GeneFamily: a comprehensive mammalian gene family database with extensive annotation and interactive visualization
Yinan Wang1,2, Yuanzheng Zhang3,4, Xueying Wang3,4
1Institutes for Systems Genetics, West China Hospital, Sichuan University, 24 South Section 1, Yihuan Road, Chengdu 610065, China.
Nucleic Acids Research
|November 18, 2025
Summary
GeneFamily is a new database simplifying mammalian gene family analysis for researchers. It offers interactive tools for exploring gene evolution and comparative genomics without needing advanced bioinformatics skills.
Area of Science:
- Genomics
- Bioinformatics
- Evolutionary Biology
Background:
- Gene families are crucial for genetic innovation and phenotypic diversity.
- Current gene family analysis requires specialized bioinformatics skills and time-intensive workflows, limiting accessibility for many researchers.
Purpose of the Study:
- To develop GeneFamily, a user-friendly database and web interface for comprehensive mammalian gene family analysis.
- To overcome technical barriers and accelerate research in gene family evolution, functional diversification, and comparative genomics.
Main Methods:
- Leveraged whole-genome data from 138 mammalian species.
- Utilized Pfam-A hidden Markov models to identify and encompass 2036 gene families.
- Developed an intuitive web interface for interactive data exploration and visualization.
Main Results:
- GeneFamily provides extensive annotations and interactive visualizations for 2036 mammalian gene families.
- Users can explore gene distributions, phylogenetic trees, sequence identities, structural features, conserved motifs, chromosomal localizations, gene collinearities, duplication events, and adaptive signatures.
- The database significantly reduces technical barriers for nonexpert users.
Conclusions:
- GeneFamily democratizes mammalian gene family research by offering accessible bioinformatics tools.
- The database accelerates discoveries in evolutionary genomics and functional diversification across mammals.
- It serves as a valuable resource for comparative genomics and understanding genetic innovation.
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