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A comparison of existing tools for ontological analysis of gene expression data

Part 4. Bioinformatics

4.5. Computational Methods for High-throughput Genetic Analysis: Expression Profiling

Short Specialist Review

  1. Purvesh Khatri,
  2. Sorin Draghici

Published Online: 15 NOV 2005

DOI: 10.1002/047001153X.g405312

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics

How to Cite

Khatri, P. and Draghici, S. 2005. A comparison of existing tools for ontological analysis of gene expression data. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. 4:4.5:59.

Author Information

  1. Wayne State University, Detroit, MI, USA

Publication History

  1. Published Online: 15 NOV 2005

Abstract

Independent of the platform and the analysis methods used, the result of a microarray experiment is, in most cases, a list of differentially expressed genes. An automatic ontological analysis approach has been recently proposed to help with the biological interpretation of such results. Currently, this approach is the de facto standard for the secondary analysis of high-throughput experiments, and a large number of tools have been developed for this purpose. We present a detailed comparison of 14 such tools using the following criteria: scope of the analysis, visualization capabilities, statistical model(s) used, correction for multiple comparisons, reference microarrays available, installation issues, and sources of annotation data. This detailed analysis of the capabilities of these tools will help researchers choose the most appropriate tool for a given type of analysis.

Keywords:

  • functional profiling;
  • ontological analysis;
  • Gene Ontology;
  • gene expression data