Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database.
BACKGROUND
Over the past decade, gene expression microarray studies have greatly expanded our knowledge of genetic mechanisms of human diseases. Meta-analysis of substantial amounts of accumulated data, by integrating valuable information from multiple studies, is becoming more important in microarray research. However, collecting data of special interest from public microarray repositories often present major practical problems. Moreover, including low-quality data may significantly reduce meta-analysis efficiency.


RESULTS
M2DB is a human curated microarray database designed for easy querying, based on clinical information and for interactive retrieval of either raw or uniformly pre-processed data, along with a set of quality-control metrics. The database contains more than 10,000 previously published Affymetrix GeneChip arrays, performed using human clinical specimens. M2DB allows online querying according to a flexible combination of five clinical annotations describing disease state and sampling location. These annotations were manually curated by controlled vocabularies, based on information obtained from GEO, ArrayExpress, and published papers. For array-based assessment control, the online query provides sets of QC metrics, generated using three available QC algorithms. Arrays with poor data quality can easily be excluded from the query interface. The query provides values from two algorithms for gene-based filtering, and raw data and three kinds of pre-processed data for downloading.


CONCLUSIONS
M2DB utilizes a user-friendly interface for QC parameters, sample clinical annotations, and data formats to help users obtain clinical metadata. This database provides a lower entry threshold and an integrated process of meta-analysis. We hope that this research will promote further evolution of microarray meta-analysis.
Cheng
Wei-Chung
WC
Department of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu, Taiwan.
Tsai
Min-Lung
ML
Chang
Cheng-Wei
CW
Huang
Ching-Lung
CL
Chen
Chaang-Ray
CR
Shu
Wun-Yi
WY
Lee
Yun-Shien
YS
Wang
Tzu-Hao
TH
Hong
Ji-Hong
JH
Li
Chia-Yang
CY
Hsu
Ian C
IC
D000465:Algorithms; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D006801:Humans; D020407:Internet; D015201:Meta-Analysis as Topic; D020411:Oligonucleotide Array Sequence Analysis; D011786:Quality Control; D012984:Software; D014584:User-Computer Interface; D018875:Vocabulary, Controlled