Gene2DGE: a Perl package for gene model renewal with digital gene expression data

Area of Science:

• Genomics
• Bioinformatics
• Transcriptomics

Background:

• Accurate transcriptome analysis requires precise definition of all genomic transcripts.
• Digital gene expression (DGE) studies reveal numerous novel transcripts beyond known gene models.
• Existing DGE studies heavily rely on current gene annotations, limiting discovery.

Purpose of the Study:

• To present Gene2DGE, a Perl software package for updating gene models using DGE data.
• To enable ab initio prediction for refining and renewing gene models in transcriptome analysis.
• To identify novel transcribed regions and potential new genes.

Main Methods:

• Applied Gene2DGE to mouse blastomere transcriptome data.
• Utilized read clustering to define 98,532 read-enriched regions (RERs).
• Employed an ab initio method for gene model refinement and novel exon identification.

Main Results:

• Refined 2,104 exonic regions, extending into un-annotated areas.
• Identified 13,291 potential exons within intronic regions.
• Renewed 4,788 gene models (39% of total transcribed genes) and discovered 12,613 intergenic RERs.

Conclusions:

• Gene2DGE is an effective tool for renewing known gene models through ab initio prediction.
• The study significantly improved mouse transcriptome annotation.
• Identified potential novel genes and transcribed regions, advancing transcriptome dissection.