DrugDependentGene (DDG) Database Tutorial

For up to date issues or problems with this database please see the wiki.

About DDG

This enhancement to the NIF is funded by National Institute of Drug Abuse (NIDA). Its purpose is to facilitate discovery and use of resources relevant to drug abuse research.

Resources available in this database include tables from published journal articles that are associated with studies directly testing hypotheses relevant to the neuroscience of addiction and addictive behavior.  The database’s focus is on gene expression data and exposes data from investigations using DNA microarrays, immunohistochemistry, and in-situ hybridizations. Data types include the effects of a particular drug, strain or knock out on a particular gene. Data from tables and their corresponding methods have been extracted and stored so that their contents can be queried through the NIF.  Additionally, resources have been annotated using the NIFSTD ontology to facilitate discovery. 

 

How to Find Data in DDG

Data from DDG can be found through the NIF interface by searching for keywords.  Here we search for cocaine:

 

The Data Federation tab shows many results. To access the DrugDependentGeneDB (DDG) database click on the link under the Dataset or Gene category.  Several columns of results are exposed including the Publication column, which links to the paper’s abstract; the Gene, Brain Region, Exp vs. Control, Expression, Organism, and Protocol Type columns; the Treatment column, which links to the methods, when available; and the Table column, which links to the table, when available. In this way, all data and resources provided through NIF are attributed via links to the primary source from which the data were extracted.  As some resources (see wiki) require a subscription - or for other reasons is not available - at a minimum, the link to the abstract is provided.

Additional Data

In addition to the data visible through the interface is a variety of other data that can be accessed through the Export button on the top right of the results pane.  The exported data includes the data visible on the interface as well as additional details about each result including the drug paradigm, data analysis, comments, expression description, platform, PMID, etc. Results are exported in Excel.

Narrowing Your Search

To narrow down your search results, simply add additional search terms to the search string. Here we search for, gene:AQP4 cocaine

The search results went from over 70,000 records when we searched cocaine alone, down to 9 when we searched for a particular gene and cocaine.  Adding a brain region, such as hippocampus, to this search would narrow the results down even further!

 

Please refer to the wiki for publications whose tables are available through this database.

If you would like to share your published paper’s data in this interface, please contact curation@neuinfo.org