Functional Annotation of Gene Lists in DAVID

After a list of genes are identified (e.g. differentially expressed genes), the most often asked question is what functions do these genes share? BxGenomicDB can pass the gene list to DAVID tool, where biologists can use a comprehensive set of functional annotation tools to further explore the data. Below we will look for what functional categories are enriched for genes that are highly expressed in metastasis cells vs. primary cells for prostate cancer.

The first step is to select your gene list. You can use the filter and search function in BxGenomicDB to get your list of differentially expressed genes.

Once you have the list, select all genes and click the DAVID button.

Select Gene List

Pass Gene List to DAVID

You will be brought to the pass list to DAVID window. From here, simply click the link for Functional Annotation Summary.
You have a few options from the DAVID Annotation Summary Results page. For now, let's just click the button for Functional Annotation Chart.

DAVID Functional Annotation Summary

DDAVID Functional Annotation Chart

DAVID will open a new window listing all the functional categories that are enriched. Note a few of the categories like extracellular region, blood vessel morphogenesis may have something to do with metastasis.

You can also explore other functions in DAVID. For example, Functional Annotation Clustering is very useful to combine the enriched categories which are related to each other by virtue of common genes. For more information, check the DAVID FAQ page.  

We are also working on other tools that help identified functional enrichment. Check out this new tool we developed recently. It has similar functions to DAVID, but you can download the complete list for each category, and it will search the Molecular Signatures Database which is not used by DAVID yet.