Gene ontology and GSEA

Question

[Amr]

What is the difference between the idea of Gene ontology and GSEA? I read many things but i just want an easy way to understand it

Thanks in advance

Answer 1

[Ram]

The way I see it, Gene Ontology, as the name suggests, is information on why a gene exists. Where it exists, what it does etc. are topics addressed by gene ontology. There are several terms (GO terms) that describe these aspects of the gene. As such, this can be considered a dataset - a collection of information points

GSEA stands for Gene Set Enrichment Analysis. I'm sure there are excellent explanations out there, but again, as the name suggests, this is an analysis, an action that yields information based on some raw data. It works on gene sets, which are collections of genes. It looks for enrichment of known sets of genes against an input set of genes. If you have a bunch of genes that were expressed strongly in one tissue vs another, you could perform GSEA on this bunch and that would tell you if certain known groups of genes overlap with your input set.

I'd recommend you Google these terms ("What is GSEA?", "What are GO terms?") and read through blog posts, introductory papers, major websites (KEGG) etc.

Answer 2

[Hamid Ghaedi]

Ontology: An ontology formally represents knowledge as a set of concepts within a domain and the relationships among those concepts. It can be used to reason about the entities within that domain and may be used to describe the domain.

Gene Ontology(GO) A way to capture biological knowledge for individual gene products in a written and computable form. It is A set of concepts and their relationships to each other arranged as a hierarchy. The concepts are molecular function(MF), biological process (BP), and cellular component (CC).

For example by GO, you can identify genes (or more specific gene products) that are working together to do a meaningful job like cell division. By an experiment like RNA-seq , it is possible to see what genes are dysregulated. To be able to see what pathways (consisting of a group of genes) are dysregulated we can use statistical methods like gene set enrichment analysis (GSEA)