We’re pleased to announce another incremental release of Gitools, version 2.2. Amongst the many improvements (listed at the bottom of this post) we’d like to highlight the effort that we put into improving performance, specifically with genomic data: mutual exclusion and co-occurrence statistics coupled with a new feature called “data events” – which helps to get a quick grasp of the data.

Low expression events ordered by mutual exclusion

Low expression data events events ordered by mutual exclusion

Mutual exclusivity and co-occurrence statistics 

Selective pressure of cancerogenesis on the alteration of certain pathways is expected to result in a mutually exclusive alterations pattern within a cohort of cancer samples. Similarly, other alterations may be cooperating. In order to be able to test a hypothesis directly with the prepared cancer genomics heatmap datastes we implemented a weighted permutation approach to test for mutual exclusivity and co-occurence of alterations across a group of genes which is currently available as an additional step when sorting the genes by mutual exclusivity.

If you have loaded alterations data in a Gitools heatmap with genes listed in rows, you can test for mutual exclusivity and co-occurrence via the menu Edit->Rows->Sort by mutual exclusion dialogue. Just activate the option at the lower part of the dialogue (see Screenshot 1 below). After the test has been performed for the selected genes, the results will be shown to you in a new dialogue (see Screenshot 2). For more information, see the “Mutual exclusion and Co-occurrence Test” page in the documentation.

Data Events

The mutual exclusivity sorter expects binary data: events and non-events. Therefore we have introduced “Data Events” which is an automatic way to decide which data points are (positive) events, and which are not. Given that you are viewing test-results with the p-value color scale, all data points that fall below the selected significance cut-off are events. For more examples, see the “Data Events” page in the documentation. If need be and the current event function does not serve for your purpose it is easily switched for another one using the drop-down menu.


The summary of the selected genomic alteration data (left) shows that 14 % of the selected cases (4 genes and 306 samples) are altered. At the left we can see that the same samples and genes are upregulated in 128 cases (10%)

The same event functions are available at the new selection box, that appears always at the left of the heatmap if some rows and/or columns are in selected state. In the above image, we show two examples of the selection box that is summarizing the selected genomic alteration data (left) and the selected expression data (right). In the expression data, which is median-centered, all values above the scale cut-off, highly expressed genes, are set to be data events.

mutual-exclusive-test-setupScreenshot 1: Mutual exclusive sorting and statistical test in Gitools.


Screenshot 2: An example of a mutual exclusive test result

Changelog Gitools 2.2.0 (July 8th 2014)

* Mutual exclusion plugin (new)
* SVG image export (new)
* Hierarchical cluster heatmap header with contextual menu (new)
* Selection statistics (new)
* Data events (new)
* Import string values: importing strings to categorical values (new)
* Layer groups (new)
* Recent files (new)
* New .mtabix compressed data file format (new)
* View enrichment data via contextual menu in results (new)
* View group comparison data via contextual menu in results (new)
* Parellization: use multiple cores for many tasks
* Many performance improvements
* UI improvements