Cyclebase.org

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  • Gene Name
  • BLAST
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FAQ

Table of Contents

New Cyclebase Version!

What is new in Cyclebase Version 2.0?

We recently upgraded Cyclebase and added a variety of new features:

  • Remapped all gene names, synonyms, and descriptions to match changes in genome annotations.
  • Inclusion on each Gene Details page of information on CDK substrates, predicted degradation signals, and loss-of-function phenotypes found in genome-wide screens.
  • Mappings to orthologous and paralogous genes are now included to further facilitate comparison of cell-cycle regulation across species.
  • The web interface has been improved and provides a single, gene-centric graph summarizing the available cell-cycle experiments.
  • The ability to query probe and gene sequences using BLAST.

How has the data download format changed?

The downloads available from the original Cyclebase contain serveral key differences from Cyclebase Version 2:

  • The general format for the tab-delimited export files is very similar, however several differences do exist. Please read the data formats page carefully.
  • Because gene annotations are not completely static, the original Cyclebase contains gene annotations that may be out of date.
  • Due to lack of interest in the XML file format, we have phased out these files for data download. If you prefer to continue using the old files, you can download them from the first version of Cyclebase (located here). Remember that there are differences between the old and new versions in both annotation and analysis details for each gene.

Can I still access the original Cyclebase?

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.

Program Use

How do I find a specific gene?

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:

Simple Search Picture

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.

How do I browse genes that might be of interest?

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*'.

Which flavor of BLAST does Cyclebase use?

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.

How do I link to a specific gene in Cyclebase?

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:

URL From Gene Details Page

The primary gene name used depends on the organism:

  • For Arabidopsis thaliana (taxId=3702) genes, the geneId parameter should contain a Representative Gene Model (see TAIR)
  • For Homo Sapiens (taxId=9606) genes, the geneId parameter should contain an Ensembl Gene Id
  • For Saccharomyces cerevisiae (taxId=4932) genes, the geneId parameter should contain a Systematic Name (see SGD)
  • For Schizosaccharomyces pombe (taxId=4896) genes, the geneId parameter should contain a Systematic Name GeneDB)

Where can I download data for specific genes, entire experiments, or entire organisms?

Cyclebase offers several types of data downloads:

  • Downloads are available which contain the results of analyses for an entire species. These files either contain all of the genes, 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.
  • Data from individual genes are also available for download. These downloads contain analysis results and normalized expression values for shared experiments. To download data for a specific gene, navigate to the gene of interest (for instructions see Question 1 and Question 2 above) and select the "Text File" download link in the corner of the page:

Image of Download Gene Links

What are the browser requirements for viewing Cyclebase.org?

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 (i.e., older versions of 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.

Methods

Where do I find information about the data analyses presented within Cyclebase?

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.

What percentage cutoffs are used for each phase in the cell cycle?

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:

Organism G1 S G2 M
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:

Marguerat, S., Jensen, T. S., de Lichtenberg, U., Wilhelm, B. T., Jensen, L. J., and Bähler, J. (2006) The more the merrier: comparative analysis of microarray studies on cell cycle-regulated genes in fission yeast. Yeast, 23, 261-277. [pubmed]

What does the "Periodic" tag mean and how does it get assigned?

The periodic tag is assigned to genes whose rank falls below a certain threshold. This threshold varies with the organism.

Why is the peaktime uncertain with some genes?

Peaktime can be uncertain for several reasons. This is covered under peaktime in the methods section.

How were the annotations for Gene Features (e.g., Degradation Signals) assigned?

A writeup is provided in the methods section, located here, which describes the source of each annotation type found in Cyclebase.

Misc.

Who developed Cyclebase.org?

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

I have a suggestion for a new feature, who can I contact?

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

How should I cite Cyclebase.org?

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.

Citations:

Gauthier, N. P., Jensen, L. J., Wernersson, R., Brunak, S., and Jensen, T. S. (2009) Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results. Nucleic Acids Research, Advance Access [free access]

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. [pubmed] [free access]