ArticleBMC bioinformatics2010
Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database.
Article in BMC bioinformatics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 2 of them syntheses that pooled it.
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Who cites it
20 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Identification of reference genes across physiological states for qRT-PCR through microarray meta-analysis.PloS one · 2011Pooled it
- Identification of human housekeeping genes and tissue-selective genes by microarray meta-analysis.PloS one · 2011Pooled it
- BioVDB: biological vector database for high-throughput gene expression meta-analysis.Frontiers in artificial intelligence · 2024Article
- MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature.Scientific reports · 2019Article
- Classical and Bayesian random-effects meta-analysis models with sample quality weights in gene expression studies.BMC bioinformatics · 2019Article
- Gene selection for microarray data classification via subspace learning and manifold regularization.Medical & biological engineering & computing · 2018Article
- Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism.Nucleic acids research · 2018Article
- BioDataome: a collection of uniformly preprocessed and automatically annotated datasets for data-driven biology.Database : the journal of biological databases and curation · 2018Article
- GEE: An Informatics Tool for Gene Expression Data Explore.Healthcare informatics research · 2016Article
- Omics-based identification of biomarkers for nasopharyngeal carcinoma.Disease markers · 2015Review
- NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases.Database : the journal of biological databases and curation · 2015Article
- Gene selection for cancer identification: a decision tree model empowered by particle swarm optimization algorithm.BMC bioinformatics · 2014Article
- INMEX--a web-based tool for integrative meta-analysis of expression data.Nucleic acids research · 2013Article
- Reuse of public genome-wide gene expression data.Nature reviews. Genetics · 2013Review
- A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity.Bioinformatics (Oxford, England) · 2013Article
- Human gene correlation analysis (HGCA): a tool for the identification of transcriptionally co-expressed genes.BMC research notes · 2012Article
- Comprehensive literature review and statistical considerations for microarray meta-analysis.Nucleic acids research · 2012Review
- CancerMA: a web-based tool for automatic meta-analysis of public cancer microarray data.Database : the journal of biological databases and curation · 2012Article
- eXframe: reusable framework for storage, analysis and visualization of genomics experiments.BMC bioinformatics · 2011Article
- High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses.BMC bioinformatics · 2011Article
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOver 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.
resultsM2DB 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.
conclusionM2DB 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.
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