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:
Home: It will load the GLAD4U homepage.
News/Updates: It will open a new window containing the news and updates about GLAD4U. New features will be introduced in this section.
Documentation: It will load this window. All information needed to run and interpret GLAD4U is provided in this window.
Contact Us: It will open a new window with a form to submit your information and questions. Once submitted, we will contact you in a fashionable manner.
Search*: Click to access the searching form. Enter any number of mixed Entrez-Gene IDs and gene symbols, separated by commas and without space (ex: "ALB,213,hpn,22"), and click GO. A new window will open with the results of the search. If any of the genes are found, their ID will be linked to the Entrez-Gene page, along with their score and position in the current GLAD4U list. Searching all species can take up to few minutes. This feature only works while your session is active. If GLAD4U notifies you that your session has expired, just re-run your query.
clicking this picture will expand the menu.
clicking this picture will collapse the menu.
this menu is only available on the result pages
The query page is composed of 4 parts:
Query: Enter the term(s) that you want to use to build a ranked gene list. This field is required.
E-mail: Entering your e-mail will allow you to receive updates from GLAD4U, such as the summary and the completion of your query.
DEFAULT OPTIONS*: Click "[expand]" to access the parameterizing options for GLAD4U. You can modify the following:
What score threshold to apply to the analysis: this setting determines which genes will be kept in the results, based on their scores after the hypergeometric test.
Which search space do you want to search: "All" will retrieve all genes, regardeless of the species, " Homo sapiens" will only consider human genes.
How many genes per page: the number of genes to present on each page of results.
How many publications per gene: the maximum number of supporting publications to present for each gene on the result page.
How many page links per page: the number of result pages to compute at once.
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
The results page is composed of 4 parts:
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:
will let you download all the results as a TAR archive (.tar.gz)
will let you download all the results in a Comma Separated Values (CSV) or Excel file
will let you download a text file with all the scores and corresponding Entrez-Gene IDs
clicking the next to the number of genes after the score threshold will open a new window listing all the excluded genes
Send data to functional enrichment analysis*: It will open a new window where your list of genes will be enriched using WebGestalt.
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.
Ranked gene lists:
Click " Expand all publications " to show all supporting publications for all the genes on this page. Click " Hide all publications " to hide all supporting publications for all the genes on this page.
each gene is formatted as:
Rank. Gene symbol - Full name [specie, Entrez Gene ID]
score, link to the Entrez-Gene page (new window), show/hide supporting publications
The supporting publications are not ranked, just organized by their PMIDs, from more recent to less recent.
Click "Abstract" at the end of each publication to open a new window with the corresponding article in Pubmed.
clicking this picture will expand the publications list for this gene.
clicking this picture will collapse the publications list for this gene.
Click the link "see all supporting publications in PubMed" to open a new window showing all the supporting publications for that gene within PubMed.
functional enrichment analysis is provided by the WebGestalt. Pop-up windows need to be allowed.
last edited on 08/02/2010.