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An equivalence test between features lists, based on the Sorensen-Dice index and the joint frequencies of GO term enrichment.
Flores, Pablo; Salicrú, Miquel; Sánchez-Pla, Alex; Ocaña, Jordi.
Afiliação
  • Flores P; Escuela Superior Politécnica de Chimborazo (ESPOCH), Research Group in Data Science CIDED, Panamericana Sur Km 1 1/2, Riobamba, Ecuador. p_flores@espoch.edu.ec.
  • Salicrú M; Department of Statistics and Operational Research, Faculty of Mathematics and Statistics, Universitat Politècnica de Catalunya, Barcelona, Spain. p_flores@espoch.edu.ec.
  • Sánchez-Pla A; Department of Genetics, Microbiology and Statistics, Statistics Section, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain.
  • Ocaña J; Department of Genetics, Microbiology and Statistics, Statistics Section, Universitat de Barcelona, Av. Diagonal 643, 08028, Barcelona, Spain.
BMC Bioinformatics ; 23(1): 207, 2022 May 31.
Article em En | MEDLINE | ID: mdl-35641928
BACKGROUND: In integrative bioinformatic analyses, it is of great interest to stablish the equivalence between gene or (more in general) feature lists, up to a given level and in terms of their annotations in the Gene Ontology. The aim of this article is to present an equivalence test based on the proportion of GO terms which are declared as enriched in both lists simultaneously. RESULTS: On the basis of these data, the dissimilarity between gene lists is measured by means of the Sorensen-Dice index. We present two flavours of the same test: One of them based on the asymptotic normality of the test statistic and the other based on the bootstrap method. CONCLUSIONS: The accuracy of these tests is studied by means of simulation and their possible interest is illustrated by using them over two real datasets: A collection of gene lists related to cancer and a collection of gene lists related to kidney rejection after transplantation.
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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Biologia Computacional / Neoplasias Limite: Humans Idioma: En Revista: BMC Bioinformatics Assunto da revista: INFORMATICA MEDICA Ano de publicação: 2022 Tipo de documento: Article País de afiliação: Equador País de publicação: Reino Unido
Texto completo
Adicionar na Minha BVS
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Biologia Computacional / Neoplasias Limite: Humans Idioma: En Revista: BMC Bioinformatics Assunto da revista: INFORMATICA MEDICA Ano de publicação: 2022 Tipo de documento: Article País de afiliação: Equador País de publicação: Reino Unido