The easiest way to find a specific gene of interest is to just 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.).

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:

• have a specific name (note this searches all gene synonym as well)
• are within a specific organism
• have a Rank that falls within a specific range
• that have a Peaktime that falls within a specific range
• that have a P-value for periodicity within a particular range
• that have a P-value for regulation within a particular range

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 offers several types of data downloads:

• Downloads are available which contain the results of analyses for an entire species. These files either contain the entire gene/probe set, or a subset with only those genes that Cyclebase has deemed periodic. These analysis downloads are available in the download data section.

• Cyclebase also provides entire single-experiment datasets. Entire experiment downloads are available in the download data section.

• Individual gene/probe sets are also available for download. In order to download a gene, navigate to the gene of interest (for instructions see Question 1 and Question 2 above) and select the "Text File" or "XML file" download link in the corner of the page:
  

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.

Javascript must be enabled for full functionality. Some browsers (ie. Safari) have trouble with the addition/removal of experiments on the Gene Details page. For these browsers, and browsers with javascript disabled, removing and adding experiments in the expression profile charts is disabled.

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.

Here are some XML resources on the web:

• W3Schools has a nice tutorial/reference
• W3C has the official XML specification
• Wikipedia's XML page

and here is a couple of XSD resources:

• W3Schools is a good tutorial/reference
• W3C has the official XSD specification

It is beyond the scope of this document to discuss reading XML with all languages, however here is a list of some of the more popular languages and some links to get you started:

• Java: Many different packages exist for reading and writing XML in java. Here are a few:
  • An official java.sun.com tutorial
  • The open source castor project offers excellent XML handling.
  • Apache's XMLBeans
• Perl:
  • More info can be found at the Perl XML project
  • XML.com has a short tutorial.
• .NET:
  • .NET has an XML schema definition tool that can generate object files from an XSD file
• Python:
  • Tutorials and examples can be found at PyXML

Cyclebase.org was developed by the Center for Biological Sequence Analysis at the Technical University of Denmark .

Feel free to email nick@cbs.dtu.dk for suggestions/comments.

A publication has been accepted in the database issue of Nucleic Acids Research and is free to access here. Please cite:

Gauthier, N. P., Larsen, M. E., Wernersson, R., de Lichtenberg, U., Jensen, L. J., Brunak, S., and Jensen, T. S. (2008) Cyclebase.org—a comprehensive multi-organism online database of cell-cycle experiments. Nucleic Acids Research, 36(Database issue), D854-859.