Extracting List Of Genes Associated With A Pathway In Kegg

Question

[naving2uk]

Hi, I have a list of genes from affymetrix and the ID's come out after normalizing the CEL files , how can i define their pathways from KEGG, can we do that using KEGGREST.

Answer 1

[Sam]

You can try out the SPIA packages or simpler, the KEGG mapper.

[naving2uk]

Kindly could you help me with code , I could not find method in SPIA that provide the pathway for specific genes ID's

[Sam]

If that's the case, KEGG mapper might be easier. Or you can try out the code from Giovanni, that should work too

Answer 2

[Giovanni M Dall'Olio]

Using the annotationDB system:

> library(help=org.Hs.eg.db)
> mylistofgenes = seq(1, 2000)  # Let's take a list of genes with Entrez from 1 to 2000
> Entrez2Kegg = as.data.frame(org.Hs.egPATH)
> head(Entrez2Kegg)
  gene_id path_id
1       2   04610
2       9   00232
3       9   00983
4       9   01100
5      10   00232
6      10   00983
> subset(Entrez2Kegg, gene_id %in% mylistofgenes)

For fancier analysis, you can use clusterProfiler:

> library(clusterProfiler)
> enrichKEGG(mylistofgenes)
> head(summary(enrichKEGG() ))
               ID                            Description GeneRatio  BgRatio       pvalue     p.adjust       qvalue
hsa04970 hsa04970                     Salivary secretion    44/951  90/6899 9.756050e-16 2.039015e-13 9.139879e-14
hsa00071 hsa00071                 Fatty acid degradation    28/951  44/6899 2.555377e-14 2.670369e-12 1.196992e-12
hsa04974 hsa04974       Protein digestion and absorption    41/951  89/6899 1.233173e-13 8.591108e-12 3.850962e-12
hsa04261 hsa04261 Adrenergic signaling in cardiomyocytes    56/951 149/6899 1.871330e-13 9.777698e-12 4.382851e-12
hsa04972 hsa04972                   Pancreatic secretion    42/951  96/6899 5.476728e-13 2.289272e-11 1.026166e-11
hsa04022 hsa04022             cGMP-PKG signaling pathway    59/951 167/6899 9.456849e-13 3.294136e-11 1.476596e-11