Gene details

Clicking on the Complex exon view bar opens the complex exon view. This view diplays the exons of the gene and their usage in the different transcripts relative to the true size of the exon. Exon information (sequence, phase and location) may be obtained by clicking on a specific exon. Transcript details may be opened (in a separate tab) by clicking on the transcript link.

This view shows the exons of the gene in a simplified view. The size of the exons is ignored in the view and all exons are shown in a standardized size. This provides a fast and easy overview on the differences between transcripts and the alternative exon usage with respect to different isoforms of the gene. Additionally in this view Affymetrix and Interpro features are mapped onto the exons and can be directly accessed by clicking on the bars. Again you can access exon information by clicking on a exon and proceed to transcript information by clicking on the transcript link in the leftmost column.

Interpro features: By default the Interpro features are shown in a simplified view meaning that for every exon it is only indicated whether there is a feature annotated or not. The Interpro features are subdivided according to their different source databases. To open or close the detailed view of the features for specific pattern database click on the name of the database or any feature (the black bars). In the detailed view you can click on a feature to obtain the details for it. A popup window will open showing the details of the feature containing a link to the external database to obtain more information as well as transcripts matched by a feature and the position and E-value information.

Affymetrix feature: All available Affymetrix probesets mapped onto exons are shown here. Click on one of the Affymetrix features (black bars) to obtain details on the corresponding affymetrix probeset including genomic position, number of probesets and Affymetrix quality annotation.

We incorporated additional tools into ProSAS for the analysis and visualization of exon microarray measurements. Exon microarrays enable the comprehensive expression profiling of individual exons, and thus also alternatively spliced transcripts, across different experimental conditions. In order to reliably detect alternative splicing events from microarrays we employ our ANOVA based method PASS (Kueffner et al., 2008, submitted) that is briefly described in the following.

Before applying ANOVA (ANalysis Of VAriance), we scale the raw signal values to enable the calculation of signal ratios between probesets. Scaling aims to compensate for probeset specific effects that cause each probeset to respond differently to target abundance (multiplicative and additive errors). In case of low signal probesets scaling sometimes strongly amplifies the noise in the signal thus partially obliterating the data plots.

The precision of PASS predictions has also been systematically validated against Ensembl annotated alternative transcripts. We could show that PASS was able to detect Ensembl annotated splicing events far more reliably than MIDAS provided by Affymetrix (Kueffner et al., 2008, submitted to BMC Bioinformatics). ProSAS displays raw and scaled measurements and enables the selection and visualization of individual probesets and exons in the context of known protein structures. The PASS ANOVA results allow users to quickly access alternatively spliced genes, exons and probesets. Thereby ProSAS displays alternative splicing events between different conditions and their effects on the overall structure of the affected proteins. For demonstration a dataset of 11 human tissues with 3 replicates per tissue has been imported into the ProSAS database.

Here, all the available probesets are listed with their corresponding information like which exon is matched or what the quality of the probeset (as annotated by Affymetrix) is like (CORE: best quality).