Pathway analysis of high-throughput biological data within a bayesian network framework

Senol Isci, Cengizhan Ozturk, Jon Jones, Hasan H Otu

Research output: Contribution to journalArticle

23 Citations (Scopus)

Abstract

Motivation: Most current approaches to high-throughput biological data (HTBD) analysis either perform individual gene/protein analysis or, gene/protein set enrichment analysis for a list of biologically relevant molecules. Bayesian Networks (BNs) capture linear and non-linear interactions, handle stochastic events accounting for noise, and focus on local interactions, which can be related to causal inference. Here, we describe for the first time an algorithm that models biological pathways as BNs and identifies pathways that best explain given HTBD by scoring fitness of each network.Results: Proposed method takes into account the connectivity and relatedness between nodes of the pathway through factoring pathway topology in its model. Our simulations using synthetic data demonstrated robustness of our approach. We tested proposed method, Bayesian Pathway Analysis (BPA), on human microarray data regarding renal cell carcinoma (RCC) and compared our results with gene set enrichment analysis. BPA was able to find broader and more specific pathways related to RCC.

Original languageEnglish (US)
Article numberbtr269
Pages (from-to)1667-1674
Number of pages8
JournalBioinformatics
Volume27
Issue number12
DOIs
StatePublished - Jun 1 2011

Fingerprint

Bayes Theorem
Bayesian networks
Bayesian Networks
Renal Cell Carcinoma
High Throughput
Pathway
Genes
Throughput
Biological Models
Microarrays
Proteins
Noise
Cells
Topology
Molecules
Gene
Protein
Causal Inference
Local Interaction
Nonlinear Interaction

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Pathway analysis of high-throughput biological data within a bayesian network framework. / Isci, Senol; Ozturk, Cengizhan; Jones, Jon; Otu, Hasan H.

In: Bioinformatics, Vol. 27, No. 12, btr269, 01.06.2011, p. 1667-1674.

Research output: Contribution to journalArticle

Isci, Senol ; Ozturk, Cengizhan ; Jones, Jon ; Otu, Hasan H. / Pathway analysis of high-throughput biological data within a bayesian network framework. In: Bioinformatics. 2011 ; Vol. 27, No. 12. pp. 1667-1674.
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