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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Generation of Two-color Antigen Microarrays for the Simultaneous Detection of IgG and IgM Autoantibodies
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Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human

Wei-Chung Cheng1, Min-Lung Tsai, Cheng-Wei Chang

  • 1Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan.

BMC Bioinformatics
|August 12, 2010
PubMed
Summary
This summary is machine-generated.

M2DB is a human curated microarray database that simplifies data retrieval and quality control for gene expression meta-analysis. It offers an integrated process and user-friendly interface, lowering the barrier for researchers.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Molecular Biology

Background:

  • Gene expression microarray studies have advanced understanding of human disease genetics.
  • Meta-analysis of microarray data is crucial but faces challenges with data accessibility and quality.
  • Public repositories often present difficulties in data collection and integration.

Purpose of the Study:

  • To develop a human curated microarray database (M2DB) for efficient querying and data retrieval.
  • To address practical problems in collecting and integrating data from public microarray repositories.
  • To improve the efficiency and reliability of microarray meta-analysis.

Main Methods:

  • M2DB is a curated database containing over 10,000 Affymetrix GeneChip arrays from human clinical specimens.
  • Data querying is enabled through a flexible combination of five manually curated clinical annotations.
  • Quality control metrics from three algorithms are provided for array-based assessment and data filtering.

Main Results:

  • M2DB provides easy online querying based on clinical information and interactive retrieval of raw or pre-processed data.
  • The database includes over 10,000 human clinical specimen arrays with detailed annotations.
  • Users can exclude low-quality arrays and access various data formats (raw, pre-processed) and quality metrics.

Conclusions:

  • M2DB offers a user-friendly interface for accessing clinical metadata and quality control parameters.
  • The database lowers the entry threshold for meta-analysis by providing an integrated data process.
  • M2DB aims to promote the advancement of microarray meta-analysis research.