Question: Extracting List Of Genes Associated With A Pathway In Kegg
1
gravatar for naving2uk
4.2 years ago by
naving2uk10
United Kingdom
naving2uk10 wrote:

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.

R • 2.2k views
ADD COMMENTlink modified 4.2 years ago by Giovanni M Dall'Olio26k • written 4.2 years ago by naving2uk10
1
gravatar for Sam
4.2 years ago by
Sam2.4k
New York
Sam2.4k wrote:

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

ADD COMMENTlink written 4.2 years ago by Sam2.4k

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

ADD REPLYlink written 4.2 years ago by naving2uk10

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

ADD REPLYlink written 4.2 years ago by Sam2.4k
0
gravatar for Giovanni M Dall'Olio
4.2 years ago by
London, UK
Giovanni M Dall'Olio26k wrote:

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
ADD COMMENTlink written 4.2 years ago by Giovanni M Dall'Olio26k
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