FishGET: A Fish Gene Expression and Transcriptome Database with Improved Accuracy and Visualization

Abstract

With the rapid expansion of transcriptome studies in many fishes, a great number of RNA-seq data have been published, allowing for a more systematic understanding of the general profiles and details of gene expression in fish. FishGET is dedicated to gathering and curating fish RNA-seq data in order to discover more novel RNAs, including mRNA and lncRNA, thereby getting a more complete reference transcriptome and providing more comprehensive and accurate transcriptome annotations.We obtained a total of 1362 RNA-seq paired-end data from 97 different studies, and then we performed transcript assembly, meta assembly, weighted gene co-expression network analysis (WGCNA), NR/KEGG/GO annotation, neighbor location annotation, lncRNA type annotation, homology annotation, and other types of work on the data. At the moment, zebrafish (Danio rerio), grass carp (Ctenopharyngodon idella), rainbow trout (Oncorhynchus mykiss), and a few others are among the eight fish species that make up FishGET.To promote research into fish genes at the transcriptional level, we developed a user-friendly web interface (http://bioinfo.ihb.ac.cn/fishget) that allows users to view all information and makes use of multiple types of dynamic interactive visualization services.