Cellular location of list of genes

Question

[shah.khyati231]

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.

Answer 1

[zlskidmore]

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.

Answer 2

[Alex Reynolds]

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

[Awanti]

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

Answer 3

[Abhik]

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

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

Answer 4

[cpad0112]

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

Answer 5

[EagleEye]

Use geneontology GO_CC in GeneSCF enrichment analysis.

Answer 6

[microfuge]

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