Step 1: Data input

Prism requires two inputs: a file of genomic data, and a catalog of gene annotations. Your first step is to provide the data by uploading it to the server.

The input data must be in tab-delimited text format. The first row of the file contains titles, and each subsequent row contains data corresponding to a single gene. Within a row, each column may contain the gene identifier, a gene expression or other data value, a Boolean flag indicating the presence of corrupted data, or arbitrary text (described below). Rows that begin with a pound sign (#) are considered comments, and are skipped. Here is an example of a gene expression data set formatted in this fashion.

Once you have typed in the name of your input file, press the button labeled "Upload file."

Alternatively, you may enter a data set identifier into the box labeled "Experiment lookup" and press the button labeled "Retrieve data." Once you have entered a data set into Prism, you can return to view it later on (up to seven days later) by using the data set ID assigned by Prism.

Right now, you can experiment with Prism by retrieving the sample data set mentioned above, using the data set identifier "sample."

Step 2: Catalog selection

Next, you select an annotation catalog from the list of catalogs that are stored at the server. If you'd like to use your own annotations, you have the option of uploading those as well. Note that, if you are retrieving a previously uploaded set of data, you will skip this step.

You may select a gene annotation catalog from the pull-down menu. In order for the annotation to work properly, the IDs in your data file must match the IDs in the catalog. To see whether this is the the case, you may view the annotation catalogs via the list at the bottom of the catalog upload page. If your gene IDs are different from those in the catalogs, you may upload your own. The format is simple: each row corresponds to a single gene and contains the gene's ID and corresponding annotation, with a tab character between. For a gene with more than one name, the gene ID can be a comma-separated list. If you do not have an appropriate annotation catalog, you may opt not to include annotations in the Prism output.

Step 3: Selecting column formats

By default, Prism assumes that the input data file consists entirely of gene expression data, with gene IDs in the first column. However, as mentioned above, some columns in the file may have different semantics. Therefore, after uploading a data file, Prism asks you to define the type of each column in your input file. There are four types of columns, as follows:

There are two ways to specify the type of each column in the input file: by selecting the correct radio button next to the column name, or by typing a range of column indices into the left-hand frame and typing "Update." By default, Prism assumes that the first column contains the gene ID, and all subsequent columns contain data. This is the case for the sample data file.

Step 4: Selecting output options

At the top of the page for selecting column types, there are several options that control the format of the output produced by Prism. These include the following:

Once you have selected these options (or left them with their default values), press the button labeled "Go."

Step 5: Primary Prism output

The primary Prism output page displays on the left side a heat map representation of the expression matrix. Columns in the matrix correspond to "data" columns in your input file. Each row in the matrix corresponds to a single gene, and the corresponding gene ID and annotation appears to the right. The gene ID is linked to a relevant gene expression database. Clicking on the matrix itself zooms in on a particular gene, as described below.

Note that the top of the page lists a numeric experiment identifier. You should keep track of this number, because you can use it later to return to this data set. You can also send this identifier to other users so that they can view your data.

Step 6: Zooming in on a gene

Clicking on the heat map matrix will take you to a gene-specific page. This page plots the expression level of this gene across the given set of experiments. Flagged data are marked with blue boxes. Columns that the user previously marked "Print" appear below the plot.

Prism was developed by Wei Wu and William Stafford Noble. Questions, comments and requests should be directed to cegrant@u.washington.edu. Prism is copyright 2003 by the University of Washington. It is published under the GNU public license.Prism was developed with support from the National Science Foundation award ISI-0431725.