Section 8 RSlyser

8.1 Interface

Input

  • Step 1: Input a list of genomic regions with two columns. The 1st column contains genomic regions in the format of chr:start-end (based on GRCm38/mm10), and the 2nd column for the significance information (p-values between 0 and 1).

  • Step 2: Use genomic proximity or enhancer-promoter datasets to identify linked genes.

  • Step 3 and Step 4: A subnetwork of highly-scored genes is identified from a gene network (Step 3), with the desired number of genes in the resulting subnetwork (Step 4). The significance (p-value) of observing the identified subnetwork by chance can also be estimated by a degree-preserving node permutation test.

  • More Controls: Use additional parameters to fine-tune the steps described above.

  • SUBMIT: click the SUBMIT button to execute the analysis.

Output

  • Example Output includes interactive tables and high-quality figures for the resulting subnetwork. A summary of input data and the runtime (computed on the server side) is also provided for reference.
The interface of `RSlyser`, including the `Show/Hide Info` toggle button with the help information on how to use the interface.

FIGURE 8.1: The interface of RSlyser, including the Show/Hide Info toggle button with the help information on how to use the interface.

8.2 Results

  • Under the Input: Region-Level Summary Data tab, An interactive table lists user-input summary data.
User-input summary data under the `Input: Region-Level Summary Data` tab returned for exploration.

FIGURE 8.2: User-input summary data under the Input: Region-Level Summary Data tab returned for exploration.


  • Under the Output: Linked Genes tab, An interactive table lists genes linked from the input genomic regions.
An interactive table listing genes linked from the input genomic regions under the `Output: Linked Genes` tab.

FIGURE 8.3: An interactive table listing genes linked from the input genomic regions under the Output: Linked Genes tab.


  • Under the Output: Gene Subnetwork tab, A network visualisation of the identified subnetwork is provided, along with An interactive table for the subnetwork genes.
A network visualisation of the resulting subnetwork under the `Output: Gene Subnetwork` tab, with genes/nodes color-coded by linked gene scores, which range from 1 to 10.

FIGURE 8.4: A network visualisation of the resulting subnetwork under the Output: Gene Subnetwork tab, with genes/nodes color-coded by linked gene scores, which range from 1 to 10.