About this work

ClockProfile is a web-app to provide an easy-to-use interface for temporal RNA-Seq datasets. Currently, it allows the user to visualize the temporal gene expression in liver of genesets and individual genes in several mouse KO models of clock genes (i.e. Bmal1 KO, Cry1/2 dKO and PARbZip KO. Raw RNA-Seq data is accessible at GEO (GSE135898 and GSE135875). A manuscript is currently in preparation.

Experimental data, statistical framework and web-app have been generated and developed by the Laboratory of Computational and Systems Biology at EPFL in collaboration with Fabrice David (BioInformatics Ↄompetence Center at EPFL) and the Physiology of Circadian Rhythms lab at the Institute for Molecular Bioscience, University of Queensland, Australia.

The app was implemented using Ruby on Rails, PostgreSQL for the backend and Plotly.js for plots.

The statistical framework dryR (Differential RhythmicitY analysis in R) to analyse rhythmic time series of two or more conditions have been made available at https://github.com/naef-lab/dryR.