Encyclopedia of Systems Biology

2013 Edition
| Editors: Werner Dubitzky, Olaf Wolkenhauer, Kwang-Hyun Cho, Hiroki Yokota

Ontology Analysis of Biological Networks

  • Jiguang Wang
Reference work entry
DOI: https://doi.org/10.1007/978-1-4419-9863-7_487

Definition

Ontology analysis of biological networks is the strategy to discover the biological implications via identifying significantly enriched annotated ontology terms in networks or subnetworks.

Characteristics

According to the accumulation of different types of experimental data and prior knowledge, more and more biological networks are constructed to discover the underlying mechanisms of cell in a system level. At the same time, the demand for strategies to analyze and mine biological meanings from these resulting networks increases quickly.  Function enrichment analysis is an important way to fill the requirement. An efficient way to accurately describe function of gene is to use the  ontology structure ( ontology) of GO ( Gene Ontology) terms.

The Importance of Ontology Analysis

 Ontologywhich is a formal representation of knowledge is one of the most popular words in information science recently. To uniformly represent gene and gene product across databases and species,...

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References

  1. Al-Shahrour F et al (2004) FatiGO: a web tool for finding significant associations of gene ontology terms with groups of genes. Bioinformatics 20:578–580PubMedGoogle Scholar
  2. Ashburner M et al (2000) Gene ontology: tool for the unification of biology. The gene ontology Consortium. Nat Genet 25:25–29PubMedGoogle Scholar
  3. Huang DW, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4(1):44–57Google Scholar
  4. Maere S, Heymans K, Kuiper M (2005) BiNGO: a cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21(16):3448–3449PubMedGoogle Scholar
  5. Reimand J, Kull M, Peterson H, Hansen J, Vilo J (2007) g:profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments. Nucleic Acids Res 35(Web Server issue):W193–W200PubMedGoogle Scholar
  6. Shaffer JP (1995) Multiple hypothesis testing. Ann Rev Psych 46:561–584Google Scholar
  7. Wang J et al (2011) NOA: a novel network ontology analysis method. Nucleic Acids Res 39(13):e87. doi:10.1093/nar/gkr251PubMedGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2013

Authors and Affiliations

  1. 1.Beijing Institute of GenomicsChinese Academy of ScienceBeijingChina