Volume 11 Supplement 4

UT-ORNL-KBRIN Bioinformatics Summit 2010

Open Access

Linking genotype to phenotype with Bayesian network modeling of Chlamydia infection

BMC Bioinformatics201011(Suppl 4):P19

DOI: 10.1186/1471-2105-11-S4-P19

Published: 23 July 2010


Understanding the causal pathways that link genotypes with gene expression and higher order phenotypes, such as disease susceptibility, has been a recent goal of systems genetic studies. Pairwise correlations can select genes and phenotypes that are associated with a common genetic locus; however, the directions of these links are more difficult to determine. We propose a method in which Bayesian networks are used to establish causal pathways from genotype to gene expression to phenotype and apply it to mice infected with Chlamydia psittaci.


Recombinant inbred BXD mice strains have been previously used to study the genetic differences that cause a much greater resistance to Chlamydia psittaci infection in C57BL/6J mice compared with DBA/2J mice [1]. Gene expression levels and higher order phenotypes, such as pathogen load and survival, were collected for 44 BXD strains. Directed graphs linking SNPs [2] in the BXD genomes to this data were created with QTL mapping and the Bayesian network method. Figure 1 shows a selection of the resulting causal pathways; many of the genes in these pathways are known to be associated with immune response or GTPase activity, which has been linked to Chlamydia psittaci infection [1].
Figure 1

Causal pathways linking genotype SNPs to gene expression levels to phenotypes in BXD mice infected with Chlamydia psittaci



This work was support by NIH grant AI081050 and DOD grant W81XHW-05-01-0227.

Authors’ Affiliations

Department of Molecular Sciences, University of Tennessee Health Science Center
Department of Pediatrics, University of Tennessee Health Science Center
Center of Integrative and Translational Genomics, University of Tennessee Health Science Center


  1. Miyairi I, Tatireddigari VRRA, Mahdi OS, Rose LA, Belland RJ, Lu L, Williams RW, Byrne GI: The p47 GTPases Iigp2 and Irgb10 regulate innate immunity and inflammation to murine Chlamydia psittaci infection. J Immunol 2007, 179: 1814–1824.View ArticlePubMedGoogle Scholar
  2. BXD Genotypes at the GeneNetwork[http://www.genenetwork.org/genotypes/BXD.geno]


© Ziebarth et al; licensee BioMed Central Ltd. 2010

This article is published under license to BioMed Central Ltd.