biostudies-literatureAlvarez ANIDA NIH HHS243https://www.ebi.ac.uk/biostudies/studies/S-EPMC3128037biostudies-literatureUnknown12<h4>Background</h4>A central question in cancer biology is what changes cause a healthy cell to form a tumor. Gene expression data could provide insight into this question, but it is difficult to distinguish between a gene that causes a change in gene expression from a gene that is affected by this change. Furthermore, the proteins that regulate gene expression are often themselves not regulated at the transcriptional level. Here we propose a Bayesian modeling framework we term RegNetB that uses mechanistic information about the gene regulatory network to distinguish between factors that cause a change in expression and genes that are affected by the change. We test this framework using human gene expression data describing localized prostate cancer progression.<h4>Results</h4>The top reguBMC bioinformaticsRegNetB: predicting relevant regulator-gene relationships in localized prostate tumor samples.PMC3128037U54-DA-021519Alvarez AWoolf PJfalseRegNetB: predicting relevant regulator-gene relationships in localized prostate tumor samples.<h4>Background</h4>A central question in cancer biology is what changes cause a healthy cell to form a tumor. Gene expression data could provide insight into this question, but it is difficult to distinguish between a gene that causes a change in gene expression from a gene that is affected by this change. Furthermore, the proteins that regulate gene expression are often themselves not regulated at the transcriptional level. Here we propose a Bayesian modeling framework we term RegNetB that uses mechanistic information about the gene regulatory network to distinguish between factors that cause a change in expression and genes that are affected by the change. We test this framework using human gene expression data describing localized prostate cancer progression.<h4>Results</h4>The top regu2011-01-01T00:00:00Z2011 Jun2026-04-07T14:47:57.096Z2026-04-07T14:18:30.274ZS-EPMC31280372168287910.1186/1471-2105-12-243