David Pathway Analysis

Question

[dingying85]

I am stuck in the output of DAVID pathway analysis. It seems it only gives the overlap between DE genes and the pathway, but gives no information about each pathway's size and the overlap between background and the pathway. Is there a way to get those informations? Thanks.

Answer 1

[Charles Warden]

I'm not a huge fan of David. Here are a couple other functional enrichment tools that I find easier to use and interpret:

http://gather.genome.duke.edu/

http://llama.mshri.on.ca/funcassociate/

Answer 2

[Free Man]

Are you using DAVID: Functional Annotation Tool?
DAVID does provided the information about the pathway size and the overlap between background.
Please use "Functional Annotation Chart" to view the results.
And use "Options" to customize the results which do not show the pathway size and the overlap between background by default.
Or use "Download file" to download full dataset.

Answer 3

[kmherb]

Have you tried metascape? Super user friendly! metascape.org