FishExp: A comprehensive database and analysis platform for gene expression and alternative splicing of fish species

The publicly archived RNA-seq data has grown exponentially, while its valuable information has not yet been fully discovered and utilized, such as alternative splicing and its integration with gene expression. This is especially true for fish species which play important roles in ecology, research and the food indus-try. Furthermore, there is a lack of online platform to analyze users' new data individually and jointly with existing data for the comprehensive analysis of alternative splicing and gene expression. Here, we present FishExp, a web-based data platform covering gene expression and alternative splicing in 26,081 RNA-seq experiments from 44 fishes. It allows users to query the data in a variety of ways, includ-ing gene identifier/symbol, functional term, and BLAST alignment. Moreover, users can customize exper-iments and tools to perform differential/specific expression and alternative splicing analysis, co -expression and cross-species analysis. In addition, functional enrichment is provided to confer biological significance. Notably, users are allowed to submit their own data and perform various analyses using the new data alone or alongside existing data in FishExp. Results of retrieval and analysis can be visualized on the gene-, transcript-and splicing event-level webpage in a highly interactive and intuitive manner. All data in FishExp can be downloaded for more in-depth analysis. The manually curated sample informa-tion, uniform data processing and various tools make it efficient for users to gain new insights from these large data sets, facilitating scientific hypothesis generation. FishExp is freely accessible at https://bioinfo. njau.edu.cn/fishExp.(c) 2022 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology. This is an open access article under the CC BY-NC-ND license (http://creative-commons.org/licenses/by-nc-nd/4.0/).