GENE ONTOLOGY VS PATHWAY ANALYSIS...
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...
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No, it is not. Gene ontologies are attempts to find sets of controlled vocabularies to describe gene functions, see their documentation here.
I recommend you start by reading this summary by Khatri et al.
Thank you for responding Friedderike!
In terms of Gene Enrichment Analysis....is this a way to DO pathway analysis??
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!)