Documentation

GLAD4U allows you to query the scientific literature to retrieve and prioritize a list of Entrez-Gene IDs. Its ranking algorithm relies on the hypergeometric test.

You can see an example of results here (a new window will open). This ranked list was obtained with the query laminin 5 cell migration run with the default options.

Most of the features of GLAD4U can be discovered through the mouseover help boxes provided within the different pages.

This documentation is organized in three parts:

  1. Menu
  2. Query
  3. Results

Menu [top]

* this menu is only available on the result pages


Query [top]

The query page is composed of 4 parts:

  1. Query: Enter the term(s) that you want to use to build a ranked gene list. This field is required.

  2. E-mail: Entering your e-mail will allow you to receive updates from GLAD4U, such as the summary and the completion of your query.

  3. DEFAULT OPTIONS*: Click "[expand]" to access the parameterizing options for GLAD4U. You can modify the following:


  4. Ticket number**: if you have received an email with a ticket number and would like to see if the results are available, enter your ticket number here to retrieve your results.

To run GLAD4U: after filling the query field (and optionally entering your email and modifying the options), click "Search" to start GLAD4U. Clicking "Clear" will reset all the fields in the form.

To retrieve your results: after filling the ticket number field, click "Retrieve" to get your results. Clicking "Clear" will reset the Ticket number field in the form.

* changing any of these options will increase the time needed for GLAD4U to present you with the results.

** this menu is only available on the home page


Results [top]

The results page is composed of 4 parts:

  1. Summary: It shows all the parameters used to run GLAD4U. It also provides the statistics of the run (number of publications and genes retrieved). Next to "Summary" are two icons:

  2. Send data to functional enrichment analysis*: It will open a new window where your list of genes will be enriched using WebGestalt.

  3. Navigation: click the different Page number to navigate to the corresponding page. Click "Previous" to go back to the previous pages and "Next" to build the next pages.

  4. Ranked gene lists:

* functional enrichment analysis is provided by the WebGestalt. Pop-up windows need to be allowed.


last edited on 08/02/2010.