As the largest group of vertebrates, fish serve not only as a food source and subjects of research for human, but also play a crucial role as animal models in various scientific research fields, including disease modeling, drug screening, environmental toxicology assessment, and the exploration of various life processes. Currently, the research background on fish multi-omics is rapidly advancing, and the exponential growth in multi-omics data offering unprecedented opportunities for genetic mechanism research exploration and comprehensive systematic analysis. Nevertheless, high-throughput omics data related to fish originate from diverse studies and are dispersed across literature and various databases, rendering them inconvenient for reuse.

FishCODE, an integrated database that comprehensively incorporates fish multi-omics data and offers multidimensional gene-related information. FishCODE encompasses 540 sets of transcriptome and methylome data derived from 11,216 samples within prominent scientific research domains. It extents across 35 fish species, including zebrafish, medaka and Atlantic salmon. FishCODE strives to provide exhaustive gene-related information, encompassing transcript structure and expression, gene methylation levels, protein domains, protein subcellular localization, protein interactions, associated SNP site information, and GO/KEGG annotations.

Furthermore, leveraging the extensive multi-omics data incorporated, we have developed the Fish Experimental Conditions Ontology (FECO) comprising 211 entries (see section 'DATASETS' for details), which describe the experimental context. Users can explore the built-in datasets of interest with a simple mouse click in the FECO selector or select both the built-in and uploaded data to perform cross-dataset omics analyses. Being the primary comprehensive multi-omics data information platform for fish, FishCODE offers abundant data resources and convenient avenues for leveraging omics data in scientific research across various fields.

FishCODE is open and free for everyone to use, no login required. Rest assured, the data you submit will be kept confidential and will be automatically deleted after the conversation ends. We kindly ask users to limit their requests to no more than 3 concurrent jobs when using this web server. FishCODE retains the greatest freedom for users to merge to form new data, but please do not perform omics analysis across species, and joint analysis of methylation analysis RRBS and WGBS is not recommended. The gene name uploaded by the user must be consistent with the gene id of the annotation version specified by the database, otherwise there will be a merge error!

It is worth noting that even though we manually annotated all datasets, unfortunately we cannot guarantee the correctness of the background information (because these background data sources are searched from various sources, including original database descriptions, articles, Emails, etc.), any supplements and corrections to the background of these omics data will be valued and appreciated by us.