Information-theoretic biodescriptors for proteomics maps: Applications to rodent hepatotoxicity

Subhash C. Basak, Brian D. Gute, Kevin T. Geiss, Frank A. Witzmann

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Scopus citations

Abstract

This paper describes an approach using information theory to derive a complexity measure for proteomics maps generated using 2-dimensional gel electrophoresis (2DE gel). The maps used in this study were partitioned into 5×5 grids and total protein abundance in each grid square was compared to the total abundance for the entire map. Next, Shannon's relation was applied to characterize the distribution of protein abundance across the entire map. Details of the approach are discussed, including an example of the calculations for one proteomics map containing 200 spots. Finally, results for the Map Information Content index are presented for a set of six maps calculated using 200, 500, and 1,400 protein 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 comparing maps containing a great deal of information and yield information useful in computational toxicology.

Original languageEnglish (US)
Title of host publicationComputation in Modern Science and Engineering - Proceedings of the International Conference on Computational Methods in Science and Engineering 2007 (ICCMSE 2007)
Pages10-13
Number of pages4
Edition2
DOIs
StatePublished - Dec 1 2007
EventInternational Conference on Computational Methods in Science and Engineering 2007, ICCMSE 2007 - Corfu, Greece
Duration: Sep 25 2007Sep 30 2007

Publication series

NameAIP Conference Proceedings
Number2
Volume963
ISSN (Print)0094-243X
ISSN (Electronic)1551-7616

Other

OtherInternational Conference on Computational Methods in Science and Engineering 2007, ICCMSE 2007
CountryGreece
CityCorfu
Period9/25/079/30/07

Keywords

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

ASJC Scopus subject areas

  • Physics and Astronomy(all)

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    Basak, S. C., Gute, B. D., Geiss, K. T., & Witzmann, F. A. (2007). Information-theoretic biodescriptors for proteomics maps: Applications to rodent hepatotoxicity. In Computation in Modern Science and Engineering - Proceedings of the International Conference on Computational Methods in Science and Engineering 2007 (ICCMSE 2007) (2 ed., pp. 10-13). (AIP Conference Proceedings; Vol. 963, No. 2). https://doi.org/10.1063/1.2835935