Gene Set Enrichment Analysis

Question

[ahmad]

Once I come to Gene Set analysis, I have faced some confusing about the differences between ORA, GSEA, Pathway analysis. In addition about difference gene set databases:

Which once shall I start first and using which tools? For example there are clusterProfile package, GSEA software, and EnrichR?

Is there book or reference which can i use as a reference for functional analysis?

Thank you in Advance

Answer 1

[Meisam]

Take a look at this biostar tutorial for an example workflow.

There is no golden standard package or workflow. The different tools you mentioned are all widely used with more or less similar functionalities, i.e. you can do GSEA with either one of them, or gene ontology over representation analysis with enrichR, clusterprofiler or my personal preference gprofiler2.

Answer 2

[ahmad]

Hello, In case of using ORA throught enrichGO() function I have the following questions:

1- What shall I use GeneId or GeneName? 2- Regarding background list, shall this list contain the gene with 0 reads (all my genes in countable) ? 3- is it mandatory to pass OrgDb = org.Hs.eg.db param, or background list is enough? 4- which more prior to separate downregulated from upregulate and run the function 2 times or one type for both??

Thanks in advance