ArticleNAR genomics and bioinformatics2024
IsopretGO-analysing and visualizing the functional consequences of differential splicing.
Article in NAR genomics and bioinformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Gene Ontology overrepresentation analysis (GO-ORA) is a standard approach towards characterizing salient functional characteristics of sets of differentially expressed genes (DGE) in RNA sequencing (RNA-seq) experiments. GO-ORA compares the distribution of GO annotations of the DGE to that of all genes or all expressed genes. This approach has not been available to characterize differential alternative splicing (DAS). Here, we introduce a desktop application called isopretGO for visualizing the functional implications of DGE and DAS that leverages our previously published machine-learning predictions of GO annotations for individual isoforms. We show based on an analysis of 100 RNA-seq datasets that DAS and DGE frequently have starkly different functional profiles. We present an example that shows how isopretGO can be used to identify functional shifts in RNA-seq data that can be attributed to differential splicing.
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