The eukaryotic cell division cycle is a highly regulated process that consists of a complex series of events and involves thousands of proteins. Researchers have studied the regulation of the cell cycle in several organisms, employing a wide range of high-throughput technologies, such as microarray-based mRNA expression profiling and quantitative proteomics. Due to its complexity, the cell cycle can also fail or otherwise change in many different ways if important genes are knocked down, which has been studied in several microscopy-based knockdown screens. The data from these many large-scale efforts are not easily accessed, analyzed, and combined due to their inherent heterogeneity. To address this, we have created Cyclebase, an online database that allows users to easily visualize and download results from genome-wide cell-cycle-related experiments. In Cyclebase version 3.0, we have updated the content of the database to reflect changes to genome annotation, added new mRNA and protein expression data, and integrated cell-cycle phenotype information from high-content screens and model-organism databases. The new version of Cyclebase also features a new web interface, designed around an overview figure that summarizes all the cell-cycle-related data for a gene.
The central figure provides an overview of the transcriptional and post-translational regulation during the cell cycle as well as the cell-cycle-related phenotypes:
- Inside the circle representing the phases, we summarize the available expression data, showing a running average of the data from transcriptomics time courses as a circular blue scale heat map, with a red arrow designating the estimated time of peak expression.
- When proteomics data are available (currently only for human) we show these inside of the transcriptomics data. Because proteomics time courses are not nearly as finely time resolved, we display the average expression within each of six-phases window instead of as a running average.
- The icons representing phenotypes and PTMs are placed at the point in the cell cycle that they are primarily associated with. Hovering over any part of the overview figure will provide additional information in the form of tooltips.
We provide as well the temporal mRNA expression profile of a gene according to each individual time-course experiment in the form of a line plot. The plot represents the expression value at each cell-cycle phase for the different cycles covered and the calculated peaktime is shown with a red circle
For further details please refer to the following Open Access articles about the current database and its previous versions:
- Cyclebase 3.0: A multi-organism database on cell-cycle regulation and phenotypes
- Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results.
- Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments.