| |
BiNChE: A web tool and library for chemical enrichment analysis based on the ChEBI ontology
- 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
- 参考文献:1. Ashburner, M, Ball, CA, Blake, JA, Botstein, D, Butler, H, Cherry, JM (2000) Gene Ontology: tool for the unification of biology. Nat Genet 25: pp. 25-9 CrossRef
2. Huang, DW, Sherman, BT, Lempicki, RA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37: pp. 1-13 CrossRef 3. Hastings, J, De Matos, P, Dekker, A, Ennis, M, Harsha, B, Kale, N (2013) The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res 41: pp. D456-63 46" target="_blank" title="It opens in new window">CrossRef 4. Xia, J, Wishart, DS (2010) MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. Nucleic Acids Res 38: pp. W71-7 CrossRef 5. Chagoyeny, M, Pazos, F (2011) MBRole: enrichment analysis of metabolomic data. Bioinformatics 27: pp. 730-31 CrossRef 6. Maere, S, Heymans, K, Kuiper, M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21: pp. 3448-9 CrossRef 7. Tirrell, R, Evani, U, Berman, AE, Mooney, SD, Musen, MA, Shah, NH (2010) An ontology-neutral framework for enrichment analysis. AMIA Annu Symp Proc 2010: pp. 797-801 8. Lopes, CT, Franz, M, Kazi, F, Donaldson, SL, Morris, Q, Bader, GD (2010) Cytoscape Web: an interactive web-based network browser. Bioinformatics 26: pp. 2347-8 430" target="_blank" title="It opens in new window">CrossRef 9. Yu, Y-K (2010) Robust and accurate data enrichment statistics via distribution function of sum of weights. Bioinformatics 26: pp. 2752-9 CrossRef 10. Haug, K, Salek, RM, Conesa, P, Hastings, J, de Matos, P, Rijnbeek, M (2013) MetaboLights鈥揳n open-access general-purpose repository for metabolomics studies and associated meta-data. Nucleic Acids Res 41: pp. D781-6 4" target="_blank" title="It opens in new window">CrossRef 11. Bordbar, A, Mo, ML, Nakayasu, ES, Schrimpe-Rutledge, AC, Kim, YM, Metz, TO (2012) Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation. Mol Syst Biol 8: pp. 558 CrossRef 12. Kim, YM, Schmidt, BJ, Kidwai, AS, Jones, MB, Kaiser, BLD, Brewer, HM (2013) Salmonella Modulates Metabolism during Growth under Conditions that induce expression of virulence genes. Mol BioSyst 9.6: pp. 1552-34 13. Wolf, S, Schmid, S, M眉ller-Hannemann, M, Neumann, S (2010) In silico fragmentation for computer assisted identification of metabolite mass spectra. BMC Bioinformatics 11: pp. 148-60 471-2105-11-148" target="_blank" title="It opens in new window">CrossRef 14. Chambers, J, Davies, M, Gaulton, A, Hersey, A, Velankar, S (2013) UniChem: a unified chemical structure cross-referencing and identifier tracking system. J Cheminformatics 5: pp. 1 46-5-3" target="_blank" title="It opens in new window">CrossRef
- 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.
| |
NGLC 2004-2010.National Geological Library of China All Rights Reserved.
Add:29 Xueyuan Rd,Haidian District,Beijing,PRC. Mail Add: 8324 mailbox 100083
For exchange or info please contact us via email.
| |