Data for A minimal activator-inhibitor-repressor model of the hepatic circadian clock

Datasets for A minimal activator-inhibitor-repressor model of the hepatic circadian clock Pauline Delpierre and Marc Lefranc December 12, 2025 The HughesPlosGenet2009-mrna.dat file contains time series of mRNA expression for various clock genes. They are derived from the mouse liver data1obtained by Hughes et al.[1], which are unique as they have a one-hour time resolution and last over 48 hours. To generate periodic profiles, the original data were fitted with fourth-order Fourier series, using the linalg.lstsq routine2from SciPy. They were then normalized to have an average value of 1. The resulting time series was first used by Woller et al. [2]. The NarumiPNAS2016-proteins.dat file contains time series for the abundances of some clock proteins, obtained by normalizing the mouse liver data available from the supporting information of Narumi et al. [3] to have an average value of 1. These datasets were used to fit an activator-inhibitor-repressor model of the hepatic clock, as well as an activator-repressor model [4]. References [1] Michael E Hughes, Luciano DiTacchio, Kevin R Hayes, Christopher Vollmers, S. Pulivarthy, Julie E Baggs, Satchidananda Panda, and John B Hogenesch. Harmonics of circadian gene transcription in mammals. PLoS Genet, 5(4):e1000442, Apr 2009. URL: http://dx.doi.org/10.1371/journal.pgen.1000442,doi:10.1371/journal.pgen. 1000442. [2] Aurore Woller, Hélène Duez, Bart Staels, and Marc Lefranc. A mathematical model of the liver circadian clock linking feeding and fasting cycles to clock function. Cell Rep, 17(4):1087–1097, Oct 2016. URL: http://dx.doi.org/10.1016/j.celrep.2016.09. 060,doi:10.1016/j.celrep.2016.09.060. [3] Ryohei Narumi, Yoshihiro Shimizu, Maki Ukai-Tadenuma, Koji L. Ode, Genki N. Kanda, Yuta Shinohara, Aya Sato, Katsuhiko Matsumoto, and Hiroki R. Ueda. Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins. Proc Natl Acad Sci U S A, 113(24):E3461–E3467, Jun 2016. URL: http://dx.doi.org/10.1073/pnas.1603799113,doi:10.1073/pnas.1603799113. [4] Pauline Delpierre and Marc Lefranc. A minimal activator-inhibitor-repressor model of the hepatic circadian clock. bioRxiv, 2025. URL: https://www.biorxiv.org/content/ 10.1101/2025.08.08.669290,doi:10.1101/2025.08.08.669290. 1available from the GEO database under accession number GSE11923 at https://www.ncbi.nlm.nih. gov/geo/query/acc.cgi?acc=GSE11923 2https://docs.scipy.org/doc/scipy/reference/generated/scipy.linalg.lstsq.html 1