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

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

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

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

Cheng Guo et al. iScience. .

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.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

None
Graphical abstract
Figure 1
Figure 1
The pages for statistics of datasets and expression counts (A) The number of bioprojects/samples covered by FishGET, as well as the percentage of each experiment type. (B) The data input form in the expression count page.
Figure 2
Figure 2
Implementation of FishGET (A) Data sources. For all species except zebrafish, we downloaded all Illumina paired-end RNA-seq data to date in SRA. (B) Transcriptome assembly. (C) Annotation. (D) FishGET’s architecture. (E) FishGET’s sitemap.
Figure 3
Figure 3
Advanced search page
Figure 4
Figure 4
Gene detail page of f7 (FishGET ID of zebrafish: XLOC_000007, FishGET ID of grass carp: CI01000299_06295715_06298755)
Figure 5
Figure 5
Expression page of FishGET
Figure 6
Figure 6
Coding ability prediction page of FishGET
See this image and copyright information in PMC

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