Question: Cellular location of list of genes
1
gravatar for shah.khyati231
2.6 years ago by
United States
shah.khyati23110 wrote:

Hi Folks,

 

I wanted to know if there is a way to get the cellular location for the genes lists and get their general functions.

 

 

 

gene • 1.1k views
ADD COMMENTlink modified 9 weeks ago by microfuge710 • written 2.6 years ago by shah.khyati23110
2
gravatar for zlskidmore
2.6 years ago by
zlskidmore280
United States, St. Louis, Washington University
zlskidmore280 wrote:

If I am understanding what you want correctly you could use bioMart to query this information. You would probably want to apply some filters on evidence type etc. but you should be able to get what you want from the GO database. Something like this would work in R:

library("biomaRt")

# Select appropriate database
ensembl <- useMart("ensembl")
ensembl <- useDataset("hsapiens_gene_ensembl", mart=ensembl)

# set up any filters and their appropriate values
filters <- c("hgnc_symbol")
gene <- c("PTEN", "PRLR")
values <- as.list(gene)

# select attributes to return
attributes <- c("hgnc_id", "namespace_1003", "name_1006", "go_id", "go_linkage_type", "definition_1006")

# perform biomart query
getBM(attributes=attributes, filters=filters, values=values, mart=ensembl)

or you could use biomarts web resource.

 

ADD COMMENTlink written 2.6 years ago by zlskidmore280
1
gravatar for Alex Reynolds
2.6 years ago by
Alex Reynolds20k
Seattle, WA USA
Alex Reynolds20k wrote:

Dunno about a list, but on a gene by gene basis, you might search Compartments (found via GeneCards).

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by Alex Reynolds20k

This is a really useful tool. Glad I came across this thread, as I had the same question. Thanks Alex!

ADD REPLYlink written 21 months ago by Awanti0
1
gravatar for Abhik
9 weeks ago by
Abhik30
KOLKATA
Abhik30 wrote:

Human Protein Atlas has downloadable files for subcellular location . You can find more at

http://www.proteinatlas.org/about/download

ADD COMMENTlink written 9 weeks ago by Abhik30
1
gravatar for cpad0112
9 weeks ago by
cpad01121.9k
cpad01121.9k wrote:

GO CC should give you the location. Any GO tool should give you this. In R, biomart is good enough.

ADD COMMENTlink written 9 weeks ago by cpad01121.9k
1
gravatar for EagleEye
9 weeks ago by
EagleEye4.7k
Sweden
EagleEye4.7k wrote:

Use geneontology GO_CC in GeneSCF enrichment analysis.

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by EagleEye4.7k
0
gravatar for microfuge
9 weeks ago by
microfuge710
microfuge710 wrote:

For prokaryotes, psortb is very widely used http://www.psort.org/psortb/

ADD COMMENTlink written 9 weeks ago by microfuge710
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