How To Convert List Of Entrez Ids Into Gene Name

Question

[grosy]

Hi Friends,

I have list of 10,000 Entrez IDs and I want to convert the multiple Entrez IDs into the respective gene names. Could someone suggest me the way to do this?

In a Bioconductor package called "Biomart", we can do this for individual gene. Like

library(org.Hs.eg.db)
library(annotate)
lookUp('3815', 'org.Hs.eg', 'SYMBOL') 
   $`3815` 
   [1] "KIT"
lookUp('3815', 'org.Hs.eg', 'REFSEQ') 
   $`3815`
   [1] "NM_000222" "NM_001093772" "NP_000213" "NP_001087241"

This answer I got it from SEQanswer, but then is there any way to do this for multiple Entrez IDs?

Thanks in advance.

[hojoon.compbio]

I think this may be one of the easiest way to do this task. You can convert Entrez ID into gene name by using website called "MatchMiner" (http://discover.nci.nih.gov/matchminer/MatchMinerLookup.jsp). All you need to do is to upload a file that contains all your Entrez IDs. This website will convert them into HUGO gene names.

[grosy]

Thanks @hojoon.compbio it worked... :o)

[moxu]

What is the library "annotate" and how can I install it, please?

Thanks.

[Neilfws]

It's a Bioconductor package; details and installation instructions are here:

http://bioconductor.org/packages/release/bioc/html/annotate.html

[moxu]

Great! Which function converts gene symbols to entrez gene ids, please?

Thanks.

[Neilfws]

Time for you to read some documentation I think :)

[LimMo]

Thanks for your question, this what I need

Answer 1

[David W]

This is an easy one - just pass a character vector that has more than one value:

getSYMBOL(c('3815', '3816', '2341'), data='org.Hs.eg')
    3815     3816     2341 
   "KIT"   "KLK1" "FNTAP2"

[grosy]

Yeah Thanks a lot :) but it doesn't work more than some 100 gene IDs... so all i have to do now is to

a <- read.csv("entrez ids.csv", header = TRUE)

library(org.Hs.eg.db)

library(annotate)

d= getSYMBOL(a, data='org.Hs.eg') Error in .checkKeysAreWellFormed(keys) : keys must be supplied in a character vector with no NAs

This is the error i get....

[David W]

When you read data into an R session with read.csv you get a dataframe containing rows and columns. In this case you probably have all your ids in one column which you can specify with $. Something like a$EntrezIDs. If you are new to R you should probably read some intro tutorials

[Neilfws]

I don't think the issue is number of IDs. I've retrieved tens of thousands of attributes (slowly) in one go using biomaRt.

[Alex Reynolds]

In a loop, can you pass in a vector of 100 elements at a time? (Or perhaps you need to filter out bad/NA entries?)

[grosy]

Actually i think the problem could be solved if i take the CSV file and list it in a variable... Like given in the Bioconducter package

"http://stuff.mit.edu/afs/athena/software/r_v2.14.1/lib/R/library/org.Hs.eg.db/html/org.Hs.egSYMBOL.html"

But the only problem i am facing now is to list the each value from the CSV file

[Adam]

d= getSYMBOL(na.omit(a), data='org.Hs.eg')

[cwang3444]

Hello there! I got the same issue earlier, but solved it using as.character(). Since the Entrez Gene IDs are made of numbers, they were loaded in as 'integer' initially. Hope it helps

[LimMo]

Your answer help me a lot, thanks +1

Answer 2

[David]

You have geneIDs that are NA.

use mget with ifnotfound=NA

a <- read.csv("entrez ids.csv", header = TRUE)
a.symbol <- as.vector(unlist(mget(a, envir=org.Hs.egSYMBOL, ifnotfound=NA)))

[grosy]

I am sorry i did but still it shows the same problem

a <- read.csv("C:\Users\Desktop\entrez ids _row.csv", header = TRUE) a.symbol <- as.vector(unlist(mget(a, envir=org.Hs.egSYMBOL, ifnotfound=NA)))

Error in .checkKeysAreWellFormed(keys) : keys must be supplied in a character vector with no NAs

[David]

R tells you what is wrong: "keys must be supplied in a character vector with no NAs"

Do that after read.csv

a <- a[-is.na(a)]

Answer 3

[Jordan]

Another way to do without coding is to use ID Mapping in Uniprot. You can just upload a list of entrez id's and then map it.

[grosy]

ya i tried this... But i Want is from ENTREZ ID to GENE NAME... Could you suggest me the options to be choosen to convert From Entrez ID to GENE NAME?

[Jordan]

One silly way of doing it is, mapping it to uniprot id's and then to your required Gene names. But I think you already got the answer. I usually download the ID mapping file from uniprot and write my own code for mapping in perl.