A Web-based Database Server Using 43,710 Public RNA-seq Samples for the Analysis of Gene Expression and Alternative Splicing in Livestock Animals

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2022 Oct 17

PMID 36253723

Authors

Jinding Liu

Kun Lang

Suxu Tan

Wencai Jie

Yihua Zhu

Shiqing Huang

Wen Huang

Affiliations

Soon will be listed here.

Abstract

Background: Livestock animals is of great significance in agricultural production. However, the role of specific gene expression, especially alternative splicing in determining phenotype, is not well understood. The livestock research community needs a gene expression and alternative splicing database contributing to livestock genetic improvement.

Description: We report the construction of LivestockExp ( https://bioinfo.njau.edu.cn/livestockExp ), a web-based database server for the exploration of gene expression and alternative splicing using 43,710 uniformly processed RNA-seq samples from livestock animals and several relative species across six orders. The database is equipped with basic querying functions and multiple online analysis modules including differential/specific expression analysis, co-expression network analysis, and cross-species gene expression conservation analysis. In addition to the re-analysis of public datasets, users can upload personal datasets to perform co-analysis with public datasets. The database also offers a wide range of visualization tools and diverse links to external databases enabling users to efficiently explore the results and to gain additional insights.

Conclusion: LivestockExp covers by far the largest number of livestock animal species and RNA-seq samples and provides a valuable data resource and analysis platform for the convenient utilization of public RNA-seq datasets.

Citing Articles

When Livestock Genomes Meet Third-Generation Sequencing Technology: From Opportunities to Applications.

Liu X, Zheng J, Ding J, Wu J, Zuo F, Zhang G Genes (Basel). 2024; 15(2).

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Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs.

Dwivedi S, Quiroz L, Reddy A, Spillane C, Ortiz R Int J Mol Sci. 2023; 24(20).

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