Question: photosynthesis genes of the plant 'arabidopsis'
0
gravatar for mannoulag1
2.8 years ago by
mannoulag160
mannoulag160 wrote:

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

ADD COMMENTlink modified 2.8 years ago by theobroma221.1k • written 2.8 years ago by mannoulag160
1

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

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by genomax78k

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

ADD REPLYlink modified 2.7 years ago • written 2.8 years ago by mannoulag160
1
gravatar for theobroma22
2.8 years ago by
theobroma221.1k
theobroma221.1k wrote:

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.

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by theobroma221.1k

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?

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by mannoulag160

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.

ADD REPLYlink modified 2.7 years ago • written 2.7 years ago by theobroma221.1k

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
.........
ADD REPLYlink modified 22 months ago • written 2.7 years ago by mannoulag160
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