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

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• 作者：Pablo Moreno (1)
  Stephan Beisken (1)
  Bhavana Harsha (1)
  Venkatesh Muthukrishnan (1)
  Ilinca Tudose (1)
  Adriano Dekker (1)
  Stefanie Dornfeldt (2)
  Franziska Taruttis (2) (3)
  Ivo Grosse (4) (5)
  Janna Hastings (1)
  Steffen Neumann (2)
  Christoph Steinbeck (1)
  
  1. Cheminformatics and Metabolism ; European Molecular Biology Laboratory - European Bioinformatics Institute ; Cambridge ; UK
  2. Dept. of Stress- and Developmental Biology ; Leibniz Institute of Plant Biochemistry ; Halle ; Germany
  3. Dept. of Statistical Bioinformatics ; Institute for Functional Genomics ; University of Regensburg ; Halle ; Germany
  4. Institute of Computer Science ; Martin Luther University Halle-Wittenberg ; Halle ; Germany
  5. German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig ; Leipzig ; Germany
  
• 关键词：Ontology ; Enrichment ; Small molecules
• 刊名：BMC Bioinformatics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：16
• 期：1
• 全文大小：784 KB
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• 刊物主题：Bioinformatics; Microarrays; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Combinatorial Libraries; Algorithms;
• 出版者：BioMed Central
• ISSN：1471-2105

文摘

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. Results We describe BiNChE, an enrichment analysis tool for small molecules based on the ChEBI Ontology. BiNChE displays an interactive graph that can be exported as a high-resolution image or in network formats. The tool provides plain, weighted and fragment analysis based on either the ChEBI Role Ontology or the ChEBI Structural Ontology. Conclusions BiNChE aids in the exploration of large sets of small molecules produced within Metabolomics or other Systems Biology research contexts. The open-source tool provides easy and highly interactive web access to enrichment analysis with the ChEBI ontology tool and is additionally available as a standalone library.