How to Use the Spotfire – MetaCore Integration

How to Export from Spotfire Professional and Spotfire Enterprise Client to MetaCore

Data from Spotfire Professional and the Spotfire Enterprise client can be exported to MetaCore for pathway analysis. This document will describe the steps to take to export the desired data from Spotfire to MetaCore.

The export to MetaCore option can be accessed by selecting “File->Export->To GeneGo MetaCore” (Figure 1). This will open the “Export to GeneGo MetaCore” dialog box. Some fields in this window are filled in by default (Figure 2).

Figure 1: Selecting the export to MetaCore option.

Figure 2: Default settings. Some field will remember user input (see below).

http://portal.genego.com is the default URL

Data table name in Spotfire is the default Experiment prefix

The correct MetaCore installation URL should start with “http://” and finish with “/api/soap.cgi”. The URL provided is adjusted automatically if it doesn't comply with these rules (Figure 3).

Figure 3: Entered and adjusted MetaCore URL.

The entered URL is automatically changed to comply with formatting rules.

Red circles with an exclamation point are displayed if some required fields are empty or contain incorrect data (Figure 4). A tooltip with the error description is displayed on mouse-over.

Figure 4: Red circles mark required or incorrect fields.

If some rows are marked in the Spotfire visualization, the “Export selected rows only” setting is chosen by default. The number of selected rows is also displayed (Figure 5). If nothing is selected in Spotfire, the “Export all rows” setting is chosen and “Export selected rows only” is disabled.

Figure 5: Selecting specific rows to upload to MetaCore.

1. Rows selected in Spotfire

2. “Export selected rows only” chosen by default

The “ID column”, “Data column” and “P-value column” lists contain the column names from the current data table in Spotfire (Figure 6). Select the corresponding column from each list.

Figure 6: Selecting the gene identifier column.

The “ID type” list contains all of the gene identifier types that can be recognized by MetaCore (Figure 7). Select the matching ID type to the current Spotfire data table.

Figure 7: The identifier types listed in the “ID Type” menu.

The user can choose to automatically open the data in MetaCore after the export is complete. To do so, check the “Open in MetaCore after export” checkbox (Figure 8).

Figure 8

The “Open in MetaCore” checkbox

Figure 9 contains a completed export form.

Figure 9: Complete export form.

When the “Open in MetaCore after export” option is selected, the MetaCore Data Manager is automatically opened in the default browser when the export completes. The newly exported experiment is in the Active Data folder (Figure 10). At this point the export is complete and further pathway analysis can be performed on the data within MetaCore.

Figure 10: Data Manager window.

Exported experiment is automatically activated

Some settings in the Export to GeneGo MetaCore window are saved between sessions. These include the MetaCore URL, username, password (only if the “Remember password” box is checked), and the state of the “Open in MetaCore after export” checkbox.

Figure 11: Saved fields.

These fields are saved automatically

The password is saved when the “Remember password” box is checked

Export Data from MetaCore to Spotfire

Gene lists created in MetaCore (from maps, networks, diseases, etc.) can be broadcast back to Spotfire as well. In the export panel, select Spotfire in the "To" row. Then, give the list a name and click Export (Figure 12).

Figure 12: The gene list export panel set to export to Spotfire.

After clicking Export, you will be prompted with a File Download message, click Run. A new window will open with a number of options. First, it will detect if you have Spotfire already running. If you do not, you will be prompted to click OK to start Spotfire. There are two options for opening the exported list in Spotfire. If you have a file open in Spotfire, you can mark the genes in that file that are also in the exported list. Use option 1 to perform this action. First select the column in Spotfire to use as the gene identifier column, and then click the Mark records button (Figure 13).

The second option for sending data to Spotfire is to load the list as a new visualization in Spotfire. To do this, click the “Load new” button. Then go to Spotfire, if a visualization was already open you will be prompted to save it. After doing so, the list from MetaCore will then be opened in Spotfire.

Figure 13: The Export to Spotfire options panel.

Figure 14: Visualization in Sporfire with genes marked from a MetaCore list.