R: STRINGdb, from get_enrichment() function how to get background gene list that are related to pathways?
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choijamts • 0
Last seen 21 months ago
South Korea

Hello there,

I wanted to get background gene lists of each pathway from string_db$get_enrichment() function.

But in the documentation https://bioconductor.org/packages/devel/bioc/manuals/STRINGdb/man/STRINGdb.pdf there were no information about it.

Here is my workflow:

 #1. Here I accessed to the string-db database and store it into object.

string_db <- STRINGdb$new( version="11", species=7227,
                                                score_threshold=400, input_directory="")

#2. And here i tried to get all of the string id and gene names from stringdb 
    #database and stored in "cc" object.
cc <- string_db$get_aliases()

#         STRING_id  alias
#1 7227.FBpp0070001 CG9570
#2 7227.FBpp0070002  Or19b
#[1] 750629      2

#3. As you can see there is huge number of gene lists, so lets get 50 of them for 
   #get_enrichment analysis.

cc_filter <- cc[1:50, 1:2] # First 50 genes

GOenrichment <- string_db$get_enrichment(cc_filter, category = "Component")

# [1]  1 10

# As you can see we got 1 pathway from get_enrichment() GO:CC function.

# Lets check result

#category       term number_of_genes number_of_genes_in_background ncbiTaxonId       inputGenes   preferredNames p_value   fdr                                    description
#1 Component GO.0090575               4                            87        7227 ac,sc,l(1)sc,ase ac,sc,l(1)sc,ase 0.00031 0.028 RNA polymerase II transcription factor complex

As you see here, we got 1 pathway and 10 variables, one of these variable is "number_of_genes_in_background". But the problem is that i couldn't get the background "gene list" for this pathway. Is there anyway to see that one?

Thank you

R STRINGdb • 537 views

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