Gene Set Enrichment Analysis (+ R tutorial) #57416
Unanswered
timase2021
asked this question in
Profile
Replies: 0 comments
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
-
Select Topic Area
Question
Body
hello I saw your youtube video which talks about enrichment tests, your video is very informative, and you master the subject well
so I come to you hoping to get help !. I'm stuck in an analysis
I have an assembled transcriptome. I performed analyses on this transcriptome to extract candidate sequences involved in the production of a substance. Then, I annotated both sets of data using the** Eggnog Mapper tool**. This is an example of my two first line result table.
#query | seed_ortholog | evalue | score | eggNOG_OGs | max_annot_lvl | COG_category | Description | Preferred_name | GOs | EC | KEGG_ko | KEGG_Pathway | KEGG_Module | KEGG_Reaction | KEGG_rclass | BRITE | KEGG_TC | CAZy | BiGG_Reaction | PFAMs
TRINITY_GG_10000_c0_g1_i1.p2 | 1307761.L21SP2_0427 | 1.46e-24 | 108.0 | COG3555@1|root,COG3555@2|Bacteria | 2|Bacteria | O | Aspartyl Asparaginyl beta-hydroxylase | aspH | - | - | ko:K12979 | - | - | - | - | ko00000,ko01000,ko01005 | - | - | - | Asp_Arg_Hydrox
I have organized my data in a table of COGs (Clusters of Orthologous Groups) annotation Total transcriptome COGs redundancy, candidate redundancy and a colomn for the COGs ( A,B....).
I am currently stuck on which statistical analysis to perform to determine the functions most involved in the production of the substance, and what other analyses can I perform with these two sets of data.
The eggnog annotation results didn't give the gene ID so I can't use g:profiler or ernrichGO package on R
thanks in advance
Beta Was this translation helpful? Give feedback.
All reactions