An Expression Matrix dataset from a Microarray experiment consists of rows representing genes expressed, and columns representing samples or conditions. The values in each cell characterize the expression level of a particular gene in a particular sample. Similarly, a Protein Expression Matrix dataset generated from a Mass Spec experiment consists of rows representing proteins and columns representing samples or conditions under which these proteins were expressed. The values in each cell characterize the protein expression level in a particular sample.

The Protein Expression Matrix Assay is designed to allow users to view the data in a long table, which makes it easy to create various charts and plots on a given dataset. Two sets of data are required to create a new protein expression assay: (1) a protein expression matrix dataset and (2) FASTA files (which should be uploaded prior to creating an assay -- for details see Link Protein Expression Data with Annotations).

After data has been imported into the assay design, you can join it to gene and protein annotation metadata to build broader queries and visualizations.

The protein expression matrix assay is a simple assay type consisting of two result fields: a protein id and an experimental score value. A batch-level field is used to tie the experiment to a particular FASTA or Uniprot file.

To create the default protein expression matrix assay design:

  • Go to Admin > Manage Assays and click New Assay Design.
  • Select Protein Expression Matrix and click Next.
  • Enter a Name for the design.
  • Click Save and Close.

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