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CanGEM: mining gene copy number changes in cancer
Ilari Scheinin1, Samuel Myllykangas, Ioana Borze
1Genome Informatics Unit, Biomedicum Helsinki, Finland.
Nucleic Acids Research
|October 13, 2007
Summary
CanGEM is a public database for cancer genome data, specifically focusing on gene copy number changes detected by array comparative genomic hybridization. It aids researchers in analyzing complex tumorigenesis by providing accessible, curated data and visualization tools.
Area of Science:
- Genomics
- Cancer Research
- Bioinformatics
Background:
- Tumorigenesis is a complex process involving genetic alterations.
- Gene copy number changes are key drivers of cancer development.
- Existing microarray databases lack a specific focus on copy number variations.
Purpose of the Study:
- To present CanGEM, a public, web-based database for cancer genome data.
- To facilitate the storage and analysis of quantitative microarray data and associated metadata.
- To support integrative systems biology approaches in cancer research.
Main Methods:
- Developed CanGEM, a public, web-based database.
- Implemented support for MIAME standards and standardized clinical information.
- Re-annotated microarray probes with human genome coordinates.
- Analyzed array comparative genomic hybridization (aCGH) data for gene-specific copy numbers.
- Enabled custom dataset creation and aberration frequency calculation.
Main Results:
- CanGEM provides a centralized repository for cancer-related microarray data.
- The database allows querying by clinical characteristics and gene copy number alterations.
- Users can visualize copy number data on a human genome map.
- Original data files are available for in-depth analysis.
Conclusions:
- CanGEM addresses the need for a specialized database for cancer copy number variations.
- The platform enhances the study of tumorigenesis through accessible, analyzed genomic data.
- It supports collaborative research by providing standardized data and analysis tools.
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
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Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
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