Question: GENE ONTOLOGY VS PATHWAY ANALYSIS...
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5 weeks ago by
revenge.com0 wrote:

Is gene ontology a form of pathway analysis?? I would like to know more about "pathway analysis" as it seems like a very broad topic that involves several things, like gene enrichment analysis, KEGG, gene ontology etc...

gene otology analysis pathway • 139 views
ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by revenge.com0

gene ontology a form of pathway analysis

No, it is not. Gene ontologies are attempts to find sets of controlled vocabularies to describe gene functions, see their documentation here.

I would like to know more about "pathway analysis"

I recommend you start by reading this summary by Khatri et al.

ADD REPLYlink modified 5 weeks ago by i.sudbery8.5k • written 5 weeks ago by Friederike6.0k

Thank you for responding Friedderike!

In terms of Gene Enrichment Analysis....is this a way to DO pathway analysis??

ADD REPLYlink written 5 weeks ago by revenge.com0
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Pathway analysis is similar to Gene Enrichment analysis.

GO terms are represented in a giant network (technically a directed acyclic graph) and there can be a lot of redundancy. For example, there are GO terms for inflammation, acute inflammation, response to acute inflammation, regulation of inflammation, etc.

If you take a gene set enriched in tissue from a burn wound or something, you will probably see enrichment for a ton of very similar GO terms. This can be helpful or super annoying depending on what you want to do with your analysis.

Pathway enrichment tends to be a bit more limited (since we haven't mapped out that many pathways fully), but can be really nice because you'll get a more succinct answer ("Ah, the inflammation and DNA-damage pathways are enriched!)

ADD REPLYlink written 5 weeks ago by MaxF70
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