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Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform
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FishGET: A fish gene expression and transcriptome database with improved accuracy and visualization.

Cheng Guo1,2, You Duan3,4,5, Weidong Ye1,2

  • 1Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.

Iscience
|April 24, 2023
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Summary
This summary is machine-generated.

FishGET curates fish RNA-seq data to identify novel messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs), enhancing reference transcriptomes and annotations. This resource aids fish gene expression research through a dynamic web interface.

Keywords:
Computational bioinformaticsIchthyologyTranscriptomics

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Area of Science:

  • Genomics
  • Bioinformatics
  • Transcriptomics

Background:

  • The proliferation of fish RNA-sequencing (RNA-seq) data necessitates systematic curation for a comprehensive understanding of gene expression.
  • Existing fish transcriptomes require expansion and improved annotation to support advanced research.

Purpose of the Study:

  • To establish FishGET, a curated database of fish RNA-seq data for discovering novel RNAs (mRNA, lncRNA).
  • To create a more complete reference transcriptome and enhance transcriptome annotations for fish species.
  • To provide a user-friendly platform for accessing and visualizing fish gene expression data.

Main Methods:

  • Collected and curated 1362 RNA-seq datasets from 8 fish species across 97 studies.
  • Performed transcript assembly, meta-assembly, and Weighted Gene Co-expression Network Analysis (WGCNA).
  • Conducted functional, neighbor location, lncRNA type, and homology annotations.

Main Results:

  • Successfully identified and annotated numerous novel messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs).
  • Developed a comprehensive reference transcriptome for the studied fish species.
  • Generated detailed transcriptome annotations, including functional and homology information.

Conclusions:

  • FishGET significantly enhances the completeness and accuracy of fish reference transcriptomes and annotations.
  • The curated database and web interface facilitate deeper research into fish gene expression at the transcriptional level.
  • This resource supports the discovery of new RNAs and improves the understanding of fish genomics.