Genetic Network Explorer

Genetic Network Explorer (GNE) is a systems biology software suite that helps researchers analyze and draw conclusions from gene expression data in novel ways. In its current version, the software provides the following major features:

• Database with more than 40 000 genetic interactions
• Powerful search and visualization of genetic networks
• Graphical and statistical analysis of experiment data

The development is done in close collaboration with our academic and commercial partners and new versions are made available regularly.

Powerful Search & Visualization

Searching for genetic networks is easy using gene id, gene name, source database or more. Automatic suggest functionality make it quick to find the right set of genes and powerful filtering make the search results comprehensible.

Genetic network visualization is nearly instant, fully automatic and filled with detailed information in tooltips. Additional tabular views of the search results with direct links to NCBI and PubMed provides additional drill-down functionality for all genes and edges in the search results. And it all runs in your web browser.

Experiment Analysis & Discretization

Gene expression data from experiments can also be imported into GNE. The data is first ordered into treatment, timepoint and group, and thereafter each value is interpreted as representing either an active or an inactive gene expression level. The discretized data can then be visualized and superimposed onto any genetic network.

Using the BGM threshold calculator, the discretization algorithm is calibrated with large datasets GEO. Detailed information about the exact expression levels for each gene and probe is naturally also available. And a graphical and automatic network inconsistency report.

Interaction & Experiment Database

Our database contains of 40 000 genetic interactions for mouse and man and is easily extended and edited for more. The current sources include:

• Large curated literature databases
• Chromatin IP experiments
• Computationally predicted transcription factor binding sites

Gene expression data is chosen and imported to answer specific questions. The experiment data import engine supports NCBI GDS format among others.