Affymetrix Microarray data

Question

[Fawzi Yassine]

I want to check if a certain biological process is enriched or signaled in a certain biological process (mitochondrial biogenesis) in Affymetrix Microarray data generated from an experiment subjecting mice to a certain treatment. How can I do that using Bioconductor? It was difficult to search for a specific term (e.g. mitochondrial biogenesis) using DAVID. Regards.

[venu]

• Follow this tutorial and links in there - Analysing Microarray Data In Bioconductor
• Get differentially expressed genes between your conditions
• Perform GO enrichment analysis (E.g. EnrichR, DAVID, GSEA ...)

P.S: You can/should change the title from Tutorial to Question

Answer 1

[Spacebio]

It is easier if you use RStudio with this script:

library(mygene)

genes <- read.table("YOUR_TABLE_OF_GENES", header = T,)
y <- queryMany(genes, scopes = "symbol", fields = "name", species = "human", returnall = T)
x <- y$response
write.table(x, file = "your_results.txt", row.names = F)

The field "name" retrives the biological process of the symbol you're submiting. Here you can look for more info: http://mygene.info/doc/query_service.html#fields

[Fawzi Yassine]

Thanks Spacebio, Where do I specify the databases to query (e.g. kegg, go, reactome)? Where do I specify the biological process I am looking for? regards,  

[Spacebio]

If you have a list of "entrez" or "symbol", you can try this:

 y <- queryMany(genes, scopes = "HERE_WRITE_ENTREZ_OR_SYMBOL_DEPENDING_YOUR_INPUT", fields = "go", species = "human", returnall = T)