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Data Formats

Table of Contents

General Information

Cyclebase offers several types of data available for download. If you are looking for how to find and download data, please consult the FAQ. Cyclebase will only distribute expression-profile data if the original authors have given their consent. Use of processed data requires that you cite the original authors as well as Cyclebase. All data have been processed as described here. Each exported type is offered in Tab-Delimited format.

Entire Organism Analysis Results

Entire organism data-files consist of overall organism information and Cyclebase analysis-results. The files contain both the combined analysis (across all available experiments) and the analysis of each individual experiment.

Downloads are available with for all genes and also for only those genes that Cyclebase has deemed periodic. The format of the download with only periodic genes is the same as the full gene download.

  • Those lines that are blank or begin with # are comments and should be ignored.
  • The first data after the initial comments will always be organism-info (OI) lines. These lines contain useful information about the organism's name, phase lengths, and experiments available.
  • The next comment line starts the Cyclebase analysis-results section. This section will first have an analysis-results header line (AH), followed by repeating analysis-results lines (AR). Each of the analysis-results line (tab separated) contains:
    • The common gene name
    • The systematic gene name
    • Whether or not it is deemed periodic
    • Overall analysis-results (Rank, Peaktime, P-value for Periodicity, and P-value for Regulation) across all experiments (pipe delimited).
    • Analysis results for each experiment (pipe delimited).

The following figure depicts a simple Tab-Delimited organism analysis:

Entire Organism Analysis Results Example

Full Experiment Downloads

An entire experiment data-file consists of overall experiment information, Cyclebase analysis-results, and all of the processed time-series expression-profiles for that experiment.

For the experiments that Cyclebase has not been given permission to distribute, downloaded files will only contain the overall experiment information and Cyclebase analysis-results. These 'confidential' experiment files will be formated exactly like the 'full' files, but will not contain the processed time-series expression-profiles.

  • Those lines that are blank or begin with # are comments and should be ignored.
  • The first data after the initial comments will always be 9 experiment-info (EI) lines.
  • The next comment line will always start the Cyclebase analysis-results section. This section will first have an analysis-results header line (AH), followed by repeating analysis-results lines (AR). Each of the analysis-results lines contains (tab separated):
    • The probeset name.
    • Gene common names (pipe separated).
    • Gene systematic names (pipe separated).
    • The combined Rank, Peaktime, P-value for Periodicity, and P-value for Regulation scores for this probeset across experiments (pipe separated).
    • The Rank, Peaktime, P-value for Periodicity, and P-value for Regulation scores for this probeset in this experiment (pipe separated).
  • The next comment line will start the time-series expression-profiles. The first line is a header (EH), which will specify the what each tab separated column means. The time (in percent of cell-cycle) from the M/G1 transition will follow the probeset_name, gene_common_names, and gene_systematic_names. Following the header line are expression-profile (EP) lines. Each of the EP lines will contain:
    • the probeset name
    • gene common names (pipe separated)
    • gene systematic names (pipe separated)
    • A tab separated list of expression values (normalized as described here). Note these values can are blank if there was no reading at a specific time for a specific gene/probe.

The following figure depicts a simple Tab-Delimited experiment:

Full Experiment Downloads Example

Single Gene Downloads

An individual gene export contains the gene's 'global' analysis-results, all available experiment analysis-results, and expression profiles. If multiple probesets exist for a gene, data for the probeset being viewed will be downloaded. Note that the default probeset displayed for a gene that multiple probesets target is the one with the best rank, but the option to select the additional probesets is given on the gene details page.

  • Those lines that are blank or begin with # are comments and should be ignored.
  • Immediately following the initial comments are 12 gene information (GI) lines.
  • A comment marks the end of the of the gene information lines and beings the start of the experiments that Cyclebase has been given permission to distribute. There can be zero or more shared experiments, each seperated with a blank line after the data (D1 and D2) lines. Cyclebase analysis-results (rank, peaktime, P-value for periodicity, and P-value for regulation) will be available in the EI lines. The data (D1 and D2) lines will be populated with the following:
    • D1 contains a tab-separated list of the time (in percent of cell-cycle) from the M/G1 transition.
    • D2 contains a tab separated list of expression values (normalized as described here).
  • The next comment will mark the beginning of the repeating confidential experiments. There can be zero or more confidential experiments.
  • Confidential experiments are experiments that Cyclebase has not been given permission to distribute, and will therefore have no treated expression-profile data. Cyclebase analysis-results (rank, peaktime, P-value for periodicity, and P-value for regulation) will still be available in the EI lines, but the word "CONFIDENTIAL" will be put on the data (D1 and D2) lines.

The figure below depicts a simple example of an exported gene:

Single Gene Downloads Example