When running enrichment analysis on the EnrichR website with background genes, the results showing on the web and those provided in the exported TXT file are not the same. Those on the web has the correct stats, whereas those in the exported TXT file are stats analysed without background genes.
Below shows the results from GO Molecular Function 2023 when I use the examples provided on the website:
Results copied from the web, when analysed without background genes
Index | Name | P-value | Adjusted p-value | Odds Ratio | Combined score
-- | -- | -- | -- | -- | --
4 | fatty-acyl-CoA Binding (GO:0000062) | 0.001626 | 0.3190 | 15.82 | 101.58
6 | Acyltransferase Activity, Transferring Groups Other Than Amino-Acyl Groups (GO:0016747) | 0.006961 | 0.3190 | 4.48 | 22.26
Results copied from the web, when analysed with background genes
Index | Name | P-value | Adjusted p-value | Odds Ratio | Combined score
-- | -- | -- | -- | -- | --
1 | fatty-acyl-CoA Binding (GO:0000062) | 0.0003711 | 0.1004 | 27.12 | 214.19
2 | Acyltransferase Activity, Transferring Groups Other Than Amino-Acyl Groups (GO:0016747) | 0.001135 | 0.1004 | 6.93 | 47.01
Results in the exported TXT file, when analysed with background genes
Term Overlap P-value Adjusted P-value Old P-value Old Adjusted P-value Odds Ratio Combined Score Genes
fatty-acyl-CoA Binding (GO:0000062) 3/13 0.0016262077325928145 0.3190301517265964 0 0 15.818548387096774 101.57887995484002 ALDH6A1;ACBD4;SCP2
Acyltransferase Activity, Transferring Groups Other Than Amino-Acyl Groups (GO:0016747) 5/64 0.006960657855853012 0.3190301517265964 0 0 4.48144754924416 22.261506851119684 LIPT1;OSGEPL1;SCP2;ZDHHC5;MCAT
Hi,
When running enrichment analysis on the EnrichR website with background genes, the results showing on the web and those provided in the exported TXT file are not the same. Those on the web has the correct stats, whereas those in the exported TXT file are stats analysed without background genes.
Below shows the results from GO Molecular Function 2023 when I use the examples provided on the website:
Results copied from the web, when analysed without background genes
Results copied from the web, when analysed with background genes
Results in the exported TXT file, when analysed with background genes