Functional enrichment analysis of bacteria

Functional enrichment analysis of bacteria

2

Hello,

I have gene lists from an RNA-seq experiment from E.coli bacteria. So far, I have only worked with model organisms, which are supported by biomaRt, so conversion of gene IDs and functional enrichment analysis within R was easy. Now that I am working with a bacterial dataset for which there is no biomaRt support, I am a bit uncertain. After searching around, I decided to use the DAVID web interface. From there, I exported the results from the functional annotation clustering as .txt files (using all 3 GO term databases, i.e. BP, CC and MF). These have the following structure:

Annotation Cluster 1    Enrichment Score: 2.0813446807310627
Category    Term    Count   %   PValue  Genes   List Total  Pop Hits    Pop Total   Fold Enrichment Bonferroni  Benjamini   FDR
GOTERM_CC_DIRECT ...

Annotation Cluster 2    Enrichment Score: 0.028318244118032198
Category    Term    Count   %   PValue  Genes   List Total  Pop Hits    Pop Total   Fold Enrichment Bonferroni  Benjamini   FDR
GOTERM_BP_DIRECT ...

I would like to visualize these results within R. Is there a function for example using the clusterProfiler package that I am not aware of?

Or is this maybe not the best approach and there is a more suitable one?

I would really appreciate some help!


GO enrichment


DAVID


bacteria


clusterProfiler


R

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