Cyclebase.org--a comprehensive multi-organism online database of cell-cycle experiments
Nicholas Paul Gauthier1, Malene Erup Larsen, Rasmus Wernersson
1Center for Biological Sequence Analysis, BioCentrum-DTU, Technical University of Denmark, Building 208, DK-2800 Lyngby, Denmark.
Nucleic Acids Research
|October 18, 2007
Summary
Cyclebase.org centralizes cell-cycle microarray data, making gene expression profiles accessible. This database aids researchers in analyzing cell cycle gene regulation across multiple experiments.
Area of Science:
- * Molecular Biology
- * Bioinformatics
- * Genomics
Background:
- * Numerous cell-cycle microarray studies have been published, with more anticipated.
- * Existing data are fragmented, hindering access, combination, and evaluation.
- * A centralized resource is needed to consolidate and analyze cell-cycle gene expression data.
Purpose of the Study:
- * To develop and present Cyclebase.org, a centralized database for cell-cycle microarray data.
- * To provide an intuitive interface for data retrieval and analysis.
- * To facilitate the examination of gene expression patterns throughout the cell cycle.
Main Methods:
- * Creation of a centralized database (Cyclebase.org) with a user-friendly interface.
- * Implementation of search functionalities for specific genes and genome-wide downloads.
- * Normalization of expression profiles to a common timescale for comparative analysis.
- * Application of computational analyses to determine gene periodicity and peak expression times.
Main Results:
- * Cyclebase.org offers easy access to and download of cell-cycle microarray data.
- * Gene expression profiles are visualized with normalized graphs across experiments.
- * Computational analysis identifies periodically expressed genes and their peak expression timing.
- * The database integrates evidence from multiple experiments for comprehensive insights.
Conclusions:
- * Cyclebase.org effectively centralizes and standardizes cell-cycle gene expression data.
- * The platform simplifies the analysis of complex cell-cycle dynamics.
- * Researchers can now more readily investigate gene regulation during the cell cycle.
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