expression, which were constructed using TBtools.…”

OrangeExpDB: an integrative gene expression database for Citrus spp.

“…Furthermore, the data is often fragmented. As data growth continue to accelerate, there is a need for a standardized and simplified method of accessing gene expression data [ 24 ].…”

“…Recently, numerous online databases have been established, including CPBD [ 25 ], NGDC [ 26 ], TeaPGDB [ 27 ], BarleyExpDB [ 24 ], PlantcircBase [ 28 ], GRooT [ 29 ], PHI-base [ 30 ], and MPDB [ 31 ]. Notebly, these databases not only store data, but also offer various tools for analyzing biological data, such as BLAST [ 24 , 25 ].…”

“…Recently, numerous online databases have been established, including CPBD [ 25 ], NGDC [ 26 ], TeaPGDB [ 27 ], BarleyExpDB [ 24 ], PlantcircBase [ 28 ], GRooT [ 29 ], PHI-base [ 30 ], and MPDB [ 31 ]. Notebly, these databases not only store data, but also offer various tools for analyzing biological data, such as BLAST [ 24 , 25 ]. TeaPGDB, for example, is a user-friendly platform for tea plant genome, providing access to seven tea genome sequences and five tool sets, including “Gene Search”, “BLAST”, “JBrowse”, “SSR” and “Download” [ 27 ].…”

“…PlantcircBase is a database that consolidates all plant-circRNA data [ 28 ]. Importantly, BarleyExpDB contains transcriptional profiles of barley across various growth and developmental stages, tissues, and stress conditions [ 24 ]. These databases are useful for analyzing the intricate regulatory mechanisms of various organisms.…”