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Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance.
Manjang, Kalifa; Tripathi, Shailesh; Yli-Harja, Olli; Dehmer, Matthias; Emmert-Streib, Frank.
Afiliación
  • Manjang K; Predictive Society and Data Analytics Lab, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland.
  • Tripathi S; Predictive Society and Data Analytics Lab, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland.
  • Yli-Harja O; Computational Systems Biology, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland.
  • Dehmer M; Institute for Systems Biology, Seattle, WA, USA.
  • Emmert-Streib F; Institute of Biosciences and Medical Technology, Tampere University, Tampere, Korkeakoulunkatu 10, 33720, Tampere, Finland.
Sci Rep ; 10(1): 16672, 2020 10 07.
Article en En | MEDLINE | ID: mdl-33028846
Gene ontology (GO) is an eminent knowledge base frequently used for providing biological interpretations for the analysis of genes or gene sets from biological, medical and clinical problems. Unfortunately, the interpretation of such results is challenging due to the large number of GO terms, their hierarchical and connected organization as directed acyclic graphs (DAGs) and the lack of tools allowing to exploit this structural information explicitly. For this reason, we developed the R package GOxploreR. The main features of GOxploreR are (I) easy and direct access to structural features of GO, (II) structure-based ranking of GO-terms, (III) mapping to reduced GO-DAGs including visualization capabilities and (IV) prioritizing of GO-terms. The underlying idea of GOxploreR is to exploit a graph-theoretical perspective of GO as manifested by its DAG-structure and the containing hierarchy levels for cumulating semantic information. That means all these features enhance the utilization of structural information of GO and complement existing analysis tools. Overall, GOxploreR provides exploratory as well as confirmatory tools for complementing any kind of analysis resulting in a list of GO-terms, e.g., from differentially expressed genes or gene sets, GWAS or biomarkers. Our R package GOxploreR is freely available from CRAN.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Bases de Datos Genéticas / Ontología de Genes Límite: Humans Idioma: En Revista: Sci Rep Año: 2020 Tipo del documento: Article País de afiliación: Finlandia Pais de publicación: Reino Unido
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Bases de Datos Genéticas / Ontología de Genes Límite: Humans Idioma: En Revista: Sci Rep Año: 2020 Tipo del documento: Article País de afiliación: Finlandia Pais de publicación: Reino Unido