Information-theoretic biodescriptors for proteomics maps

Development and applications in predictive toxicology

Subhash C. Basak, Brian D. Gute, Frank Witzmann

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

This paper describes an approach using information theory to derive a new complexity measure for proteomics maps generated using 2-dimensional gel electrophoresis. The maps used in this study were partitioned into 5×5 grids and the total abundance of protein material in each grid was compared to the total abundance for the entire map. Next, Shannon's relation was applied to characterize the distribution of spots across the proteomics map. Details of the approach are discussed here, including an illustrative example and an example of the calculations for a proteomics map containing 200 spots. Finally, results for the Map Information Content index are presented for a set of five maps calculated using 200 spots, 500 spots, and 1,054 spots. It is hoped that the application of information-theoretic techniques to characterize the complexity of these maps, thus reducing the amount of information presented to the researcher, will help in the analysis and comparison of maps containing a great deal of information.

Original languageEnglish
Pages (from-to)996-1001
Number of pages6
JournalWSEAS Transactions on Information Science and Applications
Volume2
Issue number7
StatePublished - Jul 2005

Fingerprint

Toxicology
Proteomics
Grid
Complexity Measure
Information theory
Information Content
Information Theory
Electrophoresis
Gels
Entire
Proteins
Protein

Keywords

  • 2-DE gel
  • Biodescriptor
  • Complexity
  • Information theory
  • Map information content
  • Proteomics
  • Proteomics maps

ASJC Scopus subject areas

  • Computer Science (miscellaneous)
  • Computational Mathematics

Cite this

Information-theoretic biodescriptors for proteomics maps : Development and applications in predictive toxicology. / Basak, Subhash C.; Gute, Brian D.; Witzmann, Frank.

In: WSEAS Transactions on Information Science and Applications, Vol. 2, No. 7, 07.2005, p. 996-1001.

Research output: Contribution to journalArticle

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