DrugTargetInspector offers you two main variants for data input. You either
may choose to download preprocessed and normalized expression data from GEO or
provide a precomputed list of scores. In the following we describe the requirements
and restrictions associated with these formats.
Gene Expression Omnibus
The Gene Expression Omnibus (GEO) is a
MIAME compliant online database for functional genomics data. Normalized data is stored
in the GEO SOFT format, whereas unprocessed data is stored in a platform dependent raw
format. Currently DrugTargetInspector supports the SOFT format for various platforms
and organisms:
When using a record from GEO DrugTargetInspector relies on the proper normalization of the stored data.
If you want to normalize the data yourself you will need to obtain and process the raw data from GEO and
upload a score file.
The SOFT format is supported for GEO Datasets (GDS) and GEO Series (GSE).
- GSE files
- are collections of related samples and provide a description of the study design.
- GDS files
- are curated collections of statistically comparable GEO samples.
These samples originate from GSE files that are curated and reassembled by GEO employees.
In the case of GSE record selection,
DrugTargetInspector requires you to distribute the contained samples into a sample
and reference set.
