photosynthesis genes of the plant 'arabidopsis'

Question

[mannoulag1]

hi, I would like to know from a miroarray, the group of genes linked to photosynthesis of this plant (arabiodpsis), there is any R package or R fonction? Thank you very much

[GenoMax]

Can you not find this information outside of a specific package or software? An example, which happens to include microarray data.

[mannoulag1]

Hi, I am not looking for photosyntheis regulatory network. I analyse my dataset using R and I want to filter these genes from my dataset, can I use the photosynthesis pathways (map00195 and map00710) from kegg database to know all the related genes? and how I do that with R. thanks

Answer 1

[theobroma22]

can I use the photosynthesis pathways (map00195 and map00710) from kegg database to know all the related genes?

Yes, you can. You can also use GO terms like photosynthesis.

how I do that with R?

There are many R packages like BiomaRt and KEGGREST that are useful for what you want to do.

[mannoulag1]

thank you theobroma22, I tested this R code to get GO terms

library("biomaRt")
# define biomart object
mart <- biomaRt::useMart(biomart = "plants_mart", dataset = "athaliana_eg_gene", host = 'plants.ensembl.org')
#query biomart
GTOGO <- biomaRt::getBM(attributes = c( "ensembl_gene_id", "go_id"), mart = mart)
head (GTOGO)
#remove genes without annotation 
GTOGO <- GTOGO[GTOGO$go_id != '',]

And to filter the genes annoted by this term (GO:0015979) photosynthesis, I tested this code, but it is non functional

result <- biomaRt::getBM(attributes = c( "ensembl_gene_id", "go_id"), filters = "go_id", values = "GO:0015979", mart = mart)

have you any idea please?

[theobroma22]

Hmm, try just using "go" instead of "go_id", for only the filters argument and for both attributes and filters if the former didn't work? Sorry, I've been away from my computer for the last month or so, and didn't execute any code for this. Perhaps take a look at the BiomaRt user manual available on bioconductor.org. Hope this helps.

[mannoulag1]

thank you very much :) this give me 2577 rows.

     ensembl_gene_id      go_id
1          AT3G02780 GO:0009536
2          AT3G02780 GO:0009507
3          AT3G02780 GO:0005829
4          AT3G02780 GO:0005739
5          AT3G02780 GO:0050992
6          AT3G02780 GO:0015995
7          AT3G02780 GO:0015979
8          AT3G02780 GO:0009908
.........