Topgo, Deseq and KEGG pathway
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Nas 1989 • 0
@nas-1989-23201
Last seen 17 months ago
south africa/ cape town

Hi All

I hope all doing well, I manage to obtain the deseq2 result and submit it to TOP GO for enrichment analysis for gene ontology, is there a way to submit significant GO TERMs for KEGG pathway analysis? Please if there any complete protocol forward link

Kind regards Nasr

annotation cancer • 203 views
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@kevin
Last seen 4 hours ago
Republic of Ireland

Hey Nasr, we are all doing just fine here. How are you?

There is a Bioconductor package, KEGGprofile, which accepts genes (not GO terms) and can conduct KEGG pathway enrichment on these genes. By default, it accepts genes as Entrez IDs. If you are starting with gene symbols, you can convert these to Entrez IDs via biomaRt.

Here is a complete workflow:

head(genes_hgnc)
[1] "TNFRSF4"      "TMEM240"      "PRDM16"       "ARHGEF16"     "AJAP1"       
[6] "RP11-108M9.5"
length(genes_hgnc)
[1] 270

# convert our HGNC gene symbols into Entrez IDs
  require(biomaRt)
  mart <- useMart('ensembl',
    dataset = 'hsapiens_gene_ensembl',
    host = 'uswest.ensembl.org')
  annot <- getBM(
    values = genes_hgnc,
    filters = 'hgnc_symbol',
    mart = mart,
    attributes = c('entrezgene_id','hgnc_symbol'))

  genes_entrez <- annot$entrezgene_id

  head(genes_entrez)
  [1] 10060    NA 81792 92949   114 23382
  length(genes_entrez)
  [1] 257


# Simple pathway analysis of target genes
  require(KEGGprofile)
  keggEnrichment <- find_enriched_pathway(
    genes_entrez,
    species = 'hsa',
    returned_pvalue = 1.0,
    returned_adjpvalue = 1.0, 
    returned_genenumber = 5)
  keggEnrichment <- keggEnrichment[[1]][order(keggEnrichment[[1]]$pvalueAdj),]

  options(scipen=99)
  head(keggEnrichment)
                                                Pathway_Name Gene_Found
05323                                   Rheumatoid arthritis          9
04060                 Cytokine-cytokine receptor interaction         15
05410                      Hypertrophic cardiomyopathy (HCM)          7
05414                                 Dilated cardiomyopathy          7
04062                            Chemokine signaling pathway         10
05412 Arrhythmogenic right ventricular cardiomyopathy (ARVC)          6
      Gene_Pathway Percentage          pvalue     pvalueAdj
05323           92       0.10 0.0000003915110 0.00004482801
04060          265       0.06 0.0000002933572 0.00004482801
05410           83       0.08 0.0000153563920 0.00117220459
05414           90       0.08 0.0000276933439 0.00158544394
04062          189       0.05 0.0000403192425 0.00184662131
05412           74       0.08 0.0000615650784 0.00206505622

Kevin

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Thanks for your reply can KEGG result be plotted? Kind regards Nasr

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Sure, you can generate a barplot of -log10(pvalueAdj). I expect you to research how to do that. There are many examples online.

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