Novel map descriptors for characterization of toxic effects in proteomics maps

Željko Bajzer, Milan Randić, Dejan Plavšić, Subhash C. Basak

Research output: Contribution to journalArticle

50 Scopus citations

Abstract

We consider a novel numerical characterization of proteomics maps based on the construction of a graph obtained by connecting all protein spots in a proteomics map that are at distance equal to, or smaller than, a critical distance Dc. We refer to the so constructed graph as a cluster graph and we calculate four associated characteristic matrices, previously considered in the literature: (1) the Euclidean-distance matrix ED; (2) the neighborhood-distance matrix ND; (3) the path-distance matrix based on the shortest paths between connected spots PD; and (4) the quotient matrix Q, the elements of which are given as the quotient of the corresponding elements of ED and ND matrices. Numerical descriptors for proteomics maps include in particular the leading eigenvalue of the Q matrix and the family of associated "higher order" matrices defined as powers of Q. These map descriptors show considerable sensitivity to perturbations of proteomics maps by toxicants.

Original languageEnglish (US)
Pages (from-to)1-9
Number of pages9
JournalJournal of Molecular Graphics and Modelling
Volume22
Issue number1
DOIs
StatePublished - Sep 1 2003

Keywords

  • Graph-theoretical descriptors
  • Matrix invariants
  • Peroxisome proliferators
  • Proteomics map
  • Quotient matrix

ASJC Scopus subject areas

  • Spectroscopy
  • Physical and Theoretical Chemistry
  • Computer Graphics and Computer-Aided Design
  • Materials Chemistry

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