Section 10 SUBNETWORK ANALYSER (SNPS) - SAS

10.1 Input Interface

Input

  • Step 1: Input a list of SNPs with dbSNP rsIDs in the first column and corresponding significance information (p-values between 0 and 1) in the second column.

  • Step 2: Specify the population to include SNPs in linkage disequilibrium. By default, input SNPs with p-values < 5e−8 are considered. Additional SNPs in linkage disequilibrium (R2 >= 0.8) can also be included according to the specified population.

  • Step 3: Use genomic proximity, quantitative trait locus mapping, or promoter capture Hi-C to identify linked genes.

  • Step 4 and Step 5: A subnetwork of highly-scored genes is identified from a gene network (Step 4), with the desired number of genes in the resulting subnetwork (Step 5). 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 returned for reference.
The interface of `SUBNETWORK ANALYSER (SNPS) - SAS`. The `Show/Hide Info` toggle button contains instructions on how to use the interface, including inputs, outputs, and other relevant information.

FIGURE 10.1: The interface of SUBNETWORK ANALYSER (SNPS) - SAS. The Show/Hide Info toggle button contains instructions on how to use the interface, including inputs, outputs, and other relevant information.

10.2 Subnetwork Results

  • Under the Input SNP-Level Summary Data tab, An interactive table displays user-input summary data.
`An interactive table` displaying user-input summary under the `Input SNP-Level Summary Data` tab returned for exploration.

FIGURE 10.2: An interactive table displaying user-input summary under the Input SNP-Level Summary Data tab returned for exploration.


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

FIGURE 10.3: An interactive table listing genes linked from input SNPs under the Output: Linked Genes tab.


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

FIGURE 10.4: A network visualisation of the resulting subnetwork, with genes/nodes color-coded by linked gene scores (ranged from 1 to 10) under the Output: Gene Subnetwork tab.