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Question: David Pathway Analysis
1
gravatar for dingying85
7.2 years ago by
dingying85 • 10
United States
dingying85 • 10 wrote:

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.
• 8.3k views
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modified 14 months ago by kmherb • 10 • written 7.2 years ago by dingying85 • 10
3
gravatar for Charles Warden
7.2 years ago by
Charles Warden ♦ 8.0k
Duarte, CA
Charles Warden ♦ 8.0k wrote:

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/
ADD COMMENT • link written 7.2 years ago by Charles Warden ♦ 8.0k
2
gravatar for Free Man
7.2 years ago by
Free Man • 170
Earth - China
Free Man • 170 wrote:

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.
ADD COMMENT • link written 7.2 years ago by Free Man • 170
0
gravatar for kmherb
14 months ago by
kmherb • 10
United States
kmherb • 10 wrote:

Have you tried metascape? Super user friendly! metascape.org
ADD COMMENT • link written 14 months ago by kmherb • 10
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