Running Enrichr in python using a background gene list

Question

[Jen]

I am trying to run Enrichr in python using a background gene list as per https://gseapy.readthedocs.io/en/latest/gseapy_example.html (2.3.2.2. Enrichr Web Service (with background input)). I got the following to work without specifying a background:

enr_bg = gp.enrichr(gene_list="3383CCGs.txt",
                 gene_sets=['KEGG_2019_Mouse'],
                 outdir=None
                )

But then I try add the background argument to the script and it doesn't work:

enr_bg_back_KEGG = gp.enrichr(gene_list="3383CCGs.txt",
                 gene_sets=['KEGG_2019_Mouse'],
                background="Background13569.txt",
                 outdir=None,
                )

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Input In [23], in <cell line: 1>()
----> 1 enr_bg_back_KEGG = gp.enrichr(gene_list="3383CCGs.txt",
      2                  gene_sets=['KEGG_2019_Mouse'],
      3                 background="Background13569.txt",
      4                  outdir=None,
      5                 )

TypeError: enrichr() got an unexpected keyword argument 'background'

Any ideas on how to input the background list into the command??

Answer 1

[bk11]

This is for human though. I just tested and it works fine. Please make sure to provide correct path to your gene_list and background

enr_bg = gp.enrichr(gene_list="gene_list.txt",
                 gene_sets=['MSigDB_Hallmark_2020','KEGG_2021_Human'],
                 # organism='human', # organism argment is ignored because user input a background
                 background= "all_human_genes.txt", #"hsapiens_gene_ensembl",
                 outdir=None, # don't write to disk
                )
enr_bg.results.head()
        Gene_set    Term    P-value Adjusted P-value    Old P-value Old adjusted P-value    Odds Ratio  Combined Score  Genes
0   MSigDB_Hallmark_2020    TNF-alpha Signaling via NF-kB   8.934977e-16    2.233744e-14    0   0   8.597135    297.902671  BTG2;BCL2A1;PLEK;IRS2;LITAF;IFIH1;PANX1;DRAM1;...
1   MSigDB_Hallmark_2020    Complement  8.934977e-16    2.233744e-14    0   0   8.597135    297.902671  FCN1;LRP1;PLEK;LIPA;CA2;CASP3;LAMP2;S100A12;FY...
2   MSigDB_Hallmark_2020    IL-6/JAK/STAT3 Signaling    1.891480e-15    3.152466e-14    0   0   15.259576   517.321263  IL4R;TGFB1;IL1R1;IFNGR1;IL10RB;ITGB3;IFNGR2;IL...
3   MSigDB_Hallmark_2020    Inflammatory Response   4.938414e-13    6.173017e-12    0   0   7.479140    211.933110  LYN;IFITM1;BTG2;IL4R;CD82;IL1R1;IFNGR2;ITGB3;F...
4   MSigDB_Hallmark_2020    heme Metabolism 3.693816e-12    3.693816e-11    0   0   7.116750    187.343901  SLC22A4;MPP1;BNIP3L;BTG2;ARHGEF12;NEK7;GDE1;FO...

[Jen]

Paths are correct. I have no idea why it's not working. Very strange. Maybe it's something to do with it being mouse? Don't know why that should make a difference.

[bk11]

It should work no matter what species it is. I saw your corresponding R code in other POST. Please so spend some time in basic R and Python; you will get there.

Selecting MOUSE gene set libraries in Enrichr

[Jen]

The reason it was not working is because I had a previous version of gseapy installed (0.9.5) which does not allow use of background gene list. I upgraded gseapy to version '1.0.6' and it worked to solve my issue.