FishGET: A fish gene expression and transcriptome database with improved accuracy and visualization

Cheng Guo; You Duan; Weidong Ye; Wanting Zhang; Yingyin Cheng; Mijuan Shi; Xiao-Qin Xia

doi:10.1016/j.isci.2023.106539

FishGET: A fish gene expression and transcriptome database with improved accuracy and visualization

iScience. 2023 Mar 31;26(4):106539. doi: 10.1016/j.isci.2023.106539. eCollection 2023 Apr 21.

Authors

Cheng Guo^{1

2}, You Duan^{3

4

5}, Weidong Ye^{1

2}, Wanting Zhang^{1

6}, Yingyin Cheng^{1

6}, Mijuan Shi^{1

6}, Xiao-Qin Xia^{1

2

6}

Affiliations

¹ Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
² College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, China.
³ The Joint Laboratory for Lung Development and Related Diseases of West China Second University Hospital, Sichuan University and School of Life Sciences of Fudan University, West China Institute of Women and Children's Health, West China Second University Hospital, Sichuan University, Chengdu, China.
⁴ Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu 610041, China.
⁵ NHC Key Laboratory of Chronobiology (Sichuan University), Chengdu, China.
⁶ The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China.

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 to discover more new 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 of 8 fishes from 97 different studies, and then we performed transcript assembly, meta-assembly, weighted gene co-expression network analysis (WGCNA), functional annotations, neighbor location annotation, lncRNA type annotation, homology annotation. To promote research into fish genes at the transcriptional level, we developed a user-friendly web interface that allows users to view all information and makes use of multiple types of dynamic interactive visualization services.

Keywords: Computational bioinformatics; Ichthyology; Transcriptomics.