Explore
EXPANSION is a new pipeline and webserver to explore the functional consequences of an input list of protein-coding alternative splice variants, for example differentially expressed (DE) instances from transcriptomics datasets. We combined information of DE protein-coding transcripts from cancer genomics with information of domain architecture, protein interaction network and gene enrichment analysis.
For more information, please refer to the about page.
Summary
- transcripts significantly up-regulated in tissues and transcripts significantly down-regulated in tissues
- domains affected in alternative spliceforms
- PTMs affected in alternative spliceforms
- binding regions affected in alternative spliceforms
In the isoform expression view, the log fold change expression of each isoform in each tissue is summarized using a bubble chart. The tissues (columns), isoforms (rows) , the bubble radius (PPDE value) and the bubble colour (LFC value).
The individual isoform structures are illustrated next to the bubble chart; proteins and their domains are represented as rectangles, and sequence divergences are represented as coloured lines according to the type of divergences. By moving on the mouse pointer over elements, a tooltip which contains the isoform expression information or structure information will appear next to the element. By clicking on the domains, PTMs and divergences an MSA viewer will appear.
By clicking on transcript ID UniProt page will be open.
For more information, please refer to the help section of this view.
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Interaction Network
In the interaction network view, the interaction of each isoform is summarized using a network architecture. In the interaction network, the proteins are represented as a blu circle, the peptides are represented as a grey circle, the small molecules are represented as a blu rectangle, the RNA molecule are represented as a blu triangle, the molecule sets are represented as blu rounded rectangle, and interactions are represented as coloured lines (edges) according to the type of interaction. By moving on the mouse pointer over elements, a tooltip which contains the interaction/interactor information will appear next to the element.
Use the range input to set the absolute value cutoff of the MI Score. Note: Updating the range input of this view will automatically update the network.
By placing the cursor over a node or edge and rotating the scroll wheel, you can zoom into the interaction network. You can also drag the mouse over an edge of the interaction network to reposition it.
For more information, please refer to the help section of this view.
Network Tools
In the enrichment pathways view, the functional enrichment analysis, also known as over-representation analysis (ORA) or gene set enrichment analysis, of each isoform is summarized using a bubble chart. The sources (columns), p-values (rows) and the bubble colour (enriched terms). It maps genes to known functional information sources and detects statistically significantly enriched terms.
By moving on the mouse pointer over elements, a tooltip which contains the functional information will appear next to the element.
For more information, please refer to the help section of this view.