Department of Bioinformatics and Computational Biology

Home > Public Software > SpliceSeq > Group View


hidden rowfor table layout
DescriptionA tool for investigating alternative mRNA splicing in next generation mRNA sequence data
Development Information
Current version2.1
PlatformsPlatform independent
LicenseFreely available for academic and commercial use
Last updatedFebruary 21, 2014
Citation Ryan, M. C., Cleland, J., Kim, R.G., Wong, W. C., Weinstein, J. N., SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts, Bioinformatics 28 (18) p.2385 (2012). 
Help and Support

Group View

The Group View is used to study aggregate splicing patterns of a group of samples. To use this view, the groups must have already been loaded into the database. (See Loading Data for information on creating groups.)

The Group View is generally similar in function to the Sample View, with the only major difference being that the Group View presents the average statistics for the members of the group. (e.g. if a group has three samples with 10, 15 and 20 reads in Exon A respectively, then the average read total for Exon A will be 15) Likewise, all numerical values such as PSI and magnitude would all be derived from average statistics.

To get to this view, first select Group View in the View Combobox in the Data Selection Bar . Next, select the group that you wish to investigate using the DataSet Combobox also in the Data Selection Bar.

When the group loads, the Results Panel will be loaded with all the splice events identified in the chosen group.

Group View Results Panel

Gene Summary Tab of the Results Panel allows you to sort, filter, display, and export the results for each gene in the currently selected group.

The columns that require further explanations are::

To access filtering functions for the table, use the Change filters button. The following filters are available:

Splice Event Tab in the Results Panel will contain a row for every splice event detected.

Columns that may require additonal explanation are:

To view the scatter plot of individual sample PSIs within the group, right click on a row in the Splice Event table and choose Show PSI Scatterplot.

To access filtering functions for the table, use the Change filters button. The following filters are available:

Uniprot Event Tab in the Results Panel contains a row for every UniProt-annotated feature region that is affected by alternative splicing.

To access filtering functions for the table, use the Change filters button. The following filters are available:

Group View Detail Panel

Graph Image Tab of the Detail Panel shows how the RNASeq reads of group of samples align onto the same splice graph on average.

The Show Values radio buttons on the left toggles the display of numerical values for every exon and splice. There are 4 options:

One additional feature provided in the Group View is the ability to investigate the distribution of values for any exon or splice. With OPKM, Total Reads, or Ratio selected, right click on an exon or splice line and then select either a scatter plot or box-and-whiskers plot. An additional window will open showing the OPKM, Total Read, or Ratio value for that exon / splice for each member of the group. These plots are helpful in determining if the exon or splice expression pattern is consistent across the group or widely variable.

Protein Sequence Tab of the Detail Panel shows the protein sequence, functional annotation, and relative expression level of the isoforms inferred from splice patterns of the gene from the group. For basic information on this tab, refer to Protein Sequence Tab.

Exon Info Tab of the Detail Panel shows the location, properties and nucleotide sequences of each exon in the gene model. More Information can be found in the GUI Overview section.