Mining DNA microarray data using a novel approach based on graph theory

Gabriel Del Rio, Theodore F. Bartley, Heberto Del-Rio, Rammohan Rao, Kun Lin Jin, David A. Greenberg, Mark Eshoo, Dale E. Bredesen

Research output: Contribution to journalArticle

13 Citations (Scopus)

Abstract

The recent demonstration that biochemical pathways from diverse organisms are arranged in scale-free, rather than random, systems [Jeong et al., Nature 407 (2000) 651-654], emphasizes the importance of developing methods for the identification of biochemical nexuses - the nodes within biochemical pathways that serve as the major input/output hubs, and therefore represent potentially important targets for modulation. Here we describe a bioinformatics approach that identifies candidate nexuses for biochemical pathways without requiring functional gene annotation; we also provide proof-of-principle experiments to support this technique. This approach, called Nexxus, may lead to the identification of new signal transduction pathways and targets for drug design.

Original languageEnglish
Pages (from-to)230-234
Number of pages5
JournalFEBS Letters
Volume509
Issue number2
DOIs
StatePublished - 7 Dec 2001

Fingerprint

Molecular Sequence Annotation
Signal transduction
Drug Design
Graph theory
Bioinformatics
Microarrays
Oligonucleotide Array Sequence Analysis
Computational Biology
Signal Transduction
Demonstrations
Genes
Modulation
DNA
Pharmaceutical Preparations
Experiments

Keywords

  • Cerebral ischemia
  • DNA microarray
  • Functional genomics
  • Graph theory
  • Yeast cell cycle
  • Yeast metabolism

Cite this

Del Rio, G., Bartley, T. F., Del-Rio, H., Rao, R., Jin, K. L., Greenberg, D. A., ... Bredesen, D. E. (2001). Mining DNA microarray data using a novel approach based on graph theory. FEBS Letters, 509(2), 230-234. https://doi.org/10.1016/S0014-5793(01)03165-9
Del Rio, Gabriel ; Bartley, Theodore F. ; Del-Rio, Heberto ; Rao, Rammohan ; Jin, Kun Lin ; Greenberg, David A. ; Eshoo, Mark ; Bredesen, Dale E. / Mining DNA microarray data using a novel approach based on graph theory. In: FEBS Letters. 2001 ; Vol. 509, No. 2. pp. 230-234.
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Del Rio, G, Bartley, TF, Del-Rio, H, Rao, R, Jin, KL, Greenberg, DA, Eshoo, M & Bredesen, DE 2001, 'Mining DNA microarray data using a novel approach based on graph theory', FEBS Letters, vol. 509, no. 2, pp. 230-234. https://doi.org/10.1016/S0014-5793(01)03165-9

Mining DNA microarray data using a novel approach based on graph theory. / Del Rio, Gabriel; Bartley, Theodore F.; Del-Rio, Heberto; Rao, Rammohan; Jin, Kun Lin; Greenberg, David A.; Eshoo, Mark; Bredesen, Dale E.

In: FEBS Letters, Vol. 509, No. 2, 07.12.2001, p. 230-234.

Research output: Contribution to journalArticle

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AU - Eshoo, Mark

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Del Rio G, Bartley TF, Del-Rio H, Rao R, Jin KL, Greenberg DA et al. Mining DNA microarray data using a novel approach based on graph theory. FEBS Letters. 2001 Dec 7;509(2):230-234. https://doi.org/10.1016/S0014-5793(01)03165-9