We recently upgraded Cyclebase and added a variety of new features:
The downloads available from the original Cyclebase contain serveral key differences from Cyclebase Version 2:
The old version is located here. Note that the newer 'gene-centric' form of Cyclebase slightly alters the ranking and overall analysis result for some genes (probes were previously ranked). Please read the previous two questions (above) for more detailed information about changes between the two versions.
The easiest way to find a specific gene of interest is to enter the name (or a synonym) of the gene into the search box:
If you are unaware of the exact gene name, try searching with for partial matches with a * character. For example, a search for 'YB*' returns all matches that begin with 'YB' (e.g., YBR088C, YBL003C, etc.).
In addition to searching gene names and descriptions, BLAST searches can also be performed for genes that exist in Cyclebase. To search using BLAST, enter the gene or probe sequence and select the BLAST radio button.
If you would like to find genes based on certain conditions (i.e., find genes that have specific peaktime ranges in a particular organism), the advanced search allows you to enter specific criteria to find genes of interest. The advanced search permits you to search for genes that:
You can further improve your advanced search by using the wildcard * character when searching for the gene name. For example you could limit your search to all gene names that have a 'MR0' inside of the name ('YMR001C', 'YMR071C', etc) by entering '*MR0*'.
Cyclebase searches using both BLASTP and BLASTX. Results are combined and, by default, are sorted by E-value. Mousing over the E-value will elicit a tooltip, which provides information on whether BLASTP or BLASTX identified the gene.
Cyclebase Version 2 now uses an easy URL formatting scheme for the details page of each gene. The URL to the gene details page for each gene requires that you encode the gene name and organism taxonomy id. The encoding looks as follows:
The primary gene name used depends on the organism:
Cyclebase offers several types of data downloads:
Cyclebase has been tested and works with all major modern browsers (e.g., Firefox, Internet Explorer, Opera). We recommend using the latest version of these browsers.
Most questions related to methodology can be found on the methods page. Information on this page details each of the data analysis (i.e., periodicity, regulation, rank, peaktime) techniques derived for each gene and presented in Cyclebase.
The boundaries between phases are based on the peaktime for genes known to belong to a given phase, rather than from cell-cycle checkpoints. These are rough estimates of phase boundaries and should not be considered well defined phase states.
From the microarray data we have estimated the duration of each phase in each organism. The G1/S boundary is placed at 0%. Each of the estimated phase lengths used in Cyclebase are:
|Arabidopsis thaliana||0 - 30%||30 - 64%||64 - 82%||82 - 100%|
|Homo sapiens||0 - 47%||47 - 70%||70 - 90%||90 - 100%|
|Saccharomyces cerevisiae||0 - 25%||25 - 50%||50 - 75%||75 - 100%|
|Schizosaccharomyces pombe||0 - 15%||15 - 30%||30 - 90%||90 - 100%|
More detailed information on how we calculate these phase lengths can be obtained from the following paper:
The periodic tag is assigned to genes whose rank falls below a certain threshold. This threshold varies with the organism.
Peaktime can be uncertain for several reasons. This is covered under peaktime in the methods section.
A writeup is provided in the methods section, located here, which describes the source of each annotation type found in Cyclebase.
Feel free to email firstname.lastname@example.org for suggestions/comments.
Two manuscripts have been published about Cyclebase. The latest publication describes significant updates made in Cyclebase Version 2.0 and is available free to access here. The original publication describing is also free to access and is available here.