What will my submission look like in ArrayExpress?

Once curation is complete your submission will be loaded into ArrayExpress . The submission E-MTAB-1084 is an example of how your submission will look in the interface. Information from the submitted MAGE-TAB is highlighted such as description, species, contact details. In addition a number of further links are provided as described below:

Protocols

protocol_view

I want to submit a MAGE-TAB file

This link provides information on the protocols used. These protocols are taken directly from the loaded MAGE-TAB.

Samples

score_view

This link provides information on the samples. The sample information is taken directly from the loaded MAGE-TAB.

MINSEQE

score_view

The data in ArrayExpress is organised in a structured and standardised format and are stored according to community guidelines, including the "Minimal Information about a Microarray Experiment" (MIAME) and the "Minimum Information about a high-throughput SeQuencing Experiment" (MINSEQE), as recommended by the Functional Genomics Data Society. The MINSEQE score indicates what information required by the MINSEQE guidelines was supplied as part of the MAGE-TAB submission. For microarray experiments the MIAME score is shown. A high MIAME or MINSEQE score indicates a well described experiment.

Files

files_view

This section displays all the files available for a given experiment. Zip archives are available containing the raw and processed data. In addition this section contains a link to the IDF, SDRF and, for microarray experiments, the array design format (ADF) file.

Links

link_view

This section might include links to external databases and GenomeSpace:

  • This submission is a sequencing submission and for sequencing submissions we transfer the raw data files to the European Nucleotide Archive (ENA) and provide a link from ArrayExpress to the ENA entry for this experiment.
  • GenomeSpace is a data analysis environment that allows you to move data between different tools in order to analyze them. To use it, you need to get a GenomeSpace account by registering on their website. Then, when you find a dataset of interest in ArrayExpress , click on the link, log into genome space, select what you want to import (at the moment we transfer IDF, SDRF and data archives by default) and this will be loaded into GenomeSpace. From there you can select a tool you want to use for the analysis GenePattern, Cytoscape , Genomica , IGV , etc) and the ArrayExpress files uploaded will be converted into the format required by the chosen tool.

Top