title: Catching transcriptional regulation by thermostatistical modeling.
abstract: Gene expression is frequently regulated by multiple transcription factors (TFs). Thermostatistical methods allow for a quantitative description of interactions between TFs, RNA polymerase and DNA, and their impact on the transcription rates. We illustrate three different scales of the thermostatistical approach: the microscale of TF molecules, the mesoscale of promoter energy levels and the macroscale of transcriptionally active and inactive cells in a cell population. We demonstrate versatility of combinatorial transcriptional activation by exemplifying logic functions, such as AND and OR gates. We discuss a metric for cell-to-cell transcriptional activation variability known as Fermi entropy. Suitability of thermostatistical modeling is illustrated by describing the experimental data on transcriptional induction of NFκB and the c-Fos protein.
authors.affiliation: Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland. Till.Frank@ucd.ie
authors.forename: Till D
authors.initials: TD
authors.lastname: Frank
authors.forename: Alex
authors.initials: A
authors.lastname: Cheong
authors.forename: Mariko
authors.initials: M
authors.lastname: Okada-Hatakeyama
authors.forename: Boris N
authors.initials: BN
authors.lastname: Kholodenko
mesh_terms: D000465:Algorithms; D000818:Animals; D003198:Computer Simulation; D019277:Entropy; D017143:Fuzzy Logic; D006801:Humans; D008957:Models, Genetic; D015233:Models, Statistical; D016328:NF-kappa B / Q000235:genetics; D011401:Promoter Regions, Genetic; D016760:Proto-Oncogene Proteins c-fos / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*; D015533:Transcriptional Activation
chemical_list: D016328:NF-kappa B; D016760:Proto-Oncogene Proteins c-fos; D014157:Transcription Factors