Global analysis of microarray data reveals intrinsic properties in gene expression and tissue selectivity.
Summary of "Global analysis of microarray data reveals intrinsic properties in gene expression and tissue selectivity."
MOTIVATION:
It is expected that individual genes have intrinsically different variability in the global expressional trend among them. Thus, the consideration of gene-specific expressional properties will help us to distinguish target-selective gene expression over non-selective over-expression.
RESULTS:
The re-standardization and integration of heterogeneous microarray datasets, available from public databases, have enabled us to determine the global expression properties of individual genes across a wide variety of experimental conditions and samples. The global averages and SDs of expression for each gene in the integrated microarray datasets were found to be intrinsic properties, which were consistent among independent collections of datasets using different microarray platforms. Using the gene-specific intrinsic parameters to rescale the microarray data, we were able to distinguish novel selective gene expression [cartilage oligomeric matrix protein (COMP) and Collagen X] in breast cancer tissues from non-selective over-expression, a difference that has not been detectable by conventional methods. Availability and Implementation: The web-based tool for GS-LAGE is available at http://lage.sookmyung.ac.kr
Affiliation
Department of Biological Sciences, Sookmyung Women's University, Seoul, Republic of Korea.
Journal Details
This article was published in the following journal.
Name: Bioinformatics (Oxford, England)
ISSN: 1367-4811
Pages: 1723-30
Links
- PubMed Source: http://www.ncbi.nlm.nih.gov/pubmed/20511364
- DOI: http://dx.doi.org/10.1093/bioinformatics/btq279
Medical and Biotech [MESH] Definitions
Microarray Analysis
The simultaneous analysis, on a microchip, of multiple samples or targets arranged in an array format.
Data Collection
Systematic gathering of data for a particular purpose from various sources, including questionnaires, interviews, observation, existing records, and electronic devices. The process is usually preliminary to statistical analysis of the data.
Global Warming
Increase in the temperature of the atmosphere near the Earth's surface and in the troposphere, which can contribute to changes in global climate patterns.
Fourier Analysis
Analysis based on the mathematical function first formulated by Jean-Baptiste-Joseph Fourier in 1807. The function, known as the Fourier transform, describes the sinusoidal pattern of any fluctuating pattern in the physical world in terms of its amplitude and its phase. It has broad applications in biomedicine, e.g., analysis of the x-ray crystallography data pivotal in identifying the double helical nature of DNA and in analysis of other molecules, including viruses, and the modified back-projection algorithm universally used in computerized tomography imaging, etc. (From Segen, The Dictionary of Modern Medicine, 1992)
Wavelet Analysis
Signal and data processing method that uses decomposition of wavelets to approximate, estimate, or compress signals with finite time and frequency domains. It represents a signal or data in terms of a fast decaying wavelet series from the original prototype wavelet, called the mother wavelet. This mathematical algorithm has been adopted widely in biomedical disciplines for data and signal processing in noise removal and audio/image compression (e.g., EEG and MRI).
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