A web-based database server using 43,710 public RNA-seq samples for the analysis of gene expression and alternative splicing in livestock animals.
Alternative splicing
Database
Gene expression
Livestock
RNA-seq
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
17 Oct 2022
17 Oct 2022
Historique:
received:
17
03
2022
accepted:
09
09
2022
entrez:
17
10
2022
pubmed:
18
10
2022
medline:
20
10
2022
Statut:
epublish
Résumé
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. 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. 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.
Sections du résumé
BACKGROUND
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
METHODS
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
CONCLUSIONS
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.
Identifiants
pubmed: 36253723
doi: 10.1186/s12864-022-08881-2
pii: 10.1186/s12864-022-08881-2
pmc: PMC9575303
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
706Subventions
Organisme : USDA Hatch Project
ID : MICL02560
Organisme : Fundamental Research Funds for Central Universities of the Central South University
ID : KYXK2021006
Informations de copyright
© 2022. The Author(s).
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