Question: Cellular location of list of genes
1
gravatar for shah.khyati231
2.7 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 • 1.2k views
ADD COMMENTlink modified 4 months ago by microfuge720 • written 2.7 years ago by shah.khyati23110
2
gravatar for zlskidmore
2.7 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 2.7 years ago by zlskidmore280
1
gravatar for Alex Reynolds
2.7 years ago by
Alex Reynolds21k
Seattle, WA USA
Alex Reynolds21k wrote:

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

ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by Alex Reynolds21k

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

ADD REPLYlink written 23 months ago by Awanti0
1
gravatar for Abhik
4 months 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 4 months ago by Abhik30
1
gravatar for cpad0112
4 months ago by
cpad01123.1k
cpad01123.1k wrote:

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

ADD COMMENTlink written 4 months ago by cpad01123.1k
1
gravatar for EagleEye
4 months ago by
EagleEye4.8k
Sweden
EagleEye4.8k wrote:

Use geneontology GO_CC in GeneSCF enrichment analysis.

ADD COMMENTlink modified 4 months ago • written 4 months ago by EagleEye4.8k
0
gravatar for microfuge
4 months ago by
microfuge720
microfuge720 wrote:

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

ADD COMMENTlink written 4 months ago by microfuge720
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 583 users visited in the last hour