FishExp is an online gene expression portal for fish species that allows users to retrieve gene expression and alternative splicing (AS) profiles, as well as perform differential/specific gene expression/AS analyses, all with flexibly customizable options. It has the following highlights:
I. Annotation improvement Gene annotations are improved to provide more isoforms and alternative splicing events, especially for non-model species.
II. Comprehensiveness A total of 26,081 RNA-seq experiments from 44 fish species are collected, processed in a uniform pipeline and stored in FishExp, which integrated gene expression and alternative splicing information. In addition, orthologous gene and AS groups among species are presented.
III. Sample curation The sample information including strain, genotype, tissue, development and treatment, are manually curated to provide accurate metadata for downstream analyses.
IV. Multi-way retrival Gene expression and splicing data can be searched with gene identifiers, symbols, various functional terms (e.g. gene ontology, protein family and pathway) and sequence similarity using BLAST program.
V. Expression analysis Differential expression/AS analysis (example ) and specific expression/AS analysis (example ) are implemented for users to find significant genes, with functional enrichments provided.
VI. High customizability Users can freely specify gene expression level metrics such as TPM or FPKM, splicing metrics such as JCEC or JC, differential expression methods such as DESeq2 or edgeR, differential splicing approaches such as rMATS unpaired/paired or MATS LRT, enrichment analysis methods such as hypergeometric test or gene set enrichment analysis (GSEA).
VII Rich visualization and external links FishExp provides a suite of data visualization tools to summarize retrieval and analysis results. It offers external links to frequently used resources, including Ensembl, NCBI, Pfam, GO, KEGG, UniProt, PubMed, miRBase, SRA and GEO.
Note that all data deposited in FishExp can be downloaded for more in-depth local analysis. Please send feedbacks and/or questions to (liujd@njau.edu.cn).

Danio rerio (zebrafish)	Oncorhynchus mykiss (rainbow trout)	Oryzias latipes (Japanese medaka)
Poecilia mexicana (shortfin molly)	Oreochromis niloticus (Nile tilapia)	Gasterosteus aculeatus (three-spined stickleback)
Ictalurus punctatus (channel catfish)	Larimichthys crocea (large yellow croaker)	Cyprinus carpio (common carp)