Using DAVID as a beginner

Question

[SylviaR]

Hello, I am using DAVID for the first time and struggling to understand it. I want to do a quick pathway analysis, but I am unsure how to use DAVID and how to report the results. I would really appreciate some help.

• I have a whole bunch of genes, some upregulated and some downregulated. Should I put them into the gene list together or apart?
• If I use the functional categories option, and click the "chart" button, what does this output mean? If I do this, the top hit is "disulfide bond", would it be correct to say that "the unregulated genes show enrichment for disulfide bonds"?
  • If that is not correct, do I need to use the "functional annotation clustering" to analyze enrichment? My top cluster contains "disulfide bond", but also "glycoprotein" and "signal". How can I report this result?

My samples are mRNA sequenced human tissue

Thank you :):)

Answer 1

[Kevin Blighe]

You can choose whether to input all genes together or to analyse them separately. In each case, the meaning is different. If you input all together, then you just get a general feeling of 'dys-regulation'. If you think about it, it is quite reasonable to assume that, in a given pathway, some genes may be up- and down-regulated.

Functional annotation clustering will perform enrichment and then perform a second step whereby it clusters the enriched terms into cluster groups, and then ranks them by the score.

Functional Annotation Chart will just perform the enrichment step and output all terms. You can filter the list by p-value.

If you are comfortable in R, I have provided a tutorial to plot the results of DAVID (this will be a Bioconductor package once I get time): Clustering of DAVID gene enrichment results from gene expression studies

Also in R, the KEGGprofile package can also do pathway enrichment.

Kevin