A Bayesian network driven approach to model the transcriptional response to nitric oxide in Saccharomyces cerevisiae.
The transcriptional response to exogenously supplied nitric oxide in Saccharomyces cerevisiae was modeled using an integrated framework of Bayesian network learning and experimental feedback. A Bayesian network learning algorithm was used to generate network models of transcriptional output, followed by model verification and revision through experimentation. Using this framework, we generated a network model of the yeast transcriptional response to nitric oxide and a panel of other environmental signals. We discovered two environmental triggers, the diauxic shift and glucose repression, that affected the observed transcriptional profile. The computational method predicted the transcriptional control of yeast flavohemoglobin YHB1 by glucose repression, which was subsequently experimentally verified. A freely available software application, ExpressionNet, was developed to derive Bayesian network models from a combination of gene expression profile clusters, genetic information and experimental conditions.
Zhu
Jingchun
J
Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America.
Jambhekar
Ashwini
A
Sarver
Aaron
A
DeRisi
Joseph
J
D000465:Algorithms; D001185:Artificial Intelligence; D001499:Bayes Theorem; D049308:Dioxygenases / Q000235:genetics; D025461:Feedback, Physiological; D053263:Gene Regulatory Networks; D005800:Genes, Fungal; D005947:Glucose / Q000378:metabolism / Q000494:pharmacology; D006420:Hemeproteins / Q000235:genetics; D008954:Models, Biological; D016571:Neural Networks, Computer; D009569:Nitric Oxide / Q000494:pharmacology*; D020411:Oligonucleotide Array Sequence Analysis; D011993:Recombinant Fusion Proteins / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000187:drug effects* / Q000235:genetics* / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D012984:Software; D014158:Transcription, Genetic / Q000187:drug effects*
D006420:Hemeproteins; D011993:Recombinant Fusion Proteins; D029701:Saccharomyces cerevisiae Proteins; D009569:Nitric Oxide; D049308:Dioxygenases; C101796:YHB1 protein, S cerevisiae; D005947:Glucose