Section 7 ENRICHMENT ANALYSER (SNPS) - EAS

7.1 Input Interface

Input

  • Step 1: Enter a list of SNPs, where the 1st column contains dbSNP rsIDs and the 2nd column for the significance information (p-values ranging between 0 and 1).

  • Step 2: Specify the population to include SNPs in linkage disequilibrium. By default, input SNPs with p-values < 5e−8 are considered, and additional SNPs in linkage disequilibrium (R2 >= 0.8) can 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: Select from a list of supported ontologies.

  • 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 enrichment results. A summary of input data and the runtime (computed on the server side) is also returned for reference.
The interface of `ENRICHMENT ANALYSER (SNPS) - EAS`. The `Show/Hide Info` toggle button contains the help information on inputs, outputs, and other information.

FIGURE 7.1: The interface of ENRICHMENT ANALYSER (SNPS) - EAS. The Show/Hide Info toggle button contains the help information on inputs, outputs, and other information.

7.2 Enrichment Results

  • Under the Input SNP Information tab, An interactive table lists the user-input SNPs.
The user-input data under the `Input SNP Information` tab returned for exploration.

FIGURE 7.2: The user-input data under the Input SNP Information tab returned for exploration.


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

FIGURE 7.3: An interactive table listing genes linked from the input SNPs under the Output: Linked Genes tab.


  • Under the Output: Enriched Terms tab, An interactive table lists enriched ontology terms.
An interactive table lists enriched ontology terms under the `Output: Enriched Terms` tab.

FIGURE 7.4: An interactive table lists enriched ontology terms under the Output: Enriched Terms tab.


  • Under the Output: Dotplot tab, A dotplot illustrates enriched ontology terms. A downloadable pdf file is also provided.
A dotplot for enriched ontology terms under the `Output: Dotplot` tab.

FIGURE 7.5: A dotplot for enriched ontology terms under the Output: Dotplot tab.


  • Under the Output: Forest Plot tab, A forest plot illustrates enriched ontology terms. A downloadable pdf file is also provided.
A forest plot for enriched ontology terms under the `Output: Forest Plot` tab.

FIGURE 7.6: A forest plot for enriched ontology terms under the Output: Forest Plot tab.