FifBase: a comprehensive fertility-associated indicators factor database for domestic animals.

Area of Science:

• Animal Reproduction and Genetics
• Bioinformatics and Database Development

Background:

• Animal fertility is crucial for productivity but influenced by complex genetic and environmental factors.
• Existing research on fertility genes is fragmented across literature, hindering comprehensive analysis.
• Novel fertility-associated genes remain undiscovered in omics datasets.

Purpose of the Study:

• To construct a centralized database (FifBase) for animal fertility-related factors.
• To integrate manually curated literature data with omics-based RNA-Seq datasets.
• To facilitate the discovery and retrieval of genes and environmental factors impacting animal fertility.

Main Methods:

• Manual curation of 3301 PubMed articles across 13 species to identify fertility-related genes and factors.
• Analysis of RNA-Seq datasets to detect novel fertility-associated genes.
• Development of the FifBase database (http://www.nwsuaflmz.com/FifBase/) for data browsing, retrieval, and download.

Main Results:

• FifBase integrates data from literature and RNA-Seq, identifying 1558 fertility-associated genes in 10 species.
• The database contains 2910 fertility-gene pairs and links genes to 58 environmental factors.
• Data includes 1088 genes from RNA-Seq and 470 from text mining, alongside gene annotations.

Conclusions:

• FifBase provides a valuable, user-friendly resource for researchers studying animal fertility.
• The database aids in identifying novel fertility genes and understanding environmental influences.
• This integrated approach supports advancements in animal reproductive science and productivity.