Medical Systems Biology

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2. Running VennMaster

The following steps lead to an Euler diagram:

1. Import a data set
2. Filter the data (only for data formats B and C)
3. Explore the Euler diagram

1. File Formats

VennMaster can import three different file formats.

A. List File Format

This is a very simple tab delimited file format with an element/group pair in each line which can easily be generated by e.g. Microsoft Excel or OpenOffice.

Toy example:
cat mammal
dog mammal
rose plant
rose spiny
dog animal
lobster animal
lobster spiny
:
:
This example can be downloaded: example1.list.

B. GoMiner Export File Format

VennMaster can import the pair of GoMiner summary export and gene-category export files. A brief summary of using GoMiner to generate these files is given in the Appendix below. An example file pair can be downloaded: go1.se go1.gce.

C. High-Throughput GoMiner Export File Format

VennMaster can import the single .gce-file which can be exported by the new high-throughput GoMiner.

D. Files for statistical analysis

VennMaster can perform a simplistic statistical analysis given appropriate input files. It may analyse whether a given intersection contains more than the expected number of elements. E.g. consider a list of differentially expressed genes from 3 different experiments. Given e.g. the fold change for each gene in each experiment, VennMaster can display the overlap of genes with at least 10 fold differential expression, and how this overlaps cadinality compares to its expected cardinality.

The input format for this type of data contains of a tab seperated file for each experiment. The File should contain an identifyer column and an arbitrary number of numerical values. The columns all should have a heading row. Numerical field should be named equaly between files of different experiments. One file might look like this:

GENE	absolute_expr	diff_expr	p-value
gene1	15	1.4	0.212
gene2	80	0.2	0.452
gene3	120	10	0.785
gene4	30	1.1	0.234
gene5	801	4	0.01452

A zipped example can be downloaded: column.zip

2. Importing the Input Files

A. List File

Choose the menu point Open List in the File menu and navigate to a file in the format described in section 1a.

B. GoMiner Export File

1. Choose Open GoMiner file from the VennMaster File menu.
2. In the first appearing file open dialog select the summary export (.se) file and press OK.
3. In the subsequent file open dialog select the gene-category export (.gce) file.
4. Continue with filtering.

C. High-Throughput GoMiner Export File

The export file format of the high-throughput GoMiner is now a single .gce file with a new column containing the false discovery rate (FDR).

3. Filtering

The number of categories can be reduced with the interactive filtering panel.

The five parameters have to be adjusted until the number of filtered categories (field #filtered categories) is satisfying. The number of filtered categories and elements are immediately adjusted when changing the filter values.

Click on the Update button to start the simulation with the current filter settings. The Reset button sets the filter settings back to the currently shown diagram. Normally the filter dialog should react immediately when changing the filter parameters. If not press on the Filterbutton.

4. Interactive Exploration

VennMaster allows the interactive exploration of the sets. When moving the mouse slowly over the polygon arrangement, the region under the mouse will be highlighted and the corresponding sets are shown in a small tool tip window. When a region is selected with the left mouse button the details of the selection are listed in the "Categories" tab of the information pane on the bottom. Right click on categories offers a menu for setting category labels and colors.

The upper panel shows the categories (for GoMiner files additional information is shown such as the TermID, nChanged, nTotal, pValue, and FDR). A double-click on a GO TermID opens a web browser with a direct link to www.geneontology.org. The lower pane shows a global information of the currently selected (intersection) set such as the number of involved groups and the number of elements in the intersection. Then all elements in the (intersection) set are listed in the lines below. With a double-click on a gene name a web browser is opened with a link to www.genecards.org. If a single polygon is selected it can be moved by drag and drop. When pressing the control button while selecting polygons, multiple regions can be selected and their corresponding elements are shown in the "Selection" region.

Set intersections for which no corresponding geometric intersection exists are listed in the "Inconsistencies" field of the information panel. Each entry consists of a list of categories { C1, C2 ..., Cn } : u with an integer u > 0 describing the number of elements in the shown intersection set.

Key Commands

VennMaster enables to copy and paste the contents of the category table and the gene list with the following key commands:

1. Select one or more cells of the category table or gene list with the mouse.
2. Press ctrl+A to select the whole table.
3. Press ctrl+C to copy the data into the clipboard.
4. Go to the target application (e.g. Excel or a word processing program) and paste the data.