ArticleBMC bioinformatics2014
MAAMD: a workflow to standardize meta-analyses and comparison of affymetrix microarray data.
Article in BMC bioinformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers, 1 of them a synthesis 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
7 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Multiple criteria optimization joint analyses of microarray experiments in lung cancer: from existing microarray data to new knowledge.Cancer medicine · 2015Pooled it
- Available Software for Meta-analyses of Genome-wide Expression Studies.Current genomics · 2019Review
- Identification of Prognostic Biomarkers by Combined mRNA and miRNA Expression Microarray Analysis in Pancreatic Cancer.Translational oncology · 2018Article
- DBNorm: normalizing high-density oligonucleotide microarray data based on distributions.BMC bioinformatics · 2017Article
- An Application of Sequential Meta-Analysis to Gene Expression Studies.Cancer informatics · 2015Article
- Key Challenges and Opportunities Associated with the Use of In Vitro Models to Detect Human DILI: Integrated Risk Assessment and Mitigation Plans.BioMed research internationalReview
- Using Kepler for Tool Integration in Microarray Analysis Workflows.Procedia computer scienceArticle
Corrections and comments
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Authors and funding
8 authors.
Funding
Abstract
backgroundMandatory deposit of raw microarray data files for public access, prior to study publication, provides significant opportunities to conduct new bioinformatics analyses within and across multiple datasets. Analysis of raw microarray data files (e.g. Affymetrix CEL files) can be time consuming, complex, and requires fundamental computational and bioinformatics skills. The development of analytical workflows to automate these tasks simplifies the processing of, improves the efficiency of, and serves to standardize multiple and sequential analyses. Once installed, workflows facilitate the tedious steps required to run rapid intra- and inter-dataset comparisons.
resultsWe developed a workflow to facilitate and standardize Meta-Analysis of Affymetrix Microarray Data analysis (MAAMD) in Kepler. Two freely available stand-alone software tools, R and AltAnalyze were embedded in MAAMD. The inputs of MAAMD are user-editable csv files, which contain sample information and parameters describing the locations of input files and required tools. MAAMD was tested by analyzing 4 different GEO datasets from mice and drosophila.MAAMD automates data downloading, data organization, data quality control assesment, differential gene expression analysis, clustering analysis, pathway visualization, gene-set enrichment analysis, and cross-species orthologous-gene comparisons. MAAMD was utilized to identify gene orthologues responding to hypoxia or hyperoxia in both mice and drosophila. The entire set of analyses for 4 datasets (34 total microarrays) finished in ~ one hour.
conclusionsMAAMD saves time, minimizes the required computer skills, and offers a standardized procedure for users to analyze microarray datasets and make new intra- and inter-dataset comparisons.
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Registered trials
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