Geneapp: A web application for visualizing alternative splicing for biomedicine

Geneapp: A web application for visualizing alternative splicing for biomedicine

Alternative Splicing (AS) is an essential mechanism for eukaryotes. However, the consequences of deleting a single exon can be dramatic for the organism and can lead to cancer in humans. Additionally, alternative 5′ and 3′ splice sites, which define the boundaries of exons, also play key roles to hu...

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Published in:Computers in biology and medicine Vol. 178; p. 108789
Main Authors: Fernandes, Miquéias, Mario de Andrade, Edson, Reis da Silva, Saymon Gazolla, Romagnoli, Vinícius dos Santos, Ortega, José Miguel, Antônio de Oliveira Mendes, Tiago
Format: Journal Article
Language:English
Published: United States Elsevier Ltd 01-08-2024
Elsevier Limited
Subjects:
Alternative splicing
Alternative Splicing - genetics
Annotations
Applications programs
Bioinformatics
Cancer
Computational Biology - methods
Data analysis
data visualization
Eukaryotes
Exons
Geneapp
Genes
Genomics
Graphs
Humans
Internet
Scientific visualization
Software
Target recognition
Visualization
Webapp
Workflow
Alternative splicing
data visualization
Geneapp
Webapp
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Summary:Alternative Splicing (AS) is an essential mechanism for eukaryotes. However, the consequences of deleting a single exon can be dramatic for the organism and can lead to cancer in humans. Additionally, alternative 5′ and 3′ splice sites, which define the boundaries of exons, also play key roles to human disorders. Therefore, Investigating AS events is crucial for understanding the molecular basis of human diseases and developing therapeutic strategies. Workflow for AS event analysis can be sampling followed by data analysis with bioinformatics to identify the different AS events in the control and case samples, data visualization for curation, and selection of relevant targets for experimental validation. The raw output of the analysis software does not favor the inspection of events by bioinformaticians requiring custom scripts for data visualization. In this work, we propose the Geneapp application with three modules: GeneappScript, GeneappServer, and GeneappExplorer. GeneappScript is a wrapper that assists in identifying AS in samples compared in two different approaches, while GeneappServer integrates data from AS analysis already performed by the user. In GeneappExplorer, the user visualizes the previous dataset by exploring AS events in genes with functional annotation. This targeted screens that Geneapp allows to perform helps in the identification of targets for experimental validation to confirm the hypotheses under study. The Geneapp is freely available for non-commercial use at https://geneapp.net to advance research on AS for bioinformatics. •Geneapp assists in the generation and visualization of Alternative Splicing data.•Includes the script to run differential AS discovery pipeline on Debian distros.•Integrates AS results at the genomic, transcriptomic, and proteomic level.•Case study shows how to gain insights in AS research with human dataset.
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ISSN:0010-4825
1879-0534
1879-0534
DOI:10.1016/j.compbiomed.2024.108789