Department of Bioinformatics and Computational Biology

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SpliceSeq

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Overview
DescriptionA tool for investigating alternative mRNA splicing in next generation mRNA sequence data
Development Information
LanguageJava
Current version2.1
PlatformsPlatform independent
LicenseFreely available for academic and commercial use
StatusActive
Last updatedFebruary 21, 2014
References
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). https://doi.org/10.1093/bioinformatics/bts452 
Help and Support
Contact binf@insilico.us.com 

Sample View

The Sample View is used to study alternative splicing patterns and their potential functional impact in single samples. To use this view, the sample must have already been loaded into the database. (See Data Loading for information on loading new samples)

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

When the sample loads, the Results Panel will be loaded with all the splice events identified in the given sample. For a single sample, a splice event occurs when multiple isoforms of the transcript are expressed in the sample (e.g. some some transcripts include exon 10 and others splice it out)

Sample View Results Panel

Gene Summary Tab in the Results Panel will contain a row for every gene that is expressed in the sample.

Clicking on a gene row will populate the Detail Panel with a splice graph representing the exons and splices that were present in the sample. When a gene is selected, the Gene Information Box will show a functional annotation of the selected gene from UniProt and/or NCBI Gene.

Columns that require further explanation are:

The items in the Results Panel can be filtered to find just the type of results that are of interest. 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 require additional explanation:

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

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

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

The Show Values radio buttons on the left toggles the display of numerical values for every exon and splice. There are 3 options:

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 sample. For basic information on this tab, refer to Protein Sequence Tab.

The below example shows that differential expression of exons 1 and 2 results in different expression of the UniProt feature region CAP.

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.