WikiGOA: Gene set enrichment analysis based on Wikipedia and the Gene Ontology

Gene sets curated to Gene Ontology terms are widely used by the transcriptomics community. Presence in Wikipedia is a common proxy for the relevance of a concept. In this work, we describe the use of Wikidata to generate a dataset comprising only gene sets with a corresponding Wikipedia page. We ref...

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Bibliographic Details
Published inbioRxiv
Main Authors Lubiana, Tiago, Thomaz Luscher Dias, Debora Guerra Peixe, Helder Takashi Imoto Nakaya
Format Paper
LanguageEnglish
Published Cold Spring Harbor Cold Spring Harbor Laboratory Press 17.09.2022
Subjects
Gene expression
Gene set enrichment analysis
Transcriptomics
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Summary:Gene sets curated to Gene Ontology terms are widely used by the transcriptomics community. Presence in Wikipedia is a common proxy for the relevance of a concept. In this work, we describe the use of Wikidata to generate a dataset comprising only gene sets with a corresponding Wikipedia page. We refer to the dataset as WikiGOA, standing for Wikipedia Gene Ontology Annotations. We use the dataset to analyze gene expression data and show that it provides readily understandable results. We envision WikiGOA to be useful for exploring complex biological datasets both in academic research and educational contexts. Competing Interest Statement The authors have declared no competing interest.
DOI:10.1101/2022.09.15.508149