ArticleBMC bioinformatics2009
A-MADMAN: annotation-based microarray data meta-analysis tool.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 2 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- An integrative approach for the identification of prognostic and predictive biomarkers in rectal cancer.Oncotarget · 2015Pooled it
- A data similarity-based strategy for meta-analysis of transcriptional profiles in cancer.PloS one · 2013Pooled it
- Available Software for Meta-analyses of Genome-wide Expression Studies.Current genomics · 2019Review
- Unified Transcriptomic Signature of Arbuscular Mycorrhiza Colonization in Roots ofFrontiers in plant science · 2018Article
- A semi-parametric statistical model for integrating gene expression profiles across different platforms.BMC bioinformatics · 2016Article
- A constitutive active MAPK/ERK pathway due to BRAFV600E positively regulates AHR pathway in PTC.Oncotarget · 2015Article
- NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases.Database : the journal of biological databases and curation · 2015Article
- Transcriptomic profiling of the development of the inflammatory response in human monocytes in vitro.PloS one · 2014Article
- INMEX--a web-based tool for integrative meta-analysis of expression data.Nucleic acids research · 2013Article
- Cross-platform microarray meta-analysis for the mouse jejunum selects novel reference genes with highly uniform levels of expression.PloS one · 2013Article
- AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities.BMC bioinformatics · 2012Article
- Comprehensive literature review and statistical considerations for microarray meta-analysis.Nucleic acids research · 2012Review
- Improving biomarker list stability by integration of biological knowledge in the learning process.BMC bioinformatics · 2012Article
- Indoleamine 2,3-dioxygenase is a signaling protein in long-term tolerance by dendritic cells.Nature immunology · 2011Article
- AnyExpress: integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm.BMC bioinformatics · 2011Article
- Assessing the quality of annotations in asthma gene expression experiments.BMC bioinformatics · 2010Article
- Metabotropic glutamate receptor-4 modulates adaptive immunity and restrains neuroinflammation.Nature medicine · 2010Article
- STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data.BMC bioinformatics · 2009Article
- A-MADMAN: annotation-based microarray data meta-analysis tool.BMC bioinformatics · 2009Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPublicly available datasets of microarray gene expression signals represent an unprecedented opportunity for extracting genomic relevant information and validating biological hypotheses. However, the exploitation of this exceptionally rich mine of information is still hampered by the lack of appropriate computational tools, able to overcome the critical issues raised by meta-analysis.
resultsThis work presents A-MADMAN, an open source web application which allows the retrieval, annotation, organization and meta-analysis of gene expression datasets obtained from Gene Expression Omnibus. A-MADMAN addresses and resolves several open issues in the meta-analysis of gene expression data.
conclusionA-MADMAN allows i) the batch retrieval from Gene Expression Omnibus and the local organization of raw data files and of any related meta-information, ii) the re-annotation of samples to fix incomplete, or otherwise inadequate, metadata and to create user-defined batches of data, iii) the integrative analysis of data obtained from different Affymetrix platforms through custom chip definition files and meta-normalization. Software and documentation are available on-line at http://compgen.bio.unipd.it/bioinfo/amadman/.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.