AFED, a comprehensive resource for Aspergillus flavus gene expression profiling

Authors: Mack, Brian; Lebar, Matthew

Submitted to: Scientific Data
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/31/2025
Publication Date: 4/18/2025
Citation: Mack, B.M., Lebar, M.D. 2025. AFED, a comprehensive resource for Aspergillus flavus gene expression profiling. Scientific Data. 2025. Article baaf033. https://doi.org/10.1093/database/baaf033.
DOI: https://doi.org/10.1093/database/baaf033

Interpretive Summary: The lack of a comprehensive and accessible database for gene expression data in Aspergillus flavus, a fungus with significant agricultural and medical importance, has hindered research and understanding of its biology. To address this need, we created the Aspergillus flavus Expression Database (AFED), a web-based interface that provides a comprehensive resource for gene expression data in A. flavus. Leveraging public RNA-Seq data from 604 samples across 52 experiments, AFED enables researchers to examine gene expression profiles across different growth conditions and life cycle stages, visualize expression profiles through interactive plots and heatmaps, and identify co-expressed genes and explore functional enrichment among them. By providing a centralized and user-friendly platform for exploring gene expression data in A. flavus, AFED facilitates a better understanding of the fungus's biology, with implications for research in fungal development and pathogenesis, secondary metabolite production, and host-fungus interactions.

Technical Abstract: Public RNA-Seq data was used to quantify gene expression abundance for 604 Aspergillus flavus samples from 52 experiments (bioprojects). Using abundance data, we created an Aspergillus flavus expression database (AFED) accessible through a web-based interface that allows for the expression profiles of genes to be conveniently examined across different growth conditions and life cycle stages. Expression profiles can be visualized through either an interactive bar plot for single gene queries or a heatmap for multiple gene queries. A gene co-expression network based on samples containing at least 10 million mapped reads is also available, which allows users to identify genes that are co-expressed with an individual gene or set of genes and displays the functional enrichment among the co-expressed genes.