BiNChE: a web tool and library for chemical enrichment analysis based on the ChEBI ontology.

Journal: BMC bioinformatics
Published Date: Feb 21, 2015

Abstract

BACKGROUND: Ontology-based enrichment analysis aids in the interpretation and understanding of large-scale biological data. Ontologies are hierarchies of biologically relevant groupings. Using ontology annotations, which link ontology classes to biological entities, enrichment analysis methods assess whether there is a significant over or under representation of entities for ontology classes. While many tools exist that run enrichment analysis for protein sets annotated with the Gene Ontology, there are only a few that can be used for small molecules enrichment analysis.

Authors

  • Pablo Moreno
    Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. pmoreno@ebi.ac.uk.
  • Stephan Beisken
    Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. beisken@ebi.ac.uk.
  • Bhavana Harsha
    Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. bh4@sanger.ac.uk.
  • Venkatesh Muthukrishnan
    Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. venkat@ebi.ac.uk.
  • Ilinca Tudose
    Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. tudose@ebi.ac.uk.
  • Adriano Dekker
    Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. adekker@ebi.ac.uk.
  • Stefanie Dornfeldt
    Dept. of Stress- and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany. stefanie.dornfeldt@student.uni-halle.de.
  • Franziska Taruttis
    Dept. of Stress- and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany. franziska_taruttis@yahoo.de.
  • Ivo Grosse
    Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle, Germany. grosse@informatik.uni-halle.de.
  • Janna Hastings
    Institute for Implementation Science in Health Care, Faculty of Medicine, University of Zurich, Zürich, Zurich, Switzerland.
  • Steffen Neumann
    Dept. of Stress- and Developmental Biology, Leibniz Institute of Plant Biochemistry, Halle, Germany. steffen.neumann@ipb-halle.de.
  • Christoph Steinbeck
    Cheminformatics and Metabolism, European Molecular Biology Laboratory - European Bioinformatics Institute, Cambridge, UK. steinbeck@ebi.ac.uk.

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