Using the gene ontology to enrich biological pathways

Antonio Sanfilippo, Bob Baddeley, Nathaniel Beagley, Jason McDermott, Roderick Riensche, Ronald Taylor, Banu Gopalan

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

Most current approaches to automatic pathway generation are based on a reverse engineering approach in which pathway plausibility is solely derived from gene expression data and not independently validated. Alternative approaches use prior biological knowledge to validate automatically inferred pathways, but the prior knowledge is usually not sufficiently tuned to the pathology of focus. We present a novel pathway generation approach that combines insights from the reverse engineering and knowledge-based approaches to increase the biological plausibility of automatically generated regulatory networks and describe an application of this approach to transcriptional data from a mouse model of neuroprotection during stroke.

Original languageEnglish
Pages (from-to)221-235
Number of pages15
JournalInternational Journal of Computational Biology and Drug Design
Volume2
Issue number3
DOIs
Publication statusPublished - Dec 2009
Externally publishedYes

Fingerprint

Gene Ontology
Reverse engineering
Ontology
Genes
Pathology
Gene expression
Stroke
Gene Expression
Neuroprotection

Keywords

  • Automatic pathway generation
  • Biological pathways
  • Gene ontology
  • Gene similarity
  • GO
  • Neuroprotection
  • Stroke

ASJC Scopus subject areas

  • Computer Science Applications
  • Drug Discovery

Cite this

Using the gene ontology to enrich biological pathways. / Sanfilippo, Antonio; Baddeley, Bob; Beagley, Nathaniel; McDermott, Jason; Riensche, Roderick; Taylor, Ronald; Gopalan, Banu.

In: International Journal of Computational Biology and Drug Design, Vol. 2, No. 3, 12.2009, p. 221-235.

Research output: Contribution to journalArticle

Sanfilippo, A, Baddeley, B, Beagley, N, McDermott, J, Riensche, R, Taylor, R & Gopalan, B 2009, 'Using the gene ontology to enrich biological pathways', International Journal of Computational Biology and Drug Design, vol. 2, no. 3, pp. 221-235. https://doi.org/10.1504/IJCBDD.2009.030114
Sanfilippo, Antonio ; Baddeley, Bob ; Beagley, Nathaniel ; McDermott, Jason ; Riensche, Roderick ; Taylor, Ronald ; Gopalan, Banu. / Using the gene ontology to enrich biological pathways. In: International Journal of Computational Biology and Drug Design. 2009 ; Vol. 2, No. 3. pp. 221-235.
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