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Question: Is DAVID an over-representation (ORA) tool for pathway analysis
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I have been reading the following 2 reviews to get an overview of all pathway analysis tools:

1) https://www.nature.com/articles/nmeth.3963

2) https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002375

Am I right in thinking that DAVID is an ORA method? I was looking at the DAVID website but it is not extremely clear.

Thanks

ADD COMMENTlink 9 months ago m93 • 150 • updated 9 months ago h.mon 25k
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Yes, I believe DAVID implements an ORA method, as defined by Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges. The best place to check would be the DAVID papers.

I don't think the terminology used by the Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges paper has stuck, for example, it is common to see GSEA being referred to as an over-representation analysis.

ADD REPLYlink 9 months ago
h.mon
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Yes, it certainly seems like a lot of the terminology evolving around pathway analysis is loosely used.

ADD REPLYlink 9 months ago
m93
• 150

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