TOPGO- how to do GO enrichment using a custom go database?

Question

[ahmad.iut]

Hello Biostars, I want to do GO-enrichment analysis for a non-model organism. I have these tab-delimited files: reference (two columns):

genename GOs

gene1 GO:1, GO:2,GO:3

gene2 GO:2,GO:4,GO:6

gene3 GO10

DEGS1: gene1 gene2 gene3

DEGS2: gene5 gene6 gene7

How could I enriched GOs in DEGS1 against reference and DEGS2 using TOPGO package in R (or any other software)?

[matz]

Hi Ahmad - Check out our GO_MWU ( https://github.com/z0on/GO_MWU ): great power, no need to spit the data into DEGs / non-DEGs (the test is ranks-based so it can use any measure according to which the genes can be ranked), intuitive graphical representation of results. Just replace commas with semicolons (;) in your GO terms file, and have a table of ALL genes (not just DEGs) with a measure to rank them, such as log-fold-change, or (my preference) "signed log pvalue" - log10(pvalue) multiplied by -1 if the gene is down-regulated. More detailed instructions on the github page (see link above).

• Misha

[Kevin Blighe]

Specificaly for topGO, the way in which you can perform enrichment against a custom 'database' is described in the manual: Gene set enrichment analysis with topGO (see 4.3 Custom annotations).

Answer 1

[ahmad mousavi]

Hi Ahmad,

You can use WEGO website, its pretty cool, and you could do GO analysis based on GO ID information. The example is like