title: Modeling the altered expression levels of genes on signaling pathways in tumors as causal bayesian networks.
abstract: This paper concerns a study indicating that the expression levels of genes in signaling pathways can be modeled using a causal Bayesian network (BN) that is altered in tumorous tissue. These results open up promising areas of future research that can help identify driver genes and therapeutic targets. So, it is most appropriate for the cancer informatics community. Our central hypothesis is that the expression levels of genes that code for proteins on a signal transduction network (STP) are causally related and that this causal structure is altered when the STP is involved in cancer. To test this hypothesis, we analyzed 5 STPs associated with breast cancer, 7 STPs associated with other cancers, and 10 randomly chosen pathways, using a breast cancer gene expression level dataset containing 529 cases and 61 controls. We identified all the genes related to each of the 22 pathways and developed separate gene expression datasets for each pathway. We obtained significant results indicating that the causal structure of the expression levels of genes coding for proteins on STPs, which are believed to be implicated in both breast cancer and in all cancers, is more altered in the cases relative to the controls than the causal structure of the randomly chosen pathways.
authors.affiliation: Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.
authors.forename: Richard
authors.initials: R
authors.lastname: Neapolitan
authors.affiliation: Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA.
authors.forename: Diyang
authors.initials: D
authors.lastname: Xue
authors.affiliation: Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA.
authors.forename: Xia
authors.initials: X
authors.lastname: Jiang
keywords: bayesian network; breast cancer; causal structure; gene expression level; signal transduction pathway