Star graphs of protein sequences and proteome mass spectra in cancer prediction

José M. Vázquez, Vanessa Aguiar, Jose A. Seoane, Ana Freire, José A. Serantes, Julián Dorado, Alejandro Pazos, Cristian R. Munteanu

Research output: Contribution to journalArticlepeer-review

41 Scopus citations

Abstract

The impact of cancer in the society has created the necessity of new and faster theoretical models that may allow earlier cancer detection. The present review gives the prediction of cancer by using the star graphs of the protein sequences and proteome mass spectra by building a Quantitative Protein - Disease Relationships (QPDRs), similar to Quantitative Structure Activity Relationship (QSAR) models. The nodes of these star graphs are represented by the amino acids of each protein or by the amplitudes of the mass spectra signals and the edged are the geometric and/or functional relationships between the nodes. The star graphs can be numerically described by the invariant values named topological indices (TIs). The transformation of the star graphs (graphical representation) of proteins into TIs (numbers) facilitates the manipulation of protein information and the search for structure-function relationships in Proteomics. The advantages of this method include simplicity, fast calculations and free resources such as S2SNet and MARCH-INSIDE tools. Thus, this ideal theoretical scheme can be easily extended to other types of diseases or even other fields, such as Genomics or Systems Biology.

Original languageEnglish (US)
Pages (from-to)275-288
Number of pages14
JournalCurrent Proteomics
Volume6
Issue number4
DOIs
StatePublished - Dec 2009
Externally publishedYes

Keywords

  • Cancer prediction
  • Complex network
  • Graphs
  • Linear discriminant analysis
  • Quantitative protein - disease relationship

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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