GeneFamily: a comprehensive mammalian gene family database with extensive annotation and interactive visualization

作者：Yinan Wang, Yuanzheng Zhang, Xueying Wang, Yen Kaow Ng, Yi Jia, Zicheng Zhao, Jiahe Liu, Shuo Yang, Bairong Shen, Shuai Cheng Li · 发表于：Nucleic Acids Research · 年份：2025 · DOI：10.1093/nar/gkaf1195 · 被引用次数：2 · 研究领域：Genomics and Phylogenetic Studies、Bioinformatics and Genomic Networks、Genome Rearrangement Algorithms

Gene families underlie genetic innovation and phenotypic diversification. However, the identification, analysis, and interpretation of gene families depend on custom bioinformatics and visualization workflows that are mainly unattainable for nonexpert users. To overcome the learning curve associated with analytical tools and the time costs involved in data collection and processing, we propose GeneFamily (https://gh.deepomics.org/), a comprehensive mammalian gene family database that incorporates extensive annotations and interactive visualizations. Leveraging whole-genome data from 138 mammalian species and Pfam-A hidden Markov models, GeneFamily encompasses 2036 gene families. Users can explore gene family distributions, phylogenetic trees, member diversities, sequence identities, structural features, conserved motifs, chromosomal localizations, neighboring regions, gene collinearities, duplication events, and adaptive signatures via an intuitive web interface. GeneFamily reduces technical barriers and accelerates research into gene family evolution, functional diversification, and comparative genomics across mammals.