Section 9 SUBNETWORK ANALYSER (GENES) - SAG

9.1 Input Interface

Input

  • Step 1: Enter a list of genes, with the 1st column for gene symbols and the 2nd column for the significance info (p-values between 0 and 1).

  • Step 2 and Step 3: Identify a subnetwork of highly-scored genes from a gene network (Step 2), with the desired number of genes in the resulting subnetwork (Step 3). 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 `SUBNETWORK ANALYSER (GENES) - SAG`. The `Show/Hide Info` toggle button contains the help information on how to use it, including inputs, outputs, and other relevant information.

FIGURE 9.1: The interface of SUBNETWORK ANALYSER (GENES) - SAG. The Show/Hide Info toggle button contains the help information on how to use it, including inputs, outputs, and other relevant information.

9.2 Subnetwork Results

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

FIGURE 9.2: The user-input summary under the Input Gene-Level Summary Data tab returned for exploration.


  • Under the Output: Gene Subnetwork tab, A network visualisation of the subnetwork is provided, along with An interactive table for the subnetwork genes.
Visualisation of the identified subnetwork, with genes/nodes color-coded by input gene significance information under the `Output: Gene Subnetwork` tab.

FIGURE 9.3: Visualisation of the identified subnetwork, with genes/nodes color-coded by input gene significance information under the Output: Gene Subnetwork tab.