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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

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Incorporating the human gene annotations in different databases significantly improved transcriptomic and genetic

Geng Chen¹, Charles Wang, Leming Shi

¹East China Normal University, Shanghai, China.

RNA (New York, N.Y.)

|February 23, 2013

Summary

Human gene annotation completeness varies across databases like RefSeq, Ensembl, and AceView. Integrating these resources enhances transcriptomic and genetic study accuracy by providing a more comprehensive gene set.

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Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Human gene annotation is vital for transcriptomic and genetic research.
The impact of diverse gene annotation databases on study outcomes requires thorough evaluation.

Purpose of the Study:

To systematically compare human gene annotations from RefSeq, Ensembl (GENCODE), and AceView.
To assess the effects of these annotations on transcriptomic and genetic analyses.
To determine if integrating annotations improves study results.

Main Methods:

Comparative analysis of gene annotations across RefSeq, Ensembl, and AceView.
Evaluation of annotation impacts on short-read mapping, gene/isoform expression profiling, and differential expression calling.
Assessment of single nucleotide polymorphism (SNP) locations within annotated gene regions.

Main Results:

Human gene annotations in RefSeq, Ensembl, and AceView are incomplete.
Significant overlap and discrepancies exist between annotations, with Ensembl and AceView annotating more genes.
Annotation differences distinctly affect transcriptomic analyses and SNP localization.
Integrating annotations yields a more complete gene set and enhances transcriptomic and genetic study outcomes.
Many trait/disease-associated SNPs previously in intergenic regions were relocated within genes in Ensembl and AceView.

Conclusions:

A comprehensive human gene annotation is crucial for accurate transcriptomic and genetic studies.
Integrating diverse annotation databases significantly improves the completeness of the human transcriptome.
Enhanced transcriptome annotation markedly boosts the overall results of transcriptomic and genetic analyses.