Section 5 Mining - RI2Genes

5.1 Input Interface

Input

  • Step 1: Enter a list of user-input genomic regions.

  • Step 2: Specify the reference genome build. Ensure that the input genomic coordinates (Step 1) are consistent with the specified genome build (Step 2).

  • Step 3: Select from a list of contexts available under different modalities (ABC, PCHiC, and QTL).

Output

  • Example Output includes interactive tables showcasing regulatory genes and their corresponding evidence. Additionally, a summary of the input data and the runtime (computed on the server side) is provided to the users.
The RI2Genes interface is displayed.

FIGURE 5.1: The RI2Genes interface is displayed.

5.2 Interactive Results

  • Under the Input Information tab, Interactive table lists user-input genomic regions.
A summary table of the user-input data displayed under the `Input Information` tab for exploration.

FIGURE 5.2: A summary table of the user-input data displayed under the Input Information tab for exploration.


  • Under the Output: Regulatory Genes tab, Regulatory Gene table lists regulatory genes. Each gene is hyperlinked to its gene-specific information page. Evidence table provides information on how regulatory genes are identified, including the contexts and regulatory interactions associated with them.
`Regulatory Gene table` within the `Output: Regulatory Genes` tab is depicted in this figure.

FIGURE 5.3: Regulatory Gene table within the Output: Regulatory Genes tab is depicted in this figure.