Diurnal is simply a database consisting of a number of array expression experiments with various genomes subjected to standard set of light and temperature conditions. In addition to the raw expression patterns, the patterns have been regressed against a common set of models in order to determine if they are rhythmic or not. The results of this modeling are also accessible via Diurnal.
What do all of the conditions mean?
The condition names are largely acronyms describing the specific experimental conditions that were imposed upon the plants. However, the naming scheme is not uniform and also varies slightly across species. A brief summary of the some of the most frequently used conditions is presented below, but greater details including age and sampled tissue can be found alongside the data at our ftp.
- LDHC - Light (12h) Dark (12h) / Hot (12h) Cold (12h)
- LLHC - Light (24h) / Hot (12h) Cold (12h)
- LDHH - Light (12h) Dark (12h) / Hot (24h)
- LLHH_LDHC or LL_LDHC - Entrained on LDHC and subjected to Light (24h) / Hot (24h)
- LLHH_LLHC or LL_LLHC - Entrained on LLHC and subjected to Light (24h) / Hot (24h)
- LLHH_LDHH or LL_LDHH - Entrained on LDHH and subjected to Light (24h) / Hot (24h)
What are the units of the values in the time series?
The time series for each probe set is calculated from the RMA expression values by exponentiating this value using base 2.
Where can I download all of the data in bulk?
Bulk data downloads are available via ftp. The data is segregated by organism and then by data type i.e. normalized expression data or best fit models for each probe.
What about loci with multiple probes sets or probe sets mapping to multiple loci?
All of the expression data is fundamentally associated with probe sets on the various arrays used in the experiments. As genome annotations change, we do our best to ensure that mappings of probe sets to loci and vice versa is as accurate as possible. In particular, some loci may have multiple probe sets that strongly align. Diurnal keeps track of this and will display the expression data for each of the probe sets when these loci are queried. However, the reverse is not true. Probe sets that align to multiple distinct regions in the genome are reduced by taking the locus of the top alignment.
How should I cite Diurnal?
You can use the original article in which Diurnal was released.
THE DIURNAL PROJECT: Diurnal and circadian expression profiling, model-based pattern matching and promoter analysis. Cold Spring Harb Symp Quant Biol. 2007;72:353-63. PMID: 18419293
Who should I contact to ask questions or give feedback regarding Diurnal?
You can send an email to firstname.lastname@example.org with Diurnal in the title.