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.
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naving2uk •
You can try out the SPIA packages or simpler, the KEGG mapper.
Kindly could you help me with code , I could not find method in SPIA that provide the pathway for specific genes ID's
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naving2uk •
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
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