Max-Planck-Institut für Informatik
max planck institut
mpii logo Minerva of the Max Planck Society

DomainGraph Documentation



A main feature of DomainGraph is the graphical representation, which can be obtained by double-clicking on a gene or protein node. This feature is especially useful for visualizing the Affymetrix probesets annotated to protein isoforms. Using the graphics, users are directly pointed to exons affected by alternative splicing, which protein isoforms are favored under a certain condition and if the alternative splicing event affects a domain-coding region or a microRNA binding site. Tooltips provide additional information, e.g. if the probeset is known to align to an alternative or constitutive exon or if the probeset is associated with an microRNA binding site. Furthermore, cross-hybridization information for the probesets is given, indicating whether the probeset is known to align to more than one genomic position (which would mean, the measeured expression could be caused by a transcript to this other genomic location).
The first screenshot shows a toy network (gene interaction network) with integrated AltAnalyze data. The graphical representation of 'FYN' is shown in the Data Panel. The black line with the red, blue and green rectangles represents the protein and its contained domains. Below, the exon structure is shown including the 3' and 5' UTRs. Next, the Affymetrix probesets are displayed: white color indicates that the probeset was not statistically analyzed by AltAnalyze but filtered out before. Gray stands for probesets that do not show differential expression. Probesets colored in red or green show differential expression in the two samples, with green indicating down-regulation in the experimental group and red indicating up-regulation in the experimental group.
The second screenshot shows a toy network (protein interaction network) with integrated Single Experiment data. As can be seen from the network, the NTNG2 protein contains 2 domains that are indicated to be spliced out (colored in pink). A closer look at the graphical representation makes this even clearer: expressed probesets are colored in yellow to red (color gradient according to expression strength) while not expressed probesets are colored in pink. As can be seen from the graphics, most of the Laminin-N domain is not expressed as is the 3rd Laminin-EGF domain (the 3rd domain colored in red). The tooltips provide additional information, e.g. on the probeset p-values, on cross-hybridization events, and on the microRNA binding sites.

Additional Information

DomainGraph provides some basic information on the proteins, which consists of the common names, contained Pfam domains, GO annotations, and OMIM annotations (for human proteins). They can be used to obtain a quick overview of the function of a specific protein. The information is available via right-click on a protein node.


There are several options available to customize the visual appearance of a domain graph, such as showing or hiding node and edge labels, or adjusting the edge width to the confidence scores. Furthermore, domain interactions can be filtered according to their confidence scores and low-confidence edges can be removed from the network. Additionally, the stepwise exploration of protein networks and their underlying domain interactions is coordinated in the options.


The analysis methods are mainly intended for domain graphs with integrated 'Single Experiment' data. Users can choose to compute the intersection, union, and difference of two graphs. These graph methods do not only take identical and different nodes and edges into account but also the biological types (i.e. an expressed domain or a spliced domain, for example) and highlight nodes and edges that are contained in both networks but with different biological types.