Selecting genes by biological pathways or gene ontology terms

 

SVA allows selecting genes by KEGG pathways or gene ontology terms.

1. Selecting by KEGG pathways

To access this function, click on menu "Filter -> Gene filter - pathway ", or click on button "Gene filter - pathway ".

You will see a dialog like this:

You have three ways to select genes:

  1. Click on the "Selected" column (the 2nd column) in the table;
  2. Search pathways through a keyword. An example is provided below.
  3. Prepare a text file including all the biological pathways that you would like to select, with per row one pathway. Then click on button "Load pathway list" and load the text file.

If you would like to remove all the selected genes, click on button "<<Deselect all".

After you select the genes, click on button "FILTER". This process will first select all the genes associated with the selected biological pathways, then select all the variants related to the selected genes, by the functional categories defined here.

2. Selecting by gene ontology (GO) terms

To access this function, click on menu "Filter -> Gene filter - gene ontology ", or click on button "Gene filter - gene ontology ".

You will see a dialog like this:

You have three ways to select genes:

  1. Click on the "Selected" column (the 2nd column) in the table;
  2. Search pathways through a keyword. An example is provided below.
  3. Prepare a text file including all the gene ontology terms that you would like to select, with per row one GO term. Then click on button "Load GO list" and load the text file.

If you would like to remove all the selected genes, click on button "<<Deselect all".

After you select the genes, click on button "FILTER". This process will first select all the genes associated with the selected GO terms, then select all the variants related to the selected genes, by the functional categories defined here.

 

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© 2011 Dongliang Ge, PhD.