mgsa protocols

mgsa specifications

Information


Unique identifier OMICS_16691
Name mgsa
Alternative name Model-based gene set analysis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.22.0
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Julien Gagneur <>

Publication for Model-based gene set analysis

mgsa IN pipelines

 (3)
2012
PMCID: 3329418
PMID: 22300537
DOI: 10.1186/1471-2105-13-23

[…] on annotation frequency and ignore semantic distance. although semantic distance is incorporated into methods such as parent-child union, elim and weight, the state-of-the-art mea methods gengo and mgsa use flattened representations of the ontology and therefore fail to explicitly incorporate semantic distance., real datasets frequently suffer from sparsity due to a variety of data collection […]

2012
PMCID: 3329418
PMID: 22300537
DOI: 10.1186/1471-2105-13-23

[…] exact test, which need to employ some type of smoothing (e.g., laplace or add one smoothing). bayesian methods that perform enrichment analysis using a prior probability distribution include mgsa and the baygo framework [26]. although these bayesian methods enable the enrichment analysis of sparse data, their lack of support for inter-instance relationships, non-hierarchical class […]

2011
PMCID: 3031556
PMID: 21305018
DOI: 10.1371/journal.pone.0016250

[…] gene-ontology analysis was performed separately on the set of genes with significantly higher expression in the neo aortic samples and those with significantly higher expression in the w6 samples by model-based gene set analysis [25] using the ontologizer [65]., individual mrna expression profiles were analyzed to reveal the effects of specific mirnas using rank-sum tests [34]. we applied […]

mgsa institution(s)
Institute for Medical Genetics, Charité-Universitätsmedizin Berlin, Berlin, Germany; Max Planck Institute for Molecular Genetics, Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Berlin, Germany; European Molecular Biology Laboratory, Heidelberg, Germany
mgsa funding source(s)
Supported by Deutsche Forschungsgemeinschaft (DFG RO 2005/4-1).

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