CircMedDB
Circadian medicine database by
Achim Kramer Lab and Lisa Buchauer Lab
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Select a study and a gene to view the options
How to use
Use the filters to select a study and the gene you are looking for.
Method
Rhythmicity of genes was analysed using the R Package MetaCycle (Wu et al, 2016) which implements the Lomb-Scargle periodogram method for detecting periodic signals in irregularly sampled time series data. Log-normalized expression data from each participant was individually processed through MetaCycle’s LS algorithm with the period fixed to 24 hours for each gene. The resulting parameter estimates for relative Amplitude, MESOR and peak phase were then averaged across all participants to generate consensus rhythmicity metrics. These are used to plot the mean cosine curve per gene and are displayed below the figure.
rAmplitude / MESOR / Peak Phase
Relative Amplitude: The difference between peak and trough expression divided by the mean expression level, representing the strength of oscillation.
Mesor: The Midline Estimating Statistic of Rhythm, which represents the average expression level around which the gene expression oscillates.
Peak Phase: The time at which the gene expression reaches its maximum expression within the circadian cycle.
Internal and External time
Users can toggle between two time reference systems: External Time, which represents the actual clock time at which samples were collected, and Internal Time, which normalizes each participant's data relative to their Dim Light Melatonin Onset (DLMO) as described in Wittenbrink et al. (2018), allowing for comparison of gene expression patterns aligned to individual circadian phase rather than external clock time.