MUGEN - Annotation
Ontologies
The gene expression data submitted to ArrayExpress as part of the MUGEN project will be annotated with the MGED Ontology (MO) terms for gene expression experiments. The MO provides terms for annotation the type of experiment e.g. in vitro, and for the factors within an experiment e.g. compound or disease. As part of the MUGEN project user annotation is being collated and used to generate new terms for the MO and other relevant ontologies such as those for describing the mouse. Rather than build new ontologies we intend to work with the developers of existing ontologies to extend them for MUGEN.
Annotation Examples
This section provides completed examples for MUGEN type experiments and provides links to these experiments in ArrayExpress as a test set of data. Three types of experiments have been identfied: in vitro (cell culture), in vivo and ex vivo. These experiments do not represent real data and are for use as examples only.
- Affymetrix in vivo example [spreadsheet in ArrayExpress]
- Affymetrix in vitro example [spreadsheet in ArrayExpress]
- Affymetrix ex vivo example [spreadsheet in ArrayExpress]
Annotation Standards
This section provides examples of the annotation required for transcriptomic experiments performed within the MUGEN NOE for submission to ArrayExpress. Three types of experiments have been identfied: in vitro (cell culture), in vivo and ex vivo. Example sample annotation is provided for each in the tables below. These are intended as a minimum annotation example, more information can be provided if needed, please contact the
for advice on experiment annotation.
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