Ontological analysis of gene expression data: current tools, limitations, and open problems

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…

• NS
  National Science Foundation

  Award: 0234806
• UD
  U.S. Department of Defense
• NI
  National Institutes of Health
• NC
  National Center for Research Resources
• DO
  Division of Biological Infrastructure